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Genetic and species-level biodiversity patterns are linked by demography and ecological opportunity
<p>The processes that give rise to species richness gradients are not well understood, but may be linked to resource-based limits on the number of species a region can support. Ecological limits placed on regional species richness should also affect population demography, suggesting that these processes could also generate genetic diversity gradients. If true, we might better understand how broad-scale biodiversity patterns are formed by identifying the common causes of genetic diversity and species richness. We develop a hypothetical framework based on the consequences of regional variation in ecological limits set by resource availability and heterogeneity to simultaneously explain spatial patterns of species richness and neutral genetic diversity. Repurposing raw genotypic data spanning 38 mammal species sampled across 801 sites in North America, we show that estimates of genome-wide genetic diversity and species richness share spatial structure. Notably, species richness hotspots tend to harbor lower levels of within-species genetic variation. A structural equation model encompassing eco-evolutionary processes related to resource availability, habitat heterogeneity, and contemporary human disturbance supports the spatial patterns we detect. These results suggest broad-scale patterns of species richness and genetic diversity could both partly be caused by intraspecific demographic and evolutionary processes acting simultaneously across species.</p>
Genetic diversity of the Nubian ibex in Oman as revealed by mitochondrial DNA
<p>The Nubian ibex (Capra nubiana) is patchily distributed across parts of Africa and Arabia. In Oman, it is one of the few free-ranging wild mammals found in the central and southern regions. Its population is declining due to habitat degradation, human expansion, poaching, and fragmentation. Here we investigated the population's genetic diversity using mitochondrial DNA (D-loop 186bp and cytochrome b 487bp). We found that the Nubian ibex in the southern region of Oman was more diverse (D-loop HD; 0.838) compared to the central region (0.511) and gene flow between them was restricted. We compared the genetic profiles of wild Nubian ibex from Oman with captive ibex. A Bayesian phylogenetic tree showed that wild Nubian ibex form a distinct clade independent from captive animals. This divergence was supported by high mean distances (D-loop 0.126,cytochrome b 0.0528) and high FST statistics (D-loop 0.725,cytochrome b 0.968). These results indicate that captive ibex are highly unlikely to have originated from the wild population in Oman and the considerable divergence suggests that the wild population in Oman should be treated as a distinct taxonomic unit. Further nuclear genetic work will be required to fully elucidate the degree of global taxonomic divergence of Nubian ibex populations.</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.
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.
Distribution. Angola, DR Congo, Malawi, Mozambique, Tanzania, and Zambia. Description. Head-body 46:5-47-8 cm (males), 44-45-5 cm (females), tail 40-43 cm (males), 38-39 cm (females), hindfoot 8:7-9-8 cm (males), 8-9 cm (females), ear 4-7-5-4 cm (males), 5-1-5-8 cm (females); weight 1-3-2 kg. The coat color is pale ocher, with brownish or grayish tones; melanistic individuals are quite common. The throat and chest are blackish, and the ventral pelage varies from creamy white to dirty white. The stripes and spots on the body vary from different hues of brown to black. The nuchal stripes run as two parallel lines from the nape to the shoulders, where they diverge and enlarge towards the elbows; they are not so conspicuously marked as in other genet species. Below them, a pair of thinner stripes and small spots are scattered on the shoulders and sides of the neck. A third pair of thinner, parallel stripes runs down the neck between the nuchal stripes, extending to about one fourth of the mid-dorsal line, where they vanish or diverge as the first row of flank spots. The black mid-dorsal line is continuous and is flanked on each side by four rows of oblong to squared spots, and by a few small-scattered spots below. There is a dorsal erectile crest. The face has a dark mask and a pair of white sub-ocular spots. The tail has seven to nine black rings, alternating with pale rings; the intervening white spaces are pigmented with a brownish tinge on the dorsal midline. The width of the pale rings relative to the dark rings in the middle of the tail is 50-75%; the tip of the tail is dark. The hindlimbs and forelimbs are black; there are white hairs on the metacarpals and metatarsals. [he posterior parts of the feet are dark. There are two pairs of teats. The posterior chamber of the auditory bulla is not ventrally inflated and has a continuous curve line on the external side. The ratio between the inter-orbital constriction and frontal width is 1-00 + 0-12. Dental formula: 13/3, C1/1,P 4/4, M 2/2 = 40. in Viverridae
Distribution. Angola, DR Congo, Malawi, Mozambique, Tanzania, and Zambia. Description. Head-body 46:5-47-8 cm (males), 44-45-5 cm (females), tail 40-43 cm (males), 38-39 cm (females), hindfoot 8:7-9-8 cm (males), 8-9 cm (females), ear 4-7-5-4 cm (males), 5-1-5-8 cm (females); weight 1-3-2 kg. The coat color is pale ocher, with brownish or grayish tones; melanistic individuals are quite common. The throat and chest are blackish, and the ventral pelage varies from creamy white to dirty white. The stripes and spots on the body vary from different hues of brown to black. The nuchal stripes run as two parallel lines from the nape to the shoulders, where they diverge and enlarge towards the elbows; they are not so conspicuously marked as in other genet species. Below them, a pair of thinner stripes and small spots are scattered on the shoulders and sides of the neck. A third pair of thinner, parallel stripes runs down the neck between the nuchal stripes, extending to about one fourth of the mid-dorsal line, where they vanish or diverge as the first row of flank spots. The black mid-dorsal line is continuous and is flanked on each side by four rows of oblong to squared spots, and by a few small-scattered spots below. There is a dorsal erectile crest. The face has a dark mask and a pair of white sub-ocular spots. The tail has seven to nine black rings, alternating with pale rings; the intervening white spaces are pigmented with a brownish tinge on the dorsal midline. The width of the pale rings relative to the dark rings in the middle of the tail is 50-75%; the tip of the tail is dark. The hindlimbs and forelimbs are black; there are white hairs on the metacarpals and metatarsals. [he posterior parts of the feet are dark. There are two pairs of teats. The posterior chamber of the auditory bulla is not ventrally inflated and has a continuous curve line on the external side. The ratio between the inter-orbital constriction and frontal width is 1-00 + 0-12. Dental formula: 13/3, C1/1,P 4/4, M 2/2 = 40.
Influence of voltine ecotype and geographic distance on genetic and haplotype variation in the Asian corn borer
<p>Diapause is an adaptive dormancy strategy by which arthropods endure extended periods of adverse climatic conditions. Seasonal variation in larval diapause initiation and duration in the Asian corn borer, <i>Ostrinia furnacalis</i>, influences adult mating generation number (voltinism) across local environmental conditions. Degree of mating period overlap between sympatric voltinism ecotypes influence hybridization level, but impact on <i>O. furnacalis</i> population genetic structure and evolution of divergent adaptive phenotypes remains uncertain. Genetic differentiation was estimated between voltinism ecotypes collected from 8 locations in Jilin Province, China [3 single generation (univoltine), 3 two generation (bivoltine), and 2 sympatric locations] in 2014. Bayesian and phylogenetic clustering partitioned mitochondrial cytochrome <i>c</i> oxidase subunit I (COI) haplotypes mostly into groups corresponding to historically uni- or bivoltine population origins, whereas samples from sympatric locations were interspersed between voltinism-specific clusters. Additionally, analyses of single nucleotide polymorphism (SNP) genotype data implicate voltinism, as opposed to geographic distance, as a factor contributing to differentiation among sample site. Temporal analysis of SNP genotypes from a sympatric location showed significant variation between adult moths collected within non-overlapping periods corresponding to bivoltine and univoltine flights. Regardless, only 11 of 257 SNP loci were predicted to be under selection, suggesting population genetic homogenization except at loci in proximity to factors responsible for locally adaptive or voltinism-specific traits. These findings provide evidence that divergent voltinism ecotype-specific traits and mitochondrial haplotypes may be maintained in allopatric as well as sympatric areas despite relatively high rates of nuclear gene flow.</p>
Distribution. SW Arabian Peninsula in SW Saudi Arabia and W Yemen and E Africa in Ethiopia, E South Sudan, Somalia, and Kenya. This distribution is temporary although and pending of genetic studies including a complete representation of the species in the analysis. in Miniopteridae
Distribution. SW Arabian Peninsula in SW Saudi Arabia and W Yemen and E Africa in Ethiopia, E South Sudan, Somalia, and Kenya. This distribution is temporary although and pending of genetic studies including a complete representation of the species in the analysis.
FIGURE 4 in Genetic investigation of three type specimens of Osmundea (Rhodomelaceae, Rhodophyta) from the Gulf of California, Mexico and California, USA
FIGURE 4. RaxML phylogram of fifteen Osmundea specimens sequenced in this study based on the rbcL gene sequences under the GTR + gamma model. Bootstrap values and Bayesian posterior probabilities are shown along the branches. Fully supported branches (bootstrap 100% and 1.0 Bayesian posterior probabilities) are indicated with an *.
FIGURE 2 in Genetic investigation of three type specimens of Osmundea (Rhodomelaceae, Rhodophyta) from the Gulf of California, Mexico and California, USA
FIGURE 2. Isotype specimen of Laurencia sinicola, UC 2041541, collected by Marchant and analyzed in this study. Bar = 3 cm.
Figure 1 in Effects of islanding on the genetics of Niviventer confucianus (Mamalia: Rodentia: Muridae) populations in the Thousand Island Lake region
Figure 1. Distribution of 13 islands and three peninsulas in the study. There are 16 populations in total. We collected samples from 5 to 10 points randomly on each island. Here, we have not shown the collection points in Figure 1 because of the different sizes of islands (i.e. collection points cannot be plotted clearly enough on small islands in Figure 1).
Figure 2 in Effects of islanding on the genetics of Niviventer confucianus (Mamalia: Rodentia: Muridae) populations in the Thousand Island Lake region
Figure 2. Bayesian clustering assignment of individual Niviventer confucianus to three clusters based on nuclear (microsatellite) genetic data. Each vertical column represents one individual, with the length of coloured segments proportional to the assignment strength of that individual to each of the three clusters. Most individuals of populations CS, G, D, DM, LW, L and TS are assigned to Cluster 1 (light grey); most individuals of populations Q, Y, JS and ZD are assigned to Cluster 2 (grey); and most individuals of populations WS, WT, ZD and CF are assigned to Cluster 3 (dark). Combined with the island distribution (Figure 1), a reasonable dispersion history of populations could be postulated: population L and TS might be the dispersion centre of Cluster 1, population Y might be the dispersion centre of Cluster 2, and population WT might be the dispersion centre of Cluster 3. Populations in Clusters 1 and 2 are more closely related based on the value of allele frequency divergence (0.0145).
Figure 1 in Morphometrics confirm taxonomic deflation in dwarf lemurs (Primates: Cheirogaleidae), as suggested by genetics
Figure 1. Sampling localities. Sampling sites of both the field samples and the museum specimens included in the analyses of this study are marked with circles. The colours indicate that individuals found at the respective site were classified as Cheirogaleus medius (yellow), Cheirogaleus major (red), and Cheirogaleus crossleyi (blue), or could not be clearly classified (white) by the analyses presented in this study. The Sambava locality is marked by two circles, as two different species were collected at this site. The asterisks denote sites that were newly sampled for this study.
Microsatellite markers for assessing genetic diversity and kinship relationships in one of the largest South American fur seal (Arctocephalus australis) populations of the Pacific Ocean
<p class="CuerpoAA">The genetic diversity of a population is the foundation of its adaptability to environmental challenges. The South American fur seal is a widely distributed pinniped in the south cone of South America. However, a large gap in the Pacific coast separates two distinct evolutionary units for the species: the Peruvian and the Southern Pacific/Atlantic populations. Throughout the Pacific, one of the main breeding colonies is located in Guafo Island, in the southern Chilean Patagonia. As the closest reproductive population to the isolated Peruvian group, Guafo's colony may potentially facilitate gene flow, contribute with new alleles and increase genetic variability to Peruvian populations', connecting the entire Pacific's distribution of the species. In this study, Guafo's Island South American fur seal population was characterized by the identification and genotyping of species-specific microsatellite markers. As a result, we confirm that Guafo's colony is a diverse group with mild evidence of genetic structure. Although a couple of family groups among seasons were observed, results indicate that half-siblings are rare and suggest that polygyny in this species is more relaxed than previously thought. Additionally, three full-sibling pairs were genetically identified within the 2017 season, which is the first genetic support that describes the presence of twins for the species. These attributes suggest that the colony at Guafo is a panmictic large group, and could serve as a potential genetic source for other isolated populations.</p>
Genetic structure, phylogeography, adaptive variation and speciation in the tropical tree genus Symphonia
<p>S9.2.1. SNP genotypes of <em>Symphonia globulifera</em> samples generated by Genotyping-by-sequencing</p> <p>S9.4.2. SNP genotypes of <em>Symphonia globulifer</em>a and Malagasy <em>Symphonia </em>samples generated by Sequenom technology</p> <p> </p>
SSR and cpDNA marker dataset genetic integrity of M.sylvestris in Saxony, Germany
<p><i>Malus sylvestris</i> (Mill.) is the only indigenous wild apple species in Central Europe. Agriculture, forestry and urbanization increasingly endanger <i>Malus sylvestris </i>natural habitats. In addition, the risks of cross-hybridization associated with increase in the cultivation of the domesticated apple <i>Malus ×domestica</i> (Borkh.), threatens the genetic integrity of <i>M. sylvestris</i>.</p> <p>The present study investigated the number of hybrids, genetic diversity and genetic structure of 292 putative <i>M. sylvestris</i> that originate from five different natural <i>M. sylvestris</i> populations in Saxony, Germany. All samples were genetically analyzed using nine nuclear microsatellite markers (ncSSR) and four maternally inherited chloroplast markers (cpDNA) along with 56 apple cultivars commonly cultivated in Saxony.</p> <p>Eighty-seven percent of the wild apple accessions were identified as pure <i>M. sylvestris</i>. The cpDNA analysis showed six private haplotypes for <i>M. sylvestris,</i> whereas three haplotypes were present in <i>M. sylvestris </i>and<i> M. ×domestica.</i> The analysis of molecular variance (AMOVA) resulted in a moderate (ncSSR) and great (cpDNA) variation among pure <i>M. sylvestris</i> and <i>M. ×domestica </i>individuals indicating a low gene flow between both species. The genetic diversity within the pure <i>M. sylvestris</i> populations was high with a weak genetic structure between the <i>M. sylvestris</i> populations indicating an unrestricted genetic exchange between these <i>M. sylvestris</i> populations.</p> <p>The clear distinguishing of <i>M. sylvestris</i> and <i>M. ×domestica</i> confirms our expectation of the existence of pure <i>M. sylvestris </i>accessions<i> </i>in this area and supports the argument for the implementation of preservation measures to protect the <i>M. sylvestris </i>populations in<i> </i>Saxony. </p>
Phenotypic plasticity and genetic diversity elucidate rarity and vulnerability of an endangered riparian plant
<p><span>Anthropogenic environmental change threatens many species and can be especially challenging for rare species given their potentially limited capacity for migration and adaptation relative to more common species.</span> The ability to acclimate via phenotypic plasticity could provide an important path to persistence, especially for rare species. We investigated the responses of an endangered plant species endemic to a highly dynamic riparian habitat in southeastern Tennessee, USA, and its most widespread congener to environmental change to elucidate their current statuses and future vulnerability. Specifically, we compared the population- and species-level plasticity of rare <i>Pityopsis ruthii</i> and common <i>P. graminifolia </i>to contrasting light, temperature, and water conditions in a growth chamber experiment to evaluate their potential to acclimate to environmental change. Contrary to our expectations, <i>P. ruthii</i> had greater phenotypic plasticity than its common congener in response to both altered light and water availability. But this plasticity was not associated with increased fitness, suggesting that it was not adaptive. Concurrently, we genotyped these individuals at nine putatively neutral microsatellite loci to contrast genetic diversity across the range of each species. As expected, <i>P. ruthii </i>exhibited reduced genetic diversity relative to its more common congener. Overall, our findings accord with the narrow range and current habitat specificity of <i>P. ruthii</i>, especially its tolerance of highly variable water, and highlight its potential vulnerability to future environmental change.</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.