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115 results for “Multi-locus”
Multi-locus DNA metabarcoding of western spotted skunk diet in the McKenzie River Ranger District of the Willamette National Forest from 2017-2019
There are increasing concerns about the declining population trends of small mammalian carnivores around the world. Their conservation and management is often challenging due to limited knowledge about their ecology and natural history. To address one of these deficiencies for western spotted skunks (Spilogale gracilis), we investigated their diet in the Oregon Cascades of the Pacific Northwest during 2017 –2019. We collected 130 spotted skunk scats opportunistically and with detection dog teams and identified prey items using DNA metabarcoding and mechanical sorting. Western spotted skunk diet consisted of invertebrates such as wasps, millipedes, and gastropods, vertebrates such as small mammals, amphibians, and birds, and plants such as Gaultheria, Rubus, and Vaccinium. Diet also consisted of items such as black-tailed deer that were likely scavenged. Comparison in diet by season revealed that spotted skunks consumed more insects during the dry season (June –August), particularly wasps (75% of scats in the dry season), and marginally more mammals during the wet season(September –May). We observed similar diet in areas with no record of human disturbance and areas with a history of logging at most spatial scales, but scats collected in areas with older forest within a skunk’s home range (1 km buffer) were more likely to contain insects. Western spotted skunks provide food web linkages between aquatic, terrestrial, and arboreal systems and serve functional roles of seed dispersal and scavenging. Due to their diverse diet and prey-switching, western spotted skunks may dampen the effects of irruptions of prey, such as wasps during dry springs and summers. By studying the natural history of western spotted skunks in the Pacific Northwest forests while they are still abundant, we provide key information necessary to achieve the conservation goal of keeping this common species common.
A multi-locus phylogeny for the Diamesinae (Chironomidae: Diptera) provides new insights into evolution of an amphitropical clade
<p>Aligned FASTA files for each locus, Concatinated Dataset, Input files for MrBayes, IqTree2, PartitionFinder and RASP. Ready trees after MrBayes and BEAST. </p>
FIGURE 2 in Comparative performance of a multi-locus barcoding approach to enhance taxonomic resolution of New Zealand mosquitoes (Diptera: Culicidae)
FIGURE 2 The statistical parsimony network showing the genetic relationships between Culex asteliae (n = 3), Culex pervigilans (n = 15) and Culex rotoruae (n = 3) based on their (a) COI sequences and (b) ITS2 sequences derived from the current study. Each COI/ITS2 singleton sequence is represented by one circle with size proportional to their frequency. The colours refer to the mosquito species to which each individual belongs. Small white circles connecting coloured circles indicate 'missing' or hypothetical singletons. The line linked two circles indicates one basepair difference on the sequence.
FIGURE 1 in Comparative performance of a multi-locus barcoding approach to enhance taxonomic resolution of New Zealand mosquitoes (Diptera: Culicidae)
FIGURE 1 The phylogenetic relationships of New Zealand endemic and exotic mosquito species based on (a) COI and (b) ITS2 sequences using maximum likelihood method. Anopheles annulipes was outgroup taxon for both trees. Only bootstrap support values greater than 50% is present at branches on the tree. The sequences collected for the current study and derived from New Zealand endemic, introduced or recently eradicated species are highlighted in bold. The specimens collected outside of New Zealand were highlighted by underlines. The complete phylogenetic trees of New Zealand endemic and exotic mosquito species based on COI and ITS2 sequences are available in Figure S3.
Data from: A multi-locus plastid phylogeny of the Aulonemia clade (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) reveals three new genera of bamboo
<p>Arthrostylidiinae (Poaceae: Bambusoideae), a subtribe of Neotropical woody bamboos with diverse morphology, comprises 200 species classified in 16 genera. Previous studies supported monophyly of the subtribe and recovered four major internal clades, however, some genera were found to be polyphyletic while others, like <em>Aulonemia</em> and <em>Colanthelia,</em> were either undersampled or not included. <em>Aulonemia</em> and <em>Colanthelia</em> are complex both in their taxonomy and morphology, and exhibit overlapping morphological characters. Prior morphological and molecular analyses suggested they share a close relationship, with <em>Colanthelia </em>emerging as monophyletic and either nested within <em>Aulonemia</em> or sister to it,<em> </em>but these studies sampled relatively few species of each genus. The aims of this study were to increase taxon sampling to test the monophyly of <em>Aulonemia</em> and <em>Colanthelia, </em>to investigate the relationships within the <em>Aulonemia </em>+ <em>Colanthelia </em>clade, and to revise their classification as appropriate towards a natural classification of the Arthrostylidiinae. We present a multi-locus plastid phylogeny of the Arthrostylidiinae with emphasis on <em>Aulonemia </em>and <em>Colanthelia</em>. We used sequences of seven plastid markers (one coding: <em>ndhF</em>; six non-coding:<em> trnC-rpoB, rps16-trnQ, trnT-trnL, rps16, trnD-trnT, </em>and <em>rpl16</em>) from 67 taxa of Bambusoideae including all genera of Arthrostylidiinae. Phylogenetic trees were inferred using both Bayesian and maximum likelihood methods. <em>Aulonemia</em> was confirmed as polyphyletic and <em>Colanthelia</em> was not supported as monophyletic. The phylogenetic position of <em>Myriocladus </em>within Arthrostylidiinae is resolved for the first time. All species of <em>Colanthelia</em> were recovered within the clade containing most species of <em>Aulonemia</em>. Four species of <em>Aulonemia</em> (<em>A. radiata</em>, <em>A. effusa</em>, <em>A. setosa</em>, and <em>A. setigera</em>) grouped in other clades within the subtribe and these placements combined with morphological evidence support the establishment of three new genera: <em>Quixiume</em>, <em>Stelanemia</em> and <em>Vianaea</em>, to accommodate the four remarkable <em>Aulonemia</em> species. An updated key for the genera of the Arthrostylidiinae is provided, as well as taxonomic treatments for the three new genera, including the description of a new species in <em>Stelanemia</em>.</p>
Fig. 1 in Extensive testing of a multi-locus sequence typing scheme for Giardia dUodenaliS assemblage A confirms its good discriminatory power
Fig. 1 DCC outbreak in Sweden, described by Ankarklev et al. [13]; GVB outbreak in Italy, described by Resi et al. [14]; and several longitudinal samples of different patients showing similar genotypes, described by Woschke et al. [15]
Data from: A method to generate multi-locus barcodes of pinned insect specimens using MiSeq
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Data from: A multi-locus plastid phylogeny of the Aulonemia clade (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) reveals three new genera of bamboo
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Dataset for METAPOPGEN 2.0: a multi-locus genetic simulator to model populations of large size
<p>Multi-locus genetic processes in subdivided populations can be complex and difficult to interpret using theoretical population genetics models. Genetic simulators offer a valid alternative to study multi-locus genetic processes in arbitrarily complex scenarios. However, the use of forward-in-time simulators in realistic scenarios involving high numbers of individuals distributed in multiple local populations is limited by computation time and memory requirements. These limitations increase with the number of simulated individuals. We developed a genetic simulator, <span>MetaPopGen</span> 2.0, to model multi-locus population genetic processes in subdivided populations of arbitrarily large size. It allows for spatial and temporal variation in demographic parameters, age structure, adult and propagule dispersal, variable mutation rates and selection on survival and fecundity. We developed <span>MetaPopGen</span> 2.0 in the R environment to facilitate its use by non-modeler ecologists and evolutionary biologists. We illustrate the capabilities of <span>MetaPopGen</span> 2.0 for studying adaptation to water salinity in the striped red mullet <i>Mullus surmuletus</i>.</p>
FIGURE 1 in Comparative performance of a multi-locus barcoding approach to enhance taxonomic resolution of New Zealand mosquitoes (Diptera: Culicidae)
FIGURE 1 (Continued)
Data from: Multi-locus homozygosity promotes actuarial senescence in a wild mammal
<ol> <li>Genome-wide homozygosity, caused for example by inbreeding, is expected to have deleterious effects on survival and/or reproduction. Evolutionary theory predicts that any fitness costs are likely to be detected in late life because natural selection will filter out negative impacts on younger individuals with greater reproductive value.</li> <li>Here we infer associations between multi-locus homozygosity, sex, disease, and age-dependent mortality risks using Bayesian analysis of the life histories of wild European badgers (<em>Meles</em> <em>meles</em>) in a population naturally infected with <em>Mycobacterium</em> <em>bovis</em> (the causative agent of bovine tuberculosis).</li> <li>We find important effects of multi-locus homozygosity on all parameters of the Gompertz-Makeham mortality hazard function, but particularly in later-life.</li> <li>Our findings confirm the predicted association between genomic homozygosity and actuarial senescence. Increased homozygosity is particularly associated with an earlier onset, and greater rates of actuarial senescence, regardless of sex. The association between homozygosity and actuarial senescence is further amplified among badgers putatively infected with bovine tuberculosis.</li> <li>These results recommend further investigation into the ecological and behavioural processes that result in genome-wide homozygosity, and focused work on whether homozygosity is harmful or beneficial during early life-stages.</li> </ol>
Data from: Multi-locus genomic signatures of local adaptation to snow across the landscape in California populations of a willow leaf beetle
<p>Organisms living in mountains contend with extreme climatic conditions, including short growing seasons and long winters with extensive snow cover. Anthropogenic climate change is driving unprecedented, rapid warming of montane regions across the globe, resulting in reduced winter snowpack. Loss of snow as a thermal buffer may have serious consequences for animals overwintering in soil, yet little is known about how variability in snowpack acts as a selective agent in montane ecosystems. Here we examine genomic variation in California populations of the leaf beetle <em>Chrysomela aeneicollis</em>, an emerging natural model system for understanding how organisms respond to climate change. We used a genotype-environment association approach to identify genomic signatures of local adaptation to microclimate in populations from three montane regions with variable snowpack and a coastal region with no snow. We found that both winter-associated environmental variation and geographic distance contribute to overall genomic variation across the landscape. We identified non-synonymous variation in novel candidate loci associated with cytoskeletal function, ion transport and membrane stability, cellular processes associated with cold tolerance in other insects. These findings provide intriguing evidence that variation in snowpack imposes selective gradients in montane ecosystems.</p>
Data from: Multi-locus genomic signatures of local adaptation to snow across the landscape in California populations of a willow leaf beetle
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Data from: Multi-locus homozygosity promotes actuarial senescence in a wild mammal
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Multi-locus genome-wide association study for grain yield and drought tolerance indices in sorghum accessions
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Dataset for METAPOPGEN 2.0: a multi-locus genetic simulator to model populations of large size
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Data from: Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs
Though Pleistocene refugia are frequently cited as drivers of species diversification, comparisons of molecular divergence among sister species typically indicate a continuum of divergence times from the late Miocene, rather than a clear pulse of speciation events at the Last Glacial Maximum (LGM). Community-scale inference methods that explicitly test for multiple vicariance events, and account for differences in ancestral effective population size and gene flow, are well suited for detecting heterogeneity of species' responses to past climate fluctuations. We apply this approach to multi-locus sequence data from five co-distributed frog species endemic to the Wet Tropics rainforests of Northeast Australia. Our results demonstrate at least two episodes of vicariance due to climate-driven forest contractions: one in the early Pleistocene and the other considerably older. Understanding how repeated cycles of rainforest contraction and expansion differentially affected lineage divergence among co-distributed species provides a framework for identifying evolutionary processes that underlie population divergence and speciation.
Data from: Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus Cichla) using multi-locus data
BACKGROUND: Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the supremacy of various species concepts and criteria. Here, we utilized multiple separate sources of molecular data, mtDNA, nuclear sequences, and microsatellites, to delimit species under a polytypic species concept (PTSC) and estimate the frequency and genomic extent of introgression in a Neotropical genus of cichlid fishes (Cichla). We compared our inferences of species boundaries and introgression under this paradigm to those when species are identified under a diagnostic species concept (DSC). RESULTS: We find that, based on extensive molecular data and an inclusive species concept, 8 separate biological entities should be recognized rather than the 15 described species of Cichla. Under the PTSC, fewer individuals are expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but more of the species exhibit introgression from at least one other species (75% vs. 60%). Under either species concept, the phylogenetic breadth of introgression in this group is notable, with both sister species and species from different major mtDNA clades exhibiting introgression. CONCLUSIONS: Introgression was observed to be a widespread phenomenon for delimited species in this group. While several instances of introgressive hybridization were observed in anthropogenically altered habitats, most were found in undisturbed natural habitats, suggesting that introgression is a natural but ephemeral part of the evolution of many tropical species. Nevertheless, even transient introgression may facilitate an increase in genetic diversity or transfer of adaptive mutations that have important consequences in the evolution of tropical biodiversity.
Data from: Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.)
Background: During the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Some species diverged, others did not. Here, we begin to address another facet of the role of the Pleistocene in generating today's diversity. We ask which processes contributed to divergence in semi-arid southern Australian birds. We isolated 11 autosomal nuclear loci and one mitochondrial locus from a total of 29 specimens of the sister species pair, Chestnut Quail-thrush Cinclosoma castanotum and Copperback Quail-thrush C. clarum. Results: A population clustering analysis confirmed the location of the current species boundary as a well-known biogeographical barrier in southern Australia, the Eyrean Barrier. Coalescent-based analyses placed the time of species divergence to the Middle Pleistocene. Gene flow between the species since divergence has been low. The analyses suggest the effective population size of the ancestor was 54 to 178 times smaller than populations since divergence. This contrasts with recent multi-locus studies in some other Australian birds (butcherbirds, ducks) where a lack of phenotypic divergence was accompanied by larger historical population sizes. Post-divergence population size histories of C. clarum and C. castanotum were inferred using the extended Bayesian skyline model. The population size of C. clarum increased substantially during the late Pleistocene and continued to increase through the Last Glacial Maximum and Holocene. The timing of this expansion across its vast range is broadly concordant with that documented in several other Australian birds. In contrast, effective population size of C. castanotum was much more constrained and may reflect its smaller range and more restricted habitat east of the Eyrean Barrier compared with that available to C. clarum to the west. Conclusions: Our results contribute to awareness of increased population sizes, following significant contractions, as having been important in shaping diversity in Australian arid and semi-arid zones. Further, we improve knowledge of the role of Pleistocene climatic shifts in areas of the planet that were not glaciated at that time but which still experienced that period's cyclical climatic fluctuations.
DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies
<p>Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts of missing data that are not distributed randomly: barcodes are sampled for all representatives, and additional markers are sampled only for a small percentage. We investigate the effects of the degree and randomness of missing data on phylogenetic accuracy using simulations for up to 100 markers in 1000-tips trees, as well as a real case: the subtribe Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous species with unresolved taxonomy. Our simulation tests show that when a strategic and representative selection of species for higher-level categories has been made for multigene sequencing (approximately one per simulated genus), the addition of this multigene backbone DNA data for as few as 5–10% of the specimens in the total data set can produce high-quality phylogenies, comparable to those resulting from 100% multigene sampling. In contrast, trees based exclusively on barcodes performed poorly. This approach was applied to a 1365-specimen data set of Polyommatina (including ca. 80% of described species), with nearly 8% of representative species included in the multigene backbone and the remaining 92% included only by mitochondrial COI barcodes, a phylogeny was generated that highlighted potential misplacements, unrecognized major clades, and placement for incertae sedis taxa. We use this information to make systematic rearrangements within Polyommatina, and to describe two new genera. Finally, we propose a systematic workflow to assess higher-level taxonomy in hyperdiverse groups. This research identifies an additional, enhanced value of DNA barcodes for improvements in higher-level systematics using large data sets.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.