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22 results for “historical phylogeography”
Fig. 3 in Reconstructed historical distribution and phylogeography unravels non-steppic origin of Caucasotachea vindobonensis (Gastropoda: Helicidae)
Fig. 3 Reconstruction of the geographic range evolution. For the geographic position of the samples and the subdivision of the range, see Fig. 1. The ultrametric ML tree shows phylogenetic relationships of the Caucasotachea vindobonensis haplotypes based on COI sequences. High branch supports for the main clades are indicated by black/gray dots (gray aLRT >0.80; black aLRT>0.95). The colored symbols at the tips indicate the current geographic origin of the haplotypes (see also Supplementary Table 1). Values at the branches indicate all alternative scenarios with likelihoods above 10% for the origin of the clades' common ancestors (BK Balkans, CP Carpatho-Pannon, PC northwestern, NW Ponto-Caspian). The ancestors were allowed to occupy a maximum of three geographic areas. Migration was permitted between all regions, but lower probability (B0.25^ instead of B1.0^) was assigned in the dispersal constraints for migration between areas not being immediately adjacent (between north-western and the Balkans)
Fig. 2 in Reconstructed historical distribution and phylogeography unravels non-steppic origin of Caucasotachea vindobonensis (Gastropoda: Helicidae)
Fig. 2 Median-joining networks of Caucasotachea vindobonensis COI haplotypes with assignment to the defined regions of species distribution
Fig. 1 in Reconstructed historical distribution and phylogeography unravels non-steppic origin of Caucasotachea vindobonensis (Gastropoda: Helicidae)
Fig. 1 Range of the Caucasotachea vindobonensis with localization of sampling sites and defined regions of species distribution used for genetic analyses
Fig. 4 in Reconstructed historical distribution and phylogeography unravels non-steppic origin of Caucasotachea vindobonensis (Gastropoda: Helicidae)
Fig. 4 Potential distribution of Caucasotachea vindobonensis during the LGM based on different climate models (CCSM4, MIROC-ESM). Warmer/darker colors indicate more suitable climatic conditions
Data from: Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)
Documenting and preserving the genetic diversity of populations, which conditions their long-term survival, has become a major issue in conservation biology. The loss of diversity often documented in declining populations is usually assumed to result from human disturbances; however, historical biogeographic events, otherwise known to strongly impact diversity, are rarely considered in this context. We apply a multi-locus phylogeographic study to investigate the late-Quaternary history of a tree frog (Hyla arborea) with declining populations in the northern and western part of its distribution range. Mitochondrial and nuclear polymorphisms reveal high genetic diversity in the Balkan Peninsula, with a spatial structure molded by the last glaciations. While two of the main refugial lineages remained limited to the Balkans (Adriatic coast, southern Balkans), a third one expanded to recolonize Northern and Western Europe, loosing much of its diversity in the process. Our findings show that mobile and a priori homogeneous taxa may also display substructure within glacial refugia ("refugia within refugia"), and emphasize the importance of the Balkans as a major European biodiversity center. Moreover, the distribution of diversity roughly coincides with regional conservation situations, consistent with the idea that historically impoverished genetic diversity may interact with anthropogenic disturbances, and increase the vulnerability of populations. Phylogeographic models seem important to fully appreciate the risks of local declines and inform conservation strategies.
Data from: An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the arboreal salamander (Aneides lugubris)
Background: Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to the California floristic province. We used multi-locus data to reconstruct the evolutionary history of A. lugubris and to discover the geographic location of major genetic breaks within the species. We also used species distribution modeling and comparative phylogeography to better understand the environmental factors that have shaped the genetic history of A. lugubris. Results: We found six major mitochondrial clades in A. lugubris. Nuclear loci supported the existence of at least three genetically distinct groups, corresponding to populations north of the San Francisco Bay and in the Sierra Nevada, in the Santa Cruz Mountains, and in the central coast and southern California. All of the genetic breaks in mitochondrial and nuclear loci corresponded to regions where historical barriers to dispersal have been observed in other species. Geologic or water barriers likely were the most important factors restricting gene flow among clades. Climatic unsuitability during glacial maximum may have contributed to the isolation of the mitochondrial clades in the central coast and southern California. A projection of our species distribution model to a future scenario with a moderate amount of climate change suggests that most of the range of A. lugubris will remain climatically suitable, but climatic conditions in the Sierra Nevada and low elevation areas in Southern California are likely to deteriorate. Conclusions: Aneides lugubris contains substantial cryptic genetic diversity as a result of historical isolation of populations. At least two (and perhaps three) evolutionarily significant units in A. lugubris merit protection; all six mitochondrial clades should be considered as management units within the species.
FIGURE 6 in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features
FIGURE 6. Species Distribution Model (SDM) of D. ensatus based on museum records. Increased shading towards green represents increasing suitable habitat.
FIGURE 2 in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features
FIGURE 2. Relationships between Dicamptodon ensatus populations and distribution of those lineages along the coast of the California region. Major mtDNA lineages are color coded and branch lengths are proportional. Support values on branches follow the format (coalescent analysis�posterior probability / Bayesian inference analysis posterior probability / bootstrap proportions maximum-likelihood analysis). The tree is a consensus gene tree from the coalescent analysis with deeper weakly supported relationships collapsed. The color bar represents nuclear genotype groups. Geographic range denoted by green shading. Stars on map denote likely ancestral haplotype regions as determined by the BPEC analysis. The approximate region of the former Wilson Grove embayment is overlaid onto the map in transparent blue.
FIGURE 1 in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features
FIGURE 1. Range map from the IUCN Red List in transparent green with sampling localities from this study marked.
FIGURE 5 in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features
FIGURE 5. Isolation by distance plot. P value calculated by Mantel test. (y = 0.00292 x + 0.07696, r2 = 0.809, P = 0.007).
FIGURE 3. a in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features
FIGURE 3. a) mtDNA TCS haplotype network of the control region. b) nuDNA haplotype TCS network of E16C7. Colors of clusters are coded to match the coalescent tree clade branches. Circle size is proportional to haplotype occurrence and numbers refer to occurrence sampled if greater then one.
Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification
<p class="MsoNormal"><span class="Fuentedeprrafopredeter1"><span>The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10 - 11 Ma. T</span></span><span class="Fuentedeprrafopredeter1"><span>oday, there is only one permanent connection between the Orinoco and Negro </span></span><span class="Fuentedeprrafopredeter1"><span>(Amazon) </span></span><span class="Fuentedeprrafopredeter1"><span>basins, known as the Casiquiare Canal</span></span><span class="Fuentedeprrafopredeter1"><span>. </span></span><span class="Fuentedeprrafopredeter1"><span>However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (<em>Paracheirodon axelrodi),</em> the most important fish in the ornamental world market, is distributed in both basins. Here we investigated </span></span><span class="Fuentedeprrafopredeter1"><em><span>P. axelrodi </span></em></span><span class="Fuentedeprrafopredeter1"><span>phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and 8 microsatellite loci were analyzed. </span></span><span class="Fuentedeprrafopredeter1"><span>As a result, we found two major genetic clusters as the most likely scenario (K=2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and </span></span><span class="Fuentedeprrafopredeter1"><span>São</span></span><span class="Fuentedeprrafopredeter1"><span> Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. </span></span><span class="Fuentedeprrafopredeter1"><span>Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. </span></span><span class="Fuentedeprrafopredeter1"><span>However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K=3-6), showing three major geographic clusters: Orinoco, Cucui, and the remaining of the Negro basin. </span></span><span class="Fuentedeprrafopredeter1"><span>Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance.</span></span></p>
Data from: Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus).
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Data from: Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)
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Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification
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Data from: An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the arboreal salamander (Aneides lugubris)
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Data from: Historical and recent processes shaping the geographic range of a rocky intertidal gastropod: phylogeography, ecology, and habitat availability
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FIGURE 4 in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features
FIGURE 4. Bayesian inference skyline plot of the mtDNA control region of D. ensatus.
Phylogeography, historical demography and systematics of the world’s smallest pythons (Pythonidae, Antaresia)
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Data from: Pleistocene sea level fluctuation and host plant habitat requirement influenced the historical phylogeography of the invasive species Amphiareus obscuriceps (Hemiptera: Anthocoridae) in its native range
Background: On account of repeated exposure and submergence of the East China Sea (ECS) land bridge, sea level fluctuation played an important role in shaping the population structure of many temperate species across the ECS during the glacial period. The flower bug Amphiareus obscuriceps (Poppius, 1909) (Hemiptera: Anthocoridae) is an invasive species native to the Sino-Japanese Region (SJR) of East Asia. We tested the hypothesis of the ECS land bridge acting as a dispersal corridor or filter for A. obscuriceps during the glacial period. Specifically, we tested whether and the extent to which dispersal ability and host plant habitat requirement influenced the genetic structure of A. obscuriceps during the exposure of the ECS land bridge. Results: Phylogenetic and network analyses indicated that A. obscuriceps is composed of two major lineages, i.e., China and Japan. Divergence time on both sides of the ECS was estimated to be approximately 1.07 (0.79-1.32) Ma, which was about the same period that the sea level increased. No significant Isolation by Distance (IBD) relationship was found between Фst and Euclidean distances in the Mantel tests, which is consistent with the hypothesis that this species has a good dispersal ability. Our Last Glacial Maximum (LGM) niche modeling of plants that constitute preferred habitats for A. obscuriceps exhibited a similar habitat gap on the exposed ECS continental shelf between China and Japan, but showed a continuous distribution across the Taiwan Strait. Conclusion: Our results suggest that ecological properties (habitat requirement and dispersal ability), together with sea level fluctuation during the Pleistocene across the ECS, have shaped the genetic structure and demographic history of A. obscuriceps in its native area. The host plant habitat requirement could also be a key to the colonization of the A. obscuriceps species during the exposure of the ECS land bridge. Our findings will shed light on the potential role of habitat requirement in the process of biological invasion in future studies.
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