Article
Biochemistry & Molecular Biology
Jennifer James, Chedly Kastally, Katharina B. Budde, Santiago C. Gonzalez-Martinez, Pascal Milesi, Tanja Pyhajarvi, Martin Lascoux
Summary: New mutations provide raw material for evolution and adaptation. The distribution of fitness effects (DFE) is of vital interest in evolutionary biology. Recent research has found striking similarities in the DFE between closely related species, prompting further investigation into the variation of DFE at the population and species level.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Olivier Cotto, Troy Daya
Summary: This study reveals that inferring the underlying genotype-fitness map from observed DFEs is challenging, as many different maps can produce the same DFE. The research also suggests that a random genotype-fitness map would result in the DFE with the largest information entropy, which matches empirical DFEs well.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Ecology
Y. Costa, I Martins, G. C. Carvalho, F. Barros
Summary: This study used monitoring data, simulation, and species distribution models to predict the impacts of sea-level rise on estuaries. The results showed that climate change could result in local extinctions and new colonization of species. It is important for managers to use predictive tools to anticipate the effects of climate change on species migration.
ECOLOGICAL INFORMATICS
(2022)
Article
Microbiology
Catherine Kitrinos, Rachel B. Bell, Brenda J. Bradley, Jason M. Kamilar
Summary: This study examined the diversity and composition of nonhuman primate hair microbiome using samples from 12 NHP species. The findings suggest that hair microbial communities are affected by both evolutionary and environmental factors and are relatively similar across nonhuman primate body sites. The results have important implications for understanding the biology and conservation of primates and the uniqueness of the human microbiome.
Article
Developmental Biology
Jordi Garcia-Ojalvo, Aydan Bulut-Karslioglu
Summary: Organisms vary in tissue size and complexity to serve their specific purposes, and correct timing is crucial for tissue development. Premature or delayed differentiation can result in tissue imbalance or malformation. Despite apparent constraints, there is flexibility in timing and differentiation trajectories within and between species.
Article
Evolutionary Biology
Mark E. Olson
Summary: Regarding the comparative method as macroevolutionary is harmful because it hides the true causal content of hypotheses. Adaptation is a population-level phenomenon involving fitness differences.
SYSTEMATIC BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Liang Frank Shao
Summary: This study proposes a novel method to address multicollinearity in panel data by transforming data into quasi-cross-sectional data, ensuring robust estimates across different specifications and estimators. The findings do not support the Kuznets hypothesis within and across countries; investment is consistently identified as the most robust determinant of income inequality, challenging existing literature. Simulations based on the estimates show that the total marginal effects of development on income inequality are likely to be positive within and between countries, indicating potential complexities within income distribution dynamics.
Article
Ecology
Salvador Arenas-Castro, Adrian Regos, Ivone Martins, Joao Honrado, Joaquim Alonso
Summary: This study assessed the effects of using different data sources on SDM performance and found that eBird data outperformed Atlas data for less widespread species. Climate predictors yielded the best performance across different data sources, especially when combined with EFAs, and the predictor contribution was mainly driven by the species range across different datasets.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Plant Sciences
Silvia Del Vecchio, Shivam Kumar Sharma, Mario Pavan, Alicia Teresa Rosario Acosta, Gianluigi Bacchetta, Francesco de Bello, Maike Isermann, Richard Michalet, Gabriella Buffa
Summary: Variability in seed traits can be significant both within and among populations, and may be difficult to predict. Considering seed trait variability in the analysis of ecological processes may help elucidate patterns of species dynamics.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Psychology, Multidisciplinary
T. Franklin Waddell, Holly Overton, Robert McKeever
Summary: This study examined the consistency of theoretical tenets when using different online data collection services for testing mass communication theory. The results showed that the model parameters were mostly consistent with the IPI theory, regardless of the data source. The methodological implications are discussed.
COMPUTERS IN HUMAN BEHAVIOR
(2022)
Article
Biochemistry & Molecular Biology
Alexander Tyshkovskiy, Siming Ma, Anastasia Shindyapina, Stanislav Tikhonov, Sang-Goo Lee, Perinur Bozaykut, Jose P. Castro, Andrei Seluanov, Nicholas J. Schork, Vera Gorbunova, Sergey E. Dmitriev, Richard A. Miller, Vadim N. Gladyshev
Summary: By analyzing the RNA-seq data of 41 mammalian species, this study identifies longevity signatures and their relationship with aging biomarkers and lifespan-extending interventions. The study reveals shared and unique mechanisms of lifespan regulation within and across species, and provides insights into discovering longevity interventions. The findings suggest the downregulated Igf1 and upregulated mitochondrial translation genes as universal longevity mechanisms, and highlight the distinct regulation of innate immune response and cellular respiration.
Article
Ecology
Andrew Siefert, Daniel C. Laughlin
Summary: Functional traits influence individual demographic performance and ultimately drive population dynamics and community assembly. However, the net effects of traits on species fitness have been largely unknown due to the lack of a framework for estimating fitness across multiple species and environments. This study presents a modelling framework that integrates trait effects on demographic performance to estimate the net effect of traits on species fitness. The approach involves modelling trait effects on individual demographic rates and integrating these effects into a population model to project fitness as a function of traits and environment. By applying this approach to trees across a temperature gradient, the study demonstrates how functional traits interact with size and temperature to shape fitness landscapes. The results highlight the importance of understanding the selective forces driving community assembly and provide a basis for predicting population and community dynamics in changing environments.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Physics, Mathematical
Zeying Chen, Jan de Gier, Iori Hiki, Tomohiro Sasamoto, Masato Usui
Summary: This study examines current fluctuations in a two-species totally asymmetric exclusion process, known as the Arndt-Heinzel-Rittenberg model, and provides an explicit multiple integral expression for a certain joint current probability distribution. Through asymptotic analysis, it is shown that the joint current distribution is a product of a Gaussian and a GUE Tracy-Widom distribution in the long time limit, as predicted by non-linear fluctuating hydrodynamics.
COMMUNICATIONS IN MATHEMATICAL PHYSICS
(2022)
Article
Microbiology
Ryan M. Imrie, Sarah K. Walsh, Katherine E. Roberts, Joanne Lello, Ben Longdon
Summary: The presence of coinfecting pathogens can affect the susceptibility of a host to infection by suppressing and activating host immunity, and competing for host resources. In this study, we investigated the influence of coinfections on host susceptibility to two different Cripaviruses across different insect host genotypes and host species. We found that these two viruses interact during coinfections within the fruit fly Drosophila melanogaster, altering host susceptibility.
Article
Education & Educational Research
Mikko Huhtiniemi, Kasper Salin, Jukka Lahti, Arja Saakslahti, Asko Tolvanen, Anthony Watt, Timo Jaakkola
Summary: The study found that Grade 5 students had lower levels of enjoyment and cognitive processes in fitness testing classes compared to general PE, and higher levels of somatic anxiety. Similarly, Grade 8 students also had lower levels of enjoyment and cognitive processes, and higher levels of somatic anxiety and worry in fitness testing classes than in general PE. Grade 5 students generally had higher enjoyment levels and lower levels of cognitive processes, somatic anxiety, and worry compared to Grade 8 students in both general PE and fitness testing classes.
PHYSICAL EDUCATION AND SPORT PEDAGOGY
(2021)
Article
Ecology
Ana Filipa Moutinho, Thomas Bataillon, Julien Y. Dutheil
EVOLUTIONARY ECOLOGY
(2020)
Article
Genetics & Heredity
Matthew Hartfield, Thomas Bataillon
G3-GENES GENOMES GENETICS
(2020)
Article
Biochemistry & Molecular Biology
Aline Muyle, Helene Martin, Niklaus Zemp, Maeva Mollion, Sophie Gallina, Raquel Tavares, Alexandre Silva, Thomas Bataillon, Alex Widmer, Sylvain Glemin, Pascal Touzet, Gabriel A. B. Marais
Summary: The study utilized a population genomics approach to investigate the potential effects of dioecy in the Silene genus. Results showed that dioecy is associated with increased genetic diversity and higher selection efficacy against deleterious mutations and for beneficial mutations. These findings remained consistent after controlling for phylogenetic inertia, differences in species census population sizes, and geographic ranges. The conclusion drawn was that dioecious Silene species show no signs of increased mutational load or genetic evidence for extinction risk.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Jun Chen, Thomas Bataillon, Sylvain Glemin, Martin Lascoux
Summary: The distribution of fitness effects (DFE) is crucial in molecular evolution, but difficult to estimate. This study introduces a new measure based on SIFT scores, showing that SIFT scores can provide valuable information about the fitness effect of new mutations and help characterize beneficial mutations.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Maria Izabel A. Cavassim, Stig U. Andersen, Thomas Bataillon, Mikkel Heide Schierup
Summary: This study investigates how homologous recombination affects the rate of adaptive evolution in bacterial genomes, revealing a positive correlation between recombination rate and the fixed proportion of adaptive mutations. The higher recombination rate leads to an increased probability of fixation of advantageous variants and a decreased probability of fixation of deleterious variants, ultimately facilitating adaptive evolution in prokaryotic species.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Plant Sciences
Jun Chen, Thomas Bataillon, Sylvain Glemin, Martin Lascoux
Summary: Life history traits have a major impact on the distribution of fitness effects (DFE) of new mutations in plants, while the influence of demography within species appears to be more limited. Methods need to be developed to estimate the joint evolution of demography, life history traits, and the DFE.
Article
Evolutionary Biology
Elise A. Lucotte, Clara Albinana, Romain Laurent, Claude Bherer, Thomas Bataillon, Bruno Toupance
Summary: This study proposes a new framework to detect a signature of sexually antagonistic selection and identifies six candidate regions in human populations. These candidate regions are associated with embryonic development.
Article
Evolutionary Biology
Thomas Bataillon, Perrine Gauthier, Palle Villesen, Sylvain Santoni, John D. Thompson, Bodil K. Ehlers
Summary: This study examines the ecological genetics of chemotypes in Mediterranean wild thyme and reveals that the genetics of ecotype determination mediates evolutionary responses. The variation in three terpene-synthase loci explains the variation in ecotype identity, and different chemotypes within each ecotype display a wider range of genotypic redundancy that dilutes phenotypic selection. Understanding the precise genetics of chemical polymorphism in thyme is crucial for our understanding of polymorphism in aromatic plants.
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
Ecology
Thomas Bataillon, Thomas H. G. Ezard, Michael Kopp, Joanna Masel
Article
Ecology
Martin Guillemet, Helene Chabas, Antoine Nicot, Francois Gatchich, Enrique Ortega-Abboud, Cornelia Buus, Lotte Hindhede, Genevieve M. Rousseau, Thomas Bataillon, Sylvain Moineau, Sylvain Gandon
Summary: This experimental study demonstrates how coevolution between bacteria and phages, along with competition among bacterial genotypes, leads to increased diversity of bacterial CRISPR immunity. The negative-frequency-dependent selection generated by coevolution plays a crucial role in maintaining host resistance diversity and driving the emergence of new resistance mutations. Furthermore, the asymmetries in competitive abilities among different host genotypes contribute to the evolution of hosts, allowing even the fittest genotypes to escape extinctions through the acquisition of new CRISPR immunity.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Hong Gao, Tobias Hamp, Jeffrey Ede, Joshua G. Schraiber, Jeremy McRae, Moriel Singer-Berk, Yanshen Yang, Anastasia S. D. Dietrich, Petko P. Fiziev, Lukas F. K. Kuderna, Laksshman Sundaram, Yibing Wu, Aashish Adhikari, Yair Field, Chen Chen, Serafim Batzoglou, Francois Aguet, Gabrielle Lemire, Rebecca Reimers, Daniel Balick, Mareike C. Janiak, Martin Kuhlwilm, Joseph D. Orkin, Shivakumara Manu, Alejandro Valenzuela, Juraj Bergman, Marjolaine Rousselle, Felipe Ennes Silva, Lidia Agueda, Julie Blanc, Marta Gut, Dorien de Vries, Ian Goodhead, R. Alan Harris, Muthuswamy Raveendran, Axel Jensen, Idriss S. Chuma, Julie E. Horvath, Christina Hvilsom, David Juan, Peter Frandsen, Fabiano R. de Melo, Fabricio Bertuol, Hazel Byrne, Iracilda Sampaio, Izeni Farias, Joao Valsecchi do Amaral, Mariluce Messias, Maria N. F. da Silva, Mihir Trivedi, Rogerio Rossi, Tomas Hrbek, Nicole Andriaholinirina, Clement J. Rabarivola, Alphonse Zaramody, Clifford J. Jolly, Jane Phillips-Conroy, Gregory Wilkerson, Christian Abee, Joe H. Simmons, Eduardo Fernandez-Duque, Sree Kanthaswamy, Fekadu Shiferaw, Dongdong Wu, Long Zhou, Yong Shao, Guojie Zhang, Julius D. Keyyu, Sascha Knauf, Minh D. Le, Esther Lizano, Stefan Merker, Arcadi Navarro, Thomas Bataillon, Tilo Nadler, Chiea Chuen Khor, Jessica Lee, Patrick Tan, Weng Khong Lim, Andrew C. Kitchener, Dietmar Zinner, Ivo Gut, Amanda Melin, Katerina Guschanski, Mikkel Heide Schierup, Robin M. D. Beck, Govindhaswamy Umapathy, Christian Roos, Jean P. Boubli, Monkol Lek, Shamil Sunyaev, Anne O'Donnell-Luria, Heidi L. Rehm, Jinbo Xu, Jeffrey Rogers, Tomas Marques-Bonet, Kyle Kai-How Farh
Article
Multidisciplinary Sciences
Lukas F. K. Kuderna, Hong Gao, Mareike C. Janiak, Martin Kuhlwilm, Joseph D. Orkin, Thomas Bataillon, Shivakumara Manu, Alejandro Valenzuela, Juraj Bergman, Marjolaine Rousselle, Felipe Ennes Silva, Lidia Agueda, Julie Blanc, Marta Gut, Dorien de Vries, Ian Goodhead, R. Alan Harris, Muthuswamy Raveendran, Axel Jensen, Idrissa S. Chuma, Julie E. Horvath, Christina Hvilsom, David Juan, Peter Frandsen, Joshua G. Schraiber, Fabiano R. de Melo, Fabricio Bertuol, Hazel Byrne, Iracilda Sampaio, Izeni Farias, Joao Valsecchi, Malu Messias, Maria N. F. da Silva, Mihir Trivedi, Rogerio Rossi, Tomas Hrbek, Nicole Andriaholinirina, Clement J. Rabarivola, Alphonse Zaramody, Clifford J. Jolly, Jane Phillips-Conroy, Gregory Wilkerson, Christian Abee, Joe H. Simmons, Eduardo Fernandez-Duque, Sree Kanthaswamy, Fekadu Shiferaw, Dongdong Wu, Long Zhou, Yong Shao, Guoji Zhang, Julius D. Keyyu, Sascha Knauf, Minh D. Le, Esther Lizano, Stefan Merker, Arcadi Navarro, Tilo Nadler, Chiea Chuen Khor, Jessica Lee, Patrick Tan, Weng Khong Lim, Andrew C. Kitchener, Dietmar Zinner, Ivo Gut, Amanda D. Melin, Katerina Guschanski, Mikkel Heide Schierup, Robin M. D. Beck, Govindhaswamy Umapathy, Christian Roos, Jean P. Boubli, Jeffrey Rogers, Kyle Kai-How Farh, Tomas Marques Bonet
Summary: The rich diversity of morphology and behavior displayed across primate species provides valuable insights into the impact of genomic diversity on biological processes. This study analyzed high-coverage whole-genome data from 233 primate species, representing a significant portion of the primate diversity, to create a phylogeny and reassess evolutionary divergence times. The study found associations between genetic diversity, climate, and sociality, but not extinction risk, and identified recurring missense mutations previously thought to be specific to humans. This research has significant implications for future primate genomic studies.
Article
Biology
Bodil K. Ehlers, Thomas Bataillon, Christian F. Damgaard
Summary: Loss of habitat, eutrophication, and reduced grazing intensity are known drivers of landscape-level changes in plant species composition, but the consequences of the massive decline in insect abundance are still not fully understood. This study shows an ongoing decrease in insect-pollinated plant species, especially at sites with low grazing intensity, across different habitat types. In addition to changes in plant diversity driven by land-use intensification, the loss of pollinators may also play a role in reducing the richness of insect-pollinated plants.
