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
Multidisciplinary Sciences
Yingnan Gao, Martin Wu
Summary: This study demonstrates the presence and prevalence of pulsed evolution in microbial genomic trait evolution using a likelihood-based framework. The findings support the predictions of punctuated equilibrium and quantum evolution theories.
Editorial Material
Biochemistry & Molecular Biology
Jenn Coughlan
Summary: As hybridization is found to be common in nature, understanding how natural selection affects hybrids is now more important for speciation. A study in PLOS Biology uses threespine stickleback to identify a genomic marker of ecological incompatibilities.
Article
Biology
Rene D. Clark, Matthew L. Aardema, Peter Andolfatto, Paul H. Barber, Akihisa Hattori, Jennifer A. Hoey, Humberto R. Montes, Malin L. Pinsky
Summary: The study found that the yellowtail clownfish has low genetic diversity at the range edge, gene flow from the core to the edge, and genomic signatures of local adaptation in candidate genes. This illustrates how spatially divergent selection can occur across the range core to the periphery despite genetic drift and moderate gene flow.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Genetics & Heredity
Nandita R. Garud, Philipp W. Messer, Dmitri A. Petrov
Summary: The debate over whether hard sweeps or soft sweeps dominate adaptation has continued, with the authors proposing that soft sweeps are prevalent in North American Drosophila melanogaster. Another study by Harris et al. has raised doubts about the reliability of soft sweeps detected, instead suggesting that hard sweeps may be more likely. However, upon reanalysis, the authors confirm that soft sweeps are the dominant mode of adaptation in North American Drosophila melanogaster.
Article
Biochemistry & Molecular Biology
Jorge L. Ramirez, Jonas Lescroart, Henrique Figueiro, Juan Pablo Torres-Florez, Priscilla M. S. Villela, Luiz L. Coutinho, Patricia D. Freitas, Warren E. Johnson, Agostinho Antunes, Pedro M. Galetti, Eduardo Eizirik
Summary: Using whole genome sequences, this study investigates the ecological differentiation among five species from the genus Leopardus, and explores their genomic features, comparative demographic history and positive selection. The results show that divergent ecological strategies are reflected in genomic features, and that the demographic history of these cats is influenced by climate fluctuations and habitat specialization, resulting in distinct evolutionary trajectories. Additionally, a gene involved in vertebrate retinal neurogenesis was found to be under positive selection in a specific species with nocturnal and arboreal specializations, indicating its importance in adaptation.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Meike J. Wittmann, Sylvain Mousset, Joachim Hermisson
Summary: Natural selection not only affects the actual loci under selection but also leaves footprints in patterns of genetic variation in linked genetic regions. We developed analytical approximations to characterize the genetic footprint of balancing selection with seasonally fluctuating allele frequencies. Fluctuating balancing selection can lead to an increase in genetic diversity near the selected site but reduces diversity further away due to recurrent bottlenecks of allelic backgrounds. Strong fluctuating balancing selection can even result in a loss of genetic variation in unlinked regions, impacting genome-wide diversity.
Article
Biochemistry & Molecular Biology
Eleanor C. Sheppard, Claudia A. Martin, Claire Armstrong, Catalina Gonzalez-Quevedo, Juan Carlos Illera, Alexander Suh, Lewis G. Spurgin, David S. Richardson
Summary: Understanding the mechanisms and genes that enable animals to adapt to pathogens is crucial. This study explores the genetic variation associated with avian pox infection in Berthelot's pipit populations. At the individual level, there was no evidence of variation in MHC class I and TLR4 being associated with pox infection. However, at the population-level, strong associations were found between avian pox prevalence and allele frequencies of SNPs located within genes involved in stress signalling and immune responses.
Article
Evolutionary Biology
Boyang Hu, Yuan Tian, Qi Li, Shikai Liu
Summary: This study investigated the genomic signatures of long-term selective breeding in Pacific oysters, revealing the impact of artificial selection on genetic diversity and genomic features. Population structure analysis and identification of selective sweeps highlighted the genetic differences between fast-growing oyster strains and wild populations. The findings provide valuable insights for understanding the genetic basis of growth regulation in Pacific oysters and will be beneficial for future genome-assisted breeding programs.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Huiying Shang, David L. Field, Ovidiu Paun, Martha Rendon-Anaya, Jaqueline Hess, Claus Vogl, Jianquan Liu, Par K. Ingvarsson, Christian Lexer, Thibault Leroy
Summary: Genomic landscapes of nucleotide diversity and differentiation are investigated to understand speciation processes. Resequencing 201 whole genomes from 8 closely related Populus species reveals extensive introgression between some species pairs. Conserved patterns of genomic divergence across species pairs are observed, with signatures of linked selection, gene flow, and standing genetic variation identified.
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
Multidisciplinary Sciences
Adan F. Mar-Silva, Pindaro Diaz-Jaimes, Cristina Dominguez-Mendoza, Omar Dominguez-Dominguez, Jonathan Valdiviezo-Rivera, Eduardo Espinoza-Herrera
Summary: This study found that oceanographic conditions and habitat characteristics have an impact on genetic structure in marine species, using Lutjanus guttatus as an example. The Gulf of Panama, as part of the Tropical Eastern Pacific, acts as a barrier to gene flow due to its complex current system and heterogeneous environment. The results suggest that adaptive selection plays a crucial role in population differentiation for Lutjanus guttatus.
Article
Biochemistry & Molecular Biology
Kaiya Provost, Stephanie Yun Shue, Meghan Forcellati, Brian Tilston Smith
Summary: Spatial models can explain genetic differentiation between populations based on factors such as geographic distance and environmental resistance. The genomic landscape of differentiation is diverse, indicating different evolutionary histories. This study compared different geographic predictors of differentiation in ten bird species and found that the characteristics of genomic landscapes varied, influenced by population structuring and admixture. Historical and contemporary mechanisms both played a role in genetic distance, with climate and habitat being particularly important. Different regions of the genome captured different evolutionary histories, suggesting that the genomic landscape of differentiation is associated with alternative geographic factors.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Shoupu He, Gaofei Sun, Xiaoli Geng, Wenfang Gong, Panhong Dai, Yinhua Jia, Weijun Shi, Zhaoe Pan, Junduo Wang, Liyuan Wang, Songhua Xiao, Baojun Chen, Shufang Cui, Chunyuan You, Zongming Xie, Feng Wang, Jie Sun, Guoyong Fu, Zhen Peng, Daowu Hu, Liru Wang, Baoyin Pang, Xiongming Du
Summary: The study revealed that extensive chromosome inversions on chromosomes A06 and A08 underlies the geographic differentiation in cultivated cotton, and haplotypic diversity from landraces is essential for adaptive evolution. Introgression and association analyses identified new fiber quality-related loci, showing that introgressed alleles from diploid cottons have a large effect on fiber quality improvement.
Article
Multidisciplinary Sciences
S. J. Love, J. A. Schweitzer, J. K. Bailey
Summary: Climate-induced evolution will determine population persistence in a changing world. We propose that isolated sky islands and adjacent mountain chains are natural laboratories for studying long-term and contemporary climatic pressures on natural populations. Our study showed that populations on sky islands have diverged from mountain chains in reproductive and productivity traits, with some convergence across sky islands. These shifts represent potentially beneficial phenotypes for population persistence in a changing world.
SCIENTIFIC REPORTS
(2023)
Article
Evolutionary Biology
Kerstin Johannesson, Erica H. Leder, Carl Andre, Sam Dupont, Susanne P. Eriksson, Karin Harding, Jonathan N. Havenhand, Marlene Jahnke, Per R. Jonsson, Charlotta Kvarnemo, Henrik Pavia, Marina Rafajlovic, Eva Marie Rodstrom, Michael Thorndyke, Anders Blomberg
Summary: The Centre for Marine Evolutionary Biology (CeMEB) at the University of Gothenburg, Sweden, was founded in 2008 with a 10-year research grant of 8.7 million euros. Over the past decade, CeMEB has made significant contributions to scientific publications, PhD theses, and organized various meetings and courses. This article reviews CeMEB's achievements, compares the initial goals with the actual achievements, and discusses future prospects for marine evolutionary biology.
EVOLUTIONARY APPLICATIONS
(2023)
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
Josefin Sefbom, Anke Kremp, Per Juel Hansen, Kerstin Johannesson, Anna Godhe, Karin Rengefors
Summary: This study examined whether multiple strains of the diatom Skeletonema marinoi from two genetically distinct Baltic Sea populations showed evidence of local adaptation to their respective environments. The results suggest that both estuarine and marine strains exhibit local adaptation strategies, with estuarine strains growing faster in high-salinity environments and marine strains outperforming estuarine strains in the marine environment.
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
Evolutionary Biology
Martin Eriksson, Alexandra Kinnby, Pierre De Wit, Marina Rafajlovic
Summary: Adaptive phenotypic plasticity can improve individual response to new environmental conditions. However, interpretation of reaction norms depends on the nature of assessed traits. This study combines modeling and empirical data to show that the presence of plasticity cannot be determined solely based on reaction norms, but requires additional knowledge of assessed traits and species biology.
EVOLUTIONARY APPLICATIONS
(2023)
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
Ricardo T. Pereyra, Marina Rafajlovic, Pierre De Wit, Matthew Pinder, Alexandra Kinnby, Mats Topel, Kerstin Johannesson
Summary: This study investigates the origin and evolution of large clones formed in a macroalgal species during range expansion. It found that large dominant clonal lineages repeatedly evolved from different sexual populations at range margins, while low but persistent clonality was observed in core populations. The study concludes that clones favored by uniparental reproductive assurance can play an important role in range expansion, resulting in a complex spatiotemporal mosaic of clonal and sexual lineages.
Article
Biochemistry & Molecular Biology
Bjorn Andersson, Olof Berglund, Helena L. Filipsson, Olga Kourtchenko, Anna Godhe, Kerstin Johannesson, Mats Topel, Matthew I. M. Pinder, Lara Hoepfner, Karin Rengefors
Summary: Phytoplankton have the ability to rapidly evolve and adapt to selection pressures. In a study of a diatom population in the Baltic Sea, it was found that copper tolerance did not differ between a mining-exposed population and a non-exposed population, but there was greater variation within the mining-exposed population. Through an artificial evolution experiment, it was observed that the mining-exposed population rapidly evolved copper tolerance due to the presence of hyper-tolerant strains.
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)
Correction
Evolutionary Biology
Pierre De Wit, Ellika Faust, Leon Green, Marlene Jahnke, Ricardo T. Pereyra, Marina Rafajlovic
EVOLUTIONARY APPLICATIONS
(2023)