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Burriel-Carranza B, Mochales-Riaño G, Talavera A, Els J, Estarellas M, Al Saadi S, Urriago Suarez JD, Olsson PO, Matschiner M, Carranza S. Clinging on the brink: Whole genomes reveal human-induced population declines and severe inbreeding in the Critically Endangered Emirati Leaf-toed Gecko (Asaccus caudivolvulus). Mol Ecol 2024; 33:e17451. [PMID: 38970417 DOI: 10.1111/mec.17451] [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: 01/03/2024] [Revised: 05/30/2024] [Accepted: 06/17/2024] [Indexed: 07/08/2024]
Abstract
Human-mediated habitat destruction has had a profound impact on increased species extinction rates and population declines worldwide. The coastal development in the United Arab Emirates (UAE) over the last two decades, serves as an example of how habitat transformation can alter the landscape of a country in just a few years. Here, we study the genomic implications of habitat transformation in the Critically Endangered Emirati Leaf-toed Gecko (Asaccus caudivolvulus), the only endemic vertebrate of the UAE. We generate a high-quality reference genome for this gecko, representing the first reference genome for the family Phyllodactylidae, and produce whole-genome resequencing data for 23 specimens from 10 different species of leaf-toed geckos. Our results show that A. caudivolvulus has consistently lower genetic diversity than any other Arabian species of Asaccus, suggesting a history of ancient population declines. However, high levels of recent inbreeding are recorded among populations in heavily developed areas, with a more than 50% increase in long runs of homozygosity within a 9-year period. Moreover, results suggest that this species does not effectively purge deleterious mutations, hence making it more vulnerable to future stochastic threats. Overall, results show that A. caudivolvulus is in urgent need of protection, and habitat preservation must be warranted to ensure the species' survival.
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Affiliation(s)
- Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Museu de Ciències Naturals de Barcelona, Barcelona, Spain
| | | | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Johannes Els
- Breeding Centre for Endangered Arabian Wildlife, Environment and Protected Areas Authority, Sharjah, United Arab Emirates
| | - Maria Estarellas
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | | | | | | | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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2
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Ripa A, Díaz-Caballero JA, Palacios-González MJ, Espinosa A, García-Zapata JL, Fernández-Garcia JL. Application of real-time PCR for the identification of the endangered species Galemys pyrenaicus through faecal samples. Mol Biol Rep 2024; 51:76. [PMID: 38180618 PMCID: PMC10770224 DOI: 10.1007/s11033-023-09010-2] [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: 10/05/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Currently, many micromammals are important targets for study. The endangered Galemys pyrenaicus is an outstanding example. Globally, their populations have suffered a substantial decline in last 20 years. In the surveyed area, the capture of desman is legally forbidden due to the high conservation concerns. Reason by non-invasive sampling through faeces is proposed for its monitoring. Furthermore, the confusion between faeces from desman and Mediterranean water shrews must be considered. Thus, the aim of this study was focused on developing RT-PCR assays to determine the presence of Galemys pyrenaicus and N. a. anomalus from non-invasive samples. METHODS AND RESULTS The study was conducted in the mountains of the System Central of Extremadura (Spain). A total of 186 samples were collected from 2018 to 2021 by experts where historically reported and/or our previous studies confirmed their presence. RT-PCR assays using hydrolysis probes were designed to detect genetic material from both desman and Mediterranean water shrews and its specificity was confirmed. The reliability of the method was further assessed by PCR sequencing of mitochondrial Cyb and d-loop, resulting fully compatible with the RT-PCR approach. Intraspecific phylogenetic relationship was reported to improve knowledge about mtDNA variability in the desman from the Central System. CONCLUSIONS We demonstrated that RT-PCR gives a gold opportunity to further map the species using faeces which minimizes disturbance and reports both population status and individual presence. Cost-effective RT-PCR combined with field-collected faeces allows us to better investigate the full range of occurrence of the species.
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Affiliation(s)
- Adriana Ripa
- Genetic and Animal Breeding, Faculty of Veterinary, Universidad de Extremadura, 10071, Cáceres, Spain
| | - José A Díaz-Caballero
- Dirección General Sostenibilidad, Consejería Para La Transición Ecológica y Sostenibilidad, Junta de Extremadura, 06800, Merida, Spain
- Área del Medio Natural, Sociedad de Gestión Pública de Extremadura (GPEX), Junta de Extremadura, Mérida, España
| | - María Jesús Palacios-González
- Dirección General Sostenibilidad, Consejería Para La Transición Ecológica y Sostenibilidad, Junta de Extremadura, 06800, Merida, Spain
| | - Antonio Espinosa
- Genetic and Animal Breeding, Faculty of Veterinary, Universidad de Extremadura, 10071, Cáceres, Spain
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3
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Ripa A, Díaz-Caballero JA, Palacios-González MJ, Zalba J, Espinosa A, García-Zapata JL, Gómez-Martín A, Tkach V, Fernández-Garcia JL. Non-Invasive Wildlife Disease Surveillance Using Real Time PCR Assays: The Case of the Endangered Galemys pyrenaicus Populations from the Central System Mountains (Extremadura, Spain). Animals (Basel) 2023; 13:ani13071136. [PMID: 37048392 PMCID: PMC10093302 DOI: 10.3390/ani13071136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
The Iberian desman (Galemys pyrenaicus) is a small semi-aquatic mammal that inhabits mountainous areas from the centre to the north of the Iberian Peninsula and the Pyrenees and is listed as endangered because it has suffered a serious decline. Since 1960, only three species of digeneans (Omphalometra flexuosa, Maritrema pyrenaica and Mathovius galemydis) and two nematodes (Aonchotheca galemydis and Paracuaria hispanica) have been reported from the desman, but no further information on health status and no data from Extremadura has been available. The aim of our study was to characterise the diversity and distribution of parasites and microbiomes of desmans in different areas of the Central System of Extremadura. Between 2019 and 2021 we collected 238 fecal samples and one tissue (intestine) sample that was obtained from a dead desman. DNA templates were processed by commercial or customised real-time PCR using TaqMan probes. Representative data were obtained for Cryptosporidium spp., Omphalometra spp., Eimeria spp., Salmonella spp., Staphylococcus spp. and Leptospira spp. Omphalometra spp. was studied using a newly developed PCR test. The screening of the dead desman allowed us to obtain, for the first time, a partial sequence of the 18SrDNA. This study is the most complete study of the desman, allowing us to identify parasites and the microbiome in populations of G. pyrenaicus using non-invasive sampling.
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Affiliation(s)
- Adriana Ripa
- Genetic and Animal Breeding, Faculty of Veterinary, University of Extremadura, 10071 Cáceres, Spain
| | - José A Díaz-Caballero
- Dirección General Sostenibilidad, Consejería Para la Transición Ecológica y Sostenibilidad, Junta de Extremadura, 06800 Merida, Spain
| | - María Jesús Palacios-González
- Dirección General Sostenibilidad, Consejería Para la Transición Ecológica y Sostenibilidad, Junta de Extremadura, 06800 Merida, Spain
| | - Javier Zalba
- Dirección General Sostenibilidad, Consejería Para la Transición Ecológica y Sostenibilidad, Junta de Extremadura, 06800 Merida, Spain
| | - Antonio Espinosa
- Genetic and Animal Breeding, Faculty of Veterinary, University of Extremadura, 10071 Cáceres, Spain
| | | | - Ana Gómez-Martín
- Genetic and Animal Breeding, Faculty of Veterinary, University of Extremadura, 10071 Cáceres, Spain
| | - Vasyl Tkach
- Department of Biology, University of North Dakota, Grand Forks, ND 58201, USA
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4
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Hogg CJ, Silver L, McLennan EA, Belov K. Koala Genome Survey: An Open Data Resource to Improve Conservation Planning. Genes (Basel) 2023; 14:genes14030546. [PMID: 36980819 PMCID: PMC10048327 DOI: 10.3390/genes14030546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Genome sequencing is a powerful tool that can inform the management of threatened species. Koalas (Phascolarctos cinereus) are a globally recognized species that captured the hearts and minds of the world during the 2019/2020 Australian megafires. In 2022, koalas were listed as ‘Endangered’ in Queensland, New South Wales, and the Australian Capital Territory. Populations have declined because of various threats such as land clearing, habitat fragmentation, and disease, all of which are exacerbated by climate change. Here, we present the Koala Genome Survey, an open data resource that was developed after the Australian megafires. A systematic review conducted in 2020 demonstrated that our understanding of genomic diversity within koala populations was scant, with only a handful of SNP studies conducted. Interrogating data showed that only 6 of 49 New South Wales areas of regional koala significance had meaningful genome-wide data, with only 7 locations in Queensland with SNP data and 4 locations in Victoria. In 2021, we launched the Koala Genome Survey to generate resequenced genomes across the Australian east coast. We have publicly released 430 koala genomes (average coverage: 32.25X, range: 11.3–66.8X) on the Amazon Web Services Open Data platform to accelerate research that can inform current and future conservation planning.
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Martin CA, Sheppard EC, Illera JC, Suh A, Nadachowska-Brzyska K, Spurgin LG, Richardson DS. Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird. Mol Ecol 2023; 32:1972-1989. [PMID: 36704917 DOI: 10.1111/mec.16865] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations and drive speciation. Across island systems, contemporary patterns of genetic diversity reflect population demography, including colonization events, bottlenecks, gene flow and genetic drift. Here, we investigate genome-wide diversity and the distribution of runs of homozygosity (ROH) using whole-genome resequencing of individuals (>22× coverage) from six populations across three archipelagos of Berthelot's pipit (Anthus berthelotii)-a passerine that has recently undergone island speciation. We show the most dramatic reduction in diversity occurs between the mainland sister species (the tawny pipit) and Berthelot's pipit and is lowest in the populations that have experienced sequential bottlenecks (i.e., the Madeiran and Selvagens populations). Pairwise sequential Markovian coalescent (PSMC) analyses estimated that Berthelot's pipit diverged from its sister species ~2 million years ago, with the Madeiran archipelago founded 50,000 years ago, and the Selvagens colonized 8000 years ago. We identify many long ROH (>1 Mb) in these most recently colonized populations. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). However, the extensive long and short ROH detected in the Selvagens suggest strong recent inbreeding and bottleneck effects, with as much as 38% of the autosomes consisting of ROH >250 kb. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.
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Affiliation(s)
- Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | | | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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Deschepper P, Vanbergen S, Zhang Y, Li Z, Hassani IM, Patel NA, Rasolofoarivao H, Singh S, Wee SL, De Meyer M, Virgilio M, Delatte H. Bactrocera dorsalis in the Indian Ocean: A tale of two invasions. Evol Appl 2023; 16:48-61. [PMID: 36699130 PMCID: PMC9850006 DOI: 10.1111/eva.13507] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
An increasing number of invasive fruit fly pests are colonizing new grounds. With this study, we aimed to uncover the invasion pathways of the oriental fruit fly, Bactrocera dorsalis into the islands of the Indian Ocean. By using genome-wide SNP data and a multipronged approach consisting of PCA, ancestry analysis, phylogenetic inference, and kinship networks, we were able to resolve two independent invasion pathways. A western invasion pathway involved the stepping-stone migration of B. dorsalis from the east African coast into the Comoros, along Mayotte and into Madagascar with a decreasing genetic diversity. The Mascarene islands (Reunion and Mauritius), on the contrary, were colonized directly from Asia and formed a distinct cluster. The low nucleotide diversity suggests that only a few genotypes invaded the Mascarenes. The presence of many long runs of homozygosity (ROH) in the introduced populations is indicative of population bottlenecks, with evidence of a more severe bottleneck for populations along the western migration pathway than on the Mascarene islands. More strict phytosanitary regulations are recommended in order to prevent the further spread of B. dorsalis.
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Affiliation(s)
- Pablo Deschepper
- Invertebrates SectionRoyal Museum for Central AfricaTervurenBelgium
| | - Sam Vanbergen
- Invertebrates SectionRoyal Museum for Central AfricaTervurenBelgium
| | - Yue Zhang
- College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Key Laboratory of Surveillance and Management for Plant Quarantine PestsMinistry of Agriculture and Rural AffairsBeijingChina
| | - Zhihong Li
- College of Plant ProtectionChina Agricultural UniversityBeijingChina
- Key Laboratory of Surveillance and Management for Plant Quarantine PestsMinistry of Agriculture and Rural AffairsBeijingChina
| | - Issa Mze Hassani
- National Research Institute for Agriculture, Fisheries and Environment, Ex‐CEFADERMdeComoros
| | | | | | - Sandeep Singh
- Department of Fruit SciencePunjab Agricultural UniversityLudhianaIndia
| | - Suk Ling Wee
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, Centre for Insect SystematicsUniversiti Kebangsaan MalaysiaBangiMalaysia
| | - Marc De Meyer
- Invertebrates SectionRoyal Museum for Central AfricaTervurenBelgium
| | | | - Hélène Delatte
- FOFIFA CENRADERU‐DRAAmbatobeMadagascar
- CIRAD, UMR PVBMTAntananarivoMadagascar
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7
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Gutiérrez J, Aleix-Mata G, Montiel EE, Cabral-de-Mello DC, Marchal JA, Sánchez A. Satellitome Analysis on Talpa aquitania Genome and Inferences about the satDNAs Evolution on Some Talpidae. Genes (Basel) 2022; 14:117. [PMID: 36672858 PMCID: PMC9859602 DOI: 10.3390/genes14010117] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
In the genus Talpa a new species, named Talpa aquitania, has been recently described. Only cytogenetic data are available for the nuclear genome of this species. In this work, we characterize the satellitome of the T. aquitania genome that presents 16 different families, including telomeric sequences, and they represent 1.24% of the genome. The first satellite DNA family (TaquSat1-183) represents 0.558%, and six more abundant families, including TaquSat1-183, comprise 1.13%, while the remaining 11 sat-DNAs represent only 0.11%. The average A + T content of the SatDNA families was 50.43% and the median monomer length was 289.24 bp. The analysis of these SatDNAs indicated that they have different grades of clusterization, homogenization, and degeneration. Most of the satDNA families are present in the genomes of the other Talpa species analyzed, while in the genomes of other more distant species of Talpidae, only some of them are present, in accordance with the library hypothesis. Moreover, chromosomal localization by FISH revealed that some satDNAs are localized preferentially on centromeric and non-centromeric heterochromatin in T. aquitania and also in the sister species T. occidentalis karyotype. The differences observed between T. aquitania and the close relative T. occidentalis and T. europaea suggested that the satellitome is a very dynamic component of the genomes and that the satDNAs could be responsible for chromosomal differences between the species. Finally, in a broad context, these data contribute to the understanding of the evolution of satellitomes on mammals.
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Affiliation(s)
- Juana Gutiérrez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Gaël Aleix-Mata
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Eugenia E. Montiel
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Diogo C. Cabral-de-Mello
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP—Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900, Brazil
| | - Juan Alberto Marchal
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
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8
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Escoda L, Hawlitschek O, González-Esteban J, Castresana J. Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity. Sci Rep 2022; 12:21390. [PMID: 36496459 PMCID: PMC9741620 DOI: 10.1038/s41598-022-25619-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq technique, which generated 1421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.
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Affiliation(s)
- Lídia Escoda
- grid.507636.10000 0004 0424 5398Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003 Barcelona, Spain
| | - Oliver Hawlitschek
- grid.507636.10000 0004 0424 5398Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003 Barcelona, Spain ,grid.517093.90000 0005 0294 9006Leibniz Institute for the Analysis of Biodiversity Change, Centre for Molecular Biodiversity Research, Zoological Museum, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | | | - Jose Castresana
- grid.507636.10000 0004 0424 5398Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003 Barcelona, Spain
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Lucati F, Miró A, Bosch J, Caner J, Jowers MJ, Rivera X, Donaire-Barroso D, Rebelo R, Ventura M. New insights on patterns of genetic admixture and phylogeographic history in Iberian high mountain populations of midwife toads. PLoS One 2022; 17:e0277298. [PMID: 36454960 PMCID: PMC9714896 DOI: 10.1371/journal.pone.0277298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/24/2022] [Indexed: 12/05/2022] Open
Abstract
Multiple Quaternary glacial refugia in the Iberian Peninsula, commonly known as "refugia within refugia", allowed diverging populations to come into contact and admix, potentially boosting substantial mito-nuclear discordances. In this study, we employ a comprehensive set of mitochondrial and nuclear markers to shed light onto the drivers of geographical differentiation in Iberian high mountain populations of the midwife toads Alytes obstetricans and A. almogavarii from the Pyrenees, Picos de Europa and Guadarrama Mountains. In the three analysed mountain regions, we detected evidence of extensive mito-nuclear discordances and/or admixture between taxa. Clustering analyses identified three major divergent lineages in the Pyrenees (corresponding to the eastern, central and central-western Pyrenees), which possibly recurrently expanded and admixed during the succession of glacial-interglacial periods that characterised the Late Pleistocene, and that currently follow a ring-shaped diversification pattern. On the other hand, populations from the Picos de Europa mountains (NW Iberian Peninsula) showed a mitochondrial affinity to central-western Pyrenean populations and a nuclear affinity to populations from the central Iberian Peninsula, suggesting a likely admixed origin for Picos de Europa populations. Finally, populations from the Guadarrama Mountain Range (central Iberian Peninsula) were depleted of genetic diversity, possibly as a consequence of a recent epidemic of chytridiomycosis. This work highlights the complex evolutionary history that shaped the current genetic composition of high mountain populations, and underscores the importance of using a multilocus approach to better infer the dynamics of population divergence.
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Affiliation(s)
- Federica Lucati
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
- Sociodemography Research Group (DemoSoc), University Pompeu Fabra (UPF), Barcelona, Spain
| | - Alexandre Miró
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
| | - Jaime Bosch
- IMIB-Research Unit of Biodiversity (CSIC/UO/PA), Universidad de Oviedo, Mieres, Spain
- Centro de Investigación, Seguimiento y Evaluación, Parque Nacional Sierra de Guadarrama, Rascafría, Spain
| | - Jenny Caner
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
| | - Michael Joseph Jowers
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
- National Institute of Ecology (NIE), Maseo-myeon, Seocheon-gun, Republic of Korea
| | - Xavier Rivera
- Catalan Society of Herpetology, Museu Blau, Barcelona, Catalonia, Spain
| | | | - Rui Rebelo
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Marc Ventura
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
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10
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Balmori-de la Puente A, Ventura J, Miñarro M, Somoano A, Hey J, Castresana J. Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola. Sci Rep 2022; 12:4065. [PMID: 35260719 PMCID: PMC8904462 DOI: 10.1038/s41598-022-07877-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/21/2022] [Indexed: 01/18/2023] Open
Abstract
Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.
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Affiliation(s)
- Alfonso Balmori-de la Puente
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain.,Àrea de Recerca en Petits Mamífers, Granollers Museum of Natural Sciences, Palaudàries, 102, 08402, Granollers, Barcelona, Spain
| | - Marcos Miñarro
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra AS-267, PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Aitor Somoano
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra AS-267, PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain.
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Xie HX, Liang XX, Chen ZQ, Li WM, Mi CR, Li M, Wu ZJ, Zhou XM, Du WG. Ancient demographics determine the effectiveness of genetic purging in endangered lizards. Mol Biol Evol 2021; 39:6468625. [PMID: 34919713 PMCID: PMC8788223 DOI: 10.1093/molbev/msab359] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The purging of deleterious alleles has been hypothesized to mitigate inbreeding depression, but its effectiveness in endangered species remains debatable. To understand how deleterious alleles are purged during population contractions, we analyzed genomes of the endangered Chinese crocodile lizard (Shinisaurus crocodilurus), which is the only surviving species of its family and currently isolated into small populations. Population genomic analyses revealed four genetically distinct conservation units and sharp declines in both effective population size and genetic diversity. By comparing the relative genetic load across populations and conducting genomic simulations, we discovered that seriously deleterious alleles were effectively purged during population contractions in this relict species, although inbreeding generally enhanced the genetic burden. However, despite with the initial purging, our simulations also predicted that seriously deleterious alleles will gradually accumulate under prolonged bottlenecking. Therefore, we emphasize the importance of maintaining a minimum population capacity and increasing the functional genetic diversity in conservation efforts to preserve populations of the crocodile lizard and other endangered species.
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Affiliation(s)
- Hong-Xin Xie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi-Xi Liang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhi-Qiang Chen
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Wei-Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chun-Rong Mi
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zheng-Jun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education (Guangxi Normal University, Guilin, 541004, China ).,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, 541006, China
| | - Xu-Ming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei-Guo Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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