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
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
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.
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
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.
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
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
Biochemistry & Molecular Biology
Gregory L. Owens, Marco Todesco, Natalia Bercovich, Jean-Sebastien Legare, Nora Mitchell, Kenneth D. Whitney, Loren H. Rieseberg
Summary: The origins of the texanus subspecies of Helianthus annuus in Texas are likely not from introgression with the local congener H. debilis, but rather from introgression with the sister species H. argophyllus. Genomic differentiation in H. a. texanus is mainly driven by large segregating inversions, some of which show signs of natural selection based on haplotype frequencies.
Article
Biochemistry & Molecular Biology
Harun Njoroge, Arjen van't Hof, Ambrose Oruni, Dimitra Pipini, Sanjay C. Nagi, Amy Lynd, Eric R. Lucas, Sean Tomlinson, Xavi Grau-Bove, Daniel McDermott, Francis T. Wat'senga, Emile Z. Manzambi, Fiacre R. Agossa, Arlette Mokuba, Seth Irish, Bilali Kabula, Charles Mbogo, Joel Bargul, Mark J. Paine, David Weetman, Martin J. Donnelly
Summary: Studies on insecticide resistance provide insights into the rapid evolutionary response of populations to contemporary selection. This study identified twin mutations and a triple-mutant haplotype that can predict mosquito resistance to pyrethroid insecticides, and found that the use of synergists in long lasting insecticidal nets can increase mortality in mosquitoes carrying the triple-mutant haplotype.
Article
Multidisciplinary Sciences
Thibault Latrille, Nicolas Rodrigue, Nicolas Lartillot
Summary: Adaptation in protein-coding sequences can be detected using either multiple sequence alignments across species or polymorphism data within a population. Traditional phylogenetic codon models have limitations due to purifying selection, but recent developments in mutation-selection codon models provide a more detailed assessment of mutation, purifying, and positive selection. This exome-wide analysis shows that proteins and sites detected to be under adaptation at the phylogenetic scale are also under adaptation at the population-genetic scale, reconciling the two approaches and enabling integrative models and analyses across individuals and populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Maaike de Jong, Alexandra Jansen van Rensburg, Samuel Whiteford, Carl J. Yung, Mark Beaumont, Chris Jiggins, Jon Bridle
Summary: Understanding the rate and extent of adaptation of populations to novel environments at ecological margins is vital for predicting the survival of biological communities in a rapidly changing global environment. Recent expansion of the UK butterfly Aricia agestis range due to climate change has led to the evolution of new interactions with a larval food plant and the loss of its ability to use its ancestral host species. Analysis of genomic regions using ddRAD reveals the association of evolutionary responses with demographic history and ecological variation, suggesting polygenic evolution associated with climate adaptation. These data also suggest that rapid responses to climate change do not rely on the availability of pre-adapted genotypes, but instead on the assembly of novel genotypes from multiple localities.
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
Andrew H. Moeller
Summary: Balancing selection maintains allelic diversity in multidrug efflux pumps of gut bacteria, which may play an important role in their adaptation and fitness. Metagenomic scans also identified other proteins influenced by balancing selection.
Article
Biology
R. Lynch, J. Loehr, V Lummaa, T. Honkola, J. Pettay, O. Vesakoski
Summary: The study found that cultural similarity is the best predictor of successful migrations, with social relationships playing a key role. The results also suggest that the primary obstacles to human migration are sociocultural rather than ecological factors.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)