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In our 23 chromosome pairs, do the 2 members of the pair have distinct or virtually identical sequences?

In our 23 chromosome pairs, do the 2 members of the pair have distinct or virtually identical sequences?



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I understand that we have 46 DNA molecules in the nucleus of our cells, arranged in 23 pairs: 22 autosomal and 1 sex chromosome pairs.

I have read in different sources that the pairs contain nearly identical members, excluding any mutations. I have also read that the pairs contain 1 member we inherited from our mothers and 1 we inherited from our fathers, which are different due to inheritance.

This seems contradictory, given that genealogical companies match up on the differences on these chromosomes.

My understanding was that meiosis creates sperm and egg cells that each carry 23 chromosomes - they are haploids. During the first steps of meiosis that creates the reproductive cells we have a combining of the parent's chromosome pair from their parents to create 4 daughter cells, each independently viable, where the recombination of the chromosome pair has occurred at somewhat predictable spots (for you perhaps :-) ) and that these spots can be related to genes. It is this step that give us our genetic variation between siblings for example. A new person's DNA is partially formed from any one of these highly varied daughter cell possibilities.

Fertilization combines the reproductive cells to produce the 46 chromosome zygote with is again diploid.

I think this understanding supports the second interpretation that our chromosome pairs are not 2 nearly identical DNA molecules but are distinct.

Have I got this right? Is there a missing process or a misunderstanding in my interpretation?


Homologous chromosomes (those that are paired up), excluding the sex pair are almost identical in size, shape and genes (members as you called them) present in them.

Genes determine traits and each homologous chromosome controls the same traits. The level of identity of a gene inside a population varies between genes. There are very conserved ones that do not change even between humans and yeast and others that vary alot event inside a species. This changes can be small in sequence length, a simple base (letter) swap or one deletion, and have a huge effect on the traits. This is how chimps and humans are very different but share 98.6% of their genome and humans are very similar and share 99.9% of their genome.

In summary, on the bigger scale homologous chromosomes are very similar (size, shape, traits inside), on the smaller scale homologous chromosomes have small changes that affect greatly.

EDIT: elaborating on when recombination occurs.

The zygote do not recombine the chromosomes it gets from it's parents. Each parent chromosomes recombine in the first step of meiosis. We do not expect them to be identifcal on the gene level (or the SNPs level). Each chromosome represent each paren't genetic material.

Lets look at parents A chromosomes
parent a Paternal: a-b-c-d-e parent b Paternal: a-B-c-D-e
parent a Maternal: a-B-C-D-e parent b Maternal: a-b-C-D-e
possible recombination (a) possible recombination (b)
(a-I) a-B-C-d-e (b-I) a-B-C-D-e
(a-II) a-b-c-D-e (b-II) a-b-c-D-e

Now the child can be any of the 4 possible combinations (and obviously all other not shown). Let's say (a-I) and (b-II). This chromosomes do not recombine until they get to the meiosis stage.


I have read in different sources that the pairs contain nearly identical members, excluding any mutations

"Nearly" is doing a lot of work there.

You have a copy of Chr 1 from your father and a copy from your mother. Your copies might have mutations as compared to your parents that happened either in you as you were developing, or in the gametes as compared to the stem cells they originated from, but most of the differences between your maternal copy and your parental copy were caused by long ago mutations that have been in your parents' families for generations, (we'd be more likely to call those polymorphisms, rather than mutations) not mutations that just happened.

Even with those differences, your two copies of Chr 1 are at least 99% identical.


Two major resources of genetic variation between siblings:

1- Random segregation of chromosomes during meiosis I. consider only mother: the mother has 46 chromosomes, 23 from grandmother and 23 from grandfather. during meiosis anaphase I, pairs of similar (homologous) chromosomes are segregated randomly. finally you have egg cells with 23 chromosomes, some from grandfather and some from grandmother. this can make 2^23 (8 millions) different combination of chromosomes for egg, and 2^23 for sperm and 2^46 (7000 billions) different combinations totally.

2- Recombination of homologous chromosomes during meiosis I. which is exchange of chromosome pieces during meiosis I metaphase, and I see you know enough about it.

Also, there are other resources of variation which are out of the level of this question.


Chapter 13: Meiosis and Sexual Life Cycles

In animals and plants, reproductive cells called GAMETES are the vehicles that transmit genes from one generation to the next.

In ASEXUAL REPRODUCTION, a single individual is the sole parent and passes copies of all its genes to its offspring without the fusion of gametes. For example, single-celled eukaryotic organisms can reproduce asexually by mitotic cell division, in which DNA is copied and allocated equally to two daughter cells. The genomes of the offspring are virtually exact copies of the parent's genome.
An individual that reproduces asexually gives rise to a CLONE, a group of genetically identical individuals. Genetic difference occasionally arise in asexually reproducing organisms as a result of changes in the DNA called mutations.

The only cells of the human body not produced by mitosis are the gametes, which develop from specialized cells called GERM CELLS in the gonads- ovaries in females and testes in males.

Plants and some species of algae exhibit a second type of life cycle called ALTERNATION OF GENERATIONS. This type includes both diploid and haploid stages that are multicellular. The multicellular diploid stage is called the sporophyte. Meiosis in the sporophyte produces haploid cells called spores. Unlike a gamete, a haploid spore doesn't fuse with another cell but divides mitotically, generating a multicellular haploid stage called the gametophyte. Cells of the gametophyte give rise to gametes by mitosis. Fusion of two haploid gametes at fertilization results in a diploid zygote, which develops into the next sporophyte generation. Therefore, in this type of life cycle, the sporophyte generation produces a gametophyte as its offspring, and the gametophyte generation produces the next sporophyte generation.

The third type of life cycle occurs in most fungi and some protists, including some algae. After gametes fuse and form a diploid zygote, meiosis occurs without a multicellular diploid offspring developing. Meiosis produces not gametes but haploid cells that then divide by mitosis and give rise to either unicellular descendants or a haploid multicellular adult organism. Subsequently, the haploid organism carries out further mitoses, producing the cells that develop into gametes. the only diploid stage found in these species is the single celled zygote.

Plants:
-alternating generations, with sporophytes that grow from spores and are diploid, and gametophytes that grow from fertilized seeds and are haploid.
-Haploid phase DOES divide
-NOTE: I incorrectly told section F3 that it is only the primitive plants that alternate generations. However, that's not strictly true. All plants have a sporophyte generation, but with flowering plants it all happens within the gametophyte

In meiosis I, homologous chromosome pairs separate, creating TWO haploid daughter cells


Contents

The word chromosome ( / ˈ k r oʊ m ə ˌ s oʊ m , - ˌ z oʊ m / [7] [8] ) comes from the Greek χρῶμα (chroma, "colour") and σῶμα (soma, "body"), describing their strong staining by particular dyes. [9] The term was coined by the German anatomist Heinrich Wilhelm Waldeyer, [10] referring to the term chromatin, which was introduced by Walther Flemming, the discoverer of cell division.

Some of the early karyological terms have become outdated. [11] [12] For example, Chromatin (Flemming 1880) and Chromosom (Waldeyer 1888), both ascribe color to a non-colored state. [13]

The German scientists Schleiden, [5] Virchow and Bütschli were among the first scientists who recognized the structures now familiar as chromosomes. [14]

In a series of experiments beginning in the mid-1880s, Theodor Boveri gave definitive contributions to elucidating that chromosomes are the vectors of heredity, with two notions that became known as ‘chromosome continuity’ and ‘chromosome individuality’. [15]

Wilhelm Roux suggested that each chromosome carries a different genetic configuration, and Boveri was able to test and confirm this hypothesis. Aided by the rediscovery at the start of the 1900s of Gregor Mendel's earlier work, Boveri was able to point out the connection between the rules of inheritance and the behaviour of the chromosomes. Boveri influenced two generations of American cytologists: Edmund Beecher Wilson, Nettie Stevens, Walter Sutton and Theophilus Painter were all influenced by Boveri (Wilson, Stevens, and Painter actually worked with him). [16]

In his famous textbook The Cell in Development and Heredity, Wilson linked together the independent work of Boveri and Sutton (both around 1902) by naming the chromosome theory of inheritance the Boveri–Sutton chromosome theory (the names are sometimes reversed). [17] Ernst Mayr remarks that the theory was hotly contested by some famous geneticists: William Bateson, Wilhelm Johannsen, Richard Goldschmidt and T.H. Morgan, all of a rather dogmatic turn of mind. Eventually, complete proof came from chromosome maps in Morgan's own lab. [18]

The number of human chromosomes was published in 1923 by Theophilus Painter. By inspection through the microscope, he counted 24 pairs, which would mean 48 chromosomes. His error was copied by others and it was not until 1956 that the true number, 46, was determined by Indonesia-born cytogeneticist Joe Hin Tjio. [19]

The prokaryotes – bacteria and archaea – typically have a single circular chromosome, but many variations exist. [20] The chromosomes of most bacteria, which some authors prefer to call genophores, can range in size from only 130,000 base pairs in the endosymbiotic bacteria Candidatus Hodgkinia cicadicola [21] and Candidatus Tremblaya princeps, [22] to more than 14,000,000 base pairs in the soil-dwelling bacterium Sorangium cellulosum. [23] Spirochaetes of the genus Borrelia are a notable exception to this arrangement, with bacteria such as Borrelia burgdorferi, the cause of Lyme disease, containing a single linear chromosome. [24]

Structure in sequences Edit

Prokaryotic chromosomes have less sequence-based structure than eukaryotes. Bacteria typically have a one-point (the origin of replication) from which replication starts, whereas some archaea contain multiple replication origins. [25] The genes in prokaryotes are often organized in operons, and do not usually contain introns, unlike eukaryotes.

DNA packaging Edit

Prokaryotes do not possess nuclei. Instead, their DNA is organized into a structure called the nucleoid. [26] [27] The nucleoid is a distinct structure and occupies a defined region of the bacterial cell. This structure is, however, dynamic and is maintained and remodeled by the actions of a range of histone-like proteins, which associate with the bacterial chromosome. [28] In archaea, the DNA in chromosomes is even more organized, with the DNA packaged within structures similar to eukaryotic nucleosomes. [29] [30]

Certain bacteria also contain plasmids or other extrachromosomal DNA. These are circular structures in the cytoplasm that contain cellular DNA and play a role in horizontal gene transfer. [5] In prokaryotes (see nucleoids) and viruses, [31] the DNA is often densely packed and organized in the case of archaea, by homology to eukaryotic histones, and in the case of bacteria, by histone-like proteins.

Bacterial chromosomes tend to be tethered to the plasma membrane of the bacteria. In molecular biology application, this allows for its isolation from plasmid DNA by centrifugation of lysed bacteria and pelleting of the membranes (and the attached DNA).

Prokaryotic chromosomes and plasmids are, like eukaryotic DNA, generally supercoiled. The DNA must first be released into its relaxed state for access for transcription, regulation, and replication.

Each eukaryotic chromosome consists of a long linear DNA molecule associated with proteins, forming a compact complex of proteins and DNA called chromatin. Chromatin contains the vast majority of the DNA of an organism, but a small amount inherited maternally, can be found in the mitochondria. It is present in most cells, with a few exceptions, for example, red blood cells.

Histones are responsible for the first and most basic unit of chromosome organization, the nucleosome.

Eukaryotes (cells with nuclei such as those found in plants, fungi, and animals) possess multiple large linear chromosomes contained in the cell's nucleus. Each chromosome has one centromere, with one or two arms projecting from the centromere, although, under most circumstances, these arms are not visible as such. In addition, most eukaryotes have a small circular mitochondrial genome, and some eukaryotes may have additional small circular or linear cytoplasmic chromosomes.

In the nuclear chromosomes of eukaryotes, the uncondensed DNA exists in a semi-ordered structure, where it is wrapped around histones (structural proteins), forming a composite material called chromatin.

Interphase chromatin Edit

The packaging of DNA into nucleosomes causes a 10 nanometer fibre which may further condense up to 30 nm fibres [32] Most of the euchromatin in interphase nuclei appears to be in the form of 30-nm fibers. [32] Chromatin structure is the more decondensed state, i.e. the 10-nm conformation allows transcription. [32]

During interphase (the period of the cell cycle where the cell is not dividing), two types of chromatin can be distinguished:

    , which consists of DNA that is active, e.g., being expressed as protein. , which consists of mostly inactive DNA. It seems to serve structural purposes during the chromosomal stages. Heterochromatin can be further distinguished into two types:
    • Constitutive heterochromatin, which is never expressed. It is located around the centromere and usually contains repetitive sequences.
    • Facultative heterochromatin, which is sometimes expressed.

    Metaphase chromatin and division Edit

    In the early stages of mitosis or meiosis (cell division), the chromatin double helix become more and more condensed. They cease to function as accessible genetic material (transcription stops) and become a compact transportable form. The loops of 30-nm chromatin fibers are thought to fold upon themselves further to form the compact metaphase chromosomes of mitotic cells. The DNA is thus condensed about 10,000 fold. [32]

    The chromosome scaffold, which is made of proteins such as condensin, TOP2A and KIF4, [33] plays an important role in holding the chromatin into compact chromosomes. Loops of 30 nm structure further condense with scaffold into higher order structures. [34]

    This highly compact form makes the individual chromosomes visible, and they form the classic four arm structure, a pair of sister chromatids attached to each other at the centromere. The shorter arms are called p arms (from the French petit, small) and the longer arms are called q arms (q follows p in the Latin alphabet q-g "grande" alternatively it is sometimes said q is short for queue meaning tail in French [35] ). This is the only natural context in which individual chromosomes are visible with an optical microscope.

    Mitotic metaphase chromosomes are best described by a linearly organized longitudinally compressed array of consecutive chromatin loops. [36]

    During mitosis, microtubules grow from centrosomes located at opposite ends of the cell and also attach to the centromere at specialized structures called kinetochores, one of which is present on each sister chromatid. A special DNA base sequence in the region of the kinetochores provides, along with special proteins, longer-lasting attachment in this region. The microtubules then pull the chromatids apart toward the centrosomes, so that each daughter cell inherits one set of chromatids. Once the cells have divided, the chromatids are uncoiled and DNA can again be transcribed. In spite of their appearance, chromosomes are structurally highly condensed, which enables these giant DNA structures to be contained within a cell nucleus.

    Human chromosomes Edit

    Chromosomes in humans can be divided into two types: autosomes (body chromosome(s)) and allosome (sex chromosome(s)). Certain genetic traits are linked to a person's sex and are passed on through the sex chromosomes. The autosomes contain the rest of the genetic hereditary information. All act in the same way during cell division. Human cells have 23 pairs of chromosomes (22 pairs of autosomes and one pair of sex chromosomes), giving a total of 46 per cell. In addition to these, human cells have many hundreds of copies of the mitochondrial genome. Sequencing of the human genome has provided a great deal of information about each of the chromosomes. Below is a table compiling statistics for the chromosomes, based on the Sanger Institute's human genome information in the Vertebrate Genome Annotation (VEGA) database. [37] Number of genes is an estimate, as it is in part based on gene predictions. Total chromosome length is an estimate as well, based on the estimated size of unsequenced heterochromatin regions.

    Chromosome Genes [38] Total base pairs % of bases Sequenced base pairs [39] % sequenced base pairs
    1 2000 247,199,719 8.0 224,999,719 91.02%
    2 1300 242,751,149 7.9 237,712,649 97.92%
    3 1000 199,446,827 6.5 194,704,827 97.62%
    4 1000 191,263,063 6.2 187,297,063 97.93%
    5 900 180,837,866 5.9 177,702,766 98.27%
    6 1000 170,896,993 5.5 167,273,993 97.88%
    7 900 158,821,424 5.2 154,952,424 97.56%
    8 700 146,274,826 4.7 142,612,826 97.50%
    9 800 140,442,298 4.6 120,312,298 85.67%
    10 700 135,374,737 4.4 131,624,737 97.23%
    11 1300 134,452,384 4.4 131,130,853 97.53%
    12 1100 132,289,534 4.3 130,303,534 98.50%
    13 300 114,127,980 3.7 95,559,980 83.73%
    14 800 106,360,585 3.5 88,290,585 83.01%
    15 600 100,338,915 3.3 81,341,915 81.07%
    16 800 88,822,254 2.9 78,884,754 88.81%
    17 1200 78,654,742 2.6 77,800,220 98.91%
    18 200 76,117,153 2.5 74,656,155 98.08%
    19 1500 63,806,651 2.1 55,785,651 87.43%
    20 500 62,435,965 2.0 59,505,254 95.31%
    21 200 46,944,323 1.5 34,171,998 72.79%
    22 500 49,528,953 1.6 34,893,953 70.45%
    X (sex chromosome) 800 154,913,754 5.0 151,058,754 97.51%
    Y (sex chromosome) 200 [40] 57,741,652 1.9 25,121,652 43.51%
    Total 21,000 3,079,843,747 100.0 2,857,698,560 92.79%

    In eukaryotes Edit

    These tables give the total number of chromosomes (including sex chromosomes) in a cell nucleus. For example, most eukaryotes are diploid, like humans who have 22 different types of autosomes, each present as two homologous pairs, and two sex chromosomes. This gives 46 chromosomes in total. Other organisms have more than two copies of their chromosome types, such as bread wheat, which is hexaploid and has six copies of seven different chromosome types – 42 chromosomes in total.

    Normal members of a particular eukaryotic species all have the same number of nuclear chromosomes (see the table). Other eukaryotic chromosomes, i.e., mitochondrial and plasmid-like small chromosomes, are much more variable in number, and there may be thousands of copies per cell.

    Asexually reproducing species have one set of chromosomes that are the same in all body cells. However, asexual species can be either haploid or diploid.

    Sexually reproducing species have somatic cells (body cells), which are diploid [2n] having two sets of chromosomes (23 pairs in humans), one set from the mother and one from the father. Gametes, reproductive cells, are haploid [n]: They have one set of chromosomes. Gametes are produced by meiosis of a diploid germ line cell. During meiosis, the matching chromosomes of father and mother can exchange small parts of themselves (crossover), and thus create new chromosomes that are not inherited solely from either parent. When a male and a female gamete merge (fertilization), a new diploid organism is formed.

    Some animal and plant species are polyploid [Xn]: They have more than two sets of homologous chromosomes. Plants important in agriculture such as tobacco or wheat are often polyploid, compared to their ancestral species. Wheat has a haploid number of seven chromosomes, still seen in some cultivars as well as the wild progenitors. The more-common pasta and bread wheat types are polyploid, having 28 (tetraploid) and 42 (hexaploid) chromosomes, compared to the 14 (diploid) chromosomes in the wild wheat. [66]

    In prokaryotes Edit

    Prokaryote species generally have one copy of each major chromosome, but most cells can easily survive with multiple copies. [67] For example, Buchnera, a symbiont of aphids has multiple copies of its chromosome, ranging from 10–400 copies per cell. [68] However, in some large bacteria, such as Epulopiscium fishelsoni up to 100,000 copies of the chromosome can be present. [69] Plasmids and plasmid-like small chromosomes are, as in eukaryotes, highly variable in copy number. The number of plasmids in the cell is almost entirely determined by the rate of division of the plasmid – fast division causes high copy number.

    In general, the karyotype is the characteristic chromosome complement of a eukaryote species. [70] The preparation and study of karyotypes is part of cytogenetics.

    Although the replication and transcription of DNA is highly standardized in eukaryotes, the same cannot be said for their karyotypes, which are often highly variable. There may be variation between species in chromosome number and in detailed organization. In some cases, there is significant variation within species. Often there is:

    1. variation between the two sexes 2. variation between the germ-line and soma (between gametes and the rest of the body) 3. variation between members of a population, due to balanced genetic polymorphism 4. geographical variation between races 5. mosaics or otherwise abnormal individuals.

    Also, variation in karyotype may occur during development from the fertilized egg.

    The technique of determining the karyotype is usually called karyotyping. Cells can be locked part-way through division (in metaphase) in vitro (in a reaction vial) with colchicine. These cells are then stained, photographed, and arranged into a karyogram, with the set of chromosomes arranged, autosomes in order of length, and sex chromosomes (here X/Y) at the end.

    Like many sexually reproducing species, humans have special gonosomes (sex chromosomes, in contrast to autosomes). These are XX in females and XY in males.

    History and analysis techniques Edit

    Investigation into the human karyotype took many years to settle the most basic question: How many chromosomes does a normal diploid human cell contain? In 1912, Hans von Winiwarter reported 47 chromosomes in spermatogonia and 48 in oogonia, concluding an XX/XO sex determination mechanism. [71] Painter in 1922 was not certain whether the diploid number of man is 46 or 48, at first favouring 46. [72] He revised his opinion later from 46 to 48, and he correctly insisted on humans having an XX/XY system. [73]

    New techniques were needed to definitively solve the problem:

    1. Using cells in culture
    2. Arresting mitosis in metaphase by a solution of colchicine
    3. Pretreating cells in a hypotonic solution 0.075 M KCl, which swells them and spreads the chromosomes
    4. Squashing the preparation on the slide forcing the chromosomes into a single plane
    5. Cutting up a photomicrograph and arranging the result into an indisputable karyogram.

    It took until 1954 before the human diploid number was confirmed as 46. [74] [75] Considering the techniques of Winiwarter and Painter, their results were quite remarkable. [76] Chimpanzees, the closest living relatives to modern humans, have 48 chromosomes as do the other great apes: in humans two chromosomes fused to form chromosome 2.

    Chromosomal aberrations are disruptions in the normal chromosomal content of a cell and are a major cause of genetic conditions in humans, such as Down syndrome, although most aberrations have little to no effect. Some chromosome abnormalities do not cause disease in carriers, such as translocations, or chromosomal inversions, although they may lead to a higher chance of bearing a child with a chromosome disorder. Abnormal numbers of chromosomes or chromosome sets, called aneuploidy, may be lethal or may give rise to genetic disorders. [77] Genetic counseling is offered for families that may carry a chromosome rearrangement.

    The gain or loss of DNA from chromosomes can lead to a variety of genetic disorders. Human examples include:

      , which is caused by the deletion of part of the short arm of chromosome 5. "Cri du chat" means "cry of the cat" in French the condition was so-named because affected babies make high-pitched cries that sound like those of a cat. Affected individuals have wide-set eyes, a small head and jaw, moderate to severe mental health problems, and are very short. , the most common trisomy, usually caused by an extra copy of chromosome 21 (trisomy 21). Characteristics include decreased muscle tone, stockier build, asymmetrical skull, slanting eyes and mild to moderate developmental disability. [78] , or trisomy-18, the second most common trisomy. [79] Symptoms include motor retardation, developmental disability and numerous congenital anomalies causing serious health problems. Ninety percent of those affected die in infancy. They have characteristic clenched hands and overlapping fingers. , also called idic(15), partial tetrasomy 15q, or inverted duplication 15 (inv dup 15). , which is very rare. It is also called the terminal 11q deletion disorder. [80] Those affected have normal intelligence or mild developmental disability, with poor expressive language skills. Most have a bleeding disorder called Paris-Trousseau syndrome. (XXY). Men with Klinefelter syndrome are usually sterile and tend to be taller and have longer arms and legs than their peers. Boys with the syndrome are often shy and quiet and have a higher incidence of speech delay and dyslexia. Without testosterone treatment, some may develop gynecomastia during puberty. , also called D-Syndrome or trisomy-13. Symptoms are somewhat similar to those of trisomy-18, without the characteristic folded hand. . This means there is an extra, abnormal chromosome. Features depend on the origin of the extra genetic material. Cat-eye syndrome and isodicentric chromosome 15 syndrome (or Idic15) are both caused by a supernumerary marker chromosome, as is Pallister–Killian syndrome. (XXX). XXX girls tend to be tall and thin and have a higher incidence of dyslexia. (X instead of XX or XY). In Turner syndrome, female sexual characteristics are present but underdeveloped. Females with Turner syndrome often have a short stature, low hairline, abnormal eye features and bone development and a "caved-in" appearance to the chest. , which is caused by partial deletion of the short arm of chromosome 4. It is characterized by growth retardation, delayed motor skills development, "Greek Helmet" facial features, and mild to profound mental health problems. . XYY boys are usually taller than their siblings. Like XXY boys and XXX girls, they are more likely to have learning difficulties.

    Sperm aneuploidy Edit

    Exposure of males to certain lifestyle, environmental and/or occupational hazards may increase the risk of aneuploid spermatozoa. [81] In particular, risk of aneuploidy is increased by tobacco smoking, [82] [83] and occupational exposure to benzene, [84] insecticides, [85] [86] and perfluorinated compounds. [87] Increased aneuploidy is often associated with increased DNA damage in spermatozoa.


    Chromosomes of Pacific hydrothermal vent invertebrates: towards a greater understanding of the relationship between chromosome and molecular evolution

    Karyotypes for several East Pacific Rise hydrothermal vent invertebrates are described here for the first time: the vestimentiferans Riftia pachyptila and Oasisia alvinae , the alvinellid polychaetes Alvinella pompejana, A. caudata and Paralvinella grasslei , the polynoid polychaetes Branchinotogluma grasslei and Branchipolynoe symmytilida , the serpulid Laminatubus alvini and the mytilid bivalve Bathymodiolus thermophilus . For comparative purposes, the karyotype of the Atlantic vent mussel Bathymodiolus azoricus is also described here for the first time. Each species has its own unique chromosomal characteristics which can be interpreted both in terms of group characteristics and species divergence. From comparisons with published results on other vent species and closely-related coastal species, we identified a positive correlation between chromosome number variation and molecular divergence at two ribosomal ribonucleic acid gene loci (the 18S and 28S rRNA). Whilst the patterns of chromosome divergence we found were generally within the ranges previously reported for these taxonomic groupings, there was an apparent inconsistency in the case of Branchipolynoe symmytilida (EPR) and Branchipolynoe seepensis (MAR), which show a greater degree of divergence at the chromosome level compared with other members of the same genus. Moreover, polychaetes as a whole showed greater variation in the number and structural divergence of chromosomes compared to Mytilids (structural information only). Our findings highlight the great potential for chromosome analysis in future taxonomic and evolutionary studies of the deep-sea vent fauna.


    I. From Whom: Ape-like Primates or Fully Human People?

    When considering human origins, the most natural place to start is on the question of whether humans have an ape-like ancestry. Before we can discuss the minutiae of the genetics of the human race, we need to ask whether our race is indeed human or whether we are simply highly evolved primates. Ever since Darwin, evolutionists have claimed that apes represent our closest living biological relatives.4 Evolutionary creationists (a.k.a. theistic evolutionists) agree and expect to find unequivocal genetic evidence of a common genealogical heritage between mankind and the orangutans, gorillas, and chimpanzees. Current evolutionary literature identifies the chimpanzee as the closest living relative of humans, and evolutionists place the split between these two lineages (from a common ape-like ancestor, not a chimpanzee) about 3 million to 13 million years ago.5

    In contrast, a plain reading of Scripture reveals a starkly different narrative on human ancestry. As has been argued in an earlier chapter, Genesis 1–2 teaches that God created man in His own image, categorically distinct from any animals, and that He did so supernaturally by forming Adam from the dust and Eve from Adam’s side. Human evolution from pre-existing ape-like creatures is not compatible with the Genesis narrative.

    Furthermore, the rest of Scripture identifies Adam and Eve as the sole progenitors of the entire human race, and Noah, his wife, his three sons, and their wives as the most immediate ancestors of modern humans.6 Shortly after the global Flood of Noah’s day, the human ancestors of the modern “races”7 or ethnic groups formed as a result of the confusion of languages at Babel (Gen 11:8–9).8 Apes as precursors to humans do not enter the picture under the creation view.

    Because of the nature of the genetic discussion that follows, the time element of creation is also critical to the ancestry question. Under the young-earth creation (YEC) view, Adam and Eve were created approximately 6,000 years ago, and the global Flood of Noah and the population bottleneck that followed occurred about 4,500 years ago. The Tower of Babel incident followed shortly (i.e., a couple centuries) after the Flood.9

    These two strikingly different accounts — evolution and YEC — for the origin of humans lead to very different expectations about the genetics of modern humans and apes. In some cases, however, the expectations are obviously the same. For instance, from an anatomical perspective, great apes are the most similar creatures to humans, and both sides can make a general prediction that, from a genetic perspective, apes should be the most similar to humans. While humans share different levels and traits of morphological similarity with gorillas, orangutans, and chimpanzees that don’t seem to indicate any clear evolutionary pattern, the current evolutionary consensus is that humans should be most similar to chimpanzees genetically — although this widely accepted paradigm has recently been disputed based on analyses of morphological traits by several evolutionists who claim that orangutans are the closest human relative.10

    As another example, both models accept the science of empirical genetic discovery. Hence, to claim that the existence of the basic science of genetics somehow validates one model over the other would be erroneous — a type-3 experiment that fails to distinguish among the competing ideas in question. Therefore, it is essential to clearly identify the specific predictions of each model in order to distinguish which genetic data actually constitute a type-1 experiment (e.g., one that differentiates YEC from evolution ) and which constitute lesser types of experiments.

    Are Humans 99% Genetically Identical to Chimpanzees?

    One common example of a type-2 experiment is predicting the genetic difference between humans and chimpanzees. The evolutionary model has very specific expectations about this figure, and a discrepancy between predictions and facts should result in the rejection of the evolutionary hypothesis. However, since the YEC model does not make specific predictions about human-ape genetic differences, a match between evolutionary expectations and scientific fact would not inform the origins debate (i.e., would not be decisive in evolution ’s favor).

    But the silence of the YEC model on human-chimp genetic differences is not a weakness of the model. We could just as well challenge the evolutionists to predict the number of animals that were taken on board Noah’s ark. This request would be fruitless and irrelevant to the debate since a global Flood and an ark are not part of the evolutionary model. However, if the YEC model failed to predict the numbers on board the ark accurately, then we would need to reevaluate aspects of the YEC model. Conversely, since human-ape ancestry is not part of the YEC model, the actual number of genetic differences between humans and chimpanzees is, at best, a type-2 experiment for testing the claim that humans descended from ape-like creatures — successful evolutionary predictions would not vindicate evolution in the origins debate, while evolutionary predictive failures could be grounds to reject the evolutionary view.

    With these experimental parameters in mind, we can now investigate the actual human-chimp genetic comparison in depth. If we think of genetic inheritance as analogous to copying the text of a book, the process of passing on genetic information from one generation to the next is similar to the process of transcribing the text of a book. To make the analogy tighter, inheritance is like copying the text of a book without having a perfect spell checker,11 and then using the corrupted copy as the template for the next round of copying.

    Biologically, the text of the genetic book is contained in a chemical substance called DNA. The DNA in our cells is, in essence, a chemical instruction manual for building and maintaining our anatomy and physiology from conception to death. The actual instructions are encoded in a 4-letter chemical alphabet, and the combination of these letters into chemical “words” and “sentences” carries biological meaning. In total, the DNA in our cells is billions of letters long — a very large biological “book.”

    When DNA is copied in sperm and egg cells prior to conception, the copying process is imperfect. The rate of copying mistakes (called mutations) has been measured in both humans and chimpanzees, and the rates are fairly similar. About 60 mutations happen each generation.12

    Using rounded numbers, if the human and chimpanzee lineages split 3–13 million years ago, and if the years from one generation to the next are about 20 years, then 150,000–650,000 generations have passed since the two species last shared a common ancestor.13 In each lineage, about 60 DNA mutations happen in each of those hundreds of thousands of generations leading to an expectation that the DNA of humans and the DNA of chimpanzees should differ by about 18–80 million DNA letters.14

    Thinking of DNA again like a book, we can measure book sizes by their word count, and if we wanted to be very technical, we could measure it by the total letter count. Since the total letter count in humans and chimpanzees is around 3 billion DNA letters,15 evolutionists expect about a 1–3% genetic (DNA) difference between these two species today.16

    The actual difference is about 12% — a number that is about ten times higher than the predicted value.17 Though the scientist responsible for identifying this fact is a young-earth creationist, this discovery is not the result of creationist manipulation of data to fit a pre-determined conclusion. If you read the fine print in the original evolutionary publication that announced the determination of the chimpanzee DNA sequence, you can reach a similar conclusion.18 Humans and chimpanzees are not 99% identical. They are only 88% identical, which means that the two species differ by nearly 400 million (400,000,000) DNA letters!19

    Thus, the question of human-chimpanzee DNA differences offers no assistance to the evolutionary model on at least three counts. First, whatever the difference is, it cannot falsify the YEC model, making it a type-2 experiment at best. Second, current evolutionary predictions for the human-chimp genetic difference fail to account for the gigantic genetic gap between these two species.

    Third, the evolutionary prediction of a 1% difference isn’t really a prediction at all. The evolutionary time at which the human and chimpanzee lineages split has been revised to fit the genetic data. Earlier predictions for the time of divergence for these species were originally in the 3 to 6 million year range,20 and the measurement of the DNA copying error rate in chimpanzees caused some investigators to (controversially) bump the time back further to

    13 million years.21 Thus, the absolute difference between humans and chimpanzees isn’t a confirmed prediction as much as it is a post hoc retrofitting of predictions to facts.

    These evolutionary problems aside, we are still left with the question of how to evaluate the YEC model on the human ancestry question. If human-ape genetic differences do not test validity of the YEC model of human origins, what experiment can? What genetic expectations follow from the specific YEC narrative?

    In short, the answer is that, if YEC is correct, then YE creationists should be able to explain human-human DNA differences and ape-ape DNA differences [as opposed to human-ape DNA differences] without any need to reference or invoke common ancestry. In other words, YE creationists make predictions for genetic differences among individuals that share a common ancestor under the YEC view (i.e., all humans), not for individuals that were created separately (i.e., humans and apes), and these predictions can be compared to the genetic facts.

    If genetic data matched these YEC expectations, would this result require rejection of the evolutionary model? Since evolutionists have spent years refining their own ideas about human-human and ape-ape genetic differences (and also believe that special creation as an alternative is unacceptable), this result would probably do nothing to settle the debate about human origins. In essence, it would be another example of a type-2 experiment — if the results are inconsistent with the YEC expectations, then perhaps the scientific elements of the YEC model should be reevaluated. But if the results confirm the YEC expectations, this discovery would probably do little to change the evolutionary claims about human-ape common ancestry.

    Since subsequent sections will explore this question further, the major remaining question in this section is whether the claimed evolutionary evidences for human-ape ancestry are valid type-1 experiments. The evidences listed on the BioLogos website are presented as such — as being unequivocal proof of common ancestry and as very inconsistent with the YEC view. The evidences in the mainstream scientific literature assume the same. But is the claim true?

    Relative Genetic Patterns/Nested Hierarchies

    Nearly every single one of the evidences presented by BioLogos and mainstream geneticists represents a type-3 experiment or, at best, type-2. For example, one of the most common evidences cited in favor of an ape ancestry in the human lineage is the relative pattern of genetic differences between humans and apes, and between humans and other species. In short, evolutionists expect natural selection to produce a branching, tree-like pattern of genealogical relationships among the living species on this planet.22 They further expect that, if humans arose via the process of natural selection from an ape-like ancestor, then genetic comparisons among humans, apes, and other species should reveal a branching, tree-like pattern as well.

    This expectation contrasts to the expectation about the percent DNA differences between humans and chimpanzees that we discussed earlier. The earlier expectation was a quantitative prediction the current expectation is a qualitative prediction. That is, qualitatively, if humans have ancestry prior to the first Homo sapiens, then evolutionists expect humans to be relatively close genetically to the great apes, then slightly less close genetically to the rest of the primates, then even less similar genetically to other mammals, and quite different genetically from invertebrates and plants. To be clear, the absolute number of differences is not so critical as long as the same relative pattern (in this case, a nested hierarchical pattern) holds true.

    For this argument to carry any scientific weight as a type-1 experiment in support of evolution , the YEC model would need to predict a different pattern. Otherwise, this argument would represent another type-3 experiment — useless to the overall origins debate.

    However, it doesn’t take much reflection to see that YEC and evolution make the same prediction about the relative genetic hierarchies found in nature. Under the YEC model, God designed the entire universe, including the various kinds of biological life that exist in it, and we would expect to find that life fits a design pattern. Since humans are made in God’s image, we can get a sense for what kinds of design patterns God might have used by examining the patterns that result from human designs. Examples of nested hierarchies abound among the designed things in our world.

    For example, designed means of transportation easily fit a relative hierarchical pattern. This fact is unequivocal. Sedans resemble SUVs more than they resemble tractor trailers, and all three vehicles have more in common than do sedans and amphibious assault vehicles. The latter two vehicles have more in common with one another than with submarines, and this simple pattern matches the type of hierarchy that we see in biology.23

    Therefore, nested hierarchical patterns are as much the expectation of the YEC view as they are of the evolutionary view. The relative hierarchy of genetic differences among humans, great apes, mammals, and invertebrates fits the YEC model at least as well as the evolutionary one. So, to claim nested hierarchical patterns in the biological world as exclusive evidence of evolution would be analogous to claiming that the existence of people proves YEC. Neither claim constitutes a legitimate scientific experiment. Both are type-3 experiments and, therefore, reveal nothing about the validity of either view, despite the confident claims of evolutionists to the contrary.24

    While these two examples (absolute and relative genetic differences between humans and the apes) do not constitute an exhaustive review of all the claimed genetic evidences for human-ape ancestry, they represent some of the most prominent, and they illustrate the Achilles’ heels of the remaining ones — failure to satisfy the requirements of a type-1 experiment.

    Human Chromosome 2 Fusion?

    Consider another example. If we return to our book analogy, just as the text of a book is broken up into chapters, so also the billions of letters in the DNA code for humans and chimpanzees are broken up into major divisions called chromosomes. However, because DNA comes from each parent, these chromosomes come in pairs.

    Evolutionists have claimed for years that the human chromosome pair number 2 is actually an accidental fusion of two pairs of ancestral chromosomes inherited from ape-like creatures.25 In short, they claim that the human-chimp ancestor had 48 chromosomes. Today, humans have 46. Since chromosomes come in two copies — e.g., the ape-like ancestor would have had 2 pairs of 24 chromosomes, and humans today have 23 pairs of chromosomes — and since humans have fewer total chromosomes than apes, evolutionists claim that one of the ancestral pairs of chromosomes fused to another ancestral pair of chromosomes. This would reduce the total chromosomes count from 48 to 46.26

    Since the YEC view makes no overt predictions about the differences between humans and chimpanzees in DNA organization or in the structure of DNA, the existence of a chromosome fusion would not have said anything relevant to the human origins debate. However, in this case evolutionists also made their claim prematurely, before all the evidence was acquired. Effectively, the evolutionary claims about the structure of human chromosome 2 represented a prediction rather than an observation.

    Recent reanalysis of human chromosome 2 has contradicted this evolutionary prediction. No evidence for a fusion exists. In fact, the alleged site where the fusion supposedly took place actually represents a highly organized, functional gene (in our analogy, think of genes as words or sentences).27 Thus, starting from the assumption of human-ape common ancestry, evolutionists have actually made a failed prediction about the structure and function of DNA within our cells.

    The failed evolutionary prediction on chromosome function extends beyond the purported fusion site. The BioLogos community has claimed that overall arrangement of DNA along chromosomes among humans and the great apes is inexplicable apart from common ancestry: “There is no good biological reason to find the same genes in the same order in unrelated organisms, and every good reason to expect very different gene orders.”28

    Do evolutionists actually have a large body of experimental results demonstrating “no good biological reason to find the same genes in the same order in unrelated organisms”? In the few cases where functional analyses have been performed, the results contradict this evolutionary assertion. The chromosomal context in which genes find themselves appears to play a significant role in how the genes function.29 In fact, human-designed computer code must also follow specific formats and contextual guidelines as well. So our previous analogy of human-designed systems as we applied to the idea of hierarchy holds true here as well. Thus, whether applied to predicted DNA differences or DNA function, the evolutionary model of common ancestry has not been vindicated.

    Conversely, the prediction of function is actually one of the few arenas in the question of human ancestry in which a type-1 experiment could be conducted. Evolutionists and creationists make very different predictions about the function of the billions of DNA letters in the human sequence, and experiments testing function would clearly distinguish which model makes better predictions, as we demonstrate below.

    Shared Genetic “Mistakes”?

    To make the point from a different angle, the members of BioLogos have made a host of claims on their website about shared “pseudogenes” and other types of purported shared biological “mistakes” in apes and humans. In fact, two of the three main “facts” that the website lists as genetic evidence for human evolution involve an implicit statement about function.30 In reality, hardly any actual experiments have been performed on the billions of DNA letters in humans and chimpanzees. “Pseudogene” actually represents a premature label for a particular segment of DNA that resembles a broken gene but which had never been experimentally tested for function. Thus, virtually all claims that BioLogos and other evolutionists have made about genetic “mistakes” are not arguments for evolution but bald assertions without a basis in experimental fact. Technically, this would make these arguments pseudoscience. However, for the sake of discussion, we’re willing to entertain these claims as predictions stemming from the assumption that evolution is true.

    Conversely, from the assumptions about human ancestry inherent to the YEC model, creationists have published a testable, predictive model of genetic function31 (see references for details). For the particular DNA differences that we examined, we expect them to function in each organism’s respective biology, whereas the evolutionary model claims that these particular DNA sequences are functionally neutral and are a reflection, therefore, of ancestry alone. Since precious few experiments have actually been done on genetic function, we now have a basis for doing a type-1 experiment in the future. By experimentally changing these sequences, we can evaluate whether or not these differences are functional — and confirm or reject the predictions of each origins model.

    For other DNA sequences, a few experiments have been performed, and the trajectory is not looking good for evolution. For example, after the human DNA sequence was elucidated in 2001, it was widely proclaimed that the vast majority of our billions of DNA letters were useless, non-functional leftovers of our evolutionary heritage and therefore called “junk” DNA.32 However, scientists didn’t actually do any experimental tests on the billions of letters until the Encyclopedia of DNA Elements (ENCODE) project was initiated in 2003. The first tier of ENCODE only examined about 1% of the human genome as an initial test, and they found preliminary evidence for pervasive function for the vast majority of those billions of letters.33 Then after extending this type of research to the entire human genome, using mostly human cell lines (not fresh tissues from living humans) they reported in 2012 that at least 80% of the genome had significant levels of biochemical function.34 It wasn’t useless junk after all.

    Many new discoveries in recent years are now pushing this level of functionality even higher. The leader of the ENCODE project, Ewan Birney, is predicting that the human genome will soon prove to be 100% functional.35 Needless to say, the traditional neo-Darwinian evolutionists outside the practical biomedical genetics community of ENCODE are outraged that the data is not supporting their dogmatic evolutionary claims.36

    In addition to these genome-wide results, other studies focusing on specific examples of “poster child” evolutionary pseudogenes regularly damage the credibility of the evolutionary claims. For example, the beta-globin pseudogene has obvious evidence for function,37 and one of the favorite pseudogene examples (e.g., vitellogenin) of the BioLogos geneticist, Dennis Venema, can also no longer be labeled a non-functional relic.

    Specifically, Venema claimed, “Humans have the remains of a gene devoted to egg yolk production in our DNA in exactly the place that evolution would predict.”38 But recent research has exposed this as nearly impossible to reconcile with the facts.39 The supposed evidence for this “egg yolk” gene is so pitiful that it’s hard to imagine how anyone could have seriously entertained this hypothesis in the first place. It’s like identifying the letter “e” in the Bible, finding the same letter in Darwin’s On the Origin of Species, and then claiming that the books were modified from a common ancestor — you really have to stretch your imagination to accept this claim. Conversely, there is so little DNA remnant of the egg yolk gene that it requires a real strain of the imagination to see why some evolutionists pursued this line of reasoning in the first place. Current data suggest that they mistook a functional DNA sequence (enhancer element) inside a genomic address messenger gene involved with brain tissue function, for a non-functional egg yolk gene “remnant.”40 Not surprisingly, the BioLogos community has downplayed the significance of these accumulating discoveries and tried to turn the tables on creationists with clever rhetorical games. Rather than admit the obvious damaging implications for evolution,41 the BioLogos staff has turned the argument around and challenged creationists to explain the remaining data that BioLogos claimed demonstrated non-function.41 In fact, Dennis Venema recently went so far as to claim, “Having the complete genome sequences for a variety of great apes makes looking for additional shared mutations a trivial exercise, and it is no exaggeration to say that there are thousands of examples that could be used.”42

    But the BioLogos rejoinder misses the big picture and the point. First, preliminary biochemical evidence for function does not exist merely for the two examples of pseudogenes that we discussed. It exists for at least

    80% of all the pseudogenes in humans.43 And the other 20% may still yet be found to be functional in some human tissue or under some physiological condition yet to be studied . . . and there are many. That’s the catch: many noncoding RNA genes (like pseudogenes) are only expressed under certain conditions.

    Second, challenging creationists to explain the remaining examples of “non-function” assumes that actual experiments have been performed that demonstrate non-function. They have not. The reality is that we have only just begun to uncover the functionality of the human genome. Consider just how many experiments would need to be performed to conclude with any sort of confidence that a particular set of DNA sequences has zero function. The number of possible scenarios in which a DNA sequence might plausibly function is now proving to be enormous. For example, in the short nine-month window of time that represents human embryonic development, a single cell turns into a fully formed baby that contains hundreds of cell types that must execute an unimaginable number of cellular tasks. Surely the developing baby calls upon enormous swaths of DNA code to execute this developmental program — and then silences or repurposes them for the remainder of its life via another type of code (a code which is being studied by investigators in a scientific field termed “epigenetics”).44 The dynamic use of DNA sequence during development is very different than the vast majority of DNA sequence use in the adult. Experimentally testing a DNA sequence during each of these unique windows of time in which sections of DNA are used and then silenced would be an enormous (and morally questionable) experiment. However, expressed RNA sequences have been analyzed in organ donors, aborted fetal tissue, and embryonic stem cells, with the latter two involving the murder of innocent babies. Nevertheless, these morbid data have only served to increase the known functionality and complexity of the human genome. In addition, until experiments are performed in living humans, which is also unethical, it is both inappropriate and scientifically uninformed to claim “non-function” for human DNA. In short, the recent decade of experimental results on human DNA sequences that demonstrate biochemical evidence for function are just the beginning of our understanding as to the complexity and function of the genome. Perhaps the most important point that can be taken from all this is the trajectory of these results — we watched the scientific community go from claiming high levels of non-function in the early 2000s to claiming evidence for nearly pervasive function just a decade later. This suggests that more experiments will only increase the percentage of human DNA sequence that performs a biological function just as the current leader of the ENCODE project is predicting. This upward trajectory does not bode well for evolution , a fact that the BioLogos community is very reticent to admit.

    Neanderthal Ancestry?

    On a side note, related to the question of human-ape ancestry is the question of the relationships between Neanderthals and modern humans. Interestingly, most people would be surprised to know that evolutionists consider Neanderthals to be fully human, hence they are given the technical name “archaic humans” as opposed to modern contemporary humans. An increasing number of publications claim to have recovered DNA from ancient human or human-like samples, and the comparison of these DNA samples with those of modern humans could inform the ancestry question.

    Though YEC advocates and evolutionists both agree that modern humans and Neanderthals had a common ancestor (YE creationists would say that Neanderthals are post-Flood descendants of Adam and Eve), these two positions disagree on when the Neanderthals lived — tens to hundreds of thousands of years ago (evolutionary model) versus about 4,500 years or less (YEC model). Evidence for a prehistoric45 human population could add credence to the evolutionary claim that human ancestry stretches far back in time — so far back that it touches on the boundaries of an alleged divergence from an ape lineage. Time is the magical key to the evolutionary equation, despite the fact that no viable human-ape transitional forms exist in the fossil record, as discussed in a separate chapter.

    Without going into great technical detail, the short answer to the question of what Neanderthal DNA implies regarding the origins issue is that Neanderthal and ancient DNA samples appear to be too degraded and often untrustworthy for use in rigorous genetic analyses. In addition, analyses are perpetually plagued with DNA contamination from microorganisms and modern human DNA from lab workers.46 Finally, no one knows the rate at which Neanderthal DNA changes from generation to generation — and it might change at a rate much faster than that reported for modern human individuals.47

    As things stand now, the most credible research comparing Neanderthals to modern humans merely shows that their DNA is human. The dating of the bones from the sites in which Neanderthals are found are not based on DNA, but other types of spurious data, and the evolutionists are constantly changing the dates of the material found in these locations — a fact in and of itself that shows how subjective the whole process really is.

    Summary

    To summarize, on the question of human-ape common ancestry, all of the claimed evolutionary evidences are type-2 or type-3 experiments that fail to eliminate the main competing hypothesis, YEC (Table 2). Instead of being a minor side issue in the bigger human ancestry debate, this very poor scientific track record for evolution represents a systematic failure across the board. In nearly every type of genetic comparison that can be performed between humans and chimpanzees, the evolutionary model has made erroneous predictions (Table 3).

    Table 2. Factually erroneous evolutionary claims about human-primate ancestry
    Evolutionary Claim Actual Data Type of Experiment
    Human-chimpanzee genetic identity is 98-99% Actual genetic identity is only 88% (i.e., 400,000,000 DNA differences exist between the two species) 2
    Humans are genetically closer to apes than to other animal species, unequivocally demonstrating common ancestry Relative hierarchies are characteristics of design 3
    Human chromosome #2 arose via fusion of two ape-like chromosomes The purported “fusion” site is actually a functional DNA element in a human gene 2
    Gene order along chromosomes has no function, therefore shared gene order demonstrates common ancestry Gene order along chromosomes does indeed perform a function 2
    Humans and chimpanzees shared genetic mistakes (e.g., pseudogenes) Pseudogenes appear to be functional DNA elements, not mistakes 2
    Humans possess the broken remnants of an ancient chicken gene (vitellogenin) No such remnant exists instead the “fragment” appears to be a functional DNA element 2
    Table 3. Grand Summary of Human-Chimpanzee Genetic Comparisons
    Type of Genetic Comparison/Analysis Evolutionary Success or Failure?
    Total DNA differences between humans and chimpanzees Failure to predict total genetic differences (a big genetic gap separates the two species)
    Relative genetic differences between humans and chimpanzees Irrelevant to debate (evolutionary comparison fails to refute the YEC model, thereby making it scientifically invalid)
    Chromosome differences between humans and chimpanzees Failure to predict chromosome differences (no evidence for claimed fusion event)
    Total genetic function in humans Current scientific trajectory points toward much more function than predicted by evolution
    Specific examples of genetic function in humans Failure to predict functional DNA sequences (pseudogenes and chromosomal gene order were mislabeled as “non-functional”)

    In an attempt to move the discussion forward and into the realm of type-1 experiments, creationists have published a testable, predictive model of DNA function from a YEC perspective on one of the few remaining areas of DNA function that has not yet been thoroughly investigated48 (see reference for technical details). If the evolutionists are as confident in their ideas as they claim, then we invite them to publish similar predictions of genetic function, and then to do a head-to-head experiment to test both of the ideas in the laboratory. If evolutionists are unwilling to engage in the experiment that we have proposed, at a minimum, they need to propose a different type-1 experiment.

    In short, on the question of human ancestry, evolutionists have a history of making erroneous scientific predictions they have yet to articulate a genuine genetic test by which to eliminate YEC from the discussion and their model does not look promising in light of the trajectory of experimental results in areas where evolution and YEC could theoretically be compared head-to-head.


    Chapter 19 - Introduction to Human Genetics

    This chapter reviews the basic principles of human genetics to serve as a basis for other studies that deal with specific genetic approaches in clinical research. Genetics is the science that deals with the storage of information within the cell, its transmission from generation to generation, and variation among individuals within a population. Human genetics research has a long history, dating to the study of quantitative traits in the nineteenth century and to the study of Mendelian traits in the first decade of the twentieth century. Medical applications have included such landmarks as newborn screening for inborn errors of metabolism, cytogenetic analysis, molecular diagnosis, and therapeutic interventions such as enzyme replacement. Medical applications historically have been limited to relatively rare disorders caused primarily by mutations in individual genes or structural abnormalities of chromosomes. Recent advances, and especially the sequencing of the human genome, have opened the possibility of understanding genetic contributions to more common disorders, such as diabetes and hypertension. Genetic approaches are now being applied to conditions in virtually all areas of medicine. Genetic information is stored in the cell as molecules of deoxyribonucleic acid (DNA). Each DNA molecule consists of a pair of helical deoxyribose–phosphate backbones connected by hydrogen bonding between nucleotide bases. There are two types of nucleotide bases, purines (adenine [A] and guanine [G]) and pyrimidines (cytosine [C] and thymine [T]).


    A Long Time Ago, in a Gamete Far, Far Away.

    Life on our planet began with single-cell organisms such as bacteria that reproduce asexually. There isn’t a mother and a father. A cell simply reproduces its genetic material and divides into two or more cells that are genetically identical to the parent cell.

    About three or four billion years ago, these single-cell organisms without a distinct nucleus (prokaryotes, or bacteria) began exchanging genetic information in a limited fashion. Then about two billion years ago, organisms such as yeast, with distinct cellular nuclei and specialized structures called organelles (eukaryotes), put their genes in pairs so that they could be divided into two structurally identical gametes (one-cell reproductive units called spores in the case of yeast) and reassembled to create a new organism. This special kind of cell division is called meiosis.

    Around 600 million years ago, animals began to evolve specialized gametes — structurally different single-cell units for females (eggs) and males (sperm). Sperm cells fertilize an egg, which then combines the genes of both parents. But such animals, including modern-day turtles, had no specialized sex chromosomes that determine the sex of the offspring. Males and females were genetically identical, and the sex was determined by the temperature at which the egg is incubated.

    And finally, starting about 300 million years ago, our ancestors began to evolve sex chromosomes.

    In humans, there are 23 pairs of chromosomes, which are structures found within the nucleus of every cell containing the tightly packed molecules known as deoxyribonucleic acid (DNA), the material that carries the genetic code.

    One pair of the 23 chromosomes, known as sex chromosomes, determines at conception whether a fertilized egg will develop into a male or female. Today, human females have one pair of identical X chromosomes. Human males, instead of a matched pair, have one X and one smaller Y chromosome.

    A human egg contains only an X chromosome. A human sperm contains either an X or a Y chromosome, thereby determining the sex of the offspring after fertilization. XX = female. XY = male.

    Dr. Page and his colleagues have spent the better part of the last two decades reconstructing the evolutionary origins of the human X and Y chromosomes. They have traced the origins of these sex chromosomes to ordinary chromosomes called autosomes in evolutionary ancestors that humans share with birds.

    “We have been distracted and deceived for the last 50 years by the existence of our sex chromosomes,” Page said. “Most genes that are actually involved in making the different anatomies of human males and females are not on the sex chromosomes. Most of them are on the autosomes. They are exactly the same in males and females. It’s just that the autosomes are read differently in males and females because of the sex chromosomes, just as the entirety of the genome is read differently in males and females.”


    In our 23 chromosome pairs, do the 2 members of the pair have distinct or virtually identical sequences? - Biology

    Cell Division (Mitosis) In Eukaryotic Cells

      I. Interphase : Period of cell cycle when cell is not dividing. (15 hours)

      A. G1 Phase: Cellular organelles begin to duplicate.

    B. S-Phase: DNA replication (chomosomes become doubled).

    II. M-Phase (Period of Cell Division): (2 hours)

      A. Karyokinesis (Mitosis or Nuclear Division):
      This includes Prophase , Metaphase , Anaphase & Telophase .

    2. Homologous Chromosomes: Paternal and Maternal

    Single chromosomes and doubled chromosomes (chromosome doublets). Beginning with prophase, the chromosomes appear as doublets. The clear pink doublets represent a set of maternal doubled chromosomes originally from the mother's egg. The striped blue doublets represent a set of paternal doubled chromosomes originally from the father's sperm. Diploid (2n) organisms such as humans have two sets of chromosomes, one haploid (n) set from the father and one haploid (n) set from the mother. Fertilization of the two haploid sex cells (egg and sperm) results in a diploid zygote (n + n = 2n). Homologous pairs of doublets are represented by one large pink and one large blue doubled chromosome of matching size, and one small pink and one small blue doublet of matching size. In this diagram there are two pairs of homologous chromosome doublets. In a human cell during prophase there are 23 pairs of homologous chromosome doublets, a total of 46 doublets and 92 chromatids. After the chromatids separate during anaphase and the cell divides during telophase, the resulting daughter cells have 23 pairs of single chromosomes, a total of 46. The single chromosomes become doubled again during the S-phase of interphase, prior to the onset of prophase.

    In this diagram the cell contains 3 pairs of homologous single chromosomes, a total of 6 chromosomes. Since the cell contains a total of 6 chromosomes, it has a chromosome number of 6. Chromosomes A & a represent one pair, B & b represent a second pair, and C & c represent a third pair. Each pair is called a homologous pair because they are matching in size and shape. One member of each pair comes from the mother (pink chromosome) and one member of each pair comes from the father (blue chromosome). Three pink chromosomes in this cell (A, B & C) represent one haploid set of maternal chromosomes from the mother. Three blue chromosomes (a, b & c) in this cell represent one haploid set of paternal chromosomes from the father. Since there are 2 sets of chromosomes in this diagram, the cell is diploid (2n).

    One chromatid of this eukaryotic chromosome doublet is unravelled, showing a twisted DNA molecule wrapped around beads of histone protein. Each protein bead contains about 200 base pairs on its surface, while the strand between consists of about 50 base pairs. Each protein bead with DNA on its surface is called a nucleosome. Each chromatid is essentially composed of a greatly coiled DNA molecule and protein. The chromatids (DNA molecules) are attached in a region known as the centromere. In these greatly oversimplified illustrations, the centromere is shown as a black dot. It simply represents an area where the sister DNA molecules (chromatids) are attached.

    3. The M-Phase (Cell Division Phase)

    1. Interphase: The cell is not dividing at this time period. The nucleus is composed of dark staining material called chromatin, a term that applies to all of the chromosomes collectively. At this stage the chromosomes are tenuous (threadlike) and are not visible as distinct bodies. A nucleolus is clearly visible inside the nucleus. This body is composed of ribosomal RNA and is the site of protein synthesis within the cell. Prior to cell division, two pairs of protein bodies called centrioles are present in the cytoplasm at one end of the cell. Centrioles are not typically present in plant cells.

    2. Prophase: One of the centrioles moves to the opposite end of the cell. The opposite ends of the cell are called poles, like the poles of the earth. Each centriole now consists of a pair of protein bodies surrounded by radiating strands of protein called the aster. Plant cells typically do not have the aster or centrioles. Also the nuclear membrane disintegrates and the chromosomes shorten and thicken so that they are visible as distinct rod-shaped bodies. At this time each chromosome is doubled and consists of two chromatids. Each chromatid is essentially composed of a greatly coiled DNA molecule and protein. The chromatids (DNA molecules) are attached in a region known as the centromere. In these greatly oversimplified illustrations, the centromere is shown as a black dot.

    3. Metaphase: The chromosome doublets become arranged in the central region of the cell known as the equator. They do not necessarily line up single file as the drawing shows. Protein threads called the spindle connect the centromere region of each chromosome doublet with the centrioles at the poles of the cells.

    4. Anaphase: The chromatids separate from each other at the centromere region and the single chromosomes move to opposite ends (poles) of the cell. When the chromatids separate from each other they are no longer called chromatids. They are now referred to as single chromosomes. The single chromosomes are actually being pulled to opposite ends of the cell as the spindle fibers shorten.

    The corms of autumn crocus ( Colchicum autumnale ), a member of the lily family (Liliaceae), contain the alkaloid colchicine, a spindle poison causing depolymerization of mitotic spindles into tubulin subunits. This essentially dissolves the spindle and stops the cell from completing its mitotic division. Because colchicine can stop plant cells from dividing after the chromatids have separated during anaphase of mitosis, it is a powerful inducer of polyploidy. Seeds and meristematic buds can be treated with colchicine, and the cells inside become polyploid with multiple sets of chromosomes (more than the diploid number). Polyploidy in plants has some tremendous commercial applications because odd polyploids (such as 3n triploids) are sterile and seedless. Polyploid plants (such as 4n tetraploids) typically produce larger flowers and fruits. In fact, many of the fruits and vegetables sold at supermarkets are polyploid varieties. Colchicine has another medical use for people because it reduces the inflammation and pain of gout. It is also used in cancer chemotherapy to stop tumor cells from dividing, thus causing remission of the cancer.

    Two additional alkaloids (vinblastine and vincristine) from the Madagascar periwinkle ( Catharanthus roseus ) are also potent spindle poisons. These alkaloids have proven to be very effective in chemotherapy treatments for leukemia and Hodgkin's disease (lymph node and spleen cancer). Like colchicine, they cause the dissolution (depolymerization) of protein microtubules which make up the mitotic spindle in dividing cells. This effectively stops the tumor cells from dividing, thus causing remission of the cancer. Before periwinkle alkaloids were used as a treatment there was virtually no hope for patients with Hodgkin's disease. Now there is a 90 percent chance of survival. This is a compelling reason for preserving the diverse flora and fauna in natural ecosystems. Who knows what cures for dreaded diseases are waiting to be discovered in tropical rain forests or other natural habitats.

    5. Telophase: The chromosomes at each end of the cell begin to organize into separate nuclei, each surrounded by a nuclear membrane. A cleavage furrow or constriction forms in the center of the cell, gradually getting deeper and deeper until the cell is divided into two separate cells. This cytoplasmic division is referred to as cytokinesis. Cytoplasmic division (cytokinesis) in a plant cell is accomplished by a partition or cell plate rather than a cleavage furrow. The following illustration shows cell plate formation in an onion root tip cell:

    6. Interphase: Now we are back to interphase again, but now there are two daughter cells. Each daughter cell is chromosomally identical with the original (mother) cell. They each have a nucleus that contains a nucleolus and chromatin. The centrioles have divided into four protein bodies and the aster has disappeared. During this phase the chromosomes will replicate and become distinct chromosome doublets as each daughter cell enters prophase.

    The five major phases of plant mitosis. Unlike animals cells, plant cells do not have centrioles or asters. During telophase, a partition or cell plate divides the cytoplasm rather than a cleavage furrow.

    5. Mitosis & Embryonic Stem Cells

    A. Starfish embryo during the morula stage. It consists of a ball of actively dividing cells superficially resembling the multiple fruit of a mulberry (hence, the name morula). At this stage, each cell is unspecialized and can potentially develop into a separate organism. A human embryo is in the morula stage as it travels down the fallopian tube. At the time of implantation on the uterine wall (officially marking the onset of pregnancy), the embryo consists of a hollow sphere or blastocyst (blastula) consisting of approximately 100 cells roughly the size of a printed period.
    Multiple fruit of the black mulberry ( Morus nigra ). The
    individual units are one-seeded drupelets rather than cells.
    B. Highly magnified view of a whitefish morula showing several stages of mitosis: 1 = prophase, 2 = metaphase, 3 = anaphase, 4 = telophase.

    Note: The undifferentiated cells of human blastocysts are called embryonic stem cells. Blastocysts can be formed in vitro through test tube fertilizations. Undifferentiated stem cells are especially remarkable because they can give rise to different tissues and organs. Through complex gene interactions, these cells can literally develop into any number of cell types found in the human body. The controversy over the use of embryonic stem cells in research involves the question of what constitutes a human being and when does life officially begin. In a recent discussion by right wing conservatives on when life begins, the term oocyte was included. I'm not sure if they meant primary as well as secondary oocytes. If the cells of morulas and blastocysts are also considered human beings (or U.S. citizens as some religious conservatives propose), then so are diploid somatic cells in living humans, the nuclei of which can be placed in denucleated egg cells. Biologists in other countries must be laughing at this absolute nonsense.

    With the sophisticated techniques of modern biotechnology, the nucleus of any undifferentiated cell has the potential to grow into a clone if it is placed in a denucleated egg cell. The bottom line here is that the cells must be placed in a carefully controlled environment in order to grow into a human. The latter cells can be grown in vivo (within in living organism) or in vitro (in a vessel outside of a living organism). Stem cells cultured in vitro, provide an unprecedented opportunity for the study and understanding of human embryology and the generation of tissues and organs. This research could provide a remarkable potential for therapy and cures for many devastating human diseases, including various forms of diabetes, cancers of human tissues, organs and bone marrow, and diseases of the central nervous system (such as Parkinson's disease and Alzheimer's disease). Depending on how they are cultured, embryonic stem cells could potentially be grown into tissues and organs that could save the life of a child or an adult human. Some opponents of embryonic stem cell research consider human morulas and blastulas to be human beings and should not be harvested, not even to save the life of a loved one. Placental and amniotic tissue may provide an alternative and less controversial source of stem cells.

    A human morula composed of 16-32 cells.

    6. Tumors: Uncontrolled Cell Division

    When cells divide abnormally they often develop into tissue masses called tumors. Tumors can be produced throughout the body and they can be malignant or benign. Malignant tumors are often referred to as cancers. Some human cancers are caused by viruses, such as certain forms of the herpes virus that causes cervical cancer. Most cancers are neoplastic tumors caused by mutations in the DNA of cells. These mutations interfere with the cell's ability to regulate and limit cell division. Dormant cells enter the M-phase of the cell cycle and begin to divide out of control. Mutations that activate cancer-causing oncogenes or repress tumor-suppressor genes can eventually lead to tumors. Cells have mechanisms that repair mistakes in their DNA however, mutations that affect repair enzymes may cause tumors to form. One of the best examples of the latter mechanism is a basal cell carcinoma.

    Excessive exposure to UV radiation from the sun can cause mutations in undifferentiated basal keratinocytes (basal cells) of the epidermis. The specific mutation is called a thymine dimer within the DNA molecule. In normal DNA, the pyrimidine base thymine only pairs with the purine base adenine. When two adjacent thymine bases bond together this causes an abnormal configuration or "kink" in the DNA. Healthy cells can recognize and repair this mistake by excision repair enzymes. In some animals the mutation is repaired by DNA photolyase enzymes that clip out (cleave) the dimer. People with a genetic propensity for skin cancers may have insufficient repair enzymes due to mutations that repress the genes for these repair mechanisms. Although malignant basal cell carninomas generally do not metastasize, they may slowly invade deep layers of the skin and adjacent tissue and eventually be quite destructive. The following image shows the invasive growth of a basal cell carcinoma (technically a morpheaform bcc) that required the removal of about 1/3 of the author's nose. Unlike the nodule growth form of some basal cell carcinomas, the morpheaform bcc proliferates into deeper tissue with aggressive, tentacle-like branches. In addition to an increased number and density of dark-staining basal cells, the latter type of skin cancer produces a proliferation of fibroblasts within the dermis and an increased collagen deposition (sclerosis) that resembles a scar. The tumor appears as a whitish, waxy, sclerotic plaque that rarely ulcerates. It does not form noticeable scabs as in other skin cancers. On the surface of the author's ala (side of nose), this carcimoma resembled a small, concave scar however, it had grown extensively into surrounding tissue. Although the sun is the vital energy source for all life on earth, it can also be a potent carcinogen.

    On a positive note for sun exposure, synthesis of vitamin D, a vitamin essential to human biological function, begins with activation of a precursor molecule in the skin by UV rays. Enzymes in the liver and kidneys then modify the activated precursor and finally produce calcitrol, the most active form of vitamin D. During most of the year, a few hours per week of sun exposure to the face and arms is sufficient to meet the body's requirement for the activated calcitrol precursor. In general, fair-skinned people live in northern latitudes with lower light intensity compared with dark-skinned people of the tropical latitudes. Dark skinned people produce greater concentrations of melanin which protects their skin from harmful rays of the sun. Basal cell carcinomas are rare in Blacks and Asians, compared with fair-skinned Whites. It has been suggested that fair-skinned people of northern latitudes might have a slight advantage in synthesizing vitamin D, especially during months of the year in regions with reduced light intensity.

    Dividing human cells can be photographed during prophase and metaphase, and all the 46 chromosome doublets can be arranged into 23 homologous pairs. A photographic or digital printed image called a karyotype is then made showing all the chromosomes neatly lined up in homologous pairs, from 1 through 23. Karotypes are very useful in determining chromosomal abnormalities, such as chromosomal deletions (missing genes) or incorrect numbers. For example, a person with Down's syndrome would have three number 21 chromosomes rather than two.

    Karyotypes can also reveal the gender of a person. In addition to the 22 pairs of chromosomes (autosomes) in human somatic (body) cells, females have a 23rd pair consisting of two X chromosomes. The 23rd pair of males consists of an X and a Y chromosome. The smaller Y chromosome contains a region of DNA on the short arm of the Y responsible for masculinization of the fetus. In females one of the two X chromosomes appears as a condensed, dark-staining Barr body inside the nucleus of somatic cells, near the nuclear membrane. This structure is named after its discoverer, Murray Barr. Since Barr bodies only appear in nuclei with more than one X chromosome, they are not present in male cells. Up until the early 1990s, the lack of Barr bodies in nuclei from cheek epithelial cells of women could disqualify them for competition in the Olympic Games.

    The calico cat is a sexual mosaic characterized by blotches of black, yellow and white fur. The genes (alleles) for black and yellow are linked to the same loci on two different X chromosomes. This is why calico cats are typically female because they have two X chromosomes, one with the black gene and one with the yellow gene. Since the black gene is dominant over yellow, how does the mosaic color pattern develop? The Barr body concept provides a nice cellular explanation for the patches of black and yellow fur. In regions with black fur, the black gene is active and the yellow gene is located on an inactive Barr body. In regions with yellow fur, the black gene is on the inactive Barr body while the yellow gene is on the active X chromosome. At an early stage in the cat's embryonic development, certain X chromosomes become inactive Barr bodies, apparantly at random. In the descendants of these cells, the same chromosomes are inactive, leaving the cells with only one functional allele for coat color. A rare calico male probably has an XXY karotype resulting in maleness, black fur and yellow fur. By the way, the white patches result from a gene interaction involving the "spotting gene," which blocks melanin synthesis entirely.

    Gender verification in the Olympic Games now employs sophisticated DNA testing rather than counting Barr bodies within the nuclei of cells. The test is designed to detect the presence of the SRY gene (sex region Y chromosome), a region of DNA on the short arm of the Y chromosome responsible for masculinization of the fetus. Cells from the buccal mucosa (squamous epithelial cells), often called "cheek cells" in general biology classes, are obtained by gently scraping the inside of the mouth with a toothpick. The DNA in the nuclei of these cells is amplified using the PCR technique (polymerase chain reaction). If present, the SRY gene will show up as a unique banding pattern by electrophoresis on agar gels.

    The following table shows different possible combinations of X and Y chromosomes in people. The gender of some of these chromosomal karyotypes and syndromes cannot be correctly identified using the Barr body technique:

    The gender of the following chromosomal karyotypes and syndromes cannot be correctly identified using the Barr body technique. In addition the SRY test is not reliable in individuals with hormonal sex variations, such as androgen insensitivity and adrenogenital syndromes. For example, an XY person with androgen insensitivity has a Y chromosome with the SRY gene. Although they produce testosterone, they have a sex-linked gene on their X chromosome resulting in the lack of testosterone receptor proteins therefore, they do not develop male characteristics. In other words, they produce androgens but do not respond to them.


    Materials and Methods

    Plant material and genetics

    Anthers of O. sativa cv. Nipponbare (2n=24) were used for western blot and immunocytological analyses. For immunocytology, a pair2 mutant from the fifth generation after regeneration, which was derived from a Tos17-tagged line NC0122 (Nonomura et al., 2004b), was also used. All materials were grown in a field in the city of Mishima, Shizuoka, Japan, or in a greenhouse at 30°C during the day and 24°C at night.

    Antibody production

    The entire coding region of PAIR2 cDNA (DDBJ Accession No. AB109238) (Nonomura et al., 2004b) was amplified by PCR using primers P609 (5′-CACCATGGTGATGGCTCAGAAGACGAAG-3′) and P610 (5′-TCACTGAACTTGAACTTGAACTTGGGAC-3′). The PCR product was cloned into the pENTR-TOPO plasmid and re-inserted into pDEST17 with a 6× histidine (6×His) repeat at the 5′-end of the multiple cloning site using the Gateway system (Invitrogen). After transformation of Escherichia coli strain BL21-AI (Invitrogen) with the plasmid, expression of the fusion protein was induced by adding L-arabinose to a final concentration of 0.2% (w/v) in LB liquid culture.

    The clone E30313, carrying the OsCenH3 cDNA in pBluescript II SK+, was kindly provided by T. Sasaki, Ministry of Agriculture, Forestry and Fisheries (MAFF) DNA Bank, Tsukubu, Japan. This clone is identical to the CenH3 cDNA (GenBank accession No. AY438639) used by Nagaki et al. (Nagaki et al., 2004). The sequence encoding the 41 N-terminal amino acids of OsCenH3 (AEPKKKLQFERSPRPSKAQRAGGGTGTSATTRSAAGTSASG) was used to generate a GST-fusion peptide. The fragment was amplified by PCR using primers, Tz1 (5′-GGAATTCCCGCGGAGCCCAAGAAGAAGC-3′) and Tz2 (5′-GAGTCGACCCTGAAGCCGATGTTCCAG-3′), then digested with EcoRI and SalI, and ligated between the EcoRI and SalI sites of the GST-tagged protein expression vector pGEX-6P-2 (Amersham Biosciences). Expression of the fusion peptide was induced in E. coli BL21(DE3) by addition of 0.1 mM IPTG to the culture medium.

    The recombinant peptides expressed were extracted 4 or 6 hours after induction using the BugBuster protein extraction reagent (Novagen). The 6×His- and GST-tagged peptides in the soluble fraction were purified using a HisTrap kit and glutathione Sepharose 4B (both from Amersham Biosciences), respectively, according to the manufacturer's instructions. 250 μg of PAIR2 and 750 μg of OsCenH3 recombinant peptides were injected into a rabbit and guinea pig every two weeks, respectively. Immune sera were extracted 52 days after the first injection.

    Western blotting

    Proteins from plant tissues were extracted in 2% SDS, 6% β-mercaptoethanol, 10% glycerol and 50 mM Tris-HCl (pH 6.8), and insoluble materials were removed by centrifugation. Protein samples were separated by SDS-PAGE on a 7.5% polyacrylamide gel and electroblotted onto Hybond-P PVDF membrane (Amersham). Western blots were incubated with anti-PAIR2 antiserum diluted 1/5000 followed by anti-rabbit IgG antibodies conjugated to horseradish peroxidase (Amersham) diluted 1/25,000. Signals were detected by the ECL Plus detection system (Amersham). An anti-rat α-tubulin monoclonal antibody OBT0614S (Oxford Biotechnology) was used as a positive control.

    Indirect immunofluorescence

    Young panicles containing PMCs entering into meiosis were fixed with 4% (w/v) paraformaldehyde (PFA) in PMEG buffer (25 mM PIPES, 5 mM EGTA, 2.5 mM MgSO4, 4% glycerol, and 0.2% DMSO, pH 6.8) for 3 hours, washed six times with PMEG for 20 minutes each, and stored at 4°C. Using a single anther of a floret, the meiotic stage of the PMCs was determined by an acetic-carmine squashing method. The remaining five anthers in appropriate meiotic stages were incubated in a 20:0.75 mixture of an enzyme cocktail with 100 mg/ml cytohelicase (Sigma) for 20 minutes at 37°C, and another 5 minutes at 4°C. The enzyme cocktail contained 2% cellulase Onozuka-RS (Yakult Honsha, Japan), 0.3% pectolyase Y-23 (Kikkoman) and 0.5% Macerozyme-R10 (Yakult Honsha) in PMEG (pH 6.9). The anthers were washed five times with PMEG on a poly-L-lysine-coated glass slide, and squashed in PMEG by a needle. After the cell debris was removed, the cell suspension was covered by a cover slip. The slip was removed on dry ice, and the samples were air-dried. The slide was washed three times with PMEG for 5 minutes each, blocked with 3% BSA (Sigma) in PMEG for 30 minutes followed by a PMEG wash for 5 minutes, and used for antibody staining.

    The slide was incubated at 4°C overnight with rabbit anti-PAIR2 antibody and guinea pig anti-OsCenH3 antisera, diluted 1/3000 and 1/2000, respectively, with 3% BSA/PMEG. After three washes with PMEG for 5 minutes each, the slide was incubated in a dark chamber for 3 hours at room temperature with Alexa Fluor 488-conjugated anti-rabbit IgG and Alexa Fluor 568-conjugated anti-guinea pig IgG (both from Molecular Probes) diluted 1/200 with 3% BSA/PMEG, followed by three washes with PMEG for 5 minutes each. Then, 40 μg/ml of propidium iodide (Sigma) or 4′,6-diamidino-2-phenylindole (DAPI) (Sigma) in Vectashield solution (Vector) was applied to counter-stain the chromatin or, alternatively, the chromatin was immunologically stained with mouse anti-histone pan antibody (1/1000 dilution Roche) and anti-mouse IgG-Cy5 conjugate (1/200 dilution Amersham). The signals were observed using a Fluoview FV300 CLSM system (Olympus). Captured images were enhanced and pseudo-colored by Photoshop 7.0 software (Adobe).

    To stain spindle microtubules, monoclonal antibody against rat-α-tubulin subunit (OBT0614S Oxford Biotechnology) was used. A condition to stain the spindle has been described previously (Nonomura et al., 2004a).

    BrdU incorporation and detection

    Fresh young panicles of 3-6 cm in length were cut from stems and placed in 100 μM BrdU solution in the dark for 4 hours. The panicles were fixed with 4% PFA/PMEG as described above. Anthers 0.3-0.5 mm long were isolated from flowers 1.5-2.0 mm long, which often included meiocytes from pre-meiotic S phase to early meiosis (Nonomura et al., 2004b), and then digested with the enzyme mixture used for PMC preparation on a poly-L-lysine-coated glass slide as described above. Mouse anti-BrdU monoclonal antibody (Becton Dickinson) was diluted 1/3000 and used to detect incorporated BrdU in the PMCs.

    Electron microscope observation and immunogold localization

    For transmission EM, a flower including the PMCs at zygotene was fixed with 2.5% glutaraldehyde/PBS at 4°C for 2 hours. After five washes with PBS at 4°C for 1 hour each, samples were incubated at 4°C overnight to remove the glutaraldehyde completely. Flowers were briefly washed three times with PBS, fixed with 1% osmium tetroxide/PBS at room temperature for 1 hour, dehydrated in an ethanol series, and embedded in Epon resin. For immunogold localization, a flower was fixed with 0.1% glutaraldehyde/4% PFA/0.1 M phosphate buffer for 3 hours, then washed three times with 0.14 M sucrose/0.1 M phosphate buffer. Samples were incubated at 4°C overnight, then dehydrated through an ethanol series and embedded in LR White acrylic medium (Polysciences). After standard procedures to make ultrathin sections for EM observation, the sections were mounted on nickel mesh grids.

    For immunogold localization, sections were washed with PBS for 10 seconds and with 1%BSA/PBS for 30 minutes, and incubated in 1/100 diluted anti-PAIR antiserum/1%BSA/PBS at 4°C overnight. After three washes with PBS for 30 minutes each, sections were incubated in a 1/10 dilution of the goat anti-rabbit IgG, and conjugated with a 20 nm gold colloidal particle (EY laboratories) in 1% BSA/PBS at 4°C for 2 hours. After three washes with PBS for 30 minutes each, sections were fixed with 1% glutaraldehyde/PBS for 10 minutes, washed with distilled water five times for 5 minutes each and air-dried. Samples were stained with saturated uranyl acetate for 2 minutes followed by lead citrate for 5 minutes, as described by Dobson et al. (Dobson et al., 1994). Micrographs were obtained with a JEM100S EM (JOEL).


    An Introduction to Genetic Analysis. 7th edition.

    If two breaks occur in one chromosome, sometimes the region between the breaks rotates 180 degrees before rejoining with the two end fragments. Such an event creates a chromosomal mutation called an inversion. Unlike deletions and duplications, inversions do not change the overall amount of the genetic material, so inversions are generally viable and show no particular abnormalities at the phenotypic level. In some cases, one of the chromosome breaks is within a gene of essential function, and then that breakpoint acts as a lethal gene mutation linked to the inversion. In such a case, the inversion could not be bred to homozygosity. However, many inversions can be made homozygous furthermore, inversions can be detected in haploid organisms. In these cases, the breakpoint is clearly not in an essential region. Some of the possible outcomes of inversion at the DNA level are shown in Figure 17-14.

    Figure 17-14

    Effects of inversions at the DNA level. Genes are represented by A, B, C, and D. Template strand is dark green nontemplate strand is light green jagged lines indicate break in DNA. The letter P stands for promoter thick arrow indicates the position (more. )

    Most analyses of inversions use heterozygous inversions𠅍iploids in which one chromosome has the standard sequence and one carries the inversion. Microscopic observation of meioses in inversion heterozygotes reveals the location of the inverted segment because one chromosome twists once at the ends of the inversion to pair with the other, untwisted chromosome in this way the paired homologs form an inversion loop (Figure 17-15).

    Figure 17-15

    The chromosomes of inversion heterozygotes pair in a loop at meiosis. (a) Diagrammatic representation each chromosome is actually a pair of sister chromatids. (b) Electron micrographs of synaptonemal complexes at prophase I of meiosis in a mouse heterozygous (more. )

    The location of the centromere relative to the inverted segment determines the genetic behavior of the chromosome. If the centromere is outside the inversion, then the inversion is said to be paracentric, whereas inversions spanning the centromere are pericentric:

    How do inversions behave genetically? Crossing-over within the inversion loop of a paracentric inversion connects homologous centromeres in a dicentric bridge while also producing an acentric fragment𠅊 fragment without a centromere. Then, as the chromosomes separate in anaphase I, the centromeres remain linked by the bridge, which orients the centromeres so that the noncrossover chromatids lie farthest apart. The acentric fragment cannot align itself or move and is, consequently, lost. Tension eventually breaks the bridge, forming two chromosomes with terminal deletions (Figure 17-16). The gametes containing such deleted chromosomes may be inviable but, even if viable, the zygotes that they eventually form are inviable. Hence, a crossover event, which normally generates the recombinant class of meiotic products, instead produces lethal products. The overall result is a lower recombinant frequency. In fact, for genes within the inversion, the RF is zero. For genes flanking the inversion, the RF is reduced in proportion to the relative size of the inversion.

    Figure 17-16

    Meiotic products resulting from a single crossover within a paracentric inversion loop. Two nonsister chromatids cross over within the loop.

    Inversions affect recombination in another way too. Inversion heterozygotes often have mechanical pairing problems in the region of the inversion these pairing problems reduce the frequency of crossing-over and hence the recombinant frequency in the region.

    The net genetic effect of a pericentric inversion is the same as that of a paracentric one𠅌rossover products are not recovered𠅋ut for different reasons. In a pericentric inversion, because the centromeres are contained within the inverted region, the chromosomes that have crossed over disjoin in the normal fashion, without the creation of a bridge. However, the crossover produces chromatids that contain a duplication and a deficiency for different parts of the chromosome (Figure 17-17). In this case, if a nucleus carrying a crossover chromosome is fertilized, the zygote dies because of its genetic imbalance. Again, the result is the selective recovery of noncrossover chromosomes in viable progeny.

    Figure 17-17

    Meiotic products resulting from a meiosis with a single crossover within a pericentric inversion loop.

    MESSAGE

    Two mechanisms reduce the number of recombinant products among the progeny of inversion heterozygotes: elimination of the products of crossovers in the inversion loop and inhibition of pairing in the region of the inversion.

    It is worth adding a note about homozygous inversions. In such cases the homologous inverted chromosomes pair and cross over normally, there are no bridges, and the meiotic products are viable. However, an interesting effect is that the linkage map will show the inverted gene order.

    Geneticists use inversions to create duplications of specific chromosome regions for various experimental purposes. For example, consider a heterozygous pericentric inversion with one breakpoint at the tip (T) of the chromosome, as shown in Figure 17-18. A crossover in the loop produces a chromatid type in which the entire left arm is duplicated if the tip is nonessential, a duplication stock is generated for investigation. Another way to make a duplication (and a deficiency) is to use two paracentric inversions with overlapping breakpoints (Figure 17-19). A complex loop is formed, and a crossover within the inversion produces the duplication and the deletion. These manipulations are possible only in organisms with thoroughly mapped chromosomes for which large sets of standard rearrangements are available.

    Figure 17-18

    Generation of a viable nontandem duplication from a pericentric inversion close to a dispensable chromosome tip.

    Figure 17-19

    Generation of a nontandem duplication by crossing-over between two overlapping inversions.

    We have seen that genetic analysis and meiotic chromosome cytology are both good ways of detecting inversions. As with most rearrangements, there is also the possibility of detection through mitotic chromosome analysis. A key operational feature is to look for new arm ratios. Consider a chromosome that has mutated as follows:

    Note that the ratio of the long to the short arm has been changed from about 4 to about 1 by the pericentric inversion. Paracentric inversions do not alter the arm ratio, but they may be detected microscopically if banding or other chromosome landmarks are available.

    MESSAGE

    The main diagnostic features of inversions are inversion loops, reduction of recombinant frequency, and reduced fertility from unbalanced or deleted meiotic products, all observed in individuals heterozygous for inversions. Some inversions may be directly observed as an inverted arrangement of chromosomal landmarks.

    Inversions are found in about 2 percent of humans. The heterozygous inversion carriers generally show no adverse phenotype but produce the expected array of abnormal meiotic products from crossing-over in the inversion loop. Let us consider pericentric inversions as an example. Persons heterozygous for pericentric inversions produce offspring with the duplication�letion chromosomes predicted these offspring show varying degrees of abnormalities depending on the lengths of the chromosome regions affected. Some phenotypes caused by duplication�letion chromosomes are so abnormal as to be incapable of survival to birth and are lost as spontaneous abortions. However, there is a way to study the abnormal meiotic products that does not depend on survival to term. Human sperm placed in contact with unfertilized eggs of the golden hamster penetrate the eggs but fail to fertilize them. The sperm nucleus does not fuse with the egg nucleus, and, if the cell is prepared for cytogenetic examination, the human chromosomes are easily visible as a distinct group (Figure 17-20). This technique makes it possible to study the chromosomal products of a male meiosis directly and is particularly useful in the study of meiotic products of men who have chromosome mutations.

    Figure 17-20

    Human sperm and hamster oocytes are fused to permit study of the chromosomes in the meiotic products of human males. (After original art by Renພ Martin.)

    In one case, a man heterozygous for an inversion of chromosome 3 underwent sperm analysis. The inversion was a large one with a high potential for crossing-over in the loop. Four chromosome 3 types were found in the man’s sperm—normal, inversion, and two recombinant types (Figure 17-21). The sperm contained the four types in the following frequencies:

    Figure 17-21

    (a) Four different chromosomes 3 found in sperm of a man heterozygous for a large pericentric inversion. The duplication-deletion types result from a crossover in the inversion loop. (b) Two complete sperm chromosome sets containing the two duplication�letion (more. )

    The duplication-q�letion-p recombinant chromosome had been observed previously in several abnormal children, but the duplication-p�letion-q type had never been seen, and probably zygotes receiving it are too abnormal to survive to term. Presumably, deletion of the larger q fragment has more severe consequences than deletion of the smaller p fragment.

    By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.


    Contents

    The term ploidy is a back-formation from haploidy and diploidy. "Ploid" is a combination of Ancient Greek -πλόος (-plóos, “-fold”) and -ειδής (-eidḗs), from εἶδος (eîdos, "form, likeness"). [a] The principal meaning of the Greek word ᾰ̔πλόος (haplóos) is "single", [10] from ἁ- (ha-, “one, same”). [11] διπλόος (diplóos) means "duplex" or "two-fold". Diploid therefore means "duplex-shaped" (compare "humanoid", "human-shaped").

    Polish botanist Eduard Strasburger coined the terms haploid and diploid in 1905. [b] Some authors suggest that Strasburger based the terms on August Weismann's conception of the id (or germ plasm), [14] [15] [16] hence haplo-id and diplo-id. The two terms were brought into the English language from German through William Henry Lang's 1908 translation of a 1906 textbook by Strasburger and colleagues. [17] [ citation needed ]

    Haploid and monoploid Edit

    A comparison of sexual reproduction in predominantly haploid organisms and predominantly diploid organisms.

    1) A haploid organism is on the left and a diploid organism is on the right.
    2 and 3) Haploid egg and sperm carrying the dominant purple gene and the recessive blue gene, respectively. These gametes are produced by simple mitosis of cells in the germ line.
    4 and 5) Diploid sperm and egg carrying the recessive blue gene and the dominant purple gene, respectively. These gametes are produced by meiosis, which halves the number of chromosomes in the diploid germ cells.
    6) The short-lived diploid state of haploid organisms, a zygote generated by the union of two haploid gametes during sex.
    7) The diploid zygote which has just been fertilized by the union of haploid egg and sperm during sex.
    8) Cells of the diploid structure quickly undergo meiosis to produce spores containing the meiotically halved number of chromosomes, restoring haploidy. These spores express either the mother's dominant gene or the father's recessive gene and proceed by mitotic division to build a new entirely haploid organism.
    9) The diploid zygote proceeds by mitotic division to build a new entirely diploid organism. These cells possess both the purple and blue genes, but only the purple gene is expressed since it is dominant over the recessive blue gene.

    The term haploid is used with two distinct but related definitions. In the most generic sense, haploid refers to having the number of sets of chromosomes normally found in a gamete. [18] Because two gametes necessarily combine during sexual reproduction to form a single zygote from which somatic cells are generated, healthy gametes always possess exactly half the number of sets of chromosomes found in the somatic cells, and therefore "haploid" in this sense refers to having exactly half the number of sets of chromosomes found in a somatic cell. By this definition, an organism whose gametic cells contain a single copy of each chromosome (one set of chromosomes) may be considered haploid while the somatic cells, containing two copies of each chromosome (two sets of chromosomes), are diploid. This scheme of diploid somatic cells and haploid gametes is widely used in the animal kingdom and is the simplest to illustrate in diagrams of genetics concepts. But this definition also allows for haploid gametes with more than one set of chromosomes. As given above, gametes are by definition haploid, regardless of the actual number of sets of chromosomes they contain. An organism whose somatic cells are tetraploid (four sets of chromosomes), for example, will produce gametes by meiosis that contain two sets of chromosomes. These gametes might still be called haploid even though they are numerically diploid.

    An alternative usage defines "haploid" as having a single copy of each chromosome – that is, one and only one set of chromosomes. [19] In this case, the nucleus of a eukaryotic cell is only said to be haploid if it has a single set of chromosomes, each one not being part of a pair. By extension a cell may be called haploid if its nucleus has one set of chromosomes, and an organism may be called haploid if its body cells (somatic cells) have one set of chromosomes per cell. By this definition haploid therefore would not be used to refer to the gametes produced by the tetraploid organism in the example above, since these gametes are numerically diploid. The term monoploid is often used as a less ambiguous way to describe a single set of chromosomes by this second definition, haploid and monoploid are identical and can be used interchangeably.

    Gametes (sperm and ova) are haploid cells. The haploid gametes produced by most organisms combine to form a zygote with n pairs of chromosomes, i.e. 2n chromosomes in total. The chromosomes in each pair, one of which comes from the sperm and one from the egg, are said to be homologous. Cells and organisms with pairs of homologous chromosomes are called diploid. For example, most animals are diploid and produce haploid gametes. During meiosis, sex cell precursors have their number of chromosomes halved by randomly "choosing" one member of each pair of chromosomes, resulting in haploid gametes. Because homologous chromosomes usually differ genetically, gametes usually differ genetically from one another. [ citation needed ]

    All plants and many fungi and algae switch between a haploid and a diploid state, with one of the stages emphasized over the other. This is called alternation of generations. Most fungi and algae are haploid during the principal stage of their life cycle, as are some primitive plants like mosses. More recently evolved plants, like the gymnosperms and angiosperms, spend the majority of their life cycle in the diploid stage. Most animals are diploid, but male bees, wasps, and ants are haploid organisms because they develop from unfertilized, haploid eggs, while females (workers and queens) are diploid, making their system haplodiploid.

    In some cases there is evidence that the n chromosomes in a haploid set have resulted from duplications of an originally smaller set of chromosomes. This "base" number – the number of apparently originally unique chromosomes in a haploid set – is called the monoploid number, [20] also known as basic or cardinal number, [21] or fundamental number. [22] [23] As an example, the chromosomes of common wheat are believed to be derived from three different ancestral species, each of which had 7 chromosomes in its haploid gametes. The monoploid number is thus 7 and the haploid number is 3 × 7 = 21. In general n is a multiple of x. The somatic cells in a wheat plant have six sets of 7 chromosomes: three sets from the egg and three sets from the sperm which fused to form the plant, giving a total of 42 chromosomes. As a formula, for wheat 2n = 6x = 42, so that the haploid number n is 21 and the monoploid number x is 7. The gametes of common wheat are considered to be haploid, since they contain half the genetic information of somatic cells, but they are not monoploid, as they still contain three complete sets of chromosomes (n = 3x). [24]

    In the case of wheat, the origin of its haploid number of 21 chromosomes from three sets of 7 chromosomes can be demonstrated. In many other organisms, although the number of chromosomes may have originated in this way, this is no longer clear, and the monoploid number is regarded as the same as the haploid number. Thus in humans, x = n = 23.

    Diploid Edit

    Diploid cells have two homologous copies of each chromosome, usually one from the mother and one from the father. All or nearly all mammals are diploid organisms. The suspected tetraploid (possessing four-chromosome sets) plains viscacha rat (Tympanoctomys barrerae) and golden viscacha rat (Pipanacoctomys aureus) [25] have been regarded as the only known exceptions (as of 2004). [26] However, some genetic studies have rejected any polyploidism in mammals as unlikely, and suggest that amplification and dispersion of repetitive sequences best explain the large genome size of these two rodents. [27] All normal diploid individuals have some small fraction of cells that display polyploidy. Human diploid cells have 46 chromosomes (the somatic number, 2n) and human haploid gametes (egg and sperm) have 23 chromosomes (n). Retroviruses that contain two copies of their RNA genome in each viral particle are also said to be diploid. Examples include human foamy virus, human T-lymphotropic virus, and HIV. [28]

    Polyploidy Edit

    Polyploidy is the state where all cells have multiple sets of chromosomes beyond the basic set, usually 3 or more. Specific terms are triploid (3 sets), tetraploid (4 sets), pentaploid (5 sets), hexaploid (6 sets), heptaploid [2] or septaploid [3] (7 sets), octoploid (8 sets), nonaploid (9 sets), decaploid (10 sets), undecaploid (11 sets), dodecaploid (12 sets), tridecaploid (13 sets), tetradecaploid (14 sets), etc. [29] [30] [31] [32] Some higher ploidies include hexadecaploid (16 sets), dotriacontaploid (32 sets), and tetrahexacontaploid (64 sets), [33] though Greek terminology may be set aside for readability in cases of higher ploidy (such as "16-ploid"). [31] Polytene chromosomes of plants and fruit flies can be 1024-ploid. [34] [35] Ploidy of systems such as the salivary gland, elaiosome, endosperm, and trophoblast can exceed this, up to 1048576-ploid in the silk glands of the commercial silkworm Bombyx mori. [36]

    The chromosome sets may be from the same species or from closely related species. In the latter case, these are known as allopolyploids (or amphidiploids, which are allopolyploids that behave as if they were normal diploids). Allopolyploids are formed from the hybridization of two separate species. In plants, this probably most often occurs from the pairing of meiotically unreduced gametes, and not by diploid–diploid hybridization followed by chromosome doubling. [37] The so-called Brassica triangle is an example of allopolyploidy, where three different parent species have hybridized in all possible pair combinations to produce three new species.

    Polyploidy occurs commonly in plants, but rarely in animals. Even in diploid organisms, many somatic cells are polyploid due to a process called endoreduplication, where duplication of the genome occurs without mitosis (cell division). The extreme in polyploidy occurs in the fern genus Ophioglossum, the adder's-tongues, in which polyploidy results in chromosome counts in the hundreds, or, in at least one case, well over one thousand.

    It is possible for polyploid organisms to revert to lower ploidy by haploidisation.

    In bacteria and archaea Edit

    Polyploidy is a characteristic of the bacterium Deinococcus radiodurans [38] and of the archaeon Halobacterium salinarum. [39] These two species are highly resistant to ionizing radiation and desiccation, conditions that induce DNA double-strand breaks. [40] [41] This resistance appears to be due to efficient homologous recombinational repair.

    Variable or indefinite ploidy Edit

    Depending on growth conditions, prokaryotes such as bacteria may have a chromosome copy number of 1 to 4, and that number is commonly fractional, counting portions of the chromosome partly replicated at a given time. This is because under exponential growth conditions the cells are able to replicate their DNA faster than they can divide.

    In ciliates, the macronucleus is called ampliploid, because only part of the genome is amplified. [42]

    Mixoploidy Edit

    Mixoploidy is the case where two cell lines, one diploid and one polyploid, coexist within the same organism. Though polyploidy in humans is not viable, mixoploidy has been found in live adults and children. [43] There are two types: diploid-triploid mixoploidy, in which some cells have 46 chromosomes and some have 69, [44] and diploid-tetraploid mixoploidy, in which some cells have 46 and some have 92 chromosomes. It is a major topic of cytology.

    Dihaploidy and polyhaploidy Edit

    Dihaploid and polyhaploid cells are formed by haploidisation of polyploids, i.e., by halving the chromosome constitution.

    Dihaploids (which are diploid) are important for selective breeding of tetraploid crop plants (notably potatoes), because selection is faster with diploids than with tetraploids. Tetraploids can be reconstituted from the diploids, for example by somatic fusion.

    The term "dihaploid" was coined by Bender [45] to combine in one word the number of genome copies (diploid) and their origin (haploid). The term is well established in this original sense, [46] [47] but it has also been used for doubled monoploids or doubled haploids, which are homozygous and used for genetic research. [48]

    Euploidy and aneuploidy Edit

    Euploidy (Greek eu, "true" or "even") is the state of a cell or organism having one or more than one set of the same set of chromosomes, possibly excluding the sex-determining chromosomes. For example, most human cells have 2 of each of the 23 homologous monoploid chromosomes, for a total of 46 chromosomes. A human cell with one extra set of the 23 normal chromosomes (functionally triploid) would be considered euploid. Euploid karyotypes would consequentially be a multiple of the haploid number, which in humans is 23.

    Aneuploidy is the state where one or more individual chromosomes of a normal set are absent or present in more than their usual number of copies (excluding the absence or presence of complete sets, which is considered euploidy). Unlike euploidy, aneuploid karyotypes will not be a multiple of the haploid number. In humans, examples of aneuploidy include having a single extra chromosome (as in Down syndrome, where affected individuals have three copies of chromosome 21) or missing a chromosome (as in Turner syndrome, where affected individuals have only one sex chromosome). Aneuploid karyotypes are given names with the suffix -somy (rather than -ploidy, used for euploid karyotypes), such as trisomy and monosomy.

    Homoploid Edit

    Homoploid means "at the same ploidy level", i.e. having the same number of homologous chromosomes. For example, homoploid hybridization is hybridization where the offspring have the same ploidy level as the two parental species. This contrasts with a common situation in plants where chromosome doubling accompanies or occurs soon after hybridization. Similarly, homoploid speciation contrasts with polyploid speciation. [ citation needed ]

    Zygoidy and azygoidy Edit

    Zygoidy is the state in which the chromosomes are paired and can undergo meiosis. The zygoid state of a species may be diploid or polyploid. [49] [50] In the azygoid state the chromosomes are unpaired. It may be the natural state of some asexual species or may occur after meiosis. In diploid organisms the azygoid state is monoploid. (See below for dihaploidy.)

    More than one nucleus per cell Edit

    In the strictest sense, ploidy refers to the number of sets of chromosomes in a single nucleus rather than in the cell as a whole. Because in most situations there is only one nucleus per cell, it is commonplace to speak of the ploidy of a cell, but in cases in which there is more than one nucleus per cell, more specific definitions are required when ploidy is discussed. Authors may at times report the total combined ploidy of all nuclei present within the cell membrane of a syncytium, [36] though usually the ploidy of each nucleus is described individually. For example, a fungal dikaryon with two separate haploid nuclei is distinguished from a diploid cell in which the chromosomes share a nucleus and can be shuffled together. [51]

    Ancestral ploidy levels Edit

    It is possible on rare occasions for ploidy to increase in the germline, which can result in polyploid offspring and ultimately polyploid species. This is an important evolutionary mechanism in both plants and animals and is known as a primary driver of speciation. [8] As a result, it may become desirable to distinguish between the ploidy of a species or variety as it presently breeds and that of an ancestor. The number of chromosomes in the ancestral (non-homologous) set is called the monoploid number (x), and is distinct from the haploid number (n) in the organism as it now reproduces.

    Common wheat (Triticum aestivum) is an organism in which x and n differ. Each plant has a total of six sets of chromosomes (with two sets likely having been obtained from each of three different diploid species that are its distant ancestors). The somatic cells are hexaploid, 2n = 6x = 42 (where the monoploid number x = 7 and the haploid number n = 21). The gametes are haploid for their own species, but triploid, with three sets of chromosomes, by comparison to a probable evolutionary ancestor, einkorn wheat. [ citation needed ]

    Tetraploidy (four sets of chromosomes, 2n = 4x) is common in many plant species, and also occurs in amphibians, reptiles, and insects. For example, species of Xenopus (African toads) form a ploidy series, featuring diploid (X. tropicalis, 2n=20), tetraploid (X. laevis, 4n=36), octaploid (X. wittei, 8n=72), and dodecaploid (X. ruwenzoriensis, 12n=108) species. [52]

    Over evolutionary time scales in which chromosomal polymorphisms accumulate, these changes become less apparent by karyotype – for example, humans are generally regarded as diploid, but the 2R hypothesis has confirmed two rounds of whole genome duplication in early vertebrate ancestors.

    Haplodiploidy Edit

    Ploidy can also vary between individuals of the same species or at different stages of the life cycle. [53] [54] In some insects it differs by caste. In humans, only the gametes are haploid, but in many of the social insects, including ants, bees, and termites, certain individuals develop from unfertilized eggs, making them haploid for their entire lives, even as adults. In the Australian bulldog ant, Myrmecia pilosula, a haplodiploid species, haploid individuals of this species have a single chromosome and diploid individuals have two chromosomes. [55] In Entamoeba, the ploidy level varies from 4n to 40n in a single population. [56] Alternation of generations occurs in most plants, with individuals "alternating" ploidy level between different stages of their sexual life cycle.

    Tissue-specific polyploidy Edit

    In large multicellular organisms, variations in ploidy level between different tissues, organs, or cell lineages are common. Because the chromosome number is generally reduced only by the specialized process of meiosis, the somatic cells of the body inherit and maintain the chromosome number of the zygote by mitosis. However, in many situations somatic cells double their copy number by means of endoreduplication as an aspect of cellular differentiation. For example, the hearts of two-year-old human children contain 85% diploid and 15% tetraploid nuclei, but by 12 years of age the proportions become approximately equal, and adults examined contained 27% diploid, 71% tetraploid and 2% octaploid nuclei. [57]

    There is continued study and debate regarding the fitness advantages or disadvantages conferred by different ploidy levels. A study comparing the karyotypes of endangered or invasive plants with those of their relatives found that being polyploid as opposed to diploid is associated with a 14% lower risk of being endangered, and a 20% greater chance of being invasive. [58] Polyploidy may be associated with increased vigor and adaptability. [59] Some studies suggest that selection is more likely to favor diploidy in host species and haploidy in parasite species. [60]

    When a germ cell with an uneven number of chromosomes undergoes meiosis, the chromosomes cannot be evenly divided between the daughter cells, resulting in aneuploid gametes. Triploid organisms, for instance, are usually sterile. Because of this, triploidy is commonly exploited in agriculture to produce seedless fruit such as bananas and watermelons. If the fertilization of human gametes results in three sets of chromosomes, the condition is called triploid syndrome.

    1. A phenotypic male with one Barr body.
    Term Description
    Ploidy number Number of chromosome sets
    Monoploid number (x) Number of chromosomes found in a single complete set
    Chromosome number Total number of chromosomes in all sets combined
    Zygotic number Number of chromosomes in zygotic cells
    Haploid or gametic number (n) Number of chromosomes found in gametes
    Diploid number Chromosome number of a diploid organism
    Tetraploid number Chromosome number of a tetraploid organism

    The common potato (Solanum tuberosum) is an example of a tetraploid organism, carrying four sets of chromosomes. During sexual reproduction, each potato plant inherits two sets of 12 chromosomes from the pollen parent, and two sets of 12 chromosomes from the ovule parent. The four sets combined provide a full complement of 48 chromosomes. The haploid number (half of 48) is 24. The monoploid number equals the total chromosome number divided by the ploidy level of the somatic cells: 48 chromosomes in total divided by a ploidy level of 4 equals a monoploid number of 12. Hence, the monoploid number (12) and haploid number (24) are distinct in this example.

    However, commercial potato crops (as well as many other crop plants) are commonly propagated vegetatively (by asexual reproduction through mitosis), [61] in which case new individuals are produced from a single parent, without the involvement of gametes and fertilization, and all the offspring are genetically identical to each other and to the parent, including in chromosome number. The parents of these vegetative clones may still be capable of producing haploid gametes in preparation for sexual reproduction, but these gametes are not used to create the vegetative offspring by this route.

    Examples of various ploidy levels in species with x=11
    Species Ploidy Number of chromosomes
    Eucalyptus spp. Diploid 2x = 22
    Banana (Musa spp.) Triploid 3x = 33
    Coffea arabica Tetraploid 4x = 44
    Sequoia sempervirens Hexaploid 6x = 66
    Opuntia ficus-indica Octoploid 8x = 88
    List of common organisms by chromosome count
    Species Number of chromosomes Ploidy number
    Vinegar/fruit fly 8 2
    Wheat 14, 28 or 42 2, 4 or 6
    Crocodilian 32, 34, or 42 2
    Apple 34, 51, or 68 2, 3 or 4
    Human 46 2
    Horse 64 2
    Chicken 78 2
    Gold fish 100 or more 2 or polyploid
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    Some eukaryotic genome-scale or genome size databases and other sources which may list the ploidy levels of many organisms: