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154 results for “spatial genetic structure”
Weak spatial-genetic structure in a native invasive, the southern pine beetle (Dendroctonus frontalis), across the eastern United States
<p>The southern pine beetle<i>, Dendroctonus frontalis</i>, is a native pest of pine trees that has recently expanded its range into the northeastern United States. Understanding its colonization, dispersal, and connectivity will be critical for mitigating negative economic and ecological impacts in the newly invaded areas. Characterization of spatial-genetic structure can contribute to this; however, previous studies have reached different conclusions about regional population genetic structure, with one study reporting a weak east-west pattern, and the most recent reporting absence of structure. Here we systematically assessed several explanations for the absence of spatial-genetic structure. To do this, we developed nine new microsatellite markers and combined them with an existing 24-locus data matrix for the same individuals. We then reanalyzed this full dataset alongside datasets in which certain loci were omitted with the goal of creating more favorable signal to noise ratios. We also partitioned the data based on the sex of <i>D. frontalis</i> individuals, and then employed a broad suite of genotypic clustering and isolation-by-distance (IBD) analyses. We found that neither inadequate information content in the molecular marker set, nor unfavorable signal-to-noise ratio, nor insensitivity of the analytical approaches could explain the absence of structure. Regardless of dataset composition, there was little evidence for clusters (i.e., distinct geo-genetic groups) or clines (i.e., gradients of increasing allele frequency differences over larger geographic distances), with one exception: significant IBD was repeatedly detected using an individual-based measure of relatedness whenever datasets included males (but not for female-only datasets). This is strongly indicative of broad-scale female-biased dispersal, which has not previously been reported for <i>D. frontalis</i>, in part owing to logistical limitations of direct approaches (e.g., capture-mark-recapture). Weak spatial-genetic structure suggests long-distance connectivity and that gene flow is high, but additional research is needed to understand range expansion dynamics in this species using alternate approaches.</p>
Limited seed dispersal shapes fine-scale spatial genetic structure in a Neotropical dioecious large-seeded palm
<p><span>Seed and pollen dispersal contribute to gene flow and shape the genetic patterns of plants over fine spatial scales. We inferred fine-scale spatial genetic structure (FSGS) and estimated realized dispersal distances in Phytelephas aequatorialis, a Neotropical dioecious large-seeded palm. We aimed to explore how seed and pollen dispersal shape this genetic pattern in a focal population. For this purpose, we genotyped 138 seedlings and 99 adults with 20 newly developed microsatellite markers. We tested if rodent-mediated seed dispersal has a stronger influence than insect-mediated pollen dispersal in shaping FSGS. We also tested if pollen dispersal was influenced by the density of male palms around mother palms in order to further explore this ecological process in large-seeded plants. Rodent-mediated dispersal of these large seeds occurred mostly over short distances (mean 34.76 ± 34.06 m) while pollen dispersal distances were two times higher (mean 67.91 ± 38.29 m). The spatial extent of FSGS up to 35 m and the fact that seed dispersal did not increase the distance at which male alleles disperse suggest that spatially limited seed dispersal is the main factor shaping FSGS and contributes only marginally to gene flow within the population. Pollen dispersal distances depended on the density of male palms, decreasing when individuals show a clumped distribution and increasing when they are scattered. Our results show that limited seed dispersal mediated by rodents shapes FSGS in P. aequatorialis, while more extensive pollen dispersal accounts for a larger contribution to gene flow and may maintain high genetic diversity.</span></p>
Historic and contemporary biogeographic perspectives on range-wide spatial genetic structure in a widespread seagrass
<p>This raw data set contains multilocus genotypes for 1,312 individual samples from 44 locations.</p> <p>Aim: Historical and contemporary processes drive spatial patterns of genetic diversity. These include climate-driven range shifts and gene flow mediated by biogeographical influences on dispersal. Assessments that integrate these drivers are uncommon, but critical for testing biogeographic hypotheses. Here, we characterise intraspecific genetic diversity and its spatial structure across the entire distribution of a temperate seagrass to test marine biogeographic concepts for southern Australia.</p> <p>Location: Temperate Australian coastal waters</p> <p>Methods: Predictive modelling was used to contrast the current <em>Posidonia australis</em> distribution to its historical distribution during the Last Glacial Maximum (LGM). Spatial genetic structure was estimated for 44 sampled meadows from across the geographical range of the species using nine microsatellite loci. </p> <p>Results: Historical and contemporary distributions were similar, with the exception of the Bass Strait. Genetic clustering was consistent with the three currently recognised biogeographic provinces and largely consistent with the finer-scale <span>IMCRA </span>bioregions. Discrepancies were found within the Flindersian province and southwest IMCRA bioregion, while two regions of admixture coincided with transitional bioregions. Clonal diversity was highly variable, but positively associated with latitude. Genetic differentiation among meadows was significantly associated with oceanographic distance.</p> <p>Main conclusions: Our approach suggests how shared seascape drivers have influenced the capacity of <em>P. australis</em> to effectively track sea level changes associated with natural climate cycles over millennia, <span>and in particular, the recolonisation of meadows across the Continental Shelf following the LGM</span>. Genetic structure associated with IMCRA bioregions reflects the presence of stable biogeographic barriers, such as oceanic upwellings. This study highlights the importance of biogeography to infer the role of historical drivers in shaping extant diversity and structure. </p>
Data from: Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales
<p>Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate population persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and thus has direct implications for the spatial scales of management plans. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach based on mitochondrial control region sequences and 4,339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units – the Atlantic, eastern Gulf, and western Gulf – that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighboring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.</p>
Data from: Investigating the spatial, demographic, and genetic structures of Cylicodiscus gabunensis Harms, a light-demanding African timber species
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Fine-scale spatial genetic structure, mating and gene flow dispersal patterns in Parkia biglobosa populations under different levels of habitat fragmentation
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Data from: Spatial genetic structure of two conifers in a highly human-modified landscape of central Mexico
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Data from: Genetic diagnosis of a rare myrmecochorous species, Plagiorhegma dubium (Berberidaceae): historical genetic bottlenecks and strong spatial structures among populations
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Data from: Multi-scale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes
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Effects of social organisation and elevation on spatial genetic structure in a montane ant
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Historic and contemporary biogeographic perspectives on range-wide spatial genetic structure in a widespread seagrass
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Fine-scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones
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Lack of spatial and temporal genetic structure of Japanese eel (Anguilla japonica) populations
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Weak spatial-genetic structure in a native invasive, the southern pine beetle (Dendroctonus frontalis), across the eastern United States
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Limited seed dispersal shapes fine-scale spatial genetic structure in a Neotropical dioecious large-seeded palm
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Spatial discontinuity of mountain systems and genetic structure of alpine plants: the Alps-Carpathians disjunction in a comparative phylogeographical context
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Data from: Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales
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Data from: Genetic structure at three spatial scales is consistent with limited philopatry in Ricord's Rock Iguanas (Cyclura ricordii)
Cyclura ricordii is an endemic iguana from Hispaniola Island and is threatened on the IUCN Red List. The main threats are predation by introduced mammals, habitat destruction, and hunting pressure. The present study focused on two nesting sites from Pedernales Province in the Dominican Republic. The hypothesis that natal philopatry influences dispersal and nest site selection was tested. Monitoring and sampling took place in 2012 and 2013. Polymorphic markers were used to evaluate whether natal philopatry limits dispersal at multiple spatial scales. Ripley's K revealed that nests were significantly clustered at multiple scales, when both nesting sites were considered and within each nesting site. This suggests a patchy, non-random distribution of nests within nest sites. Hierarchical AMOVA revealed that nest site aggregations did not explain a significant portion of genetic variation within nesting sites. However, a small but positive correlation between geographic and genetic distance was detected using a Mantel's test. Hence, the relationship between geographic distance and genetic distance among hatchlings within nest sites, while detectable, was not strong enough to have a marked effect on fine scale genetic structure. Spatial and genetic data combined determined that the nesting sites included nesting females from multiple locations, and the hypothesis of 'natal philopatry', was not supported because females nesting in the same cluster were no more closely related to each other than to other females from the same nesting site. These findings imply that nesting aggregations are more likely associated with cryptic habitat variables contributing to optimal nesting conditions.
Data from: Temporal variation in spatial genetic structure during population outbreaks: distinguishing among different potential drivers of spatial synchrony
Spatial synchrony is a common characteristic of spatio-temporal population dynamics across many taxa. While it is known that both dispersal and spatially autocorrelated environmental variation (i.e., the Moran effect) can synchronize populations, the relative contributions of each, and how they interact, is generally unknown. Distinguishing these mechanisms and their effects on synchrony can help us to better understand spatial population dynamics, design conservation and management strategies, and predict climate change impacts. Population genetic data can be used to tease apart these two processes as the spatio-temporal genetic patterns they create are expected to be different. A challenge, however, is that genetic data are often collected at a single point in time, which may introduce context-specific bias. Spatio-temporal sampling strategies can be used to reduce bias and to improve our characterization of the drivers of spatial synchrony. Using spatio-temporal analyses of genotypic data, our objective was to identify the relative support for these two mechanisms to the spatial synchrony in population dynamics of the irruptive forest insect pest, the spruce budworm (Choristoneura fumiferana), in Quebec (Canada). AMOVA, cluster analysis, isolation by distance and sPCA were used to characterize spatio-temporal genomic variation using 1370 SBW larvae sampled over four years (2012-2015) and genotyped at 3,562 SNP loci. We found evidence of overall weak spatial genetic structure that decreased from 2012 to 2015 and a genetic diversity homogenization among the sites. We also found genetic evidence of a long-distance dispersal event over > 140 km. These results indicate that dispersal is the key mechanism involved in driving population synchrony of the outbreak. Early intervention management strategies that aim to control source populations have the potential to be effective through limiting dispersal. However, the timing of such interventions relative to outbreak progression is likely to influence their probability of success.
Data from: Genetic assessment of population structure and connectivity in the threatened Mediterranean coral Astroides calycularis (Scleractinia, Dendrophylliidae) at different spatial scales
Understanding dispersal patterns, population structure and connectivity among populations is helpful in the management and conservation of threatened species. Molecular markers are useful tools as indirect estimators of these characteristics. In this study we assess the population genetic structure of the endemic Mediterranean coral Astroides calycularis in the Alboran Sea at local and regional scales, and at three localities outside of this basin. Bayesian clustering methods, traditional F-statistics and Dest statistics were used to determine the patterns of genetic structure. Likelihood and coalescence approaches were used to infer migration patterns and effective population sizes. The results obtained reveal a high level of connectivity among localities separated by as much as one kilometer and moderate levels of genetic differentiation among more distant localities, somewhat corresponding with a stepping-stone model of gene flow and connectivity. These data suggest that connectivity among populations of this coral is mainly driven by the biology of the species, with low dispersal abilities; in addition, hydrodynamic processes, oceanographic fronts and the distribution of rocky substrate along the coastline may influence larval dispersal.
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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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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.