Effective population size (Ne ) is a key population genetic parameter that describes the amount of genetic drift in a population. Estimating Ne has been subject to much research over the last 80 ...years. Methods to estimate Ne from linkage disequilibrium (LD) were developed ~40 years ago but depend on the availability of large amounts of genetic marker data that only the most recent advances in DNA technology have made available. Here we introduce SNeP, a multithreaded tool to perform the estimate of Ne using LD using the standard PLINK input file format (.ped and.map files) or by using LD values calculated using other software. Through SNeP the user can apply several corrections to take account of sample size, mutation, phasing, and recombination rate. Each variable involved in the computation such as the binning parameters or the chromosomes to include in the analysis can be modified. When applied to published datasets, SNeP produced results closely comparable with those obtained in the original studies. The use of SNeP to estimate Ne trends can improve understanding of population demography in the recent past, provided a sufficient number of SNPs and their physical position in the genome are available. Binaries for the most common operating systems are available at https://sourceforge.net/projects/snepnetrends/.
The genomic basis of adaptation to novel environments is a fundamental problem in evolutionary biology that has gained additional importance in the light of the recent global change discussion. Here, ...we combined laboratory natural selection (experimental evolution) in Drosophila melanogaster with genome‐wide next generation sequencing of DNA pools (Pool‐Seq) to identify alleles that are favourable in a novel laboratory environment and traced their trajectories during the adaptive process. Already after 15 generations, we identified a pronounced genomic response to selection, with almost 5000 single nucleotide polymorphisms (SNP; genome‐wide false discovery rates < 0.005%) deviating from neutral expectation. Importantly, the evolutionary trajectories of the selected alleles were heterogeneous, with the alleles falling into two distinct classes: (i) alleles that continuously rise in frequency; and (ii) alleles that at first increase rapidly but whose frequencies then reach a plateau. Our data thus suggest that the genomic response to selection can involve a large number of selected SNPs that show unexpectedly complex evolutionary trajectories, possibly due to nonadditive effects.
See also the Perspective by Burke and Long
Domestication of cattle: Two or three events? Pitt, Daniel; Sevane, Natalia; Nicolazzi, Ezequiel L. ...
Evolutionary applications,
January 2019, Letnik:
12, Številka:
1
Journal Article
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Cattle have been invaluable for the transition of human society from nomadic hunter‐gatherers to sedentary farming communities throughout much of Europe, Asia and Africa since the earliest ...domestication of cattle more than 10,000 years ago. Although current understanding of relationships among ancestral populations remains limited, domestication of cattle is thought to have occurred on two or three occasions, giving rise to the taurine (Bos taurus) and indicine (Bos indicus) species that share the aurochs (Bos primigenius) as common ancestor ~250,000 years ago. Indicine and taurine cattle were domesticated in the Indus Valley and Fertile Crescent, respectively; however, an additional domestication event for taurine in the Western Desert of Egypt has also been proposed. We analysed medium density Illumina Bovine SNP array (~54,000 loci) data across 3,196 individuals, representing 180 taurine and indicine populations to investigate population structure within and between populations, and domestication and demographic dynamics using approximate Bayesian computation (ABC). Comparative analyses between scenarios modelling two and three domestication events consistently favour a model with only two episodes and suggest that the additional genetic variation component usually detected in African taurine cattle may be explained by hybridization with local aurochs in Africa after the domestication of taurine cattle in the Fertile Crescent. African indicine cattle exhibit high levels of shared genetic variation with Asian indicine cattle due to their recent divergence and with African taurine cattle through relatively recent gene flow. Scenarios with unidirectional or bidirectional migratory events between European taurine and Asian indicine cattle are also plausible, although further studies are needed to disentangle the complex human‐mediated dispersion patterns of domestic cattle. This study therefore helps to clarify the effect of past demographic history on the genetic variation of modern cattle, providing a basis for further analyses exploring alternative migratory routes for early domestic populations.
The introduction of Iberian cattle in the Americas after Columbus’ arrival imposed high selection pressures on a limited number of animals over a brief period of time. Knowledge of the genomic ...regions selected during this process may help in enhancing climatic resilience and sustainable animal production. We first determined taurine and indicine contributions to the genomic structure of modern Creole cattle. Second, we inferred their demographic history using approximate Bayesian computation (ABC), linkage disequilibrium (LD) and Ne Slope (NeS) analysis. Third, we performed whole genome scans for selection signatures based on cross‐population extended haplotype homozygosity (XP‐EHH) and population differentiation (FST) to disentangle the genetic mechanisms involved in adaptation and phenotypic change by a rapid and major environmental transition. To tackle these questions, we combined SNP array data (~54,000 SNPs) in Creole breeds with their modern putative Iberian ancestors. Reconstruction of the population history of Creoles from the end of the 15th century indicated a major demographic expansion until the introduction of zebu and commercial breeds into the Americas ~180 years ago, coinciding with a drastic Ne contraction. NeS analysis provided insights into short‐term complexity in population change and depicted a decrease/expansion episode at the end of the ABC‐inferred expansion, as well as several additional fluctuations in Ne with the attainment of the current small Ne only towards the end of the 20th century. Selection signatures for tropical adaptation pinpointed the thermoregulatory slick hair coat region, identifying a new candidate gene (GDNF), as well as novel candidate regions involved in immune function, behavioural processes, iron metabolism and adaptation to new feeding conditions. The outcomes from this study will help in future‐proofing farm animal genetic resources (FAnGR) by providing molecular tools that allow selection for improved cattle performance, resilience and welfare under climate change.
Money spiders (Linyphiidae) are an important component of conservation biological control in cereal crops, but they rely on alternative prey when pests are not abundant, such as between cropping ...cycles. To optimally benefit from these generalist predators, prey choice dynamics must first be understood.
Money spiders and their locally available prey were collected from cereal crops 2 weeks pre‐ and post‐harvest. Spider gut DNA was amplified with two novel metabarcoding primer pairs designed for spider dietary analysis, and sequenced.
The combined general and spider‐exclusion primers successfully identified prey from 15 families in the guts of the 46 linyphiid spiders screened, whilst avoiding amplification of Erigone spp. The primers show promise for application to the diets of other spider families such as Agelenidae and Pholcidae.
Distinct invertebrate communities were identified pre‐ and post‐harvest, and changes in spider diet and, to a lesser extent, prey choice reflected this. Spiders were found to consume one another more than expected, indicating their propensity towards intraguild predation, but also consumed common pest families.
Changes in spider prey choice may redress prey community changes to maintain a consistent dietary intake. Consistent provision of alternative prey via permanent refugia should be considered to sustain effective conservation biocontrol.
Distinct invertebrate communities were identified pre‐ and post‐harvest, and changes in spider diet and prey preferences reflected this.
Spider prey choice may redress prey community changes to maintain a consistent dietary intake. Consistent provision of alternative prey via permanent refugia could sustain effective conservation biocontrol.
Spiders consumed one another more than expected, indicating their propensity towards intraguild predation, but they also consumed common agricultural pests.
samβada is a genome–environment association software, designed to search for signatures of local adaptation. However, pre‐ and postprocessing of data can be labour‐intensive, preventing wider uptake ...of the method. We have now developed R.SamBada, an r‐package providing a pipeline for landscape genomic analysis based on samβada, spanning from the retrieval of environmental conditions at sampling locations to gene annotation using the Ensembl genome browser. As a result, R.SamBada standardizes the landscape genomics pipeline and eases the search for candidate genes of local adaptation, enhancing reproducibility of landscape genomic studies. The efficiency and power of the pipeline is illustrated using two examples: sheep populations from Morocco with no evident population structure and Lidia cattle from Spain displaying population substructuring. In both cases, R.SamBada enabled rapid identification and interpretation of candidate genes, which are further discussed in the light of local adaptation. The package is available in the r CRAN package repository and on GitHub (github.com/SolangeD/R.SamBada).
The Punjab urial (Ovis vignei punjabiensis) is endemic to Northern Punjab, Pakistan, and is categorized as vulnerable by the International Union for Conservation of Nature Red List of Threatened ...Species. The urial population has declined by 30% over the last 3 generations. We used non‐invasive fecal samples to identify individuals and estimate population size of Punjab urial in the Kalabagh Game Reserve, Pakistan. We genotyped samples using 12 microsatellite markers to assess genetic variation, population structure, and demographic changes. Microsatellite analysis revealed high levels of genetic variation in urials in terms of expected and observed heterozygosity and allelic diversity. The population structure of the Punjab urial in the Kalabagh Game Reserve, based solely on microsatellite variation using Bayesian clustering, indicated 3 different clusters in the reserve. Results revealed that the urial population may be facing inbreeding pressure because its ancestral effective population size has declined from between 20,000 and 50,000 to ≤1,000 animals today. This reduction has partly occurred because of a bottleneck that occurred about 10,000 years ago. Results also indicate that 1 urial population cluster has the signature of a bottleneck, which may be due to population isolation. The 3 urial clusters are small and broadly dispersed in a large territory, meaning they could be extirpated without any opportunity for natural re‐population through dispersion. The results of our study support a management strategy that encourages maintaining connectivity between urial localities within the Kalabagh Game Reserve, increased diversity so the effective population size may recover from the historical decline, and the use of data generated here as a baseline of urial genetic diversity in the reserve for monitoring diversity over the long term.
The Punjab urial inhabiting the Kalabagh Game Reserve in Pakistan is presenting a population decline due to illegal hunting. This population experienced drastic bottlenecks during its history. Future viability of this population will strongly depend on it remaining open to the influx of reproducing animals from outside of the reserve so that genetic variation can be maintained.
Mixed signals from hybrid genomes Orozco‐terWengel, Pablo A; Bruford, Michael W
Molecular ecology,
August 2014, Letnik:
23, Številka:
16
Journal Article
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Admixture results from interbreeding between individuals from different populations or species that were previously genetically isolated from each other (Fig. ). Identifying admixture events in the ...genome is not always a straightforward task, because the genetic signature left behind fades with time as recombination events fragment the genomic segments introduced during the interbreeding event. Additionally, when the genetic architecture of populations or species that admix is not very different (e.g. they coalesce to a common ancestor recently), admixture signatures may be difficult to detect. Ignoring the effects of admixture can, however, pose severe problems for population genetic analyses that rely on the distribution of polymorphic markers across the genome. In this issue of Molecular Ecology, Bosse et al. () analyse genomic data from modern pigs to understand hybridization processes that occurred between domestic pigs from European and Asiatic origin, and between pigs and wild boars. Their results are interesting regarding the fine‐scale distribution of admixture across the pig genome, and the way in which this admixture biases estimates of the effective population size in European domestic pigs. The implications of these results are significant, as they serve as a cautionary note on genomic analyses that depend on the distribution of polymorphic variants in potentially admixed populations.
Species delimitation is one of the most contested areas in modern biology, with widespread disagreement about almost every aspect of the definition and implementation of the “species” label. While ...this debate is intellectually stimulating, it also has real implications for conservation, where its impacts on taxonomic inflation or inertia can mean that specific populations receive adequate conservation measures or are ignored. Recently, the rise of next generation sequencing and phylogenomics has revolutionised phylogenetic understanding of many organismal groups but has simultaneously highlighted the porosity of genomes in terms of admixture across previously delineated species barriers. The extraordinary power of genomic data is increasingly being used to delineate species, and several publications in this domain have recently attracted significant attention and criticism. Here we revisit the question of species delimitation, but from a genomic context. We ask how and whether the large amounts of data provided by genomic methods can resolve the longstanding discussion on the validity and application of phylogenetic and allied species concepts, and how some recent examples can inform this debate. We argue that conserving adaptive potential is a priority for conservation, and no single species concept currently does that adequately on its own. Genomic data holds the potential to add unprecedented detail, but frequently falls short of this potential.
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