Population genomics of rapid evolution in natural populations: polygenic selection in response to power station thermal effluents

Abstract Background: Valeriana officinalis L. is one of the most important medicinal plant with a mild sedative, nervine, antispasmodic and relaxant effect. Despite a substantial number of studies on this species, population genomics has not yet been analyzed. The main aim of this study was: characterization of genetic variation of natural populations of V. officinalis in Poland and comparison of variation of wild populations and the cultivated form using Next Generation Sequencing based DArTseq technique. We also would like to establish foundations for genetic monitoring of the species in the future and to develop genetic fingerprint profile for samples deposited in gene bank and in natural sites in order to assess the degree of their genetic integrity and population structure preservation in the future.Results: The major and also the most astounding result of our work is the low level of observed heterozygosity of individual plants from natural populations despite the fact that the species is widespread in the studied area. Inbreeding, in naturally outcrossing species such as valerian, decreases the reproductive success. The analysis of the population structure indicated the potential presence of metapopulation in a broad area of Poland and the formation of a distinct gene pool in Bieszczady Mountains. The results also indicate the presence of individuals of the cultivated form in natural populations in the region where the species is cultivated for the needs of the pharmaceutical industry and this could lead to structural and genetic imbalance in wild populations.Conclusions: The DArTseq technology can be applied effectively in genetic studies of V. officinalis. The genetic variability of wild populations is in fact significantly lower than assumed. Individuals from the cultivated population are found in the natural environment and their impact on wild populations should be monitored.

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Complex Traits in Natural Populations

A Primer of Population Genetics and Genomics ◽

10.1093/oso/9780198862291.003.0009 ◽

2020 ◽

pp. 263-290

Author(s):

Daniel L. Hartl

Keyword(s):

Complex Traits ◽

Population Genomics ◽

Association Studies ◽

Natural Populations ◽

Complex Diseases ◽

Stabilizing Selection ◽

Phenotypic Evolution ◽

Genetic Changes ◽

Number Of Genes ◽

Almost All

This chapter could as well be titled “Population Genomics,” although many aspects of population genomics are integrated throughout the other chapters. It includes estimates of mutational variance and standing variance, phenotypic evolution under directional selection as measured by the linear selection gradient, and phenotypic evolution under stabilizing selection. It explores the strengths and limitations of genome-wide association studies of quantitative trait loci (QTLs) and expression (eQTLs) to detect genetic influencing complex traits in natural populations and genetic risk factors for complex diseases such as heart disease or diabetes. The number of genes affecting complex traits is considered, as well as evidence bearing on the issue of whether complex diseases are primarily affected by a very large number of genes, almost all of small effect, and how this bears on direct-to-consumer and over-the-counter genetic testing. The population genomics of adaptation is considered, including drug resistance, domestication, and local selection versus gene flow. The chapter concludes with the population genomics of speciation as illustrated by reinforcement of mating barriers, the reproducibility of phenotypic and genetic changes, and the accumulation of genetic incompatibilities.

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Locating the Sex Determining Region of Linkage Group 12 of Guppy (Poecilia reticulata)

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401573 ◽

2020 ◽

Vol 10 (10) ◽

pp. 3639-3649

Author(s):

Deborah Charlesworth ◽

Roberta Bergero ◽

Chay Graham ◽

Jim Gardner ◽

Lengxob Yong

Keyword(s):

Poecilia Reticulata ◽

Population Genomics ◽

False Positive Rate ◽

Natural Populations ◽

Proximal Region ◽

High Rate ◽

Chromosome 12 ◽

Small Samples ◽

Autosomal Region ◽

Y Chromosomes

Despite over 100 years of study, the location of the fully sex-linked region of the guppy (Poecilia reticulata) carrying the male-determining locus, and the regions where the XY pair recombine, remain unclear. Previous population genomics studies to determine these regions used small samples from recently bottlenecked captive populations, which increase the false positive rate of associations between individuals’ sexes and SNPs. Using new data from multiple natural populations, we show that a recently proposed candidate for this species’ male-determining gene is probably not completely sex-linked, leaving the maleness factor still unidentified. Variants in the chromosome 12 region carrying the candidate gene sometimes show linkage disequilibrium with the sex-determining factor, but no consistently male-specific variant has yet been found. Our genetic mapping with molecular markers spread across chromosome 12 confirms that this is the guppy XY pair. We describe two families with recombinants between the X and Y chromosomes, which confirm that the male-determining locus is in the region identified by all previous studies, near the terminal pseudo-autosomal region (PAR), which crosses over at a very high rate in males. We correct the PAR marker order, and assign two unplaced scaffolds to the PAR. We also detect a duplication, with one copy in the male-determining region, explaining signals of sex linkage in a more proximal region.

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PRDM9 Diversity at Fine Geographical Scale Reveals Contrasting Evolutionary Patterns and Functional Constraints in Natural Populations of House Mice

Molecular Biology and Evolution ◽

10.1093/molbev/msz091 ◽

2019 ◽

Vol 36 (8) ◽

pp. 1686-1700 ◽

Cited By ~ 4

Author(s):

Covadonga Vara ◽

Laia Capilla ◽

Luca Ferretti ◽

Alice Ledda ◽

Rosa A Sánchez-Guillén ◽

...

Keyword(s):

Reproductive Isolation ◽

Evolutionary Biology ◽

Evolutionary Dynamics ◽

Rapid Evolution ◽

Natural Populations ◽

Global Scale ◽

House Mice ◽

Functional Constraints ◽

Evolutionary Patterns ◽

Data Set

Abstract One of the major challenges in evolutionary biology is the identification of the genetic basis of postzygotic reproductive isolation. Given its pivotal role in this process, here we explore the drivers that may account for the evolutionary dynamics of the PRDM9 gene between continental and island systems of chromosomal variation in house mice. Using a data set of nearly 400 wild-caught mice of Robertsonian systems, we identify the extent of PRDM9 diversity in natural house mouse populations, determine the phylogeography of PRDM9 at a local and global scale based on a new measure of pairwise genetic divergence, and analyze selective constraints. We find 57 newly described PRDM9 variants, this diversity being especially high on Madeira Island, a result that is contrary to the expectations of reduced variation for island populations. Our analysis suggest that the PRDM9 allelic variability observed in Madeira mice might be influenced by the presence of distinct chromosomal fusions resulting from a complex pattern of introgression or multiple colonization events onto the island. Importantly, we detect a significant reduction in the proportion of PRDM9 heterozygotes in Robertsonian mice, which showed a high degree of similarity in the amino acids responsible for protein–DNA binding. Our results suggest that despite the rapid evolution of PRDM9 and the variability detected in natural populations, functional constraints could facilitate the accumulation of allelic combinations that maintain recombination hotspot symmetry. We anticipate that our study will provide the basis for examining the role of different PRDM9 genetic backgrounds in reproductive isolation in natural populations.

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Rapid evolution in insect pests: the importance of space and time in population genomics studies

Current Opinion in Insect Science ◽

10.1016/j.cois.2017.12.008 ◽

2018 ◽

Vol 26 ◽

pp. 8-16 ◽

Cited By ~ 21

Author(s):

Benjamin Pélissié ◽

Michael S Crossley ◽

Zachary Paul Cohen ◽

Sean D Schoville

Keyword(s):

Population Genomics ◽

Insect Pests ◽

Rapid Evolution ◽

Space And Time

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Rapid evolution of cold tolerance in stickleback

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.0923 ◽

2010 ◽

Vol 278 (1703) ◽

pp. 233-238 ◽

Cited By ~ 101

Author(s):

Rowan D. H. Barrett ◽

Antoine Paccard ◽

Timothy M. Healy ◽

Sara Bergek ◽

Patricia M. Schulte ◽

...

Keyword(s):

Cold Tolerance ◽

Gasterosteus Aculeatus ◽

Field Experiments ◽

Rapid Evolution ◽

Natural Populations ◽

Temperature Tolerance ◽

Ancestral Population ◽

Biological Communities ◽

Evolutionary Consequences ◽

Short Time

Climate change is predicted to lead to increased average temperatures and greater intensity and frequency of high and low temperature extremes, but the evolutionary consequences for biological communities are not well understood. Studies of adaptive evolution of temperature tolerance have typically involved correlative analyses of natural populations or artificial selection experiments in the laboratory. Field experiments are required to provide estimates of the timing and strength of natural selection, enhance understanding of the genetics of adaptation and yield insights into the mechanisms driving evolutionary change. Here, we report the experimental evolution of cold tolerance in natural populations of threespine stickleback fish ( Gasterosteus aculeatus ). We show that freshwater sticklebacks are able to tolerate lower minimum temperatures than marine sticklebacks and that this difference is heritable. We transplanted marine sticklebacks to freshwater ponds and measured the rate of evolution after three generations in this environment. Cold tolerance evolved at a rate of 0.63 haldanes to a value 2.5°C lower than that of the ancestral population, matching values found in wild freshwater populations. Our results suggest that cold tolerance is under strong selection and that marine sticklebacks carry sufficient genetic variation to adapt to changes in temperature over remarkably short time scales.

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Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource

Molecular Biology and Evolution ◽

10.1093/molbev/msab259 ◽

2021 ◽

Author(s):

Martin Kapun ◽

Joaquin C B Nunez ◽

María Bogaerts-Márquez ◽

Jesús Murga-Moreno ◽

Margot Paris ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Population Genomics ◽

Natural Populations ◽

Easy Access ◽

Data Repository ◽

Bioinformatics Pipeline ◽

Space And Time ◽

Sequencing Technologies ◽

Spatio Temporal ◽

Demographic Inference

Abstract Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

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