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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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2
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LaFond J, Martin KR, Dahn H, Richmond JQ, Murphy RW, Rollinson N, Savage AE. Invasive Bullfrogs Maintain MHC Polymorphism Including Alleles Associated with Chytrid Fungal Infection. Integr Comp Biol 2022; 62:262-274. [PMID: 35588059 DOI: 10.1093/icb/icac044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/19/2022] [Accepted: 05/16/2022] [Indexed: 11/14/2022] Open
Abstract
Maintenance of genetic diversity at adaptive loci may facilitate invasions by non-native species by allowing populations to adapt to novel environments, despite the loss of diversity at neutral loci that typically occurs during founder events. To evaluate this prediction, we compared genetic diversity at major histocompatibility complex (MHC) and cytochrome b (cytb) loci from 20 populations of the American bullfrog (Rana catesbeiana) across theinvasive and native ranges in North America and quantified the presence of the pathogen Batrachochytrium dendrobatidis (Bd). Compared to native populations, invasive populations had significantly higher Bd prevalence and intensity, significantly higher pairwise MHC and cytb FST, and significantly lower cytb diversity, but maintained similar levels of MHC diversity. The two most common MHC alleles (LiCA_B and Rapi_33) were associated with a significant decreased risk of Bd infection, and we detected positive selection acting on four peptide binding residues. Phylogenetic analysis suggested invasive populations likely arose from a single founding population in the American Midwest with a possible subsequent invasion in the northwest. Overall, our study suggests that the maintenance of diversity at adaptive loci may contribute to invasion success and highlights the importance of quantifying diversity at functional loci to assess the evolutionary potential of invasive populations.
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Affiliation(s)
- Jacob LaFond
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
- Department of Biology, University of Tampa, Tampa, FL 33606, USA
| | - Katherine R Martin
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - Hollis Dahn
- Department of Biology, University of Toronto, Toronto, ON, Canada
| | - Jonathan Q Richmond
- U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego, CA 92101, USA
| | - Robert W Murphy
- Department of Biology, University of Toronto, Toronto, ON, Canada
| | - Njal Rollinson
- Department of Biology, University of Toronto, Toronto, ON, Canada
| | - Anna E Savage
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
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3
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Abstract
SignificanceThe dynamics of deleterious variation under contrasting demographic scenarios remain poorly understood in spite of their relevance in evolutionary and conservation terms. Here we apply a genomic approach to study differences in the burden of deleterious alleles between the endangered Iberian lynx (Lynx pardinus) and the widespread Eurasian lynx (Lynx lynx). Our analysis unveils a significantly lower deleterious burden in the former species that should be ascribed to genetic purging, that is, to the increased opportunities of selection against recessive homozygotes due to the inbreeding caused by its smaller population size, as illustrated by our analytical predictions. This research provides theoretical and empirical evidence on the evolutionary relevance of genetic purging under certain demographic conditions.
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4
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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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Escoda L, Castresana J. The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species. Evol Appl 2021; 14:1898-1913. [PMID: 34295371 PMCID: PMC8288019 DOI: 10.1111/eva.13249] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/19/2021] [Accepted: 04/27/2021] [Indexed: 01/23/2023] Open
Abstract
The Pyrenean desman (Galemys pyrenaicus) is a small semiaquatic mammal endemic to the Iberian Peninsula. Despite its limited range, this species presents a strong genetic structure due to past isolation in glacial refugia and subsequent bottlenecks. Additionally, some populations are highly fragmented today as a consequence of river barriers, causing substantial levels of inbreeding. These features make the Pyrenean desman a unique model in which to study the genomic footprints of differentiation, bottlenecks and extreme isolation in an endangered species. To understand these processes, the complete genome of the Pyrenean desman was sequenced and assembled using a Bloom filter-based approach. An analysis of the 1.83 Gb reference genome and the sequencing of five additional individuals from different evolutionary units allowed us to detect its main genomic characteristics. The population differentiation of the species was reflected in highly distinctive demographic trajectories. In addition, a severe population bottleneck during the postglacial recolonization of the eastern Pyrenees created one of the lowest genomic heterozygosity values recorded in a mammal. Moreover, isolation and inbreeding gave rise to a high proportion of runs of homozygosity (ROH). Despite these extremely low levels of genetic diversity, two key multigene families from an eco-evolutionary perspective, the major histocompatibility complex and olfactory receptor genes, showed heterozygosity excess in the majority of individuals, revealing that functional diversity can be maintained up to a certain extent. Furthermore, these two classes of genes were significantly less abundant than expected within ROH. In conclusion, the genomic landscape of each analysed Pyrenean desman turned out to be strikingly distinctive and was a clear reflection of its recent ancestry and current conservation conditions. These results may help characterize the genomic health of each individual, and can be crucial for the conservation and management of the species.
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Affiliation(s)
- Lídia Escoda
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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6
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Ghani MU, Bo L, Buyang A, Yanchun X, Hussain S, Yasir M. Molecular Characterization of MHC Class I Genes in Four Species of the Turdidae Family to Assess Genetic Diversity and Selection. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5585687. [PMID: 33937397 PMCID: PMC8055405 DOI: 10.1155/2021/5585687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022]
Abstract
In vertebrate animals, the molecules encoded by major histocompatibility complex (MHC) genes play an essential role in the adaptive immunity. MHC class I deals with intracellular pathogens (virus) in birds. MHC class I diversity depends on the consequence of local and global environment selective pressure and gene flow. Here, we evaluated the MHC class I gene in four species of the Turdidae family from a broad geographical area of northeast China. We isolated 77 MHC class I sequences, including 47 putatively functional sequences and 30 pseudosequences from 80 individuals. Using the method based on analysis of cloned amplicons (n = 25) for each species, we found two and seven MHC I sequences per individual indicating more than one MHC I locus identified in all sampled species. Results revealed an overall elevated genetic diversity at MHC class I, evidence of different selection patterns among the domains of PBR and non-PBR. Alleles are found to be divergent with overall polymorphic sites per species ranging between 58 and 70 (out of 291 sites). Moreover, transspecies alleles were evident due to convergent evolution or recent speciation for the genus. Phylogenetic relationships among MHC I show an intermingling of alleles clustering among the Turdidae family rather than between other passerines. Pronounced MHC I gene diversity is essential for the existence of species. Our study signifies a valuable tool for the characterization of evolutionary relevant difference across a population of birds with high conservational concerns.
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Affiliation(s)
- Muhammad Usman Ghani
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Li Bo
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - An Buyang
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Science, Kyushu University, Fukuoka 810-0000, Japan
| | - Xu Yanchun
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Shakeel Hussain
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Muhammad Yasir
- Department of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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7
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Li X, Liu T, Li A, Zhang L, Dai W, Jin L, Sun K, Feng J. Genetic polymorphisms and the independent evolution of major histocompatibility complex class II‐
DRB
in sibling bat species
Rhinolophus episcopus
and
Rhinolophus siamensis. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiaolin Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- Key Laboratory of Vegetation Ecology Ministry of Education Changchun China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- College of Life Science Jilin Agricultural University Changchun China
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8
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Biedrzycka A, Konopiński M, Hoffman E, Trujillo A, Zalewski A. Comparing raccoon major histocompatibility complex diversity in native and introduced ranges: Evidence for the importance of functional immune diversity for adaptation and survival in novel environments. Evol Appl 2020; 13:752-767. [PMID: 32211065 PMCID: PMC7086054 DOI: 10.1111/eva.12898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 09/27/2019] [Accepted: 10/16/2019] [Indexed: 12/21/2022] Open
Abstract
The adaptive potential of invasive species is related to the genetic diversity of the invader, which is influenced by genetic drift and natural selection. Typically, the genetic diversity of invaders is studied with neutral genetic markers; however, the expectation of reduced diversity has not been consistently supported by empirical studies. Here, we describe and interpret genetic diversity at both neutral microsatellite loci and the immune-related MHC-DRB locus of native and invasive populations of raccoon to better understand of how drift and selection impact patterns of genetic diversity during the invasion process. We found that despite the loss of many MHC (major histocompatibility complex) alleles in comparison with native populations, functional MHC supertypes are preserved in the invasive region. In the native raccoon population, the number of supertypes within individuals was higher than expected under a neutral model. The high level of individual functional divergence may facilitate the adaptation to local conditions in the invasive range. In the invasive populations, we also detected increased population structure at microsatellites compared to the MHC locus, further suggesting that balancing selection is acting on adaptively important regions of the raccoon genome. Finally, we found that alleles known to exhibit resistance to rabies in the native range, Prlo-DRB*4, Prlo-DRB*16 and Prlo-DRB*102, were the most common alleles in the European populations, suggesting directional selection is acting on this locus. Our research shows empirical support for the importance of functional immune diversity for adaptation and survival in novel environments.
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Affiliation(s)
| | - Maciej Konopiński
- Institute of Nature ConservationPolish Academy of SciencesKrakówPoland
| | - Eric Hoffman
- Department of BiologyUniversity of Central FloridaOrlandoFLUSA
| | - Alexa Trujillo
- Department of BiologyUniversity of Central FloridaOrlandoFLUSA
| | - Andrzej Zalewski
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
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9
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Vlček J, Štefka J. Association between louse abundance and MHC II supertypes in Galápagos mockingbirds. Parasitol Res 2020; 119:1597-1605. [PMID: 32006226 DOI: 10.1007/s00436-020-06617-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/22/2020] [Indexed: 01/30/2023]
Abstract
Major histocompatibility complex class II (MHC II) is an essential molecule triggering the adaptive immune response by the presentation of pathogens to helper T cells. The association between individual MHC II variants and various parasites has become a frequent finding in studies of vertebrate populations. However, although bird ectoparasites have a significant effect on their host's fitness, and the host's immune system can regulate ectoparasitic infections, no study has yet investigated the association between MHC II polymorphism and ectoparasite infection in the populations of free-living birds. Here, we test whether an association exists between the abundance of a chewing louse (Myrsidea nesomimi) and MHC II polymorphism of its hosts, the Galápagos mockingbirds (Mimus). We have found that the presence of two MHC II supertypes (functionally differentiated clusters) was significantly associated with louse abundance. This pattern supports the theory that a co-evolutionary interaction stands behind the maintenance of MHC polymorphism. Moreover, we have found a positive correlation between louse abundance and heterophil/lymphocyte ratio (an indicator of immunological stress) that serves as an additional piece of evidence that ectoparasite burden is affected by immunological state of Galápagos mockingbirds.
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Affiliation(s)
- Jakub Vlček
- Institute of Parasitology, Biology Centre CAS, Branišovská 1160/31, 37005, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, Branišovská, 1760, České Budějovice, Czech Republic.
| | - Jan Štefka
- Institute of Parasitology, Biology Centre CAS, Branišovská 1160/31, 37005, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská, 1760, České Budějovice, Czech Republic
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10
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Bartocillo AMF, Nishita Y, Abramov AV, Masuda R. Molecular evolution of MHC class II DRB exon 2 in Japanese and Russian raccoon dogs, Nyctereutes procyonoides (Carnivora: Canidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractRaccoon dogs, Nyctereutes procyonoides, are native to East Asia, but have been introduced into western Russia and eastern Europe. To determine allelic diversity and elucidate the evolution of major histocompatibility complex (MHC) class II genes in the raccoon dog, we analysed a 237-bp region of DRB exon 2 from 36 individuals of native and introduced populations from Japan and Russia. We detected 23 DRB alleles (Nypr-DRBs), 22 of which were novel. Some alleles were found across the species’ range, while others were geographically restricted. For both native and introduced populations, the ratio of non-synonymous to synonymous substitution rates for codons at predicted antigen-binding sites was significantly greater than 2, indicating that Nypr-DRBs have evolved under positive selection. Mixed effect model evolution analysis and an algorithm to detect recombination showed five positively selected codons and one recombination breakpoint, respectively. Overall, our results suggest that the diversity of MHC class II DRB in N. procyonoides was influenced and maintained by recombination, pathogen-driven positive selection, geographical barriers and the founder effect. A Bayesian phylogenetic tree revealed no evidence of trans-species polymorphism (TSP), but instead showed monophyly for the Nypr-DRB alleles within a larger clade of canid sequences. The lack of TSP may have been due to long-term divergence of raccoon dogs from other canids, or to their having encountered different sets of pathogens due to occupying a different ecological niche.
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Affiliation(s)
- Aye Mee F Bartocillo
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Kita-Ku, Sapporo, Japan
| | - Yoshinori Nishita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo, Japan
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. Saint Petersburg, Russia
| | - Ryuichi Masuda
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo, Japan
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11
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Stefan T, Matthews L, Prada JM, Mair C, Reeve R, Stear MJ. Divergent Allele Advantage Provides a Quantitative Model for Maintaining Alleles with a Wide Range of Intrinsic Merits. Genetics 2019; 212:553-564. [PMID: 30952668 PMCID: PMC6553829 DOI: 10.1534/genetics.119.302022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/30/2019] [Indexed: 01/28/2023] Open
Abstract
The Major Histocompatibility Complex (MHC) is the most genetically diverse region of the genome in most vertebrates. Some form of balancing selection is necessary to account for the extreme diversity, but the precise mechanism of balancing selection is unknown. Due to the way MHC molecules determine immune recognition, overdominance (also referred to as heterozygote advantage) has been suggested as the main driving force behind this unrivalled diversity. However, both theoretical results and simulation models have shown that overdominance in its classical form cannot maintain large numbers of alleles unless all alleles confer unrealistically similar levels of fitness. There is increasing evidence that heterozygotes containing genetically divergent alleles allow for broader antigen presentation to immune cells, providing a selective mechanism for MHC polymorphism. By framing competing models of overdominance within a general framework, we show that a model based on Divergent Allele Advantage (DAA) provides a superior mechanism for maintaining alleles with a wide range of intrinsic merits, as intrinsically less-fit MHC alleles that are more divergent can survive under DAA. Specifically, our results demonstrate that a quantitative mechanism built from the DAA hypothesis is able to maintain polymorphism in the MHC. Applying such a model to both livestock breeding and conservation could provide a better way of identifying superior heterozygotes, and quantifying the advantages of genetic diversity at the MHC.
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Affiliation(s)
- Thorsten Stefan
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
- Institute of Applied Mathematics and Statistics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Louise Matthews
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
| | - Joaquin M Prada
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
| | - Colette Mair
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
| | - Michael J Stear
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom
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12
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DeCandia AL, Henger CS, Krause A, Gormezano LJ, Weckel M, Nagy C, Munshi-South J, vonHoldt BM. Genetics of urban colonization: neutral and adaptive variation in coyotes (Canis latrans) inhabiting the New York metropolitan area. JOURNAL OF URBAN ECOLOGY 2019. [DOI: 10.1093/jue/juz002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Alexandra L DeCandia
- Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, USA
| | - Carol S Henger
- Louis Calder Center—Biological Field Station, Fordham University, 31 Whippoorwill Road, Armonk, NY, USA
| | - Amelia Krause
- Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, USA
| | - Linda J Gormezano
- American Museum of Natural History, Central Park West & 79th Street, New York, NY, USA
| | - Mark Weckel
- American Museum of Natural History, Central Park West & 79th Street, New York, NY, USA
| | | | - Jason Munshi-South
- Louis Calder Center—Biological Field Station, Fordham University, 31 Whippoorwill Road, Armonk, NY, USA
| | - Bridgett M vonHoldt
- Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, USA
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Abduriyim S, Nishita Y, Kosintsev PA, Raichev E, Väinölä R, Kryukov AP, Abramov AV, Kaneko Y, Masuda R. Evolution of MHC class I genes in Eurasian badgers, genus Meles (Carnivora, Mustelidae). Heredity (Edinb) 2019; 122:205-218. [PMID: 29959426 PMCID: PMC6327056 DOI: 10.1038/s41437-018-0100-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 11/09/2022] Open
Abstract
Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7-21 putatively functional MHCI sequences in each of the badger species, and 2-7 sequences per individual, indicating the existence of 1-4 loci. MHCI exon 2 and 3 sequences encoding domains α1 and α2 exhibited different clade topologies in phylogenetic networks. Non-synonymous nucleotide substitutions at codons for antigen-binding sites exceeded synonymous substitutions for domain α1 but not for domain α2, suggesting that the domains α1 and α2 likely had different evolutionary histories in these species. Positive selection and recombination seem to have shaped the variation in domain α2, whereas positive selection was dominant in shaping the variation in domain α1. In the separate phylogenetic analyses for exon 2, exon 3, and intron 2, each showed three clades of Meles alleles, with rampant trans-species polymorphism, indicative of the long-term maintenance of ancestral MHCI polymorphism by balancing selection.
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Affiliation(s)
- Shamshidin Abduriyim
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yoshinori Nishita
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Pavel A Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Ekaterinburg, 620144, Russia
| | - Evgeniy Raichev
- Agricultural Faculty, Trakia University, 6000, Stara Zagora, Bulgaria
| | - Risto Väinölä
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, FI-00014, Helsinki, Finland
| | - Alexey P Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, 199034, Russia
| | - Yayoi Kaneko
- Carnivore Ecology and Conservation Research Group, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Ryuichi Masuda
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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