Article
Biochemistry & Molecular Biology
Christelle Fraiesse, Iva Popovic, Clement Mazoyer, Bruno Spataro, Stephane Delmotte, Jonathan Romiguier, Etienne Loire, Alexis Simon, Nicolas Galtier, Laurent Duret, Nicolas Bierne, Xavier Vekemans, Camille Roux
Summary: DILS is a deployable statistical analysis platform that conducts demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework, and is also accessible via a Web interface. Its hierarchical analysis method identifies different demographic and genomic models, and identifies loci associated with barriers to gene flow.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Ecology
Miguel A. Cruz, Sara Magalhaes, Elio Sucena, Flore Zele
Summary: The study found that host-associated incompatibility contributes 1.5 times more than Wolbachia-induced incompatibility in reducing hybrid production, and the two sources of incompatibility act through different mechanisms in an additive fashion. In addition, near-complete F1 hybrid sterility was observed between populations of the two forms, with no contribution from Wolbachia.
Article
Biology
Dusica Brisevac, Carolina M. Peralta, Tobias S. Kaiser
Summary: This study reveals the genetic basis for the reproductive timing difference in closely related species, which is controlled by a gene involved in both circadian and lunar timing. The genetic differentiation in reproductive timing is attributed to four quantitative trait loci on three different chromosomes, suggesting the involvement of complex structural variations.
Article
Marine & Freshwater Biology
Ivana Jezkova, Javier Montero-Pau, Raquel Ortells, Manuel Serra
Summary: Freshwater zooplankter Brachionus plicatilis is able to adapt to different habitats and shows a high degree of population structuring. This study investigates the evolution of reproductive isolation in populations with gene flow. The results show signs of incipient reproductive isolation in a third of the populations, but no correlation with environmental distance or genetic/geographic predictors. The overall inbreeding coefficient suggests decreasing within-population cross preferences over time.
Article
Zoology
Marketa Sasinkova, Ondrej Balvin, Jana Vandrovcova, Christian Massino, Alfons R. Weig, Klaus Reinhardt, Oliver Otti, Tomas Bartonicka
Summary: This study investigated the reproductive isolation mechanisms between bedbugs parasitizing humans and bats. The results showed that despite differences in sperm storage capability and egg-laying rates, there was no post-copulatory reproductive isolation between HL and BL lineages.
FRONTIERS IN ZOOLOGY
(2023)
Article
Plant Sciences
Inna Osmolovsky, Mariana Shifrin, Inbal Gamliel, Jonathan Belmaker, Yuval Sapir
Summary: The continuous process of speciation results in different species at different stages of reproductive isolation. Studying the royal irises, a young group of species in the process of speciation, provides insight into the early steps of speciation. Pre-pollination barriers, such as eco-geographic divergence and phenological differentiation, were found to be the major contributors to reproductive isolation among the Iris species. Post-pollination barriers had negligible contributions to reproductive isolation. The study suggests that pre-zygotic barriers play a crucial role in speciation.
Review
Plant Sciences
Ludi Wang, Dmitry A. Filatov
Summary: Hybridisation between different species can result in maladapted or nonviable offspring due to genetic incompatibilities. Mating with close relatives or self-fertilisation can lead to inbreeding depression. Therefore, organisms need to carefully choose their mating partners to avoid both of these problems. In plants, pollen-pistil interactions play a crucial role in avoiding inbreeding and hybridisation with other species. This review focuses on the mechanisms of pollen-pistil interactions and their importance in maintaining species integrity.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Hirzi Luqman, Alex Widmer, Simone Fior, Daniel Wegmann
Summary: Adaptive genetic variation is influenced by both selective and neutral forces, and accurate identification of adaptive loci requires consideration of demographic history. A new analytical framework, LSD, leverages demographic models to infer selection signatures through deviations in demographic parameters, providing insights into the environment in which selection acts and aiding in understanding selective processes underlying local adaptation. By implementing LSD and conducting simulations, it was demonstrated to have high power in identifying selected loci, outperforming traditional genome-scan methods under complex demographies, and accurately inferring the directionality of selection for identified candidates.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Ecology
Kyle Christie, Linnea S. Fraser, David B. Lowry
Summary: Speciation is driven by reproductive isolating barriers, with prezygotic barriers generally stronger than postzygotic ones. Ecological divergence and extrinsic factors play important roles in plant speciation and species boundary maintenance.
Article
Genetics & Heredity
Jeremy Guez, Guillaume Achaz, Francois Bienvenu, Jean Cury, Bruno Toupance, Evelyne Heyer, Flora Jay, Frederic Austerlitz
Summary: The impact of cultural transmission on reproductive success has been observed in various human and animal populations. It can lead to a positive correlation between the progeny size of parents and children. This study investigates the evolutionary effects of cultural transmission on genomic diversity, including changes in effective population size, distorted coalescent tree topologies, and nonhomogeneous branch length reduction. Long-lasting cultural transmission stabilizes effective population size but results in biased demographic inference based on site frequency spectra.
Article
Ecology
Satomi Tsuboko-Ishii, Ronald S. Burton
Summary: This study found the presence of precopulatory behavioral isolation in tidepool copepod species, indicating that interspecific differences in behavior during the mating process can lead to mating failure. These findings suggest that prezygotic behavioral factors play an important role in the isolation of copepod species.
Article
Plant Sciences
S. McCarren, S. D. Johnson, G. L. Theron, A. Coetzee, R. Turner, J. Midgley
Summary: Differences in floral traits might play a role in reproductive isolation between two Erica species in South Africa. The two sister species, Erica shannonea and Erica ampullacea, have overlapping flowering phenology but are pollinated by different species of flies due to differences in flower orientation. Both species require pollinator visits for seed production and are therefore potentially influenced by pollinators in flower evolution.
Article
Biochemistry & Molecular Biology
Kyle E. Jaynes, Edward A. Myers, Vaclav Gvozdik, David C. Blackburn, Daniel M. Portik, Eli Greenbaum, Gregory F. M. Jongsma, Mark-Oliver Rodel, Gabriel Badjedjea, Abraham Bamba-Kaya, Ninda L. Baptista, Jeannot B. Akuboy, Raffael Ernst, Marcel T. Kouete, Chifundera Kusamba, Franck M. Masudi, Patrick J. McLaughlin, Lotanna M. Nneji, Abiodun B. Onadeko, Johannes Penner, Pedro Vaz Pinto, Bryan L. Stuart, Elie Tobi, Ange-Ghislain Zassi-Boulou, Adam D. Leache, Matthew K. Fujita, Rayna C. Bell
Summary: Secondary sympatry amongst sister lineages is closely associated with genetic and ecological divergence, suggesting that closely related species require differences in ecological and/or reproductive isolation traits to coexist in secondary sympatry. In this study, three giant tree frog species showed species-level divergence coinciding with a period of large-scale forest fragmentation during the late Pliocene. Environmental niche models revealed that the three species occupy distinct environmental niches and display modest morphological differentiation, particularly in tympanum diameter and male advertisement call. Additionally, climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers have generated phylogeographic structure at the intraspecific level throughout the Pleistocene and Holocene.
Article
Ecology
Francesco Piccioni, Celine Casenave, Meili Baragatti, Bertrand Cloez, Brigitte Vincon-Leite
Summary: This study proposes an automated calibration method that combines Approximate Bayesian Computation, Random Forest, and Sensitivity Analysis for the complex hydro-ecological model Delft3D-BLOOM. The method is validated using real-time monitoring data and demonstrates its accuracy in calibrating the model.
ECOLOGICAL INFORMATICS
(2022)
Article
Ecology
Cody K. K. Porter, Craig W. W. Benkman
Summary: Theoretical models suggest that strong performance trade-offs coinciding with reproduction are most likely to lead to speciation, especially when gene flow is extensive. However, reproductive isolation weakens as resource availability increases relative to breeding demands.
AMERICAN NATURALIST
(2022)
Article
Plant Sciences
Guillaume Martin, Aurelien Cottin, Franc-Christophe Baurens, Karine Labadie, Catherine Hervouet, Frederic Salmon, Nilda Paulo-de-la-Reberdiere, Ines Van den Houwe, Julie Sardos, Jean-Marc Aury, Angelique D'Hont, Nabila Yahiaoui
Summary: The study found that different genetic pools of Musa species played an important role in banana domestication, including two contributors of unknown origin. By analyzing sequencing data of 226 Musaceae accessions, the genetic composition of many varieties, including diploid and triploid cultivated bananas, was identified. Some varieties had simple genetic mosaics composed of Musa acuminata subspecies banksii and zebrina, as well as the New Guinean species Musa schizocarpa. Furthermore, the study found that the genetic composition of many varieties was related to their geographical origin, revealing the process of banana cultivation and diversification in New Guinea and Southeast Asia.
Article
Multidisciplinary Sciences
Xuexue Liu, Andaine Seguin-Orlando, Lorelei Collin, Gaetan Tressieres, Stephanie Schiavinato, Laure Tonasso-Calviere, Jean-Marc Aury, Aude Perdereau, Stefanie Wagner, Pierre Clavel, Oscar Lepetz, Jianfei Pan, Yuehui Ma, Jacob Enk, Alison Devault, Jennifer Klunk, Sebastien Lepetz, Benoit Clavel, Lin Jiang, Patrick Wincker, Yvette Running Horse Collin, Clio Der Sarkissian, Ludovic Orlando
Summary: Age profiling of archaeological bone assemblages is challenging due to the incomplete fossil record and the lack of universal skeletal markers for age. This study explores the use of DNA methylation clocks to estimate the age-at-death of ancient individuals, using a clock based on 31,836 CpG sites and dental age markers in horses. Results show the potential for reliable age predictions and the assessment of castration practices in the past, providing insights into past animal management and ritual practices.
Article
Plant Sciences
Guillaume Martin, Franc-Christophe Baurens, Karine Labadie, Catherine Hervouet, Frederic Salmon, Franck Marius, Nilda Paulo-de-la-Reberdiere, Ines van den Houwe, Jean-Marc Aury, Angelique D'Hont, Nabila Yahiaoui
Summary: By analyzing SNP genotyping data from whole-genome sequencing of 178 banana individuals, including cultivars and wild bananas, this study revealed differences in parentage relationships and gamete contributions among diploid and triploid banana cultivars. It also identified ancestral pedigree relationships between different interspecific banana cultivars.
Article
Plant Sciences
Gregoire Le Provost, Celine Lalanne, Isabelle Lesur, Jean-Marc Louvet, Sylvain Delzon, Antoine Kremer, Karine Labadie, Jean-Marc Aury, Corinne Da Silva, Thomas Moritz, Christophe Plomion
Summary: This study investigates the gene expression network underlying dormancy regulation in natural populations of sessile oak along an elevation gradient in the Pyrenees Mountains. The results show that low- and high-altitude populations have evolved different molecular strategies to minimize frost damage and maximize growth period in response to temperature.
Article
Biochemistry & Molecular Biology
Jean-Francois Gout, Yue Hao, Parul Johri, Olivier Arnaiz, Thomas G. Doak, Simran Bhullar, Arnaud Couloux, Frederic Guerin, Sophie Malinsky, Alexey Potekhin, Natalia Sawka, Linda Sperling, Karine Labadie, Eric Meyer, Sandra Duharcourt, Michael Lynch
Summary: Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages, but the maintenance of WGD-derived paralogs is still debated. The analysis of 13 Paramecium species revealed that gene retention biases and strong selective pressures against post-WGD gene loss play a major role in maintaining duplicate genes. Paramecium is an exceptional model organism in evolutionary cell biology, and this dataset of 13 species sharing an ancestral WGD will be useful for future studies.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Stefanie Wagner, Andaine Seguin-Orlando, Jean-Charles Leple, Thibault Leroy, Celine Lalanne, Karine Labadie, Jean-Marc Aury, Sandy Poirier, Patrick Wincker, Christophe Plomion, Antoine Kremer, Ludovic Orlando
Summary: Whole genome characterizations based on ancient DNA have provided valuable insights into the evolutionary origins and adaptive processes of modern cultivars. However, there has been a lack of ancient genome sequences for trees, in contrast to the availability of multiple ancient reference genomes for important crops. This study generated the first ancient tree genomes, revealing the species composition and timing of leaf unfolding for ancient trees, and expanding the applications of ancient wood in enhancing our understanding of forest ecosystem responses to past changes.
Article
Multidisciplinary Sciences
William Timothy Treal Taylor, Pablo Librado, Mila Hunska Tasunke Icu, Carlton Shield Chief Gover, Jimmy Arterberry, Anpetu Luta Win, Akil Nujipi, Tanka Omniya, Mario Gonzalez, Bill Means, Sam High Crane, Mazasu, Barbara Dull Knife, Wakihyala Win, Cruz Tecumseh Collin, Chance Ward, Theresa A. Pasqual, Lorelei Chauvey, Laure Tonasso-Calviere, Stephanie Schiavinato, Andaine Seguin-Orlando, Antoine Fages, Naveed Khan, Clio Der Sarkissian, Xuexue Liu, Stefanie Wagner, Beth Ginondidoy Leonard, Bruce L. Manzano, Nancy O'Malley, Jennifer A. Leonard, Eloisa Bernaldez-Sanchez, Eric Barrey, Lea Charliquart, Emilie Robbe, Thibault Denoblet, Kristian Gregersen, Alisa O. Vershinina, Jaco Weinstock, Petra Rajit Sikanjic, Marjan Mashkour, Irina Shingiray, Jean-Marc Aury, Aude Perdereau, Saleh Alquraishi, Ahmed H. Alfarhan, Khaled A. S. Al-Rasheid, Tajana Trbojevit Vukicevit, Marcel Buric, Eberhard Sauer, Mary Lucas, Joan Brenner-Coltrain, John R. Bozell, Cassidee A. Thornhill, Victoria Monagle, Angela Perri, Cody Newton, W. Eugene Hall, Joshua L. Conver, Petrus Le Roux, Sasha G. Buckser, Caroline Gabe, Juan Bautista Belardi, Christina I. Barron-Ortiz, Isaac A. Hart, Christina Ryder, Matthew Sponheimer, Beth Shapiro, John Southon, Joss Hibbs, Charlotte Faulkner, Alan Outram, Laura Patterson Rosa, Katelyn Palermo, Marina Sole, Alice William, Wayne McCrory, Gabriella Lindgren, Samantha Brooks, Camille Eche, Cecile Donnadieu, Olivier Bouchez, Patrick Wincker, Gregory Hodgins, Sarah Trabert, Brandi Bethke, Patrick Roberts, Emily Lena Jones, Yvette Running Horse Collin, Ludovic Orlando
Summary: This article reveals the importance of horses in many Indigenous cultures across the American Southwest and the Great Plains, as well as how horses were integrated into Indigenous lifeways. The study shows that horses rapidly spread from the south into the northern Rockies and central plains by the first half of the 17th century CE, likely through Indigenous exchange networks. Horses were deeply integrated into Indigenous societies before the arrival of 18th-century European observers, as reflected in herd management, ceremonial practices, and culture.
Article
Multidisciplinary Sciences
Corentin Hochart, Lucas Paoli, Hans-Joachim Ruscheweyh, Guillem Salazar, Emilie Boissin, Sarah Romac, Julie Poulain, Guillaume Bourdin, Guillaume Iwankow, Clementine Moulin, Maren Ziegler, Barbara Porro, Eric J. Armstrong, Benjamin C. C. Hume, Jean-Marc Aury, Claudia Pogoreutz, David A. Paz-Garcia, Maggy M. Nugues, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Michel Flores, Didier Forcioli, Paola Furla, Eric Gilson, Fabien Lombard, Stephane Pesant, Stephanie Reynaud, Olivier P. Thomas, Romain Trouble, Patrick Wincker, Didier Zoccola, Denis Allemand, Serge Planes, Rebecca Vega Thurber, Christian R. Voolstra, Shinichi Sunagawa, Pierre E. Galand
Summary: This study investigates the ecology of Endozoicomonadaceae at an ocean basin-scale and reveals that different coral genera have distinct host-symbiont association strategies at the bacterial lineage level.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Alice Rouan, Melanie Pousse, Nadir Djerbi, Barbara Porro, Guillaume Bourdin, Quentin Carradec, Benjamin CC. Hume, Julie Poulain, Julie Le-Hoang, Eric Armstrong, Sylvain Agostini, Guillem Salazar, Hans-Joachim Ruscheweyh, Jean-Marc Aury, David A. Paz-Garcia, Ryan McMinds, Marie-Josephe Giraud-Panis, Romane Deshuraud, Alexandre Ottaviani, Lycia Die Morini, Camille Leone, Lia Wurzer, Jessica Tran, Didier Zoccola, Alexis Pey, Clementine Moulin, Emilie Boissin, Guillaume Iwankow, Sarah Romac, Colomban de Vargas, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Eric Douville, Michel Flores, Stephanie Reynaud, Olivier P. Thomas, Romain Trouble, Rebecca Vega Thurber, Serge Planes, Denis Allemand, Stephane Pesant, Pierre E. Galand, Patrick Wincker, Shinichi Sunagawa, Eric Rottinger, Paola Furla, Christian R. Voolstra, Didier Forcioli, Fabien Lombard, Eric Gilson
Summary: This study uses data from the Tara Pacific expedition to show that the history of water temperature is a key factor in the variation of coral telomere DNA length across the Pacific Ocean. Telomere lengths of short-lived, stress-sensitive Pocillopora colonies are more affected by seasonal temperature variations compared to long-lived and stress-resistant Porites colonies. Telomeres are sensitive to environmental factors, and this research reveals that water thermal regime plays a significant role in the regulation of telomere DNA length in different coral genera.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Eric J. Armstrong, Julie Le-Hoang, Quentin Carradec, Jean-Marc Aury, Benjamin Noel, Benjamin C. C. Hume, Christian R. Voolstra, Julie Poulain, Caroline Belser, David A. Paz-Garcia, Corinne Cruaud, Karine Labadie, Corinne Da Silva, Cle'mentine Moulin, Emilie Boissin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Michel Flores, Didier Forcioli, Paola Furla, Pierre E. Galand, Eric Gilson, Fabien Lombard, Stephane Pesant, Stephanie Reynaud, Matthew B. Sullivan, Shinichi Sunagawa, Olivier P. Thomas, Romain Trouble, Rebecca Vega Thurber, Didier Zoccola, Serge Planes, Denis Allemand, Patrick Wincker
Summary: Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This study used DNA and RNA analysis to investigate gene expression patterns in Pocillopora corals across a historical thermal gradient, revealing the importance of host-photosymbiont specificity and host transcriptomic plasticity in thermal acclimatization.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Caroline Belser, Julie Poulain, Karine Labadie, Frederick Gavory, Adriana Alberti, Julie Guy, Quentin Carradec, Corinne Cruaud, Corinne Da Silva, Stefan Engelen, Paul Mielle, Aude Perdereau, Gaelle R. Samson, Shahinaz E. Gas, Christian R. Voolstra, Pierre E. Galand, J. Michel Flores, Benjamin C. C. Hume, Gabriela Perna, Maren Ziegler, Hans-Joachim Ruscheweyh, Emilie Boissin, Sarah Romac, Guillaume A. Bourdin, Guillaume Iwankow, Clementine Moulin, David A. Paz Garcia, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Didier Forcioli, Paola Furla, Eric Gilson, Fabien Lombard, Stephane P. Pesant, Stephanie Reynaud, Shinichi Sunagawa, Olivier Thomas, Romain Trouble, Rebecca Vega Thurber, Didier H. Zoccola, Claude Scarpelli, E' Krame Jacoby, Pedro Oliveira, Jean-Marc Aury, Denis Allemand, Serge Planes, Patrick Wincker
Summary: Coral reef science aims to understand coral health and resilience to combat reef loss caused by environmental stress. The intricate symbiotic interactions within the coral holobiont play a vital role in coral resilience. The Tara Pacific project utilizes advanced sequencing technologies to study the biodiversity and complexity of coral holobionts across the Pacific Ocean, providing valuable insights for future investigations of coral reef dynamics and their future in the Anthropocene.
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.
Article
Multidisciplinary Sciences
Evelyn T. Todd, Aurore Fromentier, Richard Sutcliffe, Yvette Running Horse Collin, Aude Perdereau, Jean-Marc Aury, Camille Eche, Olivier Bouchez, Cecile Donnadieu, Patrick Wincker, Ted Kalbfleisch, Jessica L. Petersen, Ludovic Orlando
Summary: By studying the genomes of 430 horses, we identified over 8.7 million genomic variants, including newly sequenced genomes from Clydesdale and Shire horses. We used modern genomic variation to estimate the genomes of historically important horses and found increased genetic similarity and inbreeding in modern horses compared to the past. We also discovered previously unknown characteristics of these important historical horses by studying variants associated with appearance and behavior. Overall, our study provides insights into the history of Thoroughbred and Clydesdale breeds and highlights genomic changes in the endangered Przewalski's horse after a century of captive breeding.
Article
Biotechnology & Applied Microbiology
Benjamin Noel, France Denoeud, Alice Rouan, Carol Buitrago-Lopez, Laura Capasso, Julie Poulain, Emilie Boissin, Melanie Pousse, Corinne Da Silva, Arnaud Couloux, Eric Armstrong, Quentin Carradec, Corinne Cruaud, Karine Labadie, Julie Le-Hoang, Sylvie Tambutte, Valerie Barbe, Clementine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, J. Michel Flores, Didier Forcioli, Paola Furla, Pierre E. Galand, Fabien Lombard, Stephane Pesant, Stephanie Reynaud, Matthew B. Sullivan, Shinichi Sunagawa, Olivier P. Thomas, Romain Trouble, Rebecca Vega Thurber, Denis Allemand, Serge Planes, Eric Gilson, Didier Zoccola, Patrick Wincker, Christian R. Voolstra, Jean-Marc Aury
Summary: In the Tara Pacific expedition, we assembled two coral genomes, Porites lobata and Pocillopora cf. effusa, with greatly improved contiguity. We annotated their gene catalog and found a relatively high number of genes, 43,000 and 32,000, respectively. These duplicated genes are mainly related to the immune system and disease resistance, providing insights into the stress resilience of reef-building corals.