José A. Godoy

Estación Biológica de Doñana, CSIC · Integrative Ecology

Genome‐wide technologies open up new possibilities to clarify questions on genetic structure and phylogeographic history of taxa previously studied with microsatellite loci and mitochondrial sequences. Here, we used 736 individual red deer ( Cervus elaphus ) samples genotyped at 35,701 single nucleotide polymorphism loci (SNPs) to assess the popula...

The Iberian lynx Lynx pardinus is one of the most genetically depauperated species on earth. This is likely due to the combination of long-term small population sizes and serial historical bottlenecks. Conservation actions, including captive breeding, translocations and reintroductions, have minimised genetic risks through genetic management, which...

The Iberian lynx (Lynx pardinus) ex-situ conservation programme was established in 2001, as the species was Critically Endangered, with the aim of maintaining a healthy, genetically sound captive breeding population to prevent extinction and provide a source for future reintroductions. After a slow early progress, the programme rapidly expanded aft...

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat...

Genetic diversity is lost in small and isolated populations, affecting many globally declining species. Interspecific admixture events can increase genetic variation in the recipient species’ gene pool, but empirical examples of species-wide restoration of genetic diversity by admixture are lacking. Here we present multi-fold coverage genomic data...

Since 2015, following reintroductions, an Iberian lynx population in Vale do Guadiana (Portugal) has been breeding and expanding, bringing changes to both ecosystems and residents’ perceptions. We describe how ecological monitoring, genetic analysis and social surveys contribute to assess this new scenario of coexistence with ecological and social...

Guidelines for the Genetic Management of Iberian lynx populations

Local adaptations to the environment are an important aspect of the diversity of a species and their discovery, description and quantification has important implications for the fields of taxonomy, evolutionary and conservation biology. In this study, we scan genomes from several populations across the distributional range of the Eurasian lynx, wit...

The Iberian lynx has shown a favourable demographic trajectory in the last decade as a result of the conservation measures adopted which are still ongoing. However, the viability of the species is still compromised by genetic factors. Here, we used the GESP software that predicts the effective population size (Ne) and inbreeding accumulation (∆f) o...

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. Genetic diversity has been largely neglected in biodiversity monitoring, and when addressed is treated separately, detached from other conservation issues, such as habitat alteration du...

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prere...

At the beginning of the 20th century Crocidura cantabra was described based on one specimen from Basque Provinces, North of Spain. Later, some authors considered it a junior synonym of Crocidura suaveolens , without any data to support this statement, so the eight existing specimens were registered as records of that species. Our objective was to c...

The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of...

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...

We studied the relationship between the variability and contemporary distribution of pelage phenotypes in one of most widely distributed felid species and an array of environmental and demographic conditions. We collected 672 photographic georeferenced records of the Eurasian lynx throughout Eurasia. We assigned each lynx coat to one of five phenot...

Deleterious mutations continuously accumulate in populations, building up a burden that can threaten their survival, particularly in small populations when inbreeding exposes recessive deleterious effects. Notwithstanding, this process also triggers genetic purging, which can reduce the deleterious burden and mitigate fitness inbreeding depression....

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics,...

Auteurs : European Reference Genome Atlas (ERGA) Consortium 3

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics,...

The north-eastern European lowland population of the lynx is commonly attributed to the “Baltic population” and believed to belong to the nominative subspecies Lynx lynx lynx. Geographically, its range extends from eastern Poland throughout the Baltic states north to Fennoscandia and east to central Asia. Within its range across north-eastern Europ...

Aim Genome‐wide genetic data can provide key input for both taxonomy and conservation, but its use in this context remains limited. In this study, we performed the first genome‐wide assessment of genetic variation in two populations of the Eurasian lynx, the Balkan population, the most threatened, and the Caucasian population, a possible glacial re...

Demographic bottlenecks generally reduce genetic diversity through more intense genetic drift, but their net effect may vary along the genome due to the random nature of genetic drift and to local effects of recombination, mutation and selection. Here, we analysed the changes in genetic diversity following a bottleneck by comparing whole‐genome div...

International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve, and sustainably and equitably use, biodiversity. The CBD is a vital instrument for global conservation because it guides 195 countries and the European Union in setting priorities and allocating resources, and requires regular reporting on prog...

Background Benign juvenile idiopathic epilepsy has been described in humans but rarely in animals. The objectives of the study were to describe the clinical signs, clinical data, imaging findings, genetic examinations, treatment, long-term outcome and prognosis in Iberian lynx with juvenile epilepsy. Medical records, video recordings and diagnostic...

Mating systems are studied due to their interest in ecology and evolution. In rodents, mating strategies have been inferred from the spatio-temporal arrangement of males and females, and breeding success has usually been estimated through the number of embryos counted by palpation of pregnant females. However, these might not be trustable proxies t...

Genetic diversity is critically important for all species-domesticated and wild- to adapt to environmental change, and for ecosystem resilience to extreme events. International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve and sustainably and equitably use all levels of biodiversity-genes, species and ec...

The genus Crocidura represents a remarkable model for the study of chromosome evolution. This is the case of the lesser white-toothed shrew (Crocidura suaveolens), a representative of the Palearctic group. Although continuously distributed from Siberia to Central Europe, C. suaveolens is a rare, habitat-specialist species in the southwesternmost li...

Disentangling the contribution of long‐term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key for assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation...

Interspecific competition affects population dynamics, distributional ranges, and evolution of competing species. The competitive exclusion principle states that ecologically similar species cannot coexist unless they exhibit niche segregation. Herein, we assess whether niche segregation allows the coexistence of Crocidura russula and C. suaveolens...

Restricted seed dispersal frequently leads to fine‐scale spatial genetic structure (i.e., FSGS) within plant populations. Depending on its spatial extent and the mobility of pollinators, this inflated kinship at the immediate neighbourhood can critically impoverish pollen quality. Despite the common occurrence of positive FSGS within plant populati...

Ex situ programmes have become critical for improving the conservation of many threatened species, as they establish backup populations and provide individuals for reintroduction and reinforcement of wild populations. The Iberian lynx was considered the most threatened felid species in the world in the wake of a dramatic decline during the second h...

Accurate knowledge of the distribution of rare species remains a great challenge in conservation biology because these species are prone to extinction and the number of species becoming rare is increasing. However, the distribution of rare species is usually difficult to delimit because of their low abundances and/or small distribution ranges. Thes...

Crocidura suaveolens is a rare, habitat-specialist species in the Gulf of C?diz (southwestern Iberia), the southwesternmost limit of its distributional range. In this region, it is present only in six tidal marshes distributed in four isolated areas as a result of competitive exclusion by C. russula. These rear-edge populations of C. suaveolens cou...

Durante el siglo XX, el lince sufrió un pronunciado declive demográfico que lo llevó al borde de la extinción. La adopción de medidas de conservación a principios de los años 2000 ha paliado en parte esa grave situación. La gestión genética está contribuyendo a la recuperación de la especie. Esta se concibió inicialmente a partir del análisis de va...

Despite their potential importance, biological processes such as competitive exclusion (CE) have been largely neglected in phylogeographical studies. Here, we analyse the role of glacial events and CE in the evolutionary history of the lesser white-toothed shrew, Crocidura suaveolens, in Iberia based on cytochrome b sequences. All the Iberian sampl...

In solitary carnivorous mammals, territoriality is assumed to benefit male fitness by ensuring the exclusivity of matings within territories via mate guarding and female defence. However, this hypothesis remains empirically untested. Here, we examined this hypothesis for solitary territorial carnivores using the Iberian lynx (Lynx pardinus) as a ca...

Background Demographic bottlenecks erode genetic diversity and may increase endangered species’ extinction risk via decreased fitness and adaptive potential. The genetic status of species is generally assessed using neutral markers, whose dynamic can differ from that of functional variation due to selection. The MHC is a multigene family described...

La conservación de la biodiversidad en un escenario de cambio global acelerado constituye uno de los grandes retos de la humanidad para las próximas décadas. La genética ha pasado a ser un elemento fundamental del enfoque multidisciplinar que esta tarea requiere, dando origen al área de conocimiento de la genética de la conservación. El papel de la...

a b s t r a c t For endangered species, the availability of genealogies and a good knowledge of mating patterns are valuable resources for conservation purposes. Here we studied mating patterns in the endangered Iberian lynx, Lynx pardinus, and reconstructed a partial genealogy of the intensively monitored population in Do˜ nana from 1990 to 2013....

There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and spec...

Background The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so far have been based on 36 STR...

Abstract Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink...

Roads are widely recognized to represent a barrier to individual movements and, conversely, verges can act as potential corridors for the dispersal of many small mammals. Both barrier and corridor effects should generate a clear spatial pattern in genetic structure. Nevertheless, the effect of roads on the genetic structure of small mammal populati...

The characterization of multigene families with high copy number variation is often approached through PCR amplification with highly degenerate primers to account for all expected variants flanking the region of interest. Such an approach often introduces PCR biases that result in an unbalanced representation of targets in high-throughput sequencin...

Allelic profile completeness obtained in relation to increasing coverage. Allelic profile completeness obtained in relation to increasing coverage. The same set of individuals was assayed with the three strategies and the reads obtained for each amplicon were bootstrapped to simulate lower coverages (increasing steps of 10 reads, 100 iterations). P...

Primer design summary. Contains: i) Genebank identifiers for sequences used in primer design, ii) Haplotypes present in the region considered for the forward and reverse primer design, iii) Detailed description of the primer and pooling design: First (1.a and 1.a), all haplotypes present on the regions evaluated for primer design are evaluated to b...

Final allelic profiles per approach and their comparison. Final allelic profiles per approach along with their union and intersections, and statistics about the number of scored and missed alleles and profile completeness. (XLS)

Number, nature and position of primer mismatches per allele and strategy. Number, nature and position of primer mismatches per allele in each strategy. For each allele for which we have genomic data about the flanking region we show their alignments with each primer-pair assayed in the pooled-PCRs strategy in the first four columns. Dots indicate i...

Rank of alleles relative to the most frequent artefact. Rank of alleles relative to the most frequent artefact. Unique sequences within the amplicon are ranked by number of reads and the rank of the most frequent artefact is set at zero, so a positive value means that the alleles attained higher coverage than any artefact and vice versa. Note that...

Global alignment fasta file. MHC class I sequences alignment used for primer design. Sequences come from GenBank and the Iberian lynx transcriptomic data available at the moment. (FASTA)

Allele's coverage and probability of detection per amplification strategy. Allele's coverage (measured as the average percentage of reads corresponding to each allele copy, %reads) and probability of detection per amplification strategy. Alleles are ranked in descending %reads order. (XLS)

Genealogical records of animals (studbook) are created to avoid reproduction between closely related individuals, which could cause inbreeding, particularly for such endangered species as the Panthera onca (Linnaeus, 1758). Jaguar is the largest felid in the Americas and is considered an important ecological key species. In Mexico, wild jaguar popu...

Over the past century, human activities and their side effects have significantly threatened both ecosystems and resident species. Nevertheless, the genetic patterns of large felids that depend heavily on large and well-conserved continuous habitat remain poorly studied. Using the largest-ever contemporary genetic survey of wild jaguars (Panthera o...

The study of the demographic history of species can help to understand the negative impact of recent population declines in organisms of conservation concern. Here, we use neutral molecular markers to explore the genetic consequences of the recent population decline and posterior recovery of the Eurasian eagle owl (Bubo bubo) in the Iberian Peninsu...

The use of faecal DNA, although a promising tool for the population monitoring of mammals, has not yet become a fully exploited and standard practice, mainly because low target DNA concentration, DNA degradation, and co-purification of inhibitors demand extra laboratory procedures to improve success and reliability. Here we evaluate a simple method...

The successful introduction of the common genet (Genetta genetta) into Europe has been traditionally associated to the Muslim invasion of Iberia, although diverse evidence suggested an earlier arrival. In this study, we assessed genetic variation at 11 microsatellite loci in 199 individuals from the Mediterranean Basin and used approximate Bayesian...

Host identification from mosquito blood meals has been routinely used to identify the feeding preferences of insects in studies on transmission of vector-borne pathogens. Here, we identified for the first time the susceptibility of the endangered Iberian lynx (Lynx pardinus) to the attack of a wild mosquito female, the mosquito Anopheles atroparvus...

An epidemic of the disease chytridiomycosis, caused by the pathogenic fungus Batrachochytrium dendrobatidis, induced a massive decline of populations of the common midwife toad (Alytes obstetricans) inhabiting the Peñalara Massif (Guadarrama National Park, Central Spain) in the years 1997–2001. The disease outbreak caused the disappearance of about...

Llamamos biodiversidad al conjunto de la variedad de la vida en todos sus niveles de organización, desde los genes a los individuos, las poblaciones, las especies, las comunidades y los ecosistemas. Pero la biodiversidad es más que la suma de los elementos que componen el mundo vivo. También son biodiversidad las relaciones entre esos elementos, lo...