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2,445 results for “Genetics: population”
Dataset 2 for Large‐ and small‐scale geographic structures affecting genetic patterns across populations of an Alpine butterfly
<p>Understanding factors influencing patterns of genetic diversity and the population genetic structure of species is of particular importance in the current era of global climate change and habitat loss. These factors include the evolutionary history of a species as well as heterogeneity in the environment it occupies, which in turn can change across time. Most studies investigating spatio-temporal genetic patterns have focused on patterns across wide geographical areas rather than local variation, but the latter can nevertheless be important particularly in topographically complex areas. Here we consider these issues in the Sooty Copper butterfly (<i>Lycaena tityrus</i>) from the European Alps, using genome-wide SNPs identified through RADseq. We found strong genetic differentiation within the Alps with four genetic clusters, indicating western, central, and eastern refuges, and a strong reduction of genetic diversity from west to east. This reduction in diversity may suggest that the southwestern refuge was the largest one in comparison to other refuges. Also, the high genetic diversity in the West may result from (1) admixture of different western refuges, (2) more recent demographic changes, or (3) introgression of lowland <i>L. tityrus</i> populations. At small spatial scales, populations were structured by several landscape features and especially by high mountain ridges and large river valleys. We detected 36 outlier loci likely under altitudinal selection, including several loci related to membranes and cellular processes. We suggest that efforts to preserve alpine <i>L. tityrus </i>should focus on the genetically diverse populations in the western Alps, and that the dolomite populations should be treated as genetically distinct management units, since they appear to be currently more threatened than others. This study demonstrates the usefulness of SNP-based approaches for understanding patterns of genetic diversity, gene flow and selection in a region that is expected to be particularly vulnerable to climate change.</p>
Data - Attack of the clones: population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose
<p><em>Colletotrichum lupini</em>, causing lupin anthracnose, is one of the worst pathogens to lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the genetic diversity, evolutionary dynamics and molecular basis of host-speciation of this notorious lupin pathogen. A collection of globally representative <em>C. lupini </em>isolates was genotyped through triple digest restriction-site associated DNA sequencing (3D-RADseq), resulting in a dataset of unparalleled resolution. Phylogenetic and structural analysis could distinguish four (I – IV) independent lineages. The strong population structure, low recombination rate and slow linkage decay strongly indicate that <em>C. lupini</em> reproduces clonally. Different morphologies and virulence patterns on white and Andean lupin were observed between and within clonal lineages. Lineage II isolates were shown to have a mini chromosome which was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this mini-chromosome could indicate a function related to virulence or host-speciation. All four lineages were present in the South American Andes region, which is concluded to be the center of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seed-borne pathogen, <em>C. lupini</em> has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.</p>
Country‐wide genetic monitoring over 21 years reveals lag in genetic recovery despite spatial connectivity in an expanding carnivore (Eurasian otter, Lutra lutra) population
<p>Numerous terrestrial mammal species have experienced extensive population declines during past centuries, due largely to anthropogenic pressures. For some species, including the Eurasian otter (<em>Lutra lutra</em>), environmental and legal protection has more recently led to population growth and recolonisation of parts of their historic ranges. While heralded as conservation successes, only a few such recoveries have been examined from a genetic perspective, i.e. whether genetic variability and connectivity have been restored. We here use large-scale and long-term genetic monitoring data from UK otters, whose population underwent a well-documented population decline between the 1950s to 1970s, to explore the dynamics of a population re-expansion over a 21-year period. We genotyped otters from across Wales and England at five time points between 1994 and 2014 using 15 microsatellite loci. We used this combination of long-term temporal and large-scale spatial sampling to evaluate 3 hypotheses relating to genetic recovery; that (i) gene flow between sub-populations would increase over time, (ii) genetic diversity of previously isolated populations would increase, and that (iii) genetic structuring would weaken over time. Although we found an increase in inter-regional gene flow and admixture levels among subpopulations, there was no significant temporal change in either heterozygosity or allelic richness. Genetic structuring among the main sub-populations hence remained strong and showed a clear historical continuity. These findings highlight an underappreciated aspect of population recovery of endangered species, that genetic recovery may often lag behind the processes of spatial and demographic recovery. In other words, the restoration of physical connectivity of populations does not necessarily lead to genetic connectivity. Our findings emphasise the need for genetic data as an integral part of conservation monitoring, to enable the potential vulnerability of populations to be evaluated.</p>
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>
Eastern-flowering Dogwood population genetics and ecological/environmental data
<p class="MsoNormal">Forest fragmentation and introduced pathogens are negatively impacting trees and forests globally, including the Carolinian forest of southern Ontario, Canada. Multiple species-at-risk live in this threatened but biodiverse forest, including the endangered <em>Cornus florida</em> (Eastern flowering dogwood), which is now limited to fragmented woodlots, and has been decimated by the introduced fungal pathogen <em>Discula destructiva</em> (dogwood anthracnose). Ongoing management of <em>C. florida</em> in Canada is challenged by multiple knowledge gaps, two of which we aimed to address in this study. We first evaluated the association between anthracnose disease prevalence and a suite of ecological and environmental variables across 21 sites. Across our sites, larger trees tended to have the highest disease incidence, and trees on shallow slopes had the most crown dieback. We then quantified genetic diversity and gene flow and found that genetic structure has not been substantially impacted by habitat fragmentation, although dispersal typically covers short distances. However, genetic diversity is relatively low in smaller populations, and in younger trees. Localized dispersal and eroding genetic diversity may limit future adaptation and hence exacerbate population declines. We recommend that managers prioritize plantings in small populations, avoid shallow slopes, and track younger trees to evaluate age-related mortality.</p>
Genetic population dynamics of the critically endangered scalloped hammerhead shark (Sphyrna lewini) in the Eastern Tropical Pacific
<p><span>The scalloped hammerhead shark, </span><span><em>Sphyrna</em> <em>lewini</em></span><span>, is a Critically Endangered, migratory species known for its tendency to form iconic and visually spectacular large aggregations. Herein, we investigated the population genetic dynamics of the scalloped hammerhead across much of its distribution in the Eastern Tropical Pacific (ETP), ranging from Costa Rica to Ecuador, focusing on young‐of‐the‐year animals from putative coastal nursery areas and adult females from seasonal aggregations that form in the northern Galápagos Islands. Nuclear microsatellites and partial mitochondrial control region sequences showed little evidence of population structure, suggesting that scalloped hammerheads in this ETP region comprise a single genetic stock. Galápagos aggregations of adults were not comprised of related individuals, suggesting that kinship does not play a role in the formation of the repeated, annual gatherings at these remote offshore locations. Despite high levels of fisheries exploitation of this species in the ETP, the adult scalloped hammerheads here showed greater genetic diversity compared with adult conspecifics from other parts of the species' global distribution. A phylogeographic analysis of available, globally sourced, mitochondrial control region sequence data (</span><span>n</span><span> = 1,818 sequences) revealed that scalloped hammerheads comprise three distinct matrilines corresponding to the three major world ocean basins, highlighting the need for conservation of these evolutionarily unique lineages. This study provides the first view of the genetic properties of a scalloped hammerhead aggregation, and the largest sample size‐based investigation of population structure and phylogeography of this species in the ETP to date.</span></p>
Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
<p><span>Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (<em>Galemys</em> <em>pyrenaicus</em>). For this, we used the ddRADseq technique, which generated 1,421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.</span></p>
Data for: Species identification and population genetics of the Antarctic fish genera Lepidonotothen and Nototheniops (Perciformes, Notothenioidei)
<p>Accurate species identification is essential to assess biodiversity and species richness in ecosystems threatened by rapid and recent environmental changes, such as warming in most Antarctic waters. The <em>Lepidonotothen</em> species complex comprises demersal notothenioid fishes which inhabit the shelf areas of the Antarctic Peninsula, the Scotia Arc and sub-Antarctic islands with a circum-Antarctic distribution. Species determination in this group has often been problematic. In particular, whether <em>Lepidonotothen squamifrons</em> and <em>Lepidonotothen kempi </em>are valid as separate species has been questioned. In this study, we analysed the genetic variation among four nominal southern polar species within this complex (<em>L. kempi</em>, <em>L. squamifrons</em>, <em>Nototheniops larseni</em>, <em>Nototheniops nudifrons</em>) by means of three different markers (ND2 and tRNA mitochondrial genes and a panel of 16 nuclear microsatellites). We tested whether individuals morphologically assigned to <em>L. kempi</em> showed genetic separation from <em>L. squamifrons</em>. Our analyses indicated a lack of differentiation between <em>L. kempi</em> and <em>L. squamifrons</em>. However, a genetically distinct population was found for <em>L. squamifrons</em> at the Shag Rocks islands near South Georgia. Antarctic and sub-Antarctic islands are known to be home to many cryptic species and further studies will elucidate if the genetically differentiated population we found potentially originated from this context and can be considered as an incipient species. Our analysis contributes to further characterize the species composition of the most abundant fish suborder in the Southern Ocean, which is amongst the regions most threatened by climate change.</p>
Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population
<p>The population numbers of taiga bean goose (<i>Anser fabalis fabalis</i>) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (<i>ɸ</i><sub>ST</sub> = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise <i>F</i><sub>ST</sub>-values 0.002- 0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average <i>H</i><sub>E</sub> = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (<i>F</i><sub>IS</sub> = 0.05-0.10) and high relatedness values (<i>r </i>= 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (<i>A. brachyrhynchus</i>). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.</p>
Data from: Population connectivity patterns of genetic diversity, immune responses and exposure to infectious pneumonia in a metapopulation of desert bighorn sheep
<p>Habitat fragmentation is an important driver of biodiversity loss and can be remediated through management actions aimed at maintenance of natural connectivity in metapopulations. Connectivity may protect populations from infectious diseases by preserving immunogenetic diversity and disease resistance. However, connectivity could exacerbate the risk of infectious disease spread across vulnerable populations.</p> <p>We tracked the spread of a novel strain of <em>Mycoplasma ovipneumoniae</em> in a metapopulation of desert bighorn sheep (<em>Ovis canadensis nelsoni</em>) in the Mojave desert to investigate how variation in connectivity among populations influenced disease outcomes.</p> <p><em>M. ovipneumoniae</em> was detected throughout the metapopulation, indicating that the relative isolation of many of these populations did not protect them from pathogen invasion. However, we show that connectivity among bighorn sheep populations was correlated with higher immunogenetic diversity, a protective immune response and lower disease prevalence. Variation in protective immunity predicted infection risk in individual bighorn sheep and was associated with heterozygosity at genetic loci linked to adaptive and innate immune signalling.</p> <p>Together, these findings may indicate that population connectivity maintains immunogenetic diversity in bighorn sheep populations in this system and has direct effects on immune responses in individual bighorn sheep and their susceptibility to infection by a deadly pathogen.</p> <p>Our study suggests that the genetic benefits of population connectivity could outweigh the risk of infectious disease spread and supports conservation management that maintains natural connectivity in metapopulations.</p>
The population genetics of speciation by cascade reinforcement
<p>Species interactions drive diverse evolutionary outcomes. Speciation by cascade reinforcement represents one example of how species interactions can contribute to the proliferation of species. This process occurs when the divergence of mating traits in response to selection against interspecific hybridization incidentally leads to reproductive isolation among populations of the same species. Here, we investigated the population genetic outcomes of cascade reinforcement in North American chorus frogs (Hylidae: <em>Pseudacris</em>). Specifically, we estimated the frequency of hybridization among three taxa, assessed genetic structure within the focal species, <em>P. feriarum</em>, and ascertained the directionality of gene flow within <em>P. feriarum</em> across replicated contact zones via coalescent modeling. Through field observations and preliminary experimental crosses, we assessed whether hybridization is possible under natural and laboratory conditions. We found that hybridization occurs among <em>P. feriarum</em> and two conspecifics at a low rate in multiple contact zones and that gene flow within the former species is unidirectional from allopatry into sympatry with these other species in three of four contact zones studied. We found evidence of substantial genetic structuring within <em>P. feriarum</em> including a divergent western allopatric cluster, a behaviorally-distinct sympatric South Carolina cluster, and several genetically-overlapping clusters from the remainder of the distribution. Furthermore, we found sub-structuring between reinforced and non-reinforced populations in the two most intensely-sampled contact zones. Our literature review indicated that <em>P. feriarum</em> hybridizes with at least five heterospecifics at the periphery of its range providing a mechanism for further intraspecific diversification. This work strengthens the evidence for cascade reinforcement in this clade, revealing the geographic and genetic landscape upon which this process can contribute to the proliferation of species. </p>
The timings of host diapause and epidemic progression mediate host genetic diversity and future epidemic size in Daphnia-parasite populations
<p>Epidemics commonly exert parasite-mediated selection and cause declines in host population genetic diversity. This could lead to evolution of resistance in the long-term and smaller subsequent epidemics. Alternatively, the loss of genetic diversity could increase host vulnerability to future disease spread and larger future epidemics. Matters are made more complex by the fact that a great many host organisms produce diapausing life stages in response to environmental change (often as a result of sexual reproduction) e.g., plant seeds and invertebrate resting eggs. These diapausing stages can disrupt the relationship between past epidemics, host genetic diversity and future epidemics because they allow host dispersal through time. Specifically, temporally dispersing hosts avoid infection and thus selection from contemporary parasites, and also archive genetic variation for the future. We studied 80 epidemics in 20 semi-natural populations of the temporally dispersing crustacean Daphnia magna and its sterilising bacterial parasite Pasteuria ramosa, and half of these populations experienced a simulated environmental disturbance treatment. We found that early initiation of diapause relative to the timing of the epidemic led to greater host genetic diversity and reduced epidemic size in the subsequent year, but this was unaffected by environmental disturbance.</p>
Data for: Perishing rich, expanding poor: Demography and population genetic patterns in two congeneric butterflies
<p><span>In human-altered landscapes, specialist butterflies typically form spatially restricted populations, genetically differentiated due to dispersal restrictions. Generalists, in contrast, display minimum differentiation but high genetic diversity. While local-level actions suffice to conserve specialists and landscape-level actions are necessary for generalists, minimum information exists regarding conservation of species with intermediate features. We targeted two congeneric butterflies, the recently re-expanding <em>Argynnis adippe</em> and the strongly declining <em>A. niobe</em>, co-occurring in the pastoral landscape of the Carpathian Mountains, Czech Republic. We integrated species distribution models, mark-recapture, and microsatellite analysis to compare their habitat requirements, adult demography, dispersal, and genetic patterns, and expanded the genetic analysis across the Carpathian Arc and beyond to delimit spatial conservation units. In two mountain valleys, both species formed interconnected populations numbering thousands of individuals. Mobility patterns suggested the populations' interconnection across the Czech Carpathians. Genetic diversity was extremely poor in the non-threatened <em>A. adippe</em> and moderate in the declining <em>A. niobe</em>. No population differentiation was detected within the Czech Carpathians <span>(<span>ca 1500 km<sup>2</sup></span>). </span>Low genetic diversity and no differentiation was preserved in <em>A. adippe</em> across East Central Europe, whereas in <em>A. niobe</em>, populations from Serbia were differentiated from the Carpathian Arc + Alps. The high adult mobility linked to low differentiation probably reflect the distribution of larval resources, historically widespread but sparse and currently declining for <em>A. niobe</em> (grazing-disturbed grounds), while currently increasing for <em>A. adippe</em> (abandonment scrub, disturbed woodlands). Units as large as entire mountain systems define population boundaries, and hence conservation management units, for both species. </span></p>
Code for the population genetic models of the evolution of preference strength
<p>Sexual selection has a rich history of mathematical models that consider why preferences favor one trait phenotype over another (for population genetic models) or what specific trait value is preferred (for quantitative genetic models). Less common is exploration of the evolution of choosiness or preference strength: that is, by how much a trait is preferred. We examine both population and quantitative genetic models of the evolution of preferences, specifically developing "baseline models" of the evolution of preference strength during the Fisher process. Using a population genetic approach based on the classic model of Kirkpatrick (1982), we find selection for stronger and stronger preferences when trait variation is maintained by mutation. However, this force is quite weak and likely to be swamped by drift in moderately-sized populations. In a quantitative genetic model based on Lande (1981), unimodal preferences will generally not evolve to be increasingly strong without bounds when male traits are under stabilizing viability selection, but evolve to extreme values when viability selection is directional. Our results highlight that different shapes of fitness and preference functions lead to qualitatively different trajectories for preference strength evolution ranging from no evolution to extreme evolution of preference strength.</p>
Data from: Effective population size in a partially clonal plant is not predicted by the number of genetic individuals
<p>Estimating effective population size (<em>N</em><sub>e</sub>) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of <em>N</em><sub>e</sub> in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to <em>N</em><sub>e</sub>.</p> <p>In this study, we analysed two populations of the orchid <em>Cypripedium calceolus</em> to understand how the rate of clonal vs. sexual reproduction affected <em>N</em><sub>e</sub>. We genotyped >1,000 ramets at microsatellite and SNP loci, and estimated contemporary <em>N</em><sub>e</sub> with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower <em>N</em><sub>e</sub>. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic datasets on <em>N</em><sub>e</sub> confidence intervals. The magnitude of <em>N</em><sub>e</sub>/<em>N</em><sub>ramets </sub>and <em>N</em><sub>e</sub>/<em>N</em><sub>genets</sub> ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that <em>N</em><sub>e</sub> in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence <em>N</em><sub>e</sub>. This is especially relevant in species of conservation concern, in which population declines may not be detected by only ascertaining the number of genets.</p>
Genetic diversity and population structure from a Peruvian nucleus cattle herd using SNP data
<p>New-generation sequencing technologies, among them SNP chips for massive genotyping, have proven to be useful for the effective management of genetic resources. Also, developing nucleus herds is an effective method for genetic improvement work. To date, molecular studies in Peruvian cattle are still in their infancy. To close this gap, we here employed two SNP panels (BovineHD and Bovine100K) to determine for the first time the Peruvian nucleus herd's genetic diversity and population structure that belong to INIA. This nucleus comprises Brahman (N=16), Braunvieh (N=14), Gyr (N=11), and Fleckvieh (N=22) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N=12), were incorporated into the study. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 69.37% in Gyr to 80.81% in Braunvieh. Also, Braunvieh possessed the highest observed heterozygosity (0.53±0.17), while Brahman possessed the lowest (0.44±0.10), indicating that the former is more diverse compared to the other cattle breed groups. According to the molecular variance analysis, 83.92% of the variance occurs within individuals, whereas 16.0% occurs between populations. The pairwise FST estimates between breeds showed values that ranged from 0.054 (Braunvieh vs AFB) to 0.266 (Brahman vs AFB). Pairwise Reynold's distance showed a pattern similar to the one obtained with the FST statistics, with values ranging from 0.058 to 0.309. A dendrogram was constructed using the Neighbor-Joining clustering algorithm, and similar to the principal coordinate analysis, three groups were identified. Results showed a clear separation between <em>Bos</em> <em>indicus</em> (Brahman and Gyr) and <em>B</em>. <em>taurus</em> breeds (Braunvieh and Fleckvieh). For Fleckvieh and Braunvieh, there were two subgroups each one of them grouping with the AFB group. Similar results were obtained with ADMIXTURE analysis with K= 3 as the most optimal number for the inferred genetic structure of the populations. The results from the current study would contribute to the appropriate management avoiding loss of genetic variability in these breeds and to future improvements for this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.</p>
Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (Lupinus mutabilis), with High Quality SNPs
<p><em>Lupinus mutabilis</em> Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (F<sub>st</sub>) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative F<sub>is</sub> for both populations, demonstrating that, like other <em>Lupinus</em> species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.</p>
Data from: Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in sage grouse Centrocercus urophasianus
<p><span>Sex ratio, and the extent to which it varies over time, is an important factor in the demography, management, and conservation of wildlife populations. We estimated pre-breeding sex ratio of greater sage-grouse (Centrocercus urophasianus) in a peripheral, geographically isolated population in northwestern Colorado during two consecutive winters using closed-population, robust-design, multi-state, genetic mark-recapture models in program MARK (White and Burnham 1999). This data release includes the data files (.inp format) used in those models, as described in Shyvers et al. 2023. The data include capture histories and auxiliary data for individual greater sage-grouse collected during two study seasons: Season 1 (winter 2012-2013) and Season 2 (winter 2013-2014) and are readable using program MARK or notepad. Each data row includes the unique bird identification number (GMR-ID); the bird's encounter history for n= sampling occasions coded as a static state (M = male, F = female); the group ID; and a region covariate (0 = North, 1 = South). The data were adapted from those originally developed for Shyvers et al. 2020 and applied using Closed Robust Design Multi-state (CRDMS) Huggins' p and c w/state probabilities in program MARK to obtain estimates of Omega, enabling estimation of sex ratio with associated confidence intervals (see Shyvers et al. 2023).</span></p> <p>References:</p> <p>Shyvers, J.E., Walker, B.L., Oyler-McCance, S.J., Fike, J.A. and Noon, B.R. 2023. Genetic mark-recapture analysis reveals large annual variation in pre-breeding sex ratio of greater sage-grouse. Wildlife Biology (https://doi.org/10.1002/wlb3.01085)</p> <p>Shyvers, J.E., Walker, B.L., Oyler‐McCance, S.J., Fike, J.A. and Noon, B.R., 2020. Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in Sage Grouse Centrocercus urophasianus. Ibis, 162(3), pp.749-765.</p> <p>White, G. C., and K. P. Burnham. 1999. Program Mark: survival estimation from populations of marked animals. – Bird Study 46:120–139.</p>
Genetic diversity and sperm characteristics are not associated in two bluethroat (Luscinia svecica) populations
<p>Individual heterozygosity may influence the expression of fitness-related traits, via genome-wide or local genetic effects. Earlier studies have shown negative relationships between heterozygosity and sperm variation, predominantly in captive, highly inbred populations. Little is known about the possible influence of variation in heterozygosity on sperm traits in wild, outbred populations. We studied two populations of the bluethroat, one from the widely distributed northern subspecies (<em>Luscinia</em>. <em>s</em>. <em>svecica</em>) and the other from the smaller, more patchily distributed subspecies breeding along the French coast of Brittany (<em>L. s. namnetum</em>). The two subspecies differed significantly in body size, plumage colour, sperm traits and the degree of genetic diversity. However, there was no evidence that sperm traits (total length and motility) were influenced by the degree of heterozygosity at the individual level. In contrast, we found that male body size was positively related to heterozygosity across both populations, indicating a possible relationship between overall genetic diversity and general vigour or ability to obtain food. We conclude that sperm traits are unrelated to levels of heterozygosity in the studied outbred and weakly genetically depauperate bluethroat populations.</p>
Figure 2 in Expanding Population Edge Craniometrics and Genetics Provide Insights into Dispersal of Commensal Rats through Nusa Tenggara, Indonesia
Figure 2. Sampling locations for skulls included in the craniometric analysis.
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Allen Brain Atlas
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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.
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