Karyotype
A karyotype is a preparation of the complete set of metaphase chromosomes in the cells of a species or in an individual organism, sorted by length, centromere location and other features and for a test that detects this complement or counts the number of chromosomes. Karyotyping is the process by which a karyotype is prepared from photographs of chromosomes, in order to determine the chromosome complement of an individual, including the number of chromosomes and any abnormalities. Karyotypes describe the chromosome count of an organism and what these chromosomes look like under a light microscope. Attention is paid to  their length, the position of the centromeres, banding pattern, any differences between the sex chromosomes, and any other physical characteristics. The preparation and study of karyotypes is part of cytogenetics. The study of whole sets of chromosomes is sometimes known as "karyology". The chromosomes are depicted (by rearranging a photomicrograph) in a standard format known as a "karyogram" or "idiogram": in pairs, ordered by size and position of centromere for chromosomes of the same size. The basic number of chromosomes in the somatic cells of an individual or a species is called the "somatic number" and is designated "2n". In  the germ-line (the sex cells) the chromosome number is "n" (humans: n = 23). Thus, in humans 2n = 46. So, in normal diploid organisms, autosomal chromosomes are present in two copies. There may, or may not, be sex chromosomes. Polyploid cells have multiple copies of chromosomes and haploid cells have single copies. Karyotypes can be used for many purposes; such as to study chromosomal aberrations, cellular function, taxonomic relationships, medicine and to gather information about past evolutionary events ("karyosystematics"). History of karyotype studies. Chromosomes were first observed in plant cells by Carl Wilhelm von Nägeli in 1842. Their  behavior in animal (salamander) cells was described by Walther Flemming, the discoverer of mitosis, in 1882. The name was coined by another German anatomist, Heinrich von Waldeyer in 1888. It is New Latin from Ancient Greek κάρυον "karyon", "kernel", "seed", or "nucleus", and τύπος "typos", "general form") The next stage took place after the development of genetics in the early 20th century, when it was appreciated that chromosomes (that can be observed by karyotype) were the carrier of genes. in 1922 seems to have been the first person to define the karyotype as the phenotypic appearance of the somatic chromosomes , in contrast to their genic contents. The subsequent history of the concept can be followed in the works of C. D. Darlington and Michael JD White. 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. Painter in 1922 was not certain whether the diploid of humans was 46 or 48, at first favoring 46, but revised his opinion from 46 to 48, and he  correctly insisted on humans having an XX/XY system. Considering the techniques of the time, these results were remarkable. Joe Hin Tjio working in Albert Levan's lab found the chromosome count to be 46 using new techniques available at the time: The work took place in 1955, and was published in 1956. The karyotype of humans includes only 46 chromosomes. The other great apes have 48 chromosomes. Human chromosome 2 is now known to be a result of an end-to-end fusion of two ancestral ape chromosomes. Observations on karyotypes. Staining. The study of karyotypes is made possible  by staining. Usually, a suitable dye, such as Giemsa, is applied after cells have been arrested during cell division by a solution of colchicine usually in metaphase or prometaphase when most condensed. In order for the Giemsa stain to adhere correctly, all chromosomal proteins must be digested and removed. For humans, white blood cells are used most frequently because they are easily induced to divide and grow in tissue culture. Sometimes observations may be made on non-dividing (interphase) cells. The sex of an unborn fetus can be determined by observation of interphase cells (see amniotic centesis and Barr body ). Observations. Six different characteristics of karyotypes are usually observed and compared: A full account of a karyotype may therefore include the number, type, shape and banding of the chromosomes, as well as other cytogenetic information. Variation is often found: Human karyotype. The typical human karyotypes contain 22 pairs of autosomal chromosomes and one pair of sex chromosomes (allosomes). The most common karyotypes for females contain two X chromosomes and are denoted 46,XX; males usually have both an X and a Y chromosome denoted 46,XY. Approximately 0.018% percent of humans are intersex, sometimes due to variations in sex chromosomes. Some variations  in karyotype, whether to autosomes or allosomes, cause developmental abnormalities. Diversity and evolution of karyotypes. Although the replication and transcription of DNA is highly standardized in eukaryotes, the same cannot be said for their karyotypes, which are highly variable. There is variation between species in chromosome number, and in detailed organization, despite their construction from the same macromolecules. This variation provides the basis for a range of studies in evolutionary cytology. In some cases there is even significant variation within species. In a review, Godfrey and Masters conclude: Although much is known about karyotypes at the descriptive level, and  it is clear that changes in karyotype organization has had effects on the evolutionary course of many species, it is quite unclear what the general significance might be. Changes during development. Instead of the usual gene repression, some organisms go in for large-scale elimination of heterochromatin, or other kinds of visible adjustment to the karyotype. Number of chromosomes in a set. A spectacular example of variability between closely related species is the muntjac, which was investigated by Kurt Benirschke and Doris Wurster. The diploid number of the Chinese muntjac, "Muntiacus reevesi", was found to be 46, all telocentric. When  they looked at the karyotype of the closely related Indian muntjac, "Muntiacus muntjak", they were astonished to find it had female = 6, male = 7 chromosomes. The number of chromosomes in the karyotype between (relatively) unrelated species is hugely variable. The low record is held by the nematode "Parascaris univalens", where the haploid n = 1; and an ant: "Myrmecia pilosula". The high record would be somewhere amongst the ferns, with the adder's tongue fern "Ophioglossum" ahead with an average of 1262 chromosomes. Top score for animals might be the shortnose sturgeon "Acipenser brevirostrum" at 372 chromosomes. The  existence of supernumerary or B chromosomes means that chromosome number can vary even within one interbreeding population; and aneuploids are another example, though in this case they would not be regarded as normal members of the population. Fundamental number. The fundamental number, "FN", of a karyotype is the number of visible major chromosomal arms per set of chromosomes. Thus, FN ≤ 2 x 2n, the difference depending on the number of chromosomes considered single-armed (acrocentric or telocentric) present. Humans have FN = 82, due to the presence of five acrocentric chromosome pairs: 13, 14, 15, 21, and 22 (the  human Y chromosome is also acrocentric). The fundamental autosomal number or autosomal fundamental number, "FNa" or "AN", of a karyotype is the number of visible major chromosomal arms per set of autosomes (non-sex-linked chromosomes). Ploidy. Ploidy is the number of complete sets of chromosomes in a cell. Polyploid series in related species which consist entirely of multiples of a single basic number are known as euploid. Aneuploidy. Aneuploidy is the condition in which the chromosome number in the cells is not the typical number for the species. This would give rise to a chromosome abnormality such as an  extra chromosome or one or more chromosomes lost. Abnormalities in chromosome number usually cause a defect in development. Down syndrome and Turner syndrome are examples of this. Aneuploidy may also occur within a group of closely related species. Classic examples in plants are the genus "Crepis", where the gametic (= haploid) numbers form the series x = 3, 4, 5, 6, and 7; and "Crocus", where every number from x = 3 to x = 15 is represented by at least one species. Evidence of various kinds shows that trends of evolution have gone in different directions in different groups . In primates, the great apes have 24x2 chromosomes whereas humans have 23x2. Human chromosome 2 was formed by a merger of ancestral chromosomes, reducing the number. Chromosomal polymorphism. Some species are polymorphic for different chromosome structural forms. The structural variation may be associated with different numbers of chromosomes in different individuals, which occurs in the ladybird beetle "Chilocorus stigma", some mantids of the genus "Ameles", the European shrew "Sorex araneus". There is some evidence from the case of the mollusc "Thais lapillus" (the dog whelk) on the Brittany coast, that the two chromosome morphs are adapted to different habitats. Species  trees. The detailed study of chromosome banding in insects with polytene chromosomes can reveal relationships between closely related species: the classic example is the study of chromosome banding in Hawaiian drosophilids by Hampton L. Carson. In about , the Hawaiian Islands have the most diverse collection of drosophilid flies in the world, living from rainforests to subalpine meadows. These roughly 800 Hawaiian drosophilid species are usually assigned to two genera, "Drosophila" and "Scaptomyza", in the family Drosophilidae. The polytene banding of the 'picture wing' group, the best-studied group of Hawaiian drosophilids, enabled Carson to work out the evolutionary tree long  before genome analysis was practicable. In a sense, gene arrangements are visible in the banding patterns of each chromosome. Chromosome rearrangements, especially inversions, make it possible to see which species are closely related. The results are clear. The inversions, when plotted in tree form (and independent of all other information), show a clear "flow" of species from older to newer islands. There are also cases of colonization back to older islands, and skipping of islands, but these are much less frequent. Using K-Ar dating, the present islands date from 0.4 million years ago (mya) (Mauna Kea) to 10mya (Necker ). The oldest member of the Hawaiian archipelago still above the sea is Kure Atoll, which can be dated to 30 mya. The archipelago itself (produced by the Pacific plate moving over a hot spot) has existed for far longer, at least into the Cretaceous. Previous islands now beneath the sea (guyots) form the Emperor Seamount Chain. All of the native "Drosophila" and "Scaptomyza" species in Hawaii have apparently descended from a single ancestral species that colonized the islands, probably 20 million years ago. The subsequent adaptive radiation was spurred by a lack of competition and a wide variety of niches . Although it would be possible for a single gravid female to colonise an island, it is more likely to have been a group from the same species. There are other animals and plants on the Hawaiian archipelago which have undergone similar, if less spectacular, adaptive radiations. Chromosome banding. Chromosomes display a banded pattern when treated with some stains. Bands are alternating light and dark stripes that appear along the lengths of chromosomes. Unique banding patterns are used to identify chromosomes and to diagnose chromosomal aberrations, including chromosome breakage, loss, duplication, translocation or inverted segments. A range of different chromosome treatments  produce a range of banding patterns: G-bands, R-bands, C-bands, Q-bands, T-bands and NOR-bands. Depiction of karyotypes. Types of banding. Cytogenetics employs several techniques to visualize different aspects of chromosomes: Classic karyotype cytogenetics. In the "classic" (depicted) karyotype, a dye, often Giemsa "(G-banding)", less frequently mepacrine (quinacrine), is used to stain bands on the chromosomes. Giemsa is specific for the phosphate groups of DNA. Quinacrine binds to the adenine-thymine-rich regions. Each chromosome has a characteristic banding pattern that helps to identify them; both chromosomes in a pair will have the same banding  pattern. Karyotypes are arranged with the short arm of the chromosome on top, and the long arm on the bottom. Some karyotypes call the short and long arms "p" and "q", respectively. In addition, the differently stained regions and sub-regions are given numerical designations from proximal to distal on the chromosome arms. For example, Cri du chat syndrome involves a deletion on the short arm of chromosome 5. It is written as 46,XX,5p-. The critical region for this syndrome is deletion of p15.2 (the locus on the chromosome), which is written as 46,XX,del(5)(p15.2). Multicolor FISH (mFISH) and spectral  karyotype (SKY technique). Multicolor FISH and the older spectral karyotyping are molecular cytogenetic techniques used to simultaneously visualize all the pairs of chromosomes in an organism in different colors. Fluorescently labeled probes for each chromosome are made by labeling chromosome-specific DNA with different fluorophores. Because there are a limited number of spectrally distinct fluorophores, a combinatorial labeling method is used to generate many different colors. Fluorophore combinations are captured and analyzed by a fluorescence microscope using up to 7 narrow-banded fluorescence filters or, in the case of spectral karyotyping, by using an interferometer attached to a fluorescence microscope . In the case of an mFISH image, every combination of fluorochromes from the resulting original images is replaced by a pseudo color in a dedicated image analysis software. Thus, chromosomes or chromosome sections can be visualized and identified, allowing for the analysis of chromosomal rearrangements. In the case of spectral karyotyping, image processing software assigns a pseudo color to each spectrally different combination, allowing the visualization of the individually colored chromosomes. Multicolor FISH is used to identify structural chromosome aberrations in cancer cells and other disease conditions when Giemsa banding or other techniques are not accurate enough. Digital karyotyping. "Digital  karyotyping" is a technique used to quantify the DNA copy number on a genomic scale. Short sequences of DNA from specific loci all over the genome are isolated and enumerated. This method is also known as virtual karyotyping. Using this technique, it is possible to detect small alterations in the human genome, that cannot be detected through methods employing metaphase chromosomes. Some loci deletions are known to be related to the development of cancer. Such deletions are found through digital karyotyping using the loci associated with cancer development. Chromosome abnormalities. Chromosome abnormalities can be numerical, as in the presence  of extra or missing chromosomes, or structural, as in derivative chromosome, translocations, inversions, large-scale deletions or duplications. Numerical abnormalities, also known as aneuploidy, often occur as a result of nondisjunction during meiosis in the formation of a gamete; trisomies, in which three copies of a chromosome are present instead of the usual two, are common numerical abnormalities. Structural abnormalities often arise from errors in homologous recombination. Both types of abnormalities can occur in gametes and therefore will be present in all cells of an affected person's body, or they can occur during mitosis and give rise to a  genetic mosaic individual who has some normal and some abnormal cells. In humans. Chromosomal abnormalities that lead to disease in humans include Some disorders arise from loss of just a piece of one chromosome, including