Time and time again: unisexual salamanders (genus Ambystoma) are the oldest unisexual vertebrates

<p>Abstract</p> <p>Background</p> <p>The age of unisexual salamanders of the genus <it>Ambystoma </it>is contentious. Recent and ancient evolutionary histories of unisexual <it>Ambystoma </it>were proposed by a few separate studies that constructed phylogenies using mitochondrial DNA markers (cytochrome b gene vs. non-coding region). In contrast to other studies showing that unisexual <it>Ambystoma </it>represent the most ancient unisexual vertebrates, a recent study by Robertson et al. suggests that this lineage has a very recent origin of less than 25,000 years ago.</p> <p>Results</p> <p>We re-examined the phylogenetic relationship of the unisexuals to <it>A. barbouri </it>from various populations using both mitochondrial markers as well as the complete mitochondrial genomes of <it>A. barbouri </it>and a unisexual individual from Kentucky. Lineage dating was conducted using BEAST and MultiDivTime on a complete mitochondrial genome phylogeny. Our results support a monophyletic lineage for unisexual <it>Ambystoma </it>that shares its most recent common ancestor with an <it>A. barbouri </it>lineage from western Kentucky. In contrast to the Robertson et al.'s study, no <it>A. barbouri </it>individual shared an identical or almost identical cytochrome b haplotype with any unisexual. Molecular dating supports an early Pliocene origin for the unisexual linage (~5 million years ago). We propose that a unisexual-like cytochrome b <it>numt </it>(or pseudogene) exists in the controversial <it>A. barbouri </it>individuals from Kentucky, which was likely the cause of an erroneous phylogeny and time estimate in Robertson et al.'s study.</p> <p>Conclusion</p> <p>We reject a recent origin of unisexual <it>Ambystoma </it>and provide strong evidence that unisexual <it>Ambystoma </it>are the most ancient unisexual vertebrates known to exist. The likely presence of an ancient cytochrome b <it>numt </it>in some Kentucky <it>A. barbouri </it>represents a molecular "fossil" reinforcing the hypothesis that these individuals are some of the closest extant relatives to unisexual <it>Ambystoma</it>.</p

The prevalence of genome replacement in unisexual salamanders of the genus Ambystoma (Amphibia, Caudata) revealed by nuclear gene genealogy

<p>Abstract</p> <p>Background</p> <p>Unisexual salamanders of the genus <it>Ambystoma </it>exemplify the most ancient lineage of unisexual vertebrates and demonstrate an extremely flexible reproductive system. Unisexual <it>Ambystoma </it>interact with and incorporate genomes from two to four sexual species (<it>A. laterale</it>, <it>A. jeffersonianum</it>,<it>A. texanum</it>, and <it>A. tigrinum</it>), to generate more than 20 genome compositions or biotypes. Unisexual ploidy levels range from diploid to pentaploid, but all contain at least one <it>A. laterale </it>(L) genome. Replacement of nuclear genomes might be responsible for the evolutionary longevity of unisexual <it>Ambystoma </it>but direct evidence for the prevalence of genome replacement in natural populations is absent. Two major puzzling questions have remained unanswered over the last few decades: 1) is genome replacement a common reproductive method in various unisexual populations and, 2) is there an ancient "L" genome that persists in various unisexual genome compositions.</p> <p>Results</p> <p>We examined 194 unisexual and 89 <it>A. laterale </it>specimens from 97 localities throughout their range and constructed a genealogy of the "L" genomes using a nuclear DNA marker (L-G1C12) to answer the above questions. Six L-G1C12 haplotypes (A-F) were shared by individuals in various <it>A. laterale </it>and unisexual populations. The general geographical distribution of the haplotypes in unisexual populations conformed to those found in <it>A. laterale</it>, indicating that "L" genomes in unisexuals are obtained from sympatric or nearby populations of <it>A. laterale</it>.</p> <p>Conclusion</p> <p>Our data demonstrate that genome replacement frequently occurs in unisexual <it>Ambystoma </it>across their range, and support previous speculations that genome replacement is an important reproductive mechanism that can enhance their evolutionary longevity. Our results show that there is no ancient "L" genome in the unisexual lineages, and no particular "L" genome is favored in any unisexual individual. The presence of an "L" genome in all unisexuals implies that it is important to the maintenance of unisexuals. Nuclear gene genealogy is a powerful tool to examine the historical interaction between sperm-dependent unisexuals and their sexual sperm donors. This methodology could be applicable to many other unisexual lineages to improve our understanding of their reproduction and their ability to persist.</p

A novel nucleo-cytoplasmic hybrid clone formed via androgenesis in polyploid gibel carp

<p>Abstract</p> <p>Background</p> <p>Unisexual vertebrates have been demonstrated to reproduce by gynogenesis, hybridogenesis, parthenogenesis, or kleptogenesis, however, it is uncertain how the reproduction mode contributes to the clonal diversity. Recently, polyploid gibel carp has been revealed to possess coexisting dual modes of unisexual gynogenesis and sexual reproduction and to have numerous various clones. Using sexual reproduction mating between clone D female and clone A male and subsequent 7 generation multiplying of unisexual gynogenesis, we have created a novel clone strain with more than several hundred millions of individuals. Here, we attempt to identify genetic background of the novel clone and to explore the significant implication for clonal diversity contribution.</p> <p>Methods</p> <p>Several nuclear genome markers and one cytoplasmic marker, the mitochondrial genome sequence, were used to identify the genetic organization of the randomly sampled individuals from different generations of the novel clone.</p> <p>Results</p> <p>Chromosome number, <it>Cot</it>-1 repetitive DNA banded karyotype, microsatellite patterns, AFLP profiles and transferrin alleles uniformly indicated that nuclear genome of the novel clone is identical to that of clone A, and significantly different from that of clone D. However, the cytoplasmic marker, its complete mtDNA genome sequence, is same to that of clone D, and different from that of clone A.</p> <p>Conclusions</p> <p>The present data indicate that the novel clone is a nucleo-cytoplasmic hybrid between the known clones A and D, because it originates from the offspring of gonochoristic sexual reproduction mating between clone D female and clone A male, and contains an entire nuclear genome from the paternal clone A and a mtDNA genome (cytoplasm) from the maternal clone D. It is suggested to arise via androgenesis by a mechanism of ploidy doubling of clone A sperm in clone D ooplasm through inhibiting the first mitotic division. Significantly, the selected nucleo-cytoplasmic hybrid female still maintains its gynogenetic ability. Based on the present and previous findings, we discuss the association of rapid genetic changes and high genetic diversity with various ploidy levels and multiple reproduction modes in several unisexual and sexual complexes of vertebrates and even other invertebrates.</p

A populational survey of 45S rDNA polymorphism in the Jefferson salamander Ambystoma jeffersonianum revealed by fluorescence in situ hybridization (FISH)

The chromosomal localization of 45S ribosomal RNA genes in Ambystoma jeffersonianum was determined by fluorescence in situ hybridization with 18S rDNA fragment as a probe (FISH-rDNA). Our results revealed the presence of rDNA polymorphism among A.jeffersonianum populations in terms of number, location and FISH signal intensity on the chromosomes. Nine rDNA cytotypes were found in ten geographically isolated populations and most of them contained derivative rDNA sites. Our preliminary study provides strong indication of karyotypic diversification of A.jeffersonianum that is demonstrated by intraspecific variation of 45S rDNA cytotypes. rDNA cytotype polymorphism has been described in many other caudate amphibians. We predict that habitat isolation, low dispersal ability and decline of effective population size could facilitate the fixation and accumulation of variable rDNA cytotypes during their chromosome evolution

Identifying parental chromosomes and genomic rearrangements in animal hybrid complexes of species with small genome size using Genomic In Situ Hybridization (GISH)

Genomic In Situ Hybridization (GISH), a powerful tool to identify and to quantify genomic constituents in allopolyploids, has been widely used in plants but not in animals mainly due to technical problems in obtaining informative results. Using the allopolyploid Squalius alburnoides fish complex as a model system, we succeeded in overcoming methodological constraints when dealing with parental species with a small genome size. This hybridogenetic complex has biotypes with different genome compositions and ploidy levels, but parental chromosomes are small, morphologically very similar and therefore cannot be distinguished by conventional cytogenetic approaches. Specimens have a small genome (C-value = 1.2 pg) with a low level of highly and moderate repetitive sequences, mainly located at pericentromeric chromosome regions. Since it is well known that probe annealing depends on probe concentration and hybridization time to obtain uniform hybridization signals along the chromosome arms, we progressively increased the amount of labeled probes from 100ng up to 1µg per slide and the incubation time from overnight up to 72 h, among other minor improvements. Results showed a clear enhancement of signals with respect to previous data, allowing an accurate and reproducible assignment of the parental genomes in both diploid and triploid fish. It was thus evidenced that high probes’ concentrations and long incubation time are the key to obtain, without extra image editing, uniform and reliable hybridization signals in metaphase chromosomes of hybrid fish even involving parental species with small genome size