Carles Vilà

Carles Vilà
Spanish National Research Council | CSIC · Doñana Biological Station

PhD

About

448
Publications
117,197
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Introduction
We use molecular tools to study the evolution of diversity, and assist in its conservation.
Additional affiliations
July 2008 - present
Spanish National Research Council
Position
  • Professor
Description
  • We use molecular tools to study the evolution of diversity, and assist in its conservation
March 1998 - June 2008
Uppsala University
Position
  • Professor (Assistant)
Education
January 1987 - July 1993
University of Barcelona
Field of study
  • Biology

Publications

Publications (448)
Preprint
A bstract While the theory of micro-evolution by natural selection assigns a crucial role to competition, its role in macroevolution is less clear. Phylogenetic evidence for a decelerating accumulation of lineages suggests a feedback of lineage diversity on diversification, i.e., ecological limits to diversification. However, does this feedback onl...
Article
Full-text available
Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from t...
Article
The presence of population-specific phenotypes often reflects local adaptation or barriers to gene flow. The co-occurrence of phenotypic polymorphisms that are restricted within the range of a highly mobile species is more difficult to explain. An example of such polymorphisms is in the common quail Coturnix coturnix, a small migratory bird that mo...
Article
Full-text available
Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinsh...
Article
Mountain ranges offer opportunities for understanding how species evolved and diversified across different environmental conditions. Neotropical frogs of the genus Oreobates (Anura: Craugastoridae) are adapted to highland and lowland habitats along the Andes, but many aspects of their evolution remain unknown. We studied their evolutionary history...
Article
Full-text available
Hacia análisis genéticos de alto rendimiento de muestras fecales de fauna silvestre La secuenciación de alto rendimiento ofrece nuevas posibilidades en ecología molecular y biología de la conservación. Sin embargo, el potencial de esta técnica no ha sido totalmente explotado para estudios no invasivos, a partir de muestras fecales, de fauna en libe...
Article
Detection of hybridization and introgression is important in ecological research as in conservation and evolutionary biology. STRUCTURE is one of the most popular software to study introgression and allows estimating what proportion of the genome of each individual belongs to each ancestral population, even in cases where no reference sample from t...
Article
We present data showing that the number of salamander species in Amazonia is vastly underestimated. We used DNA sequences of up to five genes (3 mitochondrial and 2 nuclear) of 366 specimens, 189 corresponding to 89 non-Amazonian nominal species and 177 Amazonian specimens, including types or topotypes, of eight of the nine recognized species in th...
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Replicate radiations, the repeated multiplication of species associated with ecological divergence, have attracted much attention and generated as much debate. Due to the few well‐studied cases, it remains unclear whether replicate radiations are an exceptional result of evolution or a relatively common example of the power of adaptation by natural...
Article
Social networks are the result of interactions between individuals at different temporal scales. Thus, sporadic intergroup encounters and individual forays play a central role in defining the dynamics of populations in social species. We assessed the rate of intergroup encounters for three western lowland gorilla (Gorilla gorilla gorilla) groups wi...
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Full-text available
In previous centuries, wolves were extirpated across much of their range worldwide, but they started to recover in Europe since the end of last century. A general pattern of this recovery is the expansion of the range occupied by local populations. The Iberian wolf population, shared by Portugal and Spain, reached its lowest extent and abundance ar...
Article
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Allee effects reduce the viability of small populations in many different ways, which act synergistically to lead populations towards extinction vortexes. The Sierra Morena wolf population, isolated in the south of the Iberian Peninsula and composed of just one or few packs for decades, represents a good example of how diverse threats act additivel...
Article
In species with female polygamy, pair bonds are frequently established since mate guarding can determine male fertilization success. However, extending the duration of pair bonds also implies reducing the chances of finding new mates. Males face a trade-off between mate guarding and looking for new mates, which can be shaped by their body condition...
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Full-text available
Background Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for links to specific phenotypes or signals of domestication. How...
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About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ∼50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely...
Article
Full-text available
Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms d...
Article
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The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human–carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their number...
Preprint
Full-text available
Whole genome sequencing is opening the door to novel insights into the population structure and evolutionary history of poorly known species. In organisms with large genomes, which includes most amphibians, whole-genome sequencing is excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wi...
Preprint
Full-text available
Whole genome sequencing is opening the door to novel insights into the population structure and evolutionary history of poorly known species. In organisms with large genomes, which includes most amphibians, whole-genome sequencing is excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wi...
Article
Full-text available
We studied the variation in genetics, bioacustics, and morphology in Eleutherodactylus glamyrus, a regionally endemic frog species restricted to high elevations in the Sierra Maestra Massif, Western Cuba that was originally described as a cryptic species hidden under the name E. auriculatus. Genetic analysis of mtDNA sequences of the 16S and cob ge...
Article
Aim Grey wolves (Canis lupus) are widespread across the Holarctic. Here, we test the previously proposed hypothesis that extant North American wolves originate from multiple waves of colonization from Asia. We also test the hypothesis that land connections have been important in the evolutionary history of other isolated wolf populations in Japan....
Article
Full-text available
Although previous studies have addressed the question of why large brains evolved, we have limited understanding of potential beneficial or detrimental effects of enlarged brain size in the face of current threats. Using novel phylogenetic path analysis, we evaluated how brain size directly and indirectly, via its effects on life-history and ecolog...
Article
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The success of a reintroduction program is determined by the ability of individuals to reproduce and thrive. Hence, an understanding of the mating system and breeding strategies of reintroduced species can be critical to the success, evaluation and effective management of reintroduction programs. As one of the most threatened crocodile species in t...
Data
Additional information on 17 microsatellite loci used in Crocodylus intermedius paternity analysis. (DOC)
Data
Parental genotypes reconstructed for 20 Crocodylus intermedius clutches across 17 polymorphic microsatellite loci. (DOC)
Article
Full-text available
Controlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection. To date, the effects of demography have not yet been explicitly considered when identifying loci under selection during dog domestication. To investigate positive selection on the dog lineage early in the dome...
Data
Genome-wide distribution of Δπ, FST, Δ Tajima’s D in 100kb sliding windows. (PDF)
Data
FDR of individual statistics vs. the joint percentile statistic for 100kb windows, used to identify outlier windows in the empirical outlier (non-FDR) approach, for (A) Δπ, (B) FST, and (C) Δ Tajima’s D. (PNG)
Data
Outlier regions identified with the FDR-based method, ranked according to CMS1-FDR. (XLS)
Data
Bi-plots of empirical percentile vs. FDR for individual summary statistics across 100 kb windows, demonstrating that the majority of windows in the top 1% have FDR > 0.01. (A) Entire range of empirical percentile and (B) Focus on the top 20% of the empirical distribution. Horizontal and vertical dotted lines indicate the 99th percentile and 1% FDR,...
Data
Venn diagram displaying overlap of candidate gene sets obtained with FDR-based and empirical outlier (EO) methods for detecting positive selection on the dog lineage. Genes unique to empirical methods relative to FDR methods are those falling within windows with a high false discovery rate (and thus are likely to be enriched with false positives) (...
Data
Distribution of sites fixed between dogs and wolves in neutral and outlier regions according to functional class, filtered according to the requirement that the dog-specific allele be at a frequency of 0.75 or greater among a panel of 12 additional breed dogs. Numbers above bars indicate counts of fixed sites. (PDF)
Data
Description of additional candidate genes. (PDF)
Data
Comparison of distributions computed from neutral coalescent simulations based up the posterior mean parameter estimates from the inferred demographic history, [19] and 1000 samples from the joint posterior distribution for (A) Δπ, (B) FST, and (C) Δ Tajima’s D. (PDF)
Data
Distribution of overlaps between outlier regions detected between methods for FDR and empirical outlier methods. (PDF)
Data
Distribution of CMS1-FDR and the joint percentile statistic for the top and 3rd ranked regions, demonstrating that CMS1-FDR localizes the peak of the outlier region signal more precisely than the joint percentile. (PDF)
Data
All 68 outlier regions identified using the FDR-based methodology using Δπ, FST, Δ Tajima’s D that were validated with the 12-breed dog diversity panel. Columns within “This study” are based on the sequencing data generated here, while those under CanMap are computed from a ~48k SNP data set for a large set of wolves and ancient/basal dog breeds. H...
Article
Postcopulatory sexual selection plays an important role in the reproductive success of males in many species. Differences in fertilization success could affect rates of admixture and genetic introgression between divergent lineages. We investigated sperm precedence in matings in captivity involving Common quails (Coturnix coturnix) and farm quails...
Article
Full-text available
Following protection measures implemented since the 1970s, large carnivores are currently increasing in number and returning to areas from which they were absent for decades or even centuries. Monitoring programmes for these species rely extensively on non-invasive sampling and genotyping. However, attempts to connect results of such studies at lar...
Article
p>Following protection measures implemented since the 1970s, large carnivores are currently increasing in number and returning to areas from which they were absent for decades or even centuries. Monitoring programmes for these species rely extensively on non-invasive sampling and genotyping. However, attempts to connect results of such studies at l...
Article
Full-text available
The letter by Garner et al. [1] continued an important discussion regarding the role genomics might play in conservation biology. In general, we do not see a dichotomy between our point of view [2] and that put forth by Garner et al. [1]. At the heart of the issue is how to define an actual impact of genomics on applied conservation and find suitab...
Article
Full-text available
Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors...
Article
Full-text available
The gray wolf (Canis lupus) is a widely distributed top predator and ancestor of the domestic dog. The specific evolutionary relationships of dogs and extant wolves are controversial and have been explored with a variety of genomic approaches. However, these studies suffer from a paucity of samples from throughout the Holarctic range of the wolf. T...
Article
Full-text available
Kin recognition is a critical element to kin cooperation and in vertebrates it is primarily based on associative learning. Recognition of socially unfamiliar kin occurs rarely, and it is reported only in vertebrate species where promiscuity prevents recognition of first-order relatives. However, it is unknown if recognition of socially unfamiliar k...
Article
AimThe evolutionary speed hypothesis is a mechanistic explanation for the latitudinal biodiversity gradient. The recently extended integrated evolutionary speed hypothesis (IESH) proposes that temperature, water availability, population size and spatial heterogeneity influence the rate of molecular evolution which, in turn, affects diversification....
Article
Full-text available
Library preparation protocols for high-throughput DNA sequencing (HTS) include amplification steps in which errors can build up. In order to have confidence in the sequencing data, it is important to understand the effects of different Taq polymerases and PCR amplification protocols on the DNA molecules sequenced. We compared thirteen enzymes in th...
Article
The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice, and we discuss how scaling-up to genome-wide inference can benefit traditional conservation genetic approaches and provide qualitatively novel insights. Yet, the generation of genomic data and subseque...
Article
Full-text available
This chapter discusses the effects of hybridization with domestic dogs on the conservation of wild canids. Hybridization between gray wolves and dogs are the majority of the documented hybridization between wild and domestic canids, and it does not usually threaten breeding opportunities. The chapter states that hybridization between dogs and rarer...
Article
The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and in...
Article
Full-text available
Recombination rates vary in intensity and location at the species, individual, sex and chromosome levels. Despite the fundamental biological importance of this process, the selective forces that operate to shape recombination rate and patterns are unclear. Domestication offers a unique opportunity to study the interplay between recombination and se...
Article
Full-text available
Genetic biodiversity contributes to individual fitness, species' evolutionary poten-tial, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform pol-icy decisions and management actions. However, there is a lack of knowledge regarding which genetic metric...
Data
Temporal arrangement of sampling for 20 schemes tested, for weak (90%), moderate (97.5%), and strong (99%) declines.