Raquel Godinho

Raquel Godinho
CIBIO/InBIO University of Porto · EcoGenomics research group

PhD

About

194
Publications
58,678
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Introduction
I am a population geneticist heading the EcoGenomics research group at CIBIO/University of Porto. My central interests include the understanding of i) the evolutionary history of populations and species, and ii) adaptive processes, including adaptive hybridization. I also devote much attention to the development and application of non-invasive molecular approaches to investigate diversity and demography, and to monitor large carnivore species.
Additional affiliations
September 2013 - present
University of Porto
Position
  • Invited Assistant Professor
September 2004 - present
January 2004 - present
CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos

Publications

Publications (194)
Article
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The evolution of RNA-seq technologies has yielded datasets of scientific value that are often generated as condition associated biological replicates within expression studies. With expanding data archives opportunity arises to augment replicate numbers when conditions of interest overlap. Despite correction procedures for estimating transcript abu...
Article
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Advances in the field of museomics have promoted a high sampling demand for natural history collections (NHCs), eventually resulting in damage to invaluable resources to understand historical biodiversity. It is thus essential to achieve a consensus about which historical tissues present the best sources of DNA. In this study, we evaluated the perf...
Article
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In the present context of the ramping up of the global biodiversity crisis, improving our understanding on the genetic and biogeographic patterns of ill-known taxa is central to conservation planning. This is especially relevant for geographically isolated populations that suffer from little or no gene flow and an increased extinction risk. The few...
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Detailed knowledge about biodiversity distribution is critical for monitoring the biological effects of global change processes. Biodiversity knowledge gaps hamper the monitoring of conservation trends and they are especially evident in the desert biome. Mauritania constitutes a remarkable example on how remoteness and regional insecurity affect cu...
Article
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Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting ca. 25,000 years ago (ya). Here, we examined th...
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The red leopard (Panthera pardus) colour morph is a colour variant that occurs only in South Africa, where it is confined to the Central Bushveld bioregion. Red leopards have been spreading over the past 40 years, which raises the speculation that the prevalence of this phenotype is related to low dispersal of young individuals owing to high off‐ta...
Article
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Genomic tools have greatly enhanced our ability to uncover ancient interspecific gene flow, including cases involving allopatric lineages and/or lineages that have gone extinct. Recently, a genomic analysis revealed the unexpected gene flow between the African wild dog (Lycaon pictus) and the dhole (Cuon alpinus). The two species have currently hig...
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Intra- and inter-specific gene flow are natural evolutionary processes. However, human-induced hybridization is a global conservation concern across taxa, and the development of discriminant genetic markers to differentiate among gene flow processes is essential. Wolves (Canis lupus) are affected by hybridization, particularly in southern Europe, w...
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The invasive Vespa velutina has been widely referred as an effective predator of honeybees. Despite the potential risk to pollination services provision and honey production, there is no accurate quantification and assessment of its real consequences for honeybees. To date, the identification of the honeybee and other insects in the diet of V. velu...
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The evolutionary history of African ungulates has been largely explained in the light of Pleistocene climatic oscillations and the way these influenced the distribution of vegetation types, leading to range expansions and/or isolation in refugia. In contrast, comparatively fewer studies have addressed the continent’s environmental heterogeneity and...
Article
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The capercaillie Tetrao urogallus - the world's largest grouse- is a circumboreal forest species, which only two remaining populations in Spain: one in the Cantabrian mountains in the west and the other in the Pyrenees further east. Both have shown severe declines, especially in the Cantabrian population, which has recently been classified as “Crit...
Article
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Hybridisation between wild and domestic taxa raises complex questions for conservation. Genetic advances offer new methods for hybrid identification, yet social and cultural factors can influence study design, and the interpretation, application, and communication of results. A relevant illustration is hybridisation between domestic dogs (Canis lup...
Preprint
The evolution of RNA-seq technologies has yielded datasets of high scientific value that are often generated as condition associated biological replicates within differential expression studies. As the number of replicates increase, so to does confidence in identifying differentially expressed transcripts. With rapidly expanding RNA-seq data archiv...
Preprint
The Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s) 1–7 . Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM) 8,9 , until human persecutions led them to extinction 1–7 . There...
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Successful conservation depends on accurate taxonomy. Currently, the taxonomy of canids in Africa, Eurasia and Australasia is unstable as recent molecular and morphological studies have questioned earlier phenetic classifications. We review available information on several taxa of Old World and Australasian Canis with phylogenetic uncertainties (na...
Article
Investigating affiliative behaviors (e.g. proximity, grooming, cooperative behaviors) is essential to understand group cohesion and stability in animal societies, as they may foster, or be fostered by long-term social bonds and ultimately determine an individual's lifetime reproductive success. Despite growing interest in affiliative behaviors acro...
Article
Accurate estimations of adult mortality are essential for understanding population dynamics and achieving efficient management actions that are directed toward long-lived species. Several noninvasive methods may be used to monitor endangered long-lived birds like raptors, but their performance in real-world scenarios remains poorly studied. We used...
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Aim Phylogeographic studies on savanna ungulates have extensively evaluated genetic patterns mostly related to Pleistocene climatic oscillations. We address this subject through a comprehensive assessment across the pan-African range of the roan antelope, assessing whether climatic oscillations or natural physical barriers play a predominant role i...
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Habitat fragmentation and the associated landscape connectivity loss can reduce gene flow among populations, which could lead to a decrease in genetic variability, and an increase in the extinction risk of a species. The main goal of this study was to provide genetic diversity and population structure data for Pampas foxes from the southern Argenti...
Article
Generalist species are often characterized by low habitat specialization and reduced genetic structure in their populations. Here, we tested this common assumption on golden jackals in Iran, a wide country with a highly heterogeneous landscape where this carnivore is assumed to be widespread, although little is known about the ecology and populatio...
Article
Understanding population structure and spatial distribution of genetic diversity is an important aspect of developing appropriate management plans for wildlife conservation, especially for large carnivores like the puma (Puma concolor). Human persecution and habitat degradation represent the main threats to the species’ conservation in Argentina, w...
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Background Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due...
Article
The Eurasian Woodcock Scolopax rusticola is a widespread Palearctic migratory wader, with purportedly sedentary populations occurring in the Macaronesian archipelago of the Azores. Here we used microsatellite markers to investigate patterns of genetic diversity and differentiation in these insular birds, and compared Azorean populations to those fr...
Preprint
Full-text available
The evolution of RNA-Seq technologies yielded datasets that are of immense scientific value. Commonly, such data is generated within differential expression studies, where datasets derived from individual samples are grouped into conditions, and gene expression patterns quantified. The number of archived datasets is increasing and revisiting many a...
Article
Long-term monitoring studies assessing wolf population dynamics are scarce, particularly in human-dominated landscapes of southern Europe. In this work, we estimate wolf demographic parameters in northwest Portugal based on a multi-methodological approach over 20 years split into two periods (period A: 1996–2005; period B: 2007–2016). Period B take...
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Deserts are among the harshest environments on Earth. The multiple ages of different deserts and their global distribution provide a unique opportunity to study repeated adaptation at different timescales. Here, we summarize recent genomic research on the genetic mechanisms underlying desert adaptations in mammals. Several studies on different dese...
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Guinea-Bissau (GB) is a regional stronghold for primate conservation. Ten primates occur in the country, including the Western chimpanzee ( Pan troglodytes verus ) and two colobus monkeys ( Colobus polykomos and Piliocolobus badius temminckii ). Primate meat is consumed at households and bushmeat-dedicated establishments, locally named "Abafatório"...
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• One of the most celebrated textbook examples of physiological adaptations to desert environments is the unique ability that desert mammals have to produce hyperosmotic urine. Commonly perceived as an adaptation mainly observed in small rodents, the extent to which urine-concentrating ability has evolved independently in distinct mammalian lineage...
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Sarcoptic mange is globally enzootic, and non-invasive methods with high diagnostic specificity for its surveillance in wildlife are lacking. We describe the molecular detection of Sar-coptes scabiei in non-invasively collected faecal samples, targeting the 16S rDNA gene. We applied this method to 843 Iberian wolf Canis lupus signatus faecal sample...
Chapter
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Monitoring of the brown bear population in the Cantabrian Mountains has been undertaken using annual counts of the number of female bears with cubs of the year. However, the increase in the bear population and its distribution range over the past 25 years make applying this technique ever less reliable, above all in the western subpopulation. Conse...
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Roan antelope (Hippotragus equinus) is the second largest member of the Hippotraginae (Bovidae), and is widely distributed across sub-Saharan mesic woodlands. Although listed as Least Concern across its African range, population numbers are decreasing with many regional Red List statuses varying between Endangered and Locally Extinct. Although roan...
Preprint
Full-text available
Background Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due...
Preprint
Full-text available
One of the most celebrated textbook examples of physiological adaptations to desert environments is the unique ability that desert mammals have to produce hyperosmotic urine. Commonly perceived as an adaptation mainly observed in small rodents, the extent to which urine concentrating ability has independently evolved in distinct lineages, including...
Article
The hirola antelope (Beatragus hunteri) is considered to be the most endangered antelope in the world. In the ex situ translocated population at Tsavo East National Park, calf mortality and the critically low population numbers might suggest low genetic diversity and inbreeding depression. Consequently, a genetic study of the wild population is piv...
Article
Reliability of population size and density estimates is one of the most contentious issues when evaluating the conservation status of species. Non-invasive DNA monitoring, combined with spatially explicit capture-recapture approaches (SCR), is recurrently presented as a reliable procedure to achieve accurate, precise and feasible estimates. However...
Article
Full-text available
The grey wolf (Canis lupus) is one of the most widely distributed mammals in which a variety of distinct populations have been described. However, given their currently fragmented distribution and recent history of human-induced population decline, little is known about the events that led to their differentiation. Based on the analysis of whole ca...
Preprint
Full-text available
Background In the last decades, the evolution of RNA-Seq has yielded archived datasets that possess the potential for providing unprecedented inter-study insight into transcriptome evolution, once background noise has been reduced. Here we present a method to quantify intra-condition variation and to remove reference-based transcripts associated wi...
Article
Carnivores are decreasing globally due in part to anthropogenic ecological disturbances. In Argentina, human activities have fragmented wildlife habitat, thereby intensifying puma–livestock conflict and leading to population control of the predator species by hunting. We investigated genetic variability and population structure of pumas (Puma conco...
Article
The civil unrest that ravaged Angola for nearly 30 years took a heavy toll on the country's wildlife, and led to a lengthy absence of reliable information for many threatened species, including the cheetah Acinonyx jubatus and African wild dog Lycaon pictus . Using camera trapping we assessed the status of these two species in two areas of southern...
Article
Full-text available
The hirola antelope (Beatragus hunteri) is considered to be the most endangered antelope in the world. In the ex situ translocated population at Tsavo East National Park, calf mortality and the critically low population numbers might suggest low genetic diversity and inbreeding depression. Consequently, a genetic study of the wild population is piv...
Article
Full-text available
The diffusion of Neolithic technology together with the Holocene Climatic Optimum fostered the spread of human settlements and pastoral activities in North Africa, resulting in profound and enduring consequences for the dynamics of species, communities and landscapes. Here, we investigate the demographic history of the African wolf (Canis lupaster)...
Article
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The Mediterranean Basin is a global biodiversity hotspot, hosting a number of native species belonging to families that are found almost exclusively in tropical climates. Yet, whether or not these taxa were able to survive in the Mediterranean region during the Quaternary climatic oscillations remains unknown. Focusing on the European free‐tailed b...
Presentation
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El conocimiento de los límites de las poblaciones, su variabilidad genética y el movimiento de individuos entre las mismas representa un aspecto importante para la conservación de las especies silvestres. En ese marco, el objetivo general de este trabajo fue analizar la distribución de la diversidad genética del puma en Argentina, identificando gru...
Article
Haplotilapiine are members of Cichlidae (cichlid fishes), one of the most species-rich vertebrate families. Many haplotilapiines diversified via allopatric divergence, sexual selection, hybridization and ecological adaptation, making them excellent models for evolutionary research. One extraordinary example of how haplotilapiine diversified are the...
Article
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Representing a form of anthropogenic hybridization, wolf–dog interbreeding may potentially compromise the ecological and evolutionary traits of local wolf populations and corrode social tolerance towards wolves. However, estimates of the extent of wolf–dog hybridization in wolf populations are scarce, especially at a multi-pack scale and in human-d...
Article
Rüppell’s fox, Vulpes rueppellii, is one of the four fox species occurring in North Africa. Its population status and ecology remains largely unknown. Here, we collected occurrence data from camera trapping and scat-collection based mitochondrial control region sequencing to assess the distribution range and status of the species across potential h...
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Anthropogenic hybridization is widely perceived as a threat to the conservation of biodiversity. Nevertheless, to date, relevant policy and management interventions are unresolved and highly convoluted. While this is due to the inherent complexity of the issue, we hereby hypothesize that a lack of agreement concerning management goals and approache...
Article
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Genome-wide assessment of genetic diversity has the potential to increase the ability to understand admixture, inbreeding, kinship and erosion of genetic diversity affecting both captive (ex situ) and wild (in situ) populations of threatened species. The sable antelope (Hippotragus niger), native to the savannah woodlands of sub-Saharan Africa, is...
Article
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Background: Different population trajectories are expected to impact the signature of neutral and adaptive processes at multiple levels, challenging the assessment of the relative roles of different microevolutionary forces. Here, we integrate adaptive and neutral variability patterns to disentangle how adaptive diversity is driven under different...
Article
Full-text available
• Accurate analyses of the diets of predators are key to understand trophic interactions and defining conservation strategies. Diets are commonly assessed through analysis of non‐invasively collected scats, and the use of faecal DNA (fDNA) analysis can reduce the species misidentifications that could lead to biased ecological inference. • We review...