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30 results for “freshwater phylogeography”
Figure 2 in Phylogeography and distribution of the freshwater razor clams Novaculina myanmarensis and N. gangetica in Myanmar, with notes on two doubtful nominal taxa described as Novaculina members (Bivalvia: Pharidae)
Figure 2. Habitats of Novaculina myanmarensis in Myanmar (new occurrences). (A) Winyaw River, Ataran Basin [sample ID: RMBH biv1030]. (B) Downstream of the Hlaing River, Ayeyarwady Basin [sample ID: RMBH biv1015]. (C) Large oxbow lake, downstream of the Ayeyarwady River [sample ID: RMBH biv1014]. (Photos: Than Win [A] and Ilya V. Vikhrev [B-C])
Figure 1 in Phylogeography and distribution of the freshwater razor clams Novaculina myanmarensis and N. gangetica in Myanmar, with notes on two doubtful nominal taxa described as Novaculina members (Bivalvia: Pharidae)
Figure 1. Map of Novaculina spp. occurrences based on reliable georeferenced records (Table 2). The circles indicate records from our earlier work (Bolotov et al. 2018a). The stars indicate new occurrences (Ng et al. 2020; this study)
FIGURE 2 in Phylogeography of Oligosarcus acutirostris (Characiformes: Characidae): testing biogeographic hypotheses in the Northeastern Mata Atlântica freshwater ecoregion
FIGURE 2 | A. Map showing part of the Northeastern Mata Atlântica freshwater ecoregion (NMAF) and the distribution of Oligosarcus acutirostris samples analyzed in this study. Adjacent freshwater ecoregions sensu Abell et al. (2008): (327) São Francisco, (329) Paraíba do Sul, and (344) Upper Paraná. Costal paleodrainages based on Thomaz, Knowles (2018): (107) Santo Antônio + João de Tiba and (110) Mucuri + Barra Seca; B and C. Haplotype networks showing the genetic connectivity among the haplotypes of O. acutirostris, which are represented by circles, the size proportional to their frequencies. Each trace corresponds to a single mutation. Colors correspond to the sampled river basins as in Fig. 2A; B. Haplotype network based on COI dataset (604 bp, 24 specimens, 11 haplotypes). Black circles represent median vectors; C. Haplotype network based on Myh6 dataset (587 bp, 27 specimens, five haplotypes).
FIGURE 1 in Phylogeography of Oligosarcus acutirostris (Characiformes: Characidae): testing biogeographic hypotheses in the Northeastern Mata Atlântica freshwater ecoregion
FIGURE 1 | Bayesian phylogenetic trees of Oligosarcus acutirostris obtained in this study indicating the relationships among analyzes specimens. Numbers at branches are posterior probabilities. A. Topology based on mitochondrial gene cytochrome oxidase I (COI, 604 bp); B. Topology based on nuclear gene myosin heavy chain 6 cardiac muscle alpha (Myh6, 587 pb); and C. Topology based on concatenated dataset (COI+Myh6, 1,191 bp). The highlighted colors in the topologies represent each sampled river basin as indicated in the legend (below/right) and showed in Fig. 2A.
Data from: Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers
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Data from: Phylogeography of the Australian freshwater turtle Chelodina expansa reveals complex relationships among inland and coastal bioregions
We examined range-wide mitochondrial phylogeographic structure in the riverine freshwater turtle Chelodina expansa to determine if this species exhibits deep genetic divergence between coastal and inland hydrological provinces as seen in co-distributed freshwater taxa. We sequenced two mitochondrial loci, genealogical relationships were assessed using a network approach, and relationships among biogeographic regions were tested using analyses of molecular variance. Population history was evaluated using neutrality tests, indices of demographic expansion, and mismatch analyses. Twenty one haplotypes were recovered across two mitochondrial haplogroups separated by ca 4% nucleotide divergence. The haplogroups have discrete geographic boundaries but only partially support a hypothesis of deep divergence between coastal and inland bioregions. The first haplogroup comprises populations from the inland Murray-Darling Basin and from coastal catchments south of the Mary River in southeast Queensland. The second haplogroup comprises populations from coastal catchments north of the Mary River. Cryptic phylogeographic barriers separating adjacent coastal populations are congruent with those demonstrated for other freshwater taxa and may result from the combined influences of the Conondale Range and alluvial deposits at the mouth of the Mary River. Our study demonstrates that freshwater taxa commonly display genetic differentiation within a biogeographic region where no boundaries have been recognised, highlighting the need to uncover cryptic microbiogeographic regions to aid conservation of freshwater biota.
Data from: Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella, with an emphasis on dwarf Galaxias (G. pusilla)
The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this region. Here, we employed phylogenetic and phylogeographic approaches to evaluate the effect of this barrier on a group of four galaxiid fish species (Galaxiella) endemic to temperate Southern Australia. We also tested if continental shelf width has influenced connectivity among populations during low sea levels when rivers, now isolated, could have been connected. We addressed these questions by sampling each species across its range using multiple molecular markers (mitochondrial cytochrome b sequences, nuclear S7 intron sequences, and 49 allozyme loci). These data also allowed us to assess species boundaries, to refine phylogenetic affinities, and to estimate species ages. Interestingly, we found compelling evidence for cryptic species in G. pusilla, manifesting as allopatric eastern and western taxa. Our combined phylogeny and dating analysis point to an origin for the genus dating to the early Cenozoic, with three of the four species originating during the Oligocene-Miocene. Each Galaxiella species showed high levels of genetic divergences between all but the most proximate populations. Despite extensive drainage connections during recent low sea levels in southeastern Australia, populations of both species within G. pusilla maintained high levels of genetic structure. All populations experienced Late Pleistocene-Holocene population growth, possibly in response to the relaxation of arid conditions after the last glacial maximum. High levels of genetic divergence and the discovery of new cryptic species have important implications for the conservation of this already threatened group of freshwater species.
Data from: Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis
BACKGROUND: Multiple loci and population genetic methods were employed to study the phylogeographic history of the Patagonian freshwater crab Aegla neuquensis (Aeglidae: Decopoda). This taxon occurs in two large river systems in the Patagonian Steppe, from the foothills of the Andes Mountains east to the Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS: A nuclear phylogeny and multilocus nested clade phylogeographic analysis detected a fragmentation event between the Negro and Chico-Chubut river systems. This event occurred approximately 137 thousand years ago. An isolation-with-migration analysis and maximum-likelihood estimates of gene flow showed asymmetrical exchange of genetic material between these two river systems exclusively in their headwaters. We used information theory to determine the best-fit demographic history between these two river systems under an isolation-with-migration model. The best-fit model suggests that the Negro and the ancestral populations have the same effective population sizes; whereas the Chico-Chubut population is smaller and shows that gene flow from the Chico-Chubut into the Negro is four times higher than in the reverse direction. Much of the Chico-Chubut system appears to have only been recently colonized while the Negro populations appear to have been in place for most of the evolutionary history of this taxon. CONCLUSIONS/SIGNIFICANCE: Due to mitochondrial introgression, three nuclear loci provided different phylogeographic resolution than the three mitochondrial genes for an ancient fragmentation event observed in the nuclear phylogeny. However, the mitochondrial locus provided greater resolution on more recent evolutionary events. Our study, therefore, demonstrates the need to include both nuclear and mitochondrial loci for a more complete understanding of evolutionary histories and associated phylogeographic events. Our results suggest that gene flow between these systems, before and after fragmentation was through periodic paleolakes that formed in the headwaters region. Fragmentation between the Negro and Chico-Chubut systems was driven by the disappearance of these paleolakes during the Patagonian Glaciation.
Data from: Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing
The KwaZulu-Natal yellowfish (Labeobarbus natalensis) is an abundant cyprinid, endemic to KwaZulu-Natal Province, South Africa. In this study we developed a Single Nucleotide Polymorphism (SNP) dataset from double-digest Restriction-site Associated DNA (ddRAD) sequencing of samples across the distribution. We addressed several hidden challenges, primarily focussing on proper filtering of RAD data and selecting optimal parameters for data processing in polyploid lineages. We used the resulting high-quality SNP dataset to investigate the population genetic structure of L. natalensis. A small number of mitochondrial markers present in these data had disproportionate influence on the recovered genetic structure. The presence of singleton SNPs also confounded genetic structure. We found a well-supported division into northern and southern lineages, with further subdivision into five populations, one of which reflects north-south admixture. Approximate Bayesian Computation scenario testing supported a scenario where an ancestral population diverged into northern and southern lineages, which then diverged to yield the current five populations. All river systems showed similar levels of genetic diversity, which appears unrelated to drainage system size. Nucleotide diversity was highest in the smallest river system, the Mbokodweni, which, together with adjacent small coastal systems, should be considered as a key catchment for conservation.
Data from: Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus).
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Data from: Phylogeography of the Australian freshwater turtle Chelodina expansa reveals complex relationships among inland and coastal bioregions
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Data from: Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis
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Data from: Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella, with an emphasis on dwarf Galaxias (G. pusilla)
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Data from: Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing
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Data from: Phylogeography of the freshwater crab Potamon persicum (Decapoda: Potamidae): an ancestral ring species?
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Figure 8 from: Veeravechsukij N, Krailas D, Namchote S, Wiggering B, Neiber MT, Glaubrecht M (2018) Molecular phylogeography and reproductive biology of the freshwater snail Tarebia granifera in Thailand and Timor (Cerithioidea, Thiaridae): morphological disparity versus genetic diversity. Zoosystematics and Evolution 94(2): 461-493. https://doi.org/10.3897/zse.94.28981
Figure 8 Frequency of ontogenetic stages in the subhemocoelic brood pouches of female Tarebiagranifera (Lamarck, 1816) (morph B) depending on occurrence in Thailand. Blue dots: mitochondrial clade A; pink dots: mitochondrial clade B. Size classes are assigned different colours in the pie charts (see legend) and rivers are coloured according to drainage systems; numbers at the pie charts refer to the total number of dissected specimens and the number of gravid females (in parentheses). The small letters refer to the stations Chiang Mai (a), Ko Samui (b) and Phuket (c) for which meteorological data representing the different climatic regions of Thailand were analysed (see Fig. 12).
Figure 4 from: Veeravechsukij N, Krailas D, Namchote S, Wiggering B, Neiber MT, Glaubrecht M (2018) Molecular phylogeography and reproductive biology of the freshwater snail Tarebia granifera in Thailand and Timor (Cerithioidea, Thiaridae): morphological disparity versus genetic diversity. Zoosystematics and Evolution 94(2): 461-493. https://doi.org/10.3897/zse.94.28981
Figure 4 Bayesiam 50% majority-rule consensus tree showing two major mitochondrial clades in Tarebiagranifera (Lamarck, 1816). Numbers at the nodes correspond to posterior probabilities (left), maximum likelihood (middle) and maximum parsimony (right) bootstrap values. At the tips of the tree voucher numbers (see material list in the main part of the text), country codes (THA: Thailand; TIM: Timor Leste; IDN: Indonesia) and the river where specimens were collected are indicated. The inset map shows the distribution of mitochondrial clades in Thailand (clade A: blue dots; clade B: magenta dots) and major river systems. The letters a–c in the map refer to localities, for which climatic data were available (see also Fig. 12). The inset with box plots shows the altitudinal distribution of mitochondrial caldes A and B, respectively.
Figure 6 from: Veeravechsukij N, Krailas D, Namchote S, Wiggering B, Neiber MT, Glaubrecht M (2018) Molecular phylogeography and reproductive biology of the freshwater snail Tarebia granifera in Thailand and Timor (Cerithioidea, Thiaridae): morphological disparity versus genetic diversity. Zoosystematics and Evolution 94(2): 461-493. https://doi.org/10.3897/zse.94.28981
Figure 6 Results of biometric (a–d) and geometric morphometrics study (e), for four different morphs (A,B,C,Timor) of Tarebiagranifera (Lamarck, 1816). Boxplots of (a) shell height, (b) shell width, (c) height of the last three whorls and (d) index of height of last three whorls agaianst shell width. Significant differences between groups are indicated by bars above the boxplots (e) Relative variance in shell shape along PC1 and PC2. Colour corresponding planes indicate the spread of each morph in the data set.
Figure 2 from: Veeravechsukij N, Krailas D, Namchote S, Wiggering B, Neiber MT, Glaubrecht M (2018) Molecular phylogeography and reproductive biology of the freshwater snail Tarebia granifera in Thailand and Timor (Cerithioidea, Thiaridae): morphological disparity versus genetic diversity. Zoosystematics and Evolution 94(2): 461-493. https://doi.org/10.3897/zse.94.28981
Figure 2 Shells of Tarebiagranifera (Lamarck, 1816) from Timor and Thailand. a. Syntypes (MHNG 1093/72/1-4) from Timor. b–g. Morph A, i.e. specimens from Thailand corresponding to T.granifera (SUT 0514044, SUT 0516123, SUT 0515088, SUT 0515068, SUT 0515059, SUT 0516144). h–m. Morph B, i.e. specimens from Thailand corresponding to named T.lineata (Gray, 1828) (SUT 0515081, SUT 0514046, SUT 0516129, SUT 0515092, SUT 0515095, SUT 0516143). n–s. Morph C from Thailand (SUT 0515079, SUT 0516126, SUT 0515055, SUT 0515091, SUT 0516147, SUT0516142). t–y. Shells of T.granifera from Timor Leste (ZMH 119364, ZMH 119359, ZMH 119357, ZMH 119353, ZMH 119363, ZMH 119361). For locality data, see the material list in the main part of the text. Scale bar: 10 mm.
Figure 12 from: Veeravechsukij N, Krailas D, Namchote S, Wiggering B, Neiber MT, Glaubrecht M (2018) Molecular phylogeography and reproductive biology of the freshwater snail Tarebia granifera in Thailand and Timor (Cerithioidea, Thiaridae): morphological disparity versus genetic diversity. Zoosystematics and Evolution 94(2): 461-493. https://doi.org/10.3897/zse.94.28981
Figure 12 Proportions of gravid vs. non-gravid specimens of Tarebiagranifera (Lamarck, 1816) collected in different months within a given year, plotted on climate charts for localities that are representative for different climatic regimes in Thailand. (a) Chiang Mai for inland locations; (b) Ko Samui for the Gulf of Thailand; (c) Phuket for the Andaman Sea (see also Fig. 8). For colour coding, see the inset legend.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.