138 Works

Data from: Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant subfossil koala lemur Megaladapis edwardsi

Stephanie Marciniak, Mehreen R. Mughal, Laurie R. Godfrey, Richard J. Bankoff, Heritiana Randrianatoandro, Brooke E. Crowley, Christina M. Bergey, Kathleen M. Muldoon, Jeannot Randrianasy, Brigitte M. Raharivololona, Stephan C. Schuster, Ripan S. Malhi, Anne D. Yoder, , Logan Kistler & George H. Perry
No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal ‘subfossil’ remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ~160 kg), elephant birds (up to ~860 kg), and other extraordinary Malagasy megafauna that survived well into the past millennium. Yet much about the evolutionary biology of these now extinct species...

Global Diversification Dynamics Since the Jurassic: Low Dispersal and Habitat-Dependent Evolution Explain Hotspots of Diversity and Shell Disparity in River Snails (Viviparidae)

Björn Stelbrink, Romy Richter, Frank Köhler, Frank Riedel, Ellen Strong, Bert Van Bocxlaer, Christian Albrecht, Torsten Hauffe, Timothy Page, David Aldridge, Arthur Bogan, Li-Na Du, Marivene Manuel-Santos, Ristiyanti Marwoto, Alena Shirokaya & Thomas Von Rintelen
The Viviparidae, commonly known as River Snails, is a dominant group of freshwater snails with a nearly worldwide distribution that reaches its highest taxonomic and morphological diversity in Southeast Asia. The rich fossil record is indicative of a probable Middle Jurassic origin on the Laurasian supercontinent where the group started to diversify during the Cretaceous. However, it remains uncertain when and how the biodiversity hotspot in Southeast Asia was formed. Here, we used a comprehensive...

Supplementary datasets for: Prodigious polyphyly in Pleuroceridae (Gastropoda: Cerithioidea)

Nathan Whelan, Paul Johnson, Jeffrey Garner, Nicole Garrison & Ellen Strong
Phylogenomic studies with hundreds or thousands of loci are rare for most invertebrate groups, including freshwater gastropods. This can prevent understanding of phylogeny, which hinders many areas of research. Pleuroceridae is a family of freshwater snails that is highly imperiled and plays an essential role in the ecology of many freshwater systems of the eastern United States. However, the evolutionary history of the family is not understood, and the systematics of the family has not...

Data from: Post-copulatory sexual selection allows females to alleviate the fitness costs incurred when mating with senescing males

Pauline Vuarin, Alice Bouchard, Loïc Lesobre, Gwénaëlle Leveque, Toni Chalah, Michel Saint-Jalme, Frédéric Lacroix, Yves Hingrat & Gabriele Sorci
Male senescence has detrimental effects on reproductive success and offspring fitness. When females mate with multiple males during the same reproductive bout, post-copulatory sexual selection that operates either through sperm competition or cryptic female choice might allow females to skew fertilization success towards young males and as such limit the fitness costs incurred when eggs are fertilized by senescing males. Here, we experimentally tested this hypothesis. We artificially inseminated female North African houbara bustards with...

Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)

Robert Alexander Pyron, Kyle A. O'Connell, Emily Moriarty Lemmon, Alan R. Lemmon & David A. Beamer
Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (Desmognathus), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 “candidate species” presenting a complex history of...

Drosophila suzukii wing spot size is robust to developmental temperature

Ceferino Varón González, Antoine Fraimout & Vincent Debat
Phenotypic plasticity is an important mechanism allowing adaptation to new environments and as such it has been suggested to facilitate biological invasions. Under this assumption, invasive populations are predicted to exhibit stronger plastic responses than native populations. Drosophila suzukii is an invasive species whose males harbor a spot on the wing tip. In this study, by manipulating developmental temperature, we compare the phenotypic plasticity of wing spot size of two invasive populations with that of...

Mind the outgroup and bare branches in total-evidence dating: a case study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

Tamara Spasojevic, Ilari E. Sääksjärvi, Masato Ito, Stanislav Korenko, Seraina Klopfstein, Gavin R. Broad & Martin Schwarz
Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes,...

Repositories for taxonomic data: Where we are and what is missing

Aurélien Miralles, Teddy Bruy, Katherine Wolcott, Mark Scherz, Dominik Begerow, Bank Beszteri, Michael Bonkowski, Janine Felden, Birgit Gemeinholzer, Frank Glaw, Frank Oliver Glöckner, Oliver Hawlitschek, Ivaylo Kostadinov, Tim Nattkemper, Christian Printzen, Jasmin Renz, Nataliya Rybalka, Marc Stadler, Tanja Weibulat, Thomas Wilke, Susanne Renner & Miguel Vences
Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15–20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for...

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...

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...

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...

Underlying data for: Influence of temporally varying weatherability on CO2-climate coupling and ecosystem change in the late Paleozoic

Jon Richey, Isabel Montañez, Yves Goddéris, Cindy Looy, Neil Griffis & William DiMichele
This dataset contains the primary data used as input parameters in a mechanistic stomatal CO2 model (Franks et al., 2014 (Geophysical Research Letters)) and the Paleosol Barometer Uncertainty Quantifier (i.e., PBUQ; Breecker, 2013 (Geochemistry, Geophysics, Geosystems)), as well as age-adjusted CO2 data from Montañez et al., 2016 (Nature Geoscience). The stomatal parameters were measured by Richey et al., 2020 (Climate Of The Past) and the paleosol parameters are revised from Montañez et al., 2007 (Science)....

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...

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: 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: 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: 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: 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: 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...

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: 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: Reinvestigation of the type specimen of Ginkgophyllum grasseti Saporta 1875 using Reflectance Transforming Imaging

Anne-Laure Decombeix, Ignacio H. Escapa, Dario De Franceschi & Olivier Béthoux
Reflectance Transforming Imaging (RTI) produces photographs in which the angle of the light can be changed at will, allowing to investigate remotely minute details of the 3D structure of sub-planar objects. Here we apply this technique to the type specimen of Gingkophyllum grasseti, a vegetative shoot with putative ginkgophyte affinities from the early Permian of Lodève (France). Gingkophyllum grasseti, the type species of the corresponding genus, was originally described by Saporta in 1875 and has...

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