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1,659 results for “structured population”
Figure 2. Zones A–D in Mammals under a colony of great cormorants: population structure and body condition of yellow-necked mice
Figure 2. Zones A–D, in which small mammals were trapped in 2011–2014: Zone A – strongest and longest-lasting influence of the colony; Zone B – expanding part of the colony, Zone C – strong former influence; Zone D – ecotone zone between colony and surrounding forest.
Figure 5 in Spatiotemporal distribution and population structure of Clibanarius symmetricus (Randall, 1840) (Crustacea, Diogenidae) in an Amazon estuary
Figure 5. Frequency of occurrence of Clibanarius symmetricus specimens of nonovigerous females (F), ovigerous females (OF), males (M), and intersex individuals (INT) by size class (cephalothoracic shield length, in mm), collected in the Marapanim estuary, Pará, Brazil.
Landscape population genetics structure in the West Nile virus vector, Culex tarsalis
<p>RADseq raw data</p>
Data from: Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis
Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia axyridis in its native area using various population genetic statistics and methods. We found that H. axyridis native area most likely consisted of two geographically distinct genetic clusters located in eastern and western Asia. We then performed approximate Bayesian computation (ABC) analyses on controlled simulated microsatellite data sets to evaluate: (i) the risk of selecting incorrect introduction scenarios, including admixture between sources, when the populations of the native area are genetically structured and sampling is incomplete, (ii) the ability of ABC analysis to minimize such risks by explicitly including unsampled populations in the scenarios compared. Finally, we performed additional ABC analyses on real microsatellite data sets to retrace the origin of biocontrol and invasive populations of H. axyridis, taking into account the possibility that the structured native area may have been incompletely sampled. We found that the invasive population in eastern North America, which has served as the bridgehead for worldwide invasion by H. axyridis, was probably formed by an admixture between the eastern and western native clusters. This admixture may have facilitated adaptation of the bridgehead population.
Data from: Genetic variation and structure of Diaphorina citri (Hemiptera:Liviidae) in populations from México
The Asian citrus psyllid, Diaphorina citri Kuwayama, is native to Asia but has recently invaded North America. Asian citrus psyllid is a significant pest of citrus crops by its direct feeding but, more importantly, as the vector of the bacterium 'Candidatus Liberibacter asiaticus', which causes Huanglongbing disease. Asian citrus psyllid was first found in México in 2001 and 2002 and, since then, has spread quickly across the country, suggesting rapid adaptation to new environments. Yet, we lack information on the genetic variation and structure that could facilitate or inhibit adaptation. Using six microsatellite markers, we analyzed genetic variation and structure among six localities in México: three in western states near the Pacific coast and two in the Yucatán Peninsula near the Gulf of México. We found low genetic diversity (no more than three alleles per locus) and intermediate differentiation between all populations. Asian citrus psyllid populations clustered into two genetic groups, but, surprisingly, these clusters were present in western populations. The first group included El Arenal, and the second group included Autlán de Navarro, Colima, and Tecomán. Interestingly, both of the Yucatán populations shared variation from the two clusters, suggesting admixture. We infer that reproductive isolation, barriers to gene flow, local selection, and the possibility of multiple invasions have influenced the current genetic structure of Asian citrus psyllid in México.
Data from: Nuclear and mitochondrial patterns of population structure in North Pacific false killer whales (Pseudorca crassidens)
False killer whales (Pseudorca crassidens) are large Delphinids typically found in deep water far offshore. However, in the Hawaiian Archipelago there are two resident island-associated populations of false killer whales, one in the waters around the main Hawaiian Islands (MHI) and one in the waters around the Northwestern Hawaiian Islands (NWHI). We use mitochondrial DNA (mtDNA) control region sequences and genotypes from 16 nuclear (nucDNA) microsatellite loci from 206 individuals to examine levels of differentiation among the two island-associated populations and offshore animals from the central and eastern North Pacific. Both mtDNA and nucDNA exhibit highly significant differentiation between populations, confirming limited gene flow in both sexes. The mtDNA haplotypes exhibit a strong pattern of phylogeographic concordance, with island-associated populations sharing three closely related haplotypes not found elsewhere in the Pacific. However, nucDNA data suggests that NWHI animals are at least as differentiated from MHI animals as they are from offshore animals. The patterns of differentiation revealed by the two marker types suggest that the island-associated false killer whale populations likely share a common colonization history, but have limited contemporary gene flow.
Data From: Genetic structure of recently fragmented suburban populations of European stag beetle
<p>Habitat loss and fragmentation due to urbanisation can negatively affect metapopulation persistence when gene flow among populations is reduced and population sizes decrease. Inference of patterns and processes of population connectivity derived from spatial genetic analysis has proven invaluable for conservation and management. However, a more complete account of population dynamics may be obtained by combining spatial and temporal sampling. We, therefore, performed a genetic study on European stag beetle (<i>Lucanus cervus</i> L.) populations in a suburban context using samples collected in three locations and during the period 2002-2016. The sampling area has seen recent landscape changes which resulted in population declines. Through the use of a suite of FST, clustering analysis, individual assignment, and relatedness analysis we assessed fine scale spatiotemporal genetic variation within and among habitat patches using 283 individuals successfully genotyped at 17 microsatellites. Our findings suggested the three locations to hold demographically independent populations, at least over time scales of relevance to conservation, though with higher levels of gene flow in the past. Contrary to expectation from tagging studies, dispersal appeared to be mainly female-biased. Although the life cycle of stag beetle suggests its generations to be discrete, no clear temporal structure was identified, which could be attributed to the varying duration of larval development. Since population bottlenecks were detected and estimates of effective number of breeders were low, conservation actions are eminent which should include the establishment of suitable dead wood for oviposition on both local and regional scales to increase (re)colonisation success and connectivity among current populations.</p>
Data from: How obstacles perturb population fronts and alter their genetic structure
As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle's shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call 'geometry-enhanced genetic drift', complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects expected from complex environments with many obstacles.
Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing
Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype composed of tetraploid and octoploid accessions, and a southern lowland ecotype composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single nucleotide polymorphisms (SNPs), of which 1,590,653 high confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype restricted non-synonymous SNPs that are predicted to impact protein function in genes that encode CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17,228 up-copy number variants (CNVs), 112,630 down-CNVs, and 14,430 presence/absence variants (PAV) impacting a total of 9,979 genes, including two upland-specific CNV-clusters. In total, 45,719 genes were impacted by a SNP, CNV, or a PAV across the panel providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.
Figure 4 in The occurrence of facultative paedomorphosis in a lacustrine population of the Pyrenean newt (Calotriton asper): morphology and age structure
Figure 4. Stained cross-section of a phalange of an 18-year-old larva of Calotriton asper.
Figure 2 in Life cycle and population structure of the terrestrial isopod Hemilepistus klugii (Brandt, 1833) (Isopoda: Oniscidea) in Iran
Figure 2. Mean population density/m2 in Hemilepistus klugii from Varamin in the years 2008– 2009.
Figure 5 in Life cycle and population structure of the terrestrial isopod Hemilepistus klugii (Brandt, 1833) (Isopoda: Oniscidea) in Iran
Figure 5. Monthly sex ratio in Hemilepistus klugii from Varamin during the sampling period.
Figure 1 in Population structure and reproductive biology of the fiddler crab Uca urvillei (Brachyura: Ocypodidae) in Maputo Bay (south Mozambique)
Figure 1. Uca urvillei (H. Milne Edwards, 1852). Size frequency distributions of all individuals sampled during the study period.
Figure 2 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 2 Phylogenetic trees of the mtDNA control region haplotypes in C. guichenoti reconstructed with Bayesian inference. Numbers at nodes represent Bayesian posterior probabilities and neighbor-joining tree. At the right side of the figure, the numbers represent the total of individuals from different sampling locations in each haplotype.
Figure 3 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 3 Median-joining network of the mtDNA control region haplotypes of C. guichenoti. The size of each circle indicates the relative frequency of the corresponding haplotype in the whole data set.
Supplementary material 1 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Tables S1, S2, Figures S1, S2
Figure 4 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 4 Isolation by distance (IBD) relationship among C. guichenoti wild populations in five populations collected in 2009 a and seven populations collected in 2019 b.
Figure 1 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 1 Sampling localities of China (solid triangles indicate sites in 2009; solid circle indicate sites in 2019) of C. guichenoti. For full names of populations, see Table 1.
Figure 2 in Genetic diversity, population structure and demographic history of Dugesia japonica in Taihang Mountains
Figure 2. Mismatch distribution of Dugesia japonica from Taihang Mountains based on mitochondrial COI.
Figure 1 in Postembryonic development, paedomorphosis, secondary sexual dimorphism and population structure of a new Florarctus species (Tardigrada, Heterotardigrada)
Figure 1. Developmental stages of the new Florarctus species, males and females.
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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.