1
|
Lobo D, López-Bao JV, Godinho R. The population bottleneck of the Iberian wolf impacted genetic diversity but not admixture with domestic dogs: A temporal genomic approach. Mol Ecol 2023; 32:5986-5999. [PMID: 37855673 DOI: 10.1111/mec.17171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023]
Abstract
After decades of intense persecution, the Iberian wolf subspecies faced a severe bottleneck in the 1970s that considerably reduced its range and population size, nearly leading to its extinction in central and southern Iberian Peninsula. Such population decline could have impacted the genetic diversity of Iberian wolves through different processes, namely genetic drift and dynamics of hybridization with domestic dogs. By contrasting the genomes of 68 contemporary with 54 historical samples spanning the periods before and immediately after the 1970s bottleneck, we found evidence of its impact on genetic diversity and dynamics of wolf-dog hybridization. Our genome-wide assessment revealed that wolves and dogs form two well-differentiated genetic groups in Iberia and that hybridization rates did not increase during the bottleneck. However, an increased number of hybrid individuals was found over time during the population re-expansion, particularly at the edge of the wolf range. We estimated a low percentage of dog ancestry (~1.4%) in historical samples, suggesting that dog introgression was not a key driver for wolf extinction in central and southern Iberia. Our findings also unveil a significant decline in genetic diversity in contemporary samples, with the highest proportion of homozygous segments in the genome being recently inherited. Overall, our study provides unprecedented insight into the impact of a sharp decline on the Iberian wolf genome and refines our understanding of the ecological and evolutionary drivers of wolf-dog hybridization in the wild.
Collapse
Affiliation(s)
- Diana Lobo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - José Vicente López-Bao
- Biodiversity Research Institute (CSIC - Oviedo University - Principality of Asturias) Oviedo University, Mieres, Spain
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| |
Collapse
|
2
|
Pacheco H, Lopes AM, Bárcena J, Blanco E, Abrantes J, Esteves P, Choquet R, Alves PC, Santos N. Multi‐event capture‐recapture models estimate the diagnostic performance of serological tests for myxoma and rabbit haemorrhagic disease viruses in the absence of reference samples. Transbound Emerg Dis 2022; 69:e3024-e3035. [DOI: 10.1111/tbed.14657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Henrique Pacheco
- CIISA – Centro de Investigação Interdisciplinar em Sanidade Animal Faculty of Veterinary Medicine University of Lisbon Lisbon Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal
| | - Ana M. Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS)/Unidade Multidisciplinar de Investigação Biomédica (UMIB) University of Porto Porto Portugal
| | - Juan Bárcena
- Centro de Investigación en Sanidad Animal (CISA‐INIA/CSIC) Valdeolmos Madrid Spain
| | - Esther Blanco
- Centro de Investigación en Sanidad Animal (CISA‐INIA/CSIC) Valdeolmos Madrid Spain
| | - Joana Abrantes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal
- Department of Biology Faculty of Sciences University of Porto Porto Portugal
| | - Pedro Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal
- Department of Biology Faculty of Sciences University of Porto Porto Portugal
| | - Rémi Choquet
- CEFE – Centre d’Écologie Fonctionnelle et Évolutive Univ Montpellier CNRS EPHE, IRD Montpellier France
| | - Paulo Célio Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal
- Department of Biology Faculty of Sciences University of Porto Porto Portugal
- Estação Biológica de Mértola (EBM) CIBIO Mértola Portugal
| | - Nuno Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal
- Estação Biológica de Mértola (EBM) CIBIO Mértola Portugal
| |
Collapse
|
3
|
Santostasi NL, Gimenez O, Caniglia R, Fabbri E, Molinari L, Reggioni W, Ciucci P. Estimating Admixture at the Population Scale: Taking Imperfect Detectability and Uncertainty in Hybrid Classification Seriously. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nina L. Santostasi
- Department of Biology and Biotechnologies “Charles Darwin” University of Rome La Sapienza Rome Italy
| | - Olivier Gimenez
- CEFE, CNRS University of Montpellier, University Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| | - Romolo Caniglia
- Italian Institute for Environmental Protection and Research (ISPRA), Unit for Conservation Genetics (BIO–CGE), Ozzano dell'Emilia Italy
| | - Elena Fabbri
- Italian Institute for Environmental Protection and Research (ISPRA), Unit for Conservation Genetics (BIO–CGE), Ozzano dell'Emilia Italy
| | - Luigi Molinari
- Wolf Apennine Center, Appennino Tosco‐Emiliano National Park, Ligonchio Italy
| | - Willy Reggioni
- Wolf Apennine Center, Appennino Tosco‐Emiliano National Park, Ligonchio Italy
| | - Paolo Ciucci
- CEFE, CNRS University of Montpellier, University Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| |
Collapse
|
4
|
Santostasi NL, Ciucci P, Bearzi G, Bonizzoni S, Gimenez O. Assessing the dynamics of hybridization through a matrix modelling approach. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2020.109120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
5
|
Caniglia R, Galaverni M, Velli E, Mattucci F, Canu A, Apollonio M, Mucci N, Scandura M, Fabbri E. A standardized approach to empirically define reliable assignment thresholds and appropriate management categories in deeply introgressed populations. Sci Rep 2020; 10:2862. [PMID: 32071323 PMCID: PMC7028925 DOI: 10.1038/s41598-020-59521-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/28/2020] [Indexed: 11/09/2022] Open
Abstract
Anthropogenic hybridization is recognized as a major threat to the long-term survival of natural populations. While identifying F1 hybrids might be simple, the detection of older admixed individuals is far from trivial and it is still debated whether they should be targets of management. Examples of anthropogenic hybridization have been described between wolves and domestic dogs, with numerous cases detected in the Italian wolf population. After selecting appropriate wild and domestic reference populations, we used empirical and simulated 39-autosomal microsatellite genotypes, Bayesian assignment and performance analyses to develop a workflow to detect different levels of wolf x dog admixture. Membership proportions to the wild cluster (qiw) and performance indexes identified two q-thresholds which allowed to efficiently classify the analysed genotypes into three assignment classes: pure (with no or negligible domestic ancestry), older admixed (with a marginal domestic ancestry) and recent admixed (with a clearly detectable domestic ancestry) animals. Based on their potential to spread domestic variants, such classes were used to define three corresponding management categories: operational pure, introgressed and operational hybrid individuals. Our multiple-criteria approach can help wildlife managers and decision makers in more efficiently targeting the available resources for the long-term conservation of species threatened by anthropogenic hybridization.
Collapse
Affiliation(s)
- Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy.
| | | | - Edoardo Velli
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Federica Mattucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Antonio Canu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marco Apollonio
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Massimo Scandura
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| |
Collapse
|
6
|
Salvatori V, Godinho R, Braschi C, Boitani L, Ciucci P. High levels of recent wolf × dog introgressive hybridization in agricultural landscapes of central Italy. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1313-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
7
|
Robinson RA, Gardner B. Advances in modelling demographic processes: The Euring 2017 Analytical Meeting. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Robert A. Robinson
- European Union of Ring Schemes (Euring) and British Trust for OrnithologyThe Nunnery Thetford UK
| | - Beth Gardner
- School of Environmental and Forest SciencesUniversity of Washington Seattle Washington
| |
Collapse
|