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1,659 results for “structured population”
Figure 1 in Changes in abundance and community structure of the zooplankton population during the 2008 mucilage event in the northeastern Marmara Sea
Figure 1. Study area.
Figure 5 in Population structure and spatial distribution of the tiger (Panthera tigris, Felidae, Carnivora) in Southwestern Primorye (Russian Far East)
Figure 5. Layout of home ranges of the GPS-collared tigers (Hernandez-Blanco et al., 2015).
Figure 3 in Population structure and spatial distribution of the tiger (Panthera tigris, Felidae, Carnivora) in Southwestern Primorye (Russian Far East)
Figure 3. Relationship between tigers according to DNA identification.
Figure 2 in Population structure and spatial distribution of the tiger (Panthera tigris, Felidae, Carnivora) in Southwestern Primorye (Russian Far East)
Figure 2. Distribution of tiger tracks in Southwestern Primorye.
Seasonality and inter-annual stability in the population genetic structure of Batrachospermum gelatinosum (Rhodophyta)
<p>Data used for Shainker-Connelly et al. in biorxiv: https://www.biorxiv.org/content/10.1101/2024.09.20.614195v1</p>
Data and codes for "Habitat structural complexity increases age-class coexistence and population growth rate through relaxed cannibalism in medaka fish"
<p>The zip file contains readme files, as well as data and codes to reproduce results and figures from the paper.</p>
Data from: Environmental heterogeneity and not vicariant biogeographic barriers generate community wide population structure in desert adapted snakes
Genetic structure can be influenced by local adaptation to environmental heterogeneity and biogeographic barriers, resulting in discrete population clusters. Geographic distance among populations, however, can result in continuous clines of genetic divergence that appear as structured populations. Here we evaluate the relevant importance of these three factors over a landscape characterized by environmental heterogeneity and the presence of a hypothesized biogeographic barrier in producing population genetic structure within 13 codistributed snake species using a genomic dataset. We demonstrate that geographic distance and environmental heterogeneity across western North America contribute to population genomic divergence. Surprisingly, landscape features long thought to contribute to biogeographic barriers play little role in divergence community wide. Our results suggest that isolation by environment is the most important contributor to genomic divergence. Furthermore, we show that models of population clustering that incorporate spatial information consistently outperform nonspatial models, demonstrating the importance of considering geographic distances in population clustering. We argue that environmental and geographic distances as drivers of community-wide divergence should be explored before assuming the role of biogeographic barriers.
Data from: The socially parasitic ant Polyergus mexicanus has host-associated genetic population structure and related neighboring nests
<p>The genetic structure of populations can be both a cause and a consequence of ecological interactions. For parasites, genetic structure may be a consequence of preferences for host species or of mating behavior. Conversely, genetic structure can determine where conspecific interactions among parasites lay on a spectrum from cooperation to conflict. We used microsatellite loci to characterize the genetic structure of a population of the socially parasitic dulotic (aka "slave-making") ant (<i>Polyergus mexicanus</i>), which is known for its host-specificity and conspecific aggression. First, we assessed whether the pattern of host species use by the parasite has influenced parasite population structure. We found that host species use was correlated with subpopulation structure, but this correlation was imperfect: some subpopulations used one host species exclusively, while others used several. Second, we examined the viscosity of the parasite population by measuring the relatedness of pairs of neighboring parasitic ant nests at varying distances from each other. Although natural history observations of local dispersal by queens suggested the potential for viscosity, there was no strong correlation between relatedness and distance between nests. However, 35% of nests had a closely related neighboring nest, indicating that kinship could potentially affect the nature of some interactions between nests of this social parasite. Our findings confirm that ecological forces like host species selection can shape the genetic structure of parasite populations, and that such genetic structure has the potential to influence parasite-parasite interactions in social parasites via inclusive fitness.</p>
Data from: How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish
Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth (library quality), as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these "simple" decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and low sequencing depth (library A); and (2) more loci and higher sequencing depth (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. FST and DAPC were robust to varying the population map and increasing the stringency of missing data requirements. In contrast, ADMIXTURE was unable to resolve strong population differentiation when increasing these same parameters in library A. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library quality and bioinformatics parameters can have potentially important impacts on the interpretation of population subdivision. Although costly, the early investment in a high-quality library and more conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation.
A transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure
<p>File S1: Alignment of Botrychium CRY2cA sequences used to infer the genus-level phylogeny.</p> <p>File S2: Peptide sequences used to infer the orthogroups named according species names or identifiers (see Table S1).</p> <p>File S3: Alignments of the orthogroup sequences subset used to infer the phylogenomy.</p> <p>File S4: Output files from modeltest-ng named by orthogroup names.</p> <p>File S5: Output files from raxml-ng named by orthogroup names.</p>
Population structure of giant clams (sub-family: Tridacninae) across Palau: implications for conservation
<p>Giant clams (Sub-family: Tridacninae) are an important food and economic resource for the Republic of Palau. Previous surveys of giant clams conducted over 20 years ago found diverse, localized populations across Helen Reef and the Rock Islands Southern Lagoon. This study updates population structure data for Palauan giant clams and investigates the impacts of conservation on these important bivalves. We surveyed eleven sites within fringing, barrier, atoll, and oceanic reefs across the Palauan archipelago (total area = 1650m<sup>2</sup>). A total of 831 clams were measured across seven species (<i>Tridacna crocea, T. maxima, T. noae, T. squamosa, T. derasa, T. gigas, </i>and <i>Hippopus hippopus</i>). In addition, this is the first documented case of <i>T. noae</i> in Palau. Our measurements show that giant clams in Palau are among the most abundant and densely distributed compared to other Indo-Pacific reefs. <i>T. crocea </i>exhibited the highest abundance (521 individuals) and density (20.0 ± 2.9 per 50m<sup>2</sup>) of all species in this survey. However, high demand from local and international markets may have resulted in low average shell lengths and reduced abundances of adult clams within the most abundant species: <i>T. crocea, T. maxima, </i>and <i>T. squamosa</i>. Despite these harvesting pressures, Palau's incorporation of bottom-up traditional and modern conservation initiatives has positively impacted <i>T. crocea</i>, the most targeted species by local fishers. Within the Ngermedellim Marine Sanctuary, <i>T. crocea </i>exhibit high abundances of recruits and adults, suggesting that protection from fishing has increased replenishment rates and reduced mortality within this conservation area. As these bivalves continue to be exploited, we suggest that continued protection of and the implementation of size-limits will enable giant clams to remain abundant and diverse in Palau.</p>
Figure 6 in Population structure of Tachypleus tridentatus (Chelicerata: Merostomata) at a nursery beach in Puerto Princesa City, Palawan, Philippines
Figure 6. Age structure of juvenile population.
Figure 4 in Population structure of Tachypleus tridentatus (Chelicerata: Merostomata) at a nursery beach in Puerto Princesa City, Palawan, Philippines
Figure 4. Size–frequency distribution of the medium-sized individuals using a 0.1-cm interval size.
Figure 2 in Population structure of Tachypleus tridentatus (Chelicerata: Merostomata) at a nursery beach in Puerto Princesa City, Palawan, Philippines
Figure 2. Size–frequency distribution of all individuals and exuviae using a 0.2-cm interval size.
Figure 5 in Population structure of Tachypleus tridentatus (Chelicerata: Merostomata) at a nursery beach in Puerto Princesa City, Palawan, Philippines
Figure 5. Size–frequency distribution of the largest individuals using a 0.3-cm interval size.
Figure 3 in Population dynamics, age structure and sex ratio of the bromeliad-dwelling jumping spider, Psecas chapoda (Salticidae)
Figure 3. Climatic data from Itauna farm (5 km from the study site), from May 1998 to April 2000.
Figure 4 in Population genetic structure and demographic history of the Chinese endemic Mongoloniscus sinensis (Dollfus, 1901) (Isopoda: Oniscidea)
Figure 4. Pairwise mismatch distributions for six derived clades.
Figure 1 in Genetic diversity, population structure and demographic history of Dugesia japonica in Taihang Mountains
Figure 1. Geographical distribution of Dugesia japonica populations sampled in Taihang Mountains.
Fig. 1 in Population structure and reproductive behavior of Sinaloa cichlid Cichlasoma beani (Jordan, 1889) in a tropical reservoir
Fig. 1. Aguamilpa Reservoir, Nayarit, Mexico. Black dots indicate landing sites and sampling areas.
Fig. 1 in Iheringichthys labrosus (Siluriformes: Pimelodidae) in the Piquiri River, Paraná, Brazil: population structure and some aspects of its reproductive biology
Fig. 1. Localization of the sampling sites in the Piquiri River.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.