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324 results for “spatial genetics”
Data from: Fine-scale spatial genetic dynamics over the life-cycle of the tropical tree Prunus africana
Studying fine-scale spatial genetic patterns across life stages is a powerful approach to identify ecological processes acting within tree populations. We investigated spatial genetic dynamics across five life stages in the insect-pollinated and vertebrate-dispersed tropical tree Prunus africana in Kakamega Forest, Kenya. Using six highly polymorphic microsatellite loci, we assessed genetic diversity and spatial genetic structure (SGS) from seed rain and seedlings, and different sapling stages to adult trees. We found significant SGS in all stages, potentially caused by limited seed dispersal and high recruitment rates in areas with high light availability. SGS decreased from seed and early seedling stages to older juvenile stages. Interestingly, SGS was stronger in adults than in late juveniles. The initial decrease in SGS was probably driven by both random and non-random thinning of offspring clusters during recruitment. Intergenerational variation in SGS could have been driven by variation in gene flow processes, overlapping generations in the adult stage or local selection. Our study shows that complex sequential processes during recruitment contribute to SGS of tree populations.
Data from: Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual-based sampling scheme
Genetic data are increasingly used in landscape ecology for the indirect assessment of functional connectivity, i.e. the permeability of landscape to movements of organisms. Among available tools, matrix correlation analyses (e.g. Mantel tests or mixed models) are commonly used to test for the relationship between pairwise genetic distances and movement costs incurred by dispersing individuals. When organisms are spatially clustered, a population-based sampling scheme (PSS) is usually performed, so that a large number of genotypes can be used to compute pairwise genetic distances on the basis of allelic frequencies. Because of financial constraints, this kind of sampling scheme implies a drastic reduction in the number of sampled aggregates, thereby reducing sampling coverage at the landscape level. We used matrix correlation analyses on simulated and empirical genetic datasets to investigate the efficiency of an individual-based sampling scheme (ISS) in detecting isolation-by-distance and isolation-by-barrier patterns. Provided that pseudo-replication issues are taken into account (e.g. through restricted permutations in Mantel tests), we showed that the use of inter-individual measures of genotypic dissimilarity may efficiently replace inter-population measures of genetic differentiation: the sampling of only three or four individuals per aggregate may be sufficient to efficiently detect specific genetic patterns in most situations. The ISS proved to be a promising methodological alternative to the more conventional PSS, offering much flexibility in the spatial design of sampling schemes and ensuring an optimal representativeness of landscape heterogeneity in data, with few aggregates left unsampled. Each strategy offering specific advantages, a combined use of both sampling schemes is discussed.
Data from: Spatial and ecological population genetic structures within two island-endemic Aeonium species of different niche width
The Crassulacean genus Aeonium is a well-known example for plant species radiation on oceanic archipelagos. However, while allopatric speciation among islands is documented for this genus, the role of intra-island speciation due to population divergence by topographical isolation or ecological heterogeneity has not yet been addressed. The aim of this study was to investigate intraspecific genetic structures and to identify spatial and ecological drivers of genetic population differentiation on the island scale. We analyzed inter simple sequence repeat variation within two island-endemic Aeonium species of La Palma: one widespread generalist that covers a large variety of different habitat types (Ae. davidbramwellii) and one narrow ecological specialist (Ae. nobile), in order to assess evolutionary potentials on this island. Gene pool differentiation and genetic diversity patterns were associated with major landscape structures in both species, with phylogeographic implications. However, overall levels of genetic differentiation were low. For the generalist species, outlier loci detection and loci–environment correlation approaches indicated moderate signatures of divergent selection pressures linked to temperature and precipitation variables, while the specialist species missed such patterns. Our data point to incipient differentiation among populations, emphasizing that ecological heterogeneity and topographical structuring within the small scales of an island can foster evolutionary processes. Very likely, such processes have contributed to the radiation of Aeonium on the Canary Islands. There is also support for different evolutionary mechanisms between generalist and specialist species.
Data from: Estimating density for species conservation: comparing camera trap spatial count models to genetic spatial capture-recapture models
Density estimation is integral to the effective conservation and management of wildlife. Camera traps in conjunction with spatial capture-recapture (SCR) models have been used to accurately and precisely estimate densities of "marked" wildlife populations comprising identifiable individuals. The emergence of spatial count (SC) models holds promise for cost-effective density estimation of "unmarked" wildlife populations when individuals are not identifiable. We evaluated model agreement, precision, and survey costs, between i) a fully marked approach using SCR models fit using non-invasive genetic data, and ii) an unmarked approach using SC models fit using camera trap data, for a recovering population of the mesocarnivore fisher (Pekania pennanti). The SCR density estimates ranged from 2.95 to 3.42 (2.18–5.19 95% BCI) fishers 100 km−2. The SC density estimates were influenced by their priors, ranging from 0.95 (0.65–2.95 95% BCI) fishers 100 km−2 for the uninformative model to 3.60 (2.01–7.55 95% BCI) fishers 100 km−2 for the model informed by prior knowledge of a 16 km2 fisher home range. We caution against using strongly informative priors but instead recommend using a range of unweighted prior knowledge. Thin detection data was problematic for both SCR and SC models, potentially producing biased low estimates. The total cost of the genetic survey ($47 610) was two-thirds of the camera trap survey ($77 080), or comparable ($75 746) if genetic sampling effort was increased to include sex and trap-behaviour covariates in SCR models. Density estimation of unmarked populations continues to be a series of trade-offs but as methods improve and integrate, so will our estimates.
Data from: Wide variation in spatial genetic structure between natural populations of the European beech (Fagus sylvatica) and its implications for SGS comparability
Identification and quantification of spatial genetic structure (SGS) within populations remains a central element of understanding population structure at the local scale. Understanding such structure can inform on aspects of the species' biology, such as establishment patterns and gene dispersal distance, in addition to sampling design for genetic resource management and conservation. However, recent work has identified that variation in factors such as sampling methodology, population characteristics, and marker system can all lead to significant variation in SGS estimates. Consequently, the extent to which estimates of SGS can be relied upon to inform on the biology of a species or differentiate between experimental treatments is open to doubt. Following on from a recent report of unusually extensive SGS when assessed using amplified fragment length polymorphisms (AFLP) in the tree Fagus sylvatica, we explored whether this marker system led to similarly high estimates of SGS extent in other apparently similar populations of this species. In the three populations assessed, SGS extent was even stronger than this previously reported maximum, extending up to 360 m, an increase of up to 800% in comparison with the generally accepted maximum of 30 - 40 m based on the literature. Within this species, wide variation in SGS estimates exists, whether quantified as SGS intensity, extent, or the Sp parameter. Consequently, we argue that greater standardisation should be applied in sample design and SGS estimation and highlight five steps that can be taken to maximize the comparability between SGS estimates.
Data from: Low spatial genetic differentiation associated with rapid recolonization in the New Zealand fur seal Arctocephalus forsteri
Population declines resulting from anthropogenic activities are of major consequence for the long-term survival of species because the resulting loss of genetic diversity can lead to extinction via the effects of inbreeding depression, fixation of deleterious mutations, and loss of adaptive potential. Otariid pinnipeds have been exploited commercially to near extinction with some species showing higher demographic resilience and recolonization potential than others. The New Zealand fur seal (NZFS) was heavily impacted by commercial sealing between the late 18th and early 19th centuries, but has recolonized its former range in southern Australia. The species has also recolonized its former range in New Zealand, yet little is known about the pattern of recolonization. Here, we first used 11 microsatellite markers (n = 383) to investigate the contemporary population structure and dispersal patterns in the NZFS (Arctocephalus forsteri). Secondly, we model postsealing recolonization with 1 additional mtDNA cytochrome b (n = 261) marker. Our data identified 3 genetic clusters: an Australian, a subantarctic, and a New Zealand one, with a weak and probably transient subdivision within the latter cluster. Demographic history scenarios supported a recolonization of the New Zealand coastline from remote west coast colonies, which is consistent with contemporary gene flow and with the species' high resilience. The present data suggest the management of distinct genetic units in the North and South of New Zealand along a genetic gradient. Assignment of individuals to their colony of origin was limited (32%) with the present data indicating the current microsatellite markers are unlikely sufficient to assign fisheries bycatch of NZFSs to colonies.
Data from: Spatial population genetic structure of a bacterial parasite in close coevolution with its host
Knowledge of a species' population genetic structure can provide insight into fundamental ecological and evolutionary processes including gene flow, genetic drift, and adaptive evolution. Such inference is of particular importance for parasites, as an understanding of their population structure can illuminate epidemiological and coevolutionary dynamics. Here we describe the population genetic structure of the bacterium Pasteuria ramosa, a parasite that infects planktonic crustaceans of the genus Daphnia. This system has become a model for investigations of host-parasite interactions and represents an example of coevolution via negative frequency-dependent selection (a.k.a. 'Red Queen' dynamics). To sample P. ramosa, we experimentally infected a panel of Daphnia hosts with natural spore banks from the sediments of 25 ponds throughout much of the species range in Europe and Western Asia. Using 12 polymorphic VNTR loci, we identified substantial genetic diversity both within and among localities that was structured geographically among ponds. Genetic diversity was also structured among host genotypes within ponds, though this pattern varied by locality, with P. ramosa at some localities partitioned into distinct host-specific lineages, and other localities where recombination had shuffled genetic variation among different infection phenotypes. Across the sample range, there was a pattern of isolation-by-distance, and principal components analysis coupled with Procrustes rotation identified congruence between patterns of genetic variation and geography. Our findings support the hypothesis that Pasteuria is an endemic parasite coevolving closely with its host. These results provide important context for previous studies of this model system and inform hypotheses for future research.
Data from: The effect of sex-biased dispersal on opposite-sexed spatial genetic structure and inbreeding risk
Natal sex-biased dispersal has long been thought to reduce the risk of inbreeding by spatially separating opposite-sexed kin. Yet, comprehensive and quantitative evaluations of this hypothesis are lacking. In this study, we quantified the effectiveness of sex-biased dispersal as an inbreeding avoidance strategy by combining spatially explicit simulations and empirical data. We quantified the extent of kin clustering by measuring the degree of spatial autocorrelation among opposite-sexed individuals (FM structure). This allowed us to systematically explore how the extent of sex-biased dispersal, generational overlap, and mate searching distance, influenced both kin clustering, and the resulting inbreeding in the absence of complementary inbreeding avoidance strategies. Simulations revealed that when sex-biased dispersal was limited, positive FM genetic structure developed quickly and increased as the mate searching distance decreased or as generational overlap increased. Interestingly, complete long-range sex-biased dispersal did not prevent the development of FM genetic structure when generations overlapped. We found a very strong correlation between FM genetic structure and both FIS under random mating, and pedigree-based measures of inbreeding. Thus, we show that the detection of FM genetic structure can be a strong indicator of inbreeding risk. Empirical data for two species with different life history strategies yielded patterns congruent with our simulations. Our study illustrates a new application of spatial genetic autocorrelation analysis that offers a framework for quantifying the risk of inbreeding that is easily extendable to other species. Furthermore, our findings provide other researchers with a context for interpreting observed patterns of opposite-sexed spatial genetic structure.
Data from: Effects of fire regime on the population genetics of natural pine stands, in Genetic structure of forest trees in biodiversity hotspots at different spatial scales (Ph.D. thesis).
The recurrence of wildfires is predicted to increase worldwide due to climate change, resulting in severe impacts on biodiversity and ecosystem functioning. We used simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers to examine the effects of fire regime on genetic diversity, demographic history and fine-scale spatial genetic structure (SGS) of Pinus pinaster and P. halepensis, two conifers with similar adaptations to fire in the eastern Iberian Peninsula. Stands growing under high (HiFi) or low (LoFi) frequency of crown fires had similar levels of genetic diversity and similar demographic history, with bottlenecks detected in all stands in both species. HiFi populations were not genetically depleted, suggesting that adaptations such as a diverse canopy seed bank due to serotinous cones, an early age of first flowering and high gene flow buffer against possible reductions of genetic diversity. Significantly stronger SGS at SNPs in HiFi than LoFi stands of P. halepensis suggested fire-related altered dispersal possibly combined with microenvironmental selection in this fire-sensitive "seeder" species. In contrast, SGS at SNP markers was unrelated to fire regime in P. pinaster. This could be a consequence of more pronounced fire-resistance in this species enabling some adults to survive fire, hence causing a lower dependence on post-fire regeneration. Our results highlight that the impact of fire differs in species with similar life-history traits. Therefore, species-specific studies are needed to understand the role of wildfires for the evolution of future forests
Data from: The relative influence of habitat amount and configuration on genetic structure across multiple spatial scales
Despite strong interest in understanding how habitat spatial structure shapes the genetics of populations, the relative importance of habitat amount and configuration for patterns of genetic differentiation remains largely unexplored in empirical systems. In this study, we evaluate the relative influence of, and interactions among, the amount of habitat and aspects of its spatial configuration on genetic differentiation in the pitcher plant midge, Metriocnemus knabi. Larvae of this species are found exclusively within the water-filled leaves of pitcher plants (Sarracenia purpurea) in a system that is naturally patchy at multiple spatial scales (i.e., leaf, plant, cluster, peatland). Using generalized linear mixed models and multimodel inference, we estimated effects of the amount of habitat, patch size, interpatch distance, and patch isolation, measured at different spatial scales, on genetic differentiation (FST) among larval samples from leaves within plants, plants within clusters, and clusters within peatlands. Among leaves and plants, genetic differentiation appears to be driven by female oviposition behaviors and is influenced by habitat isolation at a broad (peatland) scale. Among clusters, gene flow is spatially restricted and aspects of both the amount of habitat and configuration at the focal scale are important, as is their interaction. Our results suggest that both habitat amount and configuration can be important determinants of genetic structure and that their relative influence is scale dependent.
Data from: Clone configuration and spatial genetic structure of two Halophila ovalis populations with contrasting internode lengths
Fine-scale spatial genetic structure (SGS) is predominantly determined by gene flow. While sexually reproducing plants can disperse their genes through pollen and seed grains, clonal plants can additionally disperse genes through clonal growth. Plants' clonal reproduction strategy, however, often varies within and between species. Still, the effect of differential clonal reproduction strategy on fine-scale SGS remains somewhat unclear. Halophila ovalis is a fast-growing clonal seagrass, whose internode length (which defines a species' clonal reproduction strategy) varies among populations. Using eight polymorphic microsatellites, here we compare the genetic diversity, clonal structure and fine-scale SGS of two H. ovalis populations with contrasting internode lengths (Yingluo versus Xialongwei populations). We found moderate to high genotypic and allelic richness and heterozygosities in both populations. Compared to Xialongwei population, genetic and genotypic diversity was significantly lower in Yingluo population. Although their internode length was relatively short, clones of Yingluo population spread farther than those of Xialongwei population. Sexual-to-vegetative dispersal variance ratios were 34.6 and 445.5 in Yingluo and Xialongwei populations, respectively. In both populations, clonal growth significantly intensified the SGS, especially in short distance classes. The SGS at small distance classes were weaker in Yingluo than Xialongwei, in part, due to more intermingled distribution of genets and more extensive clonal expansion in the former population. Our results indicate that vegetative dispersal variance/distance, rather than internode length, plays a crucial role in shaping the fine-scale genetic structure.
Data from: Sex-biased dispersal creates spatial genetic structure in a parthenogenetic ant with a dependent-lineage reproductive system
Reproduction and dispersal are key aspects of species life history that influence spatial genetic structure in populations. Several ant species in the genus Cataglyphis have evolved a unique breeding system in which new reproductives (that is, queens and males) are produced asexually by parthenogenesis; in contrast, non-reproductives (that is, workers) are produced via sexual reproduction by mates from distinct genetic lineages. We investigated how these two coexisting reproductive methods affect population-level spatial genetic structure using the ant Cataglyphis mauritanica as a model. We obtained genotypes for queens and their male mates from 338 colonies, and we found that the two lineages present in the study population occurred with equal frequency. Furthermore, analysis of spatial genetic structure revealed strong sex-biased dispersal. Because queens were produced by parthenogenesis and because they dispersed over short distances, there was an extreme level of spatial structuring: a mosaic of patches composed of clonal queens was formed. Males, on the other hand, dispersed over several hundred metres and, thus, across patches, ensuring successful interlineage mating.
Data from: Spatial heterogeneity in landscape structure influences dispersal and genetic structure: empirical evidence from a grasshopper in an agricultural landscape
Dispersal may be strongly influenced by landscape and habitat characteristics that could either enhance or restrict movements of organisms. Therefore, spatial heterogeneity in landscape structure could influence gene flow and the spatial structure of populations. In the past decades, agricultural intensification has led to the reduction in grassland surfaces, their fragmentation and intensification. As these changes are not homogeneously distributed in landscapes, they have resulted in spatial heterogeneity with generally less intensified hedged farmland areas remaining alongside streams and rivers. In this study, we assessed spatial pattern of abundance and population genetic structure of a flightless grasshopper species, Pezotettix giornae, based on the surveys of 363 grasslands in a 430-km² agricultural landscape of western France. Data were analysed using geostatistics and landscape genetics based on microsatellites markers and computer simulations. Results suggested that small-scale intense dispersal allows this species to survive in intensive agricultural landscapes. A complex spatial genetic structure related to landscape and habitat characteristics was also detected. Two P. giornae genetic clusters bisected by a linear hedged farmland were inferred from clustering analyses. This linear hedged farmland was characterized by high hedgerow and grassland density as well as higher grassland temporal stability that were suspected to slow down dispersal. Computer simulations demonstrated that a linear-shaped landscape feature limiting dispersal could be detected as a barrier to gene flow and generate the observed genetic pattern. This study illustrates the relevance of using computer simulations to test hypotheses in landscape genetics studies.
Data from: Tracking climate change in a dispersal-limited species: reduced spatial and genetic connectivity in a montane salamander
Tropical montane taxa are often locally adapted to very specific climatic conditions, contributing to their lower dispersal potential across complex landscapes. Climate and landscape features in montane regions affect population genetic structure in predictable ways, yet few empirical studies quantify the effects of both factors in shaping genetic structure of montane-adapted taxa. Here, we considered temporal and spatial variability in climate to explain contemporary genetic differentiation between populations of the montane salamander, Pseudoeurycea leprosa. Specifically, we used ecological niche modelling (ENM) and measured spatial connectivity and gene flow (using both mtDNA and microsatellite markers) across extant populations of P. leprosa in the Trans-Mexican Volcanic Belt (TVB). Our results indicate significant spatial and genetic isolation among populations, but we cannot distinguish between isolation by distance over time or current landscape barriers as mechanisms shaping population genetic divergences. Combining ecological niche modelling, spatial connectivity analyses, and historical and contemporary genetic signatures from different classes of genetic markers allows for inference of historical evolutionary processes and predictions of the impacts future climate change will have on the genetic diversity of montane taxa with low dispersal rates. Pseudoeurycea leprosa is one montane species among many endemic to this region and thus is a case study for the continued persistence of spatially and genetically isolated populations in the highly biodiverse TVB of central Mexico.
Increased spatial-genetic structure in a population of the clonal aquatic plant Sagittaria latifolia (Alismataceae) following disturbance
<p>The spatial genetic structure (SGS) of plant populations is determined by the outcome of key ecological processes, including pollen and seed dispersal, the intensity of local resource competition among newly recruited plants, and patterns of mortality among established plants. Changes in the magnitude of SGS over time can provide insights into the operation of these processes. We measured SGS in a population of the clonal aquatic plant, <i>Sagittaria latifolia</i> that had been disturbed by flooding, both before and after the flood. . Over the four-year interval between measurements, we found substantial changes in the magnitude of SGS. In the first measurement (pre-flood), SGS was weak, even over short distances. By contrast, there was substantial SGS in the second measurement (post-flood), particularly over short distances. This change in SGS was accompanied by near complete turnover in the genotypic composition of the population. The genotypic richness of the population (the number of unique clones scaled by the sample size) was halved over the four-year interval. The clonal subrange – the distances between shoots within clones – also shrank considerably, with more than 5% of shoots having clone-mates at distances greater than 10 m before the flood, but fewer than 5% of shoots having clone-mates at distances beyond 2 m afterwards. Clonal turnover and the re-establishment of SGS in clonal populations are both expected following local extirpation and recruitment. These data reveal the genetic signatures of disturbance and a subsequent flush of seedling recruitment and subsequent clonal expansion.</p>
History and environment shape spatial genetic variation and predict climate maladaptation in a narrowly distributed serotinous pine, Pinus muricata
<p><span></span></p> <p>Understanding the distribution of genetic diversity and differentiation in species with disjunct and isolated populations is critical for assessing how environment shapes genetic variation and the potential response to climate change. In contrast to the large distributions and population sizes of most pine species, <em>Pinus muricata</em> (Bishop pine) occurs in a small number of isolated and disjunct populations occupying a narrow band of environmental conditions along the coast of western North America. We used genotyping by sequencing to generate population genomic data for trees sampled from nearly all existing populations of <em>P. muricata</em> (12 populations, 213 individuals, 7,828 loci) to describe the spatial arrangement of genetic differentiation and diversity. We used genetic-environment association (GEA) analyses to quantify the contribution of environmental variables to local adaptation and spatial genetic structure. Based on these results, we quantified relative levels of potential maladaptation given future climate projections at 2041 – 2060 and 2081 – 2100. Our analyses reveal pronounced spatial genetic structure across the distribution, with most populations forming genetically identifiable groups across a latitudinal gradient, and remarkable evidence for differentiation among three proximally distributed stands on Santa Cruz Island. Despite occurring in small, isolated populations, <em>P. muricata</em> do not exhibit strongly reduced diversity. GEA analyses suggested that specific soil and climate variables have contributed to local adaptation. Genomic offset analyses suggest geographic variation in potential maladaptation, with northern populations experiencing higher levels under projected climate change. Overall, our results suggest that isolation and local adaptation have shaped genetic variation among disjunct populations, and illustrate the consequences of this variation for <em>P. muricata</em> under projected climate change.</p>
Life-history stage and the population genetics of the tiger mosquito Aedes albopictus at a fine spatial scale
<p>As a widespread vector of disease, the mosquito species <em>Aedes albopictus </em>Skuse<em> </em>(Diptera: Culicidae) is a high priority for both public health and invasive species research and management. Like all mosquitoes, <em>A. albopictus </em>has a complex life history with aquatic egg, larval, and pupal stages and a terrestrial adult stage. This requires targeted management strategies for each life stage, coordinated across time and space. Researchers use population genetics to inform control of <em>A. albopictus</em>. However, these studies do not consider the impact on life stage on population genetic characteristics and subsequent conclusions. Our objective was to examine whether the life stage impacted patterns of <em>A. albopictus </em>genetic diversity and differentiation at a spatial scale relevant to management efforts. We first conducted a literature review of field-caught <em>A. albopictus </em>population genetic papers and identified 74 peer-reviewed publications, none of which compared results between life stages.<em> </em>We them examined population genetic patterns of egg and adult <em>A. albopictus </em>at five sites in Wake County, North Carolina USA using 8,425 single nucleotide polymorphisms. We found that level of genetic diversity and connectivity between sites varied between adults and eggs. This warrants further study and is critical for research aimed at informing local management.</p>
Spatial pattern of genetic diversity in field populations of Fusarium incarnatum-equiseti species complex
<p><i>Fusarium</i> is associated with a number of wilt, blight, scab and rot diseases in a range of economically important staple food crops worldwide. An assessment of the genetic structure and population stratification of <i>Fusarium incarnatum-equiseti</i> species complex (FIESC) pathogen populations is important to understand the evolutionary potential of such populations in adapting to environmental change. Based on inter-simple sequence repeat polymerase chain reaction (ISSR-PCR), it was found that the pathogen population was structured into three genetic clusters for which genetic differentiation was higher within than among populations. There was high intra-population genetic diversity for population 1 (94.63%) which consisted largely of isolates collected from North Trinidad. Populations 2 and 3 had a low level of admixture among the populations based on overall population differentiation. Population 1 accounted for the highest amount of genetic variation (95.82%) followed by populations 2 and 3. Population stratification was reflected in the dendrogram topology, which consisted of three main genetic clusters and which coincided with the outcome of Bayesian and PCoA analyses. The populations were isolated by distance and Voronoi tessellations indicated physical or structural barriers to gene flow which contributed to restricted admixture between two of three populations. These findings suggest a high evolutionary potential for this FIESC pathogen population, the implications of which directly affect disease management strategies.</p>
Data from: Evaluating otter reintroduction outcomes using genetic spatial capture-recapture modified for dendritic networks
<p>River otters (Lontra canadensis) were extirpated from New Mexico by the 1950s. A limited reintroduction occurred during 2008–2010 in which 33 otters sourced from Washington (WA) were translocated to the Upper Rio Grande Basin (URG) of New Mexico. We conducted a noninvasive genetic capture-recapture survey during the winter of 2018 by collecting fecal DNA samples from river otter scats found at latrines in the URG dendritic network of perennial waterways. Our objectives were to: 1) estimate genetic diversity and effective population size; 2) genetic divergence from the WA source population and potential connectivity with regionally proximal populations; 3) spatially explicit population density and size; and 4) population growth rate since the founder event. Between February and April 2018, we collected 1,184 fecal DNA samples from 622 individual scats at 20 latrines; genotyping was attempted at 10 otter-specific microsatellite loci for a subsample of 543 samples. A bottlenecking founder effect was strongly supported, which, combined with genetic drift, reduced genetic diversity and effective population size by 20–26% and 106–170%, respectively, compared with the WA source population. Estimated population density from spatial capture-recapture models was 0.23–0.28 otter/km of waterway, or 1 otter/3.57–4.35 km of waterway, corresponding to a total population size of 83–100 otters across 359 km of the perennial dendritic network from La Mesilla, New Mexico to Alamosa National Wildlife Refuge, Colorado. Estimated average annual population growth rate since the founder event was 1.12–1.15/year. Despite successful population establishment, the URG river otter population remains small, is genetically degraded, and does not yet meet the criteria for long-term reintroduction success. Projections suggested that the population could reach the recommended minimum viable population size of ≥400 otters by the years 2030–2033, though sufficient habitat may not exist in the URG Basin to support that many otters. </p>
Holocene climate changes explain the spatial pattern in genetic diversity in populations of Cyperus papyrus from Southeast Africa wetlands
<p>Wetlands are one of the most threatened ecosystems in the world because more than 70% of the area worldwide has been lost since 1900. Wetland plant species rely greatly on water for seeds and propagules, which may lead to a downstream unidirectional dispersal and accumulation of genetic diversity downstream. However, several species show no support for unidirectional genetic diversity, revealing the complexity of population dynamics and gene flow in wetlands. Here, we used microsatellite loci to address how the past demographic dynamics shaped the contemporary spatial pattern in genetic diversity and population structure of <em>Cyperus papyrus</em> in wetlands of Southeast Africa. Using spatially explicit analysis and coalescent modelling we found no support for unidirectional dispersal. Instead, we found higher genetic diversity in populations upstream than downstream in the river basin. We also found high admixture among populations, most likely due to connections between adjacent river basins during sporadic floods, and ongoing gene flow due to bird-mediated seed dispersal. Our results suggest stepping-stone migration due to strong isolation-by-distance, but not necessarily unidirectional. Moreover, the past demographic dynamics in the Holocene shaped the current pattern of genetic diversity and structure, leading to higher genetic diversity in populations upstream of the Zambezi river basin. Our results also point to the very low genetic diversity of <em>C</em>. <em>papyrus</em> populations in Southeast Africa and the need for management and conservation strategies to guarantee the long-term persistence of the species in the region.</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.