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1,467 results for “Genetic structure”
FIGURE 8 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 8. Stomach of Juliomys pictipes (CNP 895): internal view of the dorsal half. Abbreviations: p: pilorous; ia: incisura angularis; e: esophagus; ce: cornified squamous epithelium; co: corpus; bf: bordering fold; ge: glandular epithelium; a: antrum.
FIGURE 4 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 4. Manus and pes of Juliomys pictipes from Misiones, Argentina (MLP 1.I.03.24): a. Manus, palmar surface; b. Pes, dorsal surface (note the bicolor condition); c. Pes, plantar surface.
FIGURE 2 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 2. Recording localities of Juliomys pictipes: ARGENTINA: MISIONES: 1. Parque Nacional Iguazú; 2. Parque Provincial "Ernesto Che Guevara;" 3. Reserva Privada de Usos Múltiples de la Universidad Nacional de La Plata "Valle del Arroyo Cuña Pirú"; BRAZIL: SÃO PAULO: 4. Buri; not specific locality provided; 5. Mulheres and Museros; 6. Fazenda Sakamoto, Campinho; Fazenda Sakamoto, Portão; Fazenda Intervales; 7. Fragmento Citadini; Fragmento Divisa; Três Quedas; Moacir; Paraguai; Cogumelo; 8. Floresta Nacional de Ipanema, 20 km NW Sorocaba; 9. Piedade, not specific locality provided; 10. Reserva Florestal do Morro Grande, Caucaia do Alto; 11. Riacho Grande; 12. Parque Natural Municipal da Serra do Itapety; RIO DE JANEIRO: 13. Mata do Mamede; 14. Fazenda Boa Fė; MINAS GERAIS: 15. Reserva Particular do Patrimȏnio Natural do Caraça, 25 km SW Santa Barbara; 16. Estação de Pesquisa e Desenvolvimento Ambiental de Peti. The grey area represents the approximate cover of the Atlantic Forest.
FIGURE 3 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 3. External aspect (lateral view) of a recently collected Juliomys pictipes from Misiones, Argentina (MLP 1.I.03.24).
FIGURE 7 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 7. Selected mandible traits in adult Juliomys pictipes (CIES-M 23). A. Anterior region of the horizontal ramus: note the depressed position of the diastema anterior point with respect to the alveolar plane; B. Ascending ramus region: note the short angular process. Abbreviations: cp = capsular projection, m1 = first lower molar, m2 = second lower molar, m3 = third lower molar, me = mental foramen, ml = maseteric crest, lower ridge, mu = maseteric crest, upper ridge.
FIGURE 1 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 1. Strict consensus tree of the 300 most parsimonious trees (length 1048 steps, CI = 0.483, RI = 0.606) obtained in the maximum parsimony analysis of the cytochrome b gene sequences. Numbers above branches indicate parsimony jackknife (left), Bremer support (middle), and maximum likelihood bootstrap (right) values of the nodes to their right. Only jackknife and bootstrap values> 50 % are shown. * indicates that the node in question was not recovered in the maximum likelihood analyses; in that analysis J. rimofrons and J. pictipes are sister to each other but with less than 50 % of support.
FIGURE 1. Map showing collection localities for L in Morphological diversity and genetic structure within Lerista kalumburu Storr, 1976 (Squamata: Scincomorpha: Sphenomorphidae) — taxonomic implications
FIGURE 1. Map showing collection localities for L. kalumburu. Type locality (Kalumburu) in red, collection locality for twotoed specimens (Theda Station) in yellow. Locality lacking tissue sample (Doongan Station) indicated with hollow symbol. (Google © 2010; Image NASA © 2012 Cnes/Spot Image Data S10, NOAA, U.S. Navy, NGA, CEBCO).
FIGURE 2 in Morphological diversity and genetic structure within Lerista kalumburu Storr, 1976 (Squamata: Scincomorpha: Sphenomorphidae) — taxonomic implications
FIGURE 2. Majority-rule consensus tree of L. kalumburu and outgroup taxa based on four independent runs of the concatenated dataset combining four genetic loci (12S, 16S, ND4 and ATPsβ). Posterior probabilities are detailed above the branches. Branches with <60% support were collapsed. Modal digit configurations (forelimb, hindlimb) follow L. kalumburu specimen labels.
The genetic diversity, phylogeography, and population structure of Pacific harbor seals reveal isolation at the southern end of their distribution
<p>The Pacific harbor seal (<em>Phoca vitulina richardii</em>) occurs in the Mexican Pacific region at the southernmost edge of the subspecies' distribution, along 700 km of coastline and on nine islands west of the Baja California peninsula. Its abundance corresponds to 3% of its total abundance in the north Pacific Ocean. The species is considered relatively sedentary and highly philopatric, which make it vulnerable to stochastic processes; thus, reproductive and genetic isolation of the Mexican Pacific colonies is expected. This study aimed to genetically characterize the harbor seal in the Mexican Pacific to inform conservation efforts. We estimated the levels of genetic diversity for five colonies, using a 572-base pair mitochondrial DNA control region fragment and nine microsatellite loci. We examined the population genetic structure and its phylogeographic patterns. We found 15 variable sites that defined 18 mitochondrial DNA haplotypes. Results show one of the lowest levels of diversity reported for the species (overall haplotype diversity <em>h</em> = 0.626 ± SD 0.041; overall nucleotide diversity π = 0.0018 ± SD 0.0013; mean expected heterozygosity H<sub>E</sub> = 0.537). We found a stronger genetic structure with both markers than in the larger regions of the north Pacific, from Alaska to California. The Pacific harbor seal colonies found in Mexico may have their origins in northern colonies, via a founder event. We found only four haplotypes in common with those observed (451) along the rest of the Pacific colonies, while nine of the 14 haplotypes exclusive to the Mexican Pacific are private.</p>
Dataset from: Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure
<p>Genetic variation of the entire genome represents population structure, yet individual loci can show distinct patterns. Such deviations identified through genome scans have often been attributed to effects of selection instead of randomness. This interpretation assumes that long enough genomic intervals average out randomness in underlying genealogies, which represent local genetic ancestries. However, an alternative explanation to distinct patterns has not been fully addressed: too few genealogies to average out the effect of randomness. Specifically, distinct patterns of genetic variation may be due to reduced local recombination rate, which<br>reduces the number of genealogies in a genomic window. Here, we associate distinct patterns of local genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (<em>Sylvia atricapilla</em>), using genome sequences and recombination maps. We find that distinct patterns of local genetic variation reflect haplotype structure at low-recombining regions either shared in most populations or found only in a few populations. At the former species-wide low-recombining regions, genetic variation depicts conspicuous haplotypes segregating in multiple populations. At the latter population-specific low-recombining regions, genetic variation represents variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns of haplotype structure evolve due<br>to reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolution of reduced local recombination rate. Recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.</p>
Obovaria olivaria maf filtered vcf file from: RAD-tag and mitochondrial DNA sequencing reveal the genetic structure of a widespread and regionally imperiled freshwater mussel, Obovaria olivaria (Bivalvia: Unionidae)
<p><em>Obovaria olivaria</em> is a species of freshwater mussel native to the Mississippi River and Laurentian Great Lakes-St. Lawrence River drainages of North America. This mussel has experienced population declines across large parts of its distribution and is imperiled in many jurisdictions. <em>Obovaria olivaria </em>uses the similarly imperiled <em>Acipenser fulvescens</em> (Lake Sturgeon) as a host for its glochidia. We employed mitochondrial DNA sequencing and Restriction-site Associated DNA sequencing (RAD-seq) to assess patterns of genetic diversity and population structure of <em>O. olivaria</em> from 19 collection locations including the St. Lawrence River drainage, the Great Lakes drainage, the Upper Mississippi River drainage, the Ohioan River drainage and the Mississippi Embayment. Heterozygosity was highest in Upper Mississippi and Great Lakes populations, followed by a reduction in diversity and relative effective population size in the St. Lawrence populations. Pairwise <em>F</em><sub>ST</sub> ranged from 0.00 to 0.20, and analyses of genetic structure revealed two major ancestral populations, one including all St. Lawrence River/Ottawa River sites and the other including remaining sites; however, significant admixture and isolation by river distance across the range were evident. The genetic diversity and structure of <em>O. olivaria</em> is consistent with the existing literature on <em>Acipenser fulvescens</em> and suggest that, although northern and southern <em>O. olivaria</em> populations are genetically distinct, genetic structure in <em>O. olivaria</em> is largely clinal rather than discrete across its range. Conservation and restoration efforts of <em>O. olivaria</em> should prioritize the maintenance and restoration of locations where <em>O. olivaria </em>remain, especially in northern rivers, and to ensure connectivity that will facilitate dispersal of <em>Acipenser fulvescens</em> and movement of encysted glochidia.</p>
Fig. 3 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 3. Likelihood phylogeny of concatenated supermatrix of Pogonolepis and outgroups. Numbers above branches indicate UltraFast Bootstrap values, gene Concordance Factors, and site Concordance Factors. The dashed branch was shortened for the figure. Western Australian specimens of P. muelleriana are marked with (WA), all others are from eastern states. A and B indicate informally named clades inside P. stricta.
Fig. 2 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 2. Geographic spread of the specimens of Pogonolepis at CANB sampled for molecular analysis (large, pale circles) and ranges of species according to the Australasian Virtual Herbarium (dots; see https://doi.org/10.26197/ala.6556e234- 7160-49de-bf63-5123af624e94, accessed 31 May 2022). Red: P. muelleriana; blue: P. stricta. Note that specimens of P. muel-leriana geocoded in Canberra and Hobart were likely cultivated.
Fig. 1 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 1. (a) Pogonolepis muelleriana, New South Wales, SchmidtLebuhn 1633 (CANB); (b) Pogonolepis stricta, Western Australia, Schmidt-Lebuhn 1474 (CANB).
Contrasting clonal and population genetic structure in two endangered Costa Rican Vanilla species of commercial interest
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Contrasting reproductive traits affect the genetic diversity and fine-scale genetic structure of two sympatric and epiphytic tropical bromeliads.
<p>This database contains the coordinates of individuals of <em>Aechmea mariae-reginae</em> and <em>Werauhia ampla</em> in phorophytic trees and the genotypes for 8 microsatellite loci.</p>
Next-generation phylogeography of the banded newts (Ommatotriton): A phylogenetic hypothesis for three ancient species with geographically restricted interspecific gene flow and deep intraspecific genetic structure
<p class="MsoNoSpacing">Technological developments now make it possible to employ many markers for many individuals in a phylogeographic setting, even for taxa with large and complex genomes such as salamanders. The banded newt (genus <i>Ommatotriton</i>) from the Near East has been proposed to contain three species (<i>O. nesterovi</i>, <i>O. ophryticus </i>and <i>O. vittatus</i>) with unclear phylogenetic relationships, apparently limited interspecific gene flow and deep intraspecific geographic mtDNA structure. We use parallel tagged amplicon sequencing to obtain 177 nuclear DNA markers for 35 banded newts sampled throughout the range. We determine population structure (with Bayesian clustering and principal component analysis), interspecific gene flow (by determining the distribution of species-diagnostic alleles) and phylogenetic relationships (by maximum likelihood inference of concatenated sequence data and based on a summary-coalescent approach). We confirm that the three proposed species are genetically distinct. A sister relationship between <i>O. nesterovi</i> and <i>O. ophryticus</i> is suggested. We find evidence for introgression between <i>O. nesterovi</i> and <i>O. ophryticus</i>, but this is geographically limited. Intraspecific structuring is extensive, with the only recognized banded newt subspecies, <i>O. vittatus cilicensis</i>, representing the most distinct lineage below the species level. While mtDNA mostly mirrors the pattern observed in nuclear DNA, all banded newt species show mito-nuclear discordance as well.</p>
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.
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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.