Claudio Quilodrán

M Claudio Quilodrán

Maître-assistant(e) @ Génomique computationnelle des populations
+41 22 379 93 67
Bureau 4-421 (Sciences II)
claudio.quilodran@unige.ch

Description

Présentation

Ma recherche concerne l’Écologie et l’Évolution avec une attention particulière portée à la Biologie de la Conservation. La conservation des espèces, comprise comme la préservation d’un système dynamique, influencée par de multiples processus évolutifs et menacés par des facteurs anthropiques, demeure mon principal objectif de recherche. Je m’intéresse à l’utilisation de nouveaux outils d’analyse quantitative et de modélisation, principalement en écologie et génétique des populations, afin de comprendre la biodiversité et d’identifier les mesures les plus efficaces à sa conservation.

Vous trouverez d'autres informations dans mon site personnel: http://www.claudioquilodran.com/

Projet de recherche

Hybridation interspécifique

L'hybridation est un processus naturel qui a eu un rôle important dans l'évolution de plusieurs groupes de plantes et d’animaux. Cependant, quand l'hybridation est due à un facteur humain, elle peut avoir de sérieuses conséquences pour la conservation de la biodiversité, en particulier pour des espèces endémiques rares ou menacées d’extinction, car si la taille de la population est trop petite, nous nous attendons à un remplacement progressif de leur génotype par des hybrides.

Ce projet de recherche vise à modéliser l'impact des modifications anthropiques sur l'intégrité génétique des organismes due à l’hybridation interspécifique. Nous mettons en évidence les effets potentiels des espèces introduites envahissantes et les modifications de l'habitat, en particulier causés par le changement climatique.

L'objectif de ce projet est d'estimer dans quelles conditions l'augmentation du taux d'hybridation peut affecter le risque d'extinction des organismes et ainsi, de fournir une orientation concernant le type de données requises pour proposer des stratégies de conservation.

Vous trouverez d'autres informations dans le site de mon Projet de thèse: http://ua.unige.ch/fr/agp/recherche/unige/cadmos/

Publications

Page
Local increases in admixture with hunter-gatherers followed the initial expansion of Neolithic farmers across continental Europe
2025
Science advances
Auteurs: Tsoupas A, Reyna-Blanco Carlos S, Quilodran C, Blöcher J, Brami M, Wegmann D, Burger J, Currat M
Voir la publication
The replacement of hunter-gatherer lifestyles by agriculture represents a pivotal change in human history. The initial stage of this Neolithic transition in Europe was instigated by the migration of farmers from Anatolia and the Aegean basin. In this study, we modeled the expansion of Neolithic farmers into central Europe along the continental route of dispersal. We used spatially explicit simulations of paleogenomic diversity and high-quality paleogenomic data from 67 prehistoric individuals to assess how population dynamics between Indigenous European hunter-gatherers and incoming farmers varied across space and time. Our results demonstrate that admixture between the two groups increased locally over time at each stage of the Neolithic expansion along the continental route. We estimate that the effective population size of farmers was about five times that of hunter-gatherers. In addition, we infer that sporadic long-distance migrations of early farmers contributed to their rapid dispersal, while competitive interactions with hunter-gatherers were limited.
Benchmarking the Mantel test and derived methods for testing association between distance matrices.
2023
Molecular ecology resources
Auteurs: Quilodrán CS, Currat M, Montoya-Burgos JI
Voir la publication
Testing the association between objects is central in ecology, evolution, and quantitative sciences in general. Two types of variables can describe the relationships between objects: point variables (measured on individual objects), and distance variables (measured between pairs of objects). The Mantel test and derived methods have been extensively used for distance variables. Yet, these methods have been criticized due to low statistical power and inflated type I error when spatial autocorrelation is present. Here, we assessed the statistical power between different types of tested variables and the type I error rate over a wider range of autocorrelation intensities than previously assessed, both on univariate and multivariate data. We also illustrated the performance of distance matrix statistics through computational simulations of genetic diversity. We show that the Mantel test and derived methods are not affected by inflated type I error when spatial autocorrelation affects only one variable when investigating correlations, or when either the response or the explanatory variable(s) is affected by spatial autocorrelation while investigating causal relationships. As previously noted, with autocorrelation affecting more variables, inflated type I error could be reduced by modifying the significance threshold. Additionally, the Mantel test has no problem of statistical power when the hypothesis is formulated in terms of distance variables. We highlight that transformation of variable types should be avoided because of the potential information loss and modification of the tested hypothesis. We propose a set of guidelines to help choose the appropriate method according to the type of variables and defined hypothesis.
Temporal variation in introgressed segments' length statistics computed from a limited number of ancient genomes sheds light on past admixture pulses.
2023
Molecular biology and evolution
Auteurs: Di Santo LN, Quilodran CS, Currat M
Voir la publication
Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remains a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomic data for a two-population system and described temporal neutral introgression patterns under a single- and two-pulse admixture model. We computed six summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within-genomes, as well as genome-wide introgression proportions and related measures. The first two statistics could confidently be used to infer inter-lineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of ancient genomes.
Past human expansions shaped the spatial pattern of Neanderthal ancestry.
2023
Science advances
Auteurs: Quilodrán CS, Rio J, Tsoupas A, Currat M
Voir la publication
The worldwide expansion of modern humans () started before the extinction of Neanderthals (). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source. We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.
A common statement on anthropogenic hybridization of the European wildcat (Felis silvestris)
2023
Frontiers in Ecology and Evolution
Auteurs: Nussberger B, Barbosa S, Beaumont M, Currat M, Devillard S, Heurich M, Howard-McCombe J, Mattucci F, Nowak C, Quilodran CS, Senn H, Alves PC and EUROWILDCAT Consortium
Voir la publication
Preserving natural genetic diversity and ecological function of wild species is a central goal in conservation biology. As such, anthropogenic hybridization is considered a threat to wild populations, as it can lead to changes in the genetic makeup of wild species and even to the extinction of wild genomes. In European wildcats, the genetic and ecological impacts of gene flow from domestic cats are mostly unknown at the species scale. However, in small and isolated populations, it is known to include genetic swamping of wild genomes. In this context, it is crucial to better understand the dynamics of hybridization across the species range, to inform and implement management measures that maintain the genetic diversity and integrity of the European wildcat. In the present paper, we aim to provide an overview of the current scientific understanding of anthropogenic hybridization in European wildcats, to clarify important aspects regarding the evaluation of hybridization given the available methodologies, and to propose guidelines for management and research priorities.
El Rayadito subantártico: disponibilidad del binomio Aphrastura subantarctica (Passeriformes, Furnariidae)
2022
Boletín del Museo Nacional de Historia Natural
Auteurs: Rozzi, R., Quilodrán , C. S. ., Botero-Delgadillo, E. ., Crego, R. D., Napolitano, C., Barroso, O., Torres-Mura , J. C. ., & Vásquez, R. A.
Voir la publication
El nombre de la especie de paseriforme Aphrastura subantarctica, propuesto por Rozzi et al. (2022), no está disponible, dado que la publicación donde el mismo fue propuesto no cumplió con todos los requisitos del Código Internacional de Nomenclatura Zoológica. En esta nota establecemos la disponibilidad del nombre de la especie Aphrastura subantarctica, cumpliendo esos requisitos.
The Subantarctic Rayadito (Aphrastura subantarctica), a new bird species on the southernmost islands of the Americas
2022
Scientific reports
Auteurs: Rozzi R, Quilodrán CS, Botero-Delgadillo E, Napolitano C, Torres-Mura JC, Barroso O, Crego RD, Bravo C, Ippi S, Quirici V, Mackenzie R, Suazo CG, Rivero-de-Aguilar J, Goffinet B, Kempenaers B, Poulin E, Vásquez RA
Voir la publication
We describe a new taxon of terrestrial bird of the genus Aphrastura (rayaditos) inhabiting the Diego Ramírez Archipelago, the southernmost point of the American continent. This archipelago is geographically isolated and lacks terrestrial mammalian predators as well as woody plants, providing a contrasted habitat to the forests inhabited by the other two Aphrastura spp. Individuals of Diego Ramírez differ morphologically from Aphrastura spinicauda, the taxonomic group they were originally attributed to, by their larger beaks, longer tarsi, shorter tails, and larger body mass. These birds move at shorter distances from ground level, and instead of nesting in cavities in trees, they breed in cavities in the ground, reflecting different life-histories. Both taxa are genetically differentiated based on mitochondrial and autosomal markers, with no evidence of current gene flow. Although further research is required to define how far divergence has proceeded along the speciation continuum, we propose A. subantarctica as a new taxonomic unit, given its unique morphological, genetic, and behavioral attributes in a non-forested habitat. The discovery of this endemic passerine highlights the need to monitor and conserve this still-pristine archipelago devoid of exotic species, which is now protected by the recently created Diego Ramírez Islands-Drake Passage Marine Park.
The extreme rainfall gradient of the Cape Horn Biosphere Reserve and its impact on forest bird richness
2022
Biodiversity and conservation
Auteurs: Quilodrán CS, Sandvig EM, Aguirre F, de Aguilar JR, Barroso O, Vásquez RA, Rozzi R
Voir la publication
A natural laboratory is a place supporting the conditions for hypothesis testing under non-anthropogenic settings. Located at the southern end of the Magellanic sub-Antarctic ecoregion in southwestern South America, the Cape Horn Biosphere Reserve (CHBR) has one of the most extreme rainfall gradients in the world. Subject to oceanic climate conditions, it is also characterized by moderate thermal fluctuations throughout the year. This makes it a unique natural laboratory for studying the effects of extreme rainfall variations on forest bird communities. Here, we monitor the bird species richness in the different forest types present in the CHBR. We found that species richness decreased with increasing precipitation, in which an increase of 100 mm in average annual precipitation showed about 1% decrease in species richness. Similar patterns were found among different forest types within the CHBR. These results provide a baseline to investigate the interactions between physical and biotic factors in a subpolar region that climatically contrasts with boreal forests, which is subject to continental climatic conditions. This research highlights the importance of ecological and ornithological long-term studies in the CHBR, which can contribute both to a higher resolution of the heterogeneity of climate changes in different regions of the world, and to orient conservation policies in the Magellanic sub-Antarctic ecoregion in the face of growing development pressures.
The wild ancestors of domestic animals as a neglected and threatened component of biodiversity
2022
Conservation biology : the journal of the Society for Conservation Biology
Auteurs: Smith WJ, Quilodrán CS, Jezierski MT, Sendell-Price AT, Clegg SM
Voir la publication
Domestic animals have immense economic, cultural, and practical value and have played pivotal roles in the development of human civilization. Many domesticates have, among their wild relatives, undomesticated forms representative of their ancestors. Resurgent interest in these ancestral forms has highlighted the unclear genetic status of many, and some are threatened with extinction by hybridization with domestic conspecifics. We considered the contemporary status of these ancestral forms relative to their scientific, practical, and ecological importance; the varied impacts of wild-domestic hybridization; and the challenges and potential resolutions involved in conservation efforts. Identifying and conserving ancestral forms, particularly with respect to disentangling patterns of gene flow from domesticates, is complex because of the lack of available genomic and phenotypic baselines. Comparative behavioral, ecological, and genetic studies of ancestral-type, feral, and domestic animals should be prioritized to establish the contemporary status of the former. Such baseline information will be fundamental in ensuring successful conservation efforts.
Editorial: The Genomics of Biological Invasion
2021
Front. Ecol. Evol.
Auteurs: McGaughran A, Mori E and Quilodrán CS
Voir la publication

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