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944 results for “Human population”
Data from: Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations
While terrestrial megafaunal extinctions have been well characterized worldwide, our understanding of declines in marine megafauna remains limited. Here, we use ancient DNA analyses of prehistoric (<1450–1650 AD) sea lion specimens from New Zealand's isolated Chatham Islands to assess the demographic impacts of human settlement. These data suggest there was a large population of sea lions, unique to the Chatham Islands, at the time of Polynesian settlement. This distinct mitochondrial lineage became rapidly extinct within 200 years due to overhunting, paralleling the extirpation of a similarly large endemic mainland population. Whole mitogenomic analyses confirm substantial intraspecific diversity among prehistoric lineages. Demographic models suggest that even low harvest rates would likely have driven rapid extinction of these lineages. This study indicates that surviving Phocarctos populations are remnants of a once diverse and widespread sea lion assemblage, highlighting dramatic human impacts on endemic marine biodiversity. Our findings also suggest that Phocarctos bycatch in commercial fisheries may contribute to the ongoing population decline.
Data from: A population genetic signature of human releases in an invasive ladybeetle
Biological invasions have been accelerated by a variety of human activities. Propagule pressure, the number of introduced individuals and independent introductions, is likely to be influenced by these human activities and may be an important factor for successful range expansion in new environments. We tested whether the current distribution of the predatory ladybeetle Coccinella septempunctata in the introduced range (USA) is the result of multiple historical human introductions or natural range expansion from the first established populations in the USA. To test this hypothesis, we compared historical records of propagule size, propagule number, specific introduction locations, and the date of each introduction, with estimates of genetic variation in mitochondrial DNA (COI). Our results indicated that genetic diversity in the introduced range was positively correlated with historical records of propagule size and number, and negatively correlated with distance to nearest introduction point, suggesting that multiple human releases were successful. Higher genetic diversity in populations found near introduction points suggest that initial founder effects were limited, but lower genetic diversity found farther from introduction points is likely the result of serial founder effects during secondary range expansion. These results suggest that the current distribution of C. septempunctata in the introduced range is the result of a combination of human releases and short-range expansion from multiple established populations in introduced range.
Data from: Inbreeding within human Schistosoma mansoni: do host- specific factors shape the genetic composition of parasite populations?
The size, structure and distribution of host populations are key determinants of the genetic composition of parasite populations. Despite the evolutionary and epidemiological merits, there has been little consideration of how host heterogeneities affect the evolutionary trajectories of parasite populations. We assessed the genetic composition of natural populations of the parasite Schistosoma mansoni in northern Senegal. A total of 1346 parasites were collected from 14 snail and 57 human hosts within three villages and individually genotyped using nine microsatellite markers. Human host demographic parameters (age, gender and village of residence) and co-infection with Schistosoma haematobium were documented, and S. mansoni infection intensities were quantified. F-statistics and clustering analyses revealed a random distribution (panmixia) of parasite genetic variation among villages and hosts, confirming the concept of human hosts as 'genetic mixing bowls' for schistosomes. Host gender and village of residence did not show any association with parasite genetics. Host age, however, was significantly correlated with parasite inbreeding and heterozygosity, with children being more infected by related parasites than adults. The patterns may be explained by (1) genotype-dependent 'concomitant immunity' that leads to selective recruitment of genetically unrelated worms with host age, and/or (2) the 'genetic mixing bowl' hypothesis, where older hosts have been exposed to a wider variety of parasite strains than children. The present study suggests that host-specific factors may shape the genetic composition of schistosome populations, revealing important insights into host–parasite interactions within a natural system.
Humans drive spatial variation in mortality risk for a threatened wolf population in a Canis hybrid zone
<ol> <li>Large carnivores often exhibit high survival rates in protected areas, whereas intentional and unintentional human-caused mortality may be greater in adjacent areas. These patterns can result in source-sink dynamics and limit population expansion beyond protected areas.</li> <li>We used telemetry data from 438 canids in 141 packs collected from 2002–2020 to evaluate mortality risk for wolves, coyotes, and admixed canids in a 3-species hybrid zone in and adjacent to a large protected area in Ontario, Canada. The hybrid zone is occupied by most of the remaining eastern wolves (<em>Canis lycaon</em>), a rare, threatened species that hybridizes with sympatric eastern coyotes (<em>C. latrans</em>) and Great Lakes gray wolves (<em>C. lupus</em>).</li> <li>Within Algonquin Provincial Park (APP), annual human-caused mortality from harvest and vehicles was low (0.06, 95% CI [0.03, 0.08]), whereas annual human-caused mortality was higher in adjacent areas (0.31, 95% CI [0.25, 0.37]). Smaller protected areas implemented to help protect eastern wolves did not significantly reduce mortality. Eastern wolves survived poorly relative to other canids and dispersing canids survived poorly relative to residents. Mortality risk was greater when canids were closer to roads. Mortality risk was also increased or reduced by the strength of individual-level selection or avoidance of roads relative to their availability, respectively.</li> <li>Our results provide a comprehensive evaluation of factors influencing spatial variation in mortality risk for canids to inform eastern wolf recovery efforts. Additionally, we developed a novel modeling approach for investigating the influence of resource selection on mortality risk, which highlighted that individual-level responses to risk can strongly influence population-level mortality patterns.</li> <li> <em>Synthesis and applications</em>. Despite being listed as 'threatened' under the Ontario Endangered Species Act, eastern wolves are still legally trapped and shot outside protected areas in central Ontario. Eastern wolves and dispersing canids survive poorly outside of APP, primarily from human-caused mortality. These results, along with the apparent inadequacy of the smaller protected areas, suggest that expanding the threatened eastern wolf population outside APP is unlikely under current management conditions. Protecting eastern wolves from human-caused mortality is complicated as it would require a harvest ban for all canids, including coyotes.</li> </ol>
Correspondence on Li Yumei et al.: Exaggerated false positives by popular differential expression methods when analyzing human population samples.
<p>Scripts for manuscript</p>
Data from: Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age
We investigated how population changes and fluctuations in the pink-footed goose might have been affected by climatic and anthropogenic factors. First, genomic data confirmed the existence of two separate populations: western (Iceland) and eastern (Svalbard/Denmark). Second, emographic inference suggests that the species survived the last glacial period as a single ancestral population with a low population size (100-1,000 individuals) that split into the current populations at the end of the Last Glacial Maximum with Iceland being the most plausible glacial refuge. While population changes during the last glaciation were clearly environmental, we hypothesize that more recent demographic changes are human-related: (1) the inferred population increase in the Neolithic is due to deforestation to establish new lands for agriculture, increasing available habitat for pink-footed geese (2) the decline inferred during the Middle Ages is due to human persecution and (3) improved protection explains the increasing demographic trends during the 20th century. Our results suggest both environmental (during glacial cycles) and anthropogenic effects (more recent) can be a threat to species survival.
A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.
<p>https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84133</p>
Profiling of mature stage human breastmilk cells identifies host-defense lactocyte sub-populations
<p>Breastmilk is chock-full of nutrients, immunological factors, and cells that aid infant development. Maternal cells are the least studied breastmilk component, and their unique properties are difficult to identify using traditional techniques. Here, we characterized the cells in mature stage breastmilk from healthy donors at the protein, gene, and transcriptome levels. Holistic analysis of flow cytometry, qPCR, and single cell RNA sequencing data identified the predominant cell population as epithelial with smaller populations of macrophages and T cells. Two percent of epithelial cells expressed four stem cell markers: SOX2, TRA-1-60, NANOG, and SSEA4. Furthermore, milk contained six distinct epithelial lactocyte sub-populations, including three previously unidentified sub-populations programmed towards host-defense and intestinal development. Pseudotime analysis delineated the differentiation pathways of epithelial progenitors. Together, these data define healthy human maternal breastmilk cells and provide a basis for their application in maternal and infant medicine.</p>
Supplementary Information: Human populations in the world's mountains: spatio-temporal patterns and potential controls
<p>Supplementary Information (data, code, figures) for "Human populations in the world’s mountains: spatio-temporal patterns and potential controls" (Thornton et al., 2022)</p>
The first comprehensive revision of all the species attributed to Melomys led J. I. Menzies in 1996 to resurrect the genus Paramelomys and to redefine its morphologicallimits and species content. Menzies created P. gressitti as a new species belonging to a group displaying morphological similarities and including also P. lorentzii and P. moncktoni. Monotypic Distribution. E New Guinea. Descriptive notes. Head-body 135-162 mm, hindfoot 30-34 mm; no specific data are available for body weight. Gressitt's Mosaic-tailed Rat is a medium-sized Paramelomys with a soft, thick and woolly pelage, a long narrow foot, and a tail with three hairs per scale. It exhibits a medium-sepia dorsal pelage and a gray-buff ventral one. Tail is slightly shorter (99%) than head-body length. The skull has a narrow zygomatic plate. Habitat. Moist tropical mountain forest between 2300 m and 2400 m. Food and Feeding. No information. Breeding. No information. Activity patterns. Gressitt's Mosaic-tailed Rat is terrestrial. Movements, Home range and Social organization. No information. Status and Conservation. Classified as Endangered on The IUCN Red List owing to its small geographic range (less than 3500 km?*) and the destruction ofits habitat by mining and logging activities. The major threat to Gressitt's Mosaic-tailed Rat is ongoing habitat degradation caused by nearby human populations; habitat on Mount Kandy has been destroyed by gold-miners and wood-cutters. Bibliography. Menzies (1996). in Muridae
The first comprehensive revision of all the species attributed to Melomys led J. I. Menzies in 1996 to resurrect the genus Paramelomys and to redefine its morphologicallimits and species content. Menzies created P. gressitti as a new species belonging to a group displaying morphological similarities and including also P. lorentzii and P. moncktoni. Monotypic Distribution. E New Guinea. Descriptive notes. Head-body 135-162 mm, hindfoot 30-34 mm; no specific data are available for body weight. Gressitt's Mosaic-tailed Rat is a medium-sized Paramelomys with a soft, thick and woolly pelage, a long narrow foot, and a tail with three hairs per scale. It exhibits a medium-sepia dorsal pelage and a gray-buff ventral one. Tail is slightly shorter (99%) than head-body length. The skull has a narrow zygomatic plate. Habitat. Moist tropical mountain forest between 2300 m and 2400 m. Food and Feeding. No information. Breeding. No information. Activity patterns. Gressitt's Mosaic-tailed Rat is terrestrial. Movements, Home range and Social organization. No information. Status and Conservation. Classified as Endangered on The IUCN Red List owing to its small geographic range (less than 3500 km?*) and the destruction ofits habitat by mining and logging activities. The major threat to Gressitt's Mosaic-tailed Rat is ongoing habitat degradation caused by nearby human populations; habitat on Mount Kandy has been destroyed by gold-miners and wood-cutters. Bibliography. Menzies (1996).
Data from "A population of neurons selective for human voice in the monkey brain"
<p>Preprocessed datasets associated to the research article "A population of neurons selective for human voice in the monkey brain", PNAS.</p>
A human TH17 population with a tissue-resident signature in healthy and inflamed mucosal tissues
<p>A human TH17 population with a tissue-resident signature in healthy and inflamed mucosal tissues</p> <p>https://github.com/BenaroyaResearch/OralMucosa_Woodward_Davis_and_Prlic_Analysis</p>
Data from: Strong population structure in a species manipulated by humans since the Neolithic: the European fallow deer (Dama dama dama)
Species that have been translocated and otherwise manipulated by humans may show patterns of population structure that reflect those interactions. At the same time, natural processes shape populations, including behavioural characteristics like dispersal potential and breeding system. In Europe, a key factor is the geography and history of climate change through the Pleistocene. During glacial maxima throughout that period, species in Europe with temperate distributions were forced south, becoming distributed among the isolated peninsulas represented by Anatolia, Italy and Iberia. Understanding modern patterns of diversity depends on understanding these historical population dynamics. Traditionally, European fallow deer (Dama dama dama) are thought to have been restricted to refugia in Anatolia and possibly Sicily and the Balkans. However, the distribution of this species was also greatly influenced by human-mediated translocations. We focus on fallow deer to better understand the relative influence of these natural and anthropogenic processes. We compared modern fallow deer putative populations across a broad geographic range using microsatellite and mitochondrial DNA loci. The results revealed highly insular populations, depauperate of genetic variation and significantly differentiated from each other. This is consistent with the expectations of drift acting on populations founded by small numbers of individuals, and reflects known founder populations in the north. However, there was also evidence for differentiation among (but not within) physically isolated regions in the south, including Iberia. In those regions we find evidence for a stronger influence from natural processes than may be expected for a species with such strong, known anthropogenic influence.
Data from: Population genetics reveals high connectivity of giant panda populations across human disturbance features in key nature reserve
The giant panda is an example of a species that has faced extensive historical habitat fragmentation and anthropogenic disturbance, and is assumed to be isolated in numerous subpopulations with limited gene flow between them. To investigate the population size, health and connectivity of pandas in a key habitat area, we noninvasively collected a total of 539 fresh wild giant panda fecal samples for DNA extraction within Wolong Nature Reserve, Sichuan, China. Seven validated tetra-microsatellite markers were used to analyze each sample, and a total of 142 unique genotypes were identified. Non-spatial and spatial capture-recapture models estimated the population size of the reserve at 164 and 137 individuals (95% confidence intervals 153-175 and 115-163), respectively. Relatively high levels of genetic variation and low levels of inbreeding were estimated, indicating adequate genetic diversity. Surprisingly, no significant genetic boundaries were found within the population despite the national road G350 that bisects the reserve, which is also bordered with patches of development and agricultural land. We attribute this to high rates of migration, with 4 giant panda road-crossing events confirmed within a year based on repeated captures of individuals. This likely means that giant panda populations within mountain ranges are better connected than previously thought. Increased development and tourism traffic in the area and throughout the current panda distribution poses a threat of increasing population isolation, however. Maintaining and restoring adequate habitat corridors for dispersal is thus a vital step for preserving the levels of gene flow seen in our analysis and the continued conservation of the giant panda meta-population in both Wolong and throughout their current range.
Scavenging patterns of an inbred wolf population in a landscape with a pulse of human-provided carrion
<ol> <li> <span>Scavenging is an important part of food acquisition for many carnivore species that switch between scavenging and predation</span><span>. </span><span>In landscapes with anthropogenic impact, humans provide food that scavenging species can utilize. </span> </li> <li><span>We quantified the magnitude of killing versus scavenging by gray wolves (<em>Canis</em> <em>lupus</em>) in Scandinavia where humans impact the ecosystem through hunter harvest, land use practices, and infrastructure. We investigated the cause of death of different animals utilized by wolves, and examined how the proportion of their consumption time spent scavenging was influenced by season, wolf social affiliation, level of inbreeding, density of moose (<em>Alces</em> <em>alces</em>) as their main prey, density of brown bear (<em>Ursus</em> <em>arctos</em>) as an intra-guild competitor, and human density. </span></li> <li><span>We used data from 39 GPS-collared wolves covering 3,198 study days (2001–2019), including 14,205 feeding locations within space-time clusters, and 1362 carcasses utilized by wolves. </span></li> <li><span>Most carcasses were wolf-killed (80.5%) while a small part had died from other natural causes (1.9%). The remaining had either anthropogenic mortality causes (4.7%), or the cause of death was unknown (12.9%). </span></li> <li> <span>Time spent scavenging was higher during winter than during summer and autumn. Solitary wolves spent more time scavenging than pack-living individuals, likely because individual hunting success is lower than pack success. Scavenging time increased with the mean inbreeding coefficient of the adult wolves, possibly indicating that more inbred individuals resort to scavenging, which requires less body strength. There was weak evidence for </span><span>competition between wolves and brown bears as well as a positive relationship between human density and time spent scavenging. </span> </li> <li><span>This study shows how both intrinsic and extrinsic factors drive wolf scavenging behaviour and that despite a high level of inbreeding and access to carrion of anthropogenic origin, wolves mainly utilized their own kills. </span></li> </ol>
Use of Population Descriptors in Human Genetic Research
ClinicalTrials.gov study NCT00767702. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Human Genomic Population Structure and Phenotype-genotype Variation in ADME Genes in Four Populations
ClinicalTrials.gov study NCT02789527. IPD Sharing: UNDECIDED. Countries: 4. Publications: 1.
Data from: Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations
Open the record for dataset details and reuse information.
Data from: Genetic diversity and population structure of Glossina morsitans morsitans in the active foci of human African trypanosomiasis in Zambia and Malawi
Open the record for dataset details and reuse information.
Data from: Postglacial expansion and not human persecution best explains the population structure in the endangered kea (Nestor notabilis)
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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.
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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.
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