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Data from: The early spread and epidemic ignition of HIV-1 in human populations
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Data from: Does human-induced hybridization have long-term genetic effects? Empirical testing with domesticated, wild and hybridized fish populations
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FIG. 9 in Fossil dipsadid snakes from the Guadeloupe Islands (French West-Indies) and their interactions with past human populations
FIG. 9. — Fossil and modern occurrences of the three dipsadid species identified on the Guadeloupe Islands at the different chronological intervals.
FIG. 5 in Fossil dipsadid snakes from the Guadeloupe Islands (French West-Indies) and their interactions with past human populations
FIG. 5. — Trunk vertebrae of Alsophis antillensis (Schlegel, 1837) from Gare Maritime de Basse-Terre archaeological site (US 1008) located on Basse-Terre Island (A) and from Blanchard Cave paleontological deposit (Layer 11) located on Marie-Galante Island (B). Abbreviations: cd., condyle; ct., cotyle; di., diapophysis; e. s., epizygapophyseal spine; h. k., hemal keel; m. c., medial constriction; n. s., neural spine; p. c., precondylar constriction; p. d., paracotylar depression; p. n., postero-medial notch of the zygantrum; pa., parapophysis; pz. f., prezygapophyseal facet; pz. p., prezygapophyseal process; s. d., subcentral depression; s. r., subcentral ridge; s. t., sub-cotylar tubercle; zs., zygosphene. Scale bars: 4 mm.
FIG. 3 in Fossil dipsadid snakes from the Guadeloupe Islands (French West-Indies) and their interactions with past human populations
FIG. 3. — Measurements taken of snake vertebrae: CL, greatest centrum length; GH, greatest height of the vertebra; LNS, greatest length of the neural spine; MLV, maximum length of vertebra; PRW, prezygapophyseal width; WIC, width of interzygapophyseal constriction (= NAW sensu Szyndlar 1984); Wa, greatest width of the anterior part of the neural arch; Wp, greatest width of the posterior part of the neural arch (= PO-PO sensu Szyndlar 1984).
FIG. 8 in Fossil dipsadid snakes from the Guadeloupe Islands (French West-Indies) and their interactions with past human populations
FIG. 8. — Distribution of size (centrum length) of snake vertebrae from archaeological deposits (A) and natural deposits (B) on the Guadeloupe Islands.
FIG. 1. — A in Fossil dipsadid snakes from the Guadeloupe Islands (French West-Indies) and their interactions with past human populations
FIG. 1. — A, Map of the Lesser Antilles indicating the position of the Guadeloupe archipelago; B, Map of the Guadeloupe Islands with isobaths (–200 m) from Münch et al. (2013) and locations of the studied sites: 1, cathédrale de Basse-Terre; 2, gare maritime de Basse-Terre; 3, Sainte-Rose la Ramée; 4,Trou Lolo; 5, Anse à l'Écu cave; 6, Bambous cave; 7, Morel; 8, Anse à la Gourde cave; 9, Anse à la Gourde; 10, Pointe du Helleux; 11, Anse Petite Rivière;12, Pointe Gros Rempart 6; 13, Caille à Bélasse; 14, Jean-François gully cave;15, Morne Rita;16, Tourlourous – Stade José Bade; 17, Blanchard cave; 18, Cadet 2 cave;19, Cadet 3 shelter;20, Grande-Anse de Terre de Bas.
Investigating the impact of human settlements upon the availability of larval habitats and Aedes albopictus population
<b>Description: </b><p>This experiment analysed the impact of human settlements upon Aedes albopictus populations. Surveys were conducted in natural environments (twice-logged forest) and human settlements in oil palm and logged forest. At each study site, three surveys were conducted: <br><br>1) Aquatic Habitat Survey: within the study area, all bodies of water were analysed for abiotic characteristics – container type, water volume, air temperature, water temperature, canopy cover and turbidity. <br>2) Larval Survey: for each body of water, the number of and stage of larvae/pupae was recorded. Larvae/pupae were extracted from the water, reared to adults and Ae. albopictus were identified. <br>3) Adult Population Survey: human landing catches were conducted to collect Ae. albopictus adults. Abundance and sex ratio was recorded for each location, and the wing span of each individual was taken. </p><p><b>Project: </b>This dataset was collected as part of the following SAFE research project: <a href="https://www.safeproject.net/projects/project_view/202"><b>Investigating the impact of human settlements upon the availability of larval habitats and Aedes albopictus populations</b></a></p><p><b>Funding: </b>These data were collected as part of research funded by: </p><ul><li>SAFE - Tropical Forest Ecology Masters (Studentship)</li></ul><p>This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.</p><p></p><p><b>Permits: </b>These data were collected under permit from the following authorities:</p><ul><li>Sabah Biodiversity Centre (Research licence JKM/MBS.1000-2/2 JDL.8 (59))</li><li>Medical Research & Ethics Committee (Ethics licence NMRR-17-3242-39250 (IIR))</li></ul><p></p><p><b>XML metadata: </b>GEMINI compliant metadata for this dataset is available <a href="https://www.safeproject.net/datasets/xml_metadata?id=3929764">here</a></p><p><b>Files: </b>This dataset consists of 4 files: M_Vollans_Larval_Habitats_19v2.xlsx, Larval_Adult_ID.zip, HLC_Wing_Length.zip, Larval_Habitat_Photos.zip</p><p><b>M_Vollans_Larval_Habitats_19v2.xlsx</b></p><p>This file contains dataset metadata and 4 data tables:</p><ol><li><p><b>Aquatic Habitat Survey</b> (described in worksheet AquaticHabitatSurvey)</p><p>Description: AquaticHabitatSurvey</p><p>Number of fields: 30</p><p>Number of data rows: 89</p><p>Fields: </p><ul><li><b>Date</b>: Date of survey (Field type: date)</li><li><b>Land_Type</b>: Details of Land-Type (Field type: categorical)</li><li><b>Location</b>: Details of location. OP = Oil Palm, LF = Logged Forest (Field type: categorical)</li><li><b>Replicate</b>: Details location, as named in location sheet. To 'replicate' resolution. (Field type: location)</li><li><b>Number_10m^2_Square</b>: Number 10m^2 surveyed (Field type: replicate)</li><li><b>Sampling_Region</b>: Details of 10m^2 the aquatic habitat corresponds to: in human settlements, this is the type of building, and in natural environments, the compass direction of the square from the second order point (N/S/E/W). (Field type: replicate)</li><li><b>Elevation</b>: Elevation from GPS (Field type: numeric)</li><li><b>GPS_file_name</b>: File name saved on GPS (Field type: id)</li><li><b>Access_Available</b>: Record of whether able to access the aquatic habitat (Field type: categorical)</li><li><b>Comments</b>: General comments on aquatic habitat (Field type: comments)</li><li><b>Canopy_cover</b>: Record of canopy cover. NA where inside. Data incomplete. (Field type: numeric)</li><li><b>Inside/Outside</b>: Record of whether the aquatic habitat is inside or outside (NA for natural land types, where all larval habitats are outside). (Field type: categorical)</li><li><b>Water_Turbidity</b>: Water turbidity, subjective categorization by a consistant surveyer. (Field type: categorical)</li><li><b>Water_Temperature</b>: Temperature of the water in the aquatic habitat. NOTE: potential faulty equipment. This data was not used in analysis. (Field type: numeric)</li><li><b>Air_Temperature</b>: Temperature of the air directly above the aquatic habitat. (Field type: numeric)</li><li><b>Type_Aquatic_Habitat</b>: Record of the type of aquatic habitat (Field type: categorical)</li><li><b>In_Constant_Use</b>: Record of whether the aquatic habitat is in constant use. (Field type: categorical)</li><li><b>Water_Volume</b>: Total water volume of the aquatic habitat (Field type: numeric)</li><li><b>Radius</b>: Radius of the aquatic habitat (Field type: numeric)</li><li><b>Diameter</b>: Diameter of the aquatic habitat (Field type: numeric)</li><li><b>Length</b>: Length of the aquatic habitat (Field type: numeric)</li><li><b>Width</b>: Width of the aquatic habitat (Field type: numeric)</li><li><b>Water_Depth</b>: Depth of the water in the aquatic habitat (Field type: numeric)</li><li><b>Larval/Pupal_Presence</b>: Record of whether larvae/ pupae are present in the aquatic habitat. (Field type: categorical)</li><li><b>Total_Number_Larvae/Pupae</b>: The total number of larvae / pupae found within an aquatic habitat. (Field type: numeric)</li><li><b>1/2_Instar_Larvae_Number</b>: The number of 1st and 2nd instar larvae found within an aquatic habitat. (Field type: numeric)</li><li><b>3/4_Instar_Larvae_Number</b>: The number of 3rd and 4th instar larvae found within an aquatic habitat. (Field type: numeric)</li><li><b>Pupae_Number</b>: The number of pupae found within an aquatic habitat. (Field type: numeric)</li><li><b>Further_comments</b>: Further comments on aquatic habitat. (Field type: comments)</li><li><b>Photo.folder.name</b>: Folder name containing photos of the study site. (Field type: id)</li></ul></li><li><p><b>Larva lAdult ID</b> (described in worksheet LarvalAdultID)</p><p>Description: LarvalAdultID</p><p>Number of fields: 6</p><p>Number of data rows: 76</p><p>Fields: </p><ul><li><b>Date_of_ID</b>: Date of survey (Field type: date)</li><li><b>Ae.albopictus</b>: Record of whether adults are Ae. albopictus, or some other member of the Culicidae (Field type: taxa)</li><li><b>Location</b>: Details of location. (Field type: location)</li><li><b>Wing_length</b>: Measurement of wing length. (Field type: numeric trait)</li><li><b>Photo_folder_ID</b>: Folder name containing photos for adult ID and wing length. (Field type: id)</li><li><b>Comments</b>: General comments about identification / wingspan measurement. (Field type: comments)</li></ul></li><li><p><b>HLC overview</b> (described in worksheet HLCoverview)</p><p>Description: HLCoverview</p><p>Number of fields: 8</p><p>Number of data rows: 16</p><p>Fields: </p><ul><li><b>Date</b>: Date of survey (Field type: date)</li><li><b>Location</b>: Broad location of where HLC occurred. (Field type: location)</li><li><b>Comments</b>: Qualitative details about exact location. (Field type: comments)</li><li><b>Ae.albopictus</b>: Number of Ae. albopictus obtained during a single 1.5 hour sample. (Field type: abundance)</li><li><b>Number_of_males</b>: Number of Ae. albopictus males (Field type: numeric)</li><li><b>Sex_Ratio_(M/Total)</b>: Sex Ratio (number of males / total number) (Field type: numeric)</li><li><b>Survey_complete</b>: Record if it was possible to complete the HLC survey. (Field type: categorical)</li><li><b>Further_comments</b>: Further comments (Field type: comments)</li></ul></li><li><p><b>HLC adult ID</b> (described in worksheet HLCadultID)</p><p>Description: HLCadultID</p><p>Number of fields: 8</p><p>Number of data rows: 111</p><p>Fields: </p><ul><li><b>Date</b>: Date of sampling (Field type: date)</li><li><b>Location</b>: Broad location of where HLC occurred. (Field type: location)</li><li><b>Specific_Location</b>: Qualitative details about exact location. (Field type: comments)</li><li><b>Sex</b>: Sex (Field type: categorical)</li><li><b>Wing Length</b>: Wing length measurement (Field type: numeric trait)</li><li><b>Weather</b>: Weather description (Field type: categorical)</li><li><b>Comments</b>: Comments on wing dissection issues. (Field type: comments)</li><li><b>Photo_Code</b>: Folder name containing wing length photos. (Field type: id)</li></ul></li></ol><p><b>Larval_Adult_ID.zip</b></p><p>Description: Zip file containing JPEG images to ID adult mosquitoes reared from collected larvae. </p><p><b>HLC_Wing_Length.zip</b></p><p>Description: Zip file containing JPEG images of the wingspan of adult mosquitoes collected via HLC. </p><p><b>Larval_Habitat_Photos.zip</b></p><p>Description: Zip file containing photos of some of the larval habitats encountered, and some general landscapes. </p><p><b>Date range: </b>2019-04-03 to 2019-05-06</p><p><b>Latitudinal extent: </b>4.5000 to 5.0700</p><p><b>Longitudinal extent: </b>116.7500 to 117.8200</p><p><b>Taxonomic coverage: </b><br> All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets.</p><div> -  Animalia <br> -  -  Arthropoda <br> -  -  -  Insecta <br> -  -  -  -  Diptera <br> -  -  -  -  -  Culicidae <br> -  -  -  -  -  -  <i>Aedes</i> <br> -  -  -  -  -  -  -  <i>Aedes albopictus</i> <br></div><p></p>
Genomic insights into the formation of human populations in East Asia
<p>The genotypes of 383 present-day individuals from 46 populations indigenous to China (n=337) and Nepal (n=46) using the Affymetrix Human Origins array.</p>
Raw in vitro screening data and R scripts for: A Bayesian method for population-wide cardiotoxicity hazard and risk characterization using an in vitro human model
<p>Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes are an established model for testing potential chemical hazards. Inter-individual variability in toxicodynamic sensitivity has also been demonstrated <i>in vitro</i>; however, quantitative characterization of the population-wide variability has not been fully explored. We sought to develop a method to address this gap by combining a population-based iPSC-derived cardiomyocyte model with Bayesian concentration-response modeling. A total of 136 compounds, including 44 pharmaceuticals and 82 environmental chemicals, were tested in iPSC-derived cardiomyocytes from 43 non-diseased humans. Hierarchical Bayesian population concentration-response modeling was conducted for five phenotypes reflecting cardiomyocyte function or viability. Toxicodynamic variability was quantified through the derivation of chemical- and phenotype-specific variability factors (TDVF). Toxicokinetic modeling was used for probabilistic <i>in vitro</i>-to-<i>in vivo </i>extrapolation in order to derive population-wide margins of safety (MOS) for pharmaceuticals and margins of exposure (MOE) for environmental chemicals. Pharmaceuticals were found to be active across all phenotypes. Over half of tested environmental chemicals showed activity in at least one phenotype, most commonly positive chronotropy. TDVF estimates for the functional phenotypes were greater than those for cell viability, usually exceeding the generally-assumed default of ~3. Population variability-based MOS for pharmaceuticals were correctly predicted to be relatively narrow, between 10-100; however, MOE for environmental chemicals, based on population exposure estimates, generally exceeded 1000, suggesting they pose little risk at general population exposures even to sensitive sub populations. This study represents a first of its kind human <i>in vitro</i> model that can be used to characterize toxicodynamic population variability in cardiotoxic risk.</p>
Local human population increase in the non-breeding areas of long-distance migrant bird species is only weakly associated with their declines, even for synanthropic species
<p><span>Aim: To show how recent declines in populations of long-distance migrant birds are associated with recent increases in human population growth and agricultural intensification on their tropical non-breeding grounds, except for synanthropic species, where we expect the reverse.</span></p> <p><span>Location: Breeding populations throughout Europe and North America spending the non-breeding season throughout Africa, and Central and South America, respectively. </span></p> <p><span>Methods: </span>We mapped 50 species of long-distance migrant birds from published tagging studies of 126 breeding populations and identified their breeding population trends from 2000-2015 from published Country or State census data. We then matched individual bird non-breeding locations, from each population, to local human population change and crop yield data. We used GLMs to predict whether bird population decline was associated with human population change or crop yield and whether this was dependent on if a species was synanthropic or not, controlling for absolute human population density, breeding and non-breeding location, migratory distance and phylogeny. We predicted that bird populations that spend the non-breeding season in areas of recent higher human population increase or agricultural intensification (crop yield), would show greater declines, but that declines would be less for species that frequently utilize anthropogenic habitats such as secondary woodland and farmland.</p> <p><span>Results: </span>Bird population change, even for synanthropic species, showed a significant negative relationship with relative human population change and crop yield (but this was weak, <2% and 6% of variance respectively), and this relationship was the same for the Neotropics and Africa, despite African human population change being three times larger.</p> <p><span>Main conclusions: </span>The results suggest that local human population change in the non-breeding area is likely to be only a relatively minor driver of migrant declines, and its effects may be through increases in agricultural intensification reducing carrying capacity but we currently lack local studies to confirm this.</p>
Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot
<p>As human-induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant <i>Leucadendron salignum</i> or "common sunshine conebush" as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, are characteristic of the southwestern CFR, whereas, low population structure and more recent lineage coalescence depicts the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species-level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land-usage as a significant gene flow barrier, especially in severely-threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.</p>
Data from: Low genetic diversity but strong population structure reflects multiple introductions of western flower thrips (Thysanoptera: Thripidae) into China followed by human-mediated spread
Historical invasion scenarios based on observational records are usually incomplete and biased, but these can be supplemented by population genetic data. The western flower thrips (WFT), Frankliniella occidentalis, invaded China in the last 13 years and has rapidly become one of the most serious pests in the country. To assess whether this invasion involved a single event or multiple events, we examined patterns of genetic diversity and population structure of WFT across 12 Chinese populations and a native US population based on mitochondrial DNA and/or 18 microsatellite loci. The average allelic richness and haplotype diversity in Chinese populations were significantly lower than in a population from its native range. The distribution of mitochondrial haplotypes suggested multiple independent invasions of WFT into China, including two invasions into the Beijing region. Based on microsatellite data, two distinct clusters were identified, with both of them splitting further into two clusters; in the Beijing region, the microsatellite data also provided evidence for two introductions. Both the absence of isolation by distance and the fact that distant populations were similar genetically suggest patterns of WFT movement linked to human activities. Our study therefore suggests multiple introductions of WFT into China and human-assisted spread.
Data from: Coral reef degradation is not correlated with local human population density
The global decline of reef-building corals is understood to be due to a combination of local and global stressors. However, many reef scientists assume that local factors predominate and that isolated reefs, far from human activities, are generally healthier and more resilient. Here we show that coral reef degradation is not correlated with human population density. This suggests that local factors such as fishing and pollution are having minimal effects or that their impacts are masked by global drivers such as ocean warming. Our results also suggest that the effects of local and global stressors are antagonistic, rather than synergistic as widely assumed. These findings indicate that local management alone cannot restore coral populations or increase the resilience of reefs to large-scale impacts. They also highlight the truly global reach of anthropogenic warming and the immediate need for drastic and sustained cuts in carbon emissions.
Human-induced habitat fragmentation effects on connectivity, diversity and population persistence of an endemic fish, Percilia irwini, in the Biobío river basin (Chile)
<p> </p> <p>An understanding of how genetic variability is distributed in space is fundamental for the conservation and maintenance of diversity in spatially fragmented and vulnerable populations. While fragmentation can occur from natural barriers it can also be exacerbated by anthropogenic activities such as hydroelectric power plant development. Whatever the source, fragmentation can have significant ecological effects, including the disruptions of migratory processes and gene flow among populations. In Chile, the Biobío river basin exhibits a high degree of habitat fragmentation due to the numerous hydroelectric power plants in operation, the number of which is expected to increase following new renewable energy use strategies. Here, we assessed the effects of different kinds of barriers on the genetic structure of the endemic freshwater fish <em>Percilia irwini</em>, knowledge that is critically needed to inform conservation strategies in light of current and anticipated further fragmentation initiatives in the system. We identified 8 genetic units throughout the entire Biobío system with high effective sizes. A reduced effective size estimate was however observed in a single population located between two impassable barriers. Both natural waterfalls and human made dams were important drivers of population differentiation in this system, however, dams affect genetic diversity differentially depending on their mode of operation. Evidence of population extirpation was found in two river stretches limited by upstream and downstream dams. Significant gene flow in both directions was found among populations not separated by natural or anthropogenic barriers. Our results suggest a significant vulnerability of <em>P. irwini </em>populations to future dam development and demonstrate the importance of studying basin-wide data sets with genetic metrics to understand the strength and direction of anthropogenic impacts on fish populations.</p>
Data from: What have humans done for evolutionary biology? Contributions from genes to populations
Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future.
Data from: Effects of female reproductive competition on birth rate and reproductive scheduling in a historical human population
Costly reproductive competition among females is predicted to lead to strategies that reduce these costs, such as reproductive schedules. Simultaneous births of co-resident women in human families can reduce their infant survival, but whether such competition also affects overall birth rates and whether females time their pregnancies to avoid simultaneous births remain unknown, despite being key questions for understanding how intra-female competition affects reproductive strategies. Here, we used detailed parish registers to study female reproductive competition in historical Finnish joint –families, where brothers stayed on their natal farms and sisters married out, and consequently unrelated daughters-in-law often co-resided and competed for household resources. We quantified the time-varying effects of having reproductive-aged competitor(s) on a woman's interval from marriage to first childbirth, on age-specific fertility, and on birth scheduling. Contrary to our hypothesis, the presence of one or several potential female competitors did not lead to longer first birth intervals or lower age-specific probability of reproduction. We also found no evidence that women would schedule their reproduction to avoid the real cost of simultaneous births on their offspring mortality risk; age-specific reproductive rates were unaltered by changes in the presence of other infants in the household. These results raise interesting questions regarding the evolution of fertility suppression in social mammals in different contexts, the costs and benefits of extended families for female reproductive success and strategies deployed, and the cultural practices that may help to avoid the negative outcomes of female reproductive competition in human families.
Data from: Divergent selection on, but no genetic conflict over, female and male timing and rate of reproduction in a human population
The sexes often have different phenotypic optima for important life-history traits, and because of a largely shared genome this can lead to a conflict over trait expression. In mammals, the obligate costs of reproduction are higher for females, making reproductive timing and rate especially liable to conflict between the sexes. While studies from wild vertebrates support such sexual conflict, it remains unexplored in humans. We used a pedigreed human population from preindustrial Finland to estimate sexual conflict over age at first and last reproduction, reproductive lifespan and reproductive rate. We found that the phenotypic selection gradients differed between the sexes. We next established significant heritabilities in both sexes for all traits. All traits, except reproductive rate, showed strongly positive intersexual genetic correlations and were strongly genetically correlated with fitness in both sexes. Moreover, the genetic correlations with fitness were almost identical in men and women. For reproductive rate, the intersexual correlation and the correlation with fitness were weaker but again similar between the sexes. Thus, in this population, an apparent sexual conflict at the phenotypic level did not reflect an underlying genetic conflict over the studied reproductive traits. These findings emphasize the need for incorporating genetic perspectives into studies of human life-history evolution.
Data from: Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size
In vitro and in vivo evolution experiments on Escherichia coli revealed several principles of bacterial adaptation. However, few data are available in the literature describing the behavior of E. coli in its natural environment. We attempted here to study the evolution in the human gut of a commensal dominant E. coli clone ED1a belonging to B2 phylogroup, through a longitudinal genomic study. We sequenced 24 isolates sampled at three different time points within a healthy individual over almost a year. We computed amutation rate of 6.90x10-7 per base per year of the chromosome for E. coli ED1a in healthy human gut. We observed a very limited genomic diversity, and could not detect any evidence of selection contrary to what is observed in experimental evolution over similar length of time. We therefore suggest that ED1a being well adapted to the healthy human gut evolves mostly neutrally with a low effective population size (Ne ≈ 500 – 1700).
Global acceleration of lake sediment accumulation rates associated with recent human population growth and landuse changes
<p>These datasets include the spatial coordinates and the digitized temporal rates of lake sedimentation expressed as Sediment Accumulation Rates (SAR; mm/year) and Mass Accumulation Rate (MAR; g/cm<sup>2</sup>/year) presented in Baud et al. (2021).</p> <p>Baud, A., Jenny, JP., Francus, P. and Gregory-Eaves, I. Global acceleration of lake sediment accumulation rates associated with recent human population growth and land-use changes. <em>J Paleolimnol</em> (2021). https://doi.org/10.1007/s10933-021-00217-6 </p>
ScienceDex guides
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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.