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14 results for “mito-nuclear discordance”
Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito-nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation
<p>Rapid species radiations present difficulties for phylogenetic reconstruction due to lack of phylogenetic information and processes such as deep coalescence/incomplete lineage sorting and hybridization. Phylogenomic data can overcome some of these difficulties. In this study, we use Anchored Hybrid Enrichment (AHE) nuclear phylogenomic data and mitochondrial genomes recovered from AHE bycatch with several concatenated and coalescent approaches to reconstruct the poorly-resolved radiation of the New Zealand cicada species in the genera <em>Kikihia</em> Dugdale and <em>Maoricicada</em> Dugdale. Compared to previous studies using only three to five Sanger-sequenced genes, we find increased resolution across our phylogenies, but several branches remain unresolved due to topological conflict among genes. Some nodes that are strongly supported by traditional support measures like bootstraps and posterior probabilities still show significant gene and site concordance conflict. Additionally, we find strong mito-nuclear discordance; likely the result of interspecific hybridization events in the evolutionary history of <em>Kikihia</em> and <em>Maoricicada</em>.</p>
Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito-nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation
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Data from: Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas)
Many species have Holarctic distributions that extend across Europe, Asia, and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared to the association between mtDNA and nuDNA divergence observed among different species, OW-NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito-nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within-species discord. Male-mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause elevated mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation, and that more holistic approaches are needed for species delimitation.
Data from: Evaluating summary statistics used to test for incomplete lineage sorting: mito-nuclear discordance in the reef sponge Callyspongia vaginalis
Conflicting patterns of population differentiation between the mitochondrial and nuclear genomes (mito-nuclear discordance) have become increasingly evident as multilocus datasets have become easier to generate. Incomplete lineage sorting (ILS) of nucDNA is often implicated as the cause of such discordance, stemming from the large effective population size of nucDNA relative to mtDNA. However, selection, sex-biased dispersal, and historical demography can also lead to mito-nuclear discordance. Here we compare patterns of genetic diversity and subdivision for six nuclear protein-coding gene regions to those for mtDNA in a common Caribbean coral reef sponge, Callyspongia vaginalis, along the Florida reef tract. We also evaluated a suite of summary statistics to determine which are effective metrics for comparing empirical and simulated data when testing drivers of mito-nuclear discordance in a statistical framework. While earlier work revealed three divergent and geographically subdivided mtDNA COI haplotypes separated by 2.4% sequence divergence, nuclear alleles were admixed with respect to mitochondrial clade and geography. Bayesian analysis showed substitution rates for the nuclear loci were up to 7 times faster than for mitochondrial COI. Coalescent simulations and neutrality tests suggested that mito-nuclear discordance in C. vaginalis is not the result of ILS in the nucDNA or selection on the mtDNA but is more likely caused by changes in population size. Sperm-mediated gene flow may also influence patterns of population subdivision in the nucDNA.
Data from: Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex
Background: Genetically divergent cryptic species are frequently detected by molecular methods. These discoveries are often a byproduct of molecular barcoding studies in which fragments of a selected marker are used for species identification. Highly divergent mitochondrial lineages and putative cryptic species are even detected in intensively studied animal taxa, such as the crustacean genus Daphnia. Recently, eleven such lineages, exhibiting genetic distances comparable to levels observed among well-defined species, were recorded in the D. longispina species complex, a group that contains several key taxa of freshwater ecosystems. We tested if three of those lineages represent indeed distinct species, by analyzing patterns of variation of ten nuclear microsatellite markers in six populations. Results: We observed a discordant pattern between mitochondrial and nuclear DNA, as all individuals carrying one of the divergent mitochondrial lineages grouped at the nuclear level with widespread, well-recognized species coexisting at the same localities (Daphnia galeata, D. longispina, and D. cucullata). Conclusions: A likely explanation for this pattern is the introgression of the mitochondrial genome of undescribed taxa into the common species, either in the distant past or after long-distance dispersal. The occurrence of highly divergent but rare mtDNA lineages in the gene pool of widespread species would suggest that hybridization and introgression in the D. longispina species complex is frequent even across large phylogenetic distances, and that discoveries of such distinct clades must be interpreted with caution. However, maintenance of ancient polymorphisms through selection is another plausible alternative that may cause the observed discordance and cannot be entirely excluded.
Data from: Evidence for high dispersal ability and mito-nuclear discordance in the small brown planthopper, Laodelphax striatellus
Understanding dispersal ability in pest species is critical for both theoretical aspects of evolutionary and population biology and from a practical standpoint, such as implementing effective forecasting systems. The small brown planthopper (SBPH), Laodelphax striatellus (Fallén), is an economically important pest, but few data exist on its dispersal ability. Here, we used mitochondrial and nuclear markers to elucidate the population genetic structure of SBPH and of the parasitic bacterium Wolbachia throughout temperate and subtropical China. Our results showed that the SBPH populations in China lack significant differences in genetic structure, suggesting extensive gene flow. Multilocus sequence typing revealed that Wolbachia infection was systematic and due to the same strain (wStri) within and across populations. However, the mtDNA haplogroups had a nonrandom distribution across the sampling localities, which correlated to latitudinal and climatic gradients. We explain this mito-nuclear discordance as a result of historical population recolonization or mitochondria adaptation to climate.
Data from: Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection and climate
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Data from: Evidence for high dispersal ability and mito-nuclear discordance in the small brown planthopper, Laodelphax striatellus
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Data from: Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas)
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Data from: Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex
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Data from: Deciphering the origin of mito-nuclear discordance in two sibling caddisfly species
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Data from: Evaluating summary statistics used to test for incomplete lineage sorting: mito-nuclear discordance in the reef sponge Callyspongia vaginalis
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Data from: A mirage of cryptic species: genomics uncover striking mito-nuclear discordance in the butterfly Thymelicus sylvestris
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Behavioural underpinning of mito-nuclear discordances: insights from fire salamanders
<p><span>Mito-nuclear discordances across secondary contact zones have been described in a wide range of organisms. They consist of a spatial mismatch between nuclear and mitochondrial genomes in terms of location and extension of the contact zone between distinct evolutionary lineages. Despite the evolutionary and biogeographic causes of mito-nuclear discordances have been extensively investigated, we still lack a clear understanding of their phenotypic underpinnings. Here, we test the hypothesis that mtDNA variation could be associated with behavioural variation, and that such association could contribute to asymmetric mitochondrial introgression across a secondary contact zone. We analysed behavioural variation across the mtDNA secondary contact zone of the fire salamander <em>Salamandra salamandra</em> in central Italy, which is displaced 600 km from the nuclear contact zone. We found distinct behavioural profiles in the two mitotypes co-occurring in the contact zone. The introgressed mitotype was associated with a ‘slow-thorough’ dispersal profile, characterized by a less active but more cautious and accurate exploration strategy. This pattern was consistent across life stages and contexts: aquatic larvae and terrestrial juveniles, spontaneous activity and response to novelty. These results support the intriguing hypothesis that personality traits associated with distinct mitotypes could contribute to differential mitochondrial introgression and the formation of biogeographic patterns of mito-nuclear discordance.</span></p>
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