51 Works

Within-island diversification in a passerine bird

Maëva Gabrielli, Benoit Nabholz, Thibault Leroy, Borja Milá & Christophe Thébaud
The presence of congeneric taxa on the same island suggests the possibility of in situ divergence, but can also result from multiple colonizations of previously diverged lineages. Here, using genome-wide data from a large population sample, we test the hypothesis that intra-island divergence explains the occurrence of four geographic forms meeting at hybrid zones in the Reunion grey white-eye (Zosterops borbonicus), a species complex endemic to the small volcanic island of Reunion. Using population genomic...

The contribution of ancient admixture to reproductive isolation between European sea bass lineages

Maud Duranton, François Allal, Sophie Valière, Olivier Bouchez, François Bonhomme & Pierre-Alexandre Gagnaire
Understanding how new species arise through the progressive establishment of reproductive isolation barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in reproductive isolation frequently harbor anciently diverged haplotypes that predate the reconstructed history of species divergence. The possible origins of these old alleles remain much debated, as they relate to contrasting mechanisms of speciation that are not yet fully understood....

Data from: Titmice are a better indicator of bird density in Northern European than in Western European forests

Mira H. Kajanus, Jukka T. Forsman, Maximilian G. R. Vollstädt, Vincent Devictor, Merja Elo, Aleksi Lehikoinen, Mikko Mönkkönen, James T. Thorson & Sami M. Kivelä
Population sizes of many birds are declining alarmingly and methods for estimating fluctuations in species’ abundances at a large spatial scale are needed. The possibility to derive indicators from the tendency of specific species to co-occur with others has been overlooked. Here we tested whether the abundance of resident titmice can act as a general ecological indicator of forest bird density in European forests. Titmice species are easily identifiable and have a wide distribution, which...

Data from: XY females do better than the XX in the African pygmy mouse, Mus minutoides

Paul Alan Saunders, Julie Perez, Massilva Rahmoun, Ophelie Ronce, Pierre-André Crochet & Frédéric Veyrunes
All therian mammals have a similar XY/XX sex determination system except for a dozen species. The African pygmy mouse, Mus minutoides, harbors an unconventional system in which all males are XY, and there are three types of females: the usual XX but also XX* and X*Y ones (the asterisk designates a sex reversal mutation on the X chromosome). The long-term evolution of such a system is a paradox, since X*Y females are expected to face...

Data from: Population genomics shed light on the demographic and adaptive histories of European invasion in the Pacific oyster, Crassostrea gigas

Audrey Rohfritsch, Nicolas Bierne, Pierre Boudry, Serge Heurtebise, Florence Cornette & Sylvie Lapegue
Crassostrea gigas originated from the Pacific coast of Asia but was introduced into several European countries in the early 1970s. Natural populations have now spread the length of the western seaboard of Europe. To elucidate the demographic and selective processes at play during this rapid expansion, genome-scan analysis was performed on different populations. High diversities and low differentiation were observed overall, but significant genetic differentiation was found among newly-established populations and between the newly-established northern...

How to quantify factors degrading DNA in the environment and predict degradation for effective sampling design

Thomas Naef, Anne-Laure Besnard, Lisa Lehnen, Eric J. Petit, Jaap Van Schaik & Sebastien J. Puechmaille
Extra-organismal DNA (eoDNA) from material left behind by organisms (non-invasive DNA: e.g., faeces, hair) or from environmental samples (eDNA: e.g., water, soil) is a valuable source of genetic information. However, the relatively low quality and quantity of eoDNA, which can be further degraded by environmental factors, results in reduced amplification and sequencing success. This is often compensated for through cost- and time-intensive replications of genotyping/sequencing procedures. Therefore, system- and site-specific quantifications of environmental degradation are...

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Loïc Chalmandrier, Johan Pansu, Lucie Zinger, Frederic Boyer, Eric Coissac, Alexandre Génin, Ludovic Gielly, Sébastien Lavergne, Nicolas Legay, Vincent Schilling, Pierre Taberlet, Tamara Münkemüller & Wilfried Thuiller
Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β-diversity) along ecological gradients. Here, we characterize soil microbial β-diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within...

Data from: An annotated draft genome of the mountain hare (Lepus timidus)

João Pedro Marques, Fernando A. Seixas, Jeffrey M. Good, Liliana Farelo, Colin M. Callahan, W. Ian Montgomery, Neil Reid, Paulo C. Alves, Pierre Boursot & José Melo-Ferreira
Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Oryctolagus cuniculus) reference genome. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus), and evaluate the efficacy of whole-genome re-sequencing analyses using the new reference versus using the rabbit reference genome. The genome...

Evolutionary determinants of non-seasonal breeding in wild chacma baboons

Jules Dezeure, Lugdiwine Burtschell, Alice Baniel, Alecia J. Carter, Bernard Godelle, Cowlishaw Guy & Huchard Elise
Animal reproductive phenology varies from strongly seasonal to non-seasonal, sometimes among closely related or sympatric species. While the extent of reproductive seasonality is often attributed to environmental seasonality, this fails to explain many cases of non-seasonal breeding in seasonal environments. We investigated the evolutionary determinants of non-seasonal breeding in a wild primate, the chacma baboon (Papio ursinus), living in a seasonal environment with high climatic unpredictability. We tested three hypotheses proposing that non-seasonal breeding has...

Data and code from: Multiple sex chromosome drivers in a mammal with three sex chromosomes

Paul Saunders, Julie Perez, Ophélie Ronce & Frédéric Veyrunes
Eukaryotes with separate males and females display a great diversity in the way they determine sex, but it is still unclear what evolutionary forces cause transitions between sex-determining systems. Rather that the lack of hypotheses, the problem is the scarcity of adequate biological systems to test them. Here, we take advantage of the recent evolution of a feminizing X chromosome (called X*) in the African pygmy mouse Mus minutoides, to investigate one of the evolutionary...

Genotype, spatial and morphological data of adults and progeny in a natural population of Leucadendron rubrum

Jeanne Tonnabel, Etienne K. Klein, Ophélie Ronce, Sylvie Oddou-Muratorio, François Rousset, Isabelle Olivieri, Alexandre Courtiol & Agnès Mignot
We provide a dataset containing data on both female and male plants measured in a natural population of Leucadendron rubrum about plant architecture, and leaf morphology, thus informing about sexual dimorphism in this species. Genotypes of these males and females on eight microsatellites combined with corresponding genotype data in their progeny permits to undertake parentage analyses. Finally, the spatial distribution of both parents and juveniles allows to account for potential spatial biases in sampling juveniles...

Data from: Late Oligocene caviomorph rodents from Contamana, Peruvian Amazonia

Myriam Boivin, Laurent Marivaux, Adriana M. Candela, Maëva J. Orliac, François Pujos, Rodolfo Salas-Gismondi, Julia V. Tejada-Lara & Pierre-Olivier Antoine
The Deseadan South American Land Mammal Age (late Early Oligocene – Late Oligocene) attests to a time of great diversification in the caviomorph rodent fossil record. Nevertheless, Deseadan rodent-bearing localities in Neotropical lowlands are few and poorly known. Here we describe the rodent assemblages from two Late Oligocene localities, near Contamana, Loreto, Peru. Seven taxa are new to science: Palaeosteiromys amazonensis gen. et sp. nov., Plesiosteiromys newelli gen. et sp. nov., Loretomys minutus gen. et...

Data from: Forest Giants on Different Evolutionary Branches: Ecomorphological Convergence in Helicopter Damselflies

Emmanuel F. A. Toussaint, Seth M. Bybee, Robert J. Erickson & Fabien L. Condamine
The convergent evolution of analogous features is an evolutionary process occurring independently across the tree of life. From the evolution of echolocation, prehensile tail, viviparity or winged flight, environmental factors often drive this astonishing phenomenon. However, convergent evolution is not always conspicuous or easily identified. Giant damselflies count among the largest flying insects on Earth, and have astonishing ecologies including orb-web spider plucking and oviposition in phytotelmata. One species occurs in the Afrotropics and 18...

Data from: Patterns and evolution of nucleotide landscapes in seed plants

Laurana Serres-Giardi, Khalid Belkhir, Jacques David & Sylvain Glémin
Nucleotide landscapes, which is the way base composition is distributed along a genome, strongly vary among species. The underlying causes of these variations have been much debated. Though mutational bias and selection were initially invoked, GC-biased gene conversion (gBGC), a recombination-associated process favoring the G and C over A and T bases, is increasingly recognized as a major factor. As opposed to vertebrates, evolution of GC content is less well known in plants. Most studies...

Data from: Convergent and correlated evolution of major life-history traits in the angiosperm genus Leucadendron (Proteaceae)

Jeanne Tonnabel, Agnès Mignot, Emmanuel J. P. Douzery, Anthony G. Rebelo, Frank M. Schurr, Jeremy Midgley, Nicola Illing, Fabienne Justy, Denis Orcel & Isabelle Olivieri
Natural selection is expected to cause convergence of life histories among taxa as well as correlated evolution of different life-history traits. Here, we quantify the extent of convergence of five key life-history traits (adult fire survival, seed storage, degree of sexual dimorphism, pollination mode, and seed-dispersal mode) and test hypotheses about their correlated evolution in the genus Leucadendron (Proteaceae) from the fire-prone South African fynbos. We reconstructed a new molecular phylogeny of this highly diverse...

Mandrill mothers associate with infants who look like their own offspring using phenotype matching

Marie Charpentier, Clémence Poirotte, Berta Roura-Torres, Paul Amblard-Rambert, Eric Willaume, Peter Kappeler, François Rousset & Julien Renoult
Behavioral discrimination of kin is a key process structuring social relationships in animals. In this study, we provide a first example of discrimination towards non-kin by third-parties through a mechanism of phenotype matching. In mandrills, we recently demonstrated increased facial resemblance among paternally-related juvenile and adult females indicating adaptive opportunities for paternal kin recognition. Here, we hypothesize that mothers use offspring’s facial resemblance with other infants to guide offspring’s social opportunities towards similarly-looking ones. Using...

Data from: Network structure and local adaptation in coevolving bacteria-phage interactions

James Gurney, Lafi Aldakak, Alex Betts, Claire Gougat-Barbera, Timothée Poisot, Oliver Kaltz & Michael E. Hochberg
Numerous theoretical and experimental studies have investigated antagonistic coevolution between parasites and their hosts. Although experimental tests of theory from a range of biological systems are largely concordant regarding the influence of several driving processes, we know little as to how mechanisms acting at the smallest scales (individual molecular and phenotypic changes) may result in the emergence of structures at larger scales, such as coevolutionary dynamics and local adaptation. We capitalized on methods commonly employed...

Data from: Metapopulation patterns of additive and nonadditive genetic variance in the sea bass (Dicentrarchus labrax)

Bruno Guinand, Marc Vandeputte, Mathilde Dupont-Nivet, Alain Vergnet, Pierrick Haffray, Hervé Chavanne & Béatrice Chatain
Describing and explaining the geographic within-species variation in phenotypes (“phenogeography”) in the sea over a species distribution range is central to our understanding of a variety of eco-evolutionary topics. However, phenogeographic studies that have a large potential to investigate adaptive variation are overcome by phylogeographic studies, still mainly focusing on neutral markers. How genotypic and phenotypic data could covary over large geographic scales remains poorly understood in marine species. We crossed 75 noninbred sires (five...

Data from: Women's attractiveness is linked to expected age at menopause

Jeanne Bovet, Melissa Barkat-Defradas, Valérie Durand, Charlotte Faurie & Michel Raymond
A great number of studies have shown that features linked to immediate fertility explain a large part of the variance in female attractiveness. This is consistent with an evolutionary perspective, as men are expected to prefer females at the age at which fertility peaks (at least for short-term relationships) in order to increase their reproductive success. However, for long-term relationships, a high residual reproductive value (the expected future reproductive output, linked to age at menopause)...

Data from: The inbreeding strategy of a solitary primate, Microcebus murinus

Elise Huchard, Susanne Schliehe-Diecks, Peter M. Kappeler & Cornelia Kraus
Inbreeding depression may be common in nature, reflecting either the failure of inbreeding avoidance strategies or inbreeding tolerance when avoidance is costly. The combined assessment of inbreeding risk, avoidance and depression is therefore fundamental to evaluate the inbreeding strategy of a population, that is how individuals respond to the risk of inbreeding. Here, we use the demographic and genetic monitoring of 10 generations of wild grey mouse lemurs (Microcebus murinus), small primates from Madagascar with...

Data from: Differing climatic mechanisms control transient and accumulated vegetation novelty in Europe and eastern North America

Kevin Burke, John Williams, Simon Brewer, Walter Finsinger, Thomas Giesecke, David Lorenz & Alejandro Ordonez
Understanding the mechanisms that produce novel ecosystems is of joint interest to conservation biologists and paleoecologists. Here, we define and differentiate transient from accumulated novelty and evaluate four climatic mechanisms proposed to cause species to reshuffle into novel assemblages: high climatic novelty, high spatial rates of change (displacement), high variance among displacement rates for individual climate variables, and divergence among displacement vector bearings. We use climate simulations to quantify climate novelty, displacement, and divergence across...

Unconditional care from close maternal kin in the face of parasites

Clémence Poirotte & Marie Charpentier
Several species mitigate relationships according to their conspecifics’ parasite status. Yet, such strategy of defense comes with costs of depriving individuals from valuable social bonds. Animals therefore face a trade-off between costs of pathogen exposure and benefits of social relationships. According to models of social evolution, social bonds are highly kin-biased. However, whether kinship mitigates social avoidance of contagious individuals has never been tested so far. Here, we build on previous research to demonstrate that...

Evolution in interacting species alters predator life history traits, behavior and morphology in experimental microbial communities

Johannes Cairns, Felix Moerman, Emanuel Fronhofer, Florian Altermatt & Teppo Hiltunen
Predator-prey interactions are key for the dynamics of many ecosystems. An increasing body of evidence suggests that rapid evolution and co-evolution can alter these interactions, with important ecological implications, by acting on traits determining fitness, including reproduction, anti-predatory defense and foraging efficiency. However, most studies to date have focused only on evolution in the prey species, and the predator traits in (co-)evolving systems remain poorly understood. Here we investigated changes in predator traits after ~600...

Phylogenomic and macroevolutionary evidence for an explosive radiation of a plant genus in the Miocene

Hanghui Kong, Fabien L. Condamine, Lihua Yang, AJ Harris, Chao Feng, Fang Wen & Ming Kang
Mountain systems harbor a substantial fraction of global biodiversity and, thus, provide excellent opportunities to study rapid diversification and to understand the historical processes underlying the assembly of biodiversity hotspots. The rich biodiversity in mountains is widely regarded as having arisen under the influence of geological and climatic processes as well as the complex interactions among them. However, the relative contribution of geology and climate in driving species radiation is seldom explored. Here, we studied...

Supporting data for: Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition

Romain Weppe, Maeva Orliac, Guillaume Guinot & Fabien Condamine
The Eocene-Oligocene transition (EOT) represents a period of global environmental changes particularly marked in Europe and coincides with a dramatic biotic turnover. Here, using an exceptional fossil preservation, we document and analyse the diversity dynamics of a mammal clade, Cainotherioidea (Artiodactyla), that survived the EOT and radiated rapidly immediately after. We infer their diversification history from Quercy Konzentrat-Lagerstätte (South-West France) at the species level using Bayesian birth-death models. We show that cainotherioid diversity fluctuated through...

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