Polyploidy is a condition in which the cells of an organism have more than two paired homologous sets of chromosomes. Most species whose cells have nuclei eukaryotes are diploid , meaning they have two sets of chromosomes—one set inherited from each parent. However, some organisms are polyploid , and polyploidy is especially common in plants. Most eukaryotes have diploid somatic cells , but produce haploid gametes eggs and sperm by meiosis.
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It tests the hypothesis that a tetraploid lineage originated via autopolyploidization vs. The method is based on the hypothesis that, in the case of autopolyploidy, any genetic marker in the first tetraploid ancestor is represented by two copies one for each homoeologous chromosome of the haploid complement , whereas in allopolyploidy some markers absent from one of the hybridizing species will display one copy at most. The model requires knowledge of the phylogeny topology and branch lengths of a sample of species descending from the same tetraploidization event, together with the number of homoeologous copies present in each species for a set of neutral markers.
The likelihood of a given proportion of the markers being present in both homoeologous chromosome pairs of the ancestral tetraploid is expressed as a function of the deletion rate of a marker. In the case of an autopolyploid origin, this proportion equals one. A likelihood-ratio test was carried out to test this hypothesis. The method was used to examine five microsatellite loci in eight species of Barbus sensu lato. Assuming the validity of the hypotheses on phylogenetic relationships and evolutionary rates, the test rejects the possibility that European tetraploid barbs originated through autopolyploidy.
This is the first test that can reject autopolyploidy, and it would appear particularly useful for phylogenetic studies in taxa where hybridization is known and where, consequently, undetected reticulate evolution may impair phylogenetic reconstruction. Polyploidy is a very common phenomenon in plants. Although less well studied in animals, several polyploid taxa are known. In fish, however, several ancient polyploid families or genera are made up of several sexually reproducing species Schultz, In vertebrate evolution, polyploidy is considered to have enabled the evolution of more complex forms of life by giving the opportunity for new functions to evolve Ohno, Although polyploidy is recognized as being widespread and of evolutionary importance, little is known about the origins of higher order polyploid taxa.
Distinction can be made between two kinds of eupolyploidy. Autopolyploids are formed of genomes of the same species possibly the same individual , whereas allopolyploids contain genomes from distinct taxa. Allopolyploidy is therefore associated with hybridization. The establishment of whether the origin of a tetraploid lineage is allopolyploid or autopolyploid is of crucial importance for phylogenetic studies.
If a lineage has arisen through the hybridization of two species, as in the case of allopolyploidy, phylogenetic relationships are not properly described by a tree but by a net, whose reconstruction is impossible with standard methods.
Conventionally, two approaches are used to determine whether a lineage is auto- or allopolyploid. These are: i the cytological approach, involving observations of meiotic cells; and ii the formal genetic approach based on analyses of the proportions of marker alleles transmitted in the progeny of controlled crosses. After autopolyploidization, multisomic inheritance of each chromosome type is observed, but only for a certain time. Two or three in the case of hexaploidy chromosome pairs then become independent, with the re-establishment of disomic inheritance, avoiding meiotic problems which resulted from the formation of multivalents Dewet, Cytology can no longer reveal an autopolyploid origin when disomic inheritance is complete.
Furthermore, multivalents may be observable only at early stages of meiotic division e. Conversely, multivalent formation in an allotetraploid cannot be rigorously excluded if the hybridizing species were closely related. The observation of meiotic cells is not therefore a suitable method for distinguishing between auto- and allopolyploidy.
Today, using cytological tools and allozyme data or data from Mendelian markers , information on the origin of polyploidy is only available when multivalents are observed or when multisomic inheritance is established. In such cases, one can, at best, conclude that tetraploidy occurred either via autopolyploidization or via allopolyploidization involving very close species; there is no case in which allopolyploidy can be established and autopolyploidy unequivocally rejected.
A new method is described here for discriminating between the auto- and allopolyploidy hypotheses. It is based on the fact that all the genetic markers of a tetraploid lineage were present in two copies in the haploid complement of the ancestral genome in the case of autopolyploidy, but not in the case of allopolyploidy. For a set of related tetraploid species, the mean number of copies per locus in the ancestral genome at many loci is estimated from the observed number of copies in extant species.
Autopolyploidy is rejected when the proportion of loci which were ancestrally double is significantly different from one. The new method has been applied to microsatellite data of six tetraploid species of Barbus.
A stochastic model was designed to represent the evolution of the number of copies of a set of neutral loci in the genomes of diverging tetraploid lineages. A common Poisson process of deletion is assumed for copies of any locus within any lineage. The mean number of copies in all loci in the ancestral tetraploid genome is estimated to test the autopolyploidy hypothesis.
Let n be the number of tetraploid species examined. Assuming that homologous chromosomes are identical with regard to the presence or absence of a locus i. It is assumed that the number of genomic copies in n extant species has been determined experimentally for k loci. B is taken as the most ancient tetraploid common ancestor of the species investigated thus B is the ancestral species which underwent tetraploidization, Fig. It is assumed that the number of copies of a given locus did not increase after tetraploidization; extant loci therefore existed in the genome of B.
Losses are allowed but not gains. B represents the first polyploid species; A is the most recent common ancestor of the surveyed species confounded to B in the comb model.
Branch lengths in time units are t for the comb model, t 1 ancestral branch and t 2 terminal branches for the rake model. Exact likelihood functions were derived in two particular cases, namely star-phylogeny referred to below as the comb model; Fig. Maximum likelihood estimation of parameters was performed numerically using the simplex method Press et al. An unresolved radiation of n species immediately following tetraploidization is assumed.
Let t be the time since radiation. Let b be the unknown number of copies of locus i in the ancestral species B. The likelihood function at locus i is:. In this case, time t 1 elapsed between the tetraploidization event and radiation, which occurred t 2 time units ago.
Let A be the most recent common ancestor of the n species investigated. If d i and s i are the number of two-copy and one-copy species for locus i , respectively, and if a is the number of copies of locus i in ancestor A, the likelihood function for locus i is:.
If external information on divergence times is available e. If the phylogenetic relationships among surveyed species are known, the likelihood function can be computed using the method of Felsenstein However, if external information about branch lengths is available possibly from a molecular phylogeny study , fixed branch length values can be used, considerably reducing the number of parameters to be estimated, which may be necessary when a moderate number of loci is examined.
The autopolyploidy hypothesis may be tested using the likelihood ratio on any of the above models. Let L be the maximum likelihood for one of the above models say the comb model with two parameters. The genus Barbus sensu lato Cyprinidae is a polyphyletic group with at least species native to the Old World Howes, and includes diploid, tetraploid and hexaploid lineages.
As hybridization is not rare in Barbus at least six pairs of B. It is therefore important to determine whether particular polyploid groups have an allopolyploid origin. Diploid species 48—52 chromosomes are widespread from Asia to Africa.
These small species are not well known and are probably polyphyletic. The only two groups of barbs considered to be monophyletic Berrebi et al. Tetraploid species of barb not belonging to the subgenus Barbus are known in South Africa and in east and south Asia.
Numerous other diploid and polyploid lineages exist but their phylogenetic relationships are far from established Berrebi et al. All Barbus are thought to be Asian in origin Banarescu, Tsigenopoulos, pers. Primer pairs for six microsatellite loci were isolated in two Barbus species in a previous study.
For the present study, additional species were surveyed in order to obtain their copy number for extant microsatellite loci. Assuming that homoeologous copies of the loci were actually revealed in contrast with tandem repeats for example , the test described above can be used to infer the origin of tetraploidy in Euro—Mediterranean barbs.
Chenuil et al. Four further species of the subgenus Barbus were investigated in the study reported here, and also four other cyprinid and one cobitid species. Table 1 shows the loci, the corresponding primers and the standard PCR conditions used. For five loci, the genotypes were assessed of individuals collected in the Lergue river France. The sample included the following taxa: B.
These taxa belong to the western lineage of European barbs Berrebi, For the Iberian Peninsula lineage, four individuals of each species, B. For the North African lineage, four individuals per species were sampled, respectively, in the Draa river Atlantic drainage for B. For the hexaploid species, 63 individuals of B. Other cyprinid genera included a tetraploid species, the carp Cyprinus carpio L.
One individual of each of these species was caught in the Lergue river. However, in all cases when allospecific amplification was possible, it worked with the standard conditions. A locus was determined as duplicate either two disomic loci or one tetrasomic locus when an individual displayed more than two alleles.
The results of allospecific amplification and expressed ploidy levels are recorded in Table 2. To summarize, five out of six loci are conserved between B. Barb 37, Barb 62 and Barb 79 were considered to be simple loci in the six tetraploid Barbus species but their expressed ploidy could not be unambiguously established in the four species for which samples were too small.
However, because for each locus more than four alleles were observed in the samples of the tetraploid species, and because no more than two bands were observed per individual, it is very likely that these loci are nonduplicate as will be assumed below. Loci Barb 79, Barb 65, Barb 37, Barb 59 and Barb 62 were found in species which diverged from the Barbus species investigated before tetraploidization: Barb 59, Barb 65 and Barb 79 are present in a species which is unambiguously an outgroup of barbins gudgeon and the other loci are present in V.
These five loci can therefore be used for our test. A check was made data not shown that there was no presence—absence polymorphism for loci amplifiable in species B. This was confirmed by the analysis of progeny of crosses in B.
Although microsatellites are, in general, selectively neutral, the priming sites may be embedded in coding regions; hence the present study checked the absence of codons in the flanking sequences of the microsatellite loci Chenuil et al.