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154 results for “spatial genetic structure”
Microsatellite genotypes for «Genetic diversity and spatial genetic structure support the specialist‑generalist variation hypothesis in two sympatric woodpecker species»
<p>Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (<em>Dendrocopos major</em>), lower genetic diversity was found in the specialist middle spotted woodpecker (<em>Dendrocoptes medius</em>). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.</p>
Bauder Et Al. - Landscape features fail to explain spatial genetic structure
<p> RMarkdown script and data in an Excel sheet to evaluate spatial genetic structure in white-tailed deer across Ohio and compare the support for isolation by distance (IBD) and isolation by landscape resistance (IBR) models in explaining this structure. We used genetic data from 619 individual deer from 24 counties across Ohio tested at 11 microsatellites and haplotypes from a 547-bp fragment of the mitochondrial DNA control region. We used spatial and non-spatial genetic clustering tests to evaluate genetic structure in both types of genetic data and empirically optimized landscape resistance surfaces to compare IBD and IBR using microsatellite data.</p> <p>v2 (BauderEtAl_Files_for_archiving2.zip) includes additional and updated files not in v1. </p>
Fig. 4 in Spatial genetic structure in the vulnerable smooth-coated otter (Lutrogale perspicillata, Mustelidae): towards an adaptive conservation management of the species
Fig. 4. Multidimensional Scaling (MDS) plot (stress: 0.0045) performed using average pairwise TN93 (Tamura & Nei, 1993) distances among investigated Lutrogale perspicillata groups created according to the country of origin of samples (modern + museum DNA and GenBank entries).
Fig. 3. A in Spatial genetic structure in the vulnerable smooth-coated otter (Lutrogale perspicillata, Mustelidae): towards an adaptive conservation management of the species
Fig. 3. A, Lutrogale perspicillata network computed using haplotypes (h) from the 305 bp-long sequence alignment (modern + museum DNA and GenBank entries). A scale to infer the number of sequences for each pie (i.e., haplotype) was provided together with a length bar to compute the number of mutational changes. The colour of each country and the number of each haplotype are indicated. See Table S1 for more details. B, Mismatch Distributions (MD) of the mtDNA pairwise differences (dotted: observed; line: expected) calculated for South East Asia haplogroup (Fig. 3A). Estimates of FS and R2 statistics (with related P values), r (raggedness index) and the outcome of SSD and SSD* test under a model (H0) of sudden demographic and spatial population expansion, respectively, are provided.
Fig. 2 in Spatial genetic structure in the vulnerable smooth-coated otter (Lutrogale perspicillata, Mustelidae): towards an adaptive conservation management of the species
Fig. 2. Photos of MNHN-ZM-MO-2001-350, L. p. perspicillata holotype resident in the mammal collection of the National Museum of Natural History of Paris, France. A, right side, lateral view (bar length = 20 cm); B, left forelimb, lateral view; C, basement, in French "Lutra perspicillata = Lutra leptonix Horsf., loutre de Java par m Diard, mai 1821, la tête est au lab d'anatomie", which can be translated into and interpreted as: "Lutra perspicillata = Lutra leptonix (Horsfield, 1824), Java otter from M. Diard, May 1821, skull is in the lab of anatomy" (see also Material and Methods). Photos courtesy and copyright: © MNHN - RECOLNAT - Laura Flamme - 2014.
Fig. 1 in Spatial genetic structure in the vulnerable smooth-coated otter (Lutrogale perspicillata, Mustelidae): towards an adaptive conservation management of the species
Fig. 1. Lutrogale perspicillata distribution (in yellow; see insets for Iraq and Pakistan) including sampling localities of modern (white circles) and museum (green squares) individuals. As far as the latter are concerned, we reported only sites for which samples were successfully investigated (see Table S1 for the entire sample size of this study; symbol "?" stands for unknown locality). The white stars indicate, in Iraq, the locality (TaqTaq, Kurdistan) where the sample of Omer et al. (2012) was collected, in Cambodia/Thailand and Malaysia, the country/ies of origin of EF472348 and KY117557 GenBank sequence, respectively. In Iraq, Pakistan, and supposedly Java, Indonesia, the green squares indicate localities (when known) of L. p. maxwelli, L. p. sindica, and L. p. perspicillata museum holotypes, respectively. Finally, Naga Hills at the border between Myanmar and India as well as Bahoo-Kalat River Basin between Iran and Pakistan are indicated (see text for more details). The species' geographic range was adapted from IUCN (International Union for Conservation of Nature) 2015. Lutrogale perspicillata. The IUCN Red List of Threatened Species 2019-3 was modified using CorelDraw!12 (2003). Digital images (insets) were obtained from Google Earth 7.1.5.1557 (2015 Google Inc.) and Google Earth map data (Data SIO, NOAA, U.S. Navy, NGA, GEBCO - Image Landsat). Please note that thick dotted lines mark out new borders for L. p. sindica and L. p. perspicillata subspecies as established in this study (see text for more details).
figure 1 in Spatial genetic structure in the Eurasian otter (Lutra lutra) meta-population from its core range in Italy
figure 1 The area surveyed for collection of otter samples (40° 40' N, 39° 37' N). Red spots indicate the location of the collected samples. The blue lines highlight the main rivers (order 1) and their tributaries (order 2, 3 and 4 according to waterway hierarchy). The continuous red lines represent regional boundaries. In the inset, the current otter distribution (inferred from Balestrieri et al., 2016, modified) is reported in orange and the study area is defined by the black bold square.
figure 4 in Spatial genetic structure in the Eurasian otter (Lutra lutra) meta-population from its core range in Italy
figure 4 Principal Component Analysis (pca) performed on microsatellite genotypes (dots). Circles show the well-defined spatial groups. A) pca according to the belonging of genotypes to the six river basins: the Cilento basin (green dots); the Agri basin (pink dots); the Sinni basin (blue dots); the Lao basin (red dots); the Basento basin (orange dots); the Abatemarco basin (violet dots); black dots indicate the samples outside of the main river basins. Dashed line indicates geographically contiguous but genetically different genotypes. B) pca according to clusters inferred by STRUCTURE: genotypes assigned unambiguously to K2 (green dots), to K3 (yellow dots), to K5 (violet dots). Grey dots represent samples with mixed genotypes assignable to K1 and K4.
figure 3 in Spatial genetic structure in the Eurasian otter (Lutra lutra) meta-population from its core range in Italy
figure 3 Genetic structure and distribution of the Italian otter genotypes in the study area. A) Estimated population structure based on the analysis of 11 microsatellite loci according to STRUCTURE (K = 5). Each bar represents a sample analysed. B) Geographic visualisation of genotypes in the study area performed using QGIS 3.4.1 software with base layers acquired from http://www.pnc.miniambiente. it/. Each circle represents a sample analysed. The colours indicate the percentage of assignment of an individual to each cluster: in blue, K1; in green, K2; in orange, K3; in red, K4; in violet, K5. The bold blue lines highlight the main rivers, while the tiny blue lines show all other waterways.
figure 6 Mantel test for A in Spatial genetic structure in the Eurasian otter (Lutra lutra) meta-population from its core range in Italy
figure 6 Mantel test for A) the correlation between geographic distance (GGDsq) and genetic distance (LinGD) (Rxy = 0.264, P = 0.0001) and for B) the correlation between resistance distance (a measure of ecological distance) (ECO500) and LinGD (Rxy = 0.217, P = 0.0001).
Going with the flow? Relative importance of riverine hydrologic connectivity versus tidal influence for spatial structure of genetic diversity and relatedness in a foundational submersed aquatic plant
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Asymmetrical hybridization and environmental factors influence the spatial genetic structure of a killifish hybrid zone
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Data from: Defaunation increases clustering and fine-scale spatial genetic structure in a small-seeded palm despite remaining small-bodied frugivores
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Genetic Diversity and Spatial Structure of Spartina alterniflora in on the Eastern Shore of Virginia
Nine polymorphic microsatellite loci were used to quantify the genetic characteristics (e.g., allelic richness,diversity, polyploidy, fixation index) of the S. alterniflora populations at five salt marshes on the Eastern Shore of Virginia (Northampton Co.), as well as to measure the spatial structure (size and shape of clones) of a single population in Upper Phillips Creek marsh (UPC), a marsh that experienced dieback. Over 250 individual plant samples were collected at three spatial scales for these experiments
Data from: Multi-scale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes
Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, inter-population genetic differentiation was 6–9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4–7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.
Data from: Genetic diagnosis of a rare myrmecochorous species, Plagiorhegma dubium (Berberidaceae): historical genetic bottlenecks and strong spatial structures among populations
Distribution of genetic variation over time and space is relevant to demographic histories, and tightly linked to ecological disturbances as well as evolutionary potential of an organism. Therefore, understanding the pattern of genetic diversity is a primary step in conservation and management projects for rare and threatened plant species. We used 8 microsatellite markers to examine the level of genetic diversity, spatial structure and demographic history of Plagiorhegma dubium, a rare myrmecochorous herb, populations sampled across northeast Asia and Siberia. We found low within-population genetic variation associated with historical bottlenecks. Although pairwise FST values were not much higher than the ones found in similar life form species, STRUCTURE and PCoA revealed a clear broad-scale spatial pattern of genetic structure. Bayesian clustering (best K=6) and PCoA identified three populations that are distinctive from neighboring populations in the Korean peninsula, which suggests potential units for conservation and management plans in Korea. MIGRATE-N and BAYESASS showed that both contemporary (0.003-0.045) and historical migration rates (2e-5-4.6e-4) were low. Our findings provide a good example, where genetic considerations should be integrated for conservation and management plans of rare and threatened species.
Data from: Investigating the spatial, demographic, and genetic structures of Cylicodiscus gabunensis Harms, a light-demanding African timber species
<p>Most Central African rainforest canopies consist of light-demanding tree species that hold high commercial value but also suffer locally from regeneration deficits, raising concerns about the sustainability of logging. Regeneration is influenced by factors such as past perturbations (including human activity), mating systems, and seed/pollen dispersal processes that impact demographic, spatial, and genetic structures within populations. To gain a better understanding of these interactions, we studied the spatial distribution and trunk diameter structure of <em><span>Cylicodiscus gabunensis</span></em> (Fabaceae) - a wind-dispersed, insect-pollinated, timber species - in three plots ranging from 400 to 839<span> </span>ha situated in various environmental contexts (e.g. forest types and elephant densities) across Central Africa. We also genotyped adults and juveniles using microsatellite markers to analyze the spatial genetic structure of each population and infer the selfing rate, seed and pollen dispersal capacities and selection gradients using the <span>'</span>neighborhood model<span>'</span>. The selfing rate was low (3 <span>–</span> 4<span> </span>%), and seed dispersal distances (<em><span>ds</span></em><span> </span>=<span> </span>184<span> </span>m) were much shorter than pollen dispersal distances (<em><span>dp</span></em><span> </span>><span> </span>2<span> </span>km). The three populations displayed contrasted spatial, demographic and genetic structures. One population showed no spatial aggregation or genetic structure, and a multimodal diameter structure indicating pulses of regeneration events. Two populations showed strong spatial aggregation and genetic structures. One exhibited a unimodal diameter structure indicating one ancient pulse of regeneration, while the other displayed a 'reverse J-shaped' diameter structure, typical of ongoing regeneration. In the latter, reproductive success appeared leptokurtic, three mother trees accounting for over 90<span> </span>% of the regeneration and no tree below the minimum cutting diameter implemented by logging companies had offspring. The idiosyncratic nature of population characteristics observed in <em><span>C. gabunensis</span></em> suggests that, for sustainable management, a nuanced approach is needed. This involves protecting productive seed trees in areas where natural regeneration is occurring and actively supporting regeneration in areas exhibiting deficits, especially in contexts with low elephant densities.</p>
Lack of spatial and temporal genetic structure of Japanese eel (Anguilla japonica) populations
Japanese eel (Anguilla japonica) is an important food source in East Asia whose population has dramatically declined since the 1970s. Despite past analysis with DNA sequencing, microsatellite and isozyme methods, management decisions remain hampered by contradictory findings. For example, it remains unresolved whether Japanese eels are a single panmictic population or whether they harbor significant substructure. Accurate assessment of population genetic substructure, both spatial and temporal, is essential for determining the relevant number of distinct management units appropriate for this species. In the present study, we assayed genetic variation genome-wide using Restriction Site Associated DNA Sequencing (RAD-seq) technology to analyze the population genetic structure of Japanese eels. For analysis of temporal isolation, five "cohort" samples were collected yearly from 2005 to 2009 in the Yangtze River Estuary. For analysis of spatial structure, five "arrival wave" samples were collected in China in 2009, and two arrival wave samples were collected in Japan in 2001. In each cohort of each arrival wave, five individuals were collected for a total of 55 eels sampled. In total, 214,210 loci were identified from these individuals, 106,652 of which satisfied quality checks and were retained for further analysis. There was relatively little population differentiation between arrival waves and cohorts collected either at different locations during the same year (Fst = 0.077) or at the same location collected over subsequent years (Fst = 0.082), and locations displayed no consistent isolation-by-distance.
Effects of social organisation and elevation on spatial genetic structure in a montane ant
<p><span>Studying patterns of population structure across the landscape sheds light on dispersal and demographic processes, which helps to inform conservation decisions. Here, we study how social organisation and landscape factors affect spatial patterns of genetic differentiation in an ant species living in mountainous regions. Using genome-wide SNP markers, we assess population structure in the Alpine silver ant, <em>Formica selysi</em>. This species has two social forms controlled by a supergene. The monogyne form has one queen per colony, while the polygyne form has multiple queens per colony. The two social forms co-occur in the same populations. For both social forms, we found a strong pattern of isolation-by-distance across the Alps. Within regions, genetic differentiation between populations was weaker for the monogyne form than for the polygyne form. We suggest that this pattern is due to higher dispersal and effective population sizes in the monogyne form. In addition, we found stronger isolation-by-distance and lower genetic diversity in high elevation populations, compared to lowland populations, suggesting that gene flow between F. selysi populations in the Alps occurs mostly through riparian corridors along lowland valleys. Overall, this survey highlights the need to consider intraspecific polymorphisms when assessing population connectivity and calls for special attention to the conservation of lowland habitats in mountain regions.</span></p>
Fine-scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones
<p>Analyses of the factors shaping genetic variation in widespread plant species are important for understanding evolutionary history and local adaptation and have applied significance for guiding conservation and restoration decisions. Thurber's needlegrass (<em>Achnatherum</em> <em>thurberianum</em>) is a widespread, locally abundant grass that inhabits heterogeneous arid environments of western North America and is of restoration significance. It is a common component of shrubland steppe communities in the Great Basin Desert, where drought, fire, and invasive grasses have degraded natural communities. Using a reduced representation sequencing approach, we generated SNP data at 5,677 loci across 246 individuals from 17 <em>A. thurberianum</em> populations spanning five previously delineated seed zones from the western Great Basin. Analyses revealed pronounced population genetic structure, with individuals forming consistent geographical clusters across a variety of population genetic analyses and spatial scales. Low levels of genetic diversity within populations, as well as high population estimates of linkage disequilibrium and relatedness, were consistent with self-fertilization as a contributor to population differentiation. Variance partitioning and partial redundancy analysis (pRDA) indicated local adaptation to environment as additionally influencing the spatial distribution of genetic variation. The environmental variables driving these results were similar to those implicated in recent genecological work which inferred local adaptation for seed zone delineation. Our analyses also revealed a complex evolutionary history of <em>A. thurberianum</em> in the Great Basin, where previously delineated seed zones contain distantly related populations. Our results indicate evolutionary history, mating system, and differentiation across distinct geographic and environmental scales have shaped genetic variation in <em>A. thurberianum</em> and illustrate how numerous aspects of population genetic variation might require consideration for restoration planning.</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.
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