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549 results for “population size”
Mollusc population size distribution monitoring: Fall 2004 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh, monitoring sites 1-10
This data set is the Fall 2004 report of infaunal and epifaunal mollusc species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, fixed in fomalin, transferred to and preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or small etched rulers under a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-0705a1. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population size distribution monitoring: Fall 2006 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh, monitoring sites 1-10
This data set is the Fall 2006 report of infaunal and epifaunal mollusc species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, fixed in fomalin, transferred to and preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or small etched rulers under a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-0705c1. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population size distribution monitoring: Fall 2007 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2007 report of infaunal and epifaunal mollusc species' size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-0804a1. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population size distribution monitoring: Fall 2008 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2008 report of infaunal and epifaunal mollusc species' size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-0812a1. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population size distribution monitoring: Fall 2009 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2009 report of infaunal and epifaunal mollusc species' size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-1010a1. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population size distribution monitoring: Fall 2010 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2010 report of infaunal and epifaunal mollusk species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-1101a1. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population size distribution monitoring: Fall 2011 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2011 report of infaunal and epifaunal mollusk species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-1208a1. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population size distribution monitoring: Fall 2012 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2012 report of infaunal and epifaunal mollusk species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-1302. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population size distribution monitoring: Fall 2017 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2017 report of infaunal and epifaunal mollusc species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-1807. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population size distribution monitoring: Fall 2001 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh, monitoring sites 1-10
This data set is the Fall 2001 report of infaunal and epifaunal mollusc species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, fixed in fomalin, transferred to and preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or small etched rulers under a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-0301a. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Shrimp populations variability in numbers and sizes in response to disturbance and seasons on 20 pools along the reach of Quebrada Prieta, Luquillo Experimental Forest
Shrimp populations were monitored at approximately 3 week intervals to determine the variability in numbers and sizes of each species in response to disturbance and seasons. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Population size, HIV prevalence, and antiretroviral therapy coverage among key populations in sub-Saharan Africa: collation and synthesis of survey data 2010-2023
<p>This dataset contains surveillance study estimates for population size, HIV prevalence, and ART coverage among female sex workers (FSW), men who have sex with men (MSM), people who inject drugs (PWID), and transgender men and women (TGM/W) from 2010-2023. It was created to support the UNAIDS Estimates Key Population Workbook for use by HIV estimates teams in sub-Saharan Africa. Key population surveillance reports, including Ministry of Health-led biobehavioural surveys, mapping studies, and academic studies were used to populate the database.</p> <p>The dataset was populated using existing key population size estimate databases including:</p> <ul> <li>UNAIDS Key Population Atlas</li> <li>US Centers for Disease Control and Prevention surveillance database</li> <li>Global Fund against HIV/AIDS, TB, and Malaria surveillance database</li> <li>Global.HIV database</li> <li>Systematic review databases among MSM (<a href="https://pubmed.ncbi.nlm.nih.gov/31601542/" target="_blank" rel="noopener">Stannah et al, 2019</a> and <a href="https://pubmed.ncbi.nlm.nih.gov/37453439/" target="_blank" rel="noopener">Stannah et al., 2023</a>) and PWID (<a href="https://pubmed.ncbi.nlm.nih.gov/36996857/" target="_blank" rel="noopener">Degenhardt et al., 2023</a>)</li> </ul> <p><br>and was additionally supplemented by a literature review of peer-reviewed and grey literature sources.</p> <p>The data can be <a href="https://shiny.dide.ic.ac.uk/kp-data/" target="_blank" rel="noopener">explored in this web application</a> and the <a href="https://www.medrxiv.org/content/10.1101/2022.07.27.22278071v3" target="_blank" rel="noopener">accompanying manuscript can be found here</a></p>
Dataset of the article "A new and almost perfectly accurate approximation of the eigenvalue effective population size of a dioecious population: comparisons with other estimates and detailed proofs"
<p>Dataset of the article "A new and almost perfectly accurate approximation of the eigenvalue effective population size of a dioecious population: comparisons with other estimates and detailed proofs" (https://doi.org/10.5281/zenodo.7927968), recommended by PCI Evol Biol (https://evolbiol.peercommunityin.org/articles/rec?id=651)</p>
Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees
<p>Data and results of the paper "Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees".</p> <p>- data_table_species.csv: contains life-history and geographical range descriptors, terminal branch length and genomic estimated values for each substitution category, for each species in the dataset. Contains results obtained with both the complete data set and the subsampled dataset with 88 species.</p> <p>- data_table_genes.csv: contains values of substitution count that are sums of the values obtained for every species in the alignment. Also contains the results of HyPhy RELAX analyses for each alignment.</p> <p>- data_table_genes_species.csv: contains estimated values for each substitution category for each species in each alignment. Contains results obtained with both the complete data set and the subsampled dataset with 88 species.</p> <p> </p>
Figure 4 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 4. Copepod species composition (centre) and copepodid stage structures of the dominant species (left: Oyashio region, right: Okhotsk Sea). All data are integrated means of a 0– 500 m water column based on the IONESS samples in the Oyashio region (St. 19) and Okhotsk Sea (St. OK24) from October to November 1996. Error bars for the copepodid stage indicate standard deviations of each daily duplicate.
Figure 3 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 3. Vertical distribution of zooplankton biovolume in the Oyashio region (upper panels) and Okhotsk Sea (lower panels) from September to December in 1996–1998. Note that the biovolume axes are not the same between panels. Tc: thermocline.
Data from: Long-term persistence of monotypic dengue transmission in small size isolated populations, French Polynesia, 1978-2014
<p>Understanding the transition of epidemic to endemic dengue transmission remains a challenge in regions where serotypes co-circulate and there is extensive human mobility. French Polynesia, an isolated group of 72 inhabited islands, distributed among five geographically separated subdivisions, has recorded mono-serotype epidemics since 1944, with long inter-epidemic periods of circulation. Laboratory confirmed cases have been recorded since 1978, enabling exploration of dengue epidemiology under monotypic conditions in an isolated, spatially structured geographical location. A database was constructed of confirmed dengue cases, geolocated to island for a 35-year period. Statistical analyses of viral establishment, persistence and fade-out as well as synchrony among subdivisions were performed. Seven monotypic and one heterotypic dengue epidemic occurred, followed by low-level viral circulation with a recrudescent epidemic occurring on one occasion. Incidence was asynchronous among the subdivisions. Complete viral die-out occurred on several occasions with invasion of a new serotype, but also in the absence of any novel serotype. Island population size had a strong impact on the establishment, persistence and fade-out of dengue cases and endemicity was estimated achievable only at a population size in excess of 175 000. Despite island remoteness and low population size, dengue cases were observed somewhere in French Polynesia almost constantly, in part due to the spatial structuration generating asynchrony among subdivisions. Long-term persistence of dengue virus in this group of island populations may be enabled by island hopping, although could equally be explained by a reservoir of sub-clinical infections on the most populated island, Tahiti.</p>
Data for: Effective population size mediates the impact of pollination services on pollen limitation
<p>Inadequate pollen receipt limits flowering plant reproduction worldwide. Ecological causes of pollen limitation ('PL'), like pollinator scarcity and low plant abundance, have been a primary focus of research. The genetic diversity of plant populations could impact both quantity and quality components of PL in concert with ecological factors, yet empirical examples are lacking. We evaluated joint effects of ecological factors (flower abundance, pollinator visitation) and genetic effective population size (N<sub>E</sub>) on PL across 13 populations of a common herb. We used a histological approach with 5504 styles from 1137 flowers to separate quantity and quality components of PL, and link these to reproductive output. N<sub>E</sub> and pollinator visitation interacted to shape PL, but N<sub>E</sub> had stronger direct effects. Effectively smaller populations experienced stronger quantity PL, and controlled crosses in a pollinator-free environment revealed that pollen quantity was an intrinsic population-level attribute that increased with N<sub>E</sub>. Pollinator visitation enhanced pollen quality, but only in effectively larger populations. Quantity and quality PL negatively impacted fruit and seed set, respectively.<em> </em>Results highlight that PL is dictated by plant population genetic diversity in addition to commonly evaluated ecological factors.<strong> </strong>Efforts to support pollinators will only enhance plant reproduction in genetically diverse plant populations.</p>
Population size differences can lead to biases in phylogenetic inference and introgression detection in the presence of purifying selection
<p>Phylogenetic reconstruction and introgression detection rely on an assumption about the probability distribution of gene tree topologies. Recently, evidence has emerged that population size differences can affect the probability distribution of gene tree topologies in the presence of purifying selection. Here, using the population genetic simulator SLiM, we provide evidence that in the presence of purifying selection, population size differences can lead to biases in phylogenetic inference. We also provide evidence that in the presence of purifying selection, population size differences can cause statistics used for introgression detection to exhibit patterns resembling those caused by introgression. In addition, we present a theoretical analysis showing that the occurrence of population size–dependent gene tree distributions is an inherent consequence of purifying selection. Our work underscores the importance of considering the potential confounding effect of purifying selection on phylogenetic inference and introgression detection.</p>
Data for: Harvest and decimation affect genetic drift and the effective population size in wild reindeer
<p>Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long-term viability. The effective population size (N<sub>e</sub>) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate N<sub>e</sub> of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The N<sub>e</sub>/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14-year period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2 % in 2005-2018 and 44.8 % in 2021). Increased harvest rates decreased N<sub>e</sub> in the simulations, but less sex-biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased N<sub>e</sub>. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long-term genetic viability of wildlife populations subject to disease will also depend on the population impacts of the disease and how these interact with management actions.</p>
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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.