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324 results for “spatial genetics”
Both selection and drift drive the spatial pattern of adaptive genetic variation in a wild mammal
<p><span>The major histocompatibility complex (MHC) has been intensively studied to test for the relative effects of different evolutionary forces in recent decades. Pathogen-mediated balancing selection is generally thought to explain the high polymorphism observed in MHC genes, but it is still unclear to what extent MHC diversity is shaped by selection relative to neutral drift. In this study, we genotyped MHC class II DRB genes and 15 neutral microsatellite loci across 26 geographic populations of European badgers (<em>Meles meles</em>) covering most of their geographic range. By comparing the variation of microsatellites and the diversity of MHC at different levels, we demonstrate that both balancing selection and drift have shaped the evolution of MHC genes. When only MHC allelic identity was investigated, the spatial pattern of MHC variation was similar to that of microsatellites. By contrast, when functional aspects of the MHC diversity (e.g. immunological supertypes) were considered, balancing selection appears to decrease genetic structuring across populations. Our comprehensive sampling and analytical approach enable us to conclude that the likely mechanisms of selection are heterozygote advantage and/or rare-allele advantage. This study is a clear demonstration of how both balancing selection and genetic drift simultaneously affect the evolution of MHC genes in a widely-distributed wild mammal.</span></p>
FIG. 4 in Nest-Site Fidelity and Sex-Biased Dispersal Affect Spatial Genetic Structure of Eastern Box Turtles (Terrapene carolina carolina) at Their Northern Range Edge
FIG. 4. Analysis of global structure along the river corridor from the first principal component of the sPCA represented by (A) interpolation of lagged principal scores showing genetic clines and (B) colors indicating individual scores. Coordinates have been deliberately omitted to deter poachers.
FIG. 3 in Nest-Site Fidelity and Sex-Biased Dispersal Affect Spatial Genetic Structure of Eastern Box Turtles (Terrapene carolina carolina) at Their Northern Range Edge
FIG. 3. Bubble plot showing the results of two-dimensional local spatial autocorrelation analysis for all Eastern Box Turtles (n ¼ 165) sampled in northwestern Michigan. Circles represent individuals and the size of the circle is proportional to the P-values from permutation testing, with large circles representing individuals that are significantly more related to their five nearest neighbors than expected (P, 0.05) based on a random distribution of genotypes. Figure shows the distribution of five genetic ''hotspots'' in relation to known nesting sites (NS) across the study area. Some distantly sampled individuals are omitted for figure clarity.
FIG. 2 in Nest-Site Fidelity and Sex-Biased Dispersal Affect Spatial Genetic Structure of Eastern Box Turtles (Terrapene carolina carolina) at Their Northern Range Edge
FIG. 2. Spatial genetic autocorrelograms of genetic correlation coefficients (r) as a function of distance for Eastern Box Turtles in northwestern Michigan. Plots represent (A) all individuals (n ¼ 165), (B) females only (n ¼ 104), and (C) males only (n ¼ 51). Dashed lines are permuted 95% confidence intervals across all data, and error bars are bootstrapped 95% confidence intervals within each distance class. Tables below graphs represent data for each distance class including the number of pairwise comparisons (n), the correlation coefficients (r), and the P-values (p) associated with bootstrap tests of significance for positive spatial genetic autocorrelation.
FIG. 1 in Nest-Site Fidelity and Sex-Biased Dispersal Affect Spatial Genetic Structure of Eastern Box Turtles (Terrapene carolina carolina) at Their Northern Range Edge
FIG. 1. Scatterplot showing the matrix of pairwise genetic distances and matrix of pairwise geographic distances for box turtles sampled along the river corridor. Warmer colors within the kernel density indicate higher densities of points. The line (slope ¼ 1.074727e–05; R2 ¼ 0.002992) shows the correlation trend.
Data from: Non-equilibrium conditions explain spatial variability in genetic structuring of little penguin (Eudyptula minor)
Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring.
Data from: Significant genetic boundaries and spatial dynamics of giant pandas occupying fragmented habitat across southwest China
Understanding population history and genetic structure are key drivers of ecological research. Here we studied two highly fragmented and isolated populations (Xiaoxiangling and Daxiangling) of giant pandas (Ailuropoda melanoleuca) at the extreme southwestern edge of their distribution. This area also contains the Dadu River, national road 108 and various human infrastructure and development, providing an ideal region in which we can identify the effects of different barriers on animal movements. We used partial mitochondrial control region (mtDNA) and nine microsatellite loci (nuclear DNA) data derived from 192 fecal and one blood sample collected from the wild. We found 136 genotypes corresponding to 53 unique multilocus genotypes and eight unique control region haplotypes (653 bp). Significant genetic boundaries correlated spatially with the Dadu River (K=2). We estimate that a major divergence took place between these populations 26 000 YBP, at around the similar time the rock surface of valley bottom formed in Dadu River. The national road has resulted in further recent population differentiation (Pairwise FS on mtDNA and nuclear DNA) so that in effect, four smaller sub-populations now exist. Promisingly, we identified two possible first generation migrants and their migration paths, and recommended the immediate construction of a number of corridors. Fortunately, the Chinese government has accepted our advice and is now planning corridor construction.
Data from: The ghost of introduction past: spatial and temporal variability in the genetic diversity of invasive smallmouth bass
Understanding the demographic history of introduced populations is essential for unravelling their invasive potential and adaptability to a novel environment. To this end, levels of genetic diversity within the native and invasive range of a species are often compared. Most studies, however, focus solely on contemporary samples, relying heavily on the premise that the historic population structure within the native range has been maintained over time. Here, we assess this assumption by conducting a three-way comparison of the genetic diversity of native (historic and contemporary) and invasive (contemporary) smallmouth bass (Micropterus dolomieu) populations. Analyses of a total of 572 M. dolomieu samples, representing the contemporary invasive South African range, contemporary and historical native USA range (dating back to the 1930s when these fish were first introduced into South Africa), revealed that the historical native range had higher genetic diversity levels when compared to both contemporary native and invasive ranges. These results suggest that both contemporary populations experienced a recent genetic bottleneck. Furthermore, the invasive range displayed significant population structure, whereas both historical and contemporary native USA populations revealed higher levels of admixture. Comparison of contemporary and historical samples showed both a historic introduction of M. dolomieu, as well as a more recent introduction, thereby demonstrating that undocumented introductions of this species have occurred. Although multiple introductions might have contributed to the high levels of genetic diversity in the invaded range, we discuss alternative factors that may have been responsible for the elevated levels of genetic diversity and highlight the importance of incorporating historic specimens into demographic analyses.
Data from: Phylogeography of African locust bean (Parkia biglobosa) reveals genetic divergence and spatially structured populations in West and Central Africa
The evolutionary history of African savannah tree species is crucial for the management of their genetic resources. In this study, we investigated the phylogeography of Parkia biglobosa and its modelled distribution under past and present climate conditions. This tree species is very valued and widespread in West Africa, providing edible and medicinal products. A large sample of 1 610 individuals from 84 populations, distributed across 12 countries in Western and Central Africa, were genotyped using eight nuclear microsatellites. Individual-based assignments clearly distinguished three genetic clusters, extreme West Africa (EWA), centre of West Africa CWA), and Central Africa (CA). Overall, estimates of genetic diversity were moderate to high, with lower values for populations in EWA (AR=6.4, HE=0.78 and HO=0.7) and CA (AR=5.9, HE=0.67 and HO=0.61) compared to populations in CWA (AR=7.3, HE=0.79 and HO=0.75). The overall population differentiation was found to be moderate (FST=0.09). A highly significant isolation-by-distance pattern was detected, with a marked phylogeographic signature suggesting possible effects of past climate and geographic barriers to migration. Modelling the potential distribution of the species showed a contraction during the last glaciations followed by expansion events. The exploratory Approximate Bayesian Computation conducted suggests a best-supported scenario in which the cluster CWA traced back to the ancestral populations and a first split between EWA and CWA took place about 160 000 years BP, then a second split divided CA and CWA, about 100 000 years BP. However, our genetic data do not enable to conclusively distinguish among a few alternative possible scenarios.
Data from: Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika.
A central goal of phylogeography is to identify and characterize the processes underlying divergence. One of the biggest impediments currently faced is how to capture the spatiotemporal dynamic under which a species evolved. Here we described an approach that couples species distribution models (SDMs), demographic and genetic models in a spatiotemporally explicit manner. Analyses of American Pika (Ochotona priniceps) from the sky islands of the central Rocky Mountains of North America are used to provide insights into key questions about integrative approaches in landscape genetics, population genetics and phylogeography. This includes (i) general issues surrounding the conversion of time-specific SDMs into simple continuous, dynamic landscapes from past to current, and (ii) the utility of SDMs to inform demographic models with deme-specific carrying capacities and migration potentials, as well as (iii) the contribution of the temporal dynamic of colonization history in shaping genetic patterns of contemporary populations. Our results support that the inclusion of a spatiotemporal dynamic is an important factor when studying the impact of distributional shifts on patterns of genetic data. Our results also demonstrate the utility of SDMs to generate species-specific predictions about patterns of genetic variation that account for varying degrees of habitat specialization and life-history characteristics of taxa. Nevertheless, the results highlight some key issues when converting SDMs for use in demographic models. Because the transformations have direct affects on the genetic consequence of population expansion by prescribing how habitat heterogeneity and spatiotemporal variation is related to the species-specific demographic model, it is important to consider alternative transformations when studying the genetic consequences of distributional shifts.
Data from: Limited gene dispersal and spatial genetic structure as stabilizing factors in an ant-plant mutualism
Comparative studies of the population genetics of closely associated species are necessary to properly understand the evolution of these relationships because gene flow between populations affects the partners' evolutionary potential at the local scale. As a consequence (at least for antagonistic interactions), asymmetries in the strength of the genetic structures of the partner populations can result in one partner having a co-evolutionary advantage. Here, we assess the population genetic structure of partners engaged in a species-specific and obligatory mutualism: the Neotropical ant-plant, Hirtella physophora, and its ant associate, Allomerus decemarticulatus. Although the ant cannot complete its life cycle elsewhere than on H. physophora and the plant cannot live for long without the protection provided by A. decemarticulatus, these species also have antagonistic interactions: the ants have been shown to benefit from castrating their host plant and the plant is able to retaliate against too virulent ant colonies. We found similar short dispersal distances for both partners, resulting in the local transmission of the association and, thus, inbred populations in which too virulent castrating ants face the risk of local extinction due to the absence of H. physophora offspring. On the other hand, we show that the plant populations probably experienced greater gene flow than did the ant populations, thus enhancing the evolutionary potential of the plants. We conclude that such levels of spatial structure in the partners' populations can increase the stability of the mutualistic relationship. Indeed, the local transmission of the association enables partial alignments of the partners' interests, and population connectivity allows the plant retaliation mechanisms to be locally adapted to the castration behaviour of their symbionts.
Data from: Population genetic structure of the tree-hole tick Ixodes arboricola (Acari: Ixodidae) at different spatial scales
The endophilic tick Ixodes arboricola infests cavity-nesting birds, and its dispersal strongly depends on the movements of its host. Population genetic structure of I. arboricola was studied with seven polymorphic microsatellite markers. We collected 268 ticks from 76 nest boxes in four woodlots near Antwerp, Belgium. These nest boxes are mainly used by the principal hosts of I. arboricola, the great tit Parus major and the blue tit Cyanistes caeruleus. As these birds typically return to the same cavity for roosting or breeding, ticks within nest boxes were expected to be highly related, and tick populations were expected to be spatially structured among woodlots and among nest boxes within woodlots. In line with the expectations, genetic population structure was found among woodlots and among nest boxes within woodlots. Surprisingly, there was considerable genetic variation among ticks within nest boxes. This could be explained by continuous gene flow from ticks from nearby tree holes, yet this remains to be tested. A pairwise relatedness analysis conducted for all pairs of ticks within nest boxes showed that relatedness among larvae was much higher than among later instars, which suggests that larvae are the most important instar for tick dispersal. Overall, tick populations at the studied spatial scale are not as differentiated as predicted, which may influence the scale at which host–parasite evolution occurs.
Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra- and inter-population spatial scales
<p>Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (<i>Lynx rufus</i>) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study-wide. Overall, landscape genomic effects were most frequently detected at the study-wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.</p>
Figure 2 in Historical demography and spatial genetic structure of the subterranean rodent Ctenomys magellanicus in Tierra del Fuego (Argentina)
Figure 2. Bayesian inference trees of Ctenomys genus. A, tree derived from the D-loop marker. B, tree derived from Cyt b. Numbers next to branches are bootstrap support values and Bayesian posterior probabilities, respectively.
Figure 1 in Historical demography and spatial genetic structure of the subterranean rodent Ctenomys magellanicus in Tierra del Fuego (Argentina)
Figure 1. Geographical distribution of Ctenomys magellanicus sampling sites along the study area. Squares show the two regions: north (steppe, chromosome form 2n = 34) and south (ecotone, chromosome form 2n = 36). Each region was subdivided into subpopulations: two for the north (subpopulations A and B) and four for the south (subpopulations C–F).
Estimating red fox density using non-invasive genetic sampling and spatial capture–recapture modelling
<p>Data and scripts for our paper:</p> <p>Lindsø, L.K., Dupont, P., Rød-Eriksen, L. <em>et al.</em> Estimating red fox density using non-invasive genetic sampling and spatial capture–recapture modelling. <em>Oecologia</em> <strong>198</strong>, 139–151 (2022). https://doi.org/10.1007/s00442-021-05087-3</p>
Fig. 1 in Socio-spatial organization and kin structure in ocelots from integration of camera trapping and noninvasive genetics
Fig. 1.—Map of Barro Colorado Island, Panama, showing the locations of camera traps placed along trails and at ocelot (Leopardus pardalis) latrines.
Fig. 2 in Socio-spatial organization and kin structure in ocelots from integration of camera trapping and noninvasive genetics
Fig. 2.—Cumulative frequency distributions of association index values among pairs of male versus female ocelots (Leopardus pardalis) on Barro Colorado Island, Panama. Half-weight association index values represent the strength of spatiotemporal overlap between same-sex dyads based on how often they were photographed at the same camera trap within the same 30-day interval.
Fig. 4 in Socio-spatial organization and kin structure in ocelots from integration of camera trapping and noninvasive genetics
Fig. 4.—Relatedness of individual ocelots (Leopardus pardalis) on Barro Colorado Island, Panama, depending on sex and overlap of space use. Values shown are observed mean differences in relatedness between dyads of individual ocelots with overlapping space use (vertical bold lines) versus all dyads in the sampled population, along with the cumulative distribution of simulated differences from 1,000,000 randomly generated bootstrap replicates. Reference lines represent quantiles from the simulated distribution. A) All dyads, B) male-female dyads, C) male-male dyads, and D) female-female dyads.
Fig. 3 in Socio-spatial organization and kin structure in ocelots from integration of camera trapping and noninvasive genetics
Fig. 3.—Half-weight association index values between pairs of a) female and b) male ocelots (Leopardus pardalis) from Barro Colorado Island, Panama, shown in both matrix and graphical format. Values and line weights represent the strength (on a scale of 0–1) of spatiotemporal overlap between pairs of individuals based on how often they were photographed at the same camera trap during the same 30-day period. Asterisks represent associations and double asterisks represent dissociations that differed from random expectations (P <0.05).
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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)
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DANDI Archive for NWB datasets
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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.
OpenNeuro
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