136 Works

Data from: Genetic variation and population structure in the endangered Hermann’s tortoise: the roles of geography and human-mediated processes

Melanie Perez, Barbara Livoreil, Sara Mantovani, Marie-Catherine Boisselier, Barbara Crestanello, Jawad Abdelkrim, Céline Bonillo, Vassilis Goutner, Josie Lambourdière, Massimo Pierpaoli, Bogoljub Sterijovski, Ljiljana Tomovic, Sibelle Vilaca, Stefano Mazzotti & Giorgio Bertorelle
The Hermanni’s tortoise (Testudo hermanni) is an endangered land tortoise distributed in disjoint populations across Mediterranean Europe. We investigated its genetic variation by typing one mitochondrial locus and nine nuclear microsatellites in approximately 300 individuals from 22 localities. Our goal was to understand the relative impact of natural and human-mediated processes in shaping the genetic structure, and to identify the genetic priorities for the conservation of this species. We found that i) all geographic areas...

Data from: IKey+: a new single-access key generation web service

Thomas Burguiere, Florian Causse, Visotheary Ung & Régine Vignes-Lebbe
Single-access keys are a major tool for biologists who need to identify specimens. The construction process of these keys is particularly complex (especially if the input dataset is large) so having an automatic single-access key generation tool is essential. As part of the European project ViBRANT, our aim was to develop such a tool as a web service, thus allowing end-users to integrate it directly into their workflow. IKey+generates single-access keys on demand, for single...

Data from: A combined field survey and molecular identification protocol for comparing forest arthropod biodiversity across spatial scales

Brent C. Emerson, Juliane Casquet, Heriberto López, Pedro Cardoso, Paulo A. V. Borges, Noémy Mollaret, Pedro Oromí, Dominique Strasberg & Christophe Thébaud
Obtaining fundamental biodiversity metrics such as alpha, beta and gamma diversity for arthropods is often complicated by a lack of prior taxonomic information and/or taxonomic expertise, which can result in unreliable morphologically based estimates. We provide a set of standardized ecological and molecular sampling protocols that can be employed by researchers whose taxonomic skills may be limited, and where there may be a lack of robust a priori information regarding the regional pool of species....

Data from: Time-calibrated molecular phylogeny of pteropods

Alice K. Burridge, Christine Hörnlein, Arie W. Janssen, Martin Hughes, Stephanie L. Bush, Ferdinand Marlétaz, Rebeca Gasca, Annelies C. Pierrot-Bults, Ellinor Michel, Jonathan A. Todd, Jeremy R. Young, Karen J. Osborn, Steph B.J. Menken, Katja T.C.A. Peijnenburg, Katja T. C. A. Peijnenburg & Steph B. J. Menken
Pteropods are a widespread group of holoplanktonic gastropod molluscs and are uniquely suitable for study of long-term evolutionary processes in the open ocean because they are the only living metazoan plankton with a good fossil record. Pteropods have been proposed as bioindicators to monitor the impacts of ocean acidification and in consequence have attracted considerable research interest, however, a robust evolutionary framework for the group is still lacking. Here we reconstruct their phylogenetic relationships and...

Data from: Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets

Mary E. Prendergast, Michael Buckley, Alison Crowther, Heidi Eager, Laurent Frantz, Ophélie Lebrasseur, Rainer Hutterer, Ardern Hulme-Beaman, Wim Van Neer, Katerina Douka, Margaret-Ashley Veall, Eréndira M. Quintana Morales, Verena J. Schuenemann, Ella Reiter, Richard Allen, Evangelos A. Dimopoulos, Richard M. Helm, Ceri Shipton, Ogeto Mwebi, Christiane Denys, Mark C. Horton, Stephanie Wynne-Jones, Jeffrey Fleisher, Chantal Radimilahy, Henry Wright … & Mark Horton
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological...

Data from: Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: evidence from DNA metabarcoding

Ostaizka Aizpurua, Ivana Budinski, Panagiotis Georgiakakis, Shyam Gopalakrishnan, Carlos Ibáñez, Vanessa Mata, Hugo Rebelo, Danilo Russo, Farkas Szodoray-Parádi, Violeta Zhelyazkova, Vida Zrncic, M. Thomas P. Gilbert & Antton Alberdi
The interaction between agricultural production and wildlife can shape, and even condition, the functioning of both systems. In this study we i) explored the degree to which a widespread European bat, namely the common bent-wing bat Miniopterus schreibersii, consumes crop-damaging insects at a continental scale, and ii) tested whether its dietary niche is shaped by the extension and type of agricultural fields. We employed a dual-primer DNA metabarcoding approach to characterise arthropod 16S and COI...

Data from: Habitat diversity associated with island size and environmental filtering control the species richness of rock-savanna plants in neotropical inselbergs

Ludovic Henneron, Corinne Sarthou, Jean-Christophe De Massary & Jean-François Ponge
Disentangling the multiple factors controlling species diversity is a major challenge in ecology. Island biogeography and environmental filtering are two influential theories emphasizing respectively island size and isolation, and the abiotic environment, as key drivers of species richness. However, few attempts have been made to quantify their relative importance and investigate their mechanistic basis. Here, we applied structural equation modelling, a powerful method allowing test of complex hypotheses involving multiple and indirect effects, on an...

FragSAD: A database of diversity and species abundance distributions from habitat fragments

Jonathan M. Chase, Mario Liebergesell, Alban Sagouis, Felix May, Shane A. Blowes, Åke Berg, Enrico Bernard, Berry J. Brosi, Marc W. Cadotte, Luis Cayuela, Adriano G. Chiarello, Jean-François Cosson, Will Cresswell, Filibus Danjuma Dami, Jens Dauber, Christopher R. Dickman, Raphael K. Didham, David P. Edwards, Fabio Z. Farneda, Yoni Gavish, Thiago Gonçalves-Souza, Demetrio Luis Guadagnin, Mickaël Henry, Adrià López-Baucells, Heike Kappes … & Yaron Ziv
Habitat destruction is the single greatest anthropogenic threat to biodiversity. Decades of research on this issue have led to the accumulation of hundreds of data sets comparing species assemblages in larger, intact, habitats to smaller, more fragmented, habitats. Despite this, little synthesis or consensus has been achieved, primarily because of non‐standardized sampling methodology and analyses of notoriously scale‐dependent response variables (i.e., species richness). To be able to compare and contrast the results of habitat fragmentation...

Data from: Evolution of wing shape in hornets: why is the wing venation efficient for species identification?

Adrien Perrard, Michel Baylac, James M. Carpenter & Claire Villemant
Wing venation has long been used for insect identification. Lately, the characterization of venation shape using geometric morphometrics has further improved the potential of using the wing for insect identification. However, external factors inducing variation in wing shape could obscure specific differences, preventing accurate discrimination of species in heterogeneous samples. Here, we show that interspecific difference is the main source of wing shape variation within social wasps. We found that a naive clustering of wing...

Data from: Commensal associations and benthic habitats shape macroevolution of the bivalve clade Galeommatoidea

Jingchun Li, Diarmaid Ó Foighil & Ellen E. Strong
The great diversity of marine life has been shaped by the interplay between abiotic and biotic factors. Among different biotic interactions, symbiosis is an important yet less studied phenomenon. Here, we tested how symbiotic associations affected marine diversification, using the bivalve superfamily Galeommatoidea as a study system. This superfamily contains large numbers of obligate commensal as well as free-living species and is therefore amenable to comparative approaches. We constructed a global molecular phylogeny of Galeommatoidea...

Beyond the landscape: resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area

Sophia Kimmig, Joscha Beninde, Myriam Brandt, Anna Schleimer, Stephanie Kramer-Schadt, Heribert Hofer, Konstantin Börner, Christoph Schulze, Ulrich Wittstatt, Mike Heddergott, Tania Halczok, Christoph Staubach & Alain Frantz
Urbanization affects key aspects of wildlife ecology. Dispersal in urban wildlife species may be impacted by geographical barriers but also by a species’ inherent behavioural variability. There are no functional connectivity analyses using continuous individual-based sampling across an urban-rural continuum that would allow a thorough assessment of the relative importance of physical and behavioural dispersal barriers. We used 16 microsatellite loci to genotype 374 red foxes (Vulpes vulpes) from the city of Berlin and surrounding...

Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in corn snakes (Pantherophis guttatus complex)

Edward Myers, Alexander McKelvy & Frank Burbrink
The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. This richness can be explained by numerous hypotheses affecting divergence, which include biogeographic barriers, adaptation to climatic gradients across this region, and Pleistocene speciation in glacial refugia. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while one or more of these hypotheses may explain diversification, it is likely that taxa are forming within this region in species-specific...

Data from: Landscape composition and life-history traits influence bat movement and space use: analysis of 30 years of published telemetry data

Alexis Laforge, Frederic Archaux, Aurélie Coulon, Clélia Sirami, Jérémy Froidevaux, Nicolas Gouix, Sylvie Ladet, Hilaire Martin, Kévin Barré, Fabien Claireau, Christian Kerbiriou, Charlotte Roemer & Luc Barbaro
Aim: Animal movement determines home range patterns, which in turn affect individual fitness, population dynamics and ecosystem functioning. Using temperate bats, a group of particular conservation concern, we investigated how morphological traits, habitat specialization and environmental variables affect home range sizes and daily foraging movements, using a compilation of 30 years of published bat telemetry data. Location: Northern America and Europe. Time period: 1988 – 2016. Major taxa studied: Bats. Methods: We compiled data on...

Eye size and investment in frogs and toads correlate with adult habitat, activity pattern and breeding ecology

Kate N. Thomas, David J. Gower, Rayna C. Bell, Matthew K. Fujita, Ryan K. Schott & Jeffrey W. Streicher
Frogs and toads (Amphibia: Anura) display diverse ecologies and behaviours, which are often correlated with visual capacity in other vertebrates. Additionally, anurans exhibit a broad range of relative eye sizes, which have not previously been linked to ecological factors in this group. We measured relative investment in eye size and corneal size for 220 species of anurans representing all 55 currently recognized families and tested whether they were correlated with six natural history traits hypothesized...

Contribution of genetic versus plastic responses to adaptive patterns in a widespread butterfly along a latitudinal cline

Franziska Günter, Michaël Beaulieu, Kasimir F. Freiberg, Ines Welzel, Nia Toshkova, Žagar, Tatjana Simčič & Klaus Fischer
Understanding how organisms adapt to complex environments is a central goal of evolutionary biology and ecology. This issue is of special interest in the current era of rapidly changing climatic conditions. Here, we investigate clinal variation and plastic responses in life history, morphology, and physiology in the butterfly Pieris napi along a pan-European gradient by exposing butterflies raised in captivity to different temperatures. We found clinal variation in body size, growth rates and concomitant development...

Data from: A new small, mesorostrine inioid (Cetacea, Odontoceti, Delphinida) from four late Miocene localities of the Pisco Basin, Peru

Olivier Lambert, Alberto Collareta, Aldo Benites-Palomino, Claudio Di Celma, Christian De Muizon, Mario Urbina & Giovanni Bianucci
The moderately rich past diversity of the superfamily Inioidea (Cetacea, Odontoceti) in both the Atlantic and Pacific oceans contrasts with the present survival of a single genus (Inia, Amazon river dolphin, family Iniidae) in freshwater deposits of South America and of a single species (Pontoporia blainvillei, Franciscana, family Pontoporiidae) along the eastern coast of that continent. However, part of the late Miocene to Pliocene inioid fossil record is made of relatively fragmentarily known species, for...

Data from: One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark

Pierre Feutry, Floriaan Devloo-Delva, Adrien Tran Lu Y, Stefano Mona, Rasanthi Gunasekera, Grant Johnson, Richard Pillans, Damian Jaccoud, Andrzej Kilian, David Morgan, Thor Saunders, Nicholas Bax & Peter Kyne
With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close-Kin Mark-Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost-efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare,...

Data from: Heritability and genetic correlations of personality, life history, and morphology in the grey mouse lemur (M. murinus)

Pauline Zablocki-Thomas, Anthony Herrel, Caitlin Karanewsky, Fabienne Aujard & Emmanuelle Pouydebat
The recent interest in animal personality has sparked a number of studies on the heritability of personality traits. Yet, how the sources variance these traits can be decomposed remains unclear. Moreover, whether genetic correlations with life-history traits, personality traits and other phenotypic traits exist as predicted by the pace-of-life syndrome hypothesis remains poorly understood. Our aim was to compare the heritability of personality, life-history, and morphological traits and their potential genetic correlations in a small...

The Burgess Shale paleocommunity with new insights from Marble Canyon, British Columbia

Karma Nanglu, Jean-Bernard Caron & Robert Gaines
The middle (Wuliuan Stage) Cambrian Burgess Shale is famous for its exceptional preservation of diverse and abundant soft-bodied animals through the “thick” Stephen Formation. However, with the exception of the Walcott Quarry (Fossil Ridge) and the stratigraphically older Tulip Beds (Mount Stephen) which are both in Yoho National Park (British Columbia), quantitative assessments of the Burgess Shale have remained limited. Here we first provide a detailed quantitative overview of the diversity and structure of the...

Host identity and symbiotic association affects the genetic and taxonomic diversity of the clownfish-hosting sea anemone microbiome

Benjamin Titus, Robert Laroche, Estafania Rodriguez, Herman Wirshing & Christopher Meyer
All eukaryotic life engages in symbioses with a diverse community of bacteria that are essential for performing basic life functions. In many cases, eukaryotic organisms form additional symbioses with other macroscopic eukaryotes. The tightly-linked physical interactions that characterize many macroscopic symbioses creates opportunities for microbial transfer, which likely affects the diversity and function of individual microbiomes, and may ultimately lead to microbiome convergence between distantly related taxa. Here, we sequence the microbiomes of five species...

Data from: Elevational filtering and the evolution of planthoppers (Hemiptera, Fulgoromorpha) in Papua New Guinea

Chatelain Paul, Le Cesne Maxime, Elias Marianne, Guilbert Eric & Soulier-Perkins Adeline.
Along elevational gradients, phylogenetic relatedness patterns constitute a considerable source of information, and may shed light on ecological processes that structure communities. This study focuses on community phylogenetic structure of planthoppers, specifically the species-rich and abundant Fulgoromorpha families (Hemiptera, Auchenorrhyncha), Cixiidae and Derbidae+Achilidae, along an elevational gradient on Mount Wilhelm (Papua New Guinea). In order to assess the factors driving planthoppers community composition, we recorded abundance data for planthoppers species at each elevation and we...

A third European species of grayling (Actinopterygii, Salmonidae), endemic to the Loire River basin (France), Thymallus ligericus n. sp.

Henri Persat, Steven Weiss, Elsa Froufe, Giulia Secci-Petretto & Gaël P.J. Denys
Loire grayling was already known to belong to a distinct lineage, compared to other European population, according to molecular data (enzymatic polymorphism, mtDNA sequencing and microsatellites). In this paper, we consider this lineage as a new species, Thymallus ligericus n. sp., which is endemic to the Loire drainage (France). Compared with the other species, T. ligericus n. sp. is characterized by a more elongated body, the presence of a pointed snout and a strait or...

Mammal occurrence identified from metabarcoding of two leech species from Sabah, Malaysia

R. Drinkwater, I.D. Schnell, K. Bohmann, H. Bernard, G. Veron, E. Clare, T.P. Gilbert & S.J. Rossiter
This dataset contains the results from a metabarcoding study of terrestrial leech blood meals to detect differences in the diets of two leech species, Haemadipsa picta and Haemadipsa sumatrana. Mammal taxa were identified using metabarcoding of 16s rRNA and comparisons of operational taxonomic units (OTUs) to a curated reference database from NCBI (National Center for Biotechnology Information) GenBank. All leeches were collected from the Stability of Altered Forest Ecosystems project (SAFE; www.SAFEproject.net) as part of...

Data from: Dispersal out of Wallacea spurs diversification of Pteropus flying foxes, the world’s largest bats (Mammalia: Chiroptera)

Susan M. Tsang, Sigit Wiantoro, Maria Josefa Veluz, Norimasa Sugita, Y-Lan Nguyen, Nancy B. Simmons & David J. Lohman
Aim: Islands provide opportunities for isolation and speciation. Many landmasses in the Indo-Australian Archipelago (IAA) are oceanic islands, and founder-event speciation is expected to be the predominant form of speciation of volant taxa on these islands. We studied the biogeographic history of flying foxes, a group with many endemic species and a predilection for islands, to test this hypothesis and infer the biogeographic origin of the group. Location: Australasia, Indo-Australian Archipelago, Madagascar, Pacific Islands Taxon:...

Data from: Transparency improves concealement in cryptically coloured moths

Mónica Arias, Marianne Elias, Christine Andraud, Serge Berthier & Doris Gomez
Predation is a ubiquitous and strong selective pressure on living organisms. Transparency is a predation defence widespread in water but rare on land. Some Lepidoptera display transparent patches combined with already cryptic opaque patches. A recent study showed that transparency reduced detectability of aposematic prey with conspicuous patches. However, whether transparency has any effect at reducing detectability of already cryptic prey is still unknown. We conducted field predation experiments with free avian predators where we...

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