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opencc-by-4.0Oct 2021View details →

Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation

Many adaptive traits are polygenic and frequently more loci contributing to the phenotype are segregating than needed to express the phenotypic optimum. Experimental evolution with replicated populations adapting to a new controlled environment provides a powerful approach to study polygenic adaptation. Since genetic redundancy often results in non-parallel selection responses among replicates, we propose a modified Evolve and Resequence (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred Drosophila melanogasterstrains and expose them to a very extreme, hot temperature environment (29°C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Since two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation. See the README.txt file to get a description of the uploaded files. Scripts.zip contains annotated command lines and scripts for the project (see internal README.txt file).

opencc-by-4.0Jun 2024View details →

Supplementary material for "Dynamics of a goshawk population across half a century is driven by the variation of first-year survival"

Abstract Population dynamics are driven by stochastic and density-dependent processes acting on demographic rates. Individuals differ demographically, and to capture these differences, models of population dynamics are usually structured by age and stage, rarely by sex. An effect of sex on population dynamics is expected if the dynamics of males and females differ, requiring an unequal sex ratio at birth and/or sex-specific survival probabilities. Goshawks (Accipiter gentilis) show large sexual size dimorphism and differential survival, but it is unknown whether males and females contribute differently to population dynamics. We studied a goshawk population in northern Germany over 47 years using brood monitoring data, collected feathers and nestling ringing data. We jointly analyzed the data using a two-sex integrated population model and performed retrospective and prospective population analyses to understand whether the demographic drivers of population change differ between the sexes. The population showed large fluctuations, during which the number of breeding pairs doubled, but the long-term trend of the population was slightly negative. Female survival exceeded male survival during the first year of life. Females started to reproduce at a younger age than males, productivity increased with female age, the sex ratio of nestlings was male biased and there was moderate male immigration. Despite these differences, temporal variation in sex ratio did not contribute to population dynamics and the contribution of temporal variation in survival was similar for both sexes. Variation in first-year survival was the strongest driver in this population, regulated by a weak density-dependent feedback acting through female first-year survival. Overall, the contributions of the two sexes to population dynamics were similar in this monogamous species with strong sexual size dimorphism. Read me Data files and code for carrying out all analyses and generating all figures presented in the paper. The six data files are provided in csv format. There are five code files written for R, but some of the main analyses require the NIMBLE software. The main code (IPM_Code.txt) contains a description of the data, code for loading and managing the data, and for fitting the integrated population models. The other files contain custom written functions (Functions.txt), code for performing posterior predictive tests (PPT_Code.txt), code for reporting results and performing various other analyses (Output_analyses_Code.txt), and code for generating figures (Figures_Code.txt).

opencc-by-4.0Apr 2019View details →

Retrotransposon-based genetic variation of Poa annua populations from contrasting climate conditions

Raw photographs of agarose electrophoresis. Material: six Poa annua populations. Method: inter-Primer Binding Site (iPBS) markers This is the documentation of studies described in the manuscript entitled "Retrotransposon-based genetic variation of Poa annua populations from contrasting climate conditions" accepted for publication in PeerJ journal (decision received on 02.04.2019)

opencc-by-4.0Sep 2024View details →

The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover

Zenodo deposit for Pozzi et al (2024) AJB The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover  _____________________________________________________________________________________________________________________________________ The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover Adrien C.M. Pozzi1,2, Ruth G. Shaw1, Georgiana May1,3 1 Department of Ecology, Evolution and Behavior, University of Minnesota Twin-Cities, St Paul, MN 55108. 2 Current affiliation: Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622 Villeurbanne, France. ORCID: 0000-0001-6765-4293. 3 Correspondence: Georgiana May (gmay@umn.edu) Keywords: conservation; Dalea spp.; habitat fragmentation; mutualism; nitrogen-fixing symbiosis; population level variation; native prairie legume; restoration; rhizobia Description: This Zenodo deposit is part of the MN LCCMR Healthy Prairies project granted to R. Shaw and G. May, UMN Twin-Cities. It contains the following files: ·         “Metadata & data” spreadsheet. Contains metadata and data about the Twin Valley experiment (including the position of plants, an intermediary census, growth and nodulation traits for harvested plants, data on bacterial isolates from root nodules, and source modifiers for GenBank accessions OQ732394-OQ732572). ·         “Blast alignments output.txt” text file. Contains ouput of Blastn alignements for the 16S rRNA genes of bacterial isolates against the rRNA_typestrains/16S_ribosomal_RNA 16S ribosomal RNA (Bacteria and Archaea type strains) database, to determine the genus as recommended by GenBank during sequence submission. ·         “General script.R”. R script of the general statistical analyses produced for publication. ·         “General environment.RData”. The companion RData (environment) of the above R script. ·         “Trait model script.R”. R script of the plant trait models produced for publication ·         “Trait model environment.RData”. The companion RData (environment) of the above R script. Acknowledgments: The authors thank members of the May Lab (Mai Beauclaire, Em Daily, Mara Demers, Kane Keller, Cedric Ndinga-Muniania, Liam Vertal, Monica Watson) for their help in field and lab work. We thank members of the Healthy Prairies project (Shelby Flint, Anna Peschel, Bill Peterson) who provided much of the infrastructure that made this project possible, as well as help in setting up field experiments. We also thank volunteer undergrads from University of Minnesota Morris (Amelia Nelson, Emily Job, Lily Fulton) for assistance in measuring harvested plants and counting nodules. Funding for this project was provided by the Minnesota Environment and Natural Resources Trust Fund as recommended by the Legislative-Citizen Commission on Minnesota Resources (LCCMR) Project 00086965, Healthy Prairies.

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Virgin Islands National Park: Coral Reef: Population Dynamics: Landscape-scale Variation in Scleractinian Corals

This study provides a landscape-scale context to a decadal-scale analysis of community structure on shallow reefs along 4 km of the south shore of St. John, US Virgin Islands. By focusing on 12-14 sites along ~100 km of the shores of St. John and St. Thomas, surveys conducted in 2011 were used to contrast: (1) a local-scale with a landscape-scale analysis on two islands, (2) reefs around St. John and St. Thomas, and (3) reefs on north and south shores. Reefs were censused using photoquadrats that were analyzed for percentage cover first by functional groups (coral, macraolagae and CTB), and then by coral genus. In general, among-site variation for the coarse-resolution analysis eclipsed shore and island effects, but the fine-resolution analysis revealed strong site-specific differences for multiple coral genera that could be the product of priority effects in community succession. Over the next decade these differences probably will create unique community trajectories at each site.

openCC (other)Feb 2022View details →

opencc-by-4.0Nov 2018View details →

Figure 2 in Taxonomic study and population variation of scale insects (Hemiptera: Coccidae and Diaspididae) and associated parasitoids (Hymenoptera: Chalcidoidea) in an olive grove at Rio Grande do Sul, Brazil

Figure 2. Population variation of Hemiberlesia lataniae (Hemiptera: Diaspididae) on different varieties of Olea europaea (Arbequina, Arbosana and Koroneiki), at different times of sampling, in Barra do Ribeiro (30°30′54.95″S, 51°30′20.84″W), Rio Grande do Sul, Brazil.

opencc-by-4.0Nov 2018View details →

Figure 1 in Taxonomic study and population variation of scale insects (Hemiptera: Coccidae and Diaspididae) and associated parasitoids (Hymenoptera: Chalcidoidea) in an olive grove at Rio Grande do Sul, Brazil

Figure 1. Population variation of Hemiberlesia lataniae (Hemiptera: Diaspididae) in an Olea europaea multivarietal olive grove (Arbequina, Arbosana and Koroneiki), at different sampling times, considering different phases and stage of development in Barra do Ribeiro (30°30′54.95″S, 51°30′20.84″W), Rio Grande do Sul, Brazil.

opencc-by-4.0May 2020View details →

Genetic variation in early fitness traits across European populations of silver birch (Betula pendula)

Early life phenotypic data from three Betula pendula common garden experiments spread across the species latitudinal range in Europe.

opencc-zeroDec 2018View details →

Geographic patterns in morphometric and genetic variation for coyote populations with emphasis on southeastern coyotes

Prior to 1900, coyotes (Canis latrans) were restricted to the western and central regions of North America, but by the early 2000s coyotes became ubiquitous throughout the eastern United States. Information regarding morphological and genetic structure of coyote populations in the southeastern United States is limited, and where data exist, they are rarely compared to those from other regions of North America. We assessed geographic patterns in morphology and genetics of coyotes with special consideration of coyotes in the southeastern United States. Mean body mass of coyote populations increased along a west-to-east gradient, with southeastern coyotes being intermediate to western and northeastern coyotes. Similarly, principal component analysis of body mass and linear body measurements suggested that southeastern coyotes were intermediate to western and northeastern coyotes in body size but exhibited shorter tails and ears from other populations. Genetic analyses indicated that southeastern coyotes represented a distinct genetic cluster that differentiated strongly from western and northeastern coyotes. We postulate that southeastern coyotes experienced lower immigration from western populations than did northeastern coyotes, and over time, genetically diverged from both western and northeastern populations. Coyotes colonizing eastern North America experienced different selective pressures than did stable populations in the core range and we offer that the larger body size of eastern coyotes reflect an adaptation that improved dispersal capabilities of individuals in the expanding range.

opencc-zeroJun 2020View details →

Data from: Genome wide assessment of genetic variation and population distinctiveness of the pig family in South Africa

Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K= 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92% – 98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise FSTanalysis showed genetic differentiation (P < 0.05)between the village, commercial and wild populations. A per marker per population pairwise FSTanalysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.

opencc-by-nc-4.0Feb 2017View details →

Raw Genotyping data from: Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets

Data supporting : Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets Morgane Petit, Jean-Michel Astruc, Julien Sarry, Laurence Drouilhet, Stephane Fabre, Carole Moreno, Bertrand Servin http://doi.org/10.1534/genetics.117.300123 Abstract Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and datasets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified about 50,000 crossover hotspots on the genome and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting inter-individual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly 2 other loci of smaller effects including  the KCNJ15  and FSHR genes. Finally, we compared our results to those obtained previously in a distantly related population of domestic sheep, the Soay. This comparison revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome and that the two datasets can be combined to create more precise male meiotic recombination maps in sheep. Despite their similar recombination maps, we show that Soay and Lacaune males exhibit different heritabilities and QTL effects for inter-individual variation in genome-wide recombination rates.   Data files are provided in Plink format ( https://www.cog-genomics.org/plink2 ).

opencc-by-4.0Dec 2021View details →

Figure 3 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats

Figure 3. – Projection of Procrustes coordinates and scores of canonical variate on Aphanius fasciatus shape analysis (A) and comparative transformation grids (B). LM: Mellah lagoon, M: Mellah marsh, BZ: Lagoon of Bizerte, LA: Ayata Lake.

opencc-by-4.0Dec 2021View details →

Figure 2 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats

Figure 2. – Landmarks distribution on fish body of Aphanius fasciatus. 1: Eye position, 2: Dorsal opercular limit, 3: Beginning of dorsal fin, 4: End of dorsal fin, 5: Dorsal limit of caudal peduncle, 6: Median limit of caudal peduncle, 7: Ventral limit of caudal peduncle, 8: End of anal fin, 9: Beginning of anal fin, 10: Pelvic fin insertion, 11: Ventral opercula limit, 12: Dorsal limit of pectoral fin, 13: Ventral limit of pectoral fin, 14: Mouth.

opencc-by-4.0Dec 2021View details →

Figure 1 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats

Figure 1. – Map of the west Mediterranean basin with North African sample sites. 1: Mellah lagoon (LM), 2: Mellah marsh (M), 3: Lagoon of Bizerte (BZ), 4: Ayata Lake (LA).

opencc-by-4.0Nov 2013View details →

Figs 2, 3 in Seasonal variations in ixodid tick populations on a commercial game farm in the Limpopo Province, South Africa

Figs 2, 3. Numbers of Rhipicephalus (Boophilus) decoloratus collected in wetter and drier months (2), and in warmer and cooler months (3).

opencc-zeroMar 2022View details →

Data from: Environmental drivers of population-level variation in the migratory and diving ontogeny of an Arctic top predator

The development of migratory strategies that enable juveniles to survive to recruitment is critical for species that exploit seasonal niches. For animals that forage via breath-hold diving this requires a combination of both physiological and foraging skill development. Here, we assess how migratory and dive behaviour develop over the first months of life for a migratory Arctic top predator, the harp seal, tracked using animal-borne satellite relay data loggers. We reveal similarities in migratory movements and differences in diving behaviour between juveniles from breeding populations in the Northwest Atlantic and Greenland Sea. In both regions, periods of resident and transient behaviour during migration were associated with proxies for food availability; sea ice concentration and water depth. However, while ontogenetic development of dive behaviour was similar for both groups of juveniles over the first 25 days, after this time Greenland Sea animals performed shorter and shallower dives and were more closely associated with sea ice than Northwest Atlantic animals. Together, these results highlight the role of both intrinsic and extrinsic factors in shaping early-life behaviour. Differences in the environmental conditions experienced during early-life may shape how populations respond to the rapid changes occurring in the Arctic ocean ecosystem.