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TABLE 3. Genetic distances among Margattea species from Japan. K 2 P in A new species of the Genus Margattea (Blattodea: Pseudophyllodromiidae) from Yonaguni-jima Island, the Ryukyus, Japan
<p><b>TABLE 3.</b> Genetic distances among <i>Margattea</i> species from Japan. K2P distances among COI and COII sequences are shown below the diagonal. Standard error estimates are shown above the diagonal.</p><table><tbody><tr><th>Taxa</th><th>Accession no.</th><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th></th></tr></tbody><tbody><tr><th>1.</th><td><i>M</i>. <i>ventrinigra</i> <b>sp. nov.</b></td><td>LC750813–LC750815</td><td>-</td><td>0.008</td><td>0.013</td><td>0.012</td><td>0.015</td><td></td></tr><tr><th>2. 3.</th><td><i>M</i>. <i>satsumana</i> <i>M</i>. <i>ogatai</i> _Ishigaki is.</td><td>LC750816–LC750819 LC750820–LC750822</td><td>0.050 0.099</td><td>- 0.102</td><td>0.012 -</td><td>0.012 0.005</td><td>0.016 0.014</td><td>COI</td></tr><tr><th>4.</th><td><i>M</i>. <i>ogatai</i> _Iriomote is.</td><td>LC750823–LC750825</td><td>0.090</td><td>0.099</td><td>0.018</td><td>-</td><td>0.014</td><td></td></tr><tr><th>5.</th><td><i>M</i>. <i>nimbata</i></td><td>LC750826–LC750828</td><td>0.158</td><td>0.165</td><td>0.150</td><td>0.142</td><td>-</td><td></td></tr><tr><th>Taxa</th><td>Accession no.</td><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td><td></td></tr><tr><th>1.</th><td><i>M</i>. <i>ventrinigra</i> <b>sp. nov.</b></td><td>LC750829–LC750831</td><td>-</td><td>0.009</td><td>0.012</td><td>0.012</td><td>0.019</td><td></td></tr><tr><th>2. 3.</th><td><i>M</i>. <i>satsumana</i> <i>M</i>. <i>ogatai</i> _Ishigaki is.</td><td>LC750832–LC750835 LC750836–LC750838</td><td>0.058 0.082</td><td>- 0.084</td><td>0.011 -</td><td>0.012 0.004</td><td>0.019 0.019</td><td>COII</td></tr><tr><th>4.</th><td><i>M</i>. <i>ogatai</i> _Iriomote is.</td><td>LC750839–LC750841</td><td>0.083</td><td>0.086</td><td>0.013</td><td>-</td><td>0.019</td><td></td></tr><tr><th>5.</th><td><i>M</i>. <i>nimbata</i></td><td>LC750842–LC750844</td><td>0.196</td><td>0.201</td><td>0.198</td><td>0.200</td><td>-</td><td></td></tr></tbody></table>
Data from: Relationship between genetic distances and postzygotic reproductive isolation in diploid Fragaria (Rosaceae)
Studies of reproductive isolation are important for understanding speciation and species delimitation. We studied seven components of reproductive isolation at different taxonomic and geographical levels and their relationship with genetic distance in diploid Fragaria. Isolation was only evident between different taxa at later stages (post F1 survivorship) not at the earlier ones of fruit and seed set, F1 seed germination and survivorship. Within F. vesca, isolation at the later stages was positively correlated with genetic distance, but this was not found at interspecific levels. The lack of isolation between F. vesca and the other species at the early stages provide the chance for hybrid formation, but high levels of infertility expressed among the offspring can lead to potentially opposing evolutionary outcomes. Within F. vesca, there was evidence of unexpected isolation promoting evolutionary diversification and incipient speciation. Reproductive isolation values between sympatric and allopatric species pairs were similar and indicate a lack of reinforcement in Fragaria. This, combined with the lack of correlation between genetic distance and isolation at interspecific levels shows that genetic distance is not always proportionally correlated with the degree of isolation in plants and suggests that evolutionary processes may be playing differently in plants compared to animals.
Data from: A comparison of individual-based genetic distance metrics for landscape genetics
A major aim of landscape genetics is to understand how landscapes resist gene flow and thereby influence population genetic structure. An empirical understanding of this process provides a wealth of information that can be used to guide conservation and management of species in fragmented landscapes, and also to predict how landscape change may affect population viability. Statistical approaches to infer the true model among competing alternatives are based on the strength of the relationship between pairwise genetic distances and landscape distances among sampled individuals in a population. A variety of methods have been devised to quantify individual genetic distances, but no study has yet compared their relative performance when used for model selection in landscape genetics. In this study, we used population genetic simulations to assess the accuracy of 16 individual-based genetic distance metrics under varying sample sizes and degree of population genetic structure. We found most metrics performed well when sample size and genetic structure was high. However, it was much more challenging to infer the true model when sample size and genetic structure was low. Under these conditions, we found genetic distance metrics based on principal components analysis were the most accurate (though several other metrics performed similarly), but only when they were derived from multiple principal component axes (the optimal number varied depending on the degree of population genetic structure). Our results provide guidance for which genetic distance metrics maximize model selection accuracy and thereby better inform conservation and management decisions based upon landscape genetic analysis.
Data from: Relationship between genetic distances and postzygotic reproductive isolation in diploid Fragaria (Rosaceae)
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Data from: Variation in the level of aggression, chemical and genetic distance among three supercolonies of the Argentine ant in Europe
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Data from: Population genetic structure and long-distance dispersal among seabird populations: implications for colony persistence
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Data from: A comparison of individual-based genetic distance metrics for landscape genetics
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Data from: Genetic uniformity and long-distance clonal dispersal in the invasive androgenetic Corbicula clams
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Data from: Divergence in mating signals correlates with genetic distance and behavioural responses to playback
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Data from: Current approaches using genetic distances produce poor estimates of landscape resistance to interindividual dispersal
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Data from: Parasite genetic distance and local adaptation in coevolving bacteria-bacteriophage populations
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Data from: Isolation-by-distance in landscapes: considerations for landscape genetics
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Data from: Genetic distance as an alternative to physical distance for definition of gene units in association studies
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Data from: Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove
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Data from: Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard
Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera. We investigated which of the climatic, environmental, geographical and/or historical components best predict: (1) the spatial distribution of genetic diversity, and (2) the genetic differentiation among populations. We found that genetic variation in A. ocellifera has been influenced mainly by temperature variability, which modulates connectivity among populations. Past climate conditions were important for shaping current genetic diversity, suggesting a time lag in genetic responses. Population structure in A. ocellifera was best explained by both isolation by distance and isolation by resistance (main rivers). Our findings indicate that both physical and climatic features are important for explaining the observed patterns of genetic variation across the xeric Caatinga biome.
Data from: Genetic and phenotypic divergence in an island bird: isolation by distance, by colonisation or by adaptation?
Discerning the relative roles of adaptive and non-adaptive processes in generating differences among populations and species, as well as how these processes interact, are fundamental aims in biology. Both genetic and phenotypic divergence across populations can be the product of limited dispersal and gradual genetic drift across populations (isolation by distance), of colonisation history and founder effects (isolation by colonisation) or of adaptation to different environments preventing migration between populations (isolation by adaptation). Here we attempt to differentiate between these processes using island populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three Atlantic archipelagos. Using microsatellite markers and approximate Bayesian computation, we reveal that the northwards colonisation of this species ca 8,500 years ago resulted in genetic bottlenecks in the colonised archipelagos. We then show that high levels of genetic structure exist across archipelagos, and that these are consistent with a pattern of isolation by colonisation, but not with isolation by distance or adaptation. Finally, we show that substantial morphological divergence also exists and that this is strongly concordant with patterns of genetic structure and bottleneck history, but not with environmental differences or geographic distance. Overall our data suggest that founder effects are responsible for both genetic and phenotypic changes across archipelagos. Our findings provide a rare example of how founder effects can persist over evolutionary timescales, and suggest that they may play an important role in the early stages of speciation.
Data from: Long distance dispersal and genetic structure of natural populations: an assessment of the inverse isolation hypothesis in peat mosses
It is well accepted that the shape of the dispersal kernel, especially its tail, has a substantial effect on the genetic structure of species. Theory predicts that dispersal by fat-tailed kernels reshuffles genetic material and thus preserves genetic diversity during colonization. Moreover, if efficient long distance dispersal is coupled with random colonization, an inverse isolation effect is predicted to develop in which increasing genetic diversity per colonizer is expected with increasing distance from a genetically variable source. By contrast, increasing isolation leads to decreasing genetic diversity when dispersal is via thin-tailed kernels. Here we use a well-established model group for dispersal biology (peat mosses: genus Sphagnum) with a fat-tailed dispersal kernel, and the natural laboratory of the Stockholm archipelago to study the validity of the inverse isolation hypothesis in spore-dispersed plants in island colonization. Population genetic structure of three species (S. fallax, S. fimbriatum and S. palustre) with contrasting life histories and ploidy levels were investigated on a set of islands using microsatellites. Our data show (φ'st, AMOVA, IBD) that dispersal of the two most abundant species can be well approximated by a random colonization model. We find that genetic diversity per colonizer on islands increases with distance from the mainland for S. fallax and S. fimbriatum. By contrast, S. palustre deviates from this pattern, owing to its restricted distribution in the region affecting its source pool strength. Therefore, the inverse isolation effect appears to hold in natural populations of peat mosses and, likely, in other organisms with small diaspores.
Alignment-free methods for polyploid genomes: quick and reliable genetic distance estimation
<p>Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash, a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic datasets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated haploid and polyploid short-read sequences with various levels of missing data. Mash-based estimates of genetic distance were comparable to alignment-based estimates, and were less impacted by missing data. We also used Mash to analyze publicly available short-read data for three polyploid and one diploid species, then compared Mash results to published results. For both simulated and real data, Mash accurately estimated pairwise genetic differences for polyploids as well as diploids as much as 476 times faster than alignment-based methods, though we found that Mash genetic distance estimates could be biased by per-sample read depth. Mash may be a particularly useful addition to the toolkit of polyploid geneticists for rapid confirmation of alignment-based results and for basic population genetics in reference-free systems or those with only poor quality sequence data available.</p>
Data from: Long distance dispersal and genetic structure of natural populations: an assessment of the inverse isolation hypothesis in peat mosses
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Data from: Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard
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