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Paleopolyploidy is the result of
genome duplications Polyploidy is a condition in which the cells of an organism have more than one pair of ( homologous) chromosomes. Most species whose cells have nuclei (eukaryotes) are diploid, meaning they have two sets of chromosomes, where each set contains ...
which occurred at least several million years ago (MYA). Such an event could either double the genome of a single species (
autopolyploidy Polyploidy is a condition in which the cells of an organism have more than one pair of ( homologous) chromosomes. Most species whose cells have nuclei (eukaryotes) are diploid, meaning they have two sets of chromosomes, where each set contains ...
) or combine those of two species (
allopolyploidy Polyploidy is a condition in which the cells of an organism have more than one pair of ( homologous) chromosomes. Most species whose cells have nuclei ( eukaryotes) are diploid, meaning they have two sets of chromosomes, where each set conta ...
). Because of functional redundancy, genes are rapidly silenced or lost from the duplicated genomes. Most paleopolyploids, through evolutionary time, have lost their
polyploid Polyploidy is a condition in which the cells of an organism have more than one pair of ( homologous) chromosomes. Most species whose cells have nuclei (eukaryotes) are diploid, meaning they have two sets of chromosomes, where each set contains ...
status through a process called
diploidization Diploidization is the process of converting a polyploid genome back into a diploid one. Polyploidy is a product of whole genome duplication (WGD) and is followed by diploidization as a result of genome shock. The plant kingdom has undergone multi ...
, and are currently considered diploids e.g.
baker's yeast Baker's yeast is the common name for the strains of yeast commonly used in baking bread and other bakery products, serving as a leavening agent which causes the bread to rise (expand and become lighter and softer) by converting the fermentable s ...
, ''
Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. ''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land. A winter a ...
'', and perhaps
human Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ...
s. Paleopolyploidy is extensively studied in plant lineages. It has been found that almost all flowering plants have undergone at least one round of genome duplication at some point during their evolutionary history. Ancient genome duplications are also found in the early ancestor of vertebrates (which includes the human lineage) near the origin of the
bony fishes Osteichthyes (), popularly referred to as the bony fish, is a diverse superclass of fish that have skeletons primarily composed of bone tissue. They can be contrasted with the Chondrichthyes, which have skeletons primarily composed of cartilage ...
, and another in the stem lineage of teleost fishes. Evidence suggests that baker's yeast (''
Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been ...
''), which has a compact genome, experienced polyploidization during its evolutionary history. The term ''mesopolyploid'' is sometimes used for species that have undergone whole genome multiplication events (whole genome duplication, whole genome triplification, etc.) in more recent history, such as within the last 17 million years.


Eukaryotes

Ancient genome duplications are widespread throughout
eukaryotic Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bact ...
lineages, particularly in plants. Studies suggest that the common ancestor of
Poaceae Poaceae () or Gramineae () is a large and nearly ubiquitous family of monocotyledonous flowering plants commonly known as grasses. It includes the cereal grasses, bamboos and the grasses of natural grassland and species cultivated in lawns and ...
, the grass family which includes important crop species such as maize, rice, wheat, and sugar cane, shared a whole genome duplication about . In more ancient monocot lineages one or likely multiple rounds of additional whole genome duplications had occurred, which were however not shared with the ancestral
eudicots The eudicots, Eudicotidae, or eudicotyledons are a clade of flowering plants mainly characterized by having two seed leaves upon germination. The term derives from Dicotyledons. Traditionally they were called tricolpates or non- magnoliid dico ...
. Further independent more recent whole genome duplications have occurred in the lineages leading to maize, sugar cane and wheat, but not rice, sorghum or foxtail millet. A polyploidy event is theorized to have created the ancestral line that led to all modern flowering plants. That paleopolyploidy event was studied by sequencing the genome of an ancient flowering plant, '' Amborella trichopoda''. The core eudicots also shared a common whole genome triplication (paleo-hexaploidy), which was estimated to have occurred after
monocot Monocotyledons (), commonly referred to as monocots, (Lilianae ''sensu'' Chase & Reveal) are grass and grass-like flowering plants (angiosperms), the seeds of which typically contain only one embryonic leaf, or cotyledon. They constitute one of t ...
-
eudicot The eudicots, Eudicotidae, or eudicotyledons are a clade of flowering plants mainly characterized by having two seed leaves upon germination. The term derives from Dicotyledons. Traditionally they were called tricolpates or non-magnoliid dicots ...
divergence but before the divergence of
rosids The rosids are members of a large clade (monophyletic group) of flowering plants, containing about 70,000 species, more than a quarter of all angiosperms. The clade is divided into 16 to 20 orders, depending upon circumscription and classifica ...
and
asterids In the APG IV system (2016) for the classification of flowering plants, the name asterids denotes a clade (a monophyletic group). Asterids is the largest group of flowering plants, with more than 80,000 species, about a third of the total floweri ...
. Many eudicot species have experienced additional whole genome duplications or triplications. For example, the model plant ''
Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. ''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land. A winter a ...
'', the first plant to have its entire genome sequenced, has experienced at least two additional rounds of whole genome duplication since the duplication shared by the core eudicots. The most recent event took place before the divergence of the ''Arabidopsis'' and ''
Brassica ''Brassica'' () is a genus of plants in the cabbage and mustard family (Brassicaceae). The members of the genus are informally known as cruciferous vegetables, cabbages, or mustard plants. Crops from this genus are sometimes called ''cole c ...
'' lineages, about to . Other examples include the sequenced eudicot genomes of apple, soybean, tomato, cotton, etc. Compared with plants, paleopolyploidy is much rarer in the animal kingdom. It has been identified mainly in amphibians and bony fishes. Although some studies suggested one or more common genome duplications are shared by all vertebrates (including humans), the evidence is not as strong as in the other cases because the duplications, if they exist, happened so long ago (about 400-500 Ma compared to less than 200 Ma in plants), and the matter is still under debate. The idea that vertebrates share a common whole genome duplication is known as the
2R Hypothesis The 2R hypothesis or Ohno's hypothesis, first proposed by Susumu Ohno in 1970,Ohno, Susumu (1970). ''Evolution by Gene Duplication.'' London: Allen and Unwin, . is a hypothesis that the genomes of the early vertebrate lineage underwent two complete ...
. Many researchers are interested in the reason why animal lineages, particularly mammals, have had so many fewer whole genome duplications than plant lineages. A well-supported paleopolyploidy has been found in baker's yeast (''Saccharomyces cerevisiae''), despite its small, compact genome (~13Mbp), after the divergence from ''
Kluyveromyces lactis ''Kluyveromyces lactis'' is a ''Kluyveromyces'' yeast commonly used for genetic studies and industrial applications. Its name comes from the ability to assimilate lactose and convert it into lactic acid. ''Kluyveromyces lactis'' (formerly ''Sac ...
'' and '' K. marxianus''. Through genome streamlining, yeast has lost 90% of the duplicated genome over evolutionary time and is now recognized as a diploid organism.


Detection method

Duplicated genes can be identified through
sequence homology Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a sp ...
on the DNA or protein level. Paleopolyploidy can be identified as massive gene duplication at one time using a
molecular clock The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotid ...
. To distinguish between whole-genome duplication and a collection of (more common) single
gene duplication Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. ...
events, the following rules are often applied: * Duplicated genes are located in large duplicated blocks. Single gene duplication is a random process and tends to make duplicated genes scattered throughout the genome. * Duplicated blocks are non-overlapping because they were created simultaneously. Segmental duplication within the genome can fulfill the first rule; but multiple independent segmental duplications could overlap each other. In theory, the two duplicated genes should have the same "age"; that is, the divergence of the sequence should be equal between the two genes duplicated by paleopolyploidy (
homeolog Polyploidy is a condition in which the cells of an organism have more than one pair of ( homologous) chromosomes. Most species whose cells have nuclei (eukaryotes) are diploid, meaning they have two sets of chromosomes, where each set contains ...
s).
Synonymous substitution A synonymous substitution (often called a ''silent'' substitution though they are not always silent) is the evolutionary substitution of one base for another in an exon of a gene coding for a protein, such that the produced amino acid sequence ...
rate, Ks, is often used as a molecular clock to determine the time of gene duplication. Thus, paleopolyploidy is identified as a "peak" on the duplicate number vs. Ks graph (shown on the right). However, using Ks plots to identify and document ancient polyploid events can be problematic, as the method fails to identify genome duplications that were followed by massive gene elimination and genome refinement. Other mixed model approaches that combined Ks plots with other methods are being developed to better understand paleopolyploidy. Duplication events that occurred a long time ago in the history of various evolutionary lineages can be difficult to detect because of subsequent diploidization (such that a polyploid starts to behave cytogenetically as a diploid over time) as mutations and gene translations gradually make one copy of each chromosome unlike its counterpart. This usually results in a low confidence for identifying a very ancient paleopolyploidy.


Evolutionary importance

Paleopolyploidization events lead to massive cellular changes, including doubling of the genetic material, changes in gene expression and increased cell size. Gene loss during diploidization is not completely random, but heavily selected. Genes from large gene families are duplicated. On the other hand, individual genes are not duplicated. Overall, paleopolyploidy can have both short-term and long-term evolutionary effects on an organism's fitness in the natural environment. ;Enhanced phenotypic evolution: Whole genome duplication may increase the rates and efficiency by which organisms acquire new biological traits. However, one test of this hypothesis, which compared evolutionary rates in innovation in early teleost fishes (with duplicate genomes) to early holostean fishes (without duplicated genomes) found little difference between the two. ; Genome diversity: Genome doubling provided the organism with redundant alleles that can evolve freely with little selection pressure. The duplicated genes can undergo
neofunctionalization Neofunctionalization, one of the possible outcomes of functional divergence, occurs when one gene copy, or paralog, takes on a totally new function after a gene duplication event. Neofunctionalization is an adaptive mutation process; meaning one ...
or
subfunctionalization Subfunctionalization was proposed by Stoltzfus (1999) and Force et al. (1999) as one of the possible outcomes of functional divergence that occurs after a gene duplication event, in which pairs of genes that originate from duplication, or paralog ...
which could help the organism adapt to the new environment or survive different stress conditions. ; Hybrid vigor: Polyploids often have larger cells and even larger organs. Many important crops, including wheat, maize and
cotton Cotton is a soft, fluffy staple fiber that grows in a boll, or protective case, around the seeds of the cotton plants of the genus ''Gossypium'' in the mallow family Malvaceae. The fiber is almost pure cellulose, and can contain minor pe ...
, are paleopolyploids which were selected for domestication by ancient peoples. ; Speciation: It has been suggested that many polyploidization events created new species, via a gain of adaptive traits, or by sexual incompatibility with their diploid counterparts. An example would be the recent
speciation Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within ...
of allopolyploid ''
Spartina ''Spartina'' is a taxon of plants in the grass family, frequently found in coastal salt marshes. Its species are commonly known as cordgrass or cord-grass, and are native to the coasts of the Atlantic Ocean in western and southern Europe, nort ...
'' — '' S. anglica''; the polyploid plant is so successful that it is listed as an
invasive species An invasive species otherwise known as an alien is an introduced organism that becomes overpopulated and harms its new environment. Although most introduced species are neutral or beneficial with respect to other species, invasive species ad ...
in many regions.


Allopolyploidy and autopolyploidy

There are two major divisions of
polyploidy Polyploidy is a condition in which the cells of an organism have more than one pair of ( homologous) chromosomes. Most species whose cells have nuclei (eukaryotes) are diploid, meaning they have two sets of chromosomes, where each set contains ...
, allopolyploidy and autopolyploidy. Allopolyploids arise as a result of the hybridization of two related species, while autopolyploids arise from the duplication of a species' genome as a result of hybridization of two conspecific parents, or somatic doubling in reproductive tissue of a parent. Allopolyploid species are believed to be much more prevalent in nature, possibly because allopolyploids inherit different genomes, resulting in increased
heterozygosity Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. ...
, and therefore higher fitness. These different genomes result in an increased likelihood of large genomic reorganizations, which can be either deleterious, or advantageous. Autopolyploidy, however, is generally considered to be a neutral process, though it has been hypothesized that autopolyploidy may serve as a useful mechanism for inducing speciation, and therefore assisting in the ability of an organism to quickly colonize in new habitats without undergoing the time-intensive and costly period of genomic reorganization experienced by allopolyploid species. One common source of autopolyploidy in plants stems from "perfect flowers", which are capable of self-pollination, or "selfing". This, along with errors in
meiosis Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately r ...
that lead to
aneuploidy Aneuploidy is the presence of an abnormal number of chromosomes in a cell, for example a human cell having 45 or 47 chromosomes instead of the usual 46. It does not include a difference of one or more complete sets of chromosomes. A cell with any ...
, can create an environment where autopolyploidy is very likely. This fact can be exploited in a laboratory setting by using
colchicine Colchicine is a medication used to treat gout and Behçet's disease. In gout, it is less preferred to NSAIDs or steroids. Other uses for colchicine include the management of pericarditis and familial Mediterranean fever. Colchicine is taken b ...
to inhibit
chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins ar ...
segregation during meiosis, creating synthetic autopolyploid plants. Following polyploidy events, there are several possible fates for duplicated
genes In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ...
; both copies may be retained as functional genes, change in gene function may occur in one or both copies,
gene silencing Gene silencing is the regulation of gene expression in a cell to prevent the expression of a certain gene. Gene silencing can occur during either transcription or translation and is often used in research. In particular, methods used to silence gen ...
may mask one or both copies, or complete gene loss may occur. Polyploidy events will result in higher levels of heterozygosity, and, over time, can lead to an increase in the total number of functional genes in the genome. As time passes after a genome duplication event, many genes will change function as a result of either change in duplicate gene function for both allo- and autopolyploid species, or there will be changes in gene expression caused by genomic rearrangements induced by genome duplication in allopolyploids. When both copies of a gene are retained, and thus the number of copies doubled, there is a chance that there will be a proportional increase in expression of that gene, resulting in twice as much
mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during t ...
transcript being produced. There is also the possibility that transcription of a duplicated gene will be down-regulated, resulting in less than two-fold increase in transcription of that gene, or that the duplication event will yield more than a two-fold increase in transcription. In one species, ''Glycine dolichocarpa'' (a close relative of the
soybean The soybean, soy bean, or soya bean (''Glycine max'') is a species of legume native to East Asia, widely grown for its edible bean, which has numerous uses. Traditional unfermented food uses of soybeans include soy milk, from which tofu ...
, ''Glycine max''), it has been observed that following a genome duplication roughly 500,000 years ago, there has been a 1.4 fold increase in transcription, indicating that there has been a proportional decrease in transcription relative to gene copy number following the duplication event.


Vertebrates as paleopolyploid

The hypothesis of vertebrate paleopolyploidy originated as early as the 1970s, proposed by the biologist
Susumu Ohno Susumu is a masculine Japanese given name. Notable people with the name include: * Susumu Akagi (born 1972) Japanese voice actor * Susumu Aoyagi (青柳 進, born 1968), Japanese baseball player * Susumu Chiba (born 1970), Japanese voice actor *, ...
. He reasoned that the vertebrate genome could not achieve its complexity without large scale whole-genome duplications. The "two rounds of genome duplication" hypothesis (
2R hypothesis The 2R hypothesis or Ohno's hypothesis, first proposed by Susumu Ohno in 1970,Ohno, Susumu (1970). ''Evolution by Gene Duplication.'' London: Allen and Unwin, . is a hypothesis that the genomes of the early vertebrate lineage underwent two complete ...
) came about, and gained in popularity, especially among developmental biologists. Some researchers have questioned the 2R hypothesis because it predicts that vertebrate genomes should have a 4:1 gene ratio compared with invertebrate genomes, and this is not supported by findings from the 48 vertebrate genome projects available in mid-2011. For example, the human genome consists of ~21,000 protein coding genes according to June, 2011 counts at UCSC and Ensembl genome analysis centers while an average invertebrate genome size is about 15,000 genes. The amphioxus genome sequence provided support for the hypothesis of two rounds of whole genome duplication, followed by loss of duplicate copies of most genes. Additional arguments against 2R were based on the lack of the (AB)(CD) tree topology amongst four members of a gene family in vertebrates. However, if the two genome duplications occurred close together, we would not expect to find this topology. A recent study generated the
sea lamprey The sea lamprey (''Petromyzon marinus'') is a parasitic lamprey native to the Northern Hemisphere. It is sometimes referred to as the "vampire fish". Description The sea lamprey has an eel-like body without paired fins. Its mouth is jawless, r ...
genetic map, which yielded strong support for the hypothesis that a single whole-genome duplication occurred in the basal vertebrate lineage, preceded and followed by several evolutionarily independent segmental duplications that occurred over chordate evolution.


See also

*
Gene duplication Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. ...
*
Genomics Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...
*
Karyotype A karyotype is the general appearance of the complete set of metaphase chromosomes in the cells of a species or in an individual organism, mainly including their sizes, numbers, and shapes. Karyotyping is the process by which a karyotype is disce ...
*
Ploidy Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Sets of chromosomes refer to the number of maternal and paternal chromosome copies, respective ...
*
Polyploidy Polyploidy is a condition in which the cells of an organism have more than one pair of ( homologous) chromosomes. Most species whose cells have nuclei (eukaryotes) are diploid, meaning they have two sets of chromosomes, where each set contains ...
*
Speciation Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within ...


References


Further reading

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