Article
Biochemistry & Molecular Biology
Kathrin A. Otte
Summary: This article presents a new approach to genotype-environment association (GEA) studies called genomic window analysis, which combines the information of neighboring single-nucleotide polymorphisms (SNPs) to enhance the detection of genomic signals of environmental adaptation. The method is proven to be superior to several established GEA approaches, especially in cases with small sample sizes, through simulations and real data analysis.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Biochemistry & Molecular Biology
Edson Ishengoma
Summary: Africa is the birthplace of humankind and home to the most diverse wildlife and flora. Understanding genetic variation and adaptation is crucial for the sustainable utilization of Africa's biodiversity. Despite a lag in genomics research, African scientists are increasingly interested in using omics technology to study native African species. This overview on vertebrate biodiversity in Africa aims to provide insights from prior genomics research and guide future studies.
Article
Evolutionary Biology
John K. Kelly
Summary: This study characterizes the evolution of SNPs in a population of yellow monkeyflower. It finds that most SNPs exhibit minimal change over time, consistent with neutral evolution. However, a subset of SNPs display strong fluctuations in frequency, which are driven by selection and have a ripple effect on genome-wide variation.
Article
Biochemistry & Molecular Biology
Devon A. DeRaad, Marlon E. Cobos, Abdelghafar Alkishe, Uzma Ashraf, Koffi Mensah Ahadji-Dabla, Claudia Nunez-Penichet, A. Townsend Peterson
Summary: The concept of fundamental ecological niche is crucial for various ecological questions. This study examined the potential role of genome environment association (GEA) testing in understanding genetic basis of ecological niche using genomic data from Anopheles gambiae 1000 Genomes Consortium. The results indicated that while commonly implemented GEA methods can account for confounding patterns of genetic variation, challenges remain in discerning true signals of genome environment adaptation.
Article
Biochemistry & Molecular Biology
Camille Kessler, Alice Brambilla, Dominique Waldvogel, Glauco Camenisch, Iris Biebach, Deborah M. Leigh, Christine Grossen, Daniel Croll
Summary: The study explores the impact of immune function polymorphism on health and reproductive success within species, as well as the significance of genetic diversity loss in extinction risk. Through the design of a microfluidics-based amplicon sequencing assay, comprehensive genetic variation in Alpine ibex was successfully captured, revealing unexpectedly high genetic differentiation at immunity-related loci within the species.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Soraia Barbosa, Kimberly R. Andrews, Amanda R. Goldberg, Digpal S. Gour, Paul A. Hohenlohe, Courtney J. Conway, Lisette P. Waits
Summary: This study examines the neutral and adaptive processes in species and population differentiation using recently diverged sister species of ground squirrels. The results highlight the importance of neutral and adaptive differentiation in understanding genetic structure and environmental adaptation, with implications for conservation efforts.
Article
Biochemistry & Molecular Biology
Tony Kess, J. Brian Dempson, Sarah J. Lehnert, Kara K. S. Layton, Anthony Einfeldt, Paul Bentzen, Sarah J. Salisbury, Amber M. Messmer, Steven Duffy, Daniel E. Ruzzante, Cameron M. Nugent, Moira M. Ferguson, Jong S. Leong, Ben F. Koop, Michael F. O'Connell, Ian R. Bradbury
Summary: The study on Arctic Charr in Gander Lake, Newfoundland, Canada, revealed genetic divergence between deep-water and shallow-water morphs, with genes involved in gene expression, DNA repair, cardiac function, and membrane transport being highlighted as key factors in adaptation to extreme deep-water environments.
Editorial Material
Biochemistry & Molecular Biology
Sarah J. Salisbury, M. Lisette Delgado, Anne C. Dalziel
Summary: The research highlights the importance of alternative splicing as a potential mechanism underlying local adaptation, showing that different regulatory mechanisms may affect different cellular traits to complementarily alter organismal phenotype. Genetic basis may play a role in the regulatory divergence, with DE and DS genes more likely to be hub genes and have a variety of phenotypic effects, suggesting a complex interplay of gene expression and splicing in adaptive divergence.
Article
Multidisciplinary Sciences
Tin Hang Hung, Thea So, Bansa Thammavong, Voradol Chamchumroon, Ida Theilade, Chhang Phourin, Somsanith Bouamanivong, Ida Hartvig, Hannes Gaisberger, Riina Jalonen, David H. Boshier, John J. MacKay
Summary: Rosewoods have been highly trafficked in the illegal wildlife trade since 2005. The two most sought-after species, Dalbergia cochinchinensis and Dalbergia oliveri, face significant genetic risks and limited adaptability knowledge, hindering conservation efforts. This study found differential adaptive genomic variation in response to temperature and precipitation-related variables between the two species, suggesting the need for species-specific conservation actions. The research also developed a seed source matching application to aid restoration efforts. Overall, this ecological genomic research is important for global tropical tree conservation and mitigating climate change risks.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Lucy Peters, Jisca Huisman, Loeske E. B. Kruuk, Josephine M. Pemberton, Susan E. Johnston
Summary: Sexually selected traits exhibit large variation and rapid evolution in the animal kingdom, yet genetic variation persists within populations despite directional selection. Understanding the genetic architecture of sexually selected traits, such as antler morphology in red deer, can shed light on evolutionary drivers and constraints at the genomic level. The study on red deer antler traits revealed high repeatability, heritability, and polygenic architecture, suggesting that genetic covariances among traits and pleiotropy may contribute to the maintenance of genetic variation in antler morphology.
Article
Biochemistry & Molecular Biology
Carol Buitrago-Lopez, Anny Cardenas, Benjamin C. C. Hume, Thierry Gosselin, Fabian Staubach, Manuel Aranda, Daniel J. Barshis, Yvonne Sawall, Christian R. Voolstra
Summary: Global habitat degradation has increased the need to study genetic connectivity and diversity of marine biota in order to guide conservation efforts. This study examined the population structure and holobiont assemblage of two common pocilloporid corals across the Red Sea. The results showed evidence for limited population differentiation in P. verrucosa, but complex population structure and genetic differentiation in S. pistillata, along with differences in reproductive mode and genetic adaptation at various sites. The study highlights the importance of multispecies investigations and networks of reef reserves in conserving genetic variants critical to the future survival of coral ecosystems.
Article
Biochemistry & Molecular Biology
Luke T. Dunning, Jill K. Olofsson, Alexander S. T. Papadopulos, Samuel G. S. Hibdige, Oriane Hidalgo, Ilia J. Leitch, Paulo C. Baleeiro, Sinethemba Ntshangase, Nigel Barker, Richard W. Jobson
Summary: This study investigates the genetic variations and evolutionary history of the dominant grassland species T. triandra across Asia, Africa, and Australia. The research reveals the existence of distinct ecotypes and differences in nuclear and organellar genomes, suggesting a complex process of colonization and adaptation. The study also uncovers potential adaptive introgression and selection in genes related to water use efficiency. The findings suggest that the widespread distribution of T. triandra in Australia can be attributed to its ecotypic genetic variation and genome duplication, with the importance varying depending on the geographic scale.
Editorial Material
Biochemistry & Molecular Biology
Lars Opgenoorth, Christian Rellstab
Summary: The study of drought resistance in white spruce utilized multiple data sources and analytical approaches to identify candidate genes involved in growth and resistance to extreme drought events, showcasing how diverse datasets can provide complementary evidence to overcome challenges in the research field.
Article
Plant Sciences
Josselin Montarry, Benjamin Mimee, Etienne G. J. Danchin, Georgios D. Koutsovoulos, Dave T. Ste-Croix, Eric Grenier
Summary: Plant-parasitic nematodes are a significant burden on crop production, and population genetics plays a key role in understanding their life strategies. Advances in high-throughput sequencing technologies have facilitated rapid development in genomic analyses of plant-parasitic nematodes.
Article
Biochemistry & Molecular Biology
Jose Luis Blanco-Pastor, Philippe Barre, Thomas Keep, Thomas Ledauphin, Abraham Escobar-Gutierrez, Anna Maria Roschanski, Evelyn Willner, Klaus J. Dehmer, Matthew Hegarty, Hilde Muylle, Elisabeth Veeckman, Klaas Vandepoele, Tom Ruttink, Isabel Roldan-Ruiz, Stephanie Manel, Jean-Paul Sampoux
Summary: This study identified adaptive loci in perennial ryegrass using a combination of Genome-Environment Association (GEA) and GWAS analyses, as well as a new test based on Canonical Correlation Analysis (CANCOR). The gene annotation was improved through de novo gene prediction and functional annotation of over 39,000 genes. The results revealed potential polygenic and oligogenic climatic adaptations and highlighted the utility of CANCOR for investigating gene interactions involved in polygenic adaptations.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Evolutionary Biology
Quentin Rougemont, Anne Carrier, Jeremy Le Luyer, Anne-Laure Ferchaud, John M. Farrell, Daniel Hatin, Philippe Brodeur, Louis Bernatchez
EVOLUTIONARY APPLICATIONS
(2019)
Article
Ecology
Yann Dorant, Laura Benestan, Quentin Rougemont, Eric Normandeau, Brian Boyle, Remy Rochette, Louis Bernatchez
ECOLOGY AND EVOLUTION
(2019)
Article
Plant Sciences
Thibault Leroy, Quentin Rougemont, Jean-Luc Dupouey, Catherine Bodenes, Celine Lalanne, Caroline Belser, Karine Labadie, Gregoire Le Provost, Jean-Marc Aury, Antoine Kremer, Christophe Plomion
Article
Biochemistry & Molecular Biology
Hugo Cayuela, Quentin Rougemont, Martin Laporte, Claire Merot, Eric Normandeau, Yann Dorant, Ole K. Torresen, Siv Nam Khang Hoff, Sissel Jentoft, Pascal Sirois, Martin Castonguay, Teunis Jansen, Kim Praebel, Marie Clement, Louis Bernatchez
Article
Evolutionary Biology
Laura M. Benestan, Quentin Rougemont, Caroline Senay, Eric Normandeau, Eric Parent, Rick Rideout, Louis Bernatchez, Yvan Lambert, Celine Audet, Genevieve J. Parent
Summary: This study utilized genomic markers and demographic modeling to investigate the population structure, distribution patterns, and speciation history of two cryptic redfish species, revealing their genetic distinctiveness and the influence of spatial distribution and depth on genomic variation.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Ecology
Quentin Rougemont, Victoria Dolo, Adrien Oger, Anne-Laure Besnard, Dominique Huteau, Marie-Agnes Coutellec, Charles Perrier, Sophie Launey, Guillaume Evanno
Summary: The study investigated the impact of riverscape fragmentation on genetic diversity in freshwater resident European brook lamprey. Results showed a positive relationship between genetic diversity and distance from the river source, with downstream populations sympatric with anadromous river lamprey displaying higher genetic diversity. This suggests that gene flow between ecotypes may play a role in maintaining genetic diversity in fragmented river networks.
Article
Biochemistry & Molecular Biology
Yann Dorant, Hugo Cayuela, Kyle Wellband, Martin Laporte, Quentin Rougemont, Claire Merot, Eric Normandeau, Remy Rochette, Louis Bernatchez
Article
Genetics & Heredity
Quentin Rougemont, Jean-Sebastien Moore, Thibault Leroy, Eric Normandeau, Eric B. Rondeau, Ruth E. Withler, Donald M. Van Doornik, Penelope A. Crane, Kerry A. Naish, John Carlos Garza, Terry D. Beacham, Ben F. Koop, Louis Bernatchez
Article
Biochemistry & Molecular Biology
Quentin Rougemont, Amanda Xuereb, Xavier Dallaire, Jean-Sebastien Moore, Eric Normandeau, Eric B. Rondeau, Ruth E. Withler, Donald M. Van Doornik, Penelope A. Crane, Kerry A. Naish, John Carlos Garza, Terry D. Beacham, Ben F. Koop, Louis Bernatchez
Summary: This study investigated the genomic basis of local adaptation in Coho salmon across North America and found that migration distance is the primary selective factor. Several candidate genetic variations associated with long-distance migration and altitude were also identified.
Article
Ecology
Quentin Rougemont, Charles Perrier, Anne-Laure Besnard, Isabelle Lebel, Yann Abdallah, Eric Feunteun, Elodie Reveillac, Emilien Lasne, Anthony Acou, David Jose Nachon, Fernando Cobo, Guillaume Evanno, Jean-Luc Bagliniere, Sophie Launey
Summary: Deciphering the effects of historical and recent demographic processes on genetic diversity and structure of anadromous fish is crucial for evolutionary and conservation biology. This study investigated the genetic diversity, structure, hybridization, and introgression of two species of anadromous fish with contrasting life history strategies. The findings highlight the importance of considering the recent population decline and hybridization when implementing conservation programs.
Article
Biochemistry & Molecular Biology
Yann Dorant, Martin Laporte, Quentin Rougemont, Hugo Cayuela, Remy Rochette, Louis Bernatchez
Summary: This study conducted a landscape genomics analysis on the American lobster, revealing that adaptive genetic variation can enhance the identification of population structure and the delineation of biological management units in exploited marine species.
Article
Evolutionary Biology
Amanda Xuereb, Quentin Rougemont, Xavier Dallaire, Jean-Sebastien Moore, Eric Normandeau, Berenice Bougas, Alysse Perreault-Payette, Ben F. Koop, Ruth Withler, Terry Beacham, Louis Bernatchez
Summary: This study evaluated the current conservation units (CUs) for Coho salmon in Canada using a large genomic dataset and compared patterns of genetic variation using neutral and outlier loci. The results suggest that the current CU boundaries are generally appropriate, but there may be a need for refinement in certain areas.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Quentin Rougemont, Barbara Huber, Simon H. Martin, Annabel Whibley, Catalina Estrada, Darha Solano, Robert Orpet, W. Owen McMillan, Brigitte Frerot, Mathieu Joron
Summary: By studying the speciation process of Heliconius butterflies, it is found that wing pattern divergence may play a role in speciation and be associated with hybridization and reproductive isolation.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Quentin Rougemont, Thibault Leroy, Eric B. Rondeau, Ben Koop, Louis Bernatchez
Summary: This study investigates how various factors, such as population size, recombination rates, and chromosome inheritance, impact natural selection and deleterious mutations in Coho salmon. The researchers found evidence of gene surfing and variation in polyploidy affecting the genetic load, supporting the nearly neutral theory of molecular evolution. These findings have important implications for evolutionary biology and conservation genomics.