The role of recombination on genome-wide patterns of local ancestry exemplified by supplemented Brook Charr populations

AbstractAssessing the immediate and long-term evolutionary consequences of human-mediated hybridization is of major concern for conservation biology. Several studies have documented how selection in interaction with recombination modulates introgression at a genome-wide scale, but few have considered the dynamics of this process within and between chromosomes. Here, we used an exploited freshwater fish, the Brook Charr (Salvelinus fontinalis) for which decades of stocking practices have resulted in admixture between wild populations and an introduced domestic strain to assess both the temporal dynamics and local chromosomal variation in domestic ancestry. We provide a detailed picture of the domestic ancestry patterns across the genome using about 33,000 mapped SNPs genotyped in 611 individuals from 24 supplemented populations. For each lake, we distinguished early and late-generation hybrids using admixture tracts information. To assess the selective outcomes following admixture we then evaluated the relationship between recombination and admixture proportions at three different scales: the whole genome, chromosomes and within 2Mb windows. This allowed us to detect the signature of varied evolutionary mechanisms, as reflected by the finding of genomic regions where the introgression of domestic haplotypes are favored or disfavored. Among these, the main factor modulating local ancestry was likely the presence of deleterious recessive mutations in the wild populations, which can be efficiently hidden to selection in the presence of long admixture tracts. Overall, our results emphasize the relevance of taking into consideration local ancestry information to assess both the temporal and chromosomal variation in local ancestry toward better understanding post-hybridization evolutionary outcomes.

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Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

10.1101/867754 ◽

2019 ◽

Cited By ~ 7

Author(s):

Zachary L. Fuller ◽

Veronique J.L. Mocellin ◽

Luke Morris ◽

Neal Cantin ◽

Jihanne Shepherd ◽

...

Keyword(s):

Genome Wide Association Study ◽

Balancing Selection ◽

Genome Wide Association ◽

Conservation Strategies ◽

Genome Sequences ◽

Acropora Millepora ◽

Genome Wide ◽

A Genome ◽

In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

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The role of recombination on genome‐wide patterns of local ancestry exemplified by supplemented brook charr populations

Molecular Ecology ◽

10.1111/mec.15256 ◽

2019 ◽

Vol 28 (21) ◽

pp. 4755-4769 ◽

Cited By ~ 6

Author(s):

Maeva Leitwein ◽

Hugo Cayuela ◽

Anne‐Laure Ferchaud ◽

Éric Normandeau ◽

Pierre‐Alexandre Gagnaire ◽

...

Keyword(s):

Brook Charr ◽

Local Ancestry ◽

Genome Wide

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Diversification in wild populations of the model organism Anolis carolinensis : A genome-wide phylogeographic investigation

Ecology and Evolution ◽

10.1002/ece3.2547 ◽

2016 ◽

Vol 6 (22) ◽

pp. 8115-8125 ◽

Cited By ~ 12

Author(s):

Joseph D. Manthey ◽

Marc Tollis ◽

Alan R. Lemmon ◽

Emily Moriarty Lemmon ◽

Stéphane Boissinot

Keyword(s):

Model Organism ◽

Anolis Carolinensis ◽

Wild Populations ◽

Genome Wide ◽

A Genome

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Population-specific adaptation in malaria-endemic regions of asia

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720021400060 ◽

2021 ◽

Author(s):

Elena S. Gusareva ◽

Paolo Alberto Lorenzini ◽

Nurul Adilah Binte Ramli ◽

Amit Gourav Ghosh ◽

Hie Lim Kim

Keyword(s):

System Development ◽

Asian Population ◽

Population Group ◽

Nervous System Development ◽

Evolutionary Mechanisms ◽

Population Groups ◽

Genome Wide ◽

A Genome ◽

Endemic Population ◽

Mechanisms Of Adaptation

Evolutionary mechanisms of adaptation to malaria are understudied in Asian endemic regions despite a high prevalence of malaria in the region. In our research, we performed a genome-wide screening for footprints of natural selection against malaria by comparing eight Asian population groups from malaria-endemic regions with two non-endemic population groups from Europe and Mongolia. We identified 285 adaptive genes showing robust selection signals across three statistical methods, iHS, XP-EHH, and PBS. Interestingly, most of the identified genes (82%) were found to be under selection in a single population group, while adaptive genes shared across populations were rare. This is likely due to the independent adaptation history in different endemic populations. The gene ontology (GO) analysis for the 285 adaptive genes highlighted their functional processes linked to neuronal organizations or nervous system development. These genes could be related to cerebral malaria and may reduce the inflammatory response and the severity of malaria symptoms. Remarkably, our novel population genomic approach identified population-specific adaptive genes potentially against malaria infection without the need for patient samples or individual medical records.

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A genome-wide scan study identifies a single nucleotide substitution in MC1R gene associated with white coat colour in fallow deer (Dama dama)

BMC Genetics ◽

10.1186/s12863-020-00950-3 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Gerald Reiner ◽

Tim Weber ◽

Florian Nietfeld ◽

Dominik Fischer ◽

Christine Wurmser ◽

...

Keyword(s):

Pigment Cell ◽

Coat Colour ◽

Fallow Deer ◽

Receptor Protein ◽

Gene Marker ◽

Genome Wide ◽

A Genome ◽

Gene Test ◽

In The Wild ◽

Genome Wide Scan

Abstract Background The coat colour of fallow deer is highly variable and even white animals can regularly be observed in game farming and in the wild. Affected animals do not show complete albinism but rather some residual pigmentation resembling a very pale beige dilution of coat colour. The eyes and claws of the animals are pigmented. To facilitate the conservation and management of such animals, it would be helpful to know the responsible gene and causative variant. We collected 102 samples from 22 white animals and from 80 animals with wildtype coat colour. The samples came from 12 different wild flocks or game conservations located in different regions of Germany, at the border to Luxembourg and in Poland. The genomes of one white hind and her brown calf were sequenced. Results Based on a list of colour genes of the International Federation of Pigment Cell Societies (http://www.ifpcs.org/albinism/), a variant in the MC1R gene (NM_174108.2:c.143 T > C) resulting in an amino acid exchange from leucine to proline at position 48 of the MC1R receptor protein (NP_776533.1:p.L48P) was identified as a likely cause of coat colour dilution. A gene test revealed that all animals of the white phenotype were of genotype CC whereas all pigmented animals were of genotype TT or TC. The study showed that 14% of the pigmented (brown or dark pigmented) animals carried the white allele. Conclusions A genome-wide scan study led to a molecular test to determine the coat colour of fallow deer. Identification of the MC1R gene provides a deeper insight into the mechanism of dilution. The gene marker is now available for the conservation of white fallow deer in wild and farmed animals.

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Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal

Nature Communications ◽

10.1038/s41467-021-23222-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

M. A. Stoffel ◽

S. E. Johnston ◽

J. G. Pilkington ◽

J. M. Pemberton

Keyword(s):

Inbreeding Depression ◽

Genetic Architecture ◽

Wild Populations ◽

Fitness Component ◽

Wild Mammal ◽

Life History Data ◽

Fitness Consequences ◽

Genome Wide ◽

A Genome

AbstractInbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87% and deserts where only 4% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10% increase in individual inbreeding FROH is associated with a 60% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.

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Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana

10.1101/2020.06.11.145953 ◽

2020 ◽

Author(s):

Rhonda C. Meyer ◽

Kathleen Weigelt-Fischer ◽

Dominic Knoch ◽

Marc Heuermann ◽

Yusheng Zhao ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Association Study ◽

Vegetative Growth ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Temporal Dynamics ◽

Expression Patterns ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

ABSTRACTWe assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from seven to 18 days after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGR). In addition, initial seed size was determined. The generated data sets were used jointly for a genome-wide association study that identified 238 marker-trait associations (MTAs) individually explaining up to 8 % of the total phenotypic variation. Co-localisation of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localisation of MTAs for two to nine consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasising that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.HighlightA genome-wide association study including the factor time highlighted that early plant growth in Arabidopsis is governed by several medium and many small effect loci, most of which act only during short phases of two to nine days.

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Differences in the temporal dynamics of phenotypic selection among fitness components in the wild

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.1973 ◽

2010 ◽

Vol 278 (1711) ◽

pp. 1572-1580 ◽

Cited By ~ 79

Author(s):

Adam M. Siepielski ◽

Joseph D. DiBattista ◽

Jeffrey A. Evans ◽

Stephanie M. Carlson

Keyword(s):

Adaptive Evolution ◽

Mating Success ◽

Temporal Dynamics ◽

Phenotypic Selection ◽

Wild Populations ◽

Fitness Components ◽

Average Strength ◽

Directional Evolution ◽

In The Wild

The balance of selection acting through different fitness components (e.g. fecundity, mating success, survival) determines the potential tempo and trajectory of adaptive evolution. Yet the extent to which the temporal dynamics of phenotypic selection may vary among fitness components is poorly understood. Here, we compiled a database of 3978 linear selection coefficients from temporally replicated studies of selection in wild populations to address this question. Across studies, we find that multi-year selection through mating success and fecundity is stronger than selection through survival, but varies less in direction. We also report that selection through mating success varies more in long-term average strength than selection through either survival or fecundity. The consistency in direction and stronger long-term average strength of selection through mating success and fecundity suggests that selection through these fitness components should cause more persistent directional evolution relative to selection through survival. Similar patterns were apparent for the subset of studies that evaluated the temporal dynamics of selection on traits simultaneously using several different fitness components, but few such studies exist. Taken together, these results reveal key differences in the temporal dynamics of selection acting through different fitness components, but they also reveal important limitations in our understanding of how selection drives adaptive evolution.

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Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance

Physiological Genomics ◽

10.1152/physiolgenomics.00232.2010 ◽

2011 ◽

Vol 43 (14) ◽

pp. 855-872 ◽

Cited By ~ 6

Author(s):

Ajit N. Shah ◽

Daniela Cadinu ◽

R. Michael Henke ◽

Xiantong Xin ◽

Ranita Ghosh Dastidar ◽

...

Keyword(s):

Ribosome Biogenesis ◽

Molecular Mechanisms ◽

Specific Protein ◽

Hypoxia Tolerance ◽

Deletion Mutants ◽

Yeast Saccharomyces Cerevisiae ◽

Genome Wide ◽

A Genome ◽

In The Wild ◽

Induced Changes

Hypoxia is a widely occurring condition experienced by diverse organisms under numerous physiological and disease conditions. To probe the molecular mechanisms underlying hypoxia responses and tolerance, we performed a genome-wide screen to identify mutants with enhanced hypoxia tolerance in the model eukaryote, the yeast Saccharomyces cerevisiae . Yeast provides an excellent model for genomic and proteomic studies of hypoxia. We identified five genes whose deletion significantly enhanced hypoxia tolerance. They are RAI1, NSR1, BUD21, RPL20A, and RSM22, all of which encode functions involved in ribosome biogenesis. Further analysis of the deletion mutants showed that they minimized hypoxia-induced changes in polyribosome profiles and protein synthesis. Strikingly, proteomic analysis by using the iTRAQ profiling technology showed that a substantially fewer number of proteins were changed in response to hypoxia in the deletion mutants, compared with the parent strain. Computational analysis of the iTRAQ data indicated that the activities of a group of regulators were regulated by hypoxia in the wild-type parent cells, but such regulation appeared to be diminished in the deletion strains. These results show that the deletion of one of the genes involved in ribosome biogenesis leads to the reversal of hypoxia-induced changes in gene expression and related regulators. They suggest that modifying ribosomal function is an effective mechanism to minimize hypoxia-induced specific protein changes and to confer hypoxia tolerance. These results may have broad implications in understanding hypoxia responses and tolerance in diverse eukaryotes ranging from yeast to humans.

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Population-genomic inference of the strength and timing of selection against gene flow

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1616755114 ◽

2017 ◽

Vol 114 (27) ◽

pp. 7061-7066 ◽

Cited By ~ 56

Author(s):

Simon Aeschbacher ◽

Jessica P. Selby ◽

John H. Willis ◽

Graham Coop

Keyword(s):

Gene Flow ◽

Recombination Rate ◽

Divergent Selection ◽

Adaptive Divergence ◽

Serpentine Soils ◽

Evolutionary Mechanisms ◽

Local Conditions ◽

Local Environments ◽

Genome Wide ◽

A Genome

The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations. Our theory shows that the selection density (i.e., the selection coefficient per base pair) is a key parameter underlying this relationship. We then develop a procedure for parameter estimation that accounts for the confounding effect of background selection. Applying this method to two datasets from Mimulus guttatus, we infer a strong signal of adaptive divergence in the face of gene flow between populations growing on and off phytotoxic serpentine soils. However, the genome-wide intensity of this selection is not exceptional compared with what M. guttatus populations may typically experience when adapting to local conditions. We also find that selection against genome-wide introgression from the selfing sister species M. nasutus has acted to maintain a barrier between these two species over at least the last 250 ky. Our study provides a theoretical framework for linking genome-wide patterns of divergence and recombination with the underlying evolutionary mechanisms that drive this differentiation.

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