143 Works

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: 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: 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...

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...

Pontocaspian habitat polygon shapefiles from: Decline of unique Pontocaspian biodiversity in the Black Sea Basin: a review

Aleksandre Gogaladze, Mikhail Son, Matteo Lattuada, Vitaliy Anistratenko, Vitaly Syomin, Ana Bianca Pavel, Oana Popa, Luis Popa, Jan-Johan Ter Poorten, Jacobus Biesmeijer, Niels Raes, Thomas Wilke, Arthur Francis Sands, Teodora Trichkova, Zdravko Hubenov, Maxim Vinarski, Olga Anistratenko, Tatiana Alexenko & Frank Wesselingh
The unique aquatic Pontocaspian (PC) biota of the Black Sea Basin (BSB) is in decline. The lack of detailed knowledge on the status and trends of species, populations and communities hampers a thorough risk assessment and precludes effective conservation. This paper reviews PC biodiversity trends in the BSB ( Bulgaria, Romania, Moldova, Ukraine and Russia) using endemic molluscs as a model group. We aim to assess changes in PC habitats, community structure and species distribution...

Deep-time reticulation and ancient mitochondrial genome capture during the radiation of Jamaican Anolis lizards (Squamata; Iguanidae)

Edward Myers
Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean Anolis lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the...

Moorea Biocode

Neil Davies
The core goal of the Moorea Biocode Project (MBP) is to genetically barcode every non-microbial species on Moorea. We will thus create a professionally produced, verifiable (vouchered) All Taxa Biotic Inventory (ATBI) of Moorea (Output 1), together with the informatics services needed for ATBI and biocode-enabled research in Model Ecosystems (Outcome 2). We will also design a long-term plan (business model) to ensure the financial self-sustainability of biocode services, and carry out proof of concept...

Data from: Functional homogenization of flower visitor communities with urbanization

Nicolas Deguines, Romain Julliard, Mathieu De Flores & Colin Fontaine
Land-use intensification and resulting habitat loss are put forward as the main causes of flower visitor decline. However, the impact of urbanization, the prime driver of land-use intensification in Europe, is poorly studied. In particular, our understanding of whether and how it affects the composition and functioning of flower visitor assemblages is scant, yet required to cope with increasing urbanization worldwide. Here, we use a nation-wide dataset of plant-flower visitor (Coleoptera, Diptera, Hymenoptera, Lepidoptera) interactions...

Data from: Does habitat specialization shape the evolutionary potential of wild bird populations?

Ivain Martinossi-Allibert, Joanne Clavel, Simon Ducatez, I. Le Viol & Celine Teplitsky
Because specialist species evolved in more temporally and spatially homogeneous environments than generalist species, they are supposed to experience less fluctuating selection. For this reason, we expect specialists to show lower overall genetic variation as compared to generalists. We also expect populations from specialist species to be smaller and more fragmented, with lower neutral genetic diversity. We tested these hypotheses by investigating patterns of genetic diversity along a habitat specialization gradient in wild birds, based...

Data from: Two widespread green Neottia species (Orchidaceae) show mycorrhizal preference for Sebacinales in various habitats and ontogenetic stages

Tamara Těšitelová, Milan Kotilínek, Jana Jersáková, François-Xavier Joly, Jiří Košnar, Irina Tatarenko & Marc-André Selosse
Plant dependence on fungal carbon (mycoheterotrophy) evolved repeatedly. In orchids, it is connected with a mycorrhizal shift from rhizoctonia to ectomycorrhizal fungi and a high natural 13C and 15N abundance. Some green relatives of mycoheterotrophic species show identical trends, but most of these remain unstudied, blurring our understanding of evolution to mycoheterotrophy. We analyzed mycorrhizal associations and 13C and 15N biomass content in two green species, Neottia ovata and N. cordata (tribe Neottieae), from a...

Data from: Does recognized genetic management in supportive breeding prevent genetic changes in life-history traits?

Rémi Chargé, Gabriele Sorci, Michel Saint Jalme, Loïc Lesobre, Yves Hingrat, Frédéric Lacroix & Celine Teplitsky
Supportive breeding is one of the last resort conservation strategies to avoid species extinction. Management of captive populations is challenging because several harmful genetic processes need to be avoided. Several recommendations have been proposed to limit these deleterious effects, but empirical assessments of these strategies remain scarce. We investigated the outcome of a genetic management in a supportive breeding for the Houbara Bustard. At the phenotypic level, we found an increase over generations in the...

Data from: Barb geometry of asymmetrical feathers reveals a transitional morphology in the evolution of avian flight

Teresa J. Feo, Daniel J. Field & Richard O. Prum
The geometry of feather barbs (barb length and barb angle) determines feather vane asymmetry and vane rigidity, which are both critical to a feather's aerodynamic performance. Here, we describe the relationship between barb geometry and aerodynamic function across the evolutionary history of asymmetrical flight feathers, from Mesozoic taxa outside of modern avian diversity (Microraptor, Archaeopteryx, Sapeornis, Confuciusornis and the enantiornithine Eopengornis) to an extensive sample of modern birds. Contrary to previous assumptions, we find that...

Data from: Biotic predictors complement models of bat and bird responses to climate and tree diversity in European forests

Luc Barbaro, Eric Allan, Evy Ampoorter, Bastien Castagneyrol, Yohan Charbonnier, Hans De Wandeler, Christian Kerbiriou, Harriet Milligan, Aude Vialatte, Monique Carnol, Marc Deconchat, Pallieter De Smedt, Herve Jactel, Julia Koricheva, Isabelle Le Viol, Bart Muys, Michael Scherer-Lorenzen, Kris Verheyen & Fons Van Der Plas
Bats and birds are key providers of ecosystem services in forests. How climate and habitat jointly shape their communities is well studied, but whether biotic predictors from other trophic levels may improve bird and bat diversity models is less known, especially across large bioclimatic gradients. Here, we achieved multi-taxa surveys in 209 mature forests replicated in six European countries from Spain to Finland, to investigate the importance of biotic predictors (i.e., the abundance or activity...

Data from: The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates

Iker Irisarri, Diego San Mauro, Federico Abascal, Annemarie Ohler, Miguel Vences & Rafael Zardoya
BACKGROUND: Understanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that modern frogs (Neobatrachia) experienced an acceleration of mitochondrial gene substitution rates compared to non-neobatrachian relatives, no further characterization of this phenomenon was attempted. To gain new insights on this topic, we sequenced the complete mitochondrial genomes and nine nuclear loci of one pelobatoid (Pelodytes punctatus) and five neobatrachians,...

Data from: Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes

Matthias F. Geiger, Fabian Herder, Michael T. Monaghan, Vitor Almada, Roberta Barbieri, Michel Bariche, Patrick Berrebi, Jörg Bohlen, Miriam Casal-Lopez, Gaël P. J. Denys, Agnès Dettai, Ignacio Doadrio, Elena Kalogianni, Heiko Kärst, Maurice Kottelat, Marcelo Kovačić, Martin Laporte, Massimo Lorenzoni, Zoran Marčić, Müfit Özuluğ, Anabel Perdices, Silvia Perea, Henri Persat, Stefano Porcellotti, Cesare Puzzi … & G. B. Delmastro
Incomplete knowledge of biodiversity remains a stumbling block for conservation planning, and even occurs within globally important Biodiversity Hotspots. Although technical advances have boosted the power of molecular biodiversity assessments, the link between DNA sequences and species and the analytics to discriminate entities, remain crucial. Here, we present an analysis of the first DNA barcode library for the freshwater fish fauna of the Mediterranean Biodiversity Hotspot (526 spp.), with virtually complete species coverage (498 spp.,...

Data from: The survival-reproduction association becomes stronger when conditions are good

Alexandre Robert, Mark Bolton, Frédéric Jiguet & Joël Bried
Positive covariations between survival and reproductive performance (S-R covariation) are generally interpreted in the context of fixed or dynamic demographic heterogeneity (i.e., persistent differences between individuals, or dynamic variation in resource acquisition), but the processes underlying covariations are still unknown. We used multi-event modelling to investigate how environmental and individual features influence S-R covariation patterns in a long-lived seabird, the Monteiro’s storm-petrel (Oceanodroma monteiroi). Our analysis reveals that a strong positive association between individual breeding...

Data from: An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

Dahiana Arcila, R. Alexander Pyron, James C. Tyler, Guillermo Ortí & Ricardo Betancur-R.
Time-calibrated phylogenies based on molecular data provide a framework for comparative studies. Calibration methods to combine fossil information with molecular phylogenies are, however, under active development, often generating disagreement about the best way to incorporate paleontological data into these analyses. This study provides an empirical comparison of the most widely used approach based on node-dating priors for relaxed clocks implemented in the programs BEAST and MrBayes, with two recently proposed improvements: one using a new...

To hop or not to hop? the answer is in the bird trees

Pauline Provini & Elizabeth Höfling
Birds can use different types of gaits to move on the ground: they either walk, hop, or run. Although velocity can easily explain a preference for running, it remains unclear what drives a bird species to favour hopping over walking. As many hopping birds are relatively small and arboreal, we wanted to test the link between size, arboreality and hopping ability. First, we carried out ancestral character state reconstructions of size range, hopping ability and...

Modifications of the rainforest frugivore community are associated with reduced seed removal at the community level

Olivier Boissier
Tropical rainforests worldwide are under increasing pressure from human activities, which are altering key ecosystem processes such as plant-animal interactions. However, while the direct impact of anthropogenic disturbance on animal communities has been well studied, the consequences of such defaunation for mutualistic interactions such as seed dispersal remains chiefly understood at the plant species level. We asked whether communities of endozoochorous tree species had altered seed removal in forests affected by hunting and logging and...

Redescription of the cranial skeleton of the Early Devonian (Emsian) sarcopterygian Durialepis edentatus Otto, 2007 (Dipnomorpha; Porolepiformes)

Sam Giles, Jorge Mondéjar-Fernández & Matt Friedman
Porolepiforms represent a clade of Devonian stem lungfishes, divided into the cosmine-bearing and likely paraphyletic ‘Porolepidae’ (e.g., Porolepis, Heimenia) and the cosmine-free and stratigraphically younger Holoptychiidae (e.g., Holoptychius, Glyptolepis, Laccognathus). Data on the dermoskeleton are available for both groups, but are more limited for ‘porolepids’. Here we present new information on the ‘porolepid’ Durialepis edentatus from the Emsian (Early Devonian) of Germany based on micro-CT scanning. The material comprises an articulated skull of a single...

Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera

Hojun Song, Olivier Béthoux, Seunggwan Shin, Alexander Donath, Harald Letsch, Shanlin Liu, Duane D. McKenna, Guanliang Meng, Bernhard Misof, Lars Podsiadlowski, Xin Zhou, Benjamin Wipfler & Sabrina Simon
Acoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar singing insects, such as crickets, katydids, and grasshoppers. Using phylogenomic data, we firmly establish phylogenetic relationships among the major lineages and divergence time estimates within Orthoptera, as well as the lineage-specific...

Unravelling species co-occurrence in a steppe bird community of Inner Mongolia: insights for the conservation of the endangered Jankowski’s Bunting

Zheng Han, Lishi Zhang, Yunlei Jiang, Haitao Wang & Frédéric Jiguet
Aim: To evaluate the patterns of bird assemblage and distribution in an endangered grassland system, taking into accounts both environmental and biotic effects. To further focus on an endangered songbird and associated steppe birds. Location: Inner Mongolia, China Methods: We investigated the relative importance of abiotic and biotic factors driving the abundance and co-occurrence of steppe birds in Inner Mongolia by using joint species distribution models. We examined the general patterns of species assemblage, with...

Supplementary material to: Segmental series and size: clade-wide investigation of molar proportions reveals a major evolutionary allometry in the dentition of placental mammals

Guillaume Billet & Jérémie Bardin
Iterative segments such as teeth or limbs are a widespread characteristic of living organisms. While their proportions may be governed by similar developmental rules in vertebrates, there is no emerging pattern as regards their relation to size. Placental mammals span eight orders of magnitude in body size and show a wide spectrum of dietary habits associated with size and reflected in their dentitions, especially molars. Although variation in size constitutes an important determinant for variation...

Extensive photobiont sharing in a rapidly-radiating cyanolichen clade

Manuela Dal Forno & Robert Lücking
Recent studies have uncovered remarkable diversity Dictyonema s.lat. basidiolichens, here recognized as subtribe Dictyonemateae. This group includes five genera and 148 species, but hundreds more await description. The photobionts of these lichens belong to Rhizonema, a recently resurrected cyanobacterial genus known by a single species. To further investigate photobiont diversity within Dictyonemateae, we generated 765 new cyanobacterial sequences from 635 specimens collected from 18 countries. The ITS barcoding locus supported the recognition of 200 mycobiont...

Intraspecific variation and energy channel coupling within a Chilean kelp forest

Emma Elliott Smith, Chris Harrod, Felipe Docmac, Seth Newsome & Emma Elliott Smith
The widespread importance of variable types of primary production, or energy channels, to consumer communities has become increasingly apparent. However, the mechanisms underlying this ‘multichannel’ feeding remain poorly understood, especially for aquatic ecosystems that pose unique logistical constraints given the diversity of potential energy channels. Here, we use bulk tissue isotopic analysis along with carbon isotope (δ13C) analysis of individual amino acids to characterize the relative contribution of pelagic and benthic energy sources to a...

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