Article
Biochemistry & Molecular Biology
Fushi Ke, Liette Vasseur, Huiqin Yi, Lihua Yang, Xiao Wei, Baosheng Wang, Ming Kang
Summary: The study analyzed 132 genomes from five recently divergent species in Primulina genus, showing that both gene flow and linked selection have contributed to the genome-wide variation landscape. Lineage-specific genomic islands may have facilitated adaptation of certain species to special habitats.
Article
Biochemistry & Molecular Biology
Nathan J. White, Andrew P. Beckerman, Rhonda R. Snook, Michael A. Brockhurst, Roger K. Butlin, Isobel Eyres
Summary: Local adaptation is an important evolutionary process that allows populations to adapt to their local environment. This study experimentally evolved rotifer populations under either unidimensional or multidimensional divergent selection. The results showed that populations exposed to multidimensional selection initially increased in local adaptation but later declined, while populations exposed to unidimensional selection had a slower but eventually stronger increase in local adaptation.
Review
Plant Sciences
Edgar L. Y. Wong, Dmitry A. Filatov
Summary: It is well known that closely related species can hybridize and exchange genetic material, which can either promote or hinder adaptation and speciation. The heterogeneity of genomes in most eukaryotic species, such as variations in gene density, repetitive DNA, and chromatin compactness, can determine susceptibility to gene exchange from other species. Recombination rates also greatly influence the permeability of genomic regions to interspecific introgression, with regions lacking recombination impeding genetic exchange. The presence of large rarely recombining regions in plant genomes plays a significant role in preserving species identity in hybridizing plant species.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Wei Gao, Chuan-Xin Yu, Wei-Wei Zhou, Bao-Lin Zhang, E. Anne Chambers, Hollis A. Dahn, Jie-Qiong Jin, Robert W. Murphy, Ya-Ping Zhang, Jing Che
Summary: Speciation plays a crucial role in evolution, and understanding the origins and persistence of reproductive isolation (RI) is important. This study examined two closely related toad-headed lizards using genomic data and found that divergent selection and low genetic recombination help maintain RI between the two species.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Ning Sun, Liandong Yang, Fei Tian, Honghui Zeng, Ziwen He, Kai Zhao, Cheng Wang, Minghui Meng, Chenguang Feng, Chengchi Fang, Wenqi Lv, Jing Bo, Yongtao Tang, Xiaoni Gan, Zuogang Peng, Yiyu Chen, Shunping He
Summary: This study examines genome-wide variation in two species of cyprinid fishes in Lake Sunmcuo on the Qinghai-Tibet Plateau and identifies numerous large genomic islands associated with speciation with gene flow. These islands harbor divergent genes related to olfactory receptors, indicating their potential role in food selection and assortative mating. The findings support the hypothesis of parapatric speciation rather than sympatric speciation.
NATIONAL SCIENCE REVIEW
(2022)
Article
Biology
Anastasia Stolyarova, Tatiana Neretina, Elena A. Zvyagina, Anna Fedotova, Alexey S. Kondrashov, Georgii A. Bazykin
Summary: Studying patterns of genetic variation in hyperpolymorphic species, such as the fungus Schizophyllum commune, can reveal large-scale properties of the fitness landscape that are difficult to detect in species with ordinary levels of genetic variation. In S. commune, short-range linkage disequilibrium tends to be higher between pairs of nonsynonymous variants, especially those located within the same gene and covered by haploblocks, which are segments of the genome consisting of two highly divergent haplotypes and a signature of balancing selection. LD is also higher for pairs of nonsynonymous variants encoding interacting amino acids within the protein. Additionally, there is a correlation between LDs at the same pairs of nonsynonymous mutations in different populations.
Article
Biochemistry & Molecular Biology
Matthew Barnbrook, Mario Duran-Castillo, Jo Critchley, Yvette Wilson, Alex Twyford, Andrew Hudson
Summary: The study of speciation cases involving parallel adaptations can reveal adaptive characters and their underlying genes. By studying the parallel evolution of alpine morphology in the genus Antirrhinum, it was found that two later diverged sympatric species only differ by around 2% of nuclear loci, but still maintain morphological characters typical of earlier-diverged alpine or lowland lineages and correlate with local landscape features, as expected of ecological adaptations. The morphological differences involve multiple, unlinked genes that can be easily broken up by recombination in hybrids. There is little evidence of post-pollination barriers to gene flow or recombination, suggesting that genetic isolation related to ecological adaptation is important in maintaining character combinations and might have contributed to parallel speciation. Genes involved in the earlier alpine-lowland split were also reused in parallel evolution of alpine species, consistent with introgressive hybridization, and it is speculated that many non-ecological barriers to gene flow might have been purged during the process.
Article
Genetics & Heredity
A. Gilles, Y. Thevenin, F. Dione, J. -F Martin, B. Barascud, R. Chappaz, N. Pech
Summary: This study demonstrates the early stages of hybridization between divergent lineages and predicts the emergence of future hybrid zones in the wild, generating a wide spectrum of hybrids that are a potential source of important evolutionary novelties.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Hong Cheng, Zhuangbiao Zhang, Jiayue Wen, Johannes A. Lenstra, Rasmus Heller, Yudong Cai, Yingwei Guo, Ming Li, Ran Li, Wenrong Li, Sangang He, Jintao Wang, Junjie Shao, Yuxuan Song, Lei Zhang, Masum Billah, Xihong Wang, Mingjun Liu, Yu Jiang
Summary: This study analyzed the whole-genome sequencing of 1,098 domestic sheep and 69 wild sheep, and found that introgression from wild sheep contributed to the morphological diversity of sheep breeds and individual variations within breeds. The frequency of introgressed fragments varied greatly among domestic breeds, indicating the role of selection and recombination in shaping genetic and phenotypic diversity.
Article
Genetics & Heredity
Thomas H. Q. Powell, Glen Ray Hood, Meredith M. Doellman, Pheobe M. Deneen, James J. Smith, Stewart H. Berlocher, Jeffrey L. Feder
Summary: This study investigates the genetic variation and divergence in the Rhagoletis pomonella species group (RPSG) and finds that different taxa within the group are currently diverging under gene flow. The derived species are nested within the genetic variation of hawthorn-infesting populations of R. pomonella and show marked differences in genotype clustering and differentiation among sympatric populations.
Article
Biochemistry & Molecular Biology
Ken Thompson, Catherine H. Peichel, Diana K. Rennison, Matthew R. McGee, Arianne Y. K. Albert, Timothy Vines, Anna Greenwood, Abigail Wark, Yaniv Brandvain, Molly Schumer, Dolph Schluter
Summary: This study provides evidence for the presence of environment-dependent hybrid incompatibility in stickleback fish, suggesting that extrinsic incompatibilities can evolve before intrinsic incompatibilities.
Article
Multidisciplinary Sciences
Emilie J. Richards, Joseph A. McGirr, Jeremy R. Wang, Michelle E. St. John, Jelmer W. Poelstra, Maria J. Solano, Delaney C. O'Connell, Bruce J. Turner, Christopher H. Martin
Summary: This study investigated the evolutionary origins and stages of vertebrate adaptive radiation using the genomes of 202 Caribbean pupfishes. They found evidence supporting hybrid swarm origins and temporal stages of adaptation in an adaptive radiation event on San Salvador Island, Bahamas. The research demonstrates how ancient alleles from different environmental refugia can be reassembled into new adaptive combinations, providing insights into the spatiotemporal landscape of adaptation and speciation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Evolutionary Biology
Joseph D. Manthey, John Klicka, Garth M. Spellman
Summary: The genomic signature of allopatric speciation is largely shaped by genomic architecture, with gene density and recombination rate variation regionally explaining a large portion of variance in genomic diversity, differentiation, and divergence.chromosome size has a significant impact on genetic differentiation, divergence, lineage sorting, neutral evolution, genetic diversity, and recombination rate.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Maud Thierry, Florian Charriat, Joelle Milazzo, Henri Adreit, Sebastien Ravel, Sandrine Cros-Arteil, Sonia Borron, Violaine Sella, Thomas Kroj, Renaud Ioos, Elisabeth Fournier, Didier Tharreau, Pierre Gladieux
Summary: The genetic and phenotypic diversity of the rice blast fungus was analyzed, revealing population subdivision, niche separation, and reproductive isolation between distinct lineages. Partial specialization to rice subgroups and differences in putative virulence effectors contributed to population subdivision.
Article
Biochemistry & Molecular Biology
Jose Goncalves-Dias, Akanksha Singh, Corbinian Graf, Markus G. Stetter
Summary: Crop domestication and expansion is not a linear process, but involves gene flow from locally adapted wild relatives, which provide adaptive alleles. Gene flow decreases genetic load in domesticated crop species, while also creating reproductive barriers between crop species. This study on grain amaranth demonstrates the important role of gene flow in domestication and expansion, despite genetic species barriers.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Nathan J. White, Andrew P. Beckerman, Rhonda R. Snook, Michael A. Brockhurst, Roger K. Butlin, Isobel Eyres
Summary: Local adaptation is an important evolutionary process that allows populations to adapt to their local environment. This study experimentally evolved rotifer populations under either unidimensional or multidimensional divergent selection. The results showed that populations exposed to multidimensional selection initially increased in local adaptation but later declined, while populations exposed to unidimensional selection had a slower but eventually stronger increase in local adaptation.
Article
Biodiversity Conservation
Luciano Bosso, Sonia Smeraldo, Danilo Russo, Maria Luisa Chiusano, Giorgio Bertorelle, Kerstin Johannesson, Roger K. Butlin, Roberto Danovaro, Francesca Raffini
Summary: Understanding the factors that determine the success or failure of biological invasions is crucial. This study used Ecological Niche Modelling to investigate the habitat suitability of Littorina saxatilis in Europe and found that environmental constraints and biogeography play important roles in its distribution. The results suggest that abiotic factors and local ecological features are key in determining the success of invasion.
BIOLOGICAL INVASIONS
(2022)
Article
Evolutionary Biology
Aurelien De Jode, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja Marie Westram, Roger K. Butlin, Marina Rafajlovic, Christelle Fraisse
Summary: Understanding population divergence and speciation is crucial for evolutionary biology. High species diversity in the sea is considered a paradox due to the lack of geographical barriers. However, combining genome-wide data with demographic modelling has provided new insights. Studies show that barriers to gene flow exist in the sea but divergence can also occur without strict isolation.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Evolutionary Biology
Alan Le Moan, Marina Panova, Aurelien De Jode, Olga Ortega-Martinez, Marten Duvetorp, Rui Faria, Roger Butlin, Kerstin Johannesson
Summary: Understanding the genetic targets of natural selection is a challenging goal in population genetics. Using the marine snail as an example, this study explores the genomic architecture and adaptive significance of a candidate gene.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Plant Sciences
Suo Qiu, James M. Bradley, Peijun Zhang, Roy Chaudhuri, Mark Blaxter, Roger K. Butlin, Julie D. Scholes
Summary: This study reveals diverse strategies used by Striga hermonthica to overcome different layers of host resistance. Understanding the maintenance of variation at virulence loci by balancing selection is crucial for controlling the evolution of parasite virulence.
Review
Biology
Anja M. Westram, Rui Faria, Kerstin Johannesson, Roger Butlin, Nick Barton
Summary: Local adaptation and parallel evolution are major topics in evolutionary genomics. Genetic structures that reduce recombination, such as chromosomal inversions, play an important role in local adaptation. However, the contribution of inversions to parallel evolution is still not well understood.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biology
Emma L. Berdan, Alexandre Blanckaert, Roger K. Butlin, Thomas Flatt, Tanja Slotte, Ben Wielstra
Summary: Supergenes are fascinating examples of long-term balancing selection in nature, but their origin and maintenance are still unknown. Mutation accumulation can stabilize or destabilize the system, and the evolution of balanced lethal systems requires specific conditions.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Evolutionary Biology
Katherine E. Hearn, Eva L. Koch, Sean Stankowski, Roger K. Butlin, Rui Faria, Kerstin Johannesson, Anja M. Westram
Summary: Sexual antagonism is a driving force for the evolution of sex chromosomes, and the suppression of recombination between sexually antagonistic loci and the sex-determining locus plays a crucial role in maintaining beneficial combinations of alleles. Chromosomal inversions also contribute to recombination suppression, but their specific role in sex chromosome evolution is still unclear. In this study, the researchers investigated sex determination in the intertidal snail Littorina saxatilis and found evidence for a female-heterogametic sex determination system that is restricted to one ecotype. Four putative chromosomal inversions, including two previously described and two newly discovered inversions, were found to span the putative sex chromosome pair. The associations between these inversions and sex differed between the ecotypes, suggesting the presence of distinct strata of differing ages. These findings indicate a difference in selective regime and provide insights into the interaction between sex chromosomes and the environment in L. saxatilis.
Article
Ecology
Eva L. Koch, Mark Ravinet, Anja M. Westram, Kerstin Johannesson, Roger K. Butlin
Summary: Chromosomal inversions have been shown to play an important role in local adaptation, but their importance relative to the rest of the genome is still unclear. This study used the marine snail Littorina saxatilis on three Swedish islands to estimate the contribution of inversion polymorphisms to phenotypic divergence. The results showed that the contributions of loci outside inversions are similar in magnitude to inversions, with proportions varying depending on the trait and population.
Editorial Material
Biochemistry & Molecular Biology
Anja Marie Westram, Roger Butlin
Article
Microbiology
Emma L. Berdan, Fabian Roger, Maren Wellenreuther, Alexandra Kinnby, Gunnar Cervin, Ricardo Pereyra, Mats Topel, Kerstin Johannesson, Roger K. Butlin, Carl Andre
Summary: Sandy beaches are important biogeochemical hotspots that connect marine and terrestrial ecosystems via organic matter transfer. This study investigates the microbial communities of wrackbeds and a primary consumer, the seaweed fly, along a well-studied ecological gradient. The results show the dominance of polysaccharide degraders in both microbiomes, with consistent differences between wrackbed and fly samples. Additionally, shifts in microbial communities and functionality between the North and Baltic Sea are observed, potentially due to changes in the composition of polysaccharides in different seaweed communities. This study highlights the complexity of wrackbed microbial communities and the trophic consequences of shifts in near shore algal communities.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
James Reeve, Roger K. Butlin, Eva L. Koch, Sean Stankowski, Rui Faria
Summary: Inversions play a key role in adaptation and speciation, and the intertidal snail Littorina saxatilis exhibits strong associations between inversions and phenotypic differences. Inversion polymorphisms are widespread across the species range.
Article
Biochemistry & Molecular Biology
Joao Carvalho, Hernan E. Morales, Rui Faria, Roger K. Butlin, Vitor C. Sousa
Summary: In this study, a new Approximate Bayesian Computation (ABC) method was developed to infer the demographic history using pool-seq data. The results showed that pool-seq data can distinguish between general scenarios of ecotype formation and infer relevant demographic parameters.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Ecology
Joao Carvalho, Rui Faria, Roger K. K. Butlin, Vitor C. C. Sousa
Summary: Pool-seq is a valuable tool in population genomics and molecular ecology, but it has challenges in accurately estimating allele frequencies. Researchers have developed poolHelper, an R package that simulates SNP data, taking into account unequal individual contributions and sequencing errors. This tool allows users to optimize sampling schemes for Pool-seq studies.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Review
Ecology
Emma L. Berdan, Nicholas H. Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Ines Fragata, Kimberly J. Gilbert, Paul Jay, Martin Kapun, Katie E. Lotterhos, Claire Merot, Esra Durmaz Mitchell, Marta Pascual, Catherine L. Peichel, Marina Rafajlovic, Anja M. Westram, Stephen W. Schaeffer, Kerstin Johannesson, Thomas Flatt
Summary: Inversions are structural mutations that have a significant impact on adaptation and speciation. However, their study has been challenging due to reduced recombination and the effects of drift and hitchhiking. This review examines the different mechanisms of selection that affect the evolution of inversions, emphasizing the complexity of analyzing the causes underlying their evolution.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2023)