scholarly journals Cold adaptation drives population genomic divergence in the ecological specialist, Drosophila montana

2020 ◽  
Author(s):  
R. A. W. Wiberg ◽  
V. Tyukmaeva ◽  
A. Hoikkala ◽  
M. G. Ritchie ◽  
M. Kankare
Keyword(s):  
Cold Tolerance ◽  
Cold Adaptation ◽  
Ecological Adaptation ◽  
Climatic Variables ◽  
Population Divergence ◽  
Candidate Snps ◽  
Clinal Variation ◽  
Ecological Selection ◽  
Genomic Divergence ◽  
Drosophila Montana

ABSTRACTDetecting signatures of ecological adaptation in comparative genomics is challenging, but analysing population samples with characterised geographic distributions, such as clinal variation, can help identify genes showing covariation with important ecological variation. Here we analysed patterns of geographic variation in the cold-adapted species Drosophila montana across phenotypes, genotypes and environmental conditions and searched for signatures of cold adaptation in populations’ genomic divergence. We first derived the climatic variables associated with the geographic distribution of 24 populations across two continents to trace the whole scale of environmental variation experienced by the species, and measure variation in the cold tolerance of the flies of six populations from different geographic contexts. We then performed pooled whole genome sequencing of these six populations, and used Bayesian methods to identify SNPs where genetic differentiation is associated with both climatic variables and the population phenotypic measurements. The top candidate SNPs were enriched on the X and 4th chromosomes, and they also lie near genes implicated in other studies of cold tolerance and population divergence in this species and its close relatives. We conclude that ecological adaptation has contributed to the divergence of D. montana populations throughout the genome and in particular on the X and 4th chromosomes, which also showed highest interpopulation Fst. This study demonstrates that ecological selection can drive genomic divergence at different scales, from candidate genes to chromosome-wide effects.

scholarly journals Cold adaptation drives population genomic divergence in the ecological specialist , Drosophila montana

2021 ◽  
Author(s):  
R. A. W. Wiberg ◽  
V. Tyukmaeva ◽  
A. Hoikkala ◽  
M. G. Ritchie ◽  
M. Kankare
Keyword(s):  
Cold Adaptation ◽  
Population Genomic ◽  
Genomic Divergence ◽  
Drosophila Montana

scholarly journals Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation

2018 ◽  
Vol 10 (8) ◽  
pp. 2086-2101 ◽  
Author(s):  
Darren J Parker ◽  
R Axel W Wiberg ◽  
Urmi Trivedi ◽  
Venera I Tyukmaeva ◽  
Karim Gharbi ◽  
...  
Keyword(s):  
Cold Adaptation ◽  
Genomic Divergence ◽  
Drosophila Montana

scholarly journals Inter- and intra-specific genomic divergence in Drosophila montana shows evidence for cold adaptation

2018 ◽  
Author(s):  
D. J. Parker ◽  
R. A. W. Wiberg ◽  
U. Trivedi ◽  
V. I. Tyukmaeva ◽  
K. Gharbi ◽  
...  
Keyword(s):  
Cold Adaptation ◽  
Sequence Variation ◽  
Synonymous Substitution ◽  
Drosophila Species ◽  
Cold Adapted ◽  
Outlier Loci ◽  
Genomic Divergence ◽  
Genomic Adaptation ◽  
Drosophila Montana ◽  
Selective Process

AbstractThe genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to their ecological specialism from other sources of selection and more random changes is a challenge. Here we describe the genome of Drosophila montana, the most extremely cold-adapted Drosophila species. We describe the genome, which is similar in size and gene content to most Drosophila species. We look for evidence of accelerated divergence from a previously sequenced relative, and do not find strong evidence for divergent selection on coding sequence variation. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. We also re-sequenced three populations of D. montana representing its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales.

Ecological adaptation drives wood frog population divergence in life history traits

Heredity ◽  
2021 ◽  
Author(s):  
Emily H. Le Sage ◽  
Sarah I. Duncan ◽  
Travis Seaborn ◽  
Jennifer Cundiff ◽  
Leslie J. Rissler ◽  
...  
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Ecological Adaptation ◽  
Wood Frog ◽  
Population Divergence

Patterns of Genomic Divergence and Signals of Selection in Sympatric and Allopatric Northeastern Pacific and Sea of Cortez Populations of the Sargo (Anisotremus davidsonii) and Longjaw Mudsucker (Gillichthys mirabilis)

2020 ◽  
Vol 111 (1) ◽  
pp. 57-69 ◽  
Author(s):  
Eric Garcia ◽  
W Brian Simison ◽  
Giacomo Bernardi
Keyword(s):  
Baja California ◽  
Baja California Peninsula ◽  
Population Divergence ◽  
Population Isolation ◽  
Gillichthys Mirabilis ◽  
Coding Regions ◽  
Point Conception ◽  
Outlier Loci ◽  
Genomic Divergence ◽  
Sea Of Cortez

Abstract Studying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, United States, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands of loci are genotyped from 48 Sargos and 73 mudsuckers using RADseq to characterize overall genomic divergence, and search for common patterns of putatively neutral and non-neutral structure based on outlier loci among populations with hypothesized different levels of isolation. We further search for parallels between population divergence and the total proportion of outliers, outlier FST distribution, and the proportion of outliers matching coding regions in GenBank. Statistically significant differentiation is seen across Point Conception in mudsucker (FST = 0.15), Punta Eugenia in Sargo (FST = 0.02), and on either side of the Baja California peninsula in both species (FST = 0.11 and 0.23, in Sargo and mudsucker, respectively). Each species shows structure using neutral and non-neutral loci. Finally, higher population divergence yields a more even distribution of outliers along their differentiation range but does not always translate into higher outlier proportions or higher rates in which outliers are matched to coding regions. If repeated in similar systems, observed genomic patterns might reveal speciation signatures in diverse networks of population isolation.

scholarly journals ECOLOGICAL ADAPTATION AND ECOLOGICAL SELECTION

Science ◽  
1906 ◽  
Vol 23 (582) ◽  
pp. 307-310 ◽  
Author(s):  
C. ROBERTSON
Keyword(s):  
Ecological Adaptation ◽  
Ecological Selection

scholarly journals Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex

2017 ◽  
Vol 115 (2) ◽  
pp. E236-E243 ◽  
Author(s):  
Tao Ma ◽  
Kun Wang ◽  
Quanjun Hu ◽  
Zhenxiang Xi ◽  
Dongshi Wan ◽  
...  
Keyword(s):  
Gene Flow ◽  
Species Complex ◽  
Populus Euphratica ◽  
Genomic Islands ◽  
Ecological Selection ◽  
Poplar Trees ◽  
Genomic Divergence ◽  
Genome Divergence ◽  
Genomic Regions ◽  
Time Of Divergence

How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.

scholarly journals Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jared A. Grummer ◽  
Michael C. Whitlock ◽  
Patricia M. Schulte ◽  
Eric B. Taylor
Keyword(s):  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Large Body ◽  
Population Divergence ◽  
Phenotypic Traits ◽  
Evolutionary Divergence ◽  
Metabolic Rates ◽  
Genomic Divergence ◽  
Kootenay Lake ◽  
Genomic Regions

Abstract Background Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout (Oncorhynchus mykiss)—insectivores and piscivores—that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. “Gerrards” are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fish per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence. Results Genomic divergence was high between sympatric insectivores and piscivores ($$F_{\text{ST}}$$ F ST = 0.188), and in fact higher than between insectivorous populations from Kootenay Lake and the Blackwater River ($$F_{\text{ST}}$$ F ST = 0.159) that are > 500 km apart. A window-based $$F_{\text{ST}}$$ F ST analysis did not reveal “islands” of genomic differentiation; however, the window with highest $$F_{\text{ST}}$$ F ST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small effect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs. Conclusion Our results reveal a high degree of genomic differentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect. Rather, the piscivore phenotype may be controlled by several loci of small effect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences.

scholarly journals Unique genomic traits for cold adaptation in Naganishia vishniacii, a polyextremophile yeast isolated from Antarctica

2020 ◽  
Author(s):  
Paula Nizovoy ◽  
Nicolás Bellora ◽  
Sajeet Haridas ◽  
Hui Sun ◽  
Chris Daum ◽  
...  
Keyword(s):  
Cold Tolerance ◽  
Cold Adaptation ◽  
Genetic Basis ◽  
Genomic Sequence ◽  
Yeast Species ◽  
Solar Irradiation ◽  
Dry Valleys ◽  
Genomic Features ◽  
Cold Environments ◽  
Trehalose Synthesis

Abstract Cold environments impose challenges to organisms. Polyextremophile microorganisms can survive in these conditions thanks to an array of counteracting mechanisms. Naganishia vishniacii, a yeast species hitherto only isolated from McMurdo Dry Valleys, Antarctica, is an example of a polyextremophile. Here we present the first draft genomic sequence of N. vishniacii. Using comparative genomics, we unraveled unique characteristics of cold associated adaptations. From a total of 6183 predicted coding sequences, we identified 336 genes absent in sister species, encoding solute transfers and chaperones, among others. Among genes shared by N. vishniacii and its closest related species we found orthologs encompassing possible evidence of positive selection (dN/dS > 1). Genes associated with photoprotection were found in agreement with high solar irradiation exposure. Also genes coding for desaturases and genomic features associated with cold tolerance (i.e. trehalose synthesis and lipid metabolism) were explored. Finally, biases in amino acid usage (namely enrichment of glutamine and a trend reduction of proline) were observed, possibly conferring increased protein flexibility. To the best of our knowledge, such a combination of mechanisms for cold tolerance has not been previously reported in fungi, making N. vishniacii a unique model for the study of the genetic basis and evolution of cold adaptation strategies.

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