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      Geographically structured genetic diversity in the cave beetle Darlingtonea kentuckensis Valentine, 1952 (Coleoptera, Carabidae, Trechini, Trechina)

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      Subterranean Biology

      Pensoft Publishers

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          Abstract

          Cave beetles of the eastern USA are one of many poorly studied groups of insects and nearly all previous work delimiting species is based solely on morphology. This study assesses genetic diversity in the monotypic cave carabid beetle genus Darlingtonea Valentine 1952, to test the relationship between putative geographical barriers to subterranean dispersal and the boundaries of genetically distinct groups. Approximately 400bp of the mitochondrial cytochrome oxidase I (COI) gene was sequenced from up to four individuals from each of 27 populations, sampled from caves along the escarpments of the Mississippian and Cumberland plateaus in eastern Kentucky, USA. The 81 individuals sequenced yielded 28 unique haplotypes. Hierarchical analyses of molecular variance (AMOVA) within and among geographically defined groups tested two a priori hypotheses of structure based on major and minor river drainages, as well as genetic distance clusters defined a posteriori from an unrooted analysis. High genetic differentiation (FST) between populations was found across analyses. The influence of isolation by distance could potentially account for much but not all of the variation found among geographically defined groups at both levels. High variability among the three northernmost genetic clusters (FCT), low variability among populations within clusters (FSC), and low within-cluster Mantel correlations indicate the importance of unidentified likely intra-karst barriers to gene flow separating closely grouped cave populations. Overall phylogeographic patterns are consistent with previous evidence of population isolation among cave systems in the region, revealing geographically structured cryptic diversity in Darlingtonea over its distribution. The landscape features considered a priori in this study were not predictive of the genetic breaks among the three northern clusters, which are genetically distinct despite their close geographic proximity.

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          Most cited references 24

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          HapStar: automated haplotype network layout and visualization.

          Haplotype networks are commonly used for representing associations between sequences, yet there is currently no straightforward way to create optimal layouts. Automated optimal layouts are particularly useful not only because of the time-saving element but also because they avoid both human error and human-induced biases in the presentation of figures. HapStar directly uses the network connection output data generated from Arlequin (or a simple user-generated input file) and uses a force-directed algorithm to automatically lay out the network for easy visualization. In addition, this program is able to use the alternative connections generated by Arlequin to create a minimum spanning tree. HapStar provides a straightforward user-friendly interface, and publication-ready figures can be exported simply. HapStar is freely available (under a GPLv3 licence) for download for MacOSX, UNIX and Windows, at http://fo.am/hapstar. © 2010 Blackwell Publishing Ltd.
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            Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: Gyrinophilus) inferred from gene genealogies.

            Cave organisms occupy a special place in evolutionary biology because convergent morphologies of many species demonstrate repeatability in evolution even as they obscure phylogenetic relationships. The origin of specialized cave-dwelling species also raises the issue of the relative importance of isolation vs. natural selection in speciation. Two alternative hypotheses describe the origin of subterranean species. The 'climate-relict' model proposes allopatric speciation after populations of cold-adapted species become stranded in caves due to climate change. The 'adaptive-shift' model proposes parapatric speciation driven by divergent selection between subterranean and surface habitats. Our study of the Tennessee cave salamander complex shows that the three nominal forms (Gyrinophilus palleucus palleucus, G. p. necturoides, and G. gulolineatus) arose recently and are genealogically nested within the epigean (surface-dwelling) species, G. porphyriticus. Short branch lengths and discordant gene trees were consistent with a complex history involving gene flow between diverging forms. Results of coalescent-based analysis of the distribution of haplotypes among groups reject the allopatric speciation model and support continuous or recurrent genetic exchange during divergence. These results strongly favour the hypothesis that Tennessee cave salamanders originated from spring salamanders via divergence with gene flow.
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              Mantel test in population genetics

              The comparison of genetic divergence or genetic distances, estimated by pairwise FST and related statistics, with geographical distances by Mantel test is one of the most popular approaches to evaluate spatial processes driving population structure. There have been, however, recent criticisms and discussions on the statistical performance of the Mantel test. Simultaneously, alternative frameworks for data analyses are being proposed. Here, we review the Mantel test and its variations, including Mantel correlograms and partial correlations and regressions. For illustrative purposes, we studied spatial genetic divergence among 25 populations of Dipteryx alata (“Baru”), a tree species endemic to the Cerrado, the Brazilian savannas, based on 8 microsatellite loci. We also applied alternative methods to analyze spatial patterns in this dataset, especially a multivariate generalization of Spatial Eigenfunction Analysis based on redundancy analysis. The different approaches resulted in similar estimates of the magnitude of spatial structure in the genetic data. Furthermore, the results were expected based on previous knowledge of the ecological and evolutionary processes underlying genetic variation in this species. Our review shows that a careful application and interpretation of Mantel tests, especially Mantel correlograms, can overcome some potential statistical problems and provide a simple and useful tool for multivariate analysis of spatial patterns of genetic divergence.
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                Author and article information

                Journal
                Subterranean Biology
                SB
                Pensoft Publishers
                1314-2615
                1768-1448
                March 10 2020
                March 10 2020
                : 34
                : 1-23
                Article
                10.3897/subtbiol.34.46348
                © 2020

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