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Vlček J, Espinoza‐Ulloa S, Cowles SA, Ortiz‐Catedral L, Coutu C, Chaves JA, Andrés J, Štefka J. Genomes of Galápagos Mockingbirds Reveal the Impact of Island Size and Past Demography on Inbreeding and Genetic Load in Contemporary Populations. Mol Ecol 2025; 34:e17665. [PMID: 39912126 PMCID: PMC11842953 DOI: 10.1111/mec.17665] [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] [Received: 09/27/2024] [Revised: 01/10/2025] [Accepted: 01/17/2025] [Indexed: 02/07/2025]
Abstract
Restricted range size brings about noteworthy genetic consequences that may affect the viability of a population and eventually its extinction. Particularly, the question if an increase in inbreeding can avert the accumulation of genetic load via purging is hotly debated in the conservation genetic field. Insular populations with limited range sizes represent an ideal setup for relating range size to these genetic factors. Leveraging a set of eight differently sized populations of Galápagos mockingbirds (Mimus), we investigated how island size shaped effective population size (Ne), inbreeding and genetic load. We assembled a genome of M. melanotis and genotyped three individuals per population by whole-genome resequencing. Demographic inference showed that the Ne of most populations remained high after the colonisation of the archipelago 1-2 Mya. Ne decline in M. parvulus happened only 10-20 Kya, whereas the critically endangered M. trifasciatus showed a longer history of reduced Ne. Despite these historical fluctuations, the current island size determines Ne in a linear fashion. In contrast, significant inbreeding coefficients, derived from runs of homozygosity, were identified only in the four smallest populations. The index of additive genetic load suggested purging in M. parvulus, where the smallest populations showed the lowest load. By contrast, M. trifasciatus carried the highest genetic load, possibly due to a recent rapid bottleneck. Overall, our study demonstrates a complex effect of demography on inbreeding and genetic load, providing implications in conservation genetics in general and in a conservation project of M. trifasciatus in particular.
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Affiliation(s)
- Jakub Vlček
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- Institute of Parasitology, Biology Centre CASČeské BudějoviceCzech Republic
- Department of Botany, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Sebastian Espinoza‐Ulloa
- Department of BiologyUniversity of SaskatchewanSaskatoonCanada
- Facultad de MedicinaPontificia Universidad Católica del EcuadorQuitoEcuador
| | - Sarah A. Cowles
- Department of BiologyUniversity of MiamiCoral GablesFloridaUSA
| | - Luis Ortiz‐Catedral
- School of Natural Sciences, Ecology & Conservation LabMassey UniversityAucklandNew Zealand
| | - Cathy Coutu
- Agriculture & Agri‐Food CanadaSaskatoonCanada
| | - Jaime A. Chaves
- Laboratorio de Biología Evolutiva, Instituto Biósfera, Colegio de Ciencias Biologicas y AmbientalesUniversidad San Francisco de QuitoQuitoEcuador
- Department of BiologySan Francisco State UniversitySan FranciscoCaliforniaUSA
- Galapagos Science CenterUniversidad San Francisco de QuitoQuitoEcuador
| | - Jose Andrés
- Department of BiologyUniversity of SaskatchewanSaskatoonCanada
| | - Jan Štefka
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- Institute of Parasitology, Biology Centre CASČeské BudějoviceCzech Republic
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Cui J, Batley KC, Silver LW, McLennan EA, Hogg CJ, Belov K. Spatial variation in toll-like receptor diversity in koala populations across their geographic distribution. Immunogenetics 2024; 77:5. [PMID: 39614880 PMCID: PMC11608166 DOI: 10.1007/s00251-024-01365-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Accepted: 11/25/2024] [Indexed: 01/29/2025]
Abstract
The koala (Phascolarctos cinereus) is an iconic Australian species that is listed as endangered in the northern parts of its range due to loss of habitat, disease, and road deaths. Diseases contribute significantly to the decline of koala populations, primarily Chlamydia and koala retrovirus. The distribution of these diseases across the species' range, however, is not even. Toll-like receptors (TLRs) play a crucial role in innate immunity by recognising and responding to various pathogens. Variations in TLR genes can influence an individual's susceptibility or resistance to infectious diseases. The aim of this study was to identify koala TLR diversity across the east coast of Australia using 413 re-sequenced genomes at 30 × coverage. We identified 45 single-nucleotide polymorphisms (SNP) leading to 51 alleles within ten TLR genes. Our results show that the diversity of TLR genes in the koala forms four distinct genetic groups, which are consistent with the diversity of the koala major histocompatibility complex (MHC), another key immune gene family. The bioinformatics approach presented here has broad applicability to other threatened species with existing genomic resources.
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Affiliation(s)
- Jian Cui
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Kimberley C Batley
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Luke W Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia
| | - Elspeth A McLennan
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia.
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia
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Liang C, Sun L, Zhu Y, Wu J, Zhao A, Huang T, Yan F, He K. Local chicken breeds exhibit abundant TCR-V segments but similar repertoire diversity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 157:105196. [PMID: 38762097 DOI: 10.1016/j.dci.2024.105196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/22/2024] [Accepted: 05/16/2024] [Indexed: 05/20/2024]
Abstract
The thymus-derived lymphocytes of jawed vertebrates have four T-cell receptor (TCR) chains that play a significant role in immunity. As chickens have commercial value, their immune systems require a great deal of attention. Local chicken breeds are an essential part of poultry genetic resources in China. Here, we used high-throughput sequencing to analyze the TCRα and TCRβ repertoires and their relative expression levels in the native chicken breeds Baier Buff, Longyou Partridge, Xiaoshan, and Xianju. We found that TCR Vα and TCR Vβ were expressed and included 17, 19, 17, and six segments of the Vα2, Vα3, Vβ1, and Vβ2 subgroups, respectively. V-J pairing was biased; Jα11 was utilized by nearly all Vα segments and was the most commonly used. Breed-specific V segments and V-J pairings were detected as well. The results of the principal coordinate analysis (PCoA) as well as the V-J pairing and CDR3 diversity analyses suggested that the four local chicken breeds did not significantly differ in terms of TCR diversity. Hence, they expressed not significant differentiation, and they are rich genetic resources for the development and utilization of immune-related poultry breeding.
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Affiliation(s)
- Chunhong Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Lin Sun
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Jianqing Wu
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Ayong Zhao
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Tao Huang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Feifei Yan
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China.
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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