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193 results for “Population connectivity”
Data from: Pleistocene island connectivity did not enhance dispersal or impact population size change in Galápagos geckos
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Genetic connectivity and population structure of African savanna elephants (Loxodonta africana) in Tanzania
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Fig. 1 in Connecting systematic and ecological studies using DNA barcoding in a population survey of Drosophilidae (Diptera) from Mt Oku (Cameroon)
Fig. 1. Percent success and failure in obtaining a COI sequence from specimens. A. Total number of flies in the sample. B. Date of field collection (month indicated in lowercase Roman numerals). n = number of specimens used.
Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot
<p>As human-induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant <i>Leucadendron salignum</i> or "common sunshine conebush" as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, are characteristic of the southwestern CFR, whereas, low population structure and more recent lineage coalescence depicts the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species-level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land-usage as a significant gene flow barrier, especially in severely-threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.</p>
Data from: Interactions between demography, genetics, and landscape connectivity increase extinction probability for a small population of large carnivores in a major metropolitan area
The extinction vortex is a theoretical model describing the process by which extinction risk is elevated in small, isolated populations owing to interactions between environmental, demographic, and genetic factors. However, empirical demonstrations of these interactions have been elusive. We modelled the dynamics of a small mountain lion population isolated by anthropogenic barriers in greater Los Angeles, California, to evaluate the influence of demographic, genetic, and landscape factors on extinction probability. The population exhibited strong survival and reproduction, and the model predicted stable median population growth and a 15% probability of extinction over 50 years in the absence of inbreeding depression. However, our model also predicted the population will lose 40–57% of its heterozygosity in 50 years. When we reduced demographic parameters proportional to reductions documented in another wild population of mountain lions that experienced inbreeding depression, extinction probability rose to 99.7%. Simulating greater landscape connectivity by increasing immigration to greater than or equal to one migrant per generation appears sufficient to largely maintain genetic diversity and reduce extinction probability. We provide empirical support for the central tenet of the extinction vortex as interactions between genetics and demography greatly increased extinction probability relative to the risk from demographic and environmental stochasticity alone. Our modelling approach realistically integrates demographic and genetic data to provide a comprehensive assessment of factors threatening small populations.
Data from: The highs and lows of dispersal: how connectivity and initial population size jointly shape establishment dynamics in discrete landscapes
Identifying the main factors driving introduced populations to establishment is a major challenge of invasion biology. Due to their small initial size, introduced populations are most vulnerable to extinction because of demographic stochasticity or Allee effects. While an increase in initial population size is known to increase establishment success, much remains to be understood regarding its interplay with connectivity in spatially structured environments. In order to better understand how demographic mechanisms interact at such spatial scale, we developed a stochastic model of population dynamics in discrete space to investigate the effect of connectivity and initial population size on establishment. The predictions derived from the model were then tested using experimental introductions of an insect parasitoid (Trichogramma chilonis) in spatially structured laboratory microcosms. Both theoretical and experimental results demonstrated that the connectivity of the introduction site had 1) a deleterious effect in the first generation when the introduced population was small and 2) a beneficial impact brought about by metapopulation effects in the subsequent generations. Interestingly, populations displayed a weakly pushed invasion pattern promoting early establishment, which was mainly underpinned by dispersal stochasticity and the discrete nature of the landscape. These results shed light on the critical influence of landscape connectivity on establishment dynamics.
Human-induced habitat fragmentation effects on connectivity, diversity and population persistence of an endemic fish, Percilia irwini, in the Biobío river basin (Chile)
<p> </p> <p>An understanding of how genetic variability is distributed in space is fundamental for the conservation and maintenance of diversity in spatially fragmented and vulnerable populations. While fragmentation can occur from natural barriers it can also be exacerbated by anthropogenic activities such as hydroelectric power plant development. Whatever the source, fragmentation can have significant ecological effects, including the disruptions of migratory processes and gene flow among populations. In Chile, the Biobío river basin exhibits a high degree of habitat fragmentation due to the numerous hydroelectric power plants in operation, the number of which is expected to increase following new renewable energy use strategies. Here, we assessed the effects of different kinds of barriers on the genetic structure of the endemic freshwater fish <em>Percilia irwini</em>, knowledge that is critically needed to inform conservation strategies in light of current and anticipated further fragmentation initiatives in the system. We identified 8 genetic units throughout the entire Biobío system with high effective sizes. A reduced effective size estimate was however observed in a single population located between two impassable barriers. Both natural waterfalls and human made dams were important drivers of population differentiation in this system, however, dams affect genetic diversity differentially depending on their mode of operation. Evidence of population extirpation was found in two river stretches limited by upstream and downstream dams. Significant gene flow in both directions was found among populations not separated by natural or anthropogenic barriers. Our results suggest a significant vulnerability of <em>P. irwini </em>populations to future dam development and demonstrate the importance of studying basin-wide data sets with genetic metrics to understand the strength and direction of anthropogenic impacts on fish populations.</p>
Data from: Population assignment reveals low migratory connectivity in a weakly structured songbird
Understanding migratory connectivity is essential for determining the drivers behind population dynamics and for implementing effective conservation strategies for migratory species. Genetic markers provide a means to describe migratory connectivity, however they can be uninformative for species with weak population genetic structure, which has limited their application. Here, we demonstrated a genomic approach to describing migratory connectivity in the prothonotary warbler, Protonotaria citrea, a Neotropical songbird of conservation concern. Using 26,189 SNPs, we revealed regional genetic structure between the Mississippi River Valley and the Atlantic Seaboard with overall weak genetic differentiation among populations (FST = 0.0055; 95% CI: 0.0051 - 0.0059). Genetic variation had a stronger association with geographic rather than environmental factors, with each explaining 14.5% and 8.2% of genetic variation, respectively. By varying the numbers of genomic markers used in population assignment models with individuals of known provenance, we identified a maximum assignment accuracy (89.7% to site, 94.3% to region) using a subset of 600 highly differentiated SNPs. We then assigned samples from nonbreeding sites to breeding region, and found low migratory connectivity. Our results highlight the importance of filtering markers for informative loci in models of population assignment. Quantifying migratory connectivity for weakly structured species will be useful for expanding studies to a wider-range of migratory species across taxonomic groups and may contribute to a deeper understanding of the evolution of migratory strategies.
Data from: An investigation for population maintenance mechanism in a miniature garden: genetic connectivity or independence of small islet populations of the Ryukyu five-lined skink
The Ryukyu five-lined skink (Plestiodon marginatus) is an island lizard that is even found in tiny islets with less than half a hectare of habitat area. We hypothesized that the island populations are maintained under frequent gene flow among the islands or independent of each other. To test our hypotheses, we investigated genetic structure of 21 populations from 11 land-bridge islands that were connected during the latest glacial age, and four isolated islands. Analyses using mitochondrial cytochrome b gene sequence (n = 67) and 10 microsatellite loci (n = 235) revealed moderate to high levels of genetic differentiation, existence of many private alleles/haplotypes in most islands, little contemporary migration, a positive correlation between genetic variability and island area, and a negative correlation between relatedness and island area. These evidences suggest a strong effect of independent genetic drift as opposed to gene flow, favoring the isolation hypothesis even in tiny islet populations. Isolation-by-distance effect was demonstrated and it became more prominent when the four isolated islands were excluded, suggesting that the pattern is a remnant of the land-bridge age. In a few island populations, however, the possibility of occasional overwater dispersals was partially supported and therefore could not be ruled out.
Data from: Amphibious mudskipper populations are genetically connected along coastlines, but differentiated across water
<p><strong>Aim:</strong> Many mudskippers in the family Gobiidae are obligately amphibious, requiring both aquatic and terrestrial portions of their life cycle. The terrestrial phase involves restrictions to mudflat habitats during breeding, when adults build burrows in the mud to lay eggs. The effects of this restricted out-of-water phase might be reflected in the population structure of the species. However, dispersal during the aquatic larval phase could connect distant populations. We examine one such mudskipper, <em>Periophthalmus modestus</em>, to test whether populations separated by water are more differentiated than those connected along a coastline.</p> <p><strong>Location:</strong> South and East China Sea</p> <p><strong>Taxon:</strong> <em>Periophthalmus modestus</em> (family: Gobiidae, subfamily: Oxudercinae) (Cantor 1842)</p> <p><strong>Methods:</strong> We collected 236 individuals from ten locations around the East and South China Seas. We used a targeted capture sequencing method, RADcap, to call SNPs from 365 loci. We used multiple spatial and population genetics analyses and coalescent models to address the contemporary and historic biogeography of the species.</p> <p><strong>Results:</strong> Based on observed levels of genetic variation and population structure, populations of <em>Ps. modestus </em>are connected across large distances of continuous coastline and small spans of water. Restricted long-distance dispersal across deep water has resulted in fragmentation of populations. We recovered no signal of isolation by distance, but instead, found genetic differentiation associated with regional groupings separated by large expanses of water.</p> <p><strong>Main conclusions: </strong>These results are consistent with the hypothesis that a limited dispersal phase significantly affects population structure in fishes. The restrictive amphibious life history may be a key factor in the present-day distribution and population structure of <em>Ps. modestus</em>. Interactions between organismal life history and geography are critical for explaining the population genetic structure of a species.</p>
Data from: Quantitative analysis of connectivity in populations of a semi-aquatic mammal using kinship categories and network assortativity
Analyzing the impact of anthropogenic and natural river barriers on the dispersal of aquatic and semi-aquatic species may be critical for their conservation, but no adequate genetic methods have been developed for quantifying the effect of specific barriers on current connectivity. Knowledge of kinship relationships between individuals and reconstructions of pedigrees obtained using genomic data can be extremely useful, not only for studying the social organization of animals, but also inferring how the last few generations of offspring have dispersed. In this study, we used kinship data to analyze connectivity patterns in a small semi-aquatic mammal, the Pyrenean desman, in an area comprising two river systems with close headwaters and dams of various sizes. Using a large SNP dataset from 70 specimens, we obtained kinship categories and reconstructed pedigrees. To quantify the barrier effect of specific obstacles, we constructed kinship networks and devised a method based on the assortativity coefficient, which measures the proportion between observed and expected kinship relationships across a barrier. The estimation of this parameter enabled us to infer that the most important barrier in the area was the watershed divide between the rivers, followed by a dam on one of the rivers. Other barriers did not significantly reduce the expected number of kinship relationships across them. This strategy and the information obtained with it may be crucial in determining the most important connectivity problems in an area and help develop conservation plans aimed at improving genetic exchange between populations of threatened species.
Figure 2 from: Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL (2014) Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. In: Wehrtmann IS, Bauer RT (Eds) Proceedings of the Summer Meeting of the Crustacean Society and the Latin American Association of Carcinology, Costa Rica, July 2013. ZooKeys 457: 271-288. https://doi.org/10.3897/zookeys.457.6569
Figure 2 - Dendrogram based on Neighbor-Joining distance method of COI gene sequences of individuals of Artemesia longinaris. Localities represent the analyzed specimens. Numbers are bootstrap support values (1000 replicates); values below 50% are not shown.
Figure 4 from: Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL (2014) Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. In: Wehrtmann IS, Bauer RT (Eds) Proceedings of the Summer Meeting of the Crustacean Society and the Latin American Association of Carcinology, Costa Rica, July 2013. ZooKeys 457: 271-288. https://doi.org/10.3897/zookeys.457.6569
Figure 4 - Haplotype network of Artemesia longinarisaccording to Median-Joining analysis. Each circle represent one haplotype found in the localities (53 haplotypes in 60 specimens). The size of the circle of each haplotype is proportional to its frequency in the sample. Each small dash represents a mutational step.
Figure 1 from: Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL (2014) Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. In: Wehrtmann IS, Bauer RT (Eds) Proceedings of the Summer Meeting of the Crustacean Society and the Latin American Association of Carcinology, Costa Rica, July 2013. ZooKeys 457: 271-288. https://doi.org/10.3897/zookeys.457.6569
Figure 1 - Southwest Atlantic collection sites. Map showing the localities of the specimens of Artemesia longinaris analyzed: 1 Macaé, Brazil 2 Ubatuba, Brazil 3 Santos, Brazil 4 Cananéia, Brazil 5 São Francisco do Sul, Brazil 6 Rio Grande, Brazil 7 Mar del Plata, Argentina. The gray band indicates the complete geographical distribution of Artemesia longinaris.
Figure 3 from: Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL (2014) Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. In: Wehrtmann IS, Bauer RT (Eds) Proceedings of the Summer Meeting of the Crustacean Society and the Latin American Association of Carcinology, Costa Rica, July 2013. ZooKeys 457: 271-288. https://doi.org/10.3897/zookeys.457.6569
Figure 3 - Phylogram for individuals of Artemesia longinaris inferred from Maximum Likelihood analysis of COI gene sequences. Localities represent analyzed specimens. Numbers are bootstrap support values (1000 replicates); values below 50% are not shown.
Geological and climatic factors affect the population genetic connectivity in Mirabilis himalaica (Nyctaginaceae): insight from phylogeography and dispersal corridors in the Himalaya-Hengduan Biodiversity hotspot
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Data from: Population genetics of jaguars (Panthera onca) in the Brazilian Pantanal: molecular evidence for demographic connectivity on a regional scale
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Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot
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Data from: An investigation for population maintenance mechanism in a miniature garden: genetic connectivity or independence of small islet populations of the Ryukyu five-lined skink
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Data from: Interactions between demography, genetics, and landscape connectivity increase extinction probability for a small population of large carnivores in a major metropolitan area
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Allen Brain Atlas
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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.