8 Works

Data from: Synonymous genetic variation in natural isolates of Escherichia coli does not predict where synonymous substitutions occur in a long-term experiment

Rohan Maddamsetti, Philip J. Hatcher, Stéphane Cruveiller, Claudine Médigue, Jeffrey E. Barrick & Richard E. Lenski
Synonymous genetic differences vary by more than 20-fold among genes in natural isolates of Escherichia coli. One hypothesis to explain this heterogeneity is that genes with high levels of synonymous variation mutate at higher rates than genes with low synonymous variation. If so, then one would expect to observe similar mutational patterns in evolution experiments. In fact, however, the pattern of synonymous substitutions in a long-term evolution experiment with E. coli does not support this...

Data from: Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs

Jonas Donner, Heidi Anderson, Stephen Davison, Angela M. Hughes, Julia Bouirmane, Johan Lindqvist, Katherine M. Lytle, Balasubramanian Ganesan, Claudia Ottka, Päivi Ruotanen, Maria Kaukonen, Oliver P. Forman, Neale Fretwell, Cynthia A. Cole & Hannes Lohi
Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding. Limited data on frequencies of genetic disease variants across breeds exists, and the disease heritage of mixed breed dogs remains poorly explored to date. Advances in genetic screening technologies now enable comprehensive investigations of the canine disease heritage, and generate health-related big data that can be turned into action. We pursued population screening of genetic...

Data from: Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli

Colin Raeside, Joël Gaffé, Daniel E. Deatherage, Olivier Tenaillon, Adam M. Briska, Ryan N. Ptashkin, Stéphane Cruveiller, Claudine Médigue, Richard E. Lenski, Jeffrey E. Barrick & Dominique Schneider
Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations. In a long-term evolution experiment, twelve Escherichia coli populations have been propagated in a glucose-limited environment for over 25 years. We used whole-genome mapping (optical mapping) combined with genome sequencing and PCR analysis to identify the large-scale chromosomal rearrangements in clones from each population after 40,000 generations. A total of 110 rearrangement...

Data from: Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

France Denoeud, Simon Henriet, Sutada Mungpakdee, Jean-Marc Aury, Corinne Da Silva, Henner Brinkmann, Jana Mikhaleva, Lisbeth C. Olsen, Claire Jubin, Cristian Cañestro, Jean-Marie Bouquet, Gemma Danks, Julie Poulain, Coen Campsteijn, Marcin Adamski, Ismael Cross, Fekadu Yadetie, Matthieu Muffato, Alexandra Louis, Stephen Butcher, Georgia Tsagkogeorga, Anke Konrad, Sarabdeep Singh, Marit F. Jensen, Evelyne Huynh Cong … & Daniel Chourrout
Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on...

Data from: The complex phylogeography of the Indo-Malayan Alophoixus bulbuls with the description of a putative new ring species complex

Jérôme Fuchs, Per G. P. Ericson, Céline Bonillo, Arnaud Couloux & Eric Pasquet
The Indo-Malayan bioregion has provided some of the most spectacular discoveries of new vertebrate species (e.g. saola, khanyou, bare-faced bulbul) over the last 25 years. Yet, very little is known about the processes that led to the current biodiversity in this region. We reconstructed the phylogeographic history of a group of closely related passerines, the Alophoixus bulbuls. These birds are continuously distributed in Indo-Malaya around the Thailand lowlands such that their distribution resembles a ring....

Data from: Large‐scale species delimitation method for hyperdiverse groups

Nicolas Puillandre, Maria Vittoria Modica, Y. Zhang, Lawrence Sirovich, Marie-Catherine Boisselier, Corinne Cruaud, Mandë Holford & Sarah Samadi
Accelerating the description of biodiversity is a major challenge as extinction rates increase. Integrative taxonomy combining molecular, morphological, ecological and geographical data is seen as the best route to reliably identify species. Classic molluscan taxonomic methodology proposes primary species hypotheses (PSHs) based on shell morphology. However, in hyperdiverse groups, such as the molluscan family Turridae, where most of the species remain unknown and for which homoplasy and plasticity of morphological characters is common, shell‐based PSHs...

Data from: Finding candidate genes under positive selection in non-model species: examples of genes involved in host specialization in pathogens

Gabriela Aguileta, Juliette Lengelle, Sylvain Marthey, Hélène Chiapello, François Rodolphe, Annie Gendrault, Roxana Yockteng, Elodie Vercken, Benjamin Devier, Michael Fontaine, Patrick Wincker, Carole Dossat, Corinne Cruaud, Arnaud Couloux & Tatiana Giraud
Numerous genes in diverse organisms have been shown to be under positive selection, especially genes involved in reproduction, adaptation to contrasting environments, hybrid inviability, and host-pathogen interactions. Looking for genes under positive selection in pathogens has been a priority in efforts to investigate coevolution dynamics and to develop vaccines or drugs. To elucidate the functions involved in host specialization, here we aimed at identifying candidate sequences that could have evolved under positive selection among closely...

Data from: The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Angelique D'Hont, France Denoeud, Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel, Stéphanie Bocs, Gaëtan Droc, Mathieu Rouard, Corinne Da Silva, Jabbari Kamel, Céline Cardi, Julie Poulain, Marlène Souquet, Karine Labadie, Cyril Jourda, Juliette Lengellé, Marguerite Rodier-Goud, Adriana Alberti, Maria Bernard, Margot Correa, Saravanaraj Ayyampalayam, Michael R. McKain, Jim Leebens-Mack … & Patrick Wincker
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid...

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