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20 results for “cytonuclear discordance”
Diversification, introgression, and rampant cytonuclear discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)
<p>Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the <i>Tamias quadrivittatus</i> group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (<i>T. canipes</i>, <i>T. cinereicollis</i>, <i>T. dorsalis</i>, <i>T. quadrivittatus</i>, <i>T. rufus</i>, and <i>T. umbrinus</i>) that show evidence for widespread mitochondrial introgression across species boundaries. Such evidence has historically derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group.</p>
The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt, Cynops pyrrhogaster (Amphibia: Urodela)
<p> Discrepancies in geographic variation patterns between nuclear DNA and mitochondrial DNA (mtDNA) are the result of the complicated differentiation processes in organisms and the key to understanding their true evolutionary process. The genetic differentiation of the northern and southern Izu lineages of the Japanese newt <em>Cynops pyrrhogaster</em> was investigated <span>through their single nucleotide polymorphism</span> variations by multiplexed ISSR genotyping by sequencing (MIG-seq). We found three genetic groups (Tohoku, N-Kanto, and S-Kanto) those not detected by mtDNA in the northern lineage. N-Kanto has intermediate genetic characteristics between Tohoku and S-Kanto. The western populations of N-Kanto are close to S-Kanto, whereas the eastern populations of N-Kanto are close to Tohoku. Tohoku, N-Kanto, and S-Kanto are now moderately isolated from each other and have unique genetic characteristics. An estimation of the evolutionary history by t<span>he </span><span>Approximate Bayesian Computation </span>approach suggested that Tohoku diverged from the common ancestor of S-Kanto and S-Izu. Then, S-Kanto and S-Izu split and the recent hybridization between Tohoku and S-Kanto gave rise to N-Kanto. The origin of N-Kanto through the hybridization is relatively young and seems to be related to changes in the distributions of Tohoku and S-Kanto as a result of the climatic oscillation in the Pleistocene. We concluded that the mitochondrial genome of S-Kanto was captured into Tohoku and the past original mitochondrial genome of Tohoku was entirely swept out from Tohoku through the hybridization. </p>
Data from: Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae
<p>In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that, while ILS could by itself explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are with few exceptions highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.</p>
Diversification, introgression, and rampant cytonuclear discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)
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The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt, Cynops pyrrhogaster (Amphibia: Urodela)
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Data from: Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae
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Data from: Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture dataset and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central, and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes. Here, we showed that these mtDNA lineages likely formed in allopatry during the Pleistocene, but responded differentially to climatic changes that occurred since the last interglacial (~120,000 years ago). We find that the Northern lineage maintained a stable range throughout this period, correlating with genetic distinctiveness among all genetic markers and low migration rates with the other lineages. In contrast, our results suggested that the Southern lineage expanded from Baja California Sur during the Late Pleistocene to overlap and potentially swamp a contracting Central lineage. High rates of intraspecific gene flow between Southern lineage individuals among expansion origin and expansion edge populations largely eroded Central ancestry from autosomal markers. However, male-biased dispersal in this system preserved signals of this past hybridization and introgression event in matrilineal-biased X-chromosome and mtDNA markers. Our results highlight the importance of range stability in maintaining the persistence of phylogeographic lineages, whereas unstable range dynamics can increase the tendency for lineages to merge upon secondary contact.
Data from: Microsatellite genetic structure and cytonuclear discordance in naturally fragmented populations of deer mice (Peromyscus maniculatus)
The Great Lakes impose high levels of natural fragmentation on local populations of terrestrial animals in a way rarely found within continental ecosystems. Although separated by major water barriers, woodland deer mouse (Peromyscus maniculatus gracilis) populations on the islands and on the Upper Peninsula (UP) and Lower Peninsula (LP) of Michigan have previously been shown to have a mitochondrial DNA contact zone that is incongruent with the regional landscape. We analyzed 11 microsatellite loci for 16 populations of P. m. gracilis distributed across 2 peninsulas and 6 islands in northern Michigan to address the relative importance of geographical structure and inferred postglacial colonization patterns in determining the nuclear genetic structure of this species. Results showed relatively high levels of genetic structure for this species and a significant correlation between interpopulation differentiation and separation by water but little genetic structure and no isolation-by-distance within each of the 2 peninsulas. Genetic diversity was generally high on both peninsulas but lower and correlated to island size in the Beaver Island Archipelago. These results are consistent with the genetic and demographic isolation of Lower Peninsula populations, which is a matter of concern given the dramatic decline in P. m. gracilis abundance on the Lower Peninsula in recent years.
Data from: Individual performance in relation to cytonuclear discordance in a northern contact zone between long-toed salamander (Ambystoma macrodactylum) lineages
Cytonuclear discordance in contact zones between related lineages is common, with mitochondrial clines often being displaced from clines in nuclear allele frequency. Proposed explanations for such a pattern include adaptive introgression of mtDNA or a neutral wake of mtDNA being left behind following hybrid zone movement. However, studies investigating these hypotheses are rare. Our previous survey of genetic variation in the long-toed salamander (Ambystoma macrodactylum) highlighted a potential case of cytonuclear discordance between two lineages in western Canada. Here, we use additional markers and samples to clarify the extent of this discordance. We simultaneously assess the feeding performance of individuals in a common environment to test for an association between mitotype and individual performance. The genetic results confirm a general pattern of cytonuclear discordance in the focal region. However, we also observed more limited introgression of a diagnostic nuclear marker. Intriguingly, although there were differences in individual performance associated with the transition between mitotypes, these differences were not fully explained by mitotype. Instead, the lowest performance was observed in individuals demonstrating the greatest mismatch between mtDNA and all nuclear markers, suggesting the potential for cytonuclear incompatibilities to be acting. These results highlight the complexity of understanding the causes and consequences of mtDNA introgression and cytonuclear discordance in contact zones.
Resolving relationships in Mentzelia section Bartonia (Loasaceae) in the face of cytonuclear discordance
<p>Phylogenetic studies based on two nuclear ribosomal markers created the first phylogenetic framework in which to understand evolutionary relationships in <em>Mentzelia</em> section <em>Bartonia</em> (Loasaceae), but low molecular variation resulted in several large polytomies and an incomplete understanding of species relationships. We applied a genome-skimming approach to determine whether additional genetic variation generated from high-throughput sequencing could resolve relationships in one of the largest polytomies in the section. Among 20 species sequenced, a group of six species that have pinnatisect leaf morphology were previously hypothesized to be monophyletic and we tested whether additional data would resolve the group as monophyletic. For the chloroplast genome, reads were assembled using both de novo and reference-guided approaches, whereas reference-guided approaches were taken for the nuclear ribosomal cistron region and a single anonymous nuclear locus. Significant discordance was identified among all three gene trees. Exhaustive measures were taken to ensure phylogenetic and assembly-based errors were not responsible for the observed discordance among gene trees. We attribute much of the incongruence to a low phylogenetic signal-to-noise ratio that is likely due to the group radiating recently and rapidly and perhaps unique evolutionary histories among genomes. Despite incongruence, several well-supported relationships emerged across data sets, and all hypothesis tests for a monophyletic pinnatisect group among gene trees failed to reject monophyly of the group, suggesting the pinnatisect leaf form is a synapomorphy for the clades.</p>
Resolving relationships in Mentzelia section Bartonia (Loasaceae) in the face of cytonuclear discordance
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Data from: Microsatellite genetic structure and cytonuclear discordance in naturally fragmented populations of deer mice (Peromyscus maniculatus)
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Data from: Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae)
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Data from: Cytonuclear discordance among the Southeast Asian Black rats (Rattus rattus complex)
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Data from: Individual performance in relation to cytonuclear discordance in a northern contact zone between long-toed salamander (Ambystoma macrodactylum) lineages
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Data from: Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex
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Directionally biased habitat shifts and biogeographically informative cytonuclear discordance in the Hawaiian silversword alliance (Compositae)
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Cryptic genetic diversity and cytonuclear discordance characterize contact among Canada jay (Perisoreus canadensis) morphotypes in western North America
<p>Three distinct Canada jay (<em>Perisoreus canadensis</em>) morphotypes with easily recognizable plumage traits come into contact in western North America. Recent work demonstrated high genetic structure across the species' range; however, patterns of genetic variation in these contact zones remain unknown. We categorized 605 individuals into one of three morphotypes (Pacific, Rocky Mountain, and Boreal) based on plumage, and genotyped individuals at the mtDNA control region and 12 microsatellite loci to assess the extent of hybridization between morphotypes. Our data showed cryptic genetic diversity and high cytonuclear discordance among morphotypes within contact zones, which is likely the result of recent and historical admixture. The distributions of the Boreal and Pacific morphotypes each showed a strong association with a single, distinct genetic group, whereas the Rocky Mountain morphotype exhibited higher genetic diversity and was associated with multiple genotypes. Our analyses show the importance of considering both plumage and genetic traits when examining contact zones between closely related taxa. Finally, the data presented in this study reaffirm that the Pacific morphotype is distinct from the Boreal and Rocky Mountain morphotypes based on genetic, phenotypic, and ecological data, indicating that the Pacific morphotype should be re-elevated to a full species.</p>
Cryptic genetic diversity and cytonuclear discordance characterize contact among Canada jay (Perisoreus canadensis) morphotypes in western North America
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Extensive cytonuclear discordance in a crested newt from the Balkan Peninsula glacial refugium
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