Article
Ecology
Josselin Clo, Oystein H. Opedal
Summary: This study relaxes the assumption of additivity in classical theoretical models regarding traits in inbred populations, exploring the effect of dominance on evolution. It is found that dominance components can explain a substantial part of genetic variance in inbred populations, and ignoring these components can lead to an upward bias in predicted response to selection. Additionally, genetic associations can make selfing populations more evolvable in the long term, reconciling theoretical and empirical results.
Review
Biology
Hiroyuki Shimoji, Shigeto Dobata
Summary: Reproductive division of labour is a characteristic of eusocial insects, but can be disrupted by reproductive potential of otherwise sterile nest-mates. Dominance hierarchy plays a crucial role in regulating reproduction in some species, and dominance hierarchies in eusocial insects involve more individuals than in vertebrates, requiring unique selective forces. This article provides an overview of studies on dominance hierarchies in eusocial insects, specifically focusing on paper wasps and ponerine ants. It explains the emergence of dominance hierarchies as a self-organizing process through individual memory and local behavioral interactions, which can be captured using network analyses. The adaptive significance of dominance hierarchies is also discussed from the perspective of sterile subordinates, emphasizing the importance of kin selection.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Editorial Material
Biochemistry & Molecular Biology
Filip Ruzicka, Max Reuter
Summary: A new study in Drosophila serrata reveals the association between sexually antagonistic selection on cuticular hydrocarbons and a major-effect gene.
Article
Multidisciplinary Sciences
Hanne De Kort, Sylvain Legrand, Olivier Honnay, James Buckley
Summary: This study explores the effect of transposable elements on genome-wide heterozygosity and selection signatures across an inbreeding gradient in Arabidopsis lyrata. The results show that intense inbreeding is associated with elevated heterozygosity downstream of several transposable element superfamilies, as well as signatures of balancing selection. In addition, stress-responsive genes downstream of transposable elements also exhibit increased heterozygosity. The study also reveals specific selection signatures associated with transposable element superfamilies, which are reproducible in independent evolutionary lineages of A. lyrata. These findings provide an important hypothesis for the success of self-fertilizing species.
NATURE COMMUNICATIONS
(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
Plant Sciences
Chensong Chen, Owen Powell, Eric Dinglasan, Elizabeth M. Ross, Seema Yadav, Xianming Wei, Felicity Atkin, Emily Deomano, Ben J. Hayes
Summary: Machine learning methods, including deep learning neural networks and ensemble machine learning approach, were investigated for genomic prediction in sugarcane, compared to the genomic best linear unbiased prediction (GBLUP) model. While less accurate than the extended GBLUP model, optimized machine learning models showed comparable predictive ability.
Article
Biotechnology & Applied Microbiology
Muhammad Saqib Sohail, Raymond H. Y. Louie, Matthew R. McKay, John P. Barton
Summary: Genetic linkage plays a significant role in determining the fate of new mutations and their effects on fitness in evolving populations. Resolving genetic linkage is crucial for accurately quantifying selection and understanding the impact of mutations on evolutionary histories.
NATURE BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Chung-Hsien Huang, Ching-Hung Chen, Teng-Kuan Huang, Farn Lu, Jack Yu Jen Huang, Bor-Ran Li
Summary: Assisted reproductive technology is crucial for treating infertility, and the isolation of high-quality sperm is a critical step. This study presents a new chip for high-quality sperm separation, which showed promising results in clinical experiments.
Article
Genetics & Heredity
Kay Lucek, Yvonne Willi
Summary: Using whole-genome sequences of North American Arabidopsis lyrata, this study examined the impact of demographic history and mating system on linkage disequilibrium (LD). Results showed that both range expansion and shift in mating system led to increased LD, with LD positively associated with mutational load. Certain genes were identified as LD outliers, potentially experiencing selection pressure from demographic processes. Overall, LD can serve as an indicator of mutation accumulation and may affect population expansion and range limits.
Review
Genetics & Heredity
Sam Yeaman
Summary: Observations of alleles associated with complex traits should be interpreted in the context of evolutionary processes. Genetic architecture can significantly impact evolutionary outcomes and provide insights into how evolution works. Local adaptation can lead to concentrated genetic architectures enriched for alleles of larger effect, but evolution of such architectures may be limited by various factors.
Article
Biochemistry & Molecular Biology
Petra Bulankova, Mirna Sekulic, Denis Jallet, Charlotte Nef, Cock van Oosterhout, Tom O. Delmont, Ilse Vercauteren, Cristina Maria Osuna-Cruz, Emmelien Vancaester, Thomas Mock, Koen Sabbe, Fayza Daboussi, Chris Bowler, Wim Vyverman, Klaas Vandepoele, Lieven De Veylder
Summary: Diatoms, a successful group of microalgae, exhibit high levels of intraspecific genetic variability in natural populations. Through sequencing, it was found that clonally propagated diatom cell cultures rapidly accumulate multiple haplotypes with novel protein variants from a single founder cell. Genomic changes between mother and daughter cells include copy number variation and copy-neutral loss of heterozygosity, leading to the fixation of alleles within individual daughter cells. The frequency of interhomolog mitotic recombination is affected by environmental stress conditions, contributing to the clonal variability in diatom populations.
Article
Physics, Fluids & Plasmas
Anton S. Zadorin, Olivier Rivoire
Summary: By studying the advantageous conditions and evolutionary mechanisms of sexual reproduction in different environments, we have developed a new model of sexual reproduction and drawn conclusions on the adaptiveness and evolutionary value of sexual dimorphism.
Article
Genetics & Heredity
Quinn Langdon, Daniel Powell, Bernard Kim, Shreya Banerjee, Cheyenne Payne, Tristram Dodge, Ben Moran, Paola Fascinetto-Zago, Molly Schumer
Summary: This study analyzes the drivers of variation in local ancestry across the genome in hybridization events between two species pairs of swordtail fish and finds unexpectedly high levels of repeatability. The analysis also identifies regions of the genome where minor parent ancestry is unusually low or high across species pairs, indicating shared selection sites and mechanisms.
Article
Ecology
Jeremiah W. Busch, Sarah Bodbyl-Roels, Sharif Tusuubira, John K. Kelly
Summary: Selfing populations with little genetic variation have limited evolutionary potential. This study evolved populations of Mimulus guttatus for nine generations and found that populations without pollinating bees produced more selfed seed but had reduced DNA polymorphism. Simulations showed that favored alleles at specific loci decrease neutral variation and create greater heterogeneity among chromosomes in large selfing populations.
Article
Multidisciplinary Sciences
Alexander Klassmann, Mathieu Gautier
Summary: Analysis of population genetic data often involves the search for genomic regions with signs of recent positive selection. In this study, we propose and test modifications to the concept of extended haplotype homozygosity (EHH) and its associated statistics to relax data requirements. Our findings show the indispensability of phased haplotypes for accurate estimation of within-population statistics and cross-population statistics for small samples. Ancestry information, however, is found to be less important for both types of statistics. Our modified statistics are implemented in the publicly available R package rehh.
Article
Genetics & Heredity
Aneil F. Agrawal, Matthew Hartfield
Article
Genetics & Heredity
Matthew Hartfield, Stephen I. Wright, Aneil F. Agrawal
Review
Ecology
M. Hartfield
JOURNAL OF EVOLUTIONARY BIOLOGY
(2016)
Article
Biochemical Research Methods
Matthew Hartfield, Samuel Alizon
PLOS COMPUTATIONAL BIOLOGY
(2015)
Article
Genetics & Heredity
Matthew Hartfield, Sylvain Glemin
Editorial Material
Biochemistry & Molecular Biology
Matthew Hartfield
Review
Genetics & Heredity
Matthew Hartfield, Thomas Bataillon, Sylvain Glemin
TRENDS IN GENETICS
(2017)
Editorial Material
Ecology
Matthew Hartfield
Article
Evolutionary Biology
Matthew Hartfield, Rowena Bull, Peter A. White, Andrew Lloyd, Fabio Luciani, Samuel Alizon
EVOLUTIONARY APPLICATIONS
(2014)
Article
Genetics & Heredity
Matthew Hartfield, Sylvain Glemin
Article
Genetics & Heredity
Matthew Hartfield, Thomas Bataillon
G3-GENES GENOMES GENETICS
(2020)
Article
Evolutionary Biology
Matthew Hartfield, Nina Aagaard Poulsen, Bernt Guldbrandtsen, Thomas Bataillon
Summary: This study applied the Singleton Density Score method to detect recent selection in Holstein cattle, identifying several genes as potential targets of recent selection. The research did not find strong evidence for directional selection in traits important to humans, including milk protein content, milk fat content, and stature. These results offer insights into recent genetic changes in Bos taurus and provide guidance for future studies on polygenic selection.
Article
Genetics & Heredity
Graham Gower, Aaron P. Ragsdale, Gertjan Bisschop, Ryan N. Gutenkunst, Matthew Hartfield, Ekaterina Noskova, Stephan Schiffels, Travis J. Struck, Jerome Kelleher, Kevin R. Thornton
Summary: Understanding the demographic history of populations is crucial in population genetics, but the lack of a standardized format to define population dynamic models hampers progress in the field. Therefore, we propose the Demes data model and file format to address these issues.
Article
Genetics & Heredity
Matthew Hartfield, Stephen I. Wright, Aneil F. Agrawal