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360 results for “Ecology: population”
Data from: The interplay between local ecology, divergent selection and genetic drift in population divergence of a sexually antagonistic female trait
Genetically polymorphic species offer the possibility to study maintenance of genetic variation and the potential role for genetic drift in population divergence. Indirect inference of the selection regimes operating on polymorphic traits can be achieved by comparing population divergence in neutral genetic markers with population divergence in trait frequencies. Such an approach could further be combined with ecological data to better understand agents of selection. Here, we infer the selective regimes acting on a polymorphic mating trait in an insect group; the dorsal structures (either rough or smooth) of female diving beetles. Our recent work suggests that the rough structures have a sexually antagonistic function in reducing male mating attempts. For two species (Dytiscus lapponicus and Graphoderus zonatus), we could not reject genetic drift as an explanation for population divergence in morph frequencies, while for the third (Hygrotus impressopunctatus) we found that divergent selection pulls morph frequencies apart across populations. Furthermore, population morph frequencies in H. impressopunctatus were significantly related to local bioclimatic factors, providing an additional line of evidence for local adaptation in this species. These data therefore suggest that local ecological factors and sexual conflict interact over larger spatial scales to shape population divergence in the polymorphism.
Data from: A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)
The central-marginal hypothesis (CMH) predicts that population size, genetic diversity, and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core-to-edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size, and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core-to-edge genetic patterns. These results suggest that multiple processes may influence a species' distribution based on the heterogeneity of habitat across a species' range and that replicated sampling may be needed to accurately test the CMH. Our work also emphasizes the importance of identifying the geographic range core with methods other than using the Euclidean center on a map, which may help to explain discrepancies among other empirical tests of the CMH. Assessing core to edge population genetic patterns across an entire species' range accompanied with ENM can inform our general understanding of the mechanisms leading to species' geographic range limits.
Data from: Population density and size influence pollen dispersal pattern and mating system of the predominantly outcrossed Banksia nivea (Proteaceae) in a threatened ecological community
Gene flow is a critical component of plant mating systems and influences population fitness, yet pollen dispersal can be highly variable and influenced by natural and anthropogenic fragmentation. Gene flow through pollen dispersal was investigated in two populations of contrasting size and habitat context in Banksia nivea ssp. uliginosa, a rare species in the Busselton ironstone threatened ecological community with a naturally fragmented distribution. Paternity analysis was conducted with seven microsatellite loci to determine mating system parameters and patterns of pollen dispersal. Outcrossing was high in both populations with a similar level of selfing for both populations despite differences in population size, density and vegetation matrix. Most mating occurred within 10 m of a mother plant in the small, clumped population, while more dispersed mating, up to 50 m from a mother plant, was recorded in the large, less dense population. Our results show that population density and size are important influences on mating system parameters and level of pollen dispersal.
Data files for «Wood warbler population dynamics in response to mast seeding regimes in Europe», Journal: Ecology
<p><strong>Abstract</strong></p><p>Mast seeding is the episodic, massive production of plant seeds synchronized over large areas. The resulting superabundance of seeds represents a resource pulse that can profoundly affect animal populations across trophic levels. Following years of high seed production, abundances of both seed consumers and their predators increase. Higher predator abundance leads to increased predation pressure across the trophic web, impacting non-seed consumers such as the wood warbler <i>Phylloscopus sibilatrix</i> through increased nest predation after tree mast years. Over the past 30 years, the frequency of tree seed masts has increased while wood warbler populations have declined in several regions of Europe. We hypothesised that increasing mast frequencies may have contributed to the observed population declines by creating suboptimal breeding conditions in years after masting. We measured reproductive output in four study areas in central Europe, which was between 0.61 and 1.24 fledglings lower in years following masting than non-masting. For each study area, we used matrix population models to predict population trends based on the estimated reproductive output and the local mast frequencies. We then compared the predicted with the observed population trends to assess if the frequency of mast years contributed to the population dynamics. In Wielkopolska National Park (PL) and Hessen (DE), masting occurred on average only every 4 years and populations were stable or nearly so, whereas in Jura (CH) and Białowieża National Park (PL), masting occurred every 2 and 2.5 years, respectively, and populations were declining. The simple matrix population models predicted the relative difference among local population trends over the past 10-20 years well, suggesting that the masting frequency may partly explain regional variation in population trends. Simulations suggest that further increases in mast frequency will lead to further declines in wood warbler populations. We show that changes in a natural process, such as mast seeding, may contribute to the declines of animal populations through cascading effects.</p>
State-dependent mortality, not behavior, fragments population distribution of a long-lived mammal after ecological disturbance
<p>Data and code used to produce figures and analyses for the peer-reviewed paper "State-dependent mortality, not behavior, fragments population distribution of a long-lived mammal after ecological disturbance". All demographic and GPS data were collected by the authors as part of the Wyoming Range Mule Deer Project, and spatial data were derived from publicly available GIS platforms. </p> <p>Questions about data and code can be directed to rraffer1@uwyo.edu and tlasharr@uwyo.edu.</p> <p> </p>
Subspecies and Distribution. A. [. fusciceps Gray, 1866 — NW Ecuador, W of the Andes, historically in the provinces of Esmeraldas and Carchi, from the Colombian border S to the Cordillera de Colonche in the Guayas Province (most S record is in "Puente sobre el rio Chimbo," Chimborazo Province), but today it is restricted to two remnant populations (Awa Ethnological Reserve N of the Rio Mira, and Cotacachi-Cayapas Ecological Reserve and adjacent Los Cedros Protected Forest and surrounding forests S of the Rio Mira). A. f. rufiventris Sclater, 1872 — E Panama (Atlantic slope) and W Colombia from the Uraba region in NW Antioquia, N through Cordoba, Sucre, and N Bolivar departments (N distributional limit on the S bank of the Canal del Dique, Cartagena), W of the Rio Cauca to the coast, E to the lower Rio Cauca along the W bank to SC Antioquia (the Cerro Pirre or the Rio Tucuti marks the border with A. geoffroyi grisescens), and S to the Cordillera Occidental of the Andes in SW Colombia (the most southerly record is Barabacoas, Narino Department). in Atelidae
Subspecies and Distribution. A. [. fusciceps Gray, 1866 — NW Ecuador, W of the Andes, historically in the provinces of Esmeraldas and Carchi, from the Colombian border S to the Cordillera de Colonche in the Guayas Province (most S record is in "Puente sobre el rio Chimbo," Chimborazo Province), but today it is restricted to two remnant populations (Awa Ethnological Reserve N of the Rio Mira, and Cotacachi-Cayapas Ecological Reserve and adjacent Los Cedros Protected Forest and surrounding forests S of the Rio Mira). A. f. rufiventris Sclater, 1872 — E Panama (Atlantic slope) and W Colombia from the Uraba region in NW Antioquia, N through Cordoba, Sucre, and N Bolivar departments (N distributional limit on the S bank of the Canal del Dique, Cartagena), W of the Rio Cauca to the coast, E to the lower Rio Cauca along the W bank to SC Antioquia (the Cerro Pirre or the Rio Tucuti marks the border with A. geoffroyi grisescens), and S to the Cordillera Occidental of the Andes in SW Colombia (the most southerly record is Barabacoas, Narino Department).
Data from: Population genomics of Sitka black-tailed deer supports invasive species management and ecological restoration on islands
<p>Invasive mammals represent a critical threat to island biodiversity; eradications can result in ecological restoration yet may fail in the absence of key population parameters. Over-browsing by invasive Sitka black-tailed deer (<em>Odocoileus hemionus sitkensis</em>) is causing severe ecological and cultural impacts across the Haida Gwaii archipelago (Canada). Previous eradication attempts demonstrate forest regeneration upon deer removal, but reinvasion reverses conservation gains. Here we use restriction-site associated DNA sequencing (12,947 SNPs) to investigate connectivity and gene flow of invasive deer (n=181) across 15 islands, revealing little structure throughout Haida Gwaii and identifying the large, central island of Moresby (>2,600 km2) as the greatest source of migrants. As a result, the archipelago itself should be considered the primary eradication unit, with the exception of geographically isolated islands like SGang Gwaay. Thus, limiting eradications to isolated islands combined with controlled culling and enhanced biosecurity may be the most effective strategies for achieving ecological restoration goals.</p>
Geographical and ecological variables of Pseudotaxus chienii populations
<p><em><span>Pseudotaxus chienii</span></em><span>, belonging to the monotypic genus <em>Pseudotaxus</em> (Taxaceae), is a relict conifer endemic to China. Its populations are usually small and patchily distributed, having a low capacity of natural regeneration. To gain a clearer understanding of how landscape variables affect the local adaptation of <em>P. chienii</em></span><span>, we applied EST-SSR markers in conjunction with landscape genetics methods: (1) to examine the population genetic pattern and spatial genetic structure; (2) to perform genome scan and selection scan to identify outlier loci and the associated landscape variables; and (3) to model the ecological niche under climate change. </span><span>As a result, <em>P. chienii</em> was found to have a moderate level of genetic variation and a high level of genetic differentiation. Its populations displayed a significant positive relationship between the genetic and geographical distance (i.e., "isolation by distance" pattern) and a strong fine scale spatial genetic structure within 2 km.<a name="_Hlk53775407"> A putatively adaptive locus EMS6 (functionally annotated to cellulose synthase A catalytic subunit 7) was identified, which was found significantly associated with soil Cu, K, and Pb content and the combined effects of temperature and precipitation. Moreover, <em>P. chienii</em> was predicted to experience significant range contractions in future climate change scenarios. Our results highlight the potential of specific soil metal content and climate variables as the driving force of adaptive genetic differentiation in P<em>. chienii</em>. </a><a name="_Hlk70692721">The data would also be useful to develop a conservation action plan for <em>P. chienii</em>.</a></span></p> <p> </p>
Figure 5 in Population ecology of the orb-weaver spider Eustala taquara (Keyserling) (Araneidae)
Figure 5. Circular histograms of age structure established for the population of Eustala taquara. The black vector line inside the circle indicates the mean angle or direction of the data. The transverse line on the external sector of the circle indicates the confidence interval of 95%.
Figure 3. A in Population ecology of the orb-weaver spider Eustala taquara (Keyserling) (Araneidae)
Figure 3. A two-year monthly variation in the number of Eustala taquara individuals at Serra do Japi, São Paulo, Brazil.
Figure 2 in Population ecology of the orb-weaver spider Eustala taquara (Keyserling) (Araneidae)
Figure 2. Circular histogram of abundance of the Eustala taquara population. The black vector line inside the circle indicates the mean angle; the transverse line on the external sector of the circle indicates the confidence interval (95%).
Figure 7 in Population ecology of the orb-weaver spider Eustala taquara (Keyserling) (Araneidae)
Figure 7. Ivlev's electivity index indicating the preference for or rejection of food items, according to the prey type (a, b) and body length in cm (c, d), by juveniles and subadult/adult individuals of the orb-web spider Eustala taquara. Dip = Diptera, Hym = Hymenoptera, Hem = Hemiptera, Col = Coleoptera, Ara = Araneae, Lep = Lepidoptera, Pso = Psocoptera, Thy = Thysanoptera.
Figure 6 in Population ecology of the orb-weaver spider Eustala taquara (Keyserling) (Araneidae)
Figure 6. Circular frequency histograms of adult females and adult males of Eustala taquara. The black vector line inside the circle indicates the mean angle or direction of the data. The transverse line on the external sector of the circle indicates the confidence interval of 95%.
Figure 1 in Population ecology of the orb-weaver spider Eustala taquara (Keyserling) (Araneidae)
Figure 1. Climatic diagram of Serra do Japi, São Paulo, Brazil, registering the temperature and precipitation of the period 2011–2013. Areas containing vertical lines indicate humid periods; dark areas indicate super-wet periods; and dotted areas indicate dry periods.
F I G U R E 6 in Dispersal in dendritic networks: Ecological consequences on the spatial distribution of population densities
F I G U R E 6 Euclidean distances moved by Tetrahymena individuals depending on densities in our entire dataset. Across all replicates of all landscapes (patches from different landscapes types highlighted by different symbols; see legend) we find positively densitydependent movement. The solid lines represent fits of the averaged linear mixed model (red: dendritic landscapes; blue: linear landscapes) and the shaded area shows 95% confidence intervals (see Table 4 for model selection results). [Colour figure can be viewed at wileyonlinelibrary.com]
F I G U R E 4 in Dispersal in dendritic networks: Ecological consequences on the spatial distribution of population densities
F I G U R E 4 Comparison of variation in population densities between linear and dendritic networks at day 15 of the experiment. The solid line represents the difference between inter-quartile range (IQR) over median population densities of linear and dendritic landscapes. The distribution (grey) represents the distribution of the differences between IQR over median population densities of 200,000 random re-samplings for our data. As we theoretically expect the dendritic landscapes to be more variable we can perform a one-sided test which gives a probability of p =.047 of our observed difference between IQR to median ratios to be larger than zero. [Colour figure can be viewed at wileyonlinelibrary.com]
F I G U R E 3 in Dispersal in dendritic networks: Ecological consequences on the spatial distribution of population densities
F I G U R E 3 Fit of theoretical expectations to the distribution of Tetrahymena population densities depending on network type (linear versus dendritic networks), network position (central versus inner versus outer nodes) for day 15. Violin plots show the overall distribution of the data, the white point gives the median, and the solid black line the 25% and 75% percentiles, respectively. Given the network structure (Figure 1) and the three replicates per landscape, distributions include N = 18 (9, 3) measurements for outer (inner, central) nodes of dendritic networks and N = 6 (6, 18) measurements for outer (inner, central) nodes of linear landscapes. Horizontal red and blue lines visualise fits of the theoretically expected distribution of population densities to data from the dendritic and linear networks assuming network specific dispersal rates (d) and carrying capacities (K). White squares show fits of the theoretically expected distribution of population densities assuming the same d and K values for both network types. Shaded areas, respectively, error bars, show 95% confidence intervals of the fits. [Colour figure can be viewed at wileyonlinelibrary.com]
F I G U R E 2 in Dispersal in dendritic networks: Ecological consequences on the spatial distribution of population densities
F I G U R E 2 Distribution of Tetrahymena population densities depending on network type (linear versus dendritic networks), network position (central versus inner versus outer nodes) and time (days 0, 8 and 15). Violin plots show the overall distribution of the data, the white point gives the median, and the solid black line the 25% and 75% percentiles, respectively. Given the network structure (Figure 1) and the three replicates per landscape, distributions include N = 18 (9, 3) measurements for outer (inner, central) nodes of dendritic networks and N = 6 (6, 18) measurements for outer (inner, central) nodes of linear landscapes. Horizontal lines visualise back-transformed parameter estimates of the averaged linear mixed effects model and shaded areas show 95% confidence intervals (see Table 2 for model selection results). [Colour figure can be viewed at wileyonlinelibrary.com]
F I G U R E 1 in Dispersal in dendritic networks: Ecological consequences on the spatial distribution of population densities
F I G U R E 1 Median population densities (in thousands of individuals) of Tetrahymena in corresponding dendritic (a) and linear (b) landscapes at the end of the experiment (day 15) and across the three replicate landscapes. In these landscapes, outer nodes are labelled "O," inner and central nodes are labelled "I" and "C", respectively. [Colour figure can be viewed at wileyonlinelibrary.com]
F I G U R E 5 in Dispersal in dendritic networks: Ecological consequences on the spatial distribution of population densities
F I G U R E 5 Euclidean distances moved by Tetrahymena individuals depending on network type (linear versus dendritic networks), network position (central versus inner versus outer nodes) and time (days 0, 8 and 15). Violin plots show the overall distribution of the data, the white point gives the median, and the solid black line the 25% and 75% percentiles, respectively. Given the network structure (Figure 1) and the three replicates per landscape distributions include N = 18 (9, 3) measurements for outer (inner, central) nodes of dendritic networks and N = 6 (6, 18) measurements for outer (inner, central) nodes of linear landscapes. Horizontal lines visualise back-transformed parameter estimates of the averaged linear mixed effects model and shaded areas show 95% confidence intervals (see Table 3 for model selection results). [Colour figure can be viewed at wileyonlinelibrary.com]
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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.