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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-4.0Nov 2021View details →

The genetic basis of structural colour variation in mimetic Heliconius butterflies

Raw USAXS data from discal region of Heliconius butterflies (H. erato and H. melpomene). The data comes from wings of individuals of two intercross families, one from each species and was used to estimate scale structure variation and a QTL analysis.

opencc-by-4.0Jul 2022View details →

Microsatellite genotypes for «Genetic diversity and spatial genetic structure support the specialist‑generalist variation hypothesis in two sympatric woodpecker species»

Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (Dendrocopos major), lower genetic diversity was found in the specialist middle spotted woodpecker (Dendrocoptes medius). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.

opencc-by-4.0May 2024View details →

Data for 'Genetic variation in trophic avoidance shows fruit flies are generally attracted to bacterial pathogens'

Raw data dn R code for the analysis of data dn generation of all figures in the above referenced paper. Descriptions of each data file are included wihtin the R script.

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-4.0May 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-zeroDec 2015View details →

Data from: Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments

Chilean mussel populations have been thought to be panmictic with limited genetic structure. Genotyping-by-sequencing approaches have enabled investigation of genome-wide variation that may better distinguish populations that have evolved in different environments. We investigated neutral and adaptive genetic variation in Mytilus from six locations in southern Chile with 1,240 SNP obtained with RAD-seq. Differentiation among locations with 891 neutral SNPs was low (FST = 0.005). Higher differentiation was obtained with a panel of 58 putative outlier SNPs (FST = 0.114) indicating the potential for local adaptation. This panel identified clusters of genetically related individuals and demonstrated that much of the differentiation (~92%) could be attributed to the three major regions and environments: extreme conditions in Patagonia, inner bay influenced by aquaculture (Reloncaví́), and outer bay (Chiloé Island). Patagonia samples were most distinct, but additional analysis carried out excluding this collection also revealed adaptive divergence between inner and outer bay samples. The four locations within Reloncaví́ area were most similar with all panels of markers, likely due to similar environments, high gene flow by aquaculture practices and low geographic distance. However, fine scale structure could be detected when analyses included only this zone. Our results and the SNP markers developed will be a powerful tool supporting management and programs of this harvested species.

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-zeroOct 2023View details →

Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar

<div>Summary</div> <div> </div> <div> Research Aims - The extent of Madagascar's grasslands prior to human colonization is unresolved. We used population genetic analyses of a broadly dominant C4 fire-adapted grass, Loudetia simplex, as a proxy for estimating grassland change through time. We carefully examined the utility of target-enrichment data for population genetics to make recommendations for conservation genetics. We explored the potential of estimating individual ploidy levels from target-enrichment data and how assumptions about ploidy could affect analyses.</div> <div> </div> <div> Methods - We developed a novel bioinformatic pipeline based to estimate ploidy and genotypes from target-enrichment data. We estimated standard population genetic summary statistics in addition to species trees and population structure. Extended Bayesian skyline plots provided estimates of population size through time for empirical and simulated data.</div> <div> </div> <div> Key Result - All Malagasy Loudetia simplex individuals sampled in this study formed a clade and possibly indicated an ancestral high-altitude distribution. Demographic models suggested grassland expansions occurred prior to the Last Interglacial Period and supported extensive grasslands prior to human colonization. Though there are limitations to target-enrichment data for population genetic studies, we find that analyses of population structure are reliable.</div> <div> </div> <div> Key Point - Genetic variation in Loudetia simplex supports widespread grasslands in Madagascar prior to the more recent periods of notable paleoclimatic change. However, the methods explored here could not differentiate between paleoclimatic change near the Last Glacial Maximum and anthropogenic effects. Target-enrichment data can be a valuable tool for analyses of population structure in the absence a reference genome.</div> <div> </div> <div>Societal Impact Statement</div> <div> </div> <div>Recognizing Loudetia dominated grasslands were widespread prior to human colonization highlights that open ecosystems were and continue to be an important component to Madagascar's biodiversity. Urgently required are biodiversity inventories and risk assessments for unique grassland flora and fauna under present day environmental conditions to recognize and quantify modern human impacts within ecosystems historically regarded as wastelands. Substantial financial and logistic barriers exist to implementing conservation studies using contemporary genomic tools that we seek to ameliorate by developing computational resources to leverage a cost-effective data generation strategy that requires no prior genetic knowledge of the target species.</div>

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-zeroMar 2024View details →

Data from: Dominance reversals and the maintenance of genetic variation

Beneficial reversals of dominance reduce the costs of genetic trade-offs and can enable selection to maintain genetic variation for fitness. Beneficial dominance reversals are characterized by the beneficial allele for a given context (e.g. habitat, developmental stage, trait, or sex) being dominant in that context but recessive where deleterious. This context-dependence at least partially mitigates the fitness consequence of heterozygotes carrying one non-beneficial allele for their context and can result in balancing selection that maintains alternative alleles. Dominance reversals are theoretically plausible and are supported by mounting empirical evidence. Here we highlight the importance of beneficial dominance reversals as a mechanism for the mitigation of genetic conflict and review the theory and empirical evidence for them. We identify some areas in need of further research and development and outline three methods (dominance ordination, allele-specific expression, and allele-specific ATAC-Seq) that could facilitate the identification of antagonistic genetic variation. There is ample scope for the development of new empirical methods as well as reanalysis of existing data through the lens of dominance reversals. A greater focus on this topic will expand our understanding of the mechanisms that resolve genetic conflict and whether they maintain genetic variation.

opencc-by-4.0Apr 2024View details →

Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts

Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By employing virome-enriched long-read metagenomics sequencing across 91 individuals, we identified a total of 14,438 non-redundant phage SVs, and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Strikingly, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibits a higher frequency of genetic exchange with bacterial chromosomes then virulent phages. Collectively, our findings provide novel insights into the genetic landscape of the human gut phageome.

opencc-zeroMar 2022View details →

Data accompanying Polyphenisms and polymorphisms: genetic variation in plasticity and color variation within and among bluefin killifish populations

The presence of stable color polymorphisms within populations begs the question of how genetic variation is maintained. Consistent variation among populations in coloration, especially when correlated with environmental variation, raises questions about whether environmental conditions affect either the fulcrum of those balanced polymorphisms, the plastic expression of coloration, or both. Color patterns in male bluefin killifish provoke both types of questions. Red and yellow morphs are common in all populations. Blue males are more common in tannin-stained swamps relative to clear springs. Here we combined crosses with a manipulation of light to explore how genetic variation and phenotypic plasticity shape these patterns. We found that the variation in coloration is attributable mainly to two axes of variation: (1) a red-yellow axis with yellow being dominant to red, and (2) a blue axis that can override red-yellow and is controlled by genetics, phenotypic plasticity, and genetic variation for phenotypic plasticity. The variation among populations in plasticity suggests it is adaptive in some populations but not others. The variation among sires in plasticity within the swamp population suggests balancing selection may be acting not only on the red-yellow polymorphism but also on plasticity for blue coloration.