Find research datasets worth reusing

opencc-by-4.0Apr 2020View details →

Partnerships with TNCs to Better Serve the Transportation Disadvantaged Populations Data Repository

Data repository for the STRIDE project A2 "Changing Access to Public Transportation and the Potential for Increased Travel," Thrust 2---Access for Transportation Disadvantaged Populations.

openodc-pddlApr 2020View details →

Simulated trajectories of city population: Levy walks along Buffalo, NY, street network

Simulated trajectories of the full 2000 census population of Buffalo, New York. Each simulated person was placed randomly along a road within his or her census tract of residence and then independently performed road-network-constrained, truncated Lévy walks for 8 hours of simulated time, moving at 4 km per hour. The trajectories were then sampled at 30 minute intervals. The original dataset was created for studying indexes of activity-space segregation. It is archived at <a href="https://zenodo.org/record/2865830#.XpYviKsza00">https://zenodo.org/record/2865830#.XpYviKsza00</a> and described more fully in Palmer (2013), Activity-Space Segregation: Understanding Social Divisions in Space and Time (http://arks.princeton.edu/ark:/88435/dsp01k643b130h). This version has been created to aid in testing contact-tracing apps and mobility analysis tools. The fields are: latitude: latitude longitude: longitude time: UNIX time in milliseconds ID: random ID assigned to each individual

openodc-pddlApr 2020View details →

Simulated trajectories of city population: Levy walks along Utica, NY, street network

Simulated trajectories of the 2000 census population of Utica, New York. Each of 53,971 simulated people was placed randomly along a road within his or her census tract of residence and then independently performed road-network-constrained, truncated Lévy walks for 8 hours of simulated time, moving at 4 km per hour. The trajectories were then sampled at 30 minute intervals. The original dataset was created for studying indexes of activity-space segregation. It is archived at <a href="https://zenodo.org/record/2865830#.XpYviKsza00">https://zenodo.org/record/2865830#.XpYviKsza00</a> and described more fully in Palmer (2013), Activity-Space Segregation: Understanding Social Divisions in Space and Time (http://arks.princeton.edu/ark:/88435/dsp01k643b130h). This version has been created to aid in testing contact-tracing apps and mobility analysis tools. The fields are: latitude: latitude longitude: longitude time: UNIX time in milliseconds ID: random ID assigned to each individual

opencc-zeroMar 2020View details →

Meeting radiation dosimetry capacity requirements of population-scale exposures by geostatistical sampling

This is the data repository for the PLOS ONE Manuscript: "Meeting radiation dosimetry capacity requirements of population-scale exposures by geostatistical sampling". This repository contains the following data: 1. "State-and-Subdivision-Boundary-Files.Edited-for-ArcMap-10.4.KML-Format.zip": This file contains modified U.S. state and sub-division boundary files [in KML format], which can be imported into ArcMap using its KMLtoLayer function. These files have been modified to prevent sub-division naming issues that we encountered when importing boundary data into ArcMap: A) State sub-divisions with identical names are considered a single sub-division by ArcMap (corrected by adding a letter after each sub-division of the same name, i.e. CenterA, CenterB, etc), and; B) ArcMap would only identify the sub-division by its first word if sub-division name contained spaces (corrected by converting all spaces into dashes).  2. "HPAC-Plumes.Processed.zip" and "HPAC-Plumes.Unprocessed.zip": These files contain HPAC plume coordinate (WGS1984) and dose (in cGy) values for all scenarios discussed in the manuscript. We provide "processed" and "unprocessed" HPAC plume data files. The "unprocessed" HPAC plume data is provided in its original XML format, which cannot be imported into ArcMap directly. The "processed" HPAC plumes are provided in tab-delimited X,Y,Z format (Latitude, Longitude, and Dose). We have also added a "0 cGy" contour in the "processed" plumes (surrounding the HPAC plume), as the presence of unirradiated data points adjacent to the plume was found to be crucial for accurate kriging, since these points served as boundaries for kriging. 3. "Final-Derived-Plumes.Data-Points.zip": This file contains geostatistically-derived plume coordinate (WGS1984) and dose (in cGy) values for all scenarios discussed in the manuscript. Data is in comma-delimited format (Latitude, Longitude, and Dose). Data points consist of a set of initial coordinates generated at random locations within each Census sub-division using the ArcMap tool, ‘CreateRandomPoints_management’, and subsequent points generated by densification (the geostatistical procedure that targets and localizes an additional small cohort of irradiated individuals to mitigate uncertainty in environmental measurements). These data points were assigned radiation level values corresponding to the adjacent outer HPAC contour by a script comparing each sample with its location within the HPAC plume of the same scenario. 4. “Intermediate-Derived-Plumes.Data-Points.zip” This archive contains coordinate data (WGS1984) and dose values (in cGy) for all intermediary steps of plume development (using our geostatistical method) for all scenarios. Like (3), the data is comma-delimited (Latitude, Longitude, and Dose), and were assigned radiation level values by a script comparing sampling locations with the location of the HPAC plume of the same scenario. Scenario replicate folders contains text files for each iteration step of the plume derivation process, including a file containing just the initial random sampling (“Iteration-1”), a file containing initial sampling and sampling locations selected by the first densification step (“Iteration-2”), a file containing initial sampling and sampling locations selected by the first and second densification steps (“Iteration-3”), and so on. This archive also contains a Table (“Progression-of-New-Densification-Selected-Sampling-Locations-For-All-Scenarios.xslx”) which provides a categorical breakdown of how many unique densification-selected sampling locations occur within the irradiated region (i.e. overlap the HPAC plume) for each iteration of all scenario replicates. The fraction of irradiated to unirradiated sampling locations varies among each scenario and individual replicates for the same scenario. Our analysis shows that these results depend on the population densities and exact topography of the HPAC plume which is different among each scenario. 5. "Geostatistical-Sampling-Project.All-Scripts.zip" This archive contains all programs required for this project. This includes Python scripts meant to be run within the ArcMap software environment (for random point generation and data extraction), and Perl scripts used to process HPAC and U.S. State and Sub-division boundary files, and to assign radiation values to sample locations based on a modified HPAC plume. A java program, “CompareReplicates.jar”, compares the overlapping areas between a pair of polygons that overlap one other using the ArcMap software environment, and requires access to the ArcGIS Runtime SDK (<a href="https://developers.arcgis.com/arcgis-runtime/">https://developers.arcgis.com/arcgis-runtime/</a>).

Visualization of Demographic Data for 20 Most Populous U.S. Cities

The main objective of this project is to use data visualizations to compare different demographic and community data for the 20 most populous U.S. cities. The data was obtained from the American Community Survey (ACS) and FBI crime data. The analysis is broken into a general demographic overview, a detailed crime breakdown, and a detailed income breakdown. These visualizations allow users to filter and select data to gain key insights into each city in the analysis.

Data from: Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations

ABSTRACT Understanding the driving forces that control vole population dynamics requires identifying bacterial parasites hosted by the voles and describing their dynamics at the community level. To this end, we used high-throughput DNA sequencing to identify bacterial parasites in cyclic populations of montane water voles that exhibited a population outbreak and decline in 2014-2018. An unexpectedly large number of 155 Operational Taxonomic Units (OTUs) representing at least 13 genera in 11 families was detected. Individual bacterial richness was higher during declines, and vole body condition was lower. Richness as estimated by Chao2 at the local population scale did not exhibit clear seasonal or cycle phase-related patterns, but at the vole meta-population scale, exhibited seasonal and phase-related patterns. Moreover, bacterial OTUs that were detected in the low density phase were geographically widespread and detected earlier in the outbreak; some were associated with each other. Our results demonstrate the complexity of bacterial community patterns with regard to host density variations, and indicate that investigations about how parasites interact with host populations must be conducted at several temporal and spatial scales: multiple times per year over multiple years, and at both local and long-distance dispersal scales for the host(s) under consideration. FILE DESCRIPTION: Trapping, physical, and demographic data for the 1376 Arvicola terrestris included in sequencing runs 1 to 8 This XLSX file contains the following information concerning the 1376 animals included in the eight sequencing runs: location, session numbering, animal_id,         trap_name, capture_date, species, sex (1=male, 2=female), weight (g), length_body (mm),  length_tail (mm, testes (0=abdominal, 1=scrotal), testes_length (mm), testes_width (mm), nipples (0=small, 1=lactating), vagina (0=not perforate, 1=perforate), pub_symph (0=closed, 1=open), uterus_scars (#), embryos(#), lens_weight (g), lens_weight2 (g) and sequencing labels File name: Animal_details.xlsx   Information concerning the Arvicola terrestris samples and the positive and negative controls multiplexed in the 16Sv4 MiSeq sequencing runs 1 to 8 This XLSX file contains the Run IDs, Sample IDs, Sample types, Dates & Site names, DNA extraction kit, PCR IDs, PCR replicate numbers, numbers of reads before and after filtering and the fastq file names for the 6615 PCR products multiplexed in the eight different Illumina MiSeq runs. File name: Sample_and_sequencing_informations.xlsx   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run1) This ZIP file contains the Run1 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1570 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run1.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run2) This ZIP file contains the Run2 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1668 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run2.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run3) This ZIP file contains the Run3 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1646 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run3.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run4) This ZIP file contains the Run4 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1712 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run4.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run5) This ZIP file contains the Run5 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1680 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run5.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run6) This ZIP file contains the Run6 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1704 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run6.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run7) This ZIP file contains the Run7 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1620 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run7.zip   MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run8) This ZIP file contains the Run8 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1630 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx. File name: MiSeq_Reads_16S_Arvicola_terrestris_Run8.zip   Raw abundance table of the 16v4 rRNA gene from Arvicola terrestris samples before data filtering (Run1 to 8) This CSV file contains the number of reads for each distinct variant (OTU) and each of the 6615 PCR products, including the Arvicola terrestris samples and the controls, sequenced in the MiSeq runs 1 to 8 before the data filtering. File name: Read_abundance_table_before_filtering.csv   Abundance table of the 16v4 rRNA gene from Arvicola terrestris samples after data filtering (Run1 to 8) This CSV file contains the number of reads for each distinct variant (OTU) and each Arvicola terrestris sample sequenced in the MiSeq runs 1 to 8 after the data filtering. File name: Read_abundance_table_after_filtering.csv

The boulder population of asteroid 4 Vesta

These are data described in the paper "The boulder population of asteroid 4 Vesta: Size-frequency distribution and survival time" by Schröder et al., submitted to Earth & Space Science (Wiley). The data concern boulder counts for craters on the asteroid Vesta. Boulder counts for all 69 craters in Table 1 of the paper are provided as text files with 3 columns: (1) longitude and (2) latitude, both in degrees, and (3) boulder diameter in meters. Generally, boulder identifications are only reliable above 3 image pixels (60 m), but the data files contain all boulders that we (tentatively) identified, including those smaller than 60 m. We also provide figures in PDF format, one for each crater, of the spatial boulder distribution. The figures have the format of Fig. 6 in the paper: Green, small dots represent boulders with a size between 3 and 4 pixels (60 m < d < 80 m). Red, large dots represent boulders larger than 4 pixels (d > 80 m). Boulders smaller than 60 m are not shown.

Towards a Realistic Explosion Landscape for Binary Population Synthesis

Data from:         Towards a Realistic Explosion Landscape for Binary Population Synthesis         by         Patton, Rachel A. and Sukhbold, Tuguldur         (2020).  (Submitted to MNRAS) - Detailed descriptions of calculations are provided in the paper, but   please feel free to get in touch with any of us with questions, or   if you need something that is not provided here. Contacts:     Rachel Patton = patton[dot]502[at]osu[dot]edu     Tuguldur Sukhbold = tuguldur[dot]s[at]gmail[dot]com - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Below are brief descriptions of each dataset. More details can be found in the paper. kepler_table.tar.gz (1.0GB) -These are tables for our entire set of 3496 KEPLER CO-core models, containing the final presupernova structure and composition quantities for each zone. Core masses range from 2.5 to 10.0 in increments of 0.1 Msun and the initial composition ranges from 5% carbon and 95% oxygen to 50% carbon and oxygen, in incrmeents of 1%. Each file has the naming convention "mA_B.ktbl" where A is the core mass in Msun (2.5, 2.6, etc.) and B represents the initial carbon mass fraction as the number of increments of 0.01 taken from 0.05 (5%). For example, the file 'm8.0_27.ktbl' would be for an 8 Msun core with an initial carbon mass fraction of 0.32 (= 0.05 + 27*0.01). kepler_datatset.tar.gz (30.4KB) -This folder contains four tables listing the presupernova parameters evaluated from all of our KEPLER CO-cores: M_fe, the iron core mass, M4, the mass enclosed where the entropy per baryon reaches 4 Kb, mu_4, the radial gradient of mass at the location of M4, and xi_2.5, the compactness parameter. See section#3 of our paper for details on how these were evaluated. Columns represent each CO-core mass and rows represent starting carbon mass fraction. inlist (2.8KB) -This is the inlist used to create 760 MESA (version 7624) CO-core models, presented in section#4.1. The only thing that changes between models is the CO-core mass, set by 'initial_mass' and the composition, set by 'accretion_species_xa(1)' and 'accretion_species_xa(2)'. In our grid, we covered the same mass and composition range as the KEPLER models, keeping the same mass increment but increasing the carbon mass increment from 0.01 to 0.05.

opencc-zeroMay 2020View details →

Data from: Responses of activity rhythms to temperature cues evolve in Drosophila populations selected for divergent timing of eclosion

Even though the rhythm in adult emergence and rhythm in locomotor activity are two different rhythmic phenomena that occur at distinct life-stages of the fly life cycle, previous studies have hinted at similarities in certain aspects of the organisation of the circadian clock driving these two rhythms. For instance, the period gene plays an important regulatory role in both rhythms. In an earlier study, we have shown that selection on timing of adult emergence behaviour in populations of Drosophila melanogaster leads to the co-evolution of temperature sensitivity of circadian clocks driving eclosion. In this study, we were interested in asking if temperature sensitivity of the locomotor activity rhythm has evolved in our populations with divergent timing of adult emergence rhythm, with the goal of understanding the extent of similarity (or lack of it) in circadian organisation between the two rhythms. We found that in response to simulated jetlag with temperature cycles, late chronotypes (populations selected for predominant emergence during dusk) indeed re-entrain faster than early chronotypes (populations selected for predominant emergence during dawn) to 6-h phase-delays, thereby indicating enhanced sensitivity of the activity/rest clock to temperature cues in these stocks (entrainment is the synchronisation of internal rhythms to cyclic environmental time-cues). Additionally, we found that late chronotypes show higher plasticity of phases across regimes, day-to-day stability in phases and amplitude of entrainment, all indicative of enhanced temperature sensitive activity/rest rhythms. Our results highlight remarkably similar organisation principles between emergence and activity/rest rhythms.

opencc-by-4.0Dec 2019View details →

Strong association between the 12q24 locus and sweet taste preference in the Japanese population revealed by genome-wide meta-analysis: Summary stats

Summary stats of the genome-wide meta-analysis with METAL software in the article "Strong association between the 12q24 locus and sweet taste preference in the Japanese population revealed by genome-wide meta-analysis."

opencc-zeroMar 2021View details →

The seventh macronutrient: how sodium shortfall ramifies through populations, food webs, and ecosystems

Of the 25 elements required to build most organisms, sodium has a unique set of characteristics that ramify through terrestrial ecology. In plants, sodium is found in low concentrations and has little metabolic function; in plant consumers, particularly animals, sodium is essential to running costly Na-K ATPases. Here I synthesize a diverse literature from physiology, agronomy, and ecology, toward identifying sodium's place as the "7th macronutrient", one whose shortfall targets two trophic levels—herbivores and detritivores. I propose that sodium also plays a central, though unheralded role in herbivore digestion, via its importance to maintaining microbiomes and denaturing tannins. I highlight how sodium availability is a key determinant of consumer abundance and the geography of herbivory and detritivory. And I propose a re-appraisal of the assumption that, because sodium is metabolically unimportant to most plants, it is of little use. Instead, I suggest that sodium's critical role in limiting herbivore performance makes it a commodity used by plants to manipulate their herbivores and mutualists, and by consumers like bison and elephants to generate grazing lawns: dependable sources of sodium.

opencc-zeroJun 2020View details →

Data from: Candidate gene SNP variation in floodplain populations of pedunculate oak (Quercus robur L.) near the species' southern range margin: weak differentiation yet distinct associations with water availability

Populations residing near species' low-latitude range margins (LLM) often occur in warmer and drier environments than those in the core range. Thus, their genetic composition could be shaped by climatic drivers that differ from those occurring at higher latitudes, resulting in potentially adaptive variants of conservation value. Such variants could facilitate the adaptation of populations from other portions of the geographic range to similar future conditions anticipated under ongoing climate change. However, very few studies have assessed standing genetic variation at potentially adaptive loci in natural LLM populations. We investigated standing genetic variation at SNPs located within 117 candidate genes and its links to putative climatic selection pressures across 19 pedunculate oak (Quercus robur L.) populations distributed along a regional climatic gradient near the species' southern range margin in southeastern Europe. These populations are restricted to floodplain forests along large lowland rivers, whose hydric regime is undergoing significant shifts under modern rapid climate change. The populations showed very weak geographic structure, suggesting extensive genetic connectivity and gene flow or shared ancestry. We identified eight (6.2%) positive FST-outlier loci, and genotype-environment association analyses revealed consistent associations between SNP allele frequencies and several climatic variables linked to water availability. A total of 61 associations involving 37 SNPs (28.5%) from 35 annotated genes provided important insights into putative functional mechanisms in our system. Our findings provide empirical support for the role of LLM populations as sources of potentially adaptive variation that could enhance species' resilience to climate change-related pressures.

opencc-by-4.0Jun 2020View details →

Fitness measures of maternal transplants (seed fitness) and of the F1 generation (rosette diameter) of three translocated populations of Arnica montana in southern Belgium

Fitness data measured in the framework of a genetic monitoring of translocated populations of the critically endangered Arnica montana. See Van Rossum et al. (2020) in Molecular Ecology for more details.

opencc-by-4.0Jun 2020View details →

Individual multilocus genotypes of three translocated and two source populations of Arnica montana in southern Belgium

Individual multilocus genotypes based on nine microsatellite loci measured in the framework of a genetic monitoring of translocated populations of the critically endangered Arnica montana. See Van Rossum et al. (2020) in Molecular Ecology for more details.

opencc-by-4.0Jul 2020View details →

Population scenarios for U.S. states consistent with Shared Socioeconomic Pathways

This is a data record of the input and output data associated with the following publication: Jiang, L., B.C. O'Neill, H. Zoraghein, and S. Dahlke. 2020. Population scenarios for U.S. states consistent with Shared Socioeconomic Pathways. Environmental Research Letters, <a href="https://doi.org/10.1088/1748-9326/aba5b1">https://doi.org/10.1088/1748-9326/aba5b1</a>. The accompanying code can be found here:   Zoraghein, H., R. Nawrotzki, L. Jiang, and S. Dahlke (2020). IMMM-SFA/statepop: v0.1.0 (Version v0.1.0). Zenodo. <a href="https://protect2.fireeye.com/v1/url?k=dbf32d36-8746128f-dbf30723-0cc47adc5fce-abb2658d1d55b41e&q=1&e=1c8eff6c-b006-48cb-8ff3-fd95c41a8980&u=https%3A%2F%2Fprotect-us.mimecast.com%2Fs%2FbxLNCXD7VRHXoAlVcVcXsa%3Fdomain%3Dprotect2.fireeye.com">http://doi.org/10.5281/zenodo.3956703</a>  The following detail the contents: <ul> <li>SSP<ssp_number>.zip <ul> <li><state_number>_<state_abbreviation> <ul> <li><state_number>_<state_abbreviation>_In_Mig.jpg <ul> <li>output figure for in-migration change through time for the target state</li> </ul> </li> <li><state_number>_<state_abbreviation>_Net_Mig.jpg <ul> <li>output figure for net-migration change through time for the target state</li> </ul> </li> <li><state_number>_<state_abbreviation>_Out_Mig.jpg <ul> <li>output figure for out-migration change through time for the target state</li> </ul> </li> <li><state_number>_<state_abbreviation>_proj_in_mig.csv <ul> <li>projected age and gender specific number of domestic in-migration for the state over time</li> </ul> </li> <li><state_number>_<state_abbreviation>_proj_net_mig.csv <ul> <li>projected age and gender specific number of domestic net-migration for the state over time</li> </ul> </li> <li><state_number>_<state_abbreviation>_proj_out_mig.csv <ul> <li>projected age and gender specific number of domestic out-migration for the state over time</li> </ul> </li> <li><state_number>_<state_abbreviation>_proj_pop.csv <ul> <li>projected age and gender specific number of population for the state over time</li> </ul> </li> <li><state_number>_<state_abbreviation>_total_in_mig.csv <ul> <li>projected age and gender specific in-migration from other states to the current state over time</li> </ul> </li> <li><state_number>_<state_abbreviation>_total_out_mig.csv <ul> <li>projected age and gender specific out-migration from the current state to other states over time</li> </ul> </li> <li><state_number>_<state_abbreviation>.jpg <ul> <li>figure for projected change of population for the state</li> </ul> </li> </ul> </li> </ul> </li> <li>State_inputs.zip <ul> <li><state_number>_<state_abbreviation> <ul> <li><state_number>_<state_abbreviation>_in_mig.csv <ul> <li>a table containing gender- and age-specific migration rates from all states to the current state at the base year.</li> </ul> </li> <li><state_number>_<state_abbreviation>_out_mig.csv <ul> <li>a table containing gender- and age-specific migration rates from the current state to all other states at the base year.</li> </ul> </li> <li>basePop.csv <ul> <li>a table containing gender- and age-specific counts of people in the current state at the base year (2010).</li> </ul> </li> <li>Constant_rate.csv <ul> <li>a table that constructs a constant scenario for fertility, mortality (life expectancy), urbanization level (required if we differentiate urban and rural), sex ratio at birth and net estimates of international migrants for the current state. The table is from 2010 to 2100 at 5 year intervals used for scenario building. The presented scenario, for instance, keeps everything constant at its historical record estimated from the data.</li> </ul> </li> <li>fertility.csv <ul> <li>a table containing age-specific fertility rates for the current state at the base year.</li> </ul> </li> <li>intMig.csv <ul> <li>a table containing gender- and age-specific proportions of international migrants to the current state at the base year.</li> </ul> </li> <li>mortality.csv <ul> <li>a table containing gender- and age-specific life expectancy and mortality rates for the current state at the base year (life table).</li> </ul> </li> </ul> </li> </ul> </li> </ul>

opencc-zeroDec 2019View details →

Data from: The contribution of hybridization to range‐wide population genetic structure in a Pacific coastal dune plant

Premise of the study: Interspecific hybridization can cause genetic structure across species ranges if the mating system and degree of sympatry/parapatry with close relatives varies geographically. The coastal dune endemic Camissoniopsis cheiranthifolia (Onagraceae) exhibits genetic subdivisions across its range, some of which are associated with shifts in mating system from outcrossing to selfing, while others are not. For instance, strong differentiation between large-flowered, self-incompatible (LF-SI) and large-flowered, self-compatible (LF-SC) populations occurs without much reduction in outcrossing or obvious barriers to gene flow. We hypothesized that LF-SI diverged from LF-SC via hybridization with the predominantly inland SI sister species C. bistorta. Methods: We analyzed spatial proximity using 1460 herbarium records, and genetic variation at 12 microsatellites assayed for 805 and 404 individuals from 32 C. cheiranthifolia and 18 C. bistorta populations, respectively. We also assayed nine chloroplast microsatellites for 124 and 111 individuals from 27 and 19 populations, respectively. Key results: Closer parapatry was associated with unexpectedly high genetic continuity between LF-SI C. cheiranthifolia and C. bistorta. LF-SI genotypes clustered with C. bistorta exclusive of other C. cheiranthifolia genotypes. Similarly, pairwise FST among SI C. cheiranthifolia and C. bistorta, adjusted for geographic proximity, was not higher between heterospecific than conspecific populations. Conclusions: The lack of genetic differentiation between LF-SI C. cheiranthifolia and C. bistorta populations, even those located away from the zone of parapatry, suggests that LF-SI C. cheiranthifolia instead of hybridizing with C. bistorta is rather an ecotype of C. bistorta that has adapted to coastal dune habitat independent of other lineages in C. cheiranthifolia proper.

opencc-zeroJul 2020View details →

Data from: Environmental change, if unaccounted, prevents detection of cryptic evolution in a wild population

Detecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed-effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Furthermore, such studies often lack an independent measure of evolutionary change against which to verify predictions. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in a wild population of Trinidadian guppies. Crucially, we tested our predictions against evolutionary change observed in common garden experiments performed on samples from the same population. We show that standard quantitative genetic models underestimated or failed to detect the cryptic evolution of this trait as demonstrated by the common garden experiments. The models failed because: 1) size at maturity and fitness both decreased with increases in population density, 2) offspring experienced higher population densities than their parents, and 3) selection on size was strongest at high densities. When we accounted for environmental change, predictions better matched observations in the common garden experiments, although substantial uncertainty remained. Our results demonstrate that predictions of evolution are unreliable if environmental change is not appropriately captured in models.

opencc-zeroOct 2019View details →

Data from: Adaptive landscape genetics and malaria across divergent island bird populations

Environmental conditions play a major role in shaping the spatial distributions of pathogens, which in turn can drive local adaptation and divergence in host genetic diversity. Haemosporidians, such as plasmodium (malaria) are a strong selective force, impacting survival and fitness of hosts, with geographic distributions largely determined by habitat suitability for their insect vectors. Here, we have tested whether patterns of fine-scale local adaptation to malaria are replicated across discrete, ecologically differing island populations of Berthelot's pipits Anthus berthelotii. We sequenced TLR4, an innate immunity gene that is potentially under positive selection in Berthelot's pipits, and two SNPs previously identified as being associated with malaria infection in a genome-wide association study (GWAS) in Berthelot's pipits in the Canary Islands. We determined the environmental predictors of malaria infection, using these to estimate variation in malaria risk on Porto Santo, and found some congruence with previously identified environmental risk factors on Tenerife. We also found a negative association between malaria infection and a TLR4 variant in Tenerife. In contrast, one of the GWAS SNPs showed an association with malaria risk in Porto Santo, but in the opposite direction to that found in the Canary Islands GWAS. Together, these findings suggest that disease-driven local adaptation may be an important factor in shaping variation among island populations.

opencc-zeroJul 2020View details →

Data from: Detecting the population dynamics of an autosomal sex-ratio distorter transgene in malaria vector mosquitoes

1. The development of genetically modified mosquitoes and their subsequent field release offers innovative and cost-effective approaches to reduce mosquito-borne diseases, such as malaria. A sex-distorting autosomal transgene has been developed recently in G3 mosquitoes, a lab strain of the malaria vector Anopheles gambiae s.l. The transgene expresses an endonuclease called I-PpoI during spermatogenesis, which selectively cleaves the X chromosome to result in ~95% male progeny. Following the World Health Organization Guidance Framework for the testing of genetically modified mosquitoes, we assessed the dynamics of this transgene in large cages using a joint experimental-modelling approach. 2. We performed a four-month experiment in indoor large cages to study the population genetics of the transgene. The cages were set up to mimic a simple tropical environment with a diurnal light-cycle, constant temperature, and constant humidity. We allowed the generations to overlap to engender a stable age structure in the populations. We constructed a model to mimic the experiments, and used the experimental data to infer the key model parameters. 3. We identified two fitness costs associated to the transgene. First, transgenic adult males have reduced fertility and, second, their female progeny have reduced pupal survival rates. Our results demonstrate that the transgene is likely to disappear in less than three years under our confined conditions. Model predictions suggest this will be true over a wide range of background population sizes and transgene introduction rates. 4. Synthesis and applications: Our semi-field indoor cage experiments are in line with WHO guidance recommendations in regards to the development and testing of self-limiting technologies. Since the transgenic strain (Ag(PMB)1) has been considered for genetic vector control of malaria, our results are fundamentally important for determining expectations on the persistence of the transgene post-release. Our results provide a demonstration of the self-limiting nature of the transgene, and indicate that longevity will be further reduced by fitness costs that were not previously identified. Finally, our study has showcased an alternative and effective method for characterising the phenotypic expression of a transgene in an insect pest population.