167 Works

Data from: \"De novo transcriptome assembly and polymorphism detection in ecological important widely distributed Neotropical toads from the Rhinella marina species complex (Anura: Bufonidade)\" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014

Coralie Nourisson, Miguel Carneiro, Marcelo Vallinoto & Fernando Sequeira
The toads Rhinella marina and R. schneideri are large terrestrial true toads widely distributed in the Neotropical region, which can hybridize in areas of transition between Amazon rain forest and Cerrado biomes. The former is in particular an important ecological species, and a very successful invader. Here, we report de novo transcriptome of R. marina and R. schneideri and polymorphism SNPs identified between the two species. The transcriptome sequencing was performed on an Illumina platform...

Data from: The transcriptional landscape of seasonal coat colour moult in the snowshoe hare

Mafalda S. Ferreira, Paulo C. Alves, Colin M. Callahan, João P. Marques, L. Scott Mills, Jeffrey M. Good & José Melo-Ferreira
Seasonal coat colour change is an important adaptation to seasonally changing environments but the evolution of this and other circannual traits remains poorly understood. In this study we use gene expression to understand seasonal coat colour moulting in wild snowshoe hares (Lepus americanus). We used hair colour to follow the progression of the moult, simultaneously sampling skin from three moulting stages in hares collected during the peak of the spring moult from white winter to...

Data from: De novo transcriptome assembly and polymorphism detection in two highly divergent evolutionary units of Bosca's newt (Lissotriton boscai) endemic to the Iberian Peninsula

Coralie Nourisson, Antonio Muñoz-Merida, Miguel Carneiro & Fernando Sequeira
This article reports the de novo transcriptomes of two highly divergent evolutionary units of the Iberian endemic Bosca’s newt, Lissotriton boscai. These two units are distributed allopatrically but meet in areas of secondary contact in central-southwestern coastal region of Portugal. The resources we provide include the raw sequence reads, the assembled transcripts and SNPs called for both lineages.

Data from: Distribution and functionality of copy number variation across European cattle populations

Maulik Upadhyay, Vinicius H. Da Silva, Hendrik-Jan Megens, Marleen H. P. W. Visker, Paolo Ajmone-Marsan, Valentin A. Bâlteanu, Susana Dunner, Jose Fernando Garcia, Catarina Ginja, Juha Kantanen, Martien A.M. Groenen, Richard P.M.A. Crooijmans, Vinicus H. Da Silva, Martien A. M. Groenen & Richard P. M. A. Crooijmans
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina...

Data from: Moving in the Anthropocene: global reductions in terrestrial mammalian movements

Marlee A. Tucker, Katrin Böhning-Gaese, William F. Fagan, John M. Fryxell, Bram Van Moorter, Susan C. Alberts, Abdullahi H. Ali, Andrew M. Allen, Nina Attias, Tal Avgar, Hattie Bartlam-Brooks, Buuveibaatar Bayarbaatar, Jerrold L. Belant, Alessandra Bertassoni, Dean Beyer, Laura Bidner, Floris M. Van Beest, Stephen Blake, Niels Blaum, Chloe Bracis, Danielle Brown, P. J. Nico De Bruyn, Francesca Cagnacci, Justin M. Calabrese, Constança Camilo-Alves … & Thomas Mueller
Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral...

Data from: Intensity of male-male competition predicts morph diversity in a colour polymorphic lizard

Guillem Perez I De Lanuza, Miguel A. Carretero & Enrique Font
Sexual selection is one of the main processes involved in the emergence and maintenance of heritable colour polymorphisms in a variety of taxa. Here we test whether the intensity of sexual selection, estimated from population sex ratio, predicts morph diversity in Podarcis muralis, a colour polymorphic lizard with discrete white, yellow, orange, white-orange, and yellow-orange male and female phenotypes (i.e. morphs). In a sample of 116 Pyrenean populations and 5421 lizards, sex ratios (m/f) vary...

Data from: Morphological and functional implications of sexual size dimorphism in the Moorish gecko, Tarentola mauritanica

Federico Massetti, Verónica Gomes, Anna Perera, Catarina Rato & Antigoni Kaliontzopoulou
Sexual dimorphism (SD) is a common trait in animals, appearing due to sexual selection, fecundity selection or natural selection promoting sexual niche segregation. To evaluate the relative contribution of these mechanisms in shaping phenotypic patterns, we explored morphological and functional SD in the Moorish gecko, Tarentola mauritanica (Linnaeus, 1758). This species is particularly interesting because the sex of individuals is determined by the incubation temperature of the eggs, which may pose constraints on the expression...

Data from: Allelopathy prevents competitive exclusion and promotes phytoplankton biodiversity

Aldo Barreiro Felpeto, Shovonlal Roy & Vitor Manuel Vasconcelos
It has been hypothesized that allelopathy can prevent competitive exclusion and promote phytoplankton diversity in aquatic ecosystems, where numerous species coexist on a limited number of resources. However, experimental proof-of-principle is not available to support this hypothesis. Here we present the first experimental evidence to support this hypothesis by demonstrating that allelopathy promotes the coexistence of two phytoplankton species, Ankistrodesmus falcatus and Oscillatoria sp., that compete for a single limiting nutrient. By performing long-term competition...

Data from: Evolution of alternative male morphotypes in oxyurid nematodes: a case of convergence?

Fátima Jorge, Ana Perera, Vicente Roca, Miguel Carretero, D. James Harris, Robert Poulin & M. A. Carretero
Male dimorphism has been reported across different taxa, and is usually expressed as the coexistence of a larger morph with exaggerated male traits and a smaller one with reduced traits. The evolution and maintenance of male dimorphism are still poorly understood for several of the species in which it has been observed. Here, we analyse male dimorphism in several species of reptile parasitic nematodes of the genus Spauligodon, in which a major male morph (exaggerated...

Data from: Getting there and around: host range oscillations during colonisation of the Canary Islands by the parasitic nematode Spauligodon

Fátima Jorge, Ana Perera, Robert Poulin, Vicente Roca & Miguel A. Carretero
Episodes of expansion and isolation in geographic range over space and time, during which parasites have the opportunity to expand their host range, are linked to the development of host-parasite mosaic assemblages and parasite diversification. In this study we investigated whether island colonisation events lead to host range oscillations in a taxon of host-specific parasitic nematodes of the genus Spauligodon in the Canary Islands. We further investigated if range oscillations also resulted in shifts in...

Data from: Females know better: sex-biased habitat selection by the European wildcat

Teresa Oliveira, Fermin Urra, José María Lopez-Martín, Elena Balleteros-Duperón, José Miguel Barea-Azcón, Marcos Moleón, José Maria Gil-Sánchez, Paulo Celio Alves, Francisco Díaz-Ruíz, Pablo Ferreras & Pedro Monterroso
The interactions between animals and their environment vary across species, regions, but also with gender. Sex‐specific relations between individuals and the ecosystem may entail different behavioral choices and be expressed through different patterns of habitat use. Regardless, only rarely sex‐specific traits are addressed in ecological modeling approaches. The European wildcat (Felis silvestris silvestris) is a species of conservation concern in Europe, with a highly fragmented and declining distribution across most of its range. We assessed...

Data from: A multispecies approach reveals hot-spots and cold-spots of diversity and connectivity in invertebrate species with contrasting dispersal modes

Abigail E. Cahill, Aurelien De Jode, Sophie Dubois, Zoheir Bouzaza, Didier Aurelle, Emilie Boissin, Olivier Chabrol, Romain David, Emilie Egea, Jean-Baptiste Ledoux, Bastien Merigot, Alexandra Anh-Thu Weber & Anne Chenuil
Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed...

Data from: Genome-wide associations identify novel candidate loci associated with genetic susceptibility to tuberculosis in wild boar

João Queirós, Paulo Célio Alves, Joaquín Vicente, Christian Gortázar & José De La Fuente
Tuberculosis (TB) affects a wide range of host species worldwide. Understanding host-pathogen co-evolution remains a global challenge owing to complex interactions among host genetic factors, pathogen traits and environmental conditions. We used an endemic wild boar population that had undergone a huge increase in Mycobacterium bovis infection prevalence, from 45% in 2002/06 to 83% in 2009/12, to understand the effects of host genetics on host TB outcomes and disease dynamics. Host genomic variation was characterized...

Data from: Colour patch size and measurement error using reflectance spectrometry

Arnaud Badiane, Guillem Pérez I De Lanuza, María Del Carmen García-Custodio, Pau Carazo & Enrique Font
1. Over the past twenty years, portable and relatively affordable spectrophotometers have greatly advanced the study of animal coloration. However, the small size of many colour patches poses methodological challenges that have not, to date, been assessed in the literature. Here, we tackle this issue for a reflectance spectrophotometry set-up widely used in ecology and evolution (the beam method). 2. We reviewed the literature on animal coloration reporting the use of reflectance spectrophotometry to explore...

Data from: ProtASR: an evolutionary framework for ancestral protein reconstruction with selection on folding stability

Miguel Arenas, Claudia C. Weber, David A. Liberles & Ugo Bastolla
The computational reconstruction of ancestral proteins provides information on past biological events and has practical implications for biomedicine and biotechnology. Currently available tools for ancestral sequence reconstruction (ASR) are often based on empirical amino acid substitution models that assume that all sites evolve at the same rate and under the same process. However, this assumption is frequently violated because protein evolution is highly heterogeneous due to different selective constraints among sites. Here, we present ProtASR,...

Data from: Identifying loci under selection against gene flow in isolation with migration models

Vitor C. Sousa, Miguel Carneiro, Nuno Ferrand & Jody Hey
When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional...

Data from: Cryptic speciation in the field vole: a multilocus approach confirms three highly divergent lineages in Eurasia

Joana Paupério, Jeremy S. Herman, José Melo-Ferreira, Maarit Jaarola, Paulo C. Alves & Jeremy B. Searle
Species are generally described from morphological features, but there is growing recognition of sister forms that show substantial genetic differentiation without obvious morphological variation and may therefore be considered ‘cryptic species’. Here, we investigate the field vole (Microtus agrestis), a Eurasian mammal with little apparent morphological differentiation but which, on the basis of previous sex-linked nuclear and mitochondrial DNA (mtDNA) analyses, is subdivided into a northern and a southern lineage, sufficiently divergent that they may...

Data from: Citizen science reveals unexpected continental-scale evolutionary change in a model organism

Jonathan Silvertown, Laurence Cook, Robert Cameron, Mike Dodd, Kevin McConway, Jenny Worthington, Peter Skelton, Christian Anton, Oliver Bossdorf, Bruno Baur, Menno Schilthuizen, Benoît Fontaine, Helmut Sattmann, Giorgio Bertorelle, Maria Correia, Cristina Oliveira, Beata Pokryszko, Małgorzata Ożgo, Arturs Stalažs, Eoin Gill, Üllar Rammul, Péter Sólymos, Zoltan Féher & Xavier Juan
Organisms provide some of the most sensitive indicators of climate change and evolutionary responses are becoming apparent in species with short generation times. Large datasets on genetic polymorphism that can provide an historical benchmark against which to test for recent evolutionary responses are very rare, but an exception is found in the brown-lipped banded snail (Cepaea nemoralis). This species is sensitive to its thermal environment and exhibits several polymorphisms of shell colour and banding pattern...

Data from: Using beta diversity to inform agricultural policies and conservation actions on Mediterranean farmland

Joana Santana, Miguel Porto, Luis Reino, Francisco Moreira, Paulo Flores Ribeiro, José Lima Santo, John T. Rotenberry & Pedro Beja
1. Spatial variation in species composition (β-diversity) is an important component of farmland biodiversity, which together with local richness (α-diversity) drives the number of species in a region (γ-diversity). However, β-diversity is seldom used to inform conservation, due to limited understanding of its responses to agricultural management, and lack of clear links between β-diversity changes and conservation outcomes. 2. We explored the value of β-diversity to guide conservation on farmland, by quantifying the contribution of...

Data from: The role of hybridisation in the origin and evolutionary persistence of vertebrate parthenogens: a case study of Darevskia lizards

Susana Freitas, D. James Harris, Sillero Neftali, Arakelyan Marine, Roger Butlin & Miguel Carretero
Obligate parthenogenesis is found in only 0.1% of vertebrate species, is thought to be relatively short lived and is typically of hybrid origin. However, neither the evolutionary persistence of asexuality in vertebrates, nor the conditions that allow the generation of new parthenogenetic lineages are currently well understood. It has been proposed that vertebrate parthenogenetic lineages arise from hybridisation between two divergent taxa within a specific range of phylogenetic distances (the “Balance Hypothesis”). Moreover, parthenogenetic species...

The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers

Oscar Cortes Gardyn, Catarina Ginja, Luis Telo De Gama, Amparo Martínez, Inmaculada Martín Burriel & Juan Vicente Delgado
Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received infuences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula,...

Interspecific allometry for sexual shape dimorphism: macroevolution of multivariate sexual phenotypes with application to Rensch's rule

Adams Dean, Antigoni Kaliontzopoulou, Elizabeth Glynne & Dean C. Adams
Allometric trends in the degree of sexual dimorphism with body size have long fascinated evolutionary biologists. Many male-biased clades display more prominent sexual dimorphism in larger taxa (Rensch’s rule), with most examples documenting this pattern for body size dimorphism. While sexual dimorphism in traits other than body size is equally functionally relevant, characterizing allometric patterns of sexual dimorphism in such traits is hampered by lack of an analytical framework that can accommodate multivariate phenotypes. In...

Perdigão: aerial lidar survey raster map

José Laginha Palma, Vasco Batista & Vitor Costa Gomes

Perdigão: computational mesh (ALS.SW.20)

Vasco Batista, José Laginha Palma & Vitor Costa Gomes

Perdigão: computational mesh (ALS.SW.80)

Vasco Batista, José Laginha Palma & Vitor Costa Gomes

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