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32 results for “Population Collapse”
Collapse and Continuity: A multi-proxy reconstruction of settlement organization and population trajectories in the Northern Fertile Crescent during the 4.2kya Rapid Climate Change event (dataset and R scripts)
<p>The present digital archive is the outcome of the paper: <strong>Lawrence, D., Palmisano, A., and de Gruchy, M.W., 2021. <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244871">Collapse and Continuity: A multi-proxy reconstruction of settlement organization and population trajectories in the Northern Fertile Crescent during the 4.2kya Rapid Climate Change event</a></strong><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244871">.</a> <em><strong>PLoS ONE</strong></em><strong>,</strong> <strong><em>16</em></strong>(1).</p> <p>The dataset included here provides a collection of <strong>920 </strong>radiocarbon dates and <strong>1070</strong> sites from archaeological surveys. In addition, the digital archive related to this paper provides reproducible analyses in the form of three scripts written in R statistical computing language.</p>
Data from: Unexpected stability in faunal population abundances following an estuary-wide collapse of oysters
<p>Data describing the number and lengths of fish and macroinvertebrates sampled from long-term fisheries independent sampling in Florida’s coastal waters. Original data were collected by the Florida Fish and Wildlife Conservation Commission (FWC) Fish and Wildlife Research Institute (FWRI).</p>
On the impermanence of species: The collapse of genetic incompatibilities in hybridizing populations
<p>Species pairs often become genetically incompatible during divergence, which is an important source of reproductive isolation. An idealized picture is often painted where incompatibility alleles accumulate and fix between diverging species. However, recent studies have shown both that incompatibilities can collapse with ongoing hybridization, and that incompatibility loci can be polymorphic within species. This paper suggests some general rules for the behavior of incompatibilities under hybridization. In particular, we argue that redundancy of genetic pathways can strongly affect the dynamics of intrinsic incompatibilities. Since fitness in genetically redundant systems is unaffected by introducing a few foreign alleles, higher redundancy decreases the stability of incompatibilities during hybridization, but also increases tolerance of incompatibility polymorphism within species. We use simulations and theories to show that this principle leads to two types of collapse: in redundant systems, exemplified by classical Dobzhansky-Muller incompatibilities, collapse is continuous and approaches a quasi-neutral polymorphism between broadly sympatric species, often as a result of isolation-by-distance. In non-redundant systems, exemplified by coevolution among genetic elements, incompatibilities are often stable, but can collapse abruptly with spatial traveling waves. As both types are common, the proposed principle may be useful in understanding the abundance of genetic incompatibilities in natural populations.</p>
Figure 1. - A in Possible collapse of reef shark populations in remote coral reef ecosystems in the Coral Sea (Western Pacific)
Figure 1. - A: Location of the Chesterfield and Bampton reefs in a central position among the Coral Sea, between the Australian Eastern coast and New Caledonia. B: Close up of the reefs where the 2010 and 2011 field trips were conducted; specific spots for shark surveys are shown with circles around the Bampton Reefs. C: Close up on the Chesterfield reefs with circles showing the locations for fishing and underwater visual surveys.
Figure 3 in Possible collapse of reef shark populations in remote coral reef ecosystems in the Coral Sea (Western Pacific)
Figure 3. - Comparison of average sizes of grey reef shark (C. amblyrhynchos) assessed through underwater visual censuses during the 2010 (blue) and 2011 (orange) field trips. In order to facilitate the comparison, shark numbers were linked to effort (h). Sizes above 120 cm TL are essentially rep- resented by the assessment in BF3 spot (North Avon Islet) for which densities and sizes were far above the rest of the Bampton and Chesterfield reefs.
Figure 2 in Possible collapse of reef shark populations in remote coral reef ecosystems in the Coral Sea (Western Pacific)
Figure 2. - Number of grey reef shark (C. amblyrhynchos) per size classes caught in Moorea Island (French Polynesia) and Chesterfield Islands reefs (New Caledonia), respectively, with similar techniques and fishing effort (25 h × 1 operator). The size difference was assessed as highly significantly (P <0.001), and greater in Moorea than in the Chesterfield, by a one-tailed Mann-Whitney U-test.
On the impermanence of species: The collapse of genetic incompatibilities in hybridizing populations
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Data and code for: Sea level rise causes shorebird population collapse before habitat drowns
<p>Sea level rise causes habitat loss and is considered to be a key threat to coastal species globally. Sea level rise also reduces habitat quality, potentially threatening populations already before habitat drowns and is lost. The extent and timing of changes in habitat quality for wildlife actively adapting to sea level rise, and how this affects population numbers under different emission scenarios, is unknown. Here, we combine long-term field data with models of sea level rise, marsh geomorphology, adaptive behaviour, and population dynamics to show that habitat quality is already declining on three islands due to increased flooding of shorebird nests. Also, population collapses are projected well before habitat drowns. Habitat loss, a widely used proxy, thus severely underestimates population impacts of sea level rise and coastal species will suffer much sooner than previously thought. Despite shorebirds adapting by moving to higher grounds, sea level rise will result in up to 79% fewer birds in a century, eventually leading to extinction in their prime habitat. Local gas mining exacerbates matters, as deep soil subsidence makes habitat even more vulnerable to sea level rise, effectively halving the window of opportunity for conservation action. Climate change ultimately jeopardizes the biodiversity value of this UNESCO World Heritage Area, and nature management needs to take this long-term perspective on board by in the short-term, boosting the accretion of tidal marshes or developing flood-safe alternative habitat elsewhere.</p>
Data on range-wide breeding habitat use of the critically endangered Yellow-breasted Bunting Emberiza aureola after population collapse
<p>The population of the Yellow-breasted Bunting <em>Emberiza aureola</em>, a formerly widely distributed and abundant songbird of northern Eurasia, suffered a catastrophic decline and a strong range contraction between 1980 and 2013. There is evidence that the decline was driven by illegal trapping during migration, but potential contributions of other factors to the decline, such as land-use change, have not yet been evaluated. Before effects of land-use change can be evaluated, a basic understanding of the ecological requirements of the species is needed. We therefore compared habitat use in ten remaining breeding regions across the range, from European Russia to Japan and the Russian Far East. We also assessed large-scale variation in habitat parameters across the breeding range.</p> <p>We found large variation in habitat use, within and between populations. Differences were related to the cover and height of trees and shrubs at Yellow-breasted Bunting territories. In many regions, Yellow-breasted Buntings occupied early successional stages, including anthropogenic habitats characterized by mowing, grazing or fire regimes. We found that the probability of presence can be best predicted with the cover of shrubs, herbs and grasses. Highest probabilities were found at shrub cover values of 40 to 70 %.</p> <p>Differences in habitat use along a longitudinal gradient were small, but we found strong differences across latitudes, possibly related to habitat availability. We conclude that the remaining Yellow-breasted Bunting populations are not limited to specific habitat types. Our results provide important baseline information to model the range-wide distribution of this critically endangered species and to guide targeted conservation measures.</p>
Data on range-wide breeding habitat use of the critically endangered Yellow-breasted Bunting Emberiza aureola after population collapse
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Data and code for: Sea level rise causes shorebird population collapse before habitat drowns
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Population collapse in viviparid gastropods of the Lake Victoria ecoregion started before the Last Glacial Maximum
<p>For the purpose of reproducibility, we here provide the datasets and R script supporting the analyses of the paper "Population collapse in viviparid gastropods of the Lake Victoria ecoregion started before the Last Glacial Maximum" by Van Bocxlaer et al. This paper has been accepted for publication in Molecular Ecology on 31 July 2020. In this study, we examine the population structure of the clade of <i>Bellamya</i> gastropods that occupies the Lake Victoria ecoregion with the aim to relate past environmental change with demography and diversification dynamics. The here provided datasets include 1) an alignment of a fragment of the gene cytochrome <i>c</i> oxidase subunit 1 for 60 specimens; 2) genotype data for 321 individuals from 39 localities for 15 microsatellite loci (total dataset); 3) a regrouped genotype dataset (282 specimens from 21 localities for 15 microsatellite loci), which was used for some analyses in our study. Analyses were performed with various programs as reported in our paper. Here we provide input and result files (33 files in total) for these analyses, complemented with an R script that readily allows reproducing the majority of our inquiries.</p>
Data from: Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localised fishery collapse in a large Sciaenid fish, Protonibea diacanthus
As pressure on coastal marine resources is increasing globally, the need to quantitatively assess vulnerable fish stocks is crucial in order to avoid the ecological consequences of stock depletions. Species of Sciaenidae (croakers, drums) are important components of tropical and temperate fisheries and are especially vulnerable to exploitation. The black-spotted croaker, Protonibea diacanthus, is the only large sciaenid in coastal waters of northern Australia where it is targeted by commercial, recreational and indigenous fishers due to its food value and predictable aggregating behaviour. Localised declines in the abundance of this species have been observed, highlighting the urgent requirement by managers for information on fine and broad-scale population connectivity. This study examined the population structure of P. diacanthus across northwestern Australia using three complementary methods: genetic variation in microsatellite markers, otolith elemental composition and parasite assemblage composition. The genetic analyses demonstrated that there were at least five genetically distinct populations across the study region, with gene flow most likely restricted by inshore biogeographic barriers such as the Dampier Peninsula. The otolith chemistry and parasite analyses also revealed strong spatial variation among locations within broad-scale regions, suggesting fine-scale location fidelity within the lifetimes of individual fish. The complementarity of the three techniques elucidated patterns of connectivity over a range of spatial and temporal scales. We conclude that fisheries stock assessments and management are required at fine scales (100's km) to account for the restricted exchange among populations (stocks) and to prevent localised extirpations of this species. Realistic management arrangements may involve the successive closure and opening of fishing areas to reduce fishing pressure.
Data from: Population collapse of habitat-forming species in the Mediterranean: a long-term study of gorgonian populations affected by recurrent marine heatwaves
<p><span><span><span><span><span><span><span><span><span><span><span>Understanding the resilience of temperate reefs to climate change requires exploring the recovery capacity of their habitat-forming species from recurrent marine heatwaves (MHWs). Here, we show that, in a Mediterranean highly enforced Marine Protected Area established more than 40 years ago, habitat-forming octocoral populations that were firstly affected by a severe MHW in 2003 have not recovered after 15 years. Contrarily, they have followed collapse trajectories that have brought them to the brink of local ecological extinction. Since 2003, impacted populations of the red gorgonian <i>Paramuricea clavata</i> (Risso, 1826) and the red coral <i>Corallium rubrum</i> (Linnaeus, 1758) have followed different trends in terms of size structure, but a similar progressive reduction in density and biomass. Concurrently, recurrent MHWs were observed in the area during the 2003-2018 study period, which may have hindered populations recovery. The studied octocorals play a unique habitat-forming role in the coralligenous assemblages (i.e., reefs endemic to the Mediterranean Sea home to approximately 10% of its species). Therefore, our results underpin the great risk that recurrent MHWs pose for the long-term integrity and functioning of these emblematic temperate reefs.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Local population collapse of Ross's and lesser snow geese driven by failing recruitment and diminished philopatry
<p>We estimated survival and per capita production of young, as well as emigration and immigration, from 1997 to 2017 in Ross's goose <em>Anser rossii</em> and lesser snow goose <em>Anser caerulescens caerulescens</em>, which are sympatric species of migratory birds that nest in the central Canadian Arctic at one of the largest breeding colonies in North America. We formed age-structured integrated population models for each species that jointly analyzed live and dead encounter data as well as breeding adult population size and fecundity data to understand drivers of population dynamics. We compared the demography between species because both species increased during the 1990s and early 2000s yet thereafter snow geese declined, while Ross's geese continued to increase, then stabilized and similarly declined. Declines in Ross's and snow goose populations were caused by reduced per capita production of young, and juvenile survival, as well as increased adult and juvenile emigration. Stronger declines in juvenile survival in snow geese explain their earlier population decline compared to Ross's geese. Despite the divergence in population trends in Ross's and snow geese, we found strong synchrony in demographic rates which suggested substantial emigration from this colony and similar responses to environmental conditions. We provide a novel m-array implementation specific to a multi-state Burnham model which greatly improved computational efficiency and convergence of posterior estimates.</p>
Data from: Population collapse of habitat-forming species in the Mediterranean: a long-term study of gorgonian populations affected by recurrent marine heatwaves
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Data from: Demographic collapse and low genetic diversity of the Irrawaddy dolphin population inhabiting the Mekong River
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Data from: Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localised fishery collapse in a large Sciaenid fish, Protonibea diacanthus
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Data from: Landscape structure and the genetic effects of a population collapse
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Data from: Hybridization following population collapse in a critically endangered antelope
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Allen Brain Atlas
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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.