Genome-Wide Screens for Molecular Convergent Evolution in Mammals

2017 ◽  
pp. 297-312
Author(s):  
Jun-Hoe Lee ◽  
Michael Hiller
Keyword(s):  
Convergent Evolution ◽  
Genome Wide

scholarly journals Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria

Archaea ◽  
2008 ◽  
Vol 2 (3) ◽  
pp. 159-167 ◽  
Author(s):  
Betsey Dexter Dyer ◽  
Michael J. Kahn ◽  
Mark D. LeBlanc
Keyword(s):  
Environmental Conditions ◽  
Convergent Evolution ◽  
Regression Tree ◽  
Classification And Regression Tree ◽  
Evolutionary Divergence ◽  
Cart Analysis ◽  
Genomic Signatures ◽  
Genome Wide ◽  
Classification And Regression ◽  
Temperature Optima

Classification and regression tree (CART) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. Although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. Temperature optima for most of the organisms examined could be distinguished by CART analyses of tetranucleotide frequencies. This suggests that pervasive (nonlinear) qualities of genomes may reflect certain environmental conditions (such as temperature) in which those genomes evolved. The predominant use of GAGA and AGGA as the discriminating tetramers in CART models suggests that purine-loading and codon biases of thermophiles may explain some of the results.

scholarly journals Genome-wide signatures of convergent evolution in echolocating mammals

Nature ◽  
2013 ◽  
Vol 502 (7470) ◽  
pp. 228-231 ◽  
Author(s):  
Joe Parker ◽  
Georgia Tsagkogeorga ◽  
James A. Cotton ◽  
Yuan Liu ◽  
Paolo Provero ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Genome Wide

scholarly journals Evolution of color phenotypes in two distantly related species of stick insect: different ecological regimes acting on similar genetic architectures

2015 ◽  
Author(s):  
Aaron Comeault ◽  
Clarissa Ferreira ◽  
Stuart Dennis ◽  
Victor Soria-Carrasco ◽  
Patrik Nosil
Keyword(s):  
Related Species ◽  
Convergent Evolution ◽  
Genetic Architecture ◽  
Stick Insect ◽  
Genomic Region ◽  
Genome Wide Association ◽  
Multiple Sources ◽  
Adaptive Landscapes ◽  
Dominance Relationships ◽  
Genome Wide

Recurrent (e.g. parallel or convergent) evolution is widely cited as evidence for natural selection’s central role in evolution but can also highlight constraints affecting evolution. Here we describe the evolution of green and melanistic color phenotypes in two species of stick insect: Timema podura and T. cristinae. We show that similar color phenotypes of these species (1) cluster in phenotypic space and (2) confer crypsis on different plant microhabitats. We then use genome-wide association mapping to determine the genetic architecture of color in T. podura, and compare this to previous results in T. cristinae. In both species, color is under simple genetic control, dominance relationships of melanistic and green alleles are the same, and SNPs associated with color phenotypes colocalize to the same genomic region. These results differ from those of ‘typical’ parallel phenotypes because the form of selection acting on color differs between species: a balance of multiple sources of selection acting within host species maintains the color polymorphism in T. cristinae whereas T. podura color phenotypes are under divergent selection between hosts. Our results highlight how different adaptive landscapes can result in the evolution of similar phenotypic variation, and suggest the same genomic region is involved.

scholarly journals Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments

2020 ◽  
Vol 117 (28) ◽  
pp. 16424-16430 ◽  
Author(s):  
Ryan Greenway ◽  
Nick Barts ◽  
Chathurika Henpita ◽  
Anthony P. Brown ◽  
Lenin Arias Rodriguez ◽  
...  
Keyword(s):  
Mitochondrial Function ◽  
Convergent Evolution ◽  
De Novo ◽  
Extreme Environments ◽  
De Novo Mutations ◽  
Poecilia Mexicana ◽  
Genome Wide ◽  
Different Populations ◽  
Mechanistic Basis ◽  
Harsh Conditions

Extreme environments test the limits of life; yet, some organisms thrive in harsh conditions. Extremophile lineages inspire questions about how organisms can tolerate physiochemical stressors and whether the repeated colonization of extreme environments is facilitated by predictable and repeatable evolutionary innovations. We identified the mechanistic basis underlying convergent evolution of tolerance to hydrogen sulfide (H2S)—a toxicant that impairs mitochondrial function—across evolutionarily independent lineages of a fish (Poecilia mexicana, Poeciliidae) from H2S-rich springs. Using comparative biochemical and physiological analyses, we found that mitochondrial function is maintained in the presence of H2S in sulfide springP. mexicanabut not ancestral lineages from nonsulfidic habitats due to convergent adaptations in the primary toxicity target and a major detoxification enzyme. Genome-wide local ancestry analyses indicated that convergent evolution of increased H2S tolerance in different populations is likely caused by a combination of selection on standing genetic variation and de novo mutations. On a macroevolutionary scale, H2S tolerance in 10 independent lineages of sulfide spring fishes across multiple genera of Poeciliidae is correlated with the convergent modification and expression changes in genes associated with H2S toxicity and detoxification. Our results demonstrate that the modification of highly conserved physiological pathways associated with essential mitochondrial processes mediates tolerance to physiochemical stress. In addition, the same pathways, genes, and—in some instances—codons are implicated in H2S adaptation in lineages that span 40 million years of evolution.

scholarly journals Convergent Evolution of Conserved Mitochondrial Pathways Underlies Repeated Adaptation to Extreme Environments

2020 ◽  
Author(s):  
Ryan Greenway ◽  
Nick Barts ◽  
Chathurika Henpita ◽  
Anthony P. Brown ◽  
Lenin Arias Rodriguez ◽  
...  
Keyword(s):  
Hydrogen Sulfide ◽  
Mitochondrial Function ◽  
Convergent Evolution ◽  
De Novo ◽  
Extreme Environments ◽  
Poecilia Mexicana ◽  
Genome Wide ◽  
Specific Variation ◽  
Different Populations ◽  
Mechanistic Basis

Extreme environments test the limits of life; yet, some organisms thrive in harsh conditions. Extremophile lineages inspire questions about how organisms can tolerate physiochemical stressors and whether the repeated colonization of extreme environments is facilitated by predictable and repeatable evolutionary innovations. We identified the mechanistic basis underlying convergent evolution of tolerance to hydrogen sulfide (H2S)—a toxicant that impairs mitochondrial function—across evolutionarily independent lineages of a fish (Poecilia mexicana, Poeciliidae) from H2S-rich springs. Using comparative biochemical and physiological analyses, we found that mitochondrial function is maintained in the presence of H2S in sulfide spring P. mexicana, but not ancestral lineages from nonsulfidic habitats, due to convergent adaptations in the primary toxicity target and a major detoxification enzyme. Genome-wide local ancestry analyses indicated that convergent evolution of increased H2S tolerance in different populations is likely caused by a combination of selection on standing genetic variation and de novo mutations. At a macroevolutionary scale, H2S tolerance in 10 independent lineages of sulfide spring fishes across multiple genera of Poeciliidae is correlated with the convergent modification and expression changes of genes associated with H2S toxicity and detoxification. Our results demonstrate that the modification of highly conserved physiological pathways associated with essential mitochondrial processes mediates tolerance to physiochemical stress. In addition, the same pathways, genes, and—in some instances—codons are implicated in H2S adaptation in lineages that span 40 million years of evolution.Significance StatementSome organisms can tolerate environments lethal for most others, but we often do not know what adaptations allow them to persist and whether the same mechanisms underly adaptation in different lineages exposed to the same stressors. Investigating fish inhabiting springs rich in toxic hydrogen sulfide (H2S), we show that tolerance is mediated by the modification of pathways that are inhibited by H2S and those that can detoxify it. Sulfide spring fishes across multiple genera have evolved similar modifications of toxicity targets and detoxification pathways, despite abundant lineage-specific variation. Our study highlights how constraints associated with the physiological consequences of a stressor limit the number of adaptive solutions and lead to repeatable evolutionary outcomes across organizational and evolutionary scales.

scholarly journals Ecological factors and morphological traits are associated with repeated genomic differentiation between lake and stream stickleback

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180241 ◽  
Author(s):  
Diana J. Rennison ◽  
Yoel E. Stuart ◽  
Daniel I. Bolnick ◽  
Catherine L. Peichel
Keyword(s):  
Convergent Evolution ◽  
Morphological Traits ◽  
Gasterosteus Aculeatus ◽  
Abiotic Factors ◽  
Ecological Factors ◽  
Morphological Data ◽  
Genome Wide ◽  
A Genome ◽  
Repeated Evolution ◽  
Wide Scale

The repeated evolution of similar phenotypes in independent populations (i.e. parallel or convergent evolution) provides an opportunity to identify genetic and ecological factors that influence the process of adaptation. Threespine stickleback fish ( Gasterosteus aculeatus ) are an excellent model for such studies, as they have repeatedly adapted to divergent habitats across the Northern hemisphere. Here, we use genomic, ecological and morphological data from 16 independent pairs of stickleback populations adapted to divergent lake and stream habitats. We combine a population genomic approach to identify regions of the genome that are likely under selection in these divergent habitats with an association mapping approach to identify regions of the genome that underlie variation in ecological factors and morphological traits. Over 37% of genomic windows are repeatedly differentiated across lake–stream pairs. Similarly, many genomic windows are associated with variation in abiotic factors, diet items and morphological phenotypes. Both the highly differentiated windows and candidate trait windows are non-randomly distributed across the genome and show some overlap. However, the overlap is not significant on a genome-wide scale. Together, our data suggest that adaptation to divergent food resources and predation regimes are drivers of differentiation in lake–stream stickleback, but that additional ecological factors are also important. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

scholarly journals Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Poecilia reticulata)

2021 ◽  
Author(s):  
Mijke J van der Zee ◽  
James R Whiting ◽  
Josephine R Paris ◽  
Ron D Bassar ◽  
Joseph Travis ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Convergent Evolution ◽  
Poecilia Reticulata ◽  
Chromosome 15 ◽  
Frequency Change ◽  
Source Population ◽  
Multivariate Approach ◽  
Rapid Adaptation ◽  
Genome Wide ◽  
Experimental Populations

It is now accepted that phenotypic evolution can occur quickly but the genetic basis of rapid adaptation to natural environments is largely unknown in multicellular organisms. Population genomic studies of experimental populations of Trinidadian guppies (Poecilia reticulata) provide a unique opportunity to study this phenomenon. Guppy populations that were transplanted from high-predation (HP) to low-predation (LP) environments have been shown to mimic naturally-colonised LP populations phenotypically in as few as 8 generations. The new phenotypes persist in subsequent generations in lab environments, indicating their high heritability. Here, we compared whole genome variation in four populations recently introduced into LP sites along with the corresponding HP source population. We examined genome-wide patterns of genetic variation to estimate past demography, and uncovered signatures of selection with a combination of genome scans and a novel multivariate approach based on allele frequency change vectors. We were able to identify a limited number of candidate loci for convergent evolution across the genome. In particular, we found a region on chromosome 15 under strong selection in three of the four populations, with our multivariate approach revealing subtle parallel changes in allele frequency in all four populations across this region. Investigating patterns of genome-wide selection in this uniquely replicated experiment offers remarkable insight into the mechanisms underlying rapid adaptation, providing a basis for comparison with other species and populations experiencing rapidly changing environments.

scholarly journals Independent molecular basis of convergent highland adaptation in maize

2015 ◽  
Author(s):  
Shohei Takuno ◽  
Peter Ralph ◽  
Kelly Swarts ◽  
Rob J Elshire ◽  
Jeffrey C Glaubitz ◽  
...  
Keyword(s):  
South America ◽  
Molecular Basis ◽  
Convergent Evolution ◽  
Rapid Expansion ◽  
Limited Evidence ◽  
Nucleotide Level ◽  
Demographic Models ◽  
Archaeological Data ◽  
Snp Data ◽  
Genome Wide

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation.} We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection, and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation, and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.

scholarly journals Genome-wide, genic, and site-specific changes associated with the convergent evolution of sociality in spiders

2021 ◽  
Author(s):  
Chao Tong ◽  
Leticia Avilés ◽  
Linda S. Rayor ◽  
Alexander S. Mikheyev ◽  
Timothy A. Linksvayer
Keyword(s):  
Molecular Evolution ◽  
Social Behavior ◽  
Social Life ◽  
Convergent Evolution ◽  
Sequence Evolution ◽  
Site Specific ◽  
Spider Species ◽  
Social Species ◽  
Genome Wide ◽  
Evolution Of Sociality

AbstractSociality is a striking phenotypic innovation that independently evolved dozens of times across animals. Sociogenomic approaches have begun to elucidate the molecular underpinnings of social life in social insects and vertebrates, but the degree to which the convergent evolution of sociality involves convergent molecular evolution remains controversial and largely unknown. Spiders are a powerful system for identifying the genomic causes and consequences of social life because sociality is estimated to have independently evolved 15 times, and each origin likely occurred recently, within the past few million years. To determine if there are statistically supported genomic signatures of protein-coding sequence evolution associated with the convergent evolution of sociality in spiders, we compared the genomes or transcriptomes of 24 spider species that vary in social organization and represent at least seven independent origins of sociality. We identified hundreds of genes that experienced shifts in patterns of molecular evolution during the convergent evolution of sociality, and these genes were enriched for several annotated functions, including neural function, neurogenesis, and behavior, as well as immune function, growth, and metabolism. We also found evidence that directional selection for specific substitutions repeatedly occurred in social species for several genes, in particular the calcium channel gene TPC1. Finally, supporting previous results, we found elevated genome-wide rates of molecular evolution in social species, resulting mainly from relaxation of selection. Altogether, we identify genome-wide, genic, and site-specific changes that repeatedly occurred during the evolution of sociality in spiders.Significance StatementThe transition from solitary to social life is a major transition in evolution that repeatedly occurred, but the genetic underpinnings are largely unknown. To identify genomic changes associated with sociality, we compared the genomes of 24 spider species, representing seven recent and independent origins of sociality. We identified hundreds of genes and many functional classes of genes that tended to experience shifts in molecular evolution, including genes that have previously been implicated in animal social behavior and human behavioral disorders. Our study shows that while the precise genetic details vary, the repeated evolution of sociality in spiders predictably leaves genome-wide signatures and involves sets of genes with conserved functions that may play general roles in the evolution of social behavior.

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