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
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
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
Marty Kardos, Gordon Luikart
Summary: The genetic architecture underlying heritability significantly impacts population viability during environmental change, with polygenic trait architectures showing higher viability compared to architectures with large-effect loci. Initial frequency of large-effect beneficial alleles also plays a crucial role in population viability, with moderately low initial allele frequencies conferring higher viability. Integrating information on trait genetic architecture into analysis will improve understanding and prediction of evolutionary and demographic responses to environmental change.
AMERICAN NATURALIST
(2021)
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)
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.
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
Evolutionary Biology
Angela P. Fuentes-Pardo, Edward D. Farrell, Mats E. Pettersson, C. Grace Sprehn, Leif Andersson
Summary: Understanding population adaptation is important for preserving biodiversity in the face of overexploitation and climate change. This study focused on Atlantic horse mackerel, a commercially and ecologically important marine fish. The researchers used genomic data and environmental information to analyze population structure and genetic basis of local adaptation. Their findings revealed low population structure but identified key genetic markers associated with adaptation, such as loci discriminating different regions. The study emphasizes the importance of understanding both life history and climate-related selective pressures in shaping population structure in marine fish.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Paula E. Adams, Anna B. Crist, Ellen M. Young, John H. Willis, Patrick C. Phillips, Janna L. Fierst
Summary: The outcrossing species C. remanei can recover from inbreeding, but the recovery is limited by the presence of a large number of segregating deleterious variants in natural populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Dominic G. G. Swift, Shannon J. J. O'Leary, R. Dean Grubbs, Bryan S. S. Frazier, Andrew T. T. Fields, Jayne M. M. Gardiner, J. Marcus Drymon, Dana M. M. Bethea, Tonya R. R. Wiley, David S. S. Portnoy
Summary: Understanding microevolutionary forces and population structure is crucial for effective management of exploited species. This study investigated the genetic structure of blacktip sharks using mitochondrial sequences and SNP-containing loci. The results revealed three genetically distinct units, suggesting regional philopatry and local adaptation. The findings highlight the importance of conserving essential habitats to maintain adaptive variation and enhance species resilience against environmental change.
Article
Biology
Mariah H. Meek, Erik A. Beever, Soraia Barbosa, Sarah W. Fitzpatrick, Nicholas K. Fletcher, Cinnamon S. Mittan-Moreau, Brendan N. Reid, Shane C. Campbell-Staton, Nancy F. Green, Jessica J. Hellmann
Summary: Adaptation to local environments is common among species and plays a crucial role in biodiversity conservation. Recent methodological advances provide tools to study local adaptation, which can help identify populations most at risk from climate change and suggest strategies for their persistence. Incorporating local adaptation into management decisions is thus important for addressing the challenges of a rapidly changing world.
Article
Biochemistry & Molecular Biology
Eric Wootton, Claude Robert, Jolle Taillon, Steeve Cote, Aaron B. A. Shafer
Summary: In this study, the relationships between measures of inbreeding, genomic constraint, and mutational load were investigated in white-tailed deer, caribou, and mountain goat. The results showed that mountain goats had higher inbreeding coefficients and more evolutionarily constrained regions compared to caribou and white-tailed deer. Additionally, white-tailed deer had the highest mutational load, followed by caribou, while mountain goats had the lowest.
Article
Biochemistry & Molecular Biology
William C. Rosenthal, John M. Fennell, Elizabeth G. Mandeville, Jason C. Burckhardt, Annika W. Walters, Catherine E. Wagner
Summary: This study examined the relative fitness and reproductive strategies of hybridizing populations of Yellowstone cutthroat trout and rainbow trout. The results showed that Yellowstone cutthroat trout outperformed rainbow trout in terms of reproduction and there was slight female preference for males of similar ancestry. These findings provide insights into the effects of natural selection and hybridization on population dynamics.
Article
Biochemistry & Molecular Biology
D. R. Trumbo, B. M. Hardy, H. J. Crockett, E. Muths, B. R. Forester, R. G. Cheek, S. J. Zimmerman, S. Corey-Rivas, L. L. Bailey, W. C. Funk
Summary: Wildlife diseases pose a major global threat to biodiversity. This study focuses on the endangered boreal toads in the southern Rocky Mountains, which suffer from lethal skin infections caused by the amphibian chytrid fungus. By using genomic analyses, researchers found low genetic diversity and population sizes, likely due to founder effects and population crashes caused by the fungus. The study also identified specific environmental factors that facilitate gene flow in the boreal toad population. Furthermore, the analysis revealed that the toads experienced stronger selection pressure from the disease than from broad-scale environmental variations.
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
Kara K. S. Layton, Brian Dempson, Paul V. R. Snelgrove, Steven J. Duffy, Amber M. Messmer, Ian G. Paterson, Nicholas W. Jeffery, Tony Kess, John B. Horne, Sarah J. Salisbury, Daniel E. Ruzzante, Paul Bentzen, David Cote, Cameron M. Nugent, Moira M. Ferguson, Jong S. Leong, Ben F. Koop, Ian R. Bradbury
EVOLUTIONARY APPLICATIONS
(2020)
Article
Evolutionary Biology
Sarah J. Lehnert, Shauna M. Baillie, John MacMillan, Ian G. Paterson, Colin F. Buhariwalla, Ian R. Bradbury, Paul Bentzen
EVOLUTIONARY APPLICATIONS
(2020)
Article
Ecology
Tony Kess, Paul Bentzen, Sarah J. Lehnert, Emma V. A. Sylvester, Sigbjorn Lien, Matthew P. Kent, Marion Sinclair-Waters, Corey Morris, Brendan Wringe, Robert Fairweather, Ian R. Bradbury
ECOLOGY AND EVOLUTION
(2020)
Article
Fisheries
Aaron P. Frenette, Tasha Harrold, Paul Bentzen, Ian G. Paterson, Rene M. Malenfant, George Nardi, Michael D. B. Burt, Michael S. Duffy
Article
Ecology
Tomos Potter, Ronald D. Bassar, Paul Bentzen, Emily W. Ruell, Julian Torres-Dowdall, Corey A. Handelsman, Cameron K. Ghalambor, Joseph Travis, David N. Reznick, Tim Coulson
Summary: The study shows that standard quantitative genetic models underestimated or failed to detect the evolution of a certain trait in a wild population. Researchers found that predictions of evolution are unreliable if environmental change is not appropriately captured in models.
AMERICAN NATURALIST
(2021)
Article
Biochemistry & Molecular Biology
Lea Blondel, Ian G. Paterson, Paul Bentzen, Andrew P. Hendry
Summary: The study demonstrates the impacts of rare extreme black swan disturbances on ecosystems, particularly on the abundance of fish and aquatic organisms as well as intraspecific diversity. Despite significant effects on phenotypic diversity, genetic diversity and population structure of guppies were mostly resistant to extreme floods, suggesting additional resilience in these populations.
Article
Environmental Sciences
K. K. S. Layton, P. V. R. Snelgrove, J. B. Dempson, T. Kess, S. J. Lehnert, P. Bentzen, S. J. Duffy, A. M. Messmer, R. R. E. Stanley, C. DiBacco, S. J. Salisbury, D. E. Ruzzante, C. M. Nugent, M. M. Ferguson, J. S. Leong, B. F. Koop, I. R. Bradbury
Summary: Despite the lack of understanding how most taxa will respond to future climate change, this research integrates genomics and environmental modeling to assess the responses of an ecologically and economically important Arctic species. The findings reveal past declines in effective population size in the Northwest Atlantic, indicating potential northward shifts and the loss of commercially important life-history variation in response to climate change. The genomic approach used here identifies both past and future declines that impact species persistence, ecosystem stability, and food security in the Arctic.
NATURE CLIMATE CHANGE
(2021)
Article
Biochemistry & Molecular Biology
Anthony L. Einfeldt, Tony Kess, Amber Messmer, Steven Duffy, Brendan F. Wringe, Jonathan Fisher, Cornelia den Heyer, Ian R. Bradbury, Daniel E. Ruzzante, Paul Bentzen
Summary: The evolution of the XY sex-determination mechanism in Atlantic halibut involved changes in the ancestral sex-determining gene DMRT1, likely coinciding with the emergence of the GSDF gene as the primary sex-determining factor. This study highlights how mutations in a small number of genetic elements can significantly impact the genomic substrate for sex-specific evolutionary forces, shedding light on the evolutionary mechanisms controlling sex determination across taxa.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Malin L. Pinsky, Anne Maria Eikeset, Cecilia Helmerson, Ian R. Bradbury, Paul Bentzen, Corey Morris, Agata T. Gondek-Wyrozemska, Helle Tessand Baalsrud, Marine Servane Ono Brieuc, Olav Sigurd Kjesbu, Jane A. Godiksen, Julia M. I. Barth, Michael Matschiner, Nils Chr. Stenseth, Kjetill S. Jakobsen, Sissel Jentoft, Bastiaan Star
Summary: This study compared whole-genome sequence data of Atlantic cod from two geographically distinct populations and found that genetic diversity did not substantially decline and effective population sizes remained high after periods of intensive exploitation and rapid decline. The research suggests that phenotypic change in these populations is not constrained by irreversible loss of genomic variation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Correction
Environmental Sciences
K. K. S. Layton, P. V. R. Snelgrove, J. B. Dempson, T. Kess, S. J. Lehnert, P. Bentzen, S. J. Duffy, A. M. Messmer, R. R. E. Stanley, C. DiBacco, S. J. Salisbury, D. E. Ruzzante, C. M. Nugent, M. M. Ferguson, J. S. Leong, B. F. Koop, I. R. Bradbury
NATURE CLIMATE CHANGE
(2021)
Article
Biochemistry & Molecular Biology
K. Beth Watson, Sarah J. Lehnert, Paul Bentzen, Tony Kess, Antony Einfeldt, Steven Duffy, Ben Perriman, Sigbjorn Lien, Matthew Kent, Ian R. Bradbury
Summary: The study identified chromosomal rearrangements in Atlantic Salmon populations in southern Newfoundland, Canada, with a particular focus on the Ssa01/Ssa23 translocation variant which was strongly correlated with population structure and temperature. The results suggest that environmental selection acting on these structural variants introduced through secondary contact may drive fine-scale local adaptation in Placentia Bay, Newfoundland, Canada.
Article
Biochemistry & Molecular Biology
Melissa K. Holborn, Anthony L. Einfeldt, Tony Kess, Steve J. Duffy, Amber M. Messmer, Barbara L. Langille, Matthew K. Brachmann, Johanne Gauthier, Paul Bentzen, Tim Martin Knutsen, Matthew Kent, Danny Boyce, Ian R. Bradbury
Summary: Teleosts exhibit extensive diversity of sex determination systems and mechanisms. In this study, the genome of the common lumpfish was sequenced and the sex determination region and master sex determination locus were identified. Anti-Mullerian hormone (AMH) was found to be the putative sex determination factor. The study provides important insights into the early evolution of sex chromosomes and has implications for lumpfish conservation and aquaculture.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Fisheries
Richard S. McBride, Elizabeth A. Fairchild, Yvonna K. Press, Scott P. Elzey, Charles F. Adams, Paul Bentzen
Summary: This study collected a large number of fish through collaboration with the commercial fishing industry to overcome the lack of information on the life history of the U.S. Atlantic Wolffish. The study found that the Atlantic Wolffish has a long lifespan and larger males. The preliminary estimates of total mortality were lower than before the moratorium, and skip spawning was observed in a small percentage of mature females. Accounting for abortive maturation improved the precision of maturity estimates.
MARINE AND COASTAL FISHERIES
(2022)
Article
Multidisciplinary Sciences
Tomos Potter, Jeff Arendt, Ronald D. Bassar, Beth Watson, Paul Bentzen, Joseph Travis, David N. Reznick
Summary: There is no consensus on why females prefer mates with rare phenotypes, but sexual selection can maintain genetic variation. We examined the fitness consequences of female preference for rare male color patterns in Trinidadian guppies over 10 generations and found that rare males have a reproductive advantage and mating with them gives females an indirect fitness advantage through the success of their sons. However, the fitness benefit disappears for grandsons as the rare phenotype becomes common. Contrary to prevailing theory, our study shows that female preference can be maintained through indirect selection.
