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Napolitano C, Sacristán I, Acuña F, Aguilar E, García S, López-Jara MJ, Cabello J, Hidalgo-Hermoso E, Poulin E, Grueber CE. Assessing micro-macroparasite selective pressures and anthropogenic disturbance as drivers of immune gene diversity in a Neotropical wild cat. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:166289. [PMID: 37591403 DOI: 10.1016/j.scitotenv.2023.166289] [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: 04/05/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023]
Abstract
Anthropogenic environmental change is reducing available habitat for wild species, providing novel selection pressures such as infectious diseases and causing species to interact in new ways. The potential for emerging infectious diseases and zoonoses at the interface between humans, domestic animals, and wild species is a key global concern. In vertebrates, diversity at the major histocompatibility complex MHC is critical to disease resilience, and its study in wild populations provides insights into eco-evolutionary dynamics that human activities alter. In natural populations, variation at MHC loci is partly maintained by balancing selection, driven by pathogenic selective pressures. We hypothesize that MHC genetic diversity differs between guigna populations inhabiting human-dominated landscapes (higher pathogen pressures) versus more natural habitats (lower pathogen pressures). We predict that MHC diversity in guignas would be highest in human-dominated landscapes compared with continuous forest habitats. We also expected to find higher MHC diversity in guignas infected with micro and macro parasites (higher parasite load) versus non infected guignas. We characterized for the first time the genetic diversity at three MHC class I and II exons in 128 wild guignas (Leopardus guigna) across their distribution range in Chile (32-46° S) and Argentina, representing landscapes with varying levels of human disturbance. We integrated MHC sequence diversity with multiple measures of anthropogenic disturbance and both micro and macro parasite infection data. We also assessed signatures of positive selection acting on MHC genes. We found significantly higher MHC class I diversity in guignas inhabiting landscapes where houses were present, and with lower percentage of vegetation cover, and also in animals with more severe cardiorespiratory helminth infection (richness and intensity) and micro-macroparasite co-infection. This comprehensive, landscape-level assessment further enhances our knowledge on the evolutionary dynamics and adaptive potential of vertebrates in the face of emerging infectious disease threats and increasing anthropogenic impacts.
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Affiliation(s)
- Constanza Napolitano
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile; Institute of Ecology and Biodiversity (IEB), Concepción, Chile; Cape Horn International Center (CHIC), Puerto Williams, Chile.
| | - Irene Sacristán
- Universidad Andres Bello, Santiago, Chile; Animal Health Research Centre, National Institute for Agricultural and Food Research and Technology (INIA), Centro Superior de Investigaciones Científicas (CSIC), Valdeolmos, Madrid, Spain
| | - Francisca Acuña
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Emilio Aguilar
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Sebastián García
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - María José López-Jara
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Javier Cabello
- Chiloé Silvestre Center for the Conservation of Biodiversity, Ancud, Chile
| | | | - Elie Poulin
- Institute of Ecology and Biodiversity (IEB), Concepción, Chile; Millennium Institute of Biodiversity of Antarctic and Subantarctic Ecosystems and Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
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Jelinek AL, Futas J, Burger PA, Horin P. Comparative genomics of the Leukocyte Receptor Complex in carnivores. Front Immunol 2023; 14:1197687. [PMID: 37234165 PMCID: PMC10206138 DOI: 10.3389/fimmu.2023.1197687] [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: 03/31/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Background The mammalian Leukocyte Receptor Complex (LRC) chromosomal region may contain gene families for the killer cell immunoglobulin-like receptor (KIR) and/or leukocyte immunoglobulin-like receptor (LILR) collections as well as various framing genes. This complex region is well described in humans, mice, and some domestic animals. Although single KIR genes are known in some Carnivora, their complements of LILR genes remain largely unknown due to obstacles in the assembly of regions of high homology in short-read based genomes. Methods As part of the analysis of felid immunogenomes, this study focuses on the search for LRC genes in reference genomes and the annotation of LILR genes in Felidae. Chromosome-level genomes based on single-molecule long-read sequencing were preferentially sought and compared to representatives of the Carnivora. Results Seven putatively functional LILR genes were found across the Felidae and in the Californian sea lion, four to five genes in Canidae, and four to nine genes in Mustelidae. They form two lineages, as seen in the Bovidae. The ratio of functional genes for activating LILRs to inhibitory LILRs is slightly in favor of inhibitory genes in the Felidae and the Canidae; the reverse is seen in the Californian sea lion. This ratio is even in all of the Mustelidae except the Eurasian otter, which has a predominance of activating LILRs. Various numbers of LILR pseudogenes were identified. Conclusions The structure of the LRC is rather conservative in felids and the other Carnivora studied. The LILR sub-region is conserved within the Felidae and has slight differences in the Canidae, but it has taken various evolutionary paths in the Mustelidae. Overall, the process of pseudogenization of LILR genes seems to be more frequent for activating receptors. Phylogenetic analysis found no direct orthologues across the Carnivora which corroborate the rapid evolution of LILRs seen in mammals.
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Affiliation(s)
- April L. Jelinek
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno (VETUNI), Brno, Czechia
| | - Jan Futas
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno (VETUNI), Brno, Czechia
- Research Group Animal Immunogenomics, Central European Institute of Technology (CEITEC) VETUNI, Brno, Czechia
| | - Pamela A. Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna (VETMEDUNI), Vienna, Austria
| | - Petr Horin
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno (VETUNI), Brno, Czechia
- Research Group Animal Immunogenomics, Central European Institute of Technology (CEITEC) VETUNI, Brno, Czechia
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Prost S, Machado AP, Zumbroich J, Preier L, Mahtani‐Williams S, Meissner R, Guschanski K, Brealey JC, Fernandes CR, Vercammen P, Hunter LTB, Abramov AV, Plasil M, Horin P, Godsall‐Bottriell L, Bottriell P, Dalton DL, Kotze A, Burger PA. Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus). Mol Ecol 2022; 31:4208-4223. [PMID: 35748392 PMCID: PMC9540975 DOI: 10.1111/mec.16577] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022]
Abstract
We live in a world characterized by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock-on impacts on vegetation regeneration and communities. Cheetahs (Acinonyx jubatus) serve important ecosystem functions as apex predators; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-wildlife conflict and illegal trafficking, there are only approximately 7100 individuals remaining in nature. We present the most comprehensive genome-wide analysis of cheetah phylogeography and conservation genomics to date, assembling samples from nearly the entire current and past species' range. We show that their phylogeography is more complex than previously thought, and that East African cheetahs (A. j. raineyi) are genetically distinct from Southern African individuals (A. j. jubatus), warranting their recognition as a distinct subspecies. We found strong genetic differentiation between all classically recognized subspecies, thus refuting earlier findings that cheetahs show only little differentiation. The strongest differentiation was observed between the Asiatic and all the African subspecies. We detected high inbreeding in the Critically Endangered Iranian (A. j. venaticus) and North-western (A. j. hecki) subspecies, and show that overall cheetahs, along with snow leopards, have the lowest genome-wide heterozygosity of all the big cats. This further emphasizes the cheetah's perilous conservation status. Our results provide novel and important information on cheetah phylogeography that can support evidence-based conservation policy decisions to help protect this species. This is especially relevant in light of ongoing and proposed translocations across subspecies boundaries, and the increasing threats of illegal trafficking.
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Affiliation(s)
- Stefan Prost
- Research Institute of Wildlife EcologyVetmeduni ViennaViennaAustria
- LOEWE‐Center for Translational Biodiversity Genomics, Senckenberg MuseumFrankfurtGermany
- South African National Biodiversity InstitutePretoriaSouth Africa
| | - Ana Paula Machado
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Julia Zumbroich
- Research Institute of Wildlife EcologyVetmeduni ViennaViennaAustria
| | - Lisa Preier
- Research Institute of Wildlife EcologyVetmeduni ViennaViennaAustria
| | | | - Rene Meissner
- Research Institute of Wildlife EcologyVetmeduni ViennaViennaAustria
- LOEWE‐Center for Translational Biodiversity Genomics, Senckenberg MuseumFrankfurtGermany
- Institute for Ecology, Evolution and DiversityGoethe UniversityFrankfurtGermany
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life LaboratoryUppsala UniversitetUppsalaSweden
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Jaelle C. Brealey
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life LaboratoryUppsala UniversitetUppsalaSweden
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Carlos Rodríguez Fernandes
- CE3C ‐ Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisbonPortugal
- Faculdade de PsicologiaUniversidade de Lisboa, Alameda da UniversidadeLisbonPortugal
| | - Paul Vercammen
- Breeding Centre for Endangered Arabian WildlifeSharjahUnited Arab Emirates
| | - Luke T. B. Hunter
- Wildlife Conservation SocietyNew YorkNew YorkUSA
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Alexei V. Abramov
- Zoological InstituteRussian Academy of SciencesSaint PetersburgRussia
| | - Martin Plasil
- Department of Animal GeneticsUniversity of Veterinary SciencesBrnoCzech Republic
- Central European Institute of TechnologyUniversity of Veterinary Sciences Brno (CEITEC Vetuni)BrnoCzech Republic
| | - Petr Horin
- Department of Animal GeneticsUniversity of Veterinary SciencesBrnoCzech Republic
- Central European Institute of TechnologyUniversity of Veterinary Sciences Brno (CEITEC Vetuni)BrnoCzech Republic
| | | | | | | | - Antoinette Kotze
- South African National Biodiversity InstitutePretoriaSouth Africa
- Genetics DepartmentUniversity of the Free StateBloemfonteinSouth Africa
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Plasil M, Futas J, Jelinek A, Burger PA, Horin P. Comparative Genomics of the Major Histocompatibility Complex (MHC) of Felids. Front Genet 2022; 13:829891. [PMID: 35309138 PMCID: PMC8924298 DOI: 10.3389/fgene.2022.829891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/15/2022] [Indexed: 12/25/2022] Open
Abstract
This review summarizes the current knowledge on the major histocompatibility complex (MHC) of the family Felidae. This family comprises an important domestic species, the cat, as well as a variety of free-living felids, including several endangered species. As such, the Felidae have the potential to be an informative model for studying different aspects of the biological functions of MHC genes, such as their role in disease mechanisms and adaptation to different environments, as well as the importance of genetic diversity for conservation issues in free-ranging or captive populations. Despite this potential, the current knowledge on the MHC in the family as a whole is fragmentary and based mostly on studies of the domestic cat and selected species of big cats. The overall structure of the domestic cat MHC is similar to other mammalian MHCs following the general scheme "centromere-MHC class I-MHC class III-MHC class II" with some differences in the gene contents. An unambiguously defined orthologue of the non-classical class I HLA-E gene has not been identified so far and the class II DQ and DP genes are missing or pseudogenized, respectively. A comparison with available genomes of other felids showed a generally high level of structural and sequence conservation of the MHC region. Very little and fragmentary information on in vitro and/or in vivo biological functions of felid MHC genes is available. So far, no association studies have indicated effects of MHC genetic diversity on a particular disease. No information is available on the role of MHC class I molecules in interactions with Natural Killer (NK) cell receptors or on the putative evolutionary interactions (co-evolution) of the underlying genes. A comparison of complex genomic regions encoding NK cell receptors (the Leukocyte Receptor Complex, LRC and the Natural Killer Cell Complex, NKC) in the available felid genomes showed a higher variability in the NKC compared to the LRC and the MHC regions. Studies of the genetic diversity of domestic cat populations and/or specific breeds have focused mainly on DRB genes. Not surprisingly, higher levels of MHC diversity were observed in stray cats compared to pure breeds, as evaluated by DRB sequencing as well as by MHC-linked microsatellite typing. Immunogenetic analysis in wild felids has only been performed on MHC class I and II loci in tigers, Namibian leopards and cheetahs. This information is important as part of current conservation tasks to assess the adaptive potential of endangered wild species at the human-wildlife interface, which will be essential for preserving biodiversity in a functional ecosystem.
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Affiliation(s)
- Martin Plasil
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Jan Futas
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - April Jelinek
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Pamela A. Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, VIA, Vienna, Austria
| | - Petr Horin
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
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5
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Immunological MHC supertypes and allelic expression: how low is the functional MHC diversity in free-ranging Namibian cheetahs? CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01143-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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6
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Characterization of major histocompatibility complex class I, and class II DRB loci of captive and wild Indian leopards (Panthera pardus fusca). Genetica 2017; 145:541-558. [DOI: 10.1007/s10709-017-9979-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/14/2017] [Indexed: 10/19/2022]
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7
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Marmesat E, Schmidt K, Saveljev AP, Seryodkin IV, Godoy JA. Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus. BMC Evol Biol 2017; 17:158. [PMID: 28676046 PMCID: PMC5496644 DOI: 10.1186/s12862-017-1006-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/23/2017] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Demographic bottlenecks erode genetic diversity and may increase endangered species' extinction risk via decreased fitness and adaptive potential. The genetic status of species is generally assessed using neutral markers, whose dynamic can differ from that of functional variation due to selection. The MHC is a multigene family described as the most important genetic component of the mammalian immune system, with broad implications in ecology and evolution. The genus Lynx includes four species differing immensely in demographic history and population size, which provides a suitable model to study the genetic consequences of demographic declines: the Iberian lynx being an extremely bottlenecked species and the three remaining ones representing common and widely distributed species. We compared variation in the most variable exon of the MHCI and MHCII-DRB loci among the four species of the Lynx genus. RESULTS The Iberian lynx was characterised by lower number of MHC alleles than its sister species (the Eurasian lynx). However, it maintained most of the functional genetic variation at MHC loci present in the remaining and genetically healthier lynx species at all nucleotide, amino acid, and supertype levels. CONCLUSIONS Species-wide functional genetic diversity can be maintained even in the face of severe population bottlenecks, which caused devastating whole genome genetic erosion. This could be the consequence of divergent alleles being retained across paralogous loci, an outcome that, in the face of frequent gene conversion, may have been favoured by balancing selection.
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Affiliation(s)
- Elena Marmesat
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), C/Américo Vespucio, 26, 41092, Sevilla, Spain
| | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, 17-230, Białowieża, Poland
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, 79 Preobrazhenskaya Str, Kirov, 610000, Russia
| | - Ivan V Seryodkin
- Laboratory of Ecology and Conservation of Animals, Pacific Institute of Geography of Far East Branch of Russian Academy of Sciences, 7 Radio Street, Vladivostok, 690041, Russia
- Far Eastern Federal University, 8 Sukhanova Street, Vladivostok, 690091, Russia
| | - José A Godoy
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), C/Américo Vespucio, 26, 41092, Sevilla, Spain.
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Heinrich SK, Hofer H, Courtiol A, Melzheimer J, Dehnhard M, Czirják GÁ, Wachter B. Cheetahs have a stronger constitutive innate immunity than leopards. Sci Rep 2017; 7:44837. [PMID: 28333126 PMCID: PMC5363065 DOI: 10.1038/srep44837] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 02/14/2017] [Indexed: 11/21/2022] Open
Abstract
As a textbook case for the importance of genetics in conservation, absence of genetic variability at the major histocompatibility complex (MHC) is thought to endanger species viability, since it is considered crucial for pathogen resistance. An alternative view of the immune system inspired by life history theory posits that a strong response should evolve in other components of the immune system if there is little variation in the MHC. In contrast to the leopard (Panthera pardus), the cheetah (Acinonyx jubatus) has a relatively low genetic variability at the MHC, yet free-ranging cheetahs are healthy. By comparing the functional competence of the humoral immune system of both species in sympatric populations in Namibia, we demonstrate that cheetahs have a higher constitutive innate but lower induced innate and adaptive immunity than leopards. We conclude (1) immunocompetence of cheetahs is higher than previously thought; (2) studying both innate and adaptive components of immune systems will enrich conservation science.
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Affiliation(s)
- Sonja K. Heinrich
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Heribert Hofer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Alexandre Courtiol
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Jörg Melzheimer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Martin Dehnhard
- Department of Reproduction Biology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Gábor Á. Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Bettina Wachter
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
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Heinrich SK, Wachter B, Aschenborn OHK, Thalwitzer S, Melzheimer J, Hofer H, Czirják GÁ. Feliform carnivores have a distinguished constitutive innate immune response. Biol Open 2016; 5:550-5. [PMID: 27044323 PMCID: PMC4874346 DOI: 10.1242/bio.014902] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Determining the immunological phenotype of endangered and threatened populations is important to identify those vulnerable to novel pathogens. Among mammals, members of the order Carnivora are particularly threatened by diseases. We therefore examined the constitutive innate immune system, the first line of protection against invading microbes, of six free-ranging carnivore species; the black-backed jackal (Canis mesomelas), the brown hyena (Hyena brunnea), the caracal (Caracal caracal), the cheetah (Acinonyx jubatus), the leopard (Panthera pardus) and the lion (Panthera leo) using a bacterial killing assay. The differences in immune responses amongst the six species were independent of their foraging behaviour, body mass or social organisation but reflected their phylogenetic relatedness. The bacterial killing capacity of black-backed jackals, a member of the suborder Caniformia, followed the pattern established for a wide variety of vertebrates. In contrast, the five representatives of the suborder Feliformia demonstrated a killing capacity at least an order of magnitude higher than any species reported previously, with a particularly high capacity in caracals and cheetahs. Our results suggest that the immunocompetence of threatened felids such as the cheetah has been underestimated and its assessment ought to consider both innate and adaptive components of the immune system. Summary: The innate immunocompetence of six free-ranging carnivores is independent of their foraging behaviour, body mass or social organisation but reflects their phylogenetic relatedness.
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Affiliation(s)
- Sonja K Heinrich
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Bettina Wachter
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Ortwin H K Aschenborn
- Bwabwata Ecological Institute, Ministry of Environment and Tourism, Zambezi, Namibia
| | - Susanne Thalwitzer
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Jörg Melzheimer
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Gábor Á Czirják
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
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Vera M, Díez-del-Molino D, García-Marín JL. Genomic survey provides insights into the evolutionary changes that occurred during European expansion of the invasive mosquitofish (Gambusia holbrooki). Mol Ecol 2016; 25:1089-105. [PMID: 26825431 DOI: 10.1111/mec.13545] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 12/10/2015] [Accepted: 01/15/2016] [Indexed: 01/26/2023]
Abstract
Biological invasions rank among the main global threats for biodiversity. The Eastern mosquitofish (Gambusia holbrooki) is considered one of the 100 world worst invasive species due to its high adaptation capability to new environments. Using the restriction-site-associated DNA tags (RADtags), introduced European locations were compared against native US mosquitofish populations to analyse genomic changes that occurred during invasive process of European locations. After filtering, 7724 RADtags containing only one SNP were retained for population studies. Comparative genomics indicated that 186 of these RADtags matched sequences in the transcriptome of Xyphophorus maculatus, the most closely related genome available. Genomic analyses showed that invasive populations show high reductions in diversity. Further, analyses of population structuring based on these data are concordant with previous analyses based on microsatellites. It is concluded that during the invasion process genetic drift was the main evolutionary force affecting patterns of diversity and population structure. While recognizing that positive selection could be masked by the strong drift during founder events, adaptive processes were evidenced in a reduced number of RADtags (<2%), with only one of these in a putative coding region. Surprisingly, balancing selection was detected in several coding RADtags, suggesting that the preservation of polymorphism in specific genes could be more important than the average population diversity for the population maintenance at any location, particularly for the survival of introduced populations.
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Affiliation(s)
- Manuel Vera
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
| | - David Díez-del-Molino
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
| | - José-Luis García-Marín
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
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Ruiz-López MJ, Monello RJ, Schuttler SG, Lance SL, Gompper ME, Eggert LS. Major Histocompatibility Complex, demographic, and environmental predictors of antibody presence in a free-ranging mammal. INFECTION GENETICS AND EVOLUTION 2014; 28:317-27. [PMID: 25446941 DOI: 10.1016/j.meegid.2014.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/30/2014] [Accepted: 10/16/2014] [Indexed: 10/24/2022]
Abstract
Major Histocompatibility Complex (MHC) variability plays a key role in pathogen resistance, but its relative importance compared to environmental and demographic factors that also influence resistance is unknown. We analyzed the MHC II DRB exon 2 for 165 raccoons (Procyon lotor) in Missouri (USA). For each animal we also determined the presence of immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies to two highly virulent pathogens, canine distemper virus (CDV) and parvovirus. We investigated the role of MHC polymorphism and other demographic and environmental factors previously associated with predicting seroconversion. In addition, using an experimental approach, we studied the relative importance of resource availability and contact rates. We found important associations between IgG antibody presence and several MHC alleles and supertypes but not between IgM antibody presence and MHC. No effect of individual MHC diversity was found. For CDV, supertype S8, one allele within S8 (Prlo-DRB(∗)222), and a second allele (Prlo-DRB(∗)204) were positively associated with being IgG+, while supertype S4 and one allele within the supertype (Prlo-DRB(∗)210) were negatively associated with being IgG+. Age, year, and increased food availability were also positively associated with being IgG+, but allele Prlo-DRB(∗)222 was a stronger predictor. For parvovirus, only one MHC allele was negatively associated with being IgG+ and age and site were stronger predictors of seroconversion. Our results show that negative-frequency dependent selection is likely acting on the raccoon MHC and that while the role of MHC in relation to other factors depends on the pathogen of interest, it may be one of the most important factors predicting successful immune response.
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Affiliation(s)
- María José Ruiz-López
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Ryan J Monello
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Stephanie G Schuttler
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO 65211, USA; Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Stacey L Lance
- Savannah River Ecology Laboratory, P O Drawer E, Aiken, SC 29802, USA
| | - Matthew E Gompper
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Lori S Eggert
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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Holmes JC, Holmer SG, Ross P, Buntzman AS, Frelinger JA, Hess PR. Polymorphisms and tissue expression of the feline leukocyte antigen class I loci FLAI-E, FLAI-H, and FLAI-K. Immunogenetics 2013; 65:675-89. [PMID: 23812210 PMCID: PMC3777221 DOI: 10.1007/s00251-013-0711-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/18/2013] [Indexed: 01/14/2023]
Abstract
Cytotoxic CD8+ T-cell immunosurveillance for intracellular pathogens, such as viruses, is controlled by classical major histocompatibility complex (MHC) class Ia molecules, and ideally, these antiviral T-cell populations are defined by the specific peptide and restricting MHC allele. Surprisingly, despite the utility of the cat in modeling human viral immunity, little is known about the feline leukocyte antigen class I complex (FLAI). Only a few coding sequences with uncertain locus origin and expression patterns have been reported. Of 19 class I genes, three loci--FLAI-E, FLAI-H, and FLAI-K--are predicted to encode classical molecules, and our objective was to evaluate their status by analyzing polymorphisms and tissue expression. Using locus-specific, PCR-based genotyping, we amplified 33 FLAI-E, FLAI-H, and FLAI-K alleles from 12 cats of various breeds, identifying, for the first time, alleles across three distinct loci in a feline species. Alleles shared the expected polymorphic and invariant sites in the α1/α2 domains, and full-length cDNA clones possessed all characteristic class Ia exons. Alleles could be assigned to a specific locus with reasonable confidence, although there was evidence of potentially confounding interlocus recombination between FLAI-E and FLAI-K. Only FLAI-E, FLAI-H, and FLAI-K origin alleles were amplified from cDNAs of multiple tissue types. We also defined hypervariable regions across these genes, which permitted the assignment of names to both novel and established alleles. As predicted, FLAI-E, FLAI-H, and FLAI-K fulfill the major criteria of class Ia genes. These data represent a necessary prerequisite for studying epitope-specific antiviral CD8+ T-cell responses in cats.
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Affiliation(s)
- Jennifer C. Holmes
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Savannah G. Holmer
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Peter Ross
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Adam S. Buntzman
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Jeffrey A. Frelinger
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Paul R. Hess
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
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Luo MF, Pan HJ, Liu ZJ, Li M. Balancing selection and genetic drift at major histocompatibility complex class II genes in isolated populations of golden snub-nosed monkey (Rhinopithecus roxellana). BMC Evol Biol 2012; 12:207. [PMID: 23083308 PMCID: PMC3532231 DOI: 10.1186/1471-2148-12-207] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 10/05/2012] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Small, isolated populations often experience loss of genetic variation due to random genetic drift. Unlike neutral or nearly neutral markers (such as mitochondrial genes or microsatellites), major histocompatibility complex (MHC) genes in these populations may retain high levels of polymorphism due to balancing selection. The relative roles of balancing selection and genetic drift in either small isolated or bottlenecked populations remain controversial. In this study, we examined the mechanisms maintaining polymorphisms of MHC genes in small isolated populations of the endangered golden snub-nosed monkey (Rhinopithecus roxellana) by comparing genetic variation found in MHC and microsatellite loci. There are few studies of this kind conducted on highly endangered primate species. RESULTS Two MHC genes were sequenced and sixteen microsatellite loci were genotyped from samples representing three isolated populations. We isolated nine DQA1 alleles and sixteen DQB1 alleles and validated expression of the alleles. Lowest genetic variation for both MHC and microsatellites was found in the Shennongjia (SNJ) population. Historical balancing selection was revealed at both the DQA1 and DQB1 loci, as revealed by excess non-synonymous substitutions at antigen binding sites (ABS) and maximum-likelihood-based random-site models. Patterns of microsatellite variation revealed population structure. FST outlier analysis showed that population differentiation at the two MHC loci was similar to the microsatellite loci. CONCLUSIONS MHC genes and microsatellite loci showed the same allelic richness pattern with the lowest genetic variation occurring in SNJ, suggesting that genetic drift played a prominent role in these isolated populations. As MHC genes are subject to selective pressures, the maintenance of genetic variation is of particular interest in small, long-isolated populations. The results of this study may contribute to captive breeding and translocation programs for endangered species.
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Affiliation(s)
- Mao-Fang Luo
- Key laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beixhenxi Road, Chaoyang, Beijing, 100101, China
- Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Graduate School of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui-Juan Pan
- College of Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Zhi-Jin Liu
- Key laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beixhenxi Road, Chaoyang, Beijing, 100101, China
| | - Ming Li
- Key laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beixhenxi Road, Chaoyang, Beijing, 100101, China
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