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Yoel E. Stuart - One of the best experts on this subject based on the ideXlab platform.
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Divergent Uses of “Parallel Evolution” during the History of The American Naturalist
The American naturalist, 2018Co-Authors: Yoel E. StuartAbstract:The mechanistic link between natural selection and Parallel Evolution is well established. Natural selection is the only known deterministic process that can regularly overcome chance and historical contingency to generate the Evolution of similar characteristics in independent populations inhabiting similar environments. However, the ready inference of natural selection from Parallel Evolution has been established only relatively recently. Here, I review the use of "Parallel Evolution" in the first 125 years of The American Naturalist and show that there were other well-accepted definitions of the term through the history of the field. I discuss the legacy of those alternative ideas and how they helped to shape Evolution and ecology as we know them today and finish by discussing a geometric use for "Parallel" that may reduce terminological confusion.
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Non)Parallel Evolution
Annual Review of Ecology Evolution and Systematics, 2018Co-Authors: Daniel I. Bolnick, Rowan D. H. Barrett, Krista B. Oke, Diana J. Rennison, Yoel E. StuartAbstract:Parallel Evolution across replicate populations has provided Evolutionary biologists with iconic examples of adaptation. When multiple populations colonize seemingly similar habitats, they may evol...
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Contrasting effects of environment and genetics generate a continuum of Parallel Evolution
Nature ecology & evolution, 2017Co-Authors: Yoel E. Stuart, Thor Veen, Jesse N. Weber, Dieta Hanson, Mark Ravinet, Brian K. Lohman, Cole J. Thompson, Tania Tasneem, Andrew Doggett, Rebecca IzenAbstract:Environmental heterogeneity in three-spined stickleback pairs contributes to deviations from Parallel Evolution, but genomic targets of selection were more Parallel between environmentally similar pairs, suggestive of a continuum of Parallel Evolution.
Jianbo Cai - One of the best experts on this subject based on the ideXlab platform.
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Parallel Evolution strategy for solving structural optimization
Engineering Structures, 1997Co-Authors: Georg Thierauf, Jianbo CaiAbstract:Abstract A method for the solution of mixed-discrete structural optimization problems based on a two-level Parallel Evolution strategy is presented. On the first level, the optimization problem is divided into two subproblems with discrete and continuous design variables, respectively. The two subproblems are solved simultaneously on a Parallel computing architecture. On the second level, each subproblem is further Parallelized by means of a Parallel subEvolutionstrategy. Periodically, the design variables in the two groups are exchanged. Examples are included to demonstrate the implementation of this method on a Parallel computer.
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A Two Level Parallel Evolution Strategy for Solving Mixed-Discrete Structural Optimization Problems
Volume 1: 21st Design Automation Conference, 1995Co-Authors: Georg Thierauf, Jianbo CaiAbstract:Abstract A method for the solution of mixed-discrete structural optimization problems based on a two level Parallel Evolution strategy is presented. On the first level, the optimization problem is divided into two subproblems with discrete and continuous design variables, respectively. The two subproblems are solved simultaneously on a Parallel computing architecture. On the second level, each subproblem is further Parallelized by means of a Parallel sub-Evolution-strategy. Periodically, the design variables in the two groups axe exchanged. Examples are included to demonstrate the implementation of this method on a 8 nodes Parallel computer.
Juha Merilä - One of the best experts on this subject based on the ideXlab platform.
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Population structure limits Parallel Evolution
2021Co-Authors: Bohao Fang, Petri Kemppainen, Paolo Momigliano, Juha MeriläAbstract:Population genetic theory predicts that small effective population sizes (Ne) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e. Parallel Evolution), is expected to be reduced. We tested these predictions in a comparative genomic study of two ecologically similar and geographically co-distributed stickleback species (viz. Gasterosteus aculeatus and Pungitius pungitius). We found that P. pungitius harbours less genetic diversity and exhibits higher levels of genetic differentiation and isolation-by-distance than G. aculeatus. Conversely, G. aculeatus exhibits a stronger degree of genetic Parallelism across freshwater populations than P. pungitius: 2996 vs. 379 SNPs located within 26 vs nine genomic regions show evidence of selection in multiple freshwater populations of G. aculeatus and P. pungitius, respectively. Most regions involved in Parallel Evolution in G. aculeatus showed increased levels of divergence, suggestive of selection on ancient haplotypes. In contrast, regions involved in freshwater adaptation in P. pungitius were younger, and often associated with reduced diversity. In accordance with theory, the results suggest that connectivity and genetic drift play crucial roles in determining the levels and geographic distribution of standing genetic variation, providing evidence that population subdivision limits local adaptation and therefore also the likelihood of Parallel Evolution.
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On the causes of geographically heterogeneous Parallel Evolution in sticklebacks
Nature ecology & evolution, 2020Co-Authors: Bohao Fang, Petri Kemppainen, Paolo Momigliano, Xueyun Feng, Juha MeriläAbstract:The three-spined stickleback (Gasterosteus aculeatus) is an important model system for the study of Parallel Evolution in the wild, having repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes but these had typically limited geographic sampling and mostly focused on the Eastern Pacific region. We analysed population genomic data from global samples of the three-spined stickleback marine and freshwater ecotypes to detect loci involved in Parallel Evolution at different geographic scales. Most signatures of Parallel Evolution were unique to the Eastern Pacific and trans-oceanic marine-freshwater differentiation was restricted to a limited number of shared genomic regions, including three chromosomal inversions. On the basis of simulations and empirical data, we demonstrate that this could result from the stochastic loss of freshwater-adapted alleles during the invasion of the Atlantic basin and selection against freshwater-adapted variants in the sea, both of which can reduce standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the elevated linkage disequilibrium associated with marine-freshwater differentiation in the Eastern Pacific is consistent with secondary contact between marine and freshwater populations that evolved in isolation from each other during past glacial periods. Thus, contrary to what earlier studies from the Eastern Pacific region have led us to believe, Parallel marine-freshwater differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range.
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Oceans apart: Heterogeneous patterns of Parallel Evolution in sticklebacks
2019Co-Authors: Bohao Fang, Petri Kemppainen, Paolo Momigliano, Juha MeriläAbstract:An important model system for the study of genomic mechanisms underlying Parallel ecological adaptation in the wild is the three-spined stickleback (Gasterosteus aculeatus), which has repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies have identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes, but these are typically based on limited geographic sampling and are biased towards studies in the Eastern Pacific. We analysed population genomic data from marine and freshwater ecotypes of three-spined sticklebacks with from a comprehensive global collection of marine and freshwater ecotypes to detect loci involved in Parallel Evolution at different geographic scales. Our findings highlight that most signatures of Parallel Evolution were unique to the Eastern Pacific. Trans-oceanic marine and freshwater differentiation was only found in a very limited number of genomic regions, including three chromosomal inversions. Using both simulations and empirical data, we demonstrate that this is likely due to both the stochastic loss of freshwater-adapted alleles during founder events during the invasion of the Atlantic basin and selection against freshwater-adapted variants in the sea, both of which have reduced the amount of standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the existence of highly elevated linkage disequilibrium associated with marine-freshwater differentiation in the Eastern Pacific is also consistent with a secondary contact scenario between marine and freshwater populations that have evolved in isolation from each other during past glacial periods. Thus, contrary to what earlier studies focused on Eastern Pacific populations have led us to believe, Parallel marine-freshwater differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range.
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Morphological divergence of North‐European nine‐spined sticklebacks (Pungitius pungitius): signatures of Parallel Evolution
Biological Journal of the Linnean Society, 2010Co-Authors: Gábor Herczeg, Mirva Tuulikki Turtiainen, Juha MeriläAbstract:Parallel Evolution is characterised by repeated, independent occurrences of similar phenotypes in a given habitat type, in different parts of the species distribution area. We studied body shape and body armour divergence between five marine, four lake, and ten pond populations of nine-spined sticklebacks [Pungitius pungitius (Linnaeus, 1758)] in Fennoscandia. We hypothesized that marine and lake populations (large water bodies, diverse fish fauna) would be similar, whereas sticklebacks in isolated ponds (small water bodies, simple fish fauna) would be divergent. We found that pond fish had deeper bodies, shorter caudal peduncles, and less body armour (viz. shorter/absent pelvic spines, reduced/absent pelvic girdle, and reduced number of lateral plates) than marine fish. Lake fish were intermediate, but more similar to marine than to pond fish. Results of our common garden experiment concurred with these patterns, suggesting a genetic basis for the observed divergence. We also found large variation among populations within habitat types, indicating that environmental variables other than those related to gross habitat characteristics might also influence nine-spined stickleback morphology. Apart from suggesting Parallel Evolution of morphological characteristics of nine-spined sticklebacks in different habitats, the results also show a number of similarities to the Evolution of three-spined stickleback (Gasterosteus aculeatus Linnaeus, 1758) morphology. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101, 403–416.
Jianquan Liu - One of the best experts on this subject based on the ideXlab platform.
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Rapid radiation of Rheum (Polygonaceae) and Parallel Evolution of morphological traits.
Molecular phylogenetics and evolution, 2012Co-Authors: Yongshuai Sun, Ailan Wang, Dongshi Wan, Qian Wang, Jianquan LiuAbstract:In this study, we examined diversification history of Rheum and tested the hypothesis that morphological traits related to plant ‘body-plans’ evolved in Parallel in this genus. We sequenced eight chloroplast DNA fragments (representing more than 8000 bps of the sequence for each species) of 34 species from the genus and 13 species from closely related genera. Phylogenetic analyses indicate that all species of Rheum form a monophyletic lineage sister to the two-species genus Oxyria, indicating that radiative diversifications have occurred in its Evolutionary history. Our dating analyses further suggest that these radiations largely coincided with the extensive uplifts of the Qinghai–Tibetan Plateau (QTP). Ancestral state reconstruction and likelihood sensitivity tests strongly indicate that both decumbent and ‘glasshouse-like’ body-plan traits evolved in Parallel in different clades. Our findings highlight the importance of the uplift of the QTP in promoting species diversification and the Parallel Evolution of morphological traits that are putatively adaptive during such an Evolutionary history.
Matthew D. Macmanes - One of the best experts on this subject based on the ideXlab platform.
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Limited evidence for Parallel Evolution among desert adapted Peromyscus deer mice.
The Journal of heredity, 2021Co-Authors: Jocelyn P. Colella, Anna Tigano, Olga Dudchenko, Arina D. Omer, Ruqayya Khan, Ivan D. Bochkov, Erez L. Aiden, Matthew D. MacmanesAbstract:Warming climate and increasing desertification urges the identification of genes involved in heat- and dehydration-tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert adapted species can highlight Parallel or convergent patterns of genome Evolution through the identification of shared signatures of selection. We generate chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for signature of Parallel Evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another desert specialist deer mouse (P. eremicus) and a widely-distributed habitat generalist (P. maniculatus), that may be locally adapted to arid conditions. We identify few shared candidate loci involved in desert adaptation and do not find support for a shared pattern of Parallel Evolution. Instead, we hypothesize divergent molecular mechanisms of desert adaptation among deer mice, potentially tied to species-specific historical demography, which may limit or enhance adaptation. We identify a number of candidate loci experiencing selective sweeps in the P. crinitus genome that are implicated in osmoregulation (Trypsin, Prostasin) and metabolic regulation (Kallikrein, eIF2-alpha kinase GCN2, APPL1/2), which may be important to accommodating hot and dry environmental conditions.
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Limited evidence for Parallel Evolution among desert adapted Peromyscus deer mice
2020Co-Authors: Jocelyn P. Colella, Anna Tigano, Olga Dudchenko, Arina D. Omer, Ruqayya Khan, Ivan D. Bochkov, Erez L. Aiden, Matthew D. MacmanesAbstract:Phenotypic plasticity enables an immediate response to changing conditions, but for most species, Evolutionary change through adaptation will be more important for long-term survival. Warming climate and increasing desertification urges the identification of genes involved in heat- and dehydration-tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert adapted species can highlight Parallel or convergent patterns of genome Evolution through the identification of shared signatures of selection. We generate chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for signature of Parallel Evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another desert specialist deer mouse (P. eremicus) and a widely-distributed habitat generalist (P. maniculatus), that may locally adapted to arid conditions. We identify few shared candidate loci involved in desert adaptation and do not find support for a shared pattern of Parallel Evolution. Instead, we hypothesize divergent molecular mechanisms of desert adaptation among deer mice, potentially tied to species-specific historical demography, which may limit or enhance adaptation. We identify a number of candidate loci experiencing selective sweeps in P. crinitus genome that are implicated in osmoregulation (Trypsin, Prostasin) and metabolic regulation (Kallikrein, eIF2-alpha kinase GCN2, APPL1/2), which may be important to accommodating hot and dry environmental conditions.
