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56 results for “multilocus genetics”
Data from: Archipelago-wide survey of Philippine forest dragons (Agamidae: Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot
We utilize robust geographical genetic sampling, a multilocus dataset, and coalescent-based species delimitation statistics to provide the first phylogenetic inferences of relationships of Philippine Gonocephalus, combined with estimates of putative species diversity in this virtually unknown island radiation. Our results reveal startling levels of undocumented diversity, genetically partitioned at a number of geographic levels across the archipelago. In this paper we present the first survey of genetic lineage diversity, coupled with an archipelago-wide elucidation of geographic structure in a unique archipelago-endemic radiation. Philippine Gonocephalus have previously escaped the attention of biogeographers, due to taxonomic confusion associated with low numbers of preserved specimens in museum collections. With new vouchered material and genetic sampling from a comprehensive, archipelago-wide vertebrate biodiversity inventory, our findings join many recent studies highlighting the unprecedented faunal diversity in one of the world's most unique biodiversity conservation hotspots.
Multilocus phylogeography, population genetics and niche evolution of Australian Brown and Black-tailed Treecreepers (Aves: Climacteris)
<p>The Carpentarian barrier across northeastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modeling of Brown and Black-tailed Treecreepers (<em>Climacteris picumnus</em> and <em>C</em>. <em>melanurus</em>), a clade with a classic distribution on either side of the Carpentarian barrier. mtDNA control region sequences exhibited reciprocal monophyly and strong differentiation (<em>F</em><sub>st</sub> = 0.91), and reveals a signature of a recent selective sweep in <em>C. picumnus. </em>No loci among 14 anonymous autosomal markers exhibited reciprocal monophyly between species, and a variety of tests support an isolation-with-migration model of divergence, albeit with low levels of gene flow across the Carpentarian barrier and a divergence time between species of ~1.7 – 2.8 MYA, depending on the model and assumptions about generation time. Paleo-ecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the last ~600 kyr and that the area of range overlap was never historically large, perhaps decreasing opportunities for extensive gene flow. The relatively long divergence time and low opportunity for gene flow may have facilitated speciation more so than in other co-distributed bird taxa across the Australian Monsoonal Tropics.</p>
Data from: Archipelago-wide survey of Philippine forest dragons (Agamidae: Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot
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Multilocus phylogeography, population genetics and niche evolution of Australian Brown and Black-tailed Treecreepers (Aves: Climacteris)
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Data from: Modeling multilocus selection in an individual-based, spatially-explicit landscape genetics framework
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Multilocus genetic data diversification patterns in Laevilitorininae
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Data from: Multilocus patterns of genetic variation across Cryptosporidium species suggest balancing selection at the gp60 locus
Cryptosporidium is an apicomplexan protozoan that parasites most vertebrates, including humans. Its gp60 gene is functionally involved in its attachement to host's cells and its high level of genetic variation has made it the reference marker for sample typing in epidemiological studies. To understand the origin of such high diversity and to determine the extent to which this classification applies to the rest of the genome, we analysed the patterns of variation at gp60 and nine other nuclear loci in isolates of three Cryptosporidium species. Most loci showed low genetic polymorphism (πS < 1%) and similar levels of between-species divergence. Contrastingly, gp60 exhibited very different features: (i) it was nearly ten times more variable than the other loci, (ii) it displayed a significant excess of polymorphisms relative to between-species differences in a Maximum-likelihood Hudson-Kreitman-Aguadé test (iii) gp60 subtypes turned out to be much older than the species they were found in and (iv) showed a significant excess of polymorphic variants shared across species from random expectations. These observations suggest that this locus evolves under balancing selection, and specifically under negative frequency-dependent selection. Interestingly, genetic variation at the other loci cluster very well within the subtypes defined by gp60, which may provide new tools to understand the genome-wide patterns of genetic variation of the parasite in the wild. These results suggest that gp60 plays an active and essential role in the life cycle of the parasite and that genetic variation at this locus might be essential for the parasite's long-term success.
Data from: Multilocus genetic diversity and historical biogeography of the endemic wall lizard from Ibiza and Formentera, Podarcis pityusensis (Squamata: Lacertidae)
Two monophyletic sister species of wall lizards inhabit the two main groups of Balearic Islands: Podarcis lilfordi from islets and small islands around Mallorca and Menorca and Podarcis pityusensis from Ibiza, Formentera and associated islets. Genetic diversity within the endangered P. lilfordi has been well characterized, but P. pityusensis has not been studied in depth. Here, 2430 bp of mtDNA and 15 microsatellite loci were analysed from P. pityusensis populations from across its natural range. Two main genetic groupings were identified, although geographical structuring differed slightly between the mtDNA and the nuclear loci. In general, individuals from islets/islands adjacent to the main island of Ibiza were genetically distinct from those from Formentera and the associated Freus islands for both mtDNA and the nuclear loci. However, most individuals from the island of Ibiza were grouped with neighbouring islets/islands for nuclear loci, but with Formentera and Freus islands for the mitochondrial locus. A time-calibrated Bayesian tree was constructed for the principal mitochondrial lineages within the Balearics, using the multispecies coalescent model, and provided statistical support for divergence of the two main P. pityusensis lineages 0.111–0.295 Ma. This suggests a mid-late Pleistocene intraspecific divergence, compared with an early Pleistocene divergence in P. lilfordi, and postdates some major increases in sea level between 0.4 and 0.6 Ma, which may have flooded Formentera. The program IMa2 provided a posterior divergence time of 0.089–0.221 Ma, which was similar to the multispecies coalescent tree estimate. More significantly, it indicated low but asymmetric effective gene copy migration rates, with higher migration from Formentera to Ibiza populations. Our findings suggest that much of the present-day diversity may have originated from a late Pleistocene colonization of one island group from the other, followed by allopatric divergence of these populations. Subsequent gene flow between these insular groups seems likely to be explained by recent human introductions. Two evolutionary significant units can be defined for P. pityusensis but these units would need to exclude the populations that have been the subjects of recent admixture.
Data from: The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation
Hybridization drives the evolutionary trajectory of many species or local populations, and assessing the geographic extent and genetic impact of interspecific gene flow may provide invaluable clues to understand population divergence or the adaptive relevance of admixture. In North America, hares (Lepus spp.) are key species for ecosystem dynamics and their evolutionary history may have been affected by hybridization. Here we reconstructed the speciation history of the three most widespread hares in North America - the snowshoe hare (Lepus americanus), the white-tailed jackrabbit (L. townsendii) and the black-tailed jackrabbit (L. californicus) - by analyzing sequence variation at eight nuclear markers and one mitochondrial DNA (mtDNA) locus (6 240 bp; 94 specimens). A multilocus-multispecies coalescent-based phylogeny suggests that L. americanus diverged ~2.7 Mya and that L. californicus and L. townsendii split more recently (~1.2 Mya). Within L. americanus a deep history of cryptic divergence (~2.0 Mya) was inferred, which coincides with major speciation events in other North American species. While the isolation-with-migration model suggested that nuclear gene flow was generally rare or absent among species or major genetic groups, coalescent simulations of mtDNA divergence revealed historical mtDNA introgression from L. californicus into the Pacific Northwest populations of L. americanus. This finding marks a history of past reticulation between these species, which may have affected other parts of the genome and influence the adaptive potential of hares during climate change.
Data from: Multilocus approaches for the measurement of selection on correlated genetic loci
The study of ecological speciation is inherently linked to the study of selection. Methods for estimating phenotypic selection within a generation based on associations between trait values and fitness (e.g. survival) of individuals are established. These methods attempt to disentangle selection acting directly on a trait from indirect selection caused by correlations with other traits via multivariate statistical approaches (i.e. inference of selection gradients). The estimation of selection on genotypic or genomic variation could also benefit from disentangling direct and indirect selection on genetic loci. However, achieving this goal is difficult with genomic data because the number of potentially correlated genetic loci (p) is very large relative to the number of individuals sampled (n). In other words, the number of model parameters exceeds the number of observations (p ≫ n). We present simulations examining the utility of whole-genome regression approaches (i.e. Bayesian sparse linear mixed models) for quantifying direct selection in cases where p ≫ n. Such models have been used for genome-wide association mapping and are common in artificial breeding. Our results show they hold promise for studies of natural selection in the wild and thus of ecological speciation. But we also demonstrate important limitations to the approach and discuss study designs required for more robust inferences.
Fig. 1 in Multilocus population analysis of Gavia immer (Aves: Gaviidae) mtDNA reveals low genetic diversity and lack of differentiation across the species breeding range
Fig. 1 Haplotype network constructed using the median joining method. Haplotype numbers are indicated. Circle patterns represent coastal sampling locations: GZ Galicia, Spain, MX Mexico, GE Germany, NJ New Jersey, US, MI Michigan, US, CA Canada, FL Florida, US. Circle surfaces are roughly proportional to the number of individuals with each haplotype (Table 3)
Data from: The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation
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Data from: Multilocus patterns of genetic variation across Cryptosporidium species suggest balancing selection at the gp60 locus
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Data from: Multilocus approaches for the measurement of selection on correlated genetic loci
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Data from: Multilocus genetic diversity and historical biogeography of the endemic wall lizard from Ibiza and Formentera, Podarcis pityusensis (Squamata: Lacertidae)
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Supplementary material 3 from: Kanesharatnam N, Benjamin SP (2019) Multilocus genetic and morphological phylogenetic analysis reveals a radiation of shiny South Asian jumping spiders (Araneae, Salticidae). ZooKeys 839: 1-81. https://doi.org/10.3897/zookeys.839.28312
: Data type: phylogeny data
Supplementary material 2 from: Kanesharatnam N, Benjamin SP (2019) Multilocus genetic and morphological phylogenetic analysis reveals a radiation of shiny South Asian jumping spiders (Araneae, Salticidae). ZooKeys 839: 1-81. https://doi.org/10.3897/zookeys.839.28312
: Data type: phylogeny data
Supplementary material 1 from: Kanesharatnam N, Benjamin SP (2019) Multilocus genetic and morphological phylogenetic analysis reveals a radiation of shiny South Asian jumping spiders (Araneae, Salticidae). ZooKeys 839: 1-81. https://doi.org/10.3897/zookeys.839.28312
: Data type: phylogeny data
Figure 6 from: Kanesharatnam N, Benjamin SP (2019) Multilocus genetic and morphological phylogenetic analysis reveals a radiation of shiny South Asian jumping spiders (Araneae, Salticidae). ZooKeys 839: 1-81. https://doi.org/10.3897/zookeys.839.28312
Figure 6 Phintelloidesalborea (A–D) A–B Female habitus A dorsal view B ventral view C, D Epigynum C ventral view D dorsal view; Phintelloidesjesudasi (E–H) E, F Female habitus E dorsal view F ventral view G, H Epigynum G ventral view H dorsal view. Scale bars: 1 mm (A, B, E, F), 0.1 mm (C, D, G, H).
Figure 9 from: Kanesharatnam N, Benjamin SP (2019) Multilocus genetic and morphological phylogenetic analysis reveals a radiation of shiny South Asian jumping spiders (Araneae, Salticidae). ZooKeys 839: 1-81. https://doi.org/10.3897/zookeys.839.28312
Figure 9 Phintelloidesbrunne (A, B). Male habitus A dorsal view B ventral view C–E Male palp C prolateral view D ventral view E retrolateral view. Scale bars: 1 mm (A, B), 0.2 mm (C–E).
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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
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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.