1
|
Boscari E, Palle SD, Vitulo N, Scapolatiello A, Schiavon L, Cariani A, Papetti C, Zane L, Marino IAM, Congiu L. MIPs: multi-locus intron polymorphisms in species identification and population genomics. Sci Rep 2024; 14:17870. [PMID: 39090215 PMCID: PMC11294542 DOI: 10.1038/s41598-024-68065-8] [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: 10/30/2023] [Accepted: 07/19/2024] [Indexed: 08/04/2024] Open
Abstract
The study of species groups in which the presence of interspecific hybridization or introgression phenomena is known or suspected involves analysing shared bi-parentally inherited molecular markers. Current methods are based on different categories of markers among which the classical microsatellites or the more recent genome wide approaches for the analyses of thousands of SNPs or hundreds of microhaplotypes through high throughput sequencing. Our approach utilizes intron-targeted amplicon sequencing to characterise multi-locus intron polymorphisms (MIPs) and assess genetic diversity. These highly variable intron regions, combined with inter-specific transferable loci, serve as powerful multiple-SNP markers potentially suitable for various applications, from species and hybrid identification to population comparisons, without prior species knowledge. We developed the first panel of MIPs highly transferable across fish genomes, effectively distinguishing between species, even those closely related, and populations with different structures. MIPs offer versatile, hypervariable nuclear markers and promise to be especially useful when multiple nuclear loci must be genotyped across different species, such as for the monitoring of interspecific hybridization. Moreover, the relatively long sequences obtained ease the development of single-locus PCR-based diagnostic markers. This method, here demonstrated in teleost fishes, can be readily applied to other taxa, unlocking a new source of genetic variation.
Collapse
Affiliation(s)
- Elisa Boscari
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy.
| | - Stefano Dalle Palle
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada le Grazie, 15, 37134, Verona, Italy
| | | | - Luca Schiavon
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy
| | - Alessia Cariani
- Department Biological, Geological and Environmental Sciences, University of Bologna, Campus of Ravenna, Via Sant'Alberto 163, 48123, Ravenna, Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Roma, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Chiara Papetti
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Roma, Italy
- Zoological Station Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Lorenzo Zane
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Roma, Italy
- National Biodiversity Future Center, Palermo, Italy
| | | | - Leonardo Congiu
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Roma, Italy
- National Biodiversity Future Center, Palermo, Italy
| |
Collapse
|
2
|
Adomako K, Sovi S, Kyei B, Hamidu JA, Olympio OS, Aggrey SE. Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology. PLoS One 2024; 19:e0297643. [PMID: 38696379 PMCID: PMC11065228 DOI: 10.1371/journal.pone.0297643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 01/05/2024] [Indexed: 05/04/2024] Open
Abstract
Indigenous and were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CS) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds (CC) reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers 21%) were in the highest PIC value range (0.45 to 0.50). The CC were more genetically diverse than the indigenous birds, with the highest expected heterozygosity value of 0.220. Between the commercial crossbreds population and the indigenous ecotypes, pairwise FST values were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.
Collapse
Affiliation(s)
- Kwaku Adomako
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Selorm Sovi
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Nutrigenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, Georgia, United States of America
| | - Bismark Kyei
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jacob Alhassan Hamidu
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Oscar Simon Olympio
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samuel E. Aggrey
- Nutrigenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, Georgia, United States of America
| |
Collapse
|
3
|
Santos BS, Marques MP, Ceríaco LMP. Lack of country-wide systematic herpetology collections in Portugal jeopardizes future research and conservation. AN ACAD BRAS CIENC 2024; 96:e20230622. [PMID: 38451598 DOI: 10.1590/0001-3765202420230622] [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: 05/31/2023] [Accepted: 08/27/2023] [Indexed: 03/08/2024] Open
Abstract
Natural History Collections (NHCs) represent the world's largest repositories of long-term biodiversity datasets. Specimen collection and voucher deposition has been the backbone of NHCs since their inception, but recent decades have seen a drastic decline in rates of growth via active collecting. Amphibians and reptiles are amongst the most threatened zoological groups on the planet and are historically underrepresented in most worldwide NHCs. As part of an ongoing project to review the Portuguese zoological collections in the country's NHCs, herpetological data from its three major museums and smaller collections was gathered and used to examine the coverage and representation of the different taxa extant in Portugal. These collections are not taxonomically, geographically, or temporally complete. Approximately 90% of the Portuguese herpetological taxa are represented in the country's NHCs, and around half of the taxa are represented by less than 50 specimens. Geographically, the collections cover less than 30% of the country's territory and almost all of the occurring taxa have less than 10% of their known distribution represented in the collections. A discussion on the implications for science of such incomplete collections and a review of the current status of Portuguese NHCs is presented.
Collapse
Affiliation(s)
- Bruna S Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- Universidade do Porto, Departamento de Biologia, Faculdade de Ciências, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Mariana P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- Universidade do Porto, Departamento de Biologia, Faculdade de Ciências, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Carnegie Museum of Natural History, 4400 Forbes Avenue, Pittsburgh, PA 15213, U.S.A
| | - Luis M P Ceríaco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Carnegie Museum of Natural History, 4400 Forbes Avenue, Pittsburgh, PA 15213, U.S.A
- Universidade Federal do Rio de Janeiro, Departamento de Vertebrados, Museu Nacional, Quinta da Boavista, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
| |
Collapse
|
4
|
Olah G, Waples RS, Stojanovic D. Influence of molecular marker type on estimating effective population size and other genetic parameters in a critically endangered parrot. Ecol Evol 2024; 14:e11102. [PMID: 38524913 PMCID: PMC10961163 DOI: 10.1002/ece3.11102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024] Open
Abstract
Genetics is a fast-moving field, and for conservation practitioners or ecologists, it can be bewildering. The choice of marker used in studies is fundamental; in the literature, preference has recently shifted from microsatellites to single nucleotide polymorphism (SNP) loci. Understanding how marker type affects estimates of population genetic parameters is important in the context of conservation, especially because the accuracy of estimates has a bearing on the actions taken to protect threatened species. We compare parameter estimates between seven microsatellites, 3761 SNP loci, and a random subset of 100 SNPs for the exact same 324 individual swift parrots, Lathamus discolor, and also use 457 additional samples from subsequent years to compare SNP estimates. Both marker types estimated a lower H O than H E. We show that microsatellites and SNPs mainly indicate a lack of spatial genetic structure, except when a priori collection locations were used on the SNP data in a discriminant analysis of principal components (DAPC). The 100-SNP subset gave comparable results to when the full dataset was used. Estimates of effective population size (N e) were comparable between markers when the same individuals were considered, but SNPs had narrower confidence intervals. This is reassuring because conservation assessments that rely on population genetic estimates based on a few microsatellites are unlikely to be nullified by the general shift toward SNPs in the literature. However, estimates between markers and datasets varied considerably when only adult samples were considered; hence, including samples of all age groups is recommended to be used when available. The estimated N e was higher for the full SNP dataset (2010-2019) than the smaller comparison data (2010-2015), which might be a better reflection of the species status. The lower precision of microsatellites may not necessarily be a barrier for most conservation applications; however, SNPs will improve confidence limits, which may be useful for practitioners.
Collapse
Affiliation(s)
- George Olah
- Fenner School of Environment and SocietyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Robin S. Waples
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Dejan Stojanovic
- Fenner School of Environment and SocietyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| |
Collapse
|
5
|
Koontz AC, Schumacher EK, Spence ES, Hoban SM. Ex situ conservation of two rare oak species using microsatellite and SNP markers. Evol Appl 2024; 17:e13650. [PMID: 38524684 PMCID: PMC10960078 DOI: 10.1111/eva.13650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/27/2023] [Accepted: 01/14/2024] [Indexed: 03/26/2024] Open
Abstract
Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.
Collapse
Affiliation(s)
| | | | - Emma S. Spence
- Morton ArboretumCenter for Tree ScienceLisleIllinoisUSA
- Cornell UniversityDepartment of Public and Ecosystem HealthIthacaNew YorkUSA
| | - Sean M. Hoban
- Morton ArboretumCenter for Tree ScienceLisleIllinoisUSA
| |
Collapse
|
6
|
Srikanthan P, Burg TM. Environmental drivers behind the genetic differentiation in mountain chickadees ( Poecile gambeli). Genome 2024; 67:53-63. [PMID: 37922513 DOI: 10.1139/gen-2023-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
Anthropogenic climate change has a large impact on wildlife populations and the scale of the impacts has been increasing. In this study, we utilised 3dRAD sequence data to investigate genetic divergence and identify the environmental drivers of genetic differentiation between 12 populations of mountain chickadees, family Paridae, sampled across North America. To examine patterns of genetic variation across the range, we conducted a discriminant analysis of principal components (DAPC), admixture analysis, and calculated pairwise Fst values. The DAPC revealed four clusters: southern California, eastern Rocky Mountains, northwestern Rocky Mountains, and Oregon/northern California. We then used BayeScEnv to highlight significant outlier SNPs associated with the five environmental variables. We identified over 150 genes linked to outlier SNPs associated with more than 15 pathways, including stress response and circadian rhythm. We also found a strong signal of isolation by distance and local temperature was highly correlated with genetic distance. Maxent simulations showed a northward range shift over the next 50 years and a decrease in suitable habitat, highlighting the need for immediate conservation action.
Collapse
Affiliation(s)
- P Srikanthan
- Department of Biology, University of Lethbridge, 4401 University Dr., Lethbridge, AB T1K 3M4, Canada
| | - T M Burg
- Department of Biology, University of Lethbridge, 4401 University Dr., Lethbridge, AB T1K 3M4, Canada
| |
Collapse
|
7
|
Pérez-González J, Carranza J, Anaya G, Broggini C, Vedel G, de la Peña E, Membrillo A. Comparative Analysis of Microsatellite and SNP Markers for Genetic Management of Red Deer. Animals (Basel) 2023; 13:3374. [PMID: 37958129 PMCID: PMC10650148 DOI: 10.3390/ani13213374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The analysis of population genetic structure and individual multilocus heterozygosity are crucial for wildlife management and conservation. Microsatellite markers have traditionally been used to assess these genetic parameters. However, single-nucleotide polymorphisms (SNPs) are becoming increasingly popular. Our goal here was to determine to what extent SNPs can provide better insights than microsatellites into the overall genetic status and population genetic processes in the species. To this end, we genotyped 210 red deer (Cervus elaphus) in the Spanish wild population with both 11 microsatellites and 31,712 SNPs. We compared parameters related to population genetic structure and individual multilocus heterozygosity obtained with both types of markers. Our results showed correlations between parameters measured using both microsatellites and SNPs, particularly those related to the level of genetic diversity and genetic differentiation. However, we found notably lower precision of microsatellites in measuring the distribution of genetic diversity among individuals. We conclude that microsatellites can be used to monitor the overall genetic status and detect broad patterns in red deer populations. Nevertheless, the greater precision of SNPs in inferring genetic structure and multilocus heterozygosity leads us to encourage scientists and wildlife managers to prioritize their use whenever possible.
Collapse
Affiliation(s)
- Javier Pérez-González
- Biology and Ethology Unit, Veterinary Faculty, University of Extremadura, 10003 Caceres, Spain
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
| | - Gabriel Anaya
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
- Department of Genetics, University of Cordoba, 14071 Cordoba, Spain
| | - Camilla Broggini
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
| | - Giovanni Vedel
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
| | - Eva de la Peña
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
- Institute for Game and Wildlife Research (IREC), 13005 Ciudad Real, Spain
| | - Alberto Membrillo
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
- Department of Specific Didactics, Faculty of Education Sciences, University of Cordoba, 14071 Cordoba, Spain
| |
Collapse
|
8
|
Mochales-Riaño G, Fontsere C, de Manuel M, Talavera A, Burriel-Carranza B, Tejero-Cicuéndez H, AlGethami RHM, Shobrak M, Marques-Bonet T, Carranza S. Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard ( Panthera pardus nimr). iScience 2023; 26:107481. [PMID: 37601769 PMCID: PMC10432787 DOI: 10.1016/j.isci.2023.107481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/21/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies.
Collapse
Affiliation(s)
| | - Claudia Fontsere
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Raed Hamoud M. AlGethami
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Mohammed Shobrak
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| |
Collapse
|
9
|
Nugent CM, Kess T, Brachmann MK, Langille BL, Holborn MK, Beck SV, Smith N, Duffy SJ, Lehnert SJ, Wringe BF, Bentzen P, Bradbury IR. Genomic and machine learning-based screening of aquaculture-associated introgression into at-risk wild North American Atlantic salmon (Salmo salar) populations. Mol Ecol Resour 2023. [PMID: 37246351 DOI: 10.1111/1755-0998.13811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/30/2023]
Abstract
The negative genetic impacts of gene flow from domestic to wild populations can be dependent on the degree of domestication and exacerbated by the magnitude of pre-existing genetic differences between wild populations and the domestication source. Recent evidence of European ancestry within North American aquaculture Atlantic salmon (Salmo salar) has elevated the potential impact of escaped farmed salmon on often at-risk wild North American salmon populations. Here, we compare the ability of single nucleotide polymorphism (SNP) and microsatellite (SSR) marker panels of different sizes (7-SSR, 100-SSR and 220K-SNP) to detect introgression of European genetic information into North American wild and aquaculture populations. Linear regression comparing admixture predictions for a set of individuals common to the three datasets showed that the 100-SSR panel and 7-SSR panels replicated the full 220K-SNP-based admixture estimates with low accuracy (r2 of .64 and .49, respectively). Additional tests explored the effects of individual sample size and marker number, which revealed that ~300 randomly selected SNPs could replicate the 220K-SNP admixture predictions with greater than 95% fidelity. We designed a custom SNP panel (301-SNP) for European admixture detection in future monitoring work and then developed and tested a python package, salmoneuadmix (https://github.com/CNuge/SalmonEuAdmix), which uses a deep neural network to make de novo estimates of individuals' European admixture proportion without the need to conduct complete admixture analysis utilizing baseline samples. The results demonstrate the mobilization of targeted SNP panels and machine learning in support of at-risk species conservation and management.
Collapse
Affiliation(s)
- Cameron M Nugent
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Matthew K Brachmann
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Barbara L Langille
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Melissa K Holborn
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| | - Samantha V Beck
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
- Biology Department, Dalhousie University, Halifax, Nova Scotia, Canada
- Institute for Biodiversity and Freshwater Conservation, University of the Highlands and Islands, Inverness, UK
| | - Nicole Smith
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Steven J Duffy
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Sarah J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Brendan F Wringe
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| | - Paul Bentzen
- Biology Department, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ian R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| |
Collapse
|
10
|
Skey ED, Ottewell KM, Spencer PB, Shaw RE. Empirical landscape genetic comparison of single nucleotide polymorphisms and microsatellites in three arid-zone mammals with high dispersal capacity. Ecol Evol 2023; 13:e10037. [PMID: 37153020 PMCID: PMC10154367 DOI: 10.1002/ece3.10037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Landscape genetics is increasingly transitioning away from microsatellites, with single nucleotide polymorphisms (SNPs) providing increased resolution for detecting patterns of spatial-genetic structure. This is particularly pertinent for research in arid-zone mammals due to challenges associated with unique life history traits, such as boom-bust population dynamics and long-distance dispersal capacities. Here, we provide a case study comparing SNPs versus microsatellites for testing three explicit landscape genetic hypotheses (isolation-by-distance, isolation-by-barrier, and isolation-by-resistance) in a suite of small, arid-zone mammals in the Pilbara region of Western Australia. Using clustering algorithms, Mantel tests, and linear mixed effects models, we compare functional connectivity between genetic marker types and across species, including one marsupial, Ningaui timealeyi, and two native rodents, Pseudomys chapmani and P. hermannsburgensis. SNPs resolved subtle genetic structuring not detected by microsatellites, particularly for N. timealeyi where two genetic clusters were identified. Furthermore, stronger signatures of isolation-by-distance and isolation-by-resistance were detected when using SNPs, and model selection based on SNPs tended to identify more complex resistance surfaces (i.e., composite surfaces of multiple environmental layers) in the best-performing models. While we found limited evidence for physical barriers to dispersal across the Pilbara for all species, we found that topography, substrate, and soil moisture were the main environmental drivers shaping functional connectivity. Our study demonstrates that new analytical and genetic tools can provide novel ecological insights into arid landscapes, with potential application to conservation management through identifying dispersal corridors to mediate the impacts of ongoing habitat fragmentation in the region.
Collapse
Affiliation(s)
- Ebony D. Skey
- Environmental & Conservation SciencesMurdoch UniversityPerthWestern AustraliaAustralia
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Kym M. Ottewell
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Peter B. Spencer
- Environmental & Conservation SciencesMurdoch UniversityPerthWestern AustraliaAustralia
| | - Robyn E. Shaw
- Environmental & Conservation SciencesMurdoch UniversityPerthWestern AustraliaAustralia
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
- Present address:
Division of Ecology and Evolution, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| |
Collapse
|
11
|
Molecular ecology meets systematic conservation planning. Trends Ecol Evol 2023; 38:143-155. [PMID: 36210287 DOI: 10.1016/j.tree.2022.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 08/29/2022] [Accepted: 09/12/2022] [Indexed: 01/06/2023]
Abstract
Integrative and proactive conservation approaches are critical to the long-term persistence of biodiversity. Molecular data can provide important information on evolutionary processes necessary for conserving multiple levels of biodiversity (genes, populations, species, and ecosystems). However, molecular data are rarely used to guide spatial conservation decision-making. Here, we bridge the fields of molecular ecology (ME) and systematic conservation planning (SCP) (the 'why') to build a foundation for the inclusion of molecular data into spatial conservation planning tools (the 'how'), and provide a practical guide for implementing this integrative approach for both conservation planners and molecular ecologists. The proposed framework enhances interdisciplinary capacity, which is crucial to achieving the ambitious global conservation goals envisioned for the next decade.
Collapse
|
12
|
Pérez-González J, Carranza J. Genetic Diversity of Wild Boar and Deer. Animals (Basel) 2022; 13:ani13010011. [PMID: 36611620 PMCID: PMC9817961 DOI: 10.3390/ani13010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Genetic diversity provides the long-term capacity of species, communities, and the biosphere to persist under change [...].
Collapse
Affiliation(s)
- Javier Pérez-González
- Biology and Ethology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain
- Correspondence: ; Tel.: +34-927-251-371
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Córdoba, Spain
| |
Collapse
|
13
|
Gutiérrez‐Pesquera LM, Tejedo M, Camacho A, Enriquez‐Urzelai U, Katzenberger M, Choda M, Pintanel P, Nicieza AG. Phenology and plasticity can prevent adaptive clines in thermal tolerance across temperate mountains: The importance of the elevation-time axis. Ecol Evol 2022; 12:e9349. [PMID: 36225839 PMCID: PMC9534760 DOI: 10.1002/ece3.9349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/10/2022] Open
Abstract
Critical thermal limits (CTmax and CTmin) decrease with elevation, with greater change in CTmin, and the risk to suffer heat and cold stress increasing at the gradient ends. A central prediction is that populations will adapt to the prevailing climatic conditions. Yet, reliable support for such expectation is scant because of the complexity of integrating phenotypic, molecular divergence and organism exposure. We examined intraspecific variation of CTmax and CTmin, neutral variation for 11 microsatellite loci, and micro- and macro-temperatures in larvae from 11 populations of the Galician common frog (Rana parvipalmata) across an elevational gradient, to assess (1) the existence of local adaptation through a PST-FST comparison, (2) the acclimation scope in both thermal limits, and (3) the vulnerability to suffer acute heat and cold thermal stress, measured at both macro- and microclimatic scales. Our study revealed significant microgeographic variation in CTmax and CTmin, and unexpected elevation gradients in pond temperatures. However, variation in CTmax and CTmin could not be attributed to selection because critical thermal limits were not correlated to elevation or temperatures. Differences in breeding phenology among populations resulted in exposure to higher and more variable temperatures at mid and high elevations. Accordingly, mid- and high-elevation populations had higher CTmax and CTmin plasticities than lowland populations, but not more extreme CTmax and CTmin. Thus, our results support the prediction that plasticity and phenological shifts may hinder local adaptation, promoting thermal niche conservatism. This may simply be a consequence of a coupled variation of reproductive timing with elevation (the "elevation-time axis" for temperature variation). Mid and high mountain populations of R. parvipalmata are more vulnerable to heat and cool impacts than lowland populations during the aquatic phase. All of this contradicts some of the existing predictions on adaptive thermal clines and vulnerability to climate change in elevational gradients.
Collapse
Affiliation(s)
| | - Miguel Tejedo
- Department of Evolutionary EcologyEstación Biológica de Doñana, CSICSevillaSpain
| | - Agustín Camacho
- Department of Evolutionary EcologyEstación Biológica de Doñana, CSICSevillaSpain
| | | | - Marco Katzenberger
- Department of Evolutionary EcologyEstación Biológica de Doñana, CSICSevillaSpain,Laboratory of Bioinformatics and Evolutionary Biology, Department of GeneticsUniversidade Federal de PernambucoRecifePrince Edward IslandBrazil
| | - Magdalena Choda
- Department of Organisms and Systems BiologyUniversity of OviedoOviedoSpain
| | - Pol Pintanel
- Department of Evolutionary EcologyEstación Biológica de Doñana, CSICSevillaSpain,Laboratorio de Ecofisiología and Museo de Zoología (QCAZ), Escuela de Ciencias BiológicasPontificia Universidad Católica del EcuadorQuitoEcuador
| | - Alfredo G. Nicieza
- Department of Organisms and Systems BiologyUniversity of OviedoOviedoSpain,Biodiversity Research Institute (IMIB)University of Oviedo‐Principality of Asturias‐CSICMieresSpain
| |
Collapse
|
14
|
Aylward M, Sagar V, Natesh M, Ramakrishnan U. How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200418. [PMID: 35430878 PMCID: PMC9014192 DOI: 10.1098/rstb.2020.0418] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/14/2022] [Indexed: 12/26/2022] Open
Abstract
Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60-70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.
Collapse
Affiliation(s)
- Megan Aylward
- National Centre for Biological Sciences, TIFR, Bangalore, India, 560065
| | - Vinay Sagar
- National Centre for Biological Sciences, TIFR, Bangalore, India, 560065
| | - Meghana Natesh
- Indian Institute of Science Education and Research, Tirupati, India, 517507
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, Bangalore, India, 560065
- Senior Fellow, DBT Wellcome Trust India Alliance, Hyderabad, Telangana, India, 500034
| |
Collapse
|
15
|
Ruocco M, Jahnke M, Silva J, Procaccini G, Dattolo E. 2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation. Front Genet 2022; 13:866758. [PMID: 35651946 PMCID: PMC9149362 DOI: 10.3389/fgene.2022.866758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, and Ebro Delta—Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein-coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, “regulation of transcription” and “signalling” were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients.
Collapse
Affiliation(s)
| | - Marlene Jahnke
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - João Silva
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | | | | |
Collapse
|
16
|
Marques AJD, Hanson JO, Camacho-Sanchez M, Martínez-Solano I, Moritz C, Tarroso P, Velo-Antón G, Veríssimo A, Carvalho SB. Range-wide genomic scans and tests for selection identify non-neutral spatial patterns of genetic variation in a non-model amphibian species (Pelobates cultripes). CONSERV GENET 2022. [DOI: 10.1007/s10592-021-01425-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
17
|
Li Y, Zhang X, Wang L, Sork VL, Mao L, Fang Y. Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China. ANNALS OF BOTANY 2022; 129:231-245. [PMID: 34893791 PMCID: PMC8796672 DOI: 10.1093/aob/mcab140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/31/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Contemporary patterns of genetic admixture reflect imprints of both ancient and recent gene flow, which can provide us with valuable information on hybridization history in response to palaeoclimate change. Here, we examine the relationships between present admixture patterns and past climatic niche suitability of two East Asian Cerris oaks (Quercus acutissima and Q. chenii) to test the hypothesis that the mid-Pliocene warm climate promoted while the Pleistocene cool climate limited hybridization among local closely related taxa. METHODS We analyse genetic variation at seven nuclear microsatellites (1111 individuals) and three chloroplast intergenic spacers (576 individuals) to determine the present admixture pattern and ancient hybridization history. We apply an information-theoretic model selection approach to explore the associations of genetic admixture degree with past climatic niche suitability at multiple spatial scales. KEY RESULTS More than 70 % of the hybrids determined by Bayesian clustering analysis and more than 90 % of the individuals with locally shared chloroplast haplotypes are concentrated within a mid-Pliocene contact zone between ~30°N and 35°N. Climatic niche suitabilities for Q. chenii during the mid-Pliocene Warm Period [mPWP, ~3.264-3.025 million years ago (mya)] and during the Last Glacial Maximum (LGM, ~0.022 mya) best explain the admixture patterns across all Q. acutissima populations and across those within the ancient contact zone, respectively. CONCLUSIONS Our results highlight that palaeoclimate change shapes present admixture patterns by influencing the extent of historical range overlap. Specifically, the mid-Pliocene warm climate promoted ancient contact, allowing widespread hybridization throughout central China. In contrast, the Pleistocene cool climate caused the local extinction of Q. chenii, reducing the probability of interspecific gene flow in most areas except those sites having a high level of ecological stability.
Collapse
Affiliation(s)
- Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xingwang Zhang
- School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
| | - Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - Lingfeng Mao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| |
Collapse
|
18
|
Szatmári L, Cserkész T, Laczkó L, Lanszki J, Pertoldi C, Abramov AV, Elmeros M, Ottlecz B, Hegyeli Z, Sramkó G. A comparison of microsatellites and genome-wide SNPs for the detection of admixture brings the first molecular evidence for hybridization between Mustela eversmanii and M. putorius (Mustelidae, Carnivora). Evol Appl 2021; 14:2286-2304. [PMID: 34603499 PMCID: PMC8477604 DOI: 10.1111/eva.13291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 11/30/2022] Open
Abstract
Introgressive hybridization can pose a serious threat to endangered species which have an overlapping distribution such as in the case of two polecat species, Mustela eversmanii and M. putorius, in Europe. The population size of steppe polecat is known to continuously shrink, whereas its sister species, the European polecat, is still somehow widespread. In this study, we perform an analysis using microsatellite (SSR) and genomic (SNP) data sets to identify natural hybrids between polecats. Four populations were genotyped for eight polymorphic SSR loci, and thousands of unlinked SNPs were generated using a reduced-representation sequencing approach, RADseq, to characterize the genetic make-up of allopatric populations and to identify hybrids in the sympatric area. We applied standard population genetic analyses to characterize the populations based on their SSR allelic frequency. Only a single sample out of 48 sympatric samples showed exact intermediacy that we identified as an F1 hybrid. Additionally, one specimen was indicated in the genomic data sets as backcrossed. Other backcrosses, indicated by SSRs, were not validated by SNPs, which highlights the higher efficacy of the genomic method to identify backcrossed individuals. The low frequency of hybridization suggests that the difference in habitat preference of the two species may act as a barrier to admixture. Therefore, it is apparently unlikely that polecat populations are threatened by significant introgression. The two species showed a clear genetic differentiation using both techniques. We found higher genetic diversity values in the sympatric steppe polecat population than in the other studies on polecat populations. Although M. putorius is a hunted species in most countries, genetic diversity values indicate worse conditions in Europe than in the protected sibling species M. eversmanii. Suspending hunting and providing protected status of the former seems to be reasonable and timely.
Collapse
Affiliation(s)
- Lajos Szatmári
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
| | - Tamás Cserkész
- Department of Zoology Hungarian Natural History Museum Budapest Hungary
- Bükk Mammalogical Society Eger Hungary
| | - Levente Laczkó
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
| | - József Lanszki
- Carnivore Ecology Research Group Szent István University, Kaposvár Campus Kaposvár Hungary
| | - Cino Pertoldi
- Department of Chemistry and Bioscience Aalborg University Aalborg Øst Denmark
- Aalborg Zoo Aalborg Denmark
| | - Alexei V Abramov
- Zoological Institute Russian Academy of Sciences Saint Petersburg Russia
| | - Morten Elmeros
- Department of Bioscience - Wildlife Ecology Aarhus University Rønde Denmark
| | | | - Zsolt Hegyeli
- Milvus Group Bird and Nature Protection Association Tîrgu Mureș Romania
| | - Gábor Sramkó
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
| |
Collapse
|
19
|
Abstract
Background and aims Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question. Methods We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined. Results The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders. Conclusions Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here.
Collapse
|