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Smallbone W, Ellison A, Poulton S, van Oosterhout C, Cable J. Depletion of MHC supertype during domestication can compromise immunocompetence. Mol Ecol 2020; 30:736-746. [PMID: 33274493 PMCID: PMC7898906 DOI: 10.1111/mec.15763] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/27/2022]
Abstract
The major histocompatibility complex (MHC) plays an important role in infectious disease resistance. The presence of certain MHC alleles and functionally similar groups of MHC alleles (i.e., supertypes) has been associated with resistance to particular parasite species. Farmed and domesticated fish stocks are often depleted in their MHC alleles and supertype diversity, possibly as a consequence of artificial selection for desirable traits, inbreeding (loss of heterozygosity), genetic drift (loss of allelic diversity) and/or reduced parasite biodiversity. Here we quantify the effects of depletion of MHC class II genotype and supertype variation on resistance to the parasite Gyrodactylus turnbulli in guppies (Poecilia reticulata). Compared to the descendants of wild‐caught guppies, ornamental fish had a significantly reduced MHC variation (i.e., the numbers of MHC alleles and supertypes per individual, and per population). In addition, ornamental fish were significantly more susceptible to G. turnbulli infections, accumulating peak intensity 10 times higher than that of their wildtype counterparts. Four out of 13 supertypes were associated with a significantly reduced parasite load, and the presence of some supertypes had a dramatic effect on the intensity of infection. Remarkably, the ornamental and wildtype fish differed in the supertypes that were associated with parasite resistance. Analysis with a genetic algorithm showed that resistance‐conferring supertypes of the wildtype and ornamental fish shared two unique amino acids in the peptide‐binding region of the MHC that were not found in any other alleles. These data show that the supertype demarcation captures some, but not all, of the variation in the immune function of the alleles. This study highlights the importance of managing functional MHC diversity in livestock, and suggests there might be some immunological redundancy among MHC supertypes.
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Affiliation(s)
| | - Amy Ellison
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Simon Poulton
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Joanne Cable
- School of Biosciences, Cardiff University, Cardiff, UK
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2
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E GX, Chen LP, Zhou DK, Yang BG, Zhang JH, Zhao YJ, Hong QH, Ma YH, Chu MX, Zhang LP, Basang WD, Zhu YB, Han YG, Na RS, Zeng Y, Zhao ZQ, Huang YF, Han JL. Evolutionary relationship and population structure of domestic Bovidae animals based on MHC-linked and neutral autosomal microsatellite markers. Mol Immunol 2020; 124:83-90. [PMID: 32544655 DOI: 10.1016/j.molimm.2020.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/21/2020] [Accepted: 05/07/2020] [Indexed: 11/26/2022]
Abstract
Major histocompatibility complex (MHC) genes are critical for disease resistance or susceptibility responsible for host-pathogen interactions determined mainly by extensive polymorphisms in the MHC genes. Here, we examined the diversity and phylogenetic pattern of MHC haplotypes reconstructed using three MHC-linked microsatellite markers in 55 populations of five Bovidae species and compared them with those based on neutral autosomal microsatellite markers (NAMs). Three-hundred-and-forty MHC haplotypes were identified in 1453 Bovidae individuals, suggesting significantly higher polymorphism and heterozygosity compared with those based on NAMs. The ambitious boundaries in population differentiation (phylogenetic network, pairwise FST and STRUCTURE analyses) within and between species assessed using the MHC haplotypes were different from those revealed by NAMs associated closely with speciation, geographical distribution, domestication and management histories. In addition, the mean FST was significantly correlated negatively with the number of observed alleles (NA), observed (HO) and expected (HE) heterozygosity and polymorphism information content (PIC) (P < 0.05) in the MHC haplotype dataset while there was no correction of the mean FST estimates (P> 0.05) between the MHC haplotype and NAMs datasets. Analysis of molecular variance (AMOVA) revealed a lower percentage of total variance (PTV) between species/groups based on the MHC-linked microsatellites than NAMs. Therefore, it was inferred that individuals within populations accumulated as many MHC variants as possible to increase their heterozygosity and thus the survival rate of their affiliated populations and species, which eventually reduced population differentiation and thereby complicated their classification and phylogenetic relationship inference. In summary, host-pathogen coevolution and heterozygote advantage, rather than demographic history, act as key driving forces shaping the MHC diversity within the populations and determining the interspecific MHC diversity.
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Affiliation(s)
- Guang-Xin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Li-Peng Chen
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Dong-Ke Zhou
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Bai-Gao Yang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Jia-Hua Zhang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Yong-Ju Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Qiong-Hua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China
| | - Yue-Hui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ming-Xing Chu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Lu-Pei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Wang-Dui Basang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Science (TAAAS)), Lhasa 850002, China
| | - Yan-Bin Zhu
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Science (TAAAS)), Lhasa 850002, China
| | - Yan-Guo Han
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Ri-Su Na
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Yan Zeng
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Zhong-Quan Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Yong-Fu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China.
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya.
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Xu W, Zhou X, Fang W, Chen X. Genetic diversity of toll-like receptor genes in the vulnerable Chinese egret (Egretta eulophotes). PLoS One 2020; 15:e0233714. [PMID: 32469968 PMCID: PMC7259618 DOI: 10.1371/journal.pone.0233714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/11/2020] [Indexed: 01/15/2023] Open
Abstract
Toll-like receptor (TLR) genes have recently been employed to assess genetic diversity, as they can be used to infer both demographic history and adaptation to environments with different pathogen pressure. Here, we sampled 120 individuals of the Chinese egret (Egretta eulophotes), a globally vulnerable species, from four breeding populations across China. We assessed the levels of genetic diversity, selection pressure, and population differentiation at seven TLR loci (TLR1LB, TLR2A, TLR3, TLR4, TLR5, TLR7, and TLR15). Using a variety of metrics (SNPs, heterozygosity, nucleotides, haplotypes), our analyses showed that genetic diversity was lower at 4 of the 7 TLR loci in the vulnerable Chinese egret compared to the more common little egret (Egretta garzetta). The selection test indicated TLRs, except for TLR5, were under purifying selection in TLR evolution, suggesting that low TLR genetic diversity in the Chinese egret may be caused by purifying selection. Moreover, analysis of molecular variance indicated low but significant population differentiation among four populations at all of the TLR loci in this egret. However, some comparisons based on fixation index analyses did not show significant population differentiation, and Bayesian clustering showed admixture. Our finding suggested that these four populations of the Chinese egret in China may be considered a single unit for conservation planning. These results, the new report of TLR genetic diversity in a long-distance migratory vulnerable Ardeid species, will provide fundamental TLR information for further studies on the conservation genetics of the Chinese egret and other Ardeids.
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Affiliation(s)
- Wei Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Xiaoping Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Wenzhen Fang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Xiaolin Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
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Antonides J, Mathur S, Sundaram M, Ricklefs R, DeWoody JA. Immunogenetic response of the bananaquit in the face of malarial parasites. BMC Evol Biol 2019; 19:107. [PMID: 31113360 PMCID: PMC6529992 DOI: 10.1186/s12862-019-1435-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 05/08/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND In the arms race between hosts and parasites, genes involved in the immune response are targets for natural selection. Toll-Like Receptor (TLR) genes play a role in parasite detection as part of the innate immune system whereas Major Histocompatibility Complex (MHC) genes encode proteins that display antigens as part of the vertebrate adaptive immune system. Thus, both gene families are under selection pressure from pathogens. The bananaquit (Coereba flaveola) is a passerine bird that is a common host of avian malarial parasites (Plasmodium sp. and Haemoproteus sp.). We assessed molecular variation of TLR and MHC genes in a wild population of bananaquits and identified allelic associations with resistance/susceptibility to parasitic infection to address hypotheses of avian immune response to haemosporidian parasites. RESULTS We found that allele frequencies are associated with infection status at the immune loci studied. A consistent general trend showed the infected groups possessed more alleles at lower frequencies, and exhibited unique alleles, compared to the uninfected group. CONCLUSIONS Our results support the theory of natural selection favoring particular alleles for resistance while maintaining overall genetic diversity in the population, a mechanism which has been demonstrated in some systems in MHC previously but understudied in TLRs.
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Affiliation(s)
- Jennifer Antonides
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, Pfendler Hall 141, West Lafayette, IN 47907 USA
| | - Samarth Mathur
- Department of Biological Sciences, Purdue University, 915 W. State St, Indiana, USA
| | - Mekala Sundaram
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, Pfendler Hall 141, West Lafayette, IN 47907 USA
| | - Robert Ricklefs
- Department of Biology, University of Missouri, 1 University Blvd, St. Louis, MO USA
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, Pfendler Hall 141, West Lafayette, IN 47907 USA
- Department of Biological Sciences, Purdue University, 915 W. State St, Indiana, USA
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Whittingham LA, Dunn PO, Freeman-Gallant CR, Taff CC, Johnson JA. Major histocompatibility complex variation and blood parasites in resident and migratory populations of the common yellowthroat. J Evol Biol 2018; 31:1544-1557. [DOI: 10.1111/jeb.13349] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/12/2018] [Accepted: 06/25/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Linda A. Whittingham
- Behavioral and Molecular Ecology Group; Department of Biological Sciences; University of Wisconsin-Milwaukee; Milwaukee WI USA
| | - Peter O. Dunn
- Behavioral and Molecular Ecology Group; Department of Biological Sciences; University of Wisconsin-Milwaukee; Milwaukee WI USA
| | | | - Conor C. Taff
- Cornell Laboratory of Ornithology; Cornell University; Ithaca NY USA
| | - Jeff A. Johnson
- Department of Biological Sciences; Institute of Applied Sciences; University of North Texas; Denton TX USA
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Brambilla A, Keller L, Bassano B, Grossen C. Heterozygosity-fitness correlation at the major histocompatibility complex despite low variation in Alpine ibex ( Capra ibex). Evol Appl 2018; 11:631-644. [PMID: 29875807 PMCID: PMC5979623 DOI: 10.1111/eva.12575] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/30/2017] [Indexed: 01/06/2023] Open
Abstract
Crucial for the long-term survival of wild populations is their ability to fight diseases. Disease outbreaks can lead to severe population size reductions, which makes endangered and reintroduced species especially vulnerable. In vertebrates, the major histocompatibility complex (MHC) plays an important role in determining the immune response. Species that went through severe bottlenecks often show very low levels of genetic diversity at the MHC. Due to the known link between the MHC and immune response, such species are expected to be at particular risk in case of disease outbreaks. However, so far, only few studies have shown that low MHC diversity is correlated with increased disease susceptibility in species after severe bottlenecks. We investigated genetic variation at the MHC and its correlations with disease resistance and other fitness-related traits in Alpine ibex (Capra ibex), a wild goat species that underwent a strong bottleneck in the last century and that is known to have extremely low genetic variability, both genome-wide and at the MHC. We studied MHC variation in male ibex of Gran Paradiso National Park, the population used as a source for all postbottleneck reintroductions. We found that individual MHC heterozygosity (based on six microsatellites) was not correlated with genome-wide neutral heterozygosity. MHC heterozygosity, but not genome-wide heterozygosity, was positively correlated with resistance to infectious keratoconjunctivitis and with body mass. Our results show that genetic variation at the MHC plays an important role in disease resistance and, hence, should be taken into account for successfully managing species conservation.
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Affiliation(s)
- Alice Brambilla
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich (ZH)Switzerland
- Alpine Wildlife Research CentreGran Paradiso National ParkNoasca (TO)Italy
| | - Lukas Keller
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich (ZH)Switzerland
| | - Bruno Bassano
- Alpine Wildlife Research CentreGran Paradiso National ParkNoasca (TO)Italy
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich (ZH)Switzerland
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Cortázar-Chinarro M, Lattenkamp EZ, Meyer-Lucht Y, Luquet E, Laurila A, Höglund J. Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian. BMC Evol Biol 2017; 17:189. [PMID: 28806900 PMCID: PMC5557520 DOI: 10.1186/s12862-017-1022-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/26/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. RESULTS Using outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. CONCLUSION Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.
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Affiliation(s)
- Maria Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
| | - Ella Z Lattenkamp
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Present address: Department of Neurogenetics of Vocal Communication, Max Planck Institute of Psycholinguistics, Box 310, 6500, Nijmegen, Netherlands
| | - Yvonne Meyer-Lucht
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Emilien Luquet
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Present address: Université Claude Bernard - Lyon I, CNRS, UMR 5023 - LEHNA, 3-6, rue Raphaël Dubois - Bâtiments Darwin C and Forel, 69622 Villeurbanne Cedex 43, Boulevard du 11 novembre, 1918, Lyon, France
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
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Population genetic diversity and geographical differentiation of MHC class II DAB genes in the vulnerable Chinese egret (Egretta eulophotes). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0876-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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