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{{short description|Photographic display of total chromosome complement in a cell}}
{{Redirect-distinguish|Idiogram|ideogram}}
A '''karyotype''' is a type of kernel(nucleus). The types (karyotypes) of the cell depends on the appearances:(sizes, numbers) of the set of all [[chromosomes]] in the cell. The cells of an organism usually has the same karyotype. Therefore the expression ‘the karyotype of organism’ makes sense.
A '''karyotyping''' is a process that is judging of the karyotype of an organism with number of chromosome complement (a complete set of chromosomes), and any abnormalities of the chromosomes and recording the type. I.e. a karyotyping is classification of cell’s nucleus or organism’s nucleus .
[[File:NHGRI human male karyotype.png|thumb|[[Micrograph]]ic karyogram of human male using [[Giemsa]] staining]]
[[File:How to read a Karyotype.png|thumb|[[Schematic]] karyogram demonstrating the basic knowledge needed to read a karyotype]]
A '''karyogram''' or '''idiogram''' is a graphical depiction of a chromosome complement, wherein chromosomes are generally organized in pairs, ordered by size and position of centromere for chromosomes of the same size. A karyogram shows which karyotype the organism have.
Karyotyping generally combines [[light microscopy]] and [[photography]] of a cell in the [[metaphase]] of the [[cell cycle]], and results in a [[photomicrograph]]ic (or simply micrographic) karyogram. In contrast, a [[schematic]] karyogram is a designed graphic representation of a karyotype. In schematic karyograms, just one of the sister [[chromatid]]s of each chromosome is generally shown for brevity, and in reality they are generally so close together that they look as one on photomicrographs as well unless the resolution is high enough to distinguish them. The study of whole sets of chromosomes is known as '''karyology'''.
Karyotypes describe the [[list of organisms by chromosome count|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 [[centromere]]s, banding pattern, any differences between the [[sex chromosome]]s, and any other physical characteristics.<ref>{{cite book |last1=King |first1=R.C. |last2=Stansfield |first2=W.D. |last3=Mulligan |first3=P.K. |title=A dictionary of genetics |url=https://archive.org/details/dictionarygeneti02king |url-access=limited |publisher=Oxford University Press |year=2006 |page=[https://archive.org/details/dictionarygeneti02king/page/n254 242] |edition=7th }}</ref> The preparation and study of karyotypes is part of [[cytogenetics]].
The basic number of chromosomes in the [[Somatic (biology)|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).<ref name="White2">{{harvnb|White|1973|p=35}}</ref><ref>{{cite book |last=Stebbins |first=G.L. |chapter=Chapter XII: The Karyotype |title=Variation and evolution in plants |url=https://archive.org/details/variationevoluti0000unse |url-access=registration |publisher=Columbia University Press |year=1950 |isbn=9780231017336 }}</ref><sup>p28</sup> 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]]. [[polyploidy|Polyploid]] cells have multiple copies of chromosomes and [[ploidy|haploid]] cells have single copies.
Karyotypes can be used for many purposes; such as to study [[chromosomal aberration]]s, [[cell biology|cellular]] function, [[Taxonomy (biology)|taxonomic]] relationships, [[medicine]] and to gather information about past [[evolutionary]] events (''[[systematics|karyosystematics]]'').<ref>{{cite web|url= http://encyclopedia2.thefreedictionary.com/Karyosystematics|title= Karyosystematics}}</ref>
== Observations on karyotypes ==
[[File:Condensation and resolution of human sister chromatids in early mitosis.svg|thumb|Chromosomes at various stages of [[mitosis]]. Karyograms are generally made by chromosomes in prometaphase or metaphase. During these phases, the two copies of each chromosome (connected at the [[centromere]]) will look as one unless the image resolution is high enough to distinguish the two.]]
[[File:Human Chromosomes (crop).jpg|thumb|Micrograph of human chromosomes before further processing. Staining with Giemsa confers a purple color to chromosomes, but micrographs are often converted to [[grayscale]] to facilitate data presentation and make comparisons of results from different laboratories.<ref>{{cite book|url=http://www.informatics.jax.org/silver/chapters/5-2.shtml|title=Mouse Genetics, Concepts and Applications. Chapter 5.2: KARYOTYPES, CHROMOSOMES, AND TRANSLOCATIONS|author=Lee M. Silver|year=1995|publisher=Oxford University Press}} Revised August 2004, January 2008</ref>]]
=== Staining ===
The study of karyotypes is made possible by [[staining]]. Usually, a suitable [[dye]], such as [[Giemsa]],<ref>A preparation which includes the dyes Methylene Blue, Eosin Y and Azure-A,B,C</ref> is applied after [[Cell (biology)|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]].<ref name="Gustashaw K.M 1991">Gustashaw K.M. 1991. Chromosome stains. In ''The ACT Cytogenetics Laboratory Manual'' 2nd ed, ed. M.J. Barch. The Association of Cytogenetic Technologists, Raven Press, New York.</ref> Sometimes observations may be made on non-dividing ([[interphase]]) cells. The sex of an unborn [[fetus]] can be predicted by observation of interphase cells (see [[Amniocentesis|amniotic centesis]] and [[Barr body]]).
=== Observations ===
Six different characteristics of karyotypes are usually observed and compared:<ref>{{cite book |last=Stebbins |first=G.L. |title=Chromosomal evolution in higher plants |url=https://archive.org/details/chromosomalevolu0000steb |url-access=registration |publisher=Arnold |___location=London |year=1971 |pages=[https://archive.org/details/chromosomalevolu0000steb/page/85 85–86]|isbn=9780713122879 }}</ref>
# Differences in absolute sizes of chromosomes. Chromosomes can vary in absolute size by as much as twenty-fold between genera of the same family. For example, the legumes ''[[Lotus tenuis]]'' and ''[[Vicia faba]]'' each have six pairs of chromosomes, yet ''V. faba'' chromosomes are many times larger. These differences probably reflect different amounts of DNA duplication.
# Differences in the position of [[centromeres]]. These differences probably came about through [[translocations]].
# Differences in relative size of chromosomes. These differences probably arose from segmental interchange of unequal lengths.
# Differences in basic number of chromosomes. These differences could have resulted from successive unequal translocations which removed all the essential genetic material from a chromosome, permitting its loss without penalty to the organism (the dislocation hypothesis) or through fusion. Humans have one pair fewer chromosomes than the great apes. Human chromosome 2 appears to have resulted from the fusion of two ancestral chromosomes, and many of the genes of those two original chromosomes have been translocated to other chromosomes.
# Differences in number and position of satellites. [[Satellite chromosome|Satellites]] are small bodies attached to a chromosome by a thin thread.
# Differences in degree and distribution of [[GC content]] ([[Guanine]]-[[Cytosine]] pairs versus [[Adenine]]-[[Thymine]]). In metaphase where the karyotype is typically studied, all DNA is condensed, but most of the time, DNA with a high GC content is usually less condensed, that is, it tends to appear as [[euchromatin]] rather than [[heterochromatin]]. GC rich DNA tends to contain more [[coding DNA]] and be more [[Transcription (DNA)|transcriptionally active]].<ref name=Romiguier2017/> GC rich DNA is lighter on [[Giemsa staining]].<ref name="ReferenceA">Thompson & Thompson Genetics in Medicine 7th Ed</ref> Euchromatin regions contain larger amounts of [[Guanine]]-[[Cytosine]] pairs (that is, it has a higher [[GC content]]). The staining technique using [[Giemsa]] staining is called [[G banding]] and therefore produces the typical "G-Bands".<ref name="ReferenceA"/>
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:
# between the sexes,
# between the [[germ-line]] and [[somatic (biology)|soma]] (between [[gametes]] and the rest of the body),
# between members of a population ([[polymorphism (biology)|chromosome polymorphism]]),
# in [[allopatric speciation|geographic specialization]], and
# in [[Mosaic (genetics)|mosaics]] or otherwise abnormal individuals.<ref name="White1"/>
== Human karyogram ==
[[File:DNA human male chromosomes.gif|thumb|Micrographic karyogram of a human male. See section text for details.]]
[[File:Human karyotype with bands and sub-bands.png|thumb|370px|Schematic karyogram of a human. Even at low magnification, it gives an overview of the [[human genome]], with numbered chromosome pairs, its main changes during the [[cell cycle]] (top center), and the [[human mitochondrial genetics|mitochondrial genome]] to scale (at bottom left). See section text for more details.]]
Both the micrographic and schematic karyograms shown in this section have a standard chromosome layout, and display darker and lighter regions as seen on [[G banding]], which is the appearance of the chromosomes after treatment with [[trypsin]] (to partially digest the chromosomes) and [[Staining (biology)|staining]] with [[Giemsa stain]]. Compared to darker regions, the lighter regions are generally more [[Transcription (biology)|transcriptionally]] active, with a greater ratio of [[coding DNA]] versus [[non-coding DNA]], and a higher [[GC content]].<ref name=Romiguier2017>{{cite journal| author=Romiguier J, Roux C| title=Analytical Biases Associated with GC-Content in Molecular Evolution. | journal=Front Genet | year= 2017 | volume= 8 | issue= | pages= 16 | pmid=28261263 | doi=10.3389/fgene.2017.00016 | pmc=5309256 | doi-access=free }} </ref>
Both the micrographic and schematic karyograms show the normal human [[diploid]] karyotype, which is the typical composition of the [[genome]] within a normal cell of the human body, and which contains 22 pairs of [[Autosome|autosomal]] chromosomes and one pair of [[sex chromosomes]] (allosomes). A major exception to diploidy in humans is [[gamete]]s (sperm and egg cells) which are haploid with 23 unpaired chromosomes, and this [[ploidy]] is not shown in these karyograms. The micrographic karyogram is converted into [[grayscale]], whereas the schematic karyogram shows the purple hue as typically seen on Giemsa stain (and is a result of its azure B component, which stains DNA purple).<ref>{{cite book|author=K. Lew|title=Comprehensive Sampling and Sample Preparation. Chapter: 3.05 - Blood Sample Collection and Handling|publisher=Academic Press|year=2012|isbn=9780123813749|url=https://www.sciencedirect.com/science/article/pii/B9780123813732000685}}</ref>
The schematic karyogram in this section is a graphical representation of the idealized karyotype. For each chromosome pair, the scale to the left shows the length in terms of million [[base pairs]], and the scale to the right shows the designations of the [[Locus (genetics)|bands and sub-bands]]. Such bands and sub-bands are used by the [[International System for Human Cytogenomic Nomenclature]] to describe locations of [[#Chromosome abnormalities|chromosome abnormalities]]. Each row of chromosomes is vertically aligned at [[centromere]] level.
===Human chromosome groups===
Based on the karyogram characteristics of size, position of the [[centromere]] and sometimes the presence of a [[chromosomal satellite]] (a segment distal to a [[secondary constriction]]), the human chromosomes are classified into the following groups:<ref>{{cite journal|last1=Erwinsyah |first1=R. |author2=Riandi |last3=Nurjhani |first3=M.|name-list-style=amp|year=2017|title=Relevance of human chromosome analysis activities against mutation concept in genetics course|journal=IOP Conference Series: Materials Science and Engineering|volume=180 |page=012285 |doi=10.1088/1757-899x/180/1/012285|s2cid=90739754 |doi-access=free}}</ref>
{|class=wikitable
! Group
! Chromosomes
! Features
|- style="background:lavenderblush"
| '''A'''
| 1–3
| Large, metacentric or submetacentric
|- style="background:honeydew"
| '''B'''
| 4-5
| Large, submetacentric
|- style="background:lightyellow"
| '''C'''
| 6–12, X
| Medium-sized, submetacentric
|- style="background:linen"
| '''D'''
| 13–15
| Medium-sized, acrocentric, with [[satellite chromosome|satellite]]
|- style="background:lightcyan"
| '''E'''
| 16–18
| Small, metacentric or submetacentric
|- style="background:lavender"
| '''F'''
| 19–20
| Very small, metacentric
|- style="background:lavenderblush"
| '''G'''
| 21–22, Y
| Very small, acrocentric (and 21, 22 with [[satellite chromosome|satellite]])
|}
Alternatively, the human genome can be classified as follows, based on pairing, sex differences, as well as ___location within the [[cell nucleus]] versus inside [[mitochondria]]:
* 22 homologous [[autosomal]] chromosome pairs (chromosomes 1 to 22). [[Homologous chromosome|Homologous]] means that they have the same genes in the same loci, and autosomal means that they are not sex chromomes.
* Two [[sex chromosome]] (in green rectangle at bottom right in the schematic karyogram, with adjacent silhouettes of typical representative [[phenotype]]s): The most common karyotypes for [[females]] contain two [[X chromosome]]s and are denoted 46,XX; [[Male|males]] usually have both an X and a [[Y chromosome]] denoted 46,XY. However, approximately 0.018% percent of humans are [[intersex]], sometimes due to variations in sex chromosomes.<ref>{{cite journal |title=How Common is Intersex? |year=2002 |pmid=12476264 |last1=Sax |first1=L. |journal=Journal of Sex Research |volume=39 |issue=3 |pages=174–178 |doi=10.1080/00224490209552139 |s2cid=33795209 }}</ref>
* The [[Human mitochondrial genetics|human mitochondrial genome]] (shown at bottom left in the schematic karyogram, to scale compared to the nuclear DNA in terms of [[base pair]]s), although this is not included in micrographic karyograms in clinical practice. Its genome is relatively tiny compared to the rest.
===Copy number===
[[File:Animal cell cycle-en.svg|thumb|The [[cell cycle]]]]
Schematic karyograms generally display a DNA copy number corresponding to the [[G0 phase|G<sub>0</sub> phase]] of the cellular state (outside of the replicative [[cell cycle]]) which is the most common state of cells. The schematic karyogram in this section also shows this state. In this state (as well as during the G<sub>1</sub> phase of the [[cell cycle]]), each cell has two autosomal chromosomes of each kind (designated 2n), where each chromosome has one copy of each [[Locus (genetics)|locus]], making a total copy number of two for each locus (2c). At top center in the schematic karyogram, it also shows the chromosome 3 pair after having undergone [[DNA synthesis]], occurring in the [[S phase]] (annotated as S) of the cell cycle. This interval includes the [[G2 phase|G<sub>2</sub> phase]] and [[metaphase]] (annotated as "Meta."). During this interval, there is still 2n, but each chromosome will have two copies of each locus, wherein each [[sister chromatid]] (chromosome arm) is connected at the centromere, for a total of 4c.<ref name="pmid30202427">{{cite journal| author=Gomes CJ, Harman MW, Centuori SM, Wolgemuth CW, Martinez JD| title=Measuring DNA content in live cells by fluorescence microscopy. | journal=Cell Div | year= 2018 | volume= 13 | issue= | article-number= 6 | pmid=30202427 | doi=10.1186/s13008-018-0039-z | pmc=6123973 | doi-access=free }} </ref> The chromosomes on micrographic karyograms are in this state as well, because they are generally micrographed in metaphase, but during this phase the two copies of each chromosome are so close to each other that they appear as one unless the image resolution is high enough to distinguish them. In reality, during the G<sub>0</sub> and G<sub>1</sub> phases, nuclear DNA is dispersed as [[chromatin]] and does not show visually distinguishable chromosomes even on micrography.
The copy number of the [[Human mitochondrial genetics|human mitochondrial genome]] per human cell varies from 0 (erythrocytes)<ref name="pmid3178814">{{cite journal| author=Shuster RC, Rubenstein AJ, Wallace DC| title=Mitochondrial DNA in anucleate human blood cells. | journal=Biochem Biophys Res Commun | year= 1988 | volume= 155 | issue= 3 | pages= 1360–5 | pmid=3178814 | doi=10.1016/s0006-291x(88)81291-9 | pmc= }} </ref> up to 1,500,000 ([[Egg cell|oocytes]]), mainly depending on the number of mitochondria per cell.<ref name="pmid28721182">{{cite journal| author=Zhang D, Keilty D, Zhang ZF, Chian RC| title=Mitochondria in oocyte aging: current understanding. | journal=Facts Views Vis Obgyn | year= 2017 | volume= 9 | issue= 1 | pages= 29–38 | pmid=28721182 | doi= | pmc=5506767 }} </ref>
== Diversity and evolution of karyotypes ==
Although the [[DNA replication|replication]] and [[transcription (genetics)|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 [[Chromatin|macromolecules]]. This variation provides the basis for a range of studies in evolutionary [[cell biology|cytology]].
In some cases there is even significant variation within species. In a review, Godfrey and Masters conclude:
{{blockquote|In our view, it is unlikely that one process or the other can independently account for the wide range of karyotype structures that are observed ... But, used in conjunction with other phylogenetic data, karyotypic fissioning may help to explain dramatic differences in diploid numbers between closely related species, which were previously inexplicable.<ref>{{cite journal |vauthors=Godfrey LR, Masters JC |title=Kinetochore reproduction theory may explain rapid chromosome evolution |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=97 |issue=18 |pages=9821–3 |date=August 2000 |pmid=10963652 |pmc=34032 |bibcode=2000PNAS...97.9821G |doi=10.1073/pnas.97.18.9821|doi-access=free }}</ref>}}
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.
{{blockquote|We have a very poor understanding of the causes of karyotype evolution, despite many careful investigations ... the general significance of karyotype evolution is obscure.|Maynard Smith<ref>Maynard Smith J. 1998. ''Evolutionary genetics''. 2nd ed, Oxford. p218-9</ref>}}
=== 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.
* Chromosome elimination. In some species, as in many [[Sciaridae|sciarid flies]], entire chromosomes are eliminated during development.<ref>{{cite journal |vauthors=Goday C, Esteban MR |title=Chromosome elimination in sciarid flies |journal=BioEssays |volume=23 |issue=3 |pages=242–50 |date=March 2001 |pmid=11223881 |doi=10.1002/1521-1878(200103)23:3<242::AID-BIES1034>3.0.CO;2-P |s2cid=43718856 }}</ref>
* Chromatin diminution (founding father: [[Theodor Boveri]]). In this process, found in some [[copepods]] and [[roundworms]] such as ''[[Ascaris suum]]'', portions of the chromosomes are cast away in particular cells. This process is a carefully organised genome rearrangement where new telomeres are constructed and certain heterochromatin regions are lost.<ref>{{cite journal |vauthors=Müller F, Bernard V, Tobler H |title=Chromatin diminution in nematodes |journal=BioEssays |volume=18 |issue=2 |pages=133–8 |date=February 1996 |pmid=8851046 |doi=10.1002/bies.950180209 |s2cid=24583845 }}</ref><ref>{{cite journal |vauthors=Wyngaard GA, Gregory TR |title=Temporal control of DNA replication and the adaptive value of chromatin diminution in copepods |journal=J. Exp. Zool. |volume=291 |issue=4 |pages=310–6 |date=December 2001 |pmid=11754011 |doi=10.1002/jez.1131|bibcode=2001JEZ...291..310W }}</ref> In ''A. suum'', all the somatic cell precursors undergo chromatin diminution.<ref>Gilbert S.F. 2006. ''Developmental biology''. Sinauer Associates, Stamford CT. 8th ed, Chapter 9</ref>
* [[X-inactivation]]. The inactivation of one X chromosome takes place during the early development of mammals (see [[Barr body]] and [[dosage compensation]]). In [[placental mammals]], the inactivation is random as between the two Xs; thus the mammalian female is a mosaic in respect of her X chromosomes. In [[marsupials]] it is always the paternal X which is inactivated. In human females some 15% of somatic cells escape inactivation,<ref>{{harvnb|King|Stansfield|Mulligan|2006}}</ref> and the number of genes affected on the inactivated X chromosome varies between cells: in [[fibroblast]] cells up about 25% of genes on the Barr body escape inactivation.<ref>{{cite journal |vauthors=Carrel L, Willard H | year = 2005 | title = X-inactivation profile reveals extensive variability in X-linked gene expression in females | journal = Nature | volume = 434 | issue = 7031| pages = 400–404 | doi = 10.1038/nature03479 | pmid = 15772666 | bibcode = 2005Natur.434..400C | s2cid = 4358447 }}</ref>
=== 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.<ref>{{cite journal |vauthors=Wurster DH, Benirschke K |title=Indian muntjac, ''Muntiacus muntjak'': a deer with a low diploid chromosome number |journal=Science |volume=168 |issue=3937 |pages=1364–6 |date=June 1970 |pmid=5444269 |doi=10.1126/science.168.3937.1364|bibcode = 1970Sci...168.1364W |s2cid=45371297 }}</ref>
{{blockquote|They simply could not believe what they saw ... They kept quiet for two or three years because they thought something was wrong with their tissue culture ... But when they obtained a couple more specimens they confirmed [their findings].|Hsu p. 73-4<ref name="Hsu"/>}}
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]]''.<ref>{{cite journal|author1=Crosland M.W.J. |author2=Crozier, R.H.|year=1986|title=''Myrmecia pilosula'', an ant with only one pair of chromosomes|journal=Science|volume=231|pages=1278|doi=10.1126/science.231.4743.1278|pmid=17839565|issue=4743|bibcode=1986Sci...231.1278C|s2cid=25465053}}</ref> The high record would be somewhere amongst the [[fern]]s, with the adder's tongue fern ''[[Ophioglossum]]'' ahead with an average of 1262 chromosomes.<ref>{{cite journal |author=Khandelwal S. |title=Chromosome evolution in the genus Ophioglossum L |journal=Botanical Journal of the Linnean Society |volume=102 |pages=205–217 |year=1990 |doi=10.1111/j.1095-8339.1990.tb01876.x |issue=3 }}</ref> Top score for animals might be the [[shortnose sturgeon]] ''[[Acipenser brevirostrum]]'' at 372 chromosomes.<ref name=Kim2005>{{cite journal |first=D.S. |last=Kim |author2=Nam, Y.K. |author3=Noh, J.K. |author4=Park, C.H. |author5=Chapman, F.A. | year = 2005 | title = Karyotype of North American shortnose sturgeon ''Acipenser brevirostrum'' with the highest chromosome number in the Acipenseriformes | journal = Ichthyological Research | volume = 52 | issue = 1 | pages = 94–97 | doi = 10.1007/s10228-004-0257-z|bibcode=2005IchtR..52...94K |s2cid=20126376 }}</ref> The existence of supernumerary or [[B chromosomes]] means that chromosome number can vary even within one interbreeding population; and [[aneuploid]]s 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.<ref name = "Matthey">{{Cite journal
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}}</ref> Thus, FN ≤ 2 × 2n, the difference depending on the number of chromosomes considered single-armed ([[Centromere#Acrocentric|acrocentric]] or [[Centromere#Telocentric|telocentric]]) present. Humans have FN = 82,<ref name = "Pellicciari">{{Cite journal
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}}</ref> due to the presence of five acrocentric chromosome pairs: [[Chromosome 13 (human)|13]], [[Chromosome 14 (human)|14]], [[Chromosome 15 (human)|15]], [[Chromosome 21 (human)|21]], and [[Chromosome 22 (human)|22]] (the human [[Y chromosome]] is also acrocentric). The fundamental autosomal number or autosomal fundamental number, ''FNa''<ref name = "Souza">{{cite journal
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}}</ref> or ''AN'',<ref name = "Weksler">{{cite journal
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| url-status = dead
}}</ref> of a karyotype is the number of visible major chromosomal arms per set of [[autosome]]s (non-[[allosome|sex-linked chromosomes]]).
=== Ploidy ===
{{for|the investigation of ancient karyotype duplications|Paleopolyploidy}}
[[Ploidy]] is the number of complete sets of chromosomes in a cell.
* [[Polyploidy]], where there are more than two sets of homologous chromosomes in the cells, occurs mainly in plants. It has been of major significance in plant evolution according to [[G. Ledyard Stebbins|Stebbins]].<ref>{{cite journal |first=G. L. |last=Stebbins |title=The significance of polyploidy in plant evolution |journal=The American Naturalist |volume=74 |pages=54–66 |year=1940 |doi=10.1086/280872 |issue=750 |bibcode=1940ANat...74...54S |s2cid=86709379 }}</ref><ref>{{harvnb|Stebbins|1950}}</ref><ref>{{cite journal |last=Comai |first=L. |title=The advantages and disadvantages of being polyploid |journal=Nature Reviews Genetics |volume=6 |issue=11 |pages=836–46 |date=November 2005 |pmid=16304599 |doi=10.1038/nrg1711 |s2cid=3329282 }}</ref><ref>{{cite journal |vauthors=Adams KL, Wendel JF |title=Polyploidy and genome evolution in plants |journal=Current Opinion in Plant Biology |volume=8 |issue=2 |pages=135–141 |date=April 2005 |pmid=15752992 |doi=10.1016/j.pbi.2005.01.001 |bibcode=2005COPB....8..135A }}</ref> The proportion of flowering plants which are polyploid was estimated by Stebbins to be 30–35%, but in grasses the average is much higher, about 70%.<ref>{{harvnb|Stebbins|1971}}</ref> Polyploidy in lower plants ([[fern]]s, [[horsetails]] and [[psilotales]]) is also common, and some species of ferns have reached levels of polyploidy far in excess of the highest levels known in flowering plants. Polyploidy in animals is much less common, but it has been significant in some groups.<ref>{{cite book |last1=Gregory |first1=T. R. |last2=Mable |first2=B. K. |chapter=Ch. 8: Polyploidy in animals |editor-first=T. Ryan |editor-last=Gregory |title=The Evolution of the Genome |chapter-url=https://books.google.com/books?id=8HtPZP9VSiMC&pg=PA427 |year=2011 |publisher=Academic Press |isbn=978-0-08-047052-8 |pages=427–517 }}</ref><p>Polyploid series in related species which consist entirely of multiples of a single basic number are known as [[euploid]].</p>
* [[Haplo-diploid sex-determination system|Haplo-diploidy]], where one sex is [[diploid]], and the other [[haploid]]. It is a common arrangement in the [[Hymenoptera]], and in some other groups.
* [[Endopolyploidy]] occurs when in adult [[Cellular differentiation|differentiated]] tissues the cells have ceased to divide by [[mitosis]], but the [[Cell nucleus|nuclei]] contain more than the original [[somatic cell|somatic]] number of [[chromosomes]].<ref>{{cite book |last=White |first=M. J. D. |title=The chromosomes |url=https://archive.org/details/chromosomes01whit |url-access=registration |publisher=Chapman & Hall |___location=London |year=1973 |edition=6th |page=[https://archive.org/details/chromosomes01whit/page/n58 45] }}</ref> In the ''endocycle'' ([[endomitosis]] or [[endoreduplication]]) chromosomes in a 'resting' nucleus undergo [[reduplication]], the daughter chromosomes separating from each other inside an ''intact'' [[nuclear membrane]].<ref name=Lilly>{{cite journal |last1=Lilly |first1=M. A. |last2=Duronio |first2=R. J. | title = New insights into cell cycle control from the ''Drosophila'' endocycle | journal = Oncogene | volume = 24 | issue = 17 | pages = 2765–75 | year = 2005 | pmid = 15838513 | doi = 10.1038/sj.onc.1208610| doi-access = free }}</ref><p>In many instances, endopolyploid nuclei contain tens of thousands of chromosomes (which cannot be exactly counted). The cells do not always contain exact multiples (powers of two), which is why the simple definition 'an increase in the number of chromosome sets caused by replication without cell division' is not quite accurate.</p><p>This process (especially studied in insects and some higher plants such as maize) may be a developmental strategy for increasing the productivity of tissues which are highly active in biosynthesis.<ref>{{cite journal |vauthors=Edgar BA, Orr-Weaver TL |title=Endoreplication cell cycles: more for less |journal=Cell |volume=105 |issue=3 |pages=297–306 |date=May 2001 |pmid=11348589 |doi=10.1016/S0092-8674(01)00334-8|s2cid=14368177 |doi-access=free }}</ref></p><p>The phenomenon occurs sporadically throughout the [[eukaryote]] kingdom from [[protozoa]] to humans; it is diverse and complex, and serves [[differentiation (cellular)|differentiation]] and [[morphogenesis]] in many ways.<ref>{{cite book |last=Nagl |first=W. |year=1978 |title=Endopolyploidy and polyteny in differentiation and evolution: towards an understanding of quantitative and qualitative variation of nuclear DNA in ontogeny and phylogeny |publisher=Elsevier |___location=New York}}</ref></p>
=== 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.<ref>Stebbins, G. Ledley, Jr. 1972. ''Chromosomal evolution in higher plants''. Nelson, London. p18</ref> 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.<ref>{{cite journal |vauthors=IJdo JW, Baldini A, Ward DC, Reeders ST, Wells RA |title=Origin of human chromosome 2: an ancestral telomere-telomere fusion |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=88 |issue=20 |pages=9051–5 |date=October 1991 |pmid=1924367 |pmc=52649 |bibcode=1991PNAS...88.9051I |doi=10.1073/pnas.88.20.9051|doi-access=free }}</ref>
=== Chromosomal polymorphism ===
Some species are [[Polymorphism (biology)|polymorphic]] for different chromosome structural forms.<ref>{{cite book |author1=Rieger, R. |author2=Michaelis, A. |author3=Green, M.M. |year=1968 |title=A glossary of genetics and cytogenetics: Classical and molecular |url=https://archive.org/details/glossaryofgeneti00rieg |url-access=registration |publisher=Springer-Verlag |___location=New York |isbn=9780387076683 }}</ref> 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]]'',<ref>{{cite journal |last1=Gustavsson |first1=Ingemar |date=3 March 1969 |title= Cytogenetics, distribution and phenotypic effects of a translocation in Swedish cattle.|url= |journal=Hereditas |volume=63 |issue= 1–2|pages=68–169 |doi= 10.1111/j.1601-5223.1969.tb02259.x|pmid=5399228 |access-date=|doi-access=free }}</ref> the European shrew ''[[Sorex araneus]]''.<ref>{{Cite journal|last=Searle|first=J. B.|date=1984-06-01|title=Three New Karyotypic Races of the Common Shrew Sorex Araneus (Mammalia: Insectivora) and a Phylogeny|journal=Systematic Biology|volume=33|issue=2|pages=184–194|doi=10.1093/sysbio/33.2.184|issn=1063-5157}}</ref> 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 [[Adaptation|adapted]] to different habitats.<ref>{{harvnb|White|1973|p=169}}</ref>
=== Species trees ===
The detailed study of chromosome banding in insects with [[polytene chromosome]]s can reveal relationships between closely related species: the classic example is the study of chromosome banding in [[Hawaiian Drosophilidae|Hawaiian drosophilids]] by [[Hampton L. Carson (biologist)|Hampton L. Carson]].
In about {{convert|6500|sqmi|km2|abbr=on}}, the [[Hawaiian Islands]] have the most diverse collection of drosophilid flies in the world, living from [[Hawaiian tropical rainforests|rainforests]] to [[Hawaiian tropical high shrublands|subalpine meadows]]. These roughly 800 Hawaiian drosophilid species are usually assigned to two genera, ''[[Drosophila]]'' and ''[[Drosophila|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 [[Chromosome inversions|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 [[radiometric dating|K-Ar]] dating, the present islands date from 0.4 million years ago (mya) ([[Mauna Kea]]) to 10mya ([[Necker Island (Northwestern Hawaiian Islands)|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 (geology)|hot spot]]) has existed for far longer, at least into the [[Cretaceous]]. Previous islands now beneath the sea ([[guyot]]s) form the [[Hawaiian-Emperor seamount chain|Emperor Seamount Chain]].<ref>{{cite book |author1=Clague, D.A. |author2=Dalrymple, G.B. |chapter=The Hawaiian-Emperor volcanic chain, Part I. Geologic evolution |editor1=Decker, R.W. |editor2=Wright, T.L. |editor3=Stauffer, P.H. |title=Volcanism in Hawaii |id=U.S. Geological Survey Professional Paper 1350 |year=1987 |pages=5–54 |chapter-url=http://pubs.usgs.gov/pp/1987/1350/pp1350_vol1.pdf |volume=1 |archive-date=10 October 2012 |access-date=28 May 2013 |archive-url=https://web.archive.org/web/20121010062038/http://pubs.usgs.gov/pp/1987/1350/pp1350_vol1.pdf |url-status=dead }}</ref>
All of the native ''Drosophila'' and ''Scaptomyza'' species in Hawai{{okina}}i 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 (biology)|competition]] and a wide variety of [[Vacant niche|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.<ref>{{cite journal |author=Carson HL |title=Chromosome tracers of the origin of species |journal=Science |volume=168 |issue=3938 |pages=1414–8 |date=June 1970 |pmid=5445927 |bibcode=1970Sci...168.1414C |doi=10.1126/science.168.3938.1414}}</ref><ref>{{cite journal |author=Carson HL |title=Chromosomal sequences and interisland colonizations in Hawaiian ''Drosophila'' |journal=Genetics |volume=103 |issue=3 |pages=465–82 |date=March 1983 |doi=10.1093/genetics/103.3.465 |pmid=17246115 |pmc=1202034 |url=http://www.genetics.org/cgi/pmidlookup?view=long&pmid=17246115}}</ref><ref>{{cite book |author=Carson H.L. |chapter=Inversions in Hawaiian ''Drosophila'' |editor1=Krimbas, C.B. |editor2=Powell, J.R. |title=Drosophila inversion polymorphism |publisher=CRC Press |___location=Boca Raton FL |year=1992 |isbn=978-0849365478 |pages=407–439 }}</ref><ref>{{cite book |author1=Kaneshiro, K.Y. |author2=Gillespie, R.G. |author3=Carson, H.L. |chapter=Chromosomes and male genitalia of Hawaiian Drosophila: tools for interpreting phylogeny and geography |editor1=Wagner, W.L. |editor2=Funk, E. |title=Hawaiian biogeography: evolution on a hot spot archipelago |chapter-url=https://archive.org/details/hawaiianbiogeogr00wagn |publisher=Smithsonian Institution Press |___location=Washington DC |year=1995 |pages=[https://archive.org/details/hawaiianbiogeogr00wagn/page/57 57–71] }}</ref>
There are other animals and plants on the Hawaiian archipelago which have undergone similar, if less spectacular, adaptive radiations.<ref>{{cite book |author=Craddock E.M. |chapter=Speciation Processes in the Adaptive Radiation of Hawaiian Plants and Animals |title=Evolutionary Biology |editor1-first=Max K. |editor1-last=Hecht |editor2-first=Ross J. |editor2-last=MacIntyre |editor3-first=Michael T. |editor3-last=Clegg |volume=31 |pages=1–43 |year=2000 |doi=10.1007/978-1-4615-4185-1_1 |isbn=978-1-4613-6877-9 }}</ref><ref>{{cite book |first=Alan C. |last=Ziegler |title=Hawaiian natural history, ecology, and evolution |url=https://books.google.com/books?id=l56J_8teG58C |year=2002 |publisher=University of Hawaii Press |isbn=978-0-8248-2190-6}}</ref>
=== 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:<ref name="Gustashaw K.M 1991"/>
* [[G-banding]] is obtained with [[Giemsa stain]] following digestion of chromosomes with [[trypsin]]. It yields a series of lightly and darkly stained bands — the dark regions tend to be heterochromatic, late-replicating and AT rich. The light regions tend to be euchromatic, early-replicating and GC rich. This method will normally produce 300–400 bands in a normal, [[human genome]]. It is the most common chromosome banding method.<ref>{{cite book | last1=Maloy | first1=Stanley R. | last2=Hughes | first2=Kelly | title=Brenner's Encyclopedia of Genetics | publication-place=San Diego, CA | date=2013 | isbn=978-0-08-096156-9 | oclc=836404630 |publisher=Academic Press }}</ref>
* R-banding is the reverse of G-banding (the R stands for "reverse"). The dark regions are euchromatic (guanine-cytosine rich regions) and the bright regions are heterochromatic (thymine-adenine rich regions).
* C-banding: Giemsa binds to [[constitutive heterochromatin]], so it stains [[centromere]]s. The name is derived from centromeric or constitutive heterochromatin. The preparations undergo alkaline denaturation prior to staining leading to an almost complete depurination of the DNA. After washing the probe the remaining DNA is renatured again and stained with Giemsa solution consisting of methylene azure, methylene violet, methylene blue, and eosin. Heterochromatin binds a lot of the dye, while the rest of the chromosomes absorb only little of it. The C-bonding proved to be especially well-suited for the characterization of plant chromosomes.
* Q-banding is a [[fluorescent]] pattern obtained using [[quinacrine]] for staining. The pattern of bands is very similar to that seen in G-banding. They can be recognized by a yellow fluorescence of differing intensity. Most part of the stained DNA is heterochromatin. Quinacrin (atebrin) binds both regions rich in AT and in GC, but only the AT-quinacrin-complex fluoresces. Since regions rich in AT are more common in heterochromatin than in euchromatin, these regions are labelled preferentially. The different intensities of the single bands mirror the different contents of AT. Other fluorochromes like DAPI or Hoechst 33258 lead also to characteristic, reproducible patterns. Each of them produces its specific pattern. In other words: the properties of the bonds and the specificity of the fluorochromes are not exclusively based on their affinity to regions rich in AT. Rather, the distribution of AT and the association of AT with other molecules like histones, for example, influences the binding properties of the fluorochromes.
* T-banding: visualize [[telomere]]s.
* Silver staining: [[Silver nitrate]] stains the [[nucleolar organization region]]-associated protein. This yields a dark region where the silver is deposited, denoting the activity of rRNA genes within the NOR.
=== Classic karyotype cytogenetics ===
[[File:PLoSBiol3.5.Fig7ChromosomesAluFish.jpg|thumb|Karyogram from a human female [[lymphocyte]] probed for the [[Alu sequence]] using [[Fluorescent in situ hybridization|FISH]]]]
In the "classic" (depicted) karyotype, a [[dye]], often [[Giemsa]] ''(G-banding)'', less frequently [[Mepacrine|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 [[Anatomical terms of ___location#Proximal and distal|proximal]] to [[Anatomical terms of ___location#Proximal and distal|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 (genetics)|locus]] on the chromosome), which is written as 46,XX,del(5)(p15.2).<ref>{{cite book|editor1=Lisa G. Shaffer |editor2=Niels Tommerup |title=ISCN 2005: An International System for Human Cytogenetic Nomenclature|publisher=S. Karger AG|___location=Switzerland|isbn=978-3-8055-8019-9|year=2005}}</ref>
===Multicolor FISH (mFISH) and spectral karyotype (SKY technique)===
[[File:Sky spectral karyotype.png|thumb|Spectral karyogram of a human female]]
Multicolor [[Fluorescence in situ hybridization|FISH]] and the older spectral karyotyping are molecular [[cytogenetic]] techniques used to simultaneously visualize all the pairs of [[chromosome]]s in an organism in different colors. [[Fluorescent]]ly labeled probes for each chromosome are made by labeling chromosome-specific DNA with different [[fluorophore]]s. 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 [[false color|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.<ref>{{cite journal |vauthors=Liehr T, Starke H, Weise A, Lehrer H, Claussen U |title=Multicolour FISH probe sets and their applications |journal=Histol. Histopathol. |volume=19 |issue=1 |pages=229–237 |date=January 2004 |pmid=14702191 }}</ref>
In the case of spectral karyotyping, image processing software assigns a [[false color|pseudo color]] to each spectrally different combination, allowing the visualization of the individually colored chromosomes.<ref>{{cite journal |vauthors=Schröck E, du Manoir S, Veldman T, etal |title=Multicolor spectral karyotyping of human chromosomes |journal=Science |volume=273 |issue=5274 |pages=494–7 |date=July 1996 |pmid=8662537 |bibcode=1996Sci...273..494S |doi=10.1126/science.273.5274.494|s2cid=22654725 }}</ref>
[[File:Spectralkaryotype98-300.jpg|thumb|left|Spectral human karyotype]]
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.<ref>{{cite journal |vauthors=Wang TL, Maierhofer C, Speicher MR, etal |title=Digital karyotyping |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue=25 |pages=16156–61 |date=December 2002 |pmid=12461184 |pmc=138581 |doi=10.1073/pnas.202610899 |bibcode = 2002PNAS...9916156W |doi-access=free }}</ref> This method is also known as [[Virtual Karyotype|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.<ref>{{Cite journal|last1=Leary|first1=Rebecca J|last2=Cummins|first2=Jordan|last3=Wang|first3=Tian-Li|last4=Velculescu|first4=Victor E|date=August 2007|title=Digital karyotyping|url=http://www.nature.com/articles/nprot.2007.276|journal=Nature Protocols|language=en|volume=2|issue=8|pages=1973–1986|doi=10.1038/nprot.2007.276|pmid=17703209|s2cid=33337972|issn=1754-2189|url-access=subscription}}</ref>
== Chromosome abnormalities ==
{{main article|Chromosome abnormalities}}
Chromosome abnormalities can be numerical, as in the presence of extra or missing chromosomes, or structural, as in [[derivative chromosome]], [[chromosomal translocation|translocations]], [[chromosomal inversion|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]]; [[trisomy|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
* [[Turner syndrome]] results from a single X chromosome (45,X or 45,X0).
* [[Klinefelter syndrome]], the most common male chromosomal disease, otherwise known as 47,XXY, is caused by an extra '''X''' chromosome.
* [[Edwards syndrome]] is caused by [[trisomy]] (three copies) of chromosome 18.
* [[Down syndrome]], a common chromosomal disease, is caused by trisomy of chromosome 21.
* [[Patau syndrome]] is caused by trisomy of chromosome 13.
* [[Trisomy 9]], believed to be the 4th most common trisomy, has many long lived affected individuals but only in a form other than a full trisomy, such as trisomy 9p syndrome or mosaic trisomy 9. They often function quite well, but tend to have trouble with speech.
* Also documented are trisomy 8 and trisomy 16, although they generally do not survive to birth.
Some disorders arise from loss of just a piece of one chromosome, including
* [[Cri du chat]] (cry of the cat), from a truncated short arm on chromosome 5. The name comes from the babies' distinctive cry, caused by abnormal formation of the larynx.
* [[1p36 deletion syndrome|1p36 Deletion syndrome]], from the loss of part of the short arm of chromosome 1.
* [[Angelman syndrome]] – 50% of cases have a segment of the long arm of chromosome 15 missing; a deletion of the maternal genes, example of [[genomic imprinting|imprinting]] disorder.
* [[Prader-Willi syndrome]] – 50% of cases have a segment of the long arm of chromosome 15 missing; a deletion of the paternal genes, example of imprinting disorder.
* Chromosomal abnormalities can also occur in [[cancer]]ous cells of an otherwise genetically normal individual; one well-documented example is the [[Philadelphia chromosome]], a translocation mutation commonly associated with [[chronic myelogenous leukemia]] and less often with [[acute lymphoblastic leukemia]].
== 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 Wilhelm Gottfried von Waldeyer-Hartz|Heinrich von Waldeyer]] in 1888. It is [[Neo-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. The term karyotype as defined by the [[phenotypic]] appearance of the [[Somatic (biology)|somatic]] chromosomes, in contrast to their [[gene|genic]] contents was introduced by [[Grigory Levitsky]] who worked with Lev Delaunay, [[Sergei Navashin]], and [[Nikolai Vavilov]].<ref>{{Cite journal |last1=Zelenin |first1=A. V. |last2=Rodionov |first2=A. V. |last3=Bolsheva |first3=N. L. |last4=Badaeva |first4=E. D. |last5=Muravenko |first5=O. V. |date=2016 |title=Genome: Origins and evolution of the term |url=http://link.springer.com/10.1134/S0026893316040178 |journal=Molecular Biology |language=en |volume=50 |issue=4 |pages=542–550 |doi=10.1134/S0026893316040178 |pmid=27668601 |s2cid=9373640 |issn=0026-8933|url-access=subscription }}</ref><ref>{{Cite journal |last1=Vermeesch |first1=Joris Robert |last2=Rauch |first2=Anita |date=2006 |title=Reply to Hochstenbach et al |journal=European Journal of Human Genetics |language=en |volume=14 |issue=10 |pages=1063–1064 |doi=10.1038/sj.ejhg.5201663 |pmid=16736034 |s2cid=46363277 |issn=1018-4813|doi-access=free }}</ref><ref>Delaunay L. N. ''Comparative karyological study of species Muscari Mill. and Bellevalia Lapeyr''. Bulletin of the Tiflis Botanical Garden. 1922, v. 2, n. 1, p. 1-32[in Russian]</ref><ref>{{cite journal |last1=Battaglia |first1=Emilio |title=Nucleosome and nucleotype: a terminological criticism |journal=Caryologia |volume=47 |issue=3–4 |pages=193–197 |year=1994 |doi=10.1080/00087114.1994.10797297}}</ref> The subsequent history of the concept can be followed in the works of [[C. D. Darlington]]<ref>Darlington C.D. 1939. ''Evolution of genetic systems''. Cambridge University Press. 2nd ed, revised and enlarged, 1958. Oliver & Boyd, Edinburgh.</ref> and [[Michael JD White]].<ref name="White2"/><ref name="White1">White M.J.D. 1973. ''Animal cytology and evolution''. 3rd ed, Cambridge University Press.</ref>
Investigation into the human karyotype took many years to settle the most basic question: how many chromosomes does a normal [[diploid]] human cell contain?<ref>{{cite journal |first1=Kottler |last1=MJ |title=From 48 to 46: cytological technique, preconception, and the counting of human chromosomes |journal=Bull Hist Med |volume=48 |issue=4 |pages=465–502 |year=1974 |pmid=4618149 }}</ref> In 1912, [[Hans von Winiwarter]] reported 47 chromosomes in [[spermatogonia]] and 48 in [[oogonia]], concluding an [[XO sex-determination system|XX/XO sex determination]] mechanism.<ref>{{cite journal |author=von Winiwarter H. |title=Études sur la spermatogenèse humaine |journal=Archives de Biologie |volume=27 |issue=93 |pages=147–9 |year=1912 }}</ref> [[Theophilus Painter|Painter]] in 1922 was not certain whether the diploid of humans was 46 or 48, at first favoring 46,<ref>{{cite journal |author=Painter T.S. |title=The spermatogenesis of man |journal=Anat. Res. |volume=23 |page=129 |year=1922 }}</ref> but revised his opinion from 46 to 48, and he correctly insisted on humans having an [[XY sex-determination system|XX/XY]] system.<ref>{{cite journal |author=Painter T.S. |title=Studies in mammalian spermatogenesis II |journal=J. Exp. Zoology |volume=37 |pages=291–336 |year=1923 |doi=10.1002/jez.1400370303 |issue=3 }}</ref> Considering the techniques of the time, these results were remarkable.
[[File:Chromosome2 merge.png|thumb|Fusion of ancestral chromosomes left distinctive remnants of telomeres, and a vestigial centromere]]
[[Joe Hin Tjio]] working in [[Albert Levan]]'s lab<ref>{{cite news|url=https://www.theguardian.com/news/2001/dec/11/guardianobituaries.medicalscience|title=Joe Hin Tjio The man who cracked the chromosome count|newspaper=[[The Guardian]]|first=Pearce |last=Wright |date=11 December 2001}}</ref> found the chromosome count to be 46 using new techniques available at the time:
# Using cells in [[tissue culture]]
# Pretreating cells in a [[Tonicity#Hypotonicity|hypotonic solution]], which swells them and spreads the chromosomes
# Arresting [[mitosis]] in [[metaphase]] by a solution of [[colchicine]]
# Squashing the preparation on the slide forcing the chromosomes into a single plane
# Cutting up a photomicrograph and arranging the result into an indisputable karyogram.
The work took place in 1955, and was published in 1956. The karyotype of humans includes only 46 chromosomes.<ref>{{cite journal |author1=Tjio J.H. |author2=Levan A. |title=The chromosome number of man |journal=Hereditas |volume=42 |issue=1–2 |pages=1–6 |year=1956 |doi=10.1111/j.1601-5223.1956.tb03010.x |pmid=345813 |doi-access=free }}</ref><ref name="Hsu">Hsu T.C. 1979. ''Human and mammalian cytogenetics: a historical perspective''. Springer-Verlag, NY.</ref> 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.<ref name="fusion">[http://www.evolutionpages.com/chromosome_2.htm Human chromosome 2 is a fusion of two ancestral. chromosomes] Alec MacAndrew; accessed 18 May 2006.</ref><ref>[https://www.youtube.com/watch?v=x-WAHpC0Ah0 Evidence of common ancestry: human chromosome 2] (video) 2007</ref>
== See also ==
* {{annotated link|Cytogenetic notation}}
* {{annotated link|Genome screen}}
== References ==
{{reflist}}
== External links ==
* {{Commons category-inline|Karyotypes}}
* [https://web.archive.org/web/20090118031402/http://learn.genetics.utah.edu/content/begin/traits/karyotype/ Making a karyotype], an online activity from the University of Utah's Genetic Science Learning Center.
* [http://www.biology.arizona.edu/human_bio/activities/karyotyping/karyotyping.html Karyotyping activity with case histories] from the University of Arizona's Biology Project.
* [http://www.biologycorner.com/worksheets/karyotype/chromosomestudy-teacher.html Printable karyotype project] from Biology Corner, a resource site for biology and science teachers.
* [https://web.archive.org/web/20050414010530/http://homepage.mac.com/wildlifeweb/cyto/text/Banding.html Chromosome Staining and Banding Techniques]
* [http://www.bjornbiosystems.com Bjorn Biosystems for Karyotyping and FISH] {{Webarchive|url=https://web.archive.org/web/20190612132411/http://bjornbiosystems.com/ |date=12 June 2019 }}
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{{Use dmy dates|date=April 2017}}
[[Category:Cell biology]]
[[Category:Chromosomes]]
[[Category:
[[Category:Evolutionary biology]]
[[Category:Genetics techniques]]
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