Find research datasets worth reusing

opencc-by-4.0Jan 2016View details →

Fig. 2 in Song Repertoire And Origins Of Crimean Population Of Chiffchaff, Phylloscopus Collybita (Sylviidae)

Fig. 2. Songs of Crimean (A) and Caucasian (B) Chiffchaffs with identical specific Crimean song elements (marked).

opencc-by-4.0Jul 2014View details →

Fig. 1 in The Seasonal Population Dynamics Of The Cyclopoid Copepods (Cyclopoida, Cyclopidae) In Ponds Of Kyiv Region (Ukraine)

Fig. 1. Seasonal population dynamics of the cyclopids in the pond near the village Khotov: 1 — abundance of cyclopids; 2 — water temperature of pond near the village Khotov during the period of the study.

opencc-by-4.0Mar 2015View details →

Fig. 3 in Differences In Skull Size Of Harbour Porpoises, Phocoena Phocoena (Cetacea), In The Sea Of Azov And The Black Sea: Evidence For Different Morphotypes And Populations

Fig. 3. The skull measurements of the harbour porpoises from the Sea of Azov and the Black Sea: 1 — zygomatic width vs rostrum width at the mid-point; 2 — parietal width vs rostrum width at the mid-point.

opencc-by-4.0Mar 2015View details →

Fig. 4 in Differences In Skull Size Of Harbour Porpoises, Phocoena Phocoena (Cetacea), In The Sea Of Azov And The Black Sea: Evidence For Different Morphotypes And Populations

Fig. 4. Черепа морских свиней, Phocoena phocoena relicta, из Азовского и Чёрного морей, вид сверху: 1 — Азовское море, самец; 2 — Азовское море, самка; 3 — Чёрное море, самец; 4 — Чёрное море, самка. Фото М. П. Чоповди.

opencc-by-4.0Mar 2015View details →

Fig. 2 in Differences In Skull Size Of Harbour Porpoises, Phocoena Phocoena (Cetacea), In The Sea Of Azov And The Black Sea: Evidence For Different Morphotypes And Populations

Fig. 2. Skull proportions of the harbour porpoises from the Sea of Azov and the Black Sea (mean ± standard deviation is presented as the box, upper and lower limits as the lines): 1 — zygomatic width as the CBL percentage; 2 — rostrum width at the mid-point as the CBL percentage.

The role of population size in folk tune complexity

<p>Demography, particularly population size, plays a key role in cultural complexity. However, the relationship between population size and complexity appears to vary across domains: while studies of technology typically find a positive correlation, the opposite is true for language, and the role of population size in complexity in the arts remains to be established. Here, we investigate the relationship between population size and complexity in music using Irish folk session tunes as a case study. Using analyses of a large online folk tune dataset, we show that popular tunes played by larger communities of musicians have diversified into a greater number of different versions which encompass more variation in melodic complexity compared with less popular tunes. However, popular tunes also tend to be intermediate in melodic complexity and variation in complexity is lower than expected given the increased number of tune versions. We also find that user preferences for individual tune versions are more skewed in popular tunes. Taken together, these results suggest that while larger populations create more frequent opportunities for musical innovation, they encourage convergence upon intermediate levels of melodic complexity due to a widespread inverse U-shaped relationship between complexity and aesthetic preference. We explore the assumptions underlying our empirical analyses further using simple simulations of tune diffusion through populations of different sizes, finding that a combination of biased copying and structured populations appears most consistent with our results. Our study demonstrates a unique relationship between population size and cultural complexity in the arts, confirming that the relationship between population size and cultural complexity is domain-dependent, rather than universal.</p>

Gene expression in male and female sticklebacks from populations with convergent and divergent throat coloration

<p class="MsoNormal">Understanding of genetic mechanisms underlying variation in sexual dichromatism remains limited, especially for carotenoid-based colors. We addressed this knowledge gap in a gene expression study with threespine stickleback. We compared male and female throat tissues across five populations, including two in which female red coloration has evolved convergently. We found that the expression of individual genes, gene ontologies, and coexpression networks associated with red female color within a population differed between California and British Columbia populations, suggesting differences in underlying mechanisms. Comparing females from each of these populations to females from populations dominated by dull females, we again found extensive expression differences. For each population, genes and networks associated with female red color showed the same patterns for males only inconsistently. The functional roles of genes showing correlated expression with female color are unclear within populations, whereas genes highlighted through inter-population comparisons include some previously suggested to function in carotenoid pathways. Among these, the most consistent patterns involved <em>TTC39B</em> (Tetratricopeptide Repeat Domain 39B), which is within a known red coloration QTL in stickleback and implicated in red coloration in other taxa.</p>

Negative temporal autocorrelation in mast seeding dynamics positively influences both the long and short-term dynamics of a wild boar population

<p><span>Temporal autocorrelation in environmental conditions influences population dynamics through its effects on vital rates. However, a comprehensive understanding of how and to what extent temporal autocorrelation shapes population dynamics is still lacking because most empirical studies have unrealistically assumed that environmental conditions are temporally independent. Mast seeding is a biological event characterized by highly fluctuating and synchronized seed production at the tree population scale, as well as a marked negative temporal autocorrelation. In the current context of global change, mast seeding events are expected to become more frequent, leading to strengthened negative temporal autocorrelations and thereby amplified cyclicality in mast seeding dynamics with cycles of length 2 years. </span><span>Theory predicts that population growth rates are maximized when the environmental cyclicality of consumer resources and their generation times are closely matched. </span><span>To test this prediction, we took advantage of the long-term monitoring of a wild boar population, a widespread seed consumer species characterized by a short generation time (ca. 2 years). As expected, simulations indicated that its stochastic population growth rate increased as mast seeding dynamics became more negatively autocorrelated. Our findings demonstrate that accounting for temporal autocorrelations in environmental conditions relative to generation time of the focal population is required, especially under global warming where the cyclicality in resource dynamics is likely to change.</span></p>

Raw data of compounds extracted by GC-MS from each population replicate's of I. uriae ticks from Iceland.

<p>Raw data representing all the compounds extracted by GC-MS from each population replicate’s of <em>I. uriae</em> ticks from three sites in Iceland. Each replicate contain a pool of 10 living flat female ticks.</p> <p>Site: name of the site where ticks were collected.</p> <p>Host: name of the host bird.</p> <p>Replicate: number of the replicate (1 to 4).</p> <p>Peak: number of the detected peaks correponding to extracted compounds.</p> <p>Retention Time: time elapsed between sample introduction and the maximum signal of the given compound.</p> <p>Area: area under the curves of each detected coumpounds on the chromatogram.</p>

Gene expression plasticity, genetic variation and fatty acid remodelling in divergent populations of a tropical bivalve species: lipid profiles

<p><span>Ocean warming challenges marine organisms' resilience, especially for species experiencing temperatures close to their upper thermal limits. A potential increase in thermal tolerance might significantly reduce the risk of population decline, which is intrinsically linked to variability in local habitat temperatures.</span></p> <p><span>Our goal was to assess the plastic and genetic potential of response to elevated temperatures in a tropical bivalve model, <em>Pinctada margaritifera</em>. We benefit from two ecotypes for which local environmental conditions are characterized by either large diurnal variations in the tide-pools (Marquesas archipelago) or lower mean temperature with stable to moderate seasonal variations (Gambier archipelago).</span><br><br><span>We explored the physiological basis of individual responses to elevated temperature<em>, </em>genetic divergence as well as plasticity and acclimation by combining lipidomic and transcriptomic approaches.</span><br><br><span>We show that <em>P. margaritifera</em> has certain capacities to adjust to long-term elevated temperatures that was thus far largely underestimated. Genetic variation across populations overlaps with gene expression and involves the mitochondrial respiration machinery, a central physiological process that contributes to species thermal sensitivity and their distribution ranges.</span><br><br><span>Our results present evidence for acclimation potential in <em>P. margaritifera</em> and urge for longer term studies to assess populations resilience in face of climate change.</span></p>

Additional files for manuscript titled 'The double round-robin population unravels the genetic architecture of grain size in barley'

<p>Additional file 1: Parental allele for barley orthologs of genes controlling grain size in rice</p> <p>Additional file 2: Cross-validation of quantitative trait loci (QTLs) detected for grain size characters in rice</p> <p>Additional file 3: Adjusted entry means of recombinant inbred lines of 45 HvDRR sub-populations</p>

opencc-zeroDec 2021View details →

Individual dietary specialization in a generalist bee varies across populations but has no effect on the richness of associated microbial communities

<p><span></span></p> <p>Despite the increasingly documented occurrence of individual specialization, the relationship between individual consumer interactions and diet-related microbial communities in wild populations is still unclear. Using data from nests of the bee <em>Ceratina australensis</em> from three different wild populations, we combine metabarcoding and network approaches to explore the existence of individual variation in resource use within and across populations, and whether dietary specialization affects the richness of pollen-associated microbes. We reveal the existence of marked dietary specialization. In the most specialized population, we also show that individuals' diet breadth was positively related to the richness of fungi, but not bacteria. Overall, individual specialization appeared to have a weak or negligible effect on the microbial richness of nests, suggesting that different mechanisms beyond environmental transmission may be at play regarding microbial acquisition in wild bees.</p>

Synthetic population for DEU

<p><strong>Synthetic populations for regions of the World (SPW) | Germany</strong></p><p><strong>Dataset information</strong></p><p>A synthetic population of a region as provided here, captures the people of the region with selected demographic attributes, their organization into households, their assigned activities for a day, the locations where the activities take place and thus where interactions among population members happen (e.g., spread of epidemics).</p> <p><strong>License</strong></p><p><a href="https://creativecommons.org/licenses/by/4.0/">CC-BY-4.0</a></p> <p><strong>Acknowledgment</strong></p><p>This project was supported by the National Science Foundation under the NSF RAPID: COVID-19 Response Support: Building Synthetic Multi-scale Networks (PI: Madhav Marathe, Co-PIs: Henning Mortveit, Srinivasan Venkatramanan; Fund Number: OAC-2027541).</p> <p><strong>Contact information</strong></p><p>Henning.Mortveit@virginia.edu</p> <p><strong>Identifiers</strong></p><table> <thead><tr> <th></th> <th></th> </tr> </thead> <tbody> <tr> <td>Region name</td> <td>Germany</td> </tr> <tr> <td>Region ID</td> <td>deu</td> </tr> <tr> <td>Model</td> <td>coarse</td> </tr> <tr> <td>Version</td> <td>0_9_0</td> </tr> </tbody> </table> <p><strong>Statistics</strong></p><table> <thead><tr> <th>Name</th> <th>Value</th> </tr> </thead> <tbody> <tr> <td>Population</td> <td>80298171.0</td> </tr> <tr> <td>Average age</td> <td>43.4</td> </tr> <tr> <td>Households</td> <td>37501987.0</td> </tr> <tr> <td>Average household size</td> <td>2.1</td> </tr> <tr> <td>Residence locations</td> <td>37501987.0</td> </tr> <tr> <td>Activity locations</td> <td>7864868.0</td> </tr> <tr> <td>Average number of activities</td> <td>5.7</td> </tr> <tr> <td>Average travel distance</td> <td>41.0</td> </tr> </tbody> </table> <p><strong>Sources</strong></p><table> <thead><tr> <th>Description</th> <th>Name</th> <th>Version</th> <th>Url</th> </tr> </thead> <tbody> <tr> <td>Activity template data</td> <td>World Bank</td> <td>2021</td> <td><a href="https://data.worldbank.org">https://data.worldbank.org</a></td> </tr> <tr> <td>Administrative boundaries</td> <td>ADCW</td> <td>7.6</td> <td><a href="https://www.adci.com/adc-worldmap">https://www.adci.com/adc-worldmap</a></td> </tr> <tr> <td>Curated POIs based on OSM</td> <td>SLIPO/OSM POIs</td> <td></td> <td><a href="http://slipo.eu/?p=1551">http://slipo.eu/?p=1551</a> <a href="https://www.openstreetmap.org/">https://www.openstreetmap.org/</a></td> </tr> <tr> <td>Household data</td> <td>DYB</td> <td></td> <td><a href="https://unstats.un.org/unsd/demographic/products/dyb/dyb_Household/dyb_household.htm">https://unstats.un.org/unsd/demographic/products/dyb/dyb_Household/dyb_household.htm</a></td> </tr> <tr> <td>Population count with demographic attributes</td> <td>GPW</td> <td>v4.11</td> <td><a href="https://sedac.ciesin.columbia.edu/data/set/gpw-v4-admin-unit-center-points-population-estimates-rev11">https://sedac.ciesin.columbia.edu/data/set/gpw-v4-admin-unit-center-points-population-estimates-rev11</a></td> </tr> </tbody> </table> <p><strong>Files description</strong></p><p><strong>Base data files (deu_data_v_0_9.zip)</strong></p><table> <thead><tr> <th>Filename</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td><code>deu_person_v_0_9.csv</code></td> <td>Data for each person including attributes such as age, gender, and household ID.</td> </tr> <tr> <td><code>deu_household_v_0_9.csv</code></td> <td>Data at household level.</td> </tr> <tr> <td><code>deu_residence_locations_v_0_9.csv</code></td> <td>Data about residence locations</td> </tr> <tr> <td><code>deu_activity_locations_v_0_9.csv</code></td> <td>Data about activity locations, including what activity types are supported at these locations</td> </tr> <tr> <td><code>deu_activity_location_assignment_v_0_9.csv</code></td> <td>For each person and for each of their activities, this file specifies the location where the activity takes place</td> </tr> </tbody> </table> <p><strong>Derived data files</strong></p><table> <thead><tr> <th>Filename</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td><code>deu_contact_matrix_v_0_9.csv</code></td> <td>A POLYMOD-type contact matrix constructed from a network representation of the location assignment data and a within-location contact model.</td> </tr> </tbody> </table> <p><strong>Validation and measures files</strong></p><table> <thead><tr> <th>Filename</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td><code>deu_household_grouping_validation_v_0_9.pdf</code></td> <td>Validation plots for household construction</td> </tr> <tr> <td><code>deu_activity_durations_{adult,child}_v_0_9.pdf</code></td> <td>Comparison of time spent on generated activities with survey data</td> </tr> <tr> <td><code>deu_activity_patterns_{adult,child}_v_0_9.pdf</code></td> <td>Comparison of generated activity patterns by the time of day with survey data</td> </tr> <tr> <td><code>deu_location_construction_0_9.pdf</code></td> <td>Validation plots for location construction</td> </tr> <tr> <td><code>deu_location_assignement_0_9.pdf</code></td> <td>Validation plots for location assignment, including travel distribution plots</td> </tr> <tr> <td><code>deu_deu_ver_0_9_0_avg_travel_distance.pdf</code></td> <td>Choropleth map visualizing average travel distance</td> </tr> <tr> <td><code>deu_deu_ver_0_9_0_travel_distr_combined.pdf</code></td> <td>Travel distance distribution</td> </tr> <tr> <td><code>deu_deu_ver_0_9_0_num_activity_loc.pdf</code></td> <td>Choropleth map visualizing number of activity locations</td> </tr> <tr> <td><code>deu_deu_ver_0_9_0_avg_age.pdf</code></td> <td>Choropleth map visualizing average age</td> </tr> <tr> <td><code>deu_deu_ver_0_9_0_pop_density_per_sqkm.pdf</code></td> <td>Choropleth map visualizing population density</td> </tr> <tr> <td><code>deu_deu_ver_0_9_0_pop_size.pdf</code></td> <td>Choropleth map visualizing population size</td> </tr> </tbody> </table>

REPIN population analysis in 49 Stenotrophomonas maltophilia genomes

<p>This dataset contains the genome sequences of 49 S. maltophilia strains (input.zip) and the processed data from four individual RAREFAN runs. RAREFAN identifies RAYTs REPINS for each supplied genome and a reference genome. Four different strains where used as a reference genome: AA1, AB550 FDARGOOS_649, ISMMS3, and Sm53. The data were processed with default RAREFAN job parameters. Links to the original RAREFAN jobs are given below.</p>

Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges

<p>The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, e.g., when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species <em>Formica polyctena</em> and <em>F. aquilonia</em>. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent-based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (ca. 500 kya) and occurred with continuous asymmetrical gene flow from <em>F. aquilonia</em> to <em>F. polyctena</em> until a recent time, when migration became negligible (2-19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.</p>

A comparison of density estimation methods for monitoring marked and unmarked animal populations

<p>These data were generated to compare different methods of estimating population density from marked and unmarked animal populations. We compare conventional live trapping with two more modern, non-invasive field methods of population estimation: genetic fingerprinting from hair-tube sampling and camera trapping for the European pine marten (Martes martes). We used arrays of camera traps, live traps, and hair tubes to collect the relevant data in the Ring of Gullion in Northern Ireland. We apply marked spatial capture-recapture models to the genetic and live trapping data where individuals were identifiable, and unmarked spatial capture-recapture (uSCR), distance sampling (CT-DS), and random encounter models (REM) to the camera trap data where individual ID was not possible. All five approaches produced plausible and relatively consistent point estimates (0.41 – 0.99 animals per km<sup>2</sup>), despite differences in precision, cost, and effort being apparent.</p> <p>In addition to the data, we provide novel code for running unmarked spatial capture-recapture (uSCR) and random encounter models (REM) to the camera trap data where individual ID was not possible. </p>

Integrated population model for the Mallard in the Netherlands

<p><span>Europe's highest densities of breeding Mallards (<em>Anas platyrhynchos</em>) are found in the Netherlands, but the breeding population there has declined by ~30% since the 1990s. The exact cause of this decline has remained unclear.</span><span> </span><span>Here, we used an integrated population model to jointly analyze Mallard population survey, nest survey, duckling survival and band-recovery data. We used this approach to holistically estimate all relevant vital rates, including duckling survival rates for years for which no explicit data were available. Mean vital rate estimates were high for nest success (0.38 ±0.01) and egg hatch rate (0.96 ±0.001), but relatively low for clutch size (8.2 ±0.05) compared to populations in other regions. Estimates for duckling survival rate for the three years for which explicit data were available were low (0.16-0.27) compared to historical observations, but were comparable to rates reported for other regions with declining populations. Finally, mean survival rate was low for ducklings (0.18 ±0.02), but high and stable for adults (0.71 ±0.03). Population growth rate was only affected by variation in duckling survival, but since this is a predominantly latent state variable, this result should be interpreted with caution. However, it does strongly indicate that none of the other vital rates, all of which were supported by data, was able to sufficiently explain the population decline. Together with a comparison with historic vital rates, these findings point to a reduced duckling survival rate as the likely cause of the decline. Candidate drivers of reduced duckling survival are increased predation pressure and reduced food availability, but this requires future study. Integrated population modeling can provide valuable insights into population dynamics even when empirical data for a key parameter are partly missing.</span></p>

opencc-by-4.0May 2022View details →

IGM Population of HFF structures using Hi-C, laminB1 DamID, 3D HIPMAp FISH and single cell SPRITE data

<p>This repository accompanies the manuscript "<strong>Integrative Genome Modeling Platform reveals essentiality of rare contact events in 3D genome organizations</strong>", to appear in Nat. Methods (2022), see also https://www.biorxiv.org/content/10.1101/2021.08.22.457288v1.</p> <p>It contains the preprocessed input data files (Hi-C, laminB1 DamID, 3D HIPMAp FISH and single cell SPRITE) for the HFF fibroblast cell line to be used in the Integrative Genome Modeling platform (IGM) developed in the Alber lab at UCLA (https://github.com/alberlab/igm).</p> <p>Also, we provide the configuration file to run IGM with those datasets, as we did in generating the HDSF population discussed in the accompanying manuscript. Such population is also provided as an "hss" file. Documentation and a simple demo/tutorial on how IGM can be run is given on the Alber lab Github @ https://github.com/alberlab/igm.</p> <p>All files can be read in using the <em>h5py</em> and <em>alabtools</em> (available @https://github.com/alberlab/alabtools) Python packages. More detailed information is provided in the manuscript and associated Supplementary Information file.  </p> <p>For any inquiry/suggestions/doubts please reach out to Lorenzo Boninsegna (bonimba@g.ucla.edu) or Dr. Frank Alber (falber@g.ucla.edu).</p> <p> </p>

Gene drives for vertebrate pest control: realistic spatial modelling of eradication probabilities and times for island mouse populations

<p>Invasive alien species continue to threaten global biodiversity. CRISPR-based gene drives, which can theoretically spread through populations despite imparting a fitness cost, could be used to suppress or eradicate pest populations. We develop an individual-based, spatially explicit, stochastic model to simulate the ability of CRISPR-based homing and X-chromosome shredding drives to eradicate populations of invasive mice (Mus muculus) from islands. Using the model, we explore the interactive effect of the efficiency of the drive constructs and the spatial ecology of the target population on the outcome of a gene-drive release. We also consider the impact of polyandrous mating and sperm competition, which could compromise the efficacy of some gene-drive strategies. Our results show that both drive strategies could be used to eradicate large populations of mice. Whereas parameters related to drive efficiency and demography strongly influence drive performance, we find that sperm competition following polyandrous mating is unlikely to impact the outcome of an eradication effort substantially. Assumptions regarding the spatial ecology of mice influenced the probability of and time required for eradication, with short-range dispersal capabilities and limited mate-search areas producing `chase' dynamics across the island characterised by cycles of local extinction and recolonization by mice. We also show that highly efficient drives are not always optimal, when dispersal capabilities are low, rapid local population supression around the introduction sites can cause loss of the gene drive before it can spread to the entire island. We conclude that, although the design of efficient gene drives is undoubtedly critical, accurate data on the spatial ecology of target species is critical for predicting the result of a gene-drive release.</p>

Population structure of the scleractinian coral, Montastraea cavernosa, in southeast Florida

The persistence of scleractinian coral populations on the Florida Reef Tract (FRT) is controlled in part by metapopulation dynamics and larval dispersal. Nine polymorphic microsatellite loci were analyzed to identify contemporary population structure and gene flow as well as historical migration rates of Montastraea cavernosa at five sites off Martin, Palm Beach, and Broward counties in southeast Florida. The sampled populations demonstrated evidence of genetic isolation by distance over a geographic range of 85 km. Population genetic structure was divided into two genetic clusters, northern and southern, with admixture along a latitudinal gradient. Historical migration models indicated likely panmixia throughout all sites sampled, identifying a potential reduction in connectivity among the sampled populations through time. Though M. cavernosa populations demonstrated evidence of historical connectivity, contemporary patterns of isolation by distance suggest that effective management will require localized actions to maximize the likelihood of sustaining individual populations in the northern FRT. Given the results of this study, coupled with recent coral mortality events in the region, we recommend regional conservation efforts and management initiatives throughout southeast Florida within a more comprehensive FRT-wide management network.