136 Works

Data from: Synchronized shift of oral, fecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction

Muriel Dietrich, Teresa Kearney, Ernest C.J. Seamark, Janusz T. Paweska & Wanda Markotter
Seasonal reproduction is a period of extreme physiological and behavioral changes, yet we know little about how it may affect host microbial communities (i.e. microbiota) and pathogen transmission. Here, we investigated shifts of the bacterial microbiota in saliva, urine and faeces during the seasonal reproduction of bats in South Africa, and test for an interaction in shedding patterns of both bacterial (Leptospira) and viral (adeno- and herpes-viruses) agents. Based on a comparative approach in two...

Data from: Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses

Jerome G. Prunier, Marc Colyn, Kim F. Nimon, Xavier Legendre & Marie Christine Flamand
Direct gradient analyses in spatial genetics provide unique opportunities to describe the inherent complexity of genetic variation in wildlife species and are the object of many methodological developments. However, multicollinearity among explanatory variables are a systemic issue in multivariate regression analyses and are likely to cause serious difficulties in properly interpreting results of direct gradient analyses, with the risk of erroneous conclusions, misdirected research and inefficient or counter-productive conservation measures. Using simulated datasets along with...

Data from: Low reproductive isolation and highly variable levels of gene flow reveal limited progress toward speciation between European river and brook lampreys

Quentin Rougemont, Arnaud Gaigher, Emilien Lasne, Jessica Côte, Maïra Coke, Anne-Laure Besnard, Sophie Launey & Guillaume Evanno
Ecologically based divergent selection is a factor that could drive reproductive isolation even in the presence of gene flow. Population pairs arrayed along a continuum of divergence provide a good opportunity to address this issue. Here we used a combination of mating trials, experimental crosses and population genetics analyses to investigate the evolution of reproductive isolation between two closely related species of lampreys with distinct life histories. We used microsatellite markers to genotype over 1000...

Data from: How the truffle got its mate: insights from genetic structure in spontaneous and planted Mediterranean populations of Tuber melanosporum

Elisa Taschen, François Rousset, Mathieu Sauve, Laure Benoit, Marie-Pierre Dubois, Franck Richard, Marc-André Selosse, M.-P. Dubois & M.-A. Selosse
The life cycles and dispersal of edible fungi are still poorly known, thus limiting our understanding of their evolution and domestication. The prized Tuber melanosporum produces fruitbodies (fleshy organs where meiospores mature) gathered in natural, spontaneously inoculated forests or harvested in plantations of nursery-inoculated trees. Yet, how fruitbodies are formed remains unclear, thus limiting yields, and how current domestication attempts affect population genetic structure is overlooked. Fruitbodies result from mating between two haploid individuals: the...

Data from: Are species’ responses to global change predicted by past niche evolution?

Sébastien Lavergne, Margaret E. K. Evans, Ian J. Burfield, Frederic Jiguet & Wilfried Thuiller
Predicting how and when adaptive evolution might rescue species from global change, and integrating this process into tools of biodiversity forecasting, has now become an urgent task. Here we explored whether recent population trends of species can be explained by their past rate of niche evolution, which can be inferred from increasingly available phylogenetic and niche data. We examined the assemblage of 409 European bird species for which estimates of demographic trends between 1970 and...

Data from: Rapid mobilization of abdominal fat in migrating eared grebes

Lorian Cobra Straker, & Joseph R. Jehl
Eared grebes Podiceps nigricollis, like shorebirds and other long-distance migrants, lay down large amounts of fat to power their journeys. To investigate the pattern of how fat and soft tissue might be mobilized, we used grebes killed in migration and applied computed tomography to reconstruct how stores in the chest, thorax, and abdomen were reduced as body weight decreased. Fat and soft tissue were each mobilized at a constant rate through the entire migration. Fat...

Data from: Testing for independence between evolutionary processes

Abdelkader Behdenna, Joël Pothier, Sophie S. Abby, Amaury Lambert & Guillaume Achaz
Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are...

Data from: High frequency echolocation, ear morphology, and the marine–freshwater transition: a comparative study of extant and extinct toothed whales

Carolina S. Gutstein, Constanza P. Figueroa-Bravo, Nicholas D. Pyenson, Roberto E. Yury-Yañez, Mario A. Cozzuol & Mauricio Canals
This study compares the bony ear morphology of freshwater and marine odontocetes (toothed whales). Odontocetes are unique among marine mammals in two important respects: 1) they use echolocation; 2) at least three lineages have independently evolved obligate freshwater habits from marine ancestries. Freshwater odontocetes include the so-called “river dolphins,” a paraphyletic group that each evolved convergent external morphological characters that distinguish them from oceanic dolphins (Delphinoidea). In addition to their convergent external morphology, “river dolphins”...

Data from: Does hunting or hiking affect wildlife communities in protected areas?

Roland Kays, Arielle W. Parsons, Megan C. Baker, Ellizabeth L. Kalies, Tavis Forrester, Robert Costello, Christopher T. Rota, Joshua J. Millspaugh & William J. McShea
Managed public wild areas have dual mandates to protect biodiversity and provide recreational opportunities for people. These goals could be at odds if recreation, ranging from hiking to legal hunting, disrupts wildlife enough to alter their space use or community structure. We evaluated the effect of managed hunting and recreation on 12 terrestrial wildlife species by employing a large citizen science camera trapping survey at 1947 sites stratified across different levels of human activities in...

Data from: Patterns of tree mortality in a temperate deciduous forest derived from a large forest dynamics plot

Erika B. Gonzalez-Akre, Victoria Meakem, Cheng-Yin Eng, Alan J. Tepley, Norman A. Bourg, William McShea, Stuart J. Davies, Kristina Anderson-Teixeira & Erika Gonzalez-Akre
Tree mortality is one of the most influential drivers of forest dynamics, and characterizing patterns of tree mortality is critical to understanding forest dynamics and ecosystem function in the present era of global change. Here, we use a unique data set of mortality in a temperate deciduous forest to characterize rates and drivers of mortality. At the 25.6-ha Center for Tropical Forest Science—Forest Global Earth Observatory forest dynamics plot at the Smithsonian Conservation Biology Institute...

Data from: Regression commonality analyses on hierarchical genetic distances.

Jérôme G. Prunier, Marc Colyn, Xavier Legendre & Marie-Christine Flamand
Landscape genetics is emerging as an important way of supporting decision-making in landscape management, in response to the deterioration of matrix permeability due to habitat loss and fragmentation. In line with unremitting methodological developments in landscape genetics, a new analytical procedure was recently proposed as a way of evaluating the effects of landscape gradients on genetic structures. This procedure is based on the computation of inter-individual hierarchical genetic distances (HGD), a metric of genetic differentiation...

Data from: Bat overpasses: an insufficient solution to restore habitat connectivity across roads

Fabien Claireau, Yves Bas, Sébastien J. Puechmaille, Jean-François Julien, Benjamin Allegrini & Christian Kerbiriou
1. Roads have many negative effects on wildlife, including their role in habitat fragmentation. Habitat fragmentation affects bats during their daily movements between roosts and foraging areas. As bats are protected in Europe, developers must implement specific mitigation measures that are hierarchically structured to achieve a null net impact. However, very few specific mitigation measures have been undertaken specifically for bats. Bat overpasses are among proposed improvements intended to reduce the impact of roads, but...

Data from: Geometric morphometrics of nested symmetries unravels hierarchical inter- and intra-individual variation in biological shapes

Yoland Savriama & Sylvain Gerber
Symmetry is a pervasive feature of organismal shape and the focus of a large body of research in Biology. Here, we consider complex patterns of symmetry where a phenotype exhibits a hierarchically structured combination of symmetries. We extend the Procrustes ANOVA for the analysis of nested symmetries and the decomposition of the overall morphological variation into components of symmetry (among-individual variation) and asymmetry (directional and fluctuating asymmetry). We illustrate its use with the Aristotle’s lantern,...

Data from: Megaphylogeny resolves global patterns of mushroom evolution

Torda Varga, Krisztina Krizsán, Csenge Földi, Bálint Dima, Marisol Sánchez-García, Santiago Sánchez-Ramírez, Gergely J. Szöllősi, János G. Szarkándi, Viktor Papp, László Albert, William Andreopoulos, Claudio Angelini, Vladimír Antonín, Kerrie W. Barry, Neale L. Bougher, Peter Buchanan, Bart Buyck, Viktória Bense, Pam Catcheside, Mansi Chovatia, Jerry Cooper, Wolfgang Dämon, Dennis Desjardin, Péter Finy, József Geml … & László G. Nagy
Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfill diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree...

Data from: Differential requirements for the RAD51 paralogs in genome repair and maintenance in human cells

Edwige B. Garcin, Stéphanie Gon, Meghan R. Sullivan, Gregory J. Brunette, Anne De Cian, Jean-Paul Concordet, Carine Giovannangeli, Wilhelm G. Dirks, Sonja Eberth, Kara A. Bernstein, Rohit Prakash, Maria Jasin & Mauro Modesti
Deficiency in several of the classical human RAD51 paralogs [RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3] is associated with cancer predisposition and Fanconi anemia. To investigate their functions, isogenic disruption mutants for each were generated in non-transformed MCF10A mammary epithelial cells and in transformed U2OS and HEK293 cells. In U2OS and HEK293 cells, viable ablated clones were readily isolated for each RAD51 paralog; in contrast, with the exception of RAD51B, RAD51 paralogs are cell-essential in MCF10A...

The mark of captivity: plastic responses in the ankle bone of a wild ungulate (Sus scrofa)

Thomas CUCCHI, Hugo Harbers, Dimitri Neaux, Katia Ortiz, Flavie Laurens, Isabelle Baly, Cécile Callou, Renate Schafberg, Ashleigh Haruda, François Lecompte, Jacqueline Studer, Sabrina Renaud, Yann Locatelli, Jean-Denis Vigne & Anthony Herrel
Deciphering the plastic (non-heritable) changes induced by human control over wild animals in the archaeological record is challenging. We hypothesized that changes in locomotor behaviour in a wild ungulate due to mobility control could be quantified in the bone anatomy. To test this, we experimented the effect of mobility reduction on the skeleton of wild boar (Sus scrofa), using the calcaneus shape as a possible phenotypic marker. We first assessed differences in shape variation and...

The only complete articulated early Miocene chameleon skull (Rusinga Island, Kenya) suggests an African origin for Madagascar’s endemic chameleons

Andrej Cernansky, Anthony Herrel, Job Kibii, Christopher Anderson, Renaud Boistel & Thomas Lehmann
We here present the first detailed study of the specimen KNM-RU 18340 from Rusinga Island (Kenya), the only known complete early Miocene chameleon skull, using micro-CT. This specimen represents one of the oldest chameleon fossils ever recovered. For the first time, the skull bone internal surfaces, their sutures, and elements contained inside the rocky matrix are observed. Our morphological comparisons and phylogenetic analyses place this specimen confidently in the genus Calumma and a new species,...

Interrogating discordance resolves relationships in the rapid radiation of Old World fruit bats (Chiroptera: Pteropodidae)

Nicolas Nesi, Stephen Rossiter, Michael McGowen, Georgia Tsagkogeorga, Burton Lim, Susan Tsang, Violaine Nicolas, Aude Lalis, Silke Riesle Sbarbaro, Sigit Wiantoro, Alan Hitch, Javier Juste, Corinna Pinzari, Frank Bonaccorso, Nancy Simmons, Annette Scanlon & Christopher Todd
The family Pteropodidae (Old World fruit bats) comprises >200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with >50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the...

Regional assemblages shaped by historical and contemporary factors: evidence from a species-rich insect group

Mengdi Hao, Qian Jin, Guanliang Meng, Caiqing Yang, Shenzhou Yang, Zhiyong Shi, Min Tang, Shanlin Liu, Yinan Li, Dan Zhang, Xu Su, Chungkun Shih, Yiran Sun, Xin Zhou & Ai-Bing Zhang
Understanding the complex diversity patterns is one of the main aims of community ecology. It is important to take both historical and contemporary factors into account in investigating the potential roles in assembling diversity patterns. Here, We compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State-Speciation and Extinction model to track the origins of these patterns. We subsequently estimate diversification...

Hybridization and transgressive exploration of colour pattern and wing morphology in Heliconius butterflies

Claire Mérot, Vincent Debat, Yann Le Poul, Richard M Merrill, Russell E Naisbit, Adélie Tholance, Chris Jiggins & Mathieu Joron
Hybridization can generate novel phenotypes distinct from those of parental lineages, a phenomenon known as transgressive trait variation. Transgressive phenotypes might negatively or positively affect hybrid fitness, and increase available variation. Closely related species of Heliconius butterflies regularly produce hybrids in nature and hybridization is thought to play a role in the diversification of novel wing colour patterns despite strong stabilizing selection due to interspecific mimicry. Here, we studied wing phenotypes in first and second...

Phenotypic divergence in two sibling species of shorebird: Common Snipe and Wilson's Snipe (Charadriiformes: Scolopacidae)

Tiago M Rodrigues, Edward Miller, Sergei V Drovetski, Robert M Zink, Jon Fjeldså & David Gonçalves
Natural selection and social selection are among the main shapers of biological diversity, but their relative importance in divergence remains understudied. Additionally, although neutral evolutionary processes may promote phenotypic divergence, their potential contribution in speciation is often overlooked in studies of comparative morphology. In this study, we investigated phenotypic differentiation in two allopatric shorebirds: the Palearctic Common Snipe Gallinago gallinago and the Nearctic Wilson’s Snipe G. delicata. Specimens of Common Snipe (n = 355 skins,...

Trait-dependency of trophic interactions in zooplankton food webs

Florian Vincent, Andrea Bertolo, Gérard Lacroix, Maud Mouchet & Eric Edeline
Anthropogenic change in the abundance or identity of dominant top predators may induce reorganizations in whole food webs. Predicting these reorganizations requires identifying the biological rules that govern trophic niches. However, we still lack a detailed understanding of the respective contributions of body size, behaviour (e.g., match between predator hunting mode and prey antipredator strategy), phylogeny and/or ontogeny in determining both the presence and strength of trophic interactions. Here, we address this question by measuring...

Tracking the Near East origins and European dispersal of the house mouse

Thomas CUCCHI, Katerina Papayianni, Sophie Cersoy, Laetitia Aznar-Cormano, Antoine Zazzo, Régis Debruyne, Rémi Berthon, Adrian Bălășescu, Alan Simmons, François Valla, Yannis Hamilakis, Fanis Mavridis, Marjan Mashkour, Jamshid Darvish, Roohollah Siahsarvi, Fereidoun Biglari, Cameron A. Petrie, Lloyd Weeks, Alireza Sardari, Sepideh Maziar, Christiane Denys, David Orton, Emma Jenkins, Melinda Zeder, Jeremy B. Searle … & Jean-Denis Vigne
The house mouse (Mus musculus) is one of the most invasive mammals and an evolutionary model. However, the timing and components of its origin and dispersal remain poorly documented. To track its synanthropisation and subsequent biological invasion during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, dating between 40,000 and 3,000 cal. BP, combining geometric morphometris numerical taxonomy with ancient mitochondrial DNA...

Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex)

Frank Burbrink, Marcelo Gehara, Alexander McKelvy & Edward Myers
Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the “gray zone” of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates of gene flow often ignore spatial information, for example when considering the location and width of hybrid zones with respect to changes...

Combined palaeohistological and isotopic inferences of thermometabolism in extinct Neosuchia, using Goniopholis and Dyrosaurus (Pseudosuchia: Crocodylomorpha) as case studies

Mathieu Faure-Brac, Romain Amiot, Christian De Muizon, Jorge Cubo & Christophe Lécuyer
The evolution of thermometabolism in pseudosuchians (Late Triassic to the present) remains a partly unsolved issue: extant taxa (crocodilians) are ectothermic, but the clade was inferred ancestrally endothermic. Here we inferred the thermometabolic regime of two neosuchian groups, Goniopholididae (Early Jurassic to Late Cretaceous) and Dyrosauridae (Middle Cretaceous to Late Eocene), close relatives of extant crocodilians, in order to elucidate the evolutionary pattern across Metasuchia (Early Jurassic to the present), a clade comprising Neosuchia (Early...

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