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Fu M, Eimes JA, Kong S, Lamichhaney S, Waldman B. Identification of major histocompatibility complex genotypes associated with resistance to an amphibian emerging infectious disease. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105470. [PMID: 37336279 DOI: 10.1016/j.meegid.2023.105470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
Amphibian chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), emerged from Asia and spread globally. By comparing functional MHC IIß1 alleles from an Asian Bd-resistant anuran species (Bufo gargarizans) with those of an Australasian Bd-susceptible species (Litoria caerulea), we identified MHC genotypes associated with Bd resistance. These alleles encode a glycine deletion (G90β1) and adjacent motifs in the deepest pathogen-derived peptide-binding groove. Every Bd-resistant individual, but no susceptible individuals, possessed at least one allele encoding the variant. We detected trans-species polymorphism at the end of the MHC IIβ1 sequences. The G90β1 deletion was encoded by different alleles in the two species, suggesting it may have evolved independently in each species rather than having been derived from a common ancestor. These results are consistent with a scenario by which MHC adaptations that confer resistance to the pathogen have evolved by convergent evolution. Immunogenetic studies such as this are critical to ongoing conservation efforts.
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Affiliation(s)
- Minjie Fu
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
| | - John A Eimes
- University College, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Sungsik Kong
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH 44243, USA
| | - Bruce Waldman
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea; Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
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2
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Lozano-Martín C, Bracamonte SE, Barluenga M. Evolution of MHC IIB Diversity Across Cichlid Fish Radiations. Genome Biol Evol 2023; 15:evad110. [PMID: 37314153 PMCID: PMC10306275 DOI: 10.1093/gbe/evad110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/12/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023] Open
Abstract
The genes of the major histocompatibility complex (MHC) are among the most polymorphic genes in vertebrates and crucial for their adaptive immune response. These genes frequently show inconsistencies between allelic genealogies and species phylogenies. This phenomenon is thought to be the result of parasite-mediated balancing selection maintaining ancient alleles through speciation events (trans-species polymorphism [TSP]). However, allele similarities may also arise from postspeciation mechanisms, such as convergence or introgression. Here, we investigated the evolution of MHC class IIB diversity in the cichlid fish radiations across Africa and the Neotropics by a comprehensive review of available MHC IIB DNA sequence information. We explored what mechanism explains the MHC allele similarities found among cichlid radiations. Our results showed extensive allele similarity among cichlid fish across continents, likely due to TSP. Functionality at MHC was also shared among species of the different continents. The maintenance of MHC alleles for long evolutionary times and their shared functionality may imply that certain MHC variants are essential in immune adaptation, even in species that diverged millions of years ago and occupy different environments.
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3
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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4
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Minias P, Palomar G, Dudek K, Babik W. Salamanders reveal novel trajectories of amphibian MHC evolution. Evolution 2022; 76:2436-2449. [PMID: 36000494 DOI: 10.1111/evo.14601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 07/06/2022] [Accepted: 07/29/2022] [Indexed: 01/22/2023]
Abstract
Genes of the major histocompatibility complex (MHC) code for immune proteins that are crucial for pathogen recognition in vertebrates. MHC research in nonmodel taxa has long been hampered by its genomic complexity that makes the locus-specific genotyping challenging. The recent progress in sequencing and genotyping methodologies allows an extensive phylogenetic coverage in studies of MHC evolution. Here, we analyzed the peptide-binding region of MHC class I (MHC-I) in 30 species of salamanders from six families representative of Urodela phylogeny. This extensive dataset revealed an extreme diversity of MHC-I in salamanders, both in terms of sequence diversity (about 3000 variants) and architecture (2-22 gene copies per species). The signal of positive selection was moderate and consistent between both peptide-binding domains, but varied greatly between genera. Positions of positively selected sites mostly coincided with human peptide-binding sites, suggesting similar structural properties of MHC-I molecules across distant vertebrate lineages. Finally, we provided evidence for the common intraexonic recombination at MHC-I and for the role of life history traits in the processes of MHC-I expansion/contraction. Our study revealed novel evolutionary trajectories of amphibian MHC and it contributes to the understanding of the mechanisms that generated extraordinary MHC diversity throughout vertebrate evolution.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, 90-237, Poland
| | - Gemma Palomar
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, 30-387, Poland.,Parasitology Unit, Department of Biomedicine and Biotechnology, Faculty of Pharmacy, Universidad de Alcalá (UAH), Alcalá de Henares, Madrid, 28805, Spain
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, 30-387, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, 30-387, Poland
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5
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Arntzen JW, Jehle R, Wielstra B. Genetic and morphological data demonstrate hybridization and backcrossing in a pair of salamanders at the far end of the speciation continuum. Evol Appl 2021; 14:2784-2793. [PMID: 34950229 PMCID: PMC8674889 DOI: 10.1111/eva.13312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/05/2021] [Accepted: 10/01/2021] [Indexed: 12/23/2022] Open
Abstract
Deeply diverged yet hybridizing species provide a system to investigate the final stages of the speciation process. We study a hybridizing pair of salamander species-the morphologically and genetically drastically different newts Triturus cristatus and T. marmoratus-with a panel of 32 nuclear and mitochondrial genetic markers. Morphologically identified hybrids are mostly of the F1 generation and mothered by T. cristatus. The sex ratio of the F1 hybrid class is reciprocally skewed, with a preponderance of females in T. cristatus-mothered hybrids and males in T. marmoratus-mothered hybrids. This amounts to the Haldane effect operating in one direction of the cross. Deeper generation hybrids are occasionally produced, possibly including F1 hybrid × backcross hybrid offspring. Interspecific gene flow is low, yet skewed toward T. cristatus. This asymmetry may be caused by hybrid zone movement, with the superseding species being predisposed to introgression. The persisting gene flow between deeply differentiated species supports the notion that full genetic isolation may be selected against. Conversely, published morphological data suggest that introgressive hybridization is detrimental, with digital malformations occurring more frequently in the area of sympatry. Finally, to assist field identification, both within the area of natural range overlap and concerning anthropogenic introductions elsewhere, we document the phenotypical variation of two generations of hybrids compared with both parental species. We suggest that fluctuating range boundaries, ecological segregation, cytonuclear incompatibilities and hybrid breakdown through Bateson-Dobzhansky-Muller incompatibilities all contribute to species integrity, despite incomplete isolation during secondary contact.
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Affiliation(s)
- Jan W. Arntzen
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Institute of BiologyLeiden UniversityLeidenThe Netherlands
| | - Robert Jehle
- School of Science, Engineering and EnvironmentUniversity of SalfordSalfordUK
| | - Ben Wielstra
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Institute of BiologyLeiden UniversityLeidenThe Netherlands
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6
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Diversity of MHC IIB genes and parasitism in hybrids of evolutionarily divergent cyprinoid species indicate heterosis advantage. Sci Rep 2021; 11:16860. [PMID: 34413384 PMCID: PMC8376869 DOI: 10.1038/s41598-021-96205-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/02/2021] [Indexed: 02/07/2023] Open
Abstract
The genes of the major histocompatibility complex (MHC) are an essential component of the vertebrate immune system and MHC genotypes may determine individual susceptibility to parasite infection. In the wild, selection that favors MHC variability can create situations in which interspecies hybrids experience a survival advantage. In a wild system of two naturally hybridizing leuciscid fish, we assessed MHC IIB genetic variability and its potential relationships to hosts' ectoparasite communities. High proportions of MHC alleles and parasites were species-specific. Strong positive selection at specific MHC codons was detected in both species and hybrids. MHC allele expression in hybrids was slightly biased towards the maternal species. Controlling for a strong seasonal effect on parasite communities, we found no clear associations between host-specific parasites and MHC alleles or MHC supertypes. Hybrids shared more MHC alleles with the more MHC-diverse parental species, but expressed intermediate numbers of MHC alleles and positively selected sites. Hybrids carried significantly fewer ectoparasites than either parent species, suggesting a hybrid advantage via potential heterosis.
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7
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Hybridization with mountain hares increases the functional allelic repertoire in brown hares. Sci Rep 2021; 11:15771. [PMID: 34349207 PMCID: PMC8338973 DOI: 10.1038/s41598-021-95357-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
Brown hares (Lepus europaeus Pallas) are able to hybridize with mountain hares (L. timidus Linnaeus) and produce fertile offspring, which results in cross-species gene flow. However, not much is known about the functional significance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic diversity in the Finnish brown hare to be small, likely due to founder effect and range expansion, while gene flow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1), might have adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study offers a rare example where an expanding species can increase its allelic variability through hybridization with a congeneric native species, offering a route to shortcut evolutionary adaptation to the local environmental conditions.
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8
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Roth AM, Keiser CN, Williams JB, Gee JM. Prevalence and intensity of avian malaria in a quail hybrid zone. Ecol Evol 2021; 11:8123-8135. [PMID: 34188875 PMCID: PMC8216944 DOI: 10.1002/ece3.7645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 01/12/2023] Open
Abstract
Hybrid zones have been described as natural laboratories by researchers who study speciation and the various mechanisms that may affect gene flow. The evolutionary consequences of hybridization depend not only on reproductive compatibility between sympatric species, but also on factors like vulnerability to each other's predators and parasites. We examined infection patterns of the blood parasite Haemoproteus lophortyx, a causative agent of avian malaria, at a site in the contact zone between California quail (Callipepla californica) and Gambel's quail (C. gambelii). Controlling for the potential influence of sex and year, we tested whether species identity predicted infection status and intensity. We found that infection prevalence was lower in California and hybrid quail compared with Gambel's quail. However, infected California and hybrid quail had higher infection intensities than Gambel's quail. California and hybrid quail exhibited no significant differences in prevalence or intensity of infection. These findings suggest that infection by H. lophortyx has the potential to influence species barrier dynamics in this system; however, more work is necessary to determine the exact evolutionary consequences of this blood parasite on hybridization.
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Affiliation(s)
| | - Carl N. Keiser
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Judson B. Williams
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
- Present address:
Department of SurgeryDuke UniversityRaleighNCUSA
| | - Jennifer M. Gee
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
- Present address:
James San Jacinto Mountains ReserveUniversity of California – RiversideUniversity of California Natural Reserve SystemIdyllwildCAUSA
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9
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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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10
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Jamie GA, Meier JI. The Persistence of Polymorphisms across Species Radiations. Trends Ecol Evol 2020; 35:795-808. [DOI: 10.1016/j.tree.2020.04.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
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11
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Ravinet M, Kume M, Ishikawa A, Kitano J. Patterns of genomic divergence and introgression between Japanese stickleback species with overlapping breeding habitats. J Evol Biol 2020; 34:114-127. [PMID: 32557887 DOI: 10.1111/jeb.13664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 11/26/2022]
Abstract
With only a few absolute geographic barriers in marine environments, the factors maintaining reproductive isolation among marine organisms remain elusive. However, spatial structuring in breeding habitat can contribute to reproductive isolation. This is particularly important for marine organisms that migrate to use fresh- or brackish water environments to breed. The Japanese Gasterosteus stickleback species, the Pacific Ocean three-spined stickleback (G. aculeatus) and the Japan Sea stickleback (G. nipponicus) overwinter in the sea, but migrate to rivers for spawning. Although they co-occur at several locations across the Japanese islands, they are reproductively isolated. Our previous studies in Bekanbeushi River showed that the Japan Sea stickleback spawns in the estuary, while the Pacific Ocean stickleback mainly spawns further upstream in freshwater. Overall genomic divergence was very high with many interspersed regions of introgression. Here, we investigated genomic divergence and introgression between the sympatric species in the much shorter Tokotan River, where they share spawning sites. The levels of genome-wide divergence were reduced and introgression was increased, suggesting that habitat isolation substantially contributes to a reduction in gene flow. We also found that genomic regions of introgression were largely shared between the two systems. Furthermore, some regions of introgression were located near loci with a heterozygote advantage for juvenile survival. Taken together, introgression may be partially driven by adaptation in this system. Although, the two species remain clearly genetically differentiated. Regions with low recombination rates showed especially low introgression. Speciation reversal is therefore likely prevented by barriers other than habitat isolation.
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Affiliation(s)
- Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Manabu Kume
- Kyoto University Field Science Education and Research Center, Kyoto, Japan
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
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12
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Talarico L, Babik W, Marta S, Pietrocini V, Mattoccia M. MHC structuring and divergent allele advantage in a urodele amphibian: a hierarchical multi-scale approach. Heredity (Edinb) 2019; 123:593-607. [PMID: 31036951 PMCID: PMC6972932 DOI: 10.1038/s41437-019-0221-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/31/2019] [Accepted: 03/31/2019] [Indexed: 12/27/2022] Open
Abstract
Proteins encoded by extraordinarily polymorphic major histocompatibility complex (MHC) genes are involved in the adaptive immune response. Balancing selection is believed to maintain MHC polymorphism in the long term, although neutral processes also play a role in shaping MHC diversity. However, the relative contribution of these processes is poorly understood. Here we characterized MHC class II variation of a low-dispersal, pond-breeding newt (Triturus carnifex) over a restricted, geographically structured area. We aimed to (1) evaluate the contribution of selection and neutral processes to shaping MHC diversity at two geographic scales, and (2) test for signatures of divergent allele advantage (DAA), which is a potentially important mechanism of balancing selection. The dominant role of selection in shaping MHC variation was suggested by the lack of correlation between MHC and neutral (microsatellite) variation. Although most variation occurred within populations for both types of markers, they differed in the extent of structuring at the two spatial scales. MHC structuring was more pronounced at local scales, suggesting the role of local selection, while structuring was not detectable at a larger scale, possibly due to the effect of balancing selection. Microsatellites showed the opposite pattern. As expected under DAA, the observed genotypes combined more sequence diversity than expected under a random association of alleles. Thus, DAA may contribute to maintaining MHC polymorphism, which is ancient, as supported by signatures of historical positive selection and trans-species polymorphism. Our results point to the importance of a multi-scale approach in studying MHC variation, especially in low-dispersal taxa, which are genetically structured at fine spatial scales.
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Affiliation(s)
- Lorenzo Talarico
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, Rome, 00133, Italy.
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Silvio Marta
- Department of Environmental Sciences and Policy, University of Milan, Via G. Celoria 26, Milan, 20133, Italy
| | - Venusta Pietrocini
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, Rome, 00133, Italy
| | - Marco Mattoccia
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, Rome, 00133, Italy
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13
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Dudek K, Gaczorek TS, Zieliński P, Babik W. Massive introgression of major histocompatibility complex (MHC) genes in newt hybrid zones. Mol Ecol 2019; 28:4798-4810. [PMID: 31574568 DOI: 10.1111/mec.15254] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 12/22/2022]
Abstract
Variation in the vertebrate major histocompatibility complex (MHC) genes is crucial for fighting pathogen assault. Because new alleles confer a selective advantage, MHC should readily introgress between species, even under limited hybridization. Using replicated transects through two hybrid zones between strongly reproductively isolated European newts, Lissotriton montandoni and L. vulgaris, we demonstrated recent and ongoing MHC class I and II introgression in the Carpathian region. The extent of introgression correlated with the age of contact. In the older zone, MHC similarity between species within transects exceeded similarity between transects within species, implying pervasive introgression - a massive exchange of MHC genes, not limited to specific variants. In simulations, the observed pattern emerged under the combined action of balancing selection and hybridization, but not when these processes acted separately. Thus, massive introgression at advanced stages of divergence can introduce novel and restore previously lost MHC variation, boosting the adaptive potential of hybridizing taxa. In consequence, MHC genes may be the last to stop introgressing between incipient species.
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Affiliation(s)
- Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Tomasz S Gaczorek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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14
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Sagonas K, Runemark A, Antoniou A, Lymberakis P, Pafilis P, Valakos ED, Poulakakis N, Hansson B. Selection, drift, and introgression shape MHC polymorphism in lizards. Heredity (Edinb) 2019; 122:468-484. [PMID: 30258107 PMCID: PMC6460769 DOI: 10.1038/s41437-018-0146-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/27/2018] [Accepted: 08/09/2018] [Indexed: 01/12/2023] Open
Abstract
The major histocompatibility complex (MHC) has long served as a model for the evolution of adaptive genetic diversity in wild populations. Pathogen-mediated selection is thought to be a main driver of MHC diversity, but it remains elusive to what degree selection shapes MHC diversity in complex biogeographical scenarios where other evolutionary processes (e.g. genetic drift and introgression) may also be acting. Here we focus on two closely related green lizard species, Lacerta trilineata and L. viridis, to address the evolutionary forces acting on MHC diversity in populations with different biogeographic structure. We characterized MHC class I exon 2 and exon 3, and neutral diversity (microsatellites), to study the relative importance of selection, drift, and introgression in shaping MHC diversity. As expected, positive selection was a significant force shaping the high diversity of MHC genes in both species. Moreover, introgression significantly increased MHC diversity in mainland populations, with a primary direction of gene flow from L. viridis to L. trilineata. Finally, we found significantly fewer MHC alleles in island populations, but maintained MHC sequence and functional diversity, suggesting that positive selection counteracted the effect of drift. Overall, our data support that different evolutionary processes govern MHC diversity in different biogeographical scenarios: positive selection occurs broadly while introgression acts in sympatry and drift when the population sizes decrease.
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Affiliation(s)
- K Sagonas
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
- Department of Human and Animal Physiology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, 15784, Athens, Greece.
| | - A Runemark
- Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - A Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, 71003, Heraklion, Crete, Greece
| | - P Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, 71409, Heraklion, Crete, Greece
| | - P Pafilis
- Department of Zoology and Marine Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, 15784, Athens, Greece
| | - E D Valakos
- Department of Human and Animal Physiology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, 15784, Athens, Greece
| | - N Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, 71409, Heraklion, Crete, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vasilika Vouton, 71003, Heraklion, Crete, Greece
| | - B Hansson
- Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
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15
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Parasites and Host Species Barriers in Animal Hybrid Zones. Trends Ecol Evol 2018; 34:19-30. [PMID: 30348471 DOI: 10.1016/j.tree.2018.09.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 12/19/2022]
Abstract
Species barriers are tested in hybrid zones when gene flow occurs between hybridizing species. Hybridization can erode species barriers, lead to the introgression of adaptive traits, or remain stable through time. Outcomes in hybrid zones are influenced by divergence between the hybridizing taxa, behavior, ecology, and geography. Parasites and pathogens play a major role in host fitness and appear to have varied impacts on species barriers in hybrid zones. We comprehensively reviewed the literature on parasitism in animal hybrid zones and present an evolutionary framework within which to consider parasite-hybrid interactions. Parasites most frequently show potential to contribute to species barrier breakdown in hybrid zones, but also frequently show potential to facilitate the maintenance of species barriers. Incorporating eco-immunology, parasite community theory, and spatiotemporal approaches will be important as genomic tools allow researchers to examine parasites and hybrid zones at greater resolution and in a diversity of natural habitats.
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16
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Fijarczyk A, Dudek K, Niedzicka M, Babik W. Balancing selection and introgression of newt immune-response genes. Proc Biol Sci 2018; 285:20180819. [PMID: 30111606 PMCID: PMC6111169 DOI: 10.1098/rspb.2018.0819] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022] Open
Abstract
The importance of interspecific introgression as a source of adaptive variation is increasingly recognized. Theory predicts that beneficial genetic variants cross species boundaries easily even when interspecific hybridization is rare and gene flow is strongly constrained throughout the genome. However, it remains unclear whether certain classes of genes are particularly prone to adaptive introgression. Genes affected by balancing selection (BS) may constitute such a class, because forms of BS that favour novel, initially rare alleles, should facilitate introgression. We tested this hypothesis in hybridizing newts by comparing 13 genes with signatures of BS, in particular an excess of common non-synonymous polymorphisms, to the genomic background (154 genes). Parapatric hybridizing taxa were less differentiated in BS candidate genes than more closely related allopatric lineages, while the opposite was observed in the control genes. Coalescent and forward simulations that explored neutral and BS scenarios under isolation and migration showed that processes other than differential gene flow are unlikely to account for this pattern. We conclude that BS, probably involving a form of novel allele advantage, promotes introgression. This mechanism may be a source of adaptively relevant variation in hybridizing species over prolonged periods.
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Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, Université Laval, 1030, Avenue de la Médecine, Québec, Canada G1V 0A6
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Marta Niedzicka
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
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Linnenbrink M, Teschke M, Montero I, Vallier M, Tautz D. Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice ( Mus musculus). Front Zool 2018; 15:15. [PMID: 29721030 PMCID: PMC5910556 DOI: 10.1186/s12983-018-0266-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022] Open
Abstract
Background The MHC class I and II loci mediate the adaptive immune response and belong to the most polymorphic loci in vertebrate genomes. In fact, the number of different alleles in a given species is often so large that it remains a challenge to provide an evolutionary model that can fully account for this. Results We provide here a general survey of MHC allele numbers in house mouse populations and two sub-species (M. m. domesticus and M. m. musculus) for H2 class I D and K, as well as class II A and E loci. Between 50 and 90% of the detected different sequences constitute new alleles, confirming that the discovery of new alleles is indeed far from complete. House mice live in separate demes with small effective population sizes, factors that were proposed to reduce, rather than enhance the possibility for the maintenance of many different alleles. To specifically investigate the occurrence of alleles within demes, we focused on the class II H2-Aa and H2-Eb exon 2 alleles in nine demes of M. m. domesticus from two different geographic regions. We find on the one hand a group of alleles that occur in different sampling regions and three quarters of these are also found in both sub-species. On the other hand, the larger group of different alleles (56%) occurs only in one of the regions and most of these (89%) only in single demes. We show that most of these region-specific alleles have apparently arisen through recombination and/or partial gene conversion from already existing alleles. Conclusions Demes can act as sources of alleles that outnumber the set of alleles that are shared across the species range. These findings support the reservoir model proposed for human MHC diversity, which states that large pools of rare MHC allele variants are continuously generated by neutral mutational mechanisms. Given that these can become important in the defense against newly emerging pathogens, the reservoir model complements the selection based models for MHC diversity and explains why the exceptional diversity exists. Electronic supplementary material The online version of this article (10.1186/s12983-018-0266-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miriam Linnenbrink
- 3Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Meike Teschke
- 1Present address: Deutsche Forschungsgemeinschaft, 53170 Bonn, Germany.,3Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Inka Montero
- 2Present address: Medical Faculty, Eberhard Karls Universität Tübingen, Tübingen, Germany.,3Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Marie Vallier
- 3Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
| | - Diethard Tautz
- 3Max-Planck Institute for Evolutionary Biology, August-Thienemannstrasse 2, 24306 Plön, Germany
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18
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Phillips KP, Cable J, Mohammed RS, Herdegen-Radwan M, Raubic J, Przesmycka KJ, van Oosterhout C, Radwan J. Immunogenetic novelty confers a selective advantage in host-pathogen coevolution. Proc Natl Acad Sci U S A 2018; 115:1552-1557. [PMID: 29339521 PMCID: PMC5816137 DOI: 10.1073/pnas.1708597115] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The major histocompatibility complex (MHC) is crucial to the adaptive immune response of vertebrates and is among the most polymorphic gene families known. Its high diversity is usually attributed to selection imposed by fast-evolving pathogens. Pathogens are thought to evolve to escape recognition by common immune alleles, and, hence, novel MHC alleles, introduced through mutation, recombination, or gene flow, are predicted to give hosts superior resistance. Although this theoretical prediction underpins host-pathogen "Red Queen" coevolution, it has not been demonstrated in the context of natural MHC diversity. Here, we experimentally tested whether novel MHC variants (both alleles and functional "supertypes") increased resistance of guppies (Poecilia reticulata) to a common ectoparasite (Gyrodactylus turnbulli). We used exposure-controlled infection trials with wild-sourced parasites, and Gyrodactylus-naïve host fish that were F2 descendants of crossed wild populations. Hosts carrying MHC variants (alleles or supertypes) that were new to a given parasite population experienced a 35-37% reduction in infection intensity, but the number of MHC variants carried by an individual, analogous to heterozygosity in single-locus systems, was not a significant predictor. Our results provide direct evidence of novel MHC variant advantage, confirming a fundamental mechanism underpinning the exceptional polymorphism of this gene family and highlighting the role of immunogenetic novelty in host-pathogen coevolution.
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Affiliation(s)
- Karl P Phillips
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, 60-614 Poznań, Poland
- School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
| | - Joanne Cable
- School of Biosciences, Cardiff University, CF10 3AX Cardiff, United Kingdom
| | - Ryan S Mohammed
- Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Magdalena Herdegen-Radwan
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Jarosław Raubic
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, 60-614 Poznań, Poland
| | - Karolina J Przesmycka
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, 60-614 Poznań, Poland
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, United Kingdom
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, 60-614 Poznań, Poland;
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19
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Wielstra B, Canestrelli D, Cvijanović M, Denoël M, Fijarczyk A, Jablonski D, Liana M, Naumov B, Olgun K, Pabijan M, Pezzarossa A, Popgeorgiev G, Salvi D, Si Y, Sillero N, Sotiropoulos K, Zieliński P, Babik W. The distributions of the six species constituting the smooth newt species complex (Lissotriton vulgaris sensu lato and L. montandoni) – an addition to the New Atlas of Amphibians and Reptiles of Europe. AMPHIBIA-REPTILIA 2018. [DOI: 10.1163/15685381-17000128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
The ‘smooth newt’, the taxon traditionally referred to as Lissotriton vulgaris, consists of multiple morphologically distinct taxa. Given the uncertainty concerning the validity and rank of these taxa, L. vulgaris sensu lato has often been treated as a single, polytypic species. A recent study, driven by genetic data, proposed to recognize five species, L. graecus, L. kosswigi, L. lantzi, L. schmidtleri and a more restricted L. vulgaris. The Carpathian newt L. montandoni was confirmed to be a closely related sister species. We propose to refer to this collective of six Lissotriton species as the smooth newt or Lissotriton vulgaris species complex. Guided by comprehensive genomic data from throughout the range of the smooth newt species complex we 1) delineate the distribution ranges, 2) provide a distribution database, and 3) produce distribution maps according to the format of the New Atlas of Amphibians and Reptiles of Europe, for the six constituent species. This allows us to 4) highlight regions where more research is needed to determine the position of contact zones.
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Affiliation(s)
- Ben Wielstra
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- 2Department of Animal and Plant Sciences, University of Sheffield, S10 2TN Sheffield, UK
- 3Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Daniele Canestrelli
- 4Department of Ecological and Biological Science, Tuscia University, 01100 Viterbo, Italy
| | - Milena Cvijanović
- 5Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Bul. Despota Stefana 142, 11060 Belgrade, Serbia
| | - Mathieu Denoël
- 6Laboratory of Fish and Amphibian Ethology, Behavioural Biology Unit, Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
| | - Anna Fijarczyk
- 7Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
- 8Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec, QC, Canada
| | - Daniel Jablonski
- 9Department of Zoology, Comenius University in Bratislava Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | | | - Borislav Naumov
- 11Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Street, 1113 Sofia, Bulgaria
| | - Kurtuluş Olgun
- 12Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, 09010 Aydın, Turkey
| | - Maciej Pabijan
- 13Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Alice Pezzarossa
- 4Department of Ecological and Biological Science, Tuscia University, 01100 Viterbo, Italy
| | - Georgi Popgeorgiev
- 14National Museum of Natural History, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd, 1000 Sofia, Bulgaria
| | - Daniele Salvi
- 15Department of Health, Life and Environmental Sciences, University of L’Aquila, Via Vetoio, 67100 Coppito, L’Aquila, Italy
- 16CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Yali Si
- 17Ministry of Education Key Laboratory for Earth System Modeling, and Department of Earth System Science, Tsinghua University, Beijing, China
- 18Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 621 Charles E. Yong Drive South, Los Angeles, CA 90095, USA
| | - Neftalí Sillero
- 19CICGE – Centro de Investigação em Ciências Geo-Espaciais, Observatório Astronómico Prof. Manuel de Barros, Alameda do Monte da Virgem, 4430-146 Vila Nova de Gaia, Portugal
| | - Konstantinos Sotiropoulos
- 20Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece
| | - Piotr Zieliński
- 7Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Wiesław Babik
- 7Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
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20
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Minias P, Bateson ZW, Whittingham LA, Johnson JA, Oyler-McCance S, Dunn PO. Extensive shared polymorphism at non-MHC immune genes in recently diverged North American prairie grouse. Immunogenetics 2017; 70:195-204. [PMID: 28770305 PMCID: PMC5818594 DOI: 10.1007/s00251-017-1024-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/25/2017] [Indexed: 12/23/2022]
Abstract
Gene polymorphisms shared between recently diverged species are thought to be widespread and most commonly reflect introgression from hybridization or retention of ancestral polymorphism through incomplete lineage sorting. Shared genetic diversity resulting from incomplete lineage sorting is usually maintained for a relatively short period of time, but under strong balancing selection it may persist for millions of years beyond species divergence (balanced trans-species polymorphism), as in the case of the major histocompatibility complex (MHC) genes. However, balancing selection is much less likely to act on non-MHC immune genes. The aim of this study was to investigate the patterns of shared polymorphism and selection at non-MHC immune genes in five grouse species from Centrocercus and Tympanuchus genera. For this purpose, we genotyped five non-MHC immune genes that do not interact directly with pathogens, but are involved in signaling and regulate immune cell growth. In contrast to previous studies with MHC, we found no evidence for balancing selection or balanced trans-species polymorphism among the non-MHC immune genes. No haplotypes were shared between genera and in most cases more similar allelic variants sorted by genus. Between species within genera, however, we found extensive shared polymorphism, which was most likely attributable to introgression or incomplete lineage sorting following recent divergence and large ancestral effective population size (i.e., weak genetic drift). Our study suggests that North American prairie grouse may have attained relatively low degree of reciprocal monophyly at nuclear loci and reinforces the rarity of balancing selection in non-MHC immune genes.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Zachary W Bateson
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, TX, USA
| | | | - Peter O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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21
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22
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Linkage Map of Lissotriton Newts Provides Insight into the Genetic Basis of Reproductive Isolation. G3-GENES GENOMES GENETICS 2017; 7:2115-2124. [PMID: 28500054 PMCID: PMC5499121 DOI: 10.1534/g3.117.041178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Linkage maps are widely used to investigate structure, function, and evolution of genomes. In speciation research, maps facilitate the study of the genetic architecture of reproductive isolation by allowing identification of genomic regions underlying reduced fitness of hybrids. Here we present a linkage map for European newts of the Lissotriton vulgaris species complex, constructed using two families of F2 L. montandoni × L. vulgaris hybrids. The map consists of 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM (1.29 cM per marker). It is notably shorter than two other maps available for salamanders, but the differences in map length are consistent with cytogenetic estimates of the number of chiasmata per chromosomal arm. Thus, large salamander genomes do not necessarily translate into long linkage maps, as previously suggested. Consequently, salamanders are an excellent model to study evolutionary consequences of recombination rate variation in taxa with large genomes and a similar number of chromosomes. A complex pattern of transmission ratio distortion (TRD) was detected: TRD occurred mostly in one family, in one breeding season, and was clustered in two genomic segments. This is consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in these two segments and suggests a role of TRD blocks in reproductive isolation. The reported linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.
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23
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Santonastaso T, Lighten J, van Oosterhout C, Jones KL, Foufopoulos J, Anthony NM. The effects of historical fragmentation on major histocompatibility complex class II β and microsatellite variation in the Aegean island reptile, Podarcis erhardii. Ecol Evol 2017; 7:4568-4581. [PMID: 28690787 PMCID: PMC5496512 DOI: 10.1002/ece3.3022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 03/16/2017] [Accepted: 03/27/2017] [Indexed: 01/29/2023] Open
Abstract
The major histocompatibility complex (MHC) plays a key role in disease resistance and is the most polymorphic gene region in vertebrates. Although habitat fragmentation is predicted to lead to a loss in MHC variation through drift, the impact of other evolutionary forces may counter this effect. Here we assess the impact of selection, drift, migration, and recombination on MHC class II and microsatellite variability in 14 island populations of the Aegean wall lizard Podarcis erhardii. Lizards were sampled from islands within the Cyclades (Greece) formed by rising sea levels as the last glacial maximum approximately 20,000 before present. Bathymetric data were used to determine the area and age of each island, allowing us to infer the corresponding magnitude and timing of genetic bottlenecks associated with island formation. Both MHC and microsatellite variation were positively associated with island area, supporting the hypothesis that drift governs neutral and adaptive variation in this system. However, MHC but not microsatellite variability declined significantly with island age. This discrepancy is likely due to the fact that microsatellites attain mutation‐drift equilibrium more rapidly than MHC. Although we detected signals of balancing selection, recombination and migration, the effects of these evolutionary processes appeared negligible relative to drift. This study demonstrates how land bridge islands can provide novel insights into the impact of historical fragmentation on genetic diversity as well as help disentangle the effects of different evolutionary forces on neutral and adaptive diversity.
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Affiliation(s)
- Trent Santonastaso
- Department of Biological Sciences University of New Orleans New Orleans LA USA
| | - Jackie Lighten
- School of Environmental 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
| | - Kenneth L Jones
- Department of Biochemistry and Molecular Genetics University of Colorado Denver School of Medicine Denver CO USA
| | - Johannes Foufopoulos
- School of the Environment and Sustainability University of Michigan Ann Arbor MI USA
| | - Nicola M Anthony
- Department of Biological Sciences University of New Orleans New Orleans LA USA
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24
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Spatial distribution of microsatellite and MHC-DRB exon 2 gene variability in the Jamaican fruit bat (Artibeus jamaicensis) in Mexico. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2016.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Substantial functional diversity accompanies limited major histocompatibility complex class II variability in golden jackal (Canis aureus): A comparison between two wild Canis species in Croatia. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2016.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Li D, Sun K, Zhao Y, Lin A, Li S, Jiang Y, Feng J. Polymorphism in the major histocompatibility complex (MHC class II B) genes of the Rufous-backed Bunting ( Emberiza jankowskii). PeerJ 2017; 5:e2917. [PMID: 28149689 PMCID: PMC5270597 DOI: 10.7717/peerj.2917] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 12/16/2016] [Indexed: 11/23/2022] Open
Abstract
Genetic diversity is one of the pillars of conservation biology research. High genetic diversity and abundant genetic variation in an organism may be suggestive of capacity to adapt to various environmental changes. The major histocompatibility complex (MHC) is known to be highly polymorphic and plays an important role in immune function. It is also considered an ideal model system to investigate genetic diversity in wildlife populations. The Rufous-backed Bunting (Emberiza jankowskii) is an endangered species that has experienced a sharp decline in both population and habitat size. Many historically significant populations are no longer present in previously populated regions, with only three breeding populations present in Inner Mongolia (i.e., the Aolunhua, Gahaitu and Lubei557 populations). Efforts focused on facilitating the conservation of the Rufous-backed Bunting (Emberiza jankowskii) are becoming increasingly important. However, the genetic diversity of E. jankowskii has not been investigated. In the present study, polymorphism in exon 2 of the MHCIIB of E. jankowskii was investigated. This polymorphism was subsequently compared with a related species, the Meadow Bunting (Emberiza cioides). A total of 1.59 alleles/individual were detected in E. jankowskii and 1.73 alleles/individual were identified in E. cioides. The maximum number of alleles per individual from the three E. jankowskii populations suggest the existence of at least three functional loci, while the maximum number of alleles per individual from the three E. cioides populations suggest the presence of at least four functional loci. Two of the alleles were shared between the E. jankowskii and E. cioides. Among the 12 unique alleles identified in E. jankowskii, 10.17 segregating sites per allele were detected, and the nucleotide diversity was 0.1865. Among the 17 unique alleles identified in E. cioides, eight segregating sites per allele were detected, and the nucleotide diversity was 0.1667. Overall, compared to other passerine birds, a relatively low level of MHC polymorphism was revealed in E. jankowskii, which was similar to that in E. cioides. Positive selection was detected by PAML/SLAC/FEL analyses in the region encoding the peptide-binding region in both species, and no recombination was detected. Phylogenetic analysis showed that the alleles from E. jankowskii and E. cioides belong to the same clade and the two species shared similar alleles, suggesting the occurrence of a trans-species polymorphism between the two Emberiza species.
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Affiliation(s)
- Dan Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun , China
| | - Yunjiao Zhao
- College of Animal Science and Technology, Jilin Agricultural University , Changchun , China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun , China
| | - Shi Li
- College of Animal Science and Technology, Jilin Agricultural University , Changchun , China
| | - Yunlei Jiang
- College of Animal Science and Technology, Jilin Agricultural University , Changchun , China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun , China
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27
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Fijarczyk A, Dudek K, Babik W. Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation. Genome Biol Evol 2016; 8:3417-3432. [PMID: 27702815 PMCID: PMC5203778 DOI: 10.1093/gbe/evw236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus. Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.
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Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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28
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Rico Y, Ethier DM, Davy CM, Sayers J, Weir RD, Swanson BJ, Nocera JJ, Kyle CJ. Spatial patterns of immunogenetic and neutral variation underscore the conservation value of small, isolated American badger populations. Evol Appl 2016; 9:1271-1284. [PMID: 27877205 PMCID: PMC5108218 DOI: 10.1111/eva.12410] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/14/2016] [Indexed: 12/29/2022] Open
Abstract
Small and isolated populations often exhibit low genetic diversity due to drift and inbreeding, but may simultaneously harbour adaptive variation. We investigate spatial distributions of immunogenetic variation in American badger subspecies (Taxidea taxus), as a proxy for evaluating their evolutionary potential across the northern extent of the species' range. We compared genetic structure of 20 microsatellites and the major histocompatibility complex (MHC DRB exon 2) to evaluate whether small, isolated populations show low adaptive polymorphism relative to large and well-connected populations. Our results suggest that gene flow plays a prominent role in shaping MHC polymorphism across large spatial scales, while the interplay between gene flow and selection was stronger towards the northern peripheries. The similarity of MHC alleles within subspecies relative to their neutral genetic differentiation suggests that adaptive divergence among subspecies can be maintained despite ongoing gene flow along subspecies boundaries. Neutral genetic diversity was low in small relative to large populations, but MHC diversity within individuals was high in small populations. Despite reduced neutral genetic variation, small and isolated populations harbour functional variation that likely contribute to the species evolutionary potential at the northern range. Our findings suggest that conservation approaches should focus on managing adaptive variation across the species range rather than protecting subspecies per se.
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Affiliation(s)
- Yessica Rico
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
- Present address: CONACYTInstituto de Ecología A.C.Centro Regional del BajíoAvenida Lázaro Cárdenas 253PátzcuaroMichoacán61600México
| | - Danielle M. Ethier
- Ontario Badger ProjectGuelphONCanada
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Christina M. Davy
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
| | | | - Richard D. Weir
- Ecosystems Protection & Sustainability BranchMinistry of EnvironmentVictoriaBCCanada
| | | | - Joseph J. Nocera
- Wildlife Research and Monitoring SectionMinistry of Natural Resources & ForestryPeterboroughONCanada
| | - Christopher J. Kyle
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
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Biedrzycka A, Sebastian A, Migalska M, Westerdahl H, Radwan J. Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird. Mol Ecol Resour 2016; 17:642-655. [DOI: 10.1111/1755-0998.12612] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 02/10/2016] [Accepted: 08/23/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Aleksandra Biedrzycka
- Institute of Nature Conservation; Polish Academy of Sciences; Al. Mickiewicza 33 31-120 Kraków Poland
| | - Alvaro Sebastian
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznań Poland
| | - Magdalena Migalska
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznań Poland
| | - Helena Westerdahl
- Department of Biology; Lund University; Ecology Building, Sölvegatan 37 223 62 Lund Sweden
| | - Jacek Radwan
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznań Poland
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30
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Sallaberry‐Pincheira N, González‐Acuña D, Padilla P, Dantas GPM, Luna‐Jorquera G, Frere E, Valdés‐Velásquez A, Vianna JA. Contrasting patterns of selection between MHC I and II across populations of Humboldt and Magellanic penguins. Ecol Evol 2016; 6:7498-7510. [PMID: 28725416 PMCID: PMC5513272 DOI: 10.1002/ece3.2502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/18/2016] [Accepted: 08/28/2016] [Indexed: 12/21/2022] Open
Abstract
The evolutionary and adaptive potential of populations or species facing an emerging infectious disease depends on their genetic diversity in genes, such as the major histocompatibility complex (MHC). In birds, MHC class I deals predominantly with intracellular infections (e.g., viruses) and MHC class II with extracellular infections (e.g., bacteria). Therefore, patterns of MHC I and II diversity may differ between species and across populations of species depending on the relative effect of local and global environmental selective pressures, genetic drift, and gene flow. We hypothesize that high gene flow among populations of Humboldt and Magellanic penguins limits local adaptation in MHC I and MHC II, and signatures of selection differ between markers, locations, and species. We evaluated the MHC I and II diversity using 454 next-generation sequencing of 100 Humboldt and 75 Magellanic penguins from seven different breeding colonies. Higher genetic diversity was observed in MHC I than MHC II for both species, explained by more than one MHC I loci identified. Large population sizes, high gene flow, and/or similar selection pressures maintain diversity but limit local adaptation in MHC I. A pattern of isolation by distance was observed for MHC II for Humboldt penguin suggesting local adaptation, mainly on the northernmost studied locality. Furthermore, trans-species alleles were found due to a recent speciation for the genus or convergent evolution. High MHC I and MHC II gene diversity described is extremely advantageous for the long-term survival of the species.
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Affiliation(s)
- Nicole Sallaberry‐Pincheira
- Laboratorio de Biodiversidad MolecularDepartamento de Ecosistemas y Medio AmbienteFacultad de Agronomía e Ingeniería ForestalPontificia Universidad Católica de ChileSantiagoChile
- Escuela de Medicina VeterinariaFacultad Ecología y Recursos NaturalesUniversidad Andrés BelloSantiagoChile
| | | | - Pamela Padilla
- Laboratorio de Biodiversidad MolecularDepartamento de Ecosistemas y Medio AmbienteFacultad de Agronomía e Ingeniería ForestalPontificia Universidad Católica de ChileSantiagoChile
| | | | - Guillermo Luna‐Jorquera
- Universidad Católica del NorteMillenium Nucleus of Ecology and Sustainable Management of Oceanic Islands ESMOICentro de Estudios Avanzados en Zonas Áridas CEAZACoquimboChile
| | - Esteban Frere
- Centro de Investigaciones de Puerto DeseadoUniversidad Nacional de la Patagonia AustralPuerto DeseadoArgentina
| | - Armando Valdés‐Velásquez
- Laboratorio de Estudios en BiodiversidadFacultad de Ciencias Biológicas y FisiológicasUniversidad Peruana Cayetano HerediaLimaPeru
| | - Juliana A. Vianna
- Laboratorio de Biodiversidad MolecularDepartamento de Ecosistemas y Medio AmbienteFacultad de Agronomía e Ingeniería ForestalPontificia Universidad Católica de ChileSantiagoChile
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31
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Pearson SK, Bradford TM, Ansari TH, Bull CM, Gardner MG. MHC genotyping from next-generation sequencing: detailed methodology for the gidgee skink, Egernia stokesii. T ROY SOC SOUTH AUST 2016. [DOI: 10.1080/03721426.2016.1216735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- S. K. Pearson
- School of Biological Sciences, Flinders University of South Australia, Bedford Park, Australia
| | - T. M. Bradford
- School of Biological Sciences, Flinders University of South Australia, Bedford Park, Australia
| | - T. H. Ansari
- School of Biological Sciences, Flinders University of South Australia, Bedford Park, Australia
| | - C. M. Bull
- School of Biological Sciences, Flinders University of South Australia, Bedford Park, Australia
| | - M. G. Gardner
- School of Biological Sciences, Flinders University of South Australia, Bedford Park, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia
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32
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Zieliński P, Nadachowska-Brzyska K, Dudek K, Babik W. Divergence history of the Carpathian and smooth newts modelled in space and time. Mol Ecol 2016; 25:3912-28. [PMID: 27288862 DOI: 10.1111/mec.13724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 12/24/2022]
Abstract
Information about demographic history is essential for the understanding of the processes of divergence and speciation. Patterns of genetic variation within and between closely related species provide insights into the history of their interactions. Here, we investigated historical demography and genetic exchange between the Carpathian (Lissotriton montandoni, Lm) and smooth (L. vulgaris, Lv) newts. We combine an extensive geographical sampling and multilocus nuclear sequence data with the approximate Bayesian computation framework to test alternative scenarios of divergence and reconstruct the temporal and spatial pattern of gene flow between species. A model of recent (last glacial period) interspecific gene flow was favoured over alternative models. Thus, despite the relatively old divergence (4-6 mya) and presumably long periods of isolation, the species have retained the ability to exchange genes. Nevertheless, the low migration rates (ca. 10(-6) per gene copy per generation) are consistent with strong reproductive isolation between the species. Models allowing demographic changes were favoured, suggesting that the effective population sizes of both species at least doubled as divergence reaching the current ca. 0.2 million in Lm and 1 million in Lv. We found asymmetry in rates of interspecific gene flow between Lm and one evolutionary lineage of Lv. We suggest that intraspecific polymorphism for hybrid incompatibilities segregating within Lv could explain this pattern and propose further tests to distinguish between alternative explanations. Our study highlights the importance of incorporating intraspecific genetic structure into the models investigating the history of divergence.
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Affiliation(s)
- P Zieliński
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - K Nadachowska-Brzyska
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - K Dudek
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - W Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
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33
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Stuglik MT, Babik W. Genomic heterogeneity of historical gene flow between two species of newts inferred from transcriptome data. Ecol Evol 2016; 6:4513-25. [PMID: 27386093 PMCID: PMC4930998 DOI: 10.1002/ece3.2152] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/02/2016] [Accepted: 04/04/2016] [Indexed: 01/31/2023] Open
Abstract
The role of gene flow in species formation is a major unresolved issue in speciation biology. Progress in this area requires information on the long-term patterns of gene flow between diverging species. Here, we used thousands of single-nucleotide polymorphisms derived from transcriptome resequencing and a method modeling the joint frequency spectrum of these polymorphisms to reconstruct patterns of historical gene flow between two Lissotriton newts: L. vulgaris (Lv) and L. montandoni (Lm). We tested several models of divergence including complete isolation and various scenarios of historical gene flow. The model of secondary contact received the highest support. According to this model, the species split from their common ancestor ca. 5.5 million years (MY) ago, evolved in isolation for ca. 2 MY, and have been exchanging genes for the last 3.5 MY Demographic changes have been inferred in both species, with the current effective population size of ca. 0.7 million in Lv and 0.2 million in Lm. The postdivergence gene flow resulted in two-directional introgression which affected the genomes of both species, but was more pronounced from Lv to Lm. Interestingly, we found evidence for genomic heterogeneity of interspecific gene flow. This study demonstrates the complexity of long-term gene flow between distinct but incompletely reproductively isolated taxa which divergence was initiated millions of years ago.
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Affiliation(s)
- Michał T. Stuglik
- Institute of Environmental SciencesJagiellonian UniversityGronostajowa 730387KrakowPoland
| | - Wiesław Babik
- Institute of Environmental SciencesJagiellonian UniversityGronostajowa 730387KrakowPoland
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34
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Faulks LK, Östman Ö. Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics. JOURNAL OF FISH BIOLOGY 2016; 88:1564-1583. [PMID: 26940068 DOI: 10.1111/jfb.12930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 01/29/2016] [Indexed: 06/05/2023]
Abstract
This study assessed the major histocompatibility complex (MHC) and neutral genetic variation and structure in two percid species, perch Perca fluviatilis and zander Sander lucioperca, in a unique brackish ecosystem, the Baltic Sea. In addition, to assess the importance of MHC diversity to disease susceptibility in these populations, comparisons were made to an introduced, disease susceptible, P. fluviatilis population in Australia. Eighty-three MHC class II B exon 2 variants were amplified: 71 variants from 92 P. fluviatilis samples, and 12 variants from 82 S. lucioperca samples. Microsatellite and MHC data revealed strong spatial genetic structure in S. lucioperca, but not P. fluviatilis, across the Baltic Sea. Both microsatellite and MHC data showed higher levels of genetic diversity in P. fluviatilis from the Baltic Sea compared to Australia, which may have facilitated the spread of an endemic virus, EHNV in the Australian population. The relatively high levels of genetic variation in the Baltic Sea populations, together with spatial genetic structure, however, suggest that there currently seems to be little risk of disease epidemics in this system. To ensure this remains the case in the face of ongoing environmental changes, fisheries and habitat disturbance, the conservation of local-scale genetic variation is recommended.
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Affiliation(s)
- L K Faulks
- Department of Ecology and Genetics - Animal Ecology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Ö Östman
- Department of Aquatic Resources - Institute of Coastal Research, Swedish University of Agricultural Sciences, Skolvägen 6, 74242, Öregrund, Sweden
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35
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Minias P, Bateson ZW, Whittingham LA, Johnson JA, Oyler-McCance S, Dunn PO. Contrasting evolutionary histories of MHC class I and class II loci in grouse--effects of selection and gene conversion. Heredity (Edinb) 2016; 116:466-76. [PMID: 26860199 DOI: 10.1038/hdy.2016.6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/18/2015] [Indexed: 11/09/2022] Open
Abstract
Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.
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Affiliation(s)
- P Minias
- Department of Teacher Training and Biodiversity Studies, University of Łódź, Łódź, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Z W Bateson
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - L A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - J A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, TX, USA
| | - S Oyler-McCance
- Fort Collins Science Center, US Geological Survey, Fort Collins, CO, USA
| | - P O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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36
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Seifertová M, Jarkovský J, Šimková A. Does the parasite-mediated selection drive the MHC class IIB diversity in wild populations of European chub (Squalius cephalus)? Parasitol Res 2015; 115:1401-15. [PMID: 26693717 DOI: 10.1007/s00436-015-4874-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/07/2015] [Indexed: 11/29/2022]
Abstract
The genes of major histocompatibility complex (MHC) provide an excellent opportunity to study host-parasite relationships because they are expected to evolve in response to parasites and variation in parasite communities. In this study, we investigated the potential role of parasite-mediated selection acting on MHC class IIB (DAB) genes in European chub (Squalius cephalus) natural populations. We found significant differences between populations in metazoan parasites, neutral and adaptive genetic diversities. The analyses based on pairwise data revealed that populations with dissimilar MHC allelic profiles were geographically distant populations with significantly different diversity in microsatellites and a dissimilar composition of parasite communities. The results from the generalized estimating equations method (GEE) on the level of individuals revealed that metazoan parasite load in European chub was influenced by the diversity of DAB alleles as well as by the diversity of neutral genetic markers and host traits reflecting condition and immunocompetence. The multivariate co-inertia analysis showed specific associations between DAB alleles and parasite species. DAB1-like alleles were more involved in associations with ectoparasites, while DAB3-like alleles were positively associated with endoparasites which could suggest potential differences between DAB genes caused by different selection pressure. Our study revealed that parasite-mediated selection is not the only variable affecting MHC diversity in European chub; however, we strongly support the role of neutral processes as the main driver of DAB diversity across populations. In addition, our study contributes to the understanding of the evolution of MHC genes in wild living fish.
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Affiliation(s)
- Mária Seifertová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic.
| | - Jiří Jarkovský
- Institute of Biostatistics and Analyses, Faculty of Medicine and Faculty of Science, Masaryk University, Kamenice 126/3, 625 00, Brno, Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
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Galov A, Fabbri E, Caniglia R, Arbanasić H, Lapalombella S, Florijančić T, Bošković I, Galaverni M, Randi E. First evidence of hybridization between golden jackal (Canis aureus) and domestic dog (Canis familiaris) as revealed by genetic markers. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150450. [PMID: 27019731 PMCID: PMC4807452 DOI: 10.1098/rsos.150450] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/03/2015] [Indexed: 05/22/2023]
Abstract
Interspecific hybridization is relatively frequent in nature and numerous cases of hybridization between wild canids and domestic dogs have been recorded. However, hybrids between golden jackals (Canis aureus) and other canids have not been described before. In this study, we combined the use of biparental (15 autosomal microsatellites and three major histocompatibility complex (MHC) loci) and uniparental (mtDNA control region and a Y-linked Zfy intron) genetic markers to assess the admixed origin of three wild-living canids showing anomalous phenotypic traits. Results indicated that these canids were hybrids between golden jackals and domestic dogs. One of them was a backcross to jackal and another one was a backcross to dog, confirming that golden jackal-domestic dog hybrids are fertile. The uniparental markers showed that the direction of hybridization, namely females of the wild species hybridizing with male domestic dogs, was common to most cases of canid hybridization. A melanistic 3bp-deletion at the K locus (β-defensin CDB103 gene), that was absent in reference golden jackal samples, but was found in a backcross to jackal with anomalous black coat, suggested its introgression from dogs via hybridization. Moreover, we demonstrated that MHC sequences, although rarely used as markers of hybridization, can be also suitable for the identification of hybrids, as long as haplotypes are exclusive for the parental species.
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Affiliation(s)
- Ana Galov
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb 10000, Croatia
- Author for correspondence: Ana Galov e-mail:
| | - Elena Fabbri
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
| | - Romolo Caniglia
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
| | - Haidi Arbanasić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb 10000, Croatia
| | - Silvana Lapalombella
- Department of Biological, Geological and Environmental Sciences University of Bologna, Via Selmi 3, Bologna 40126, Italy
| | - Tihomir Florijančić
- Department for Hunting, Fishery and Beekeeping, Faculty of Agriculture in Osijek, Josip Juraj Strossmayer University of Osijek, Kralja Petra Svačića 1d, Osijek 31000, Croatia
| | - Ivica Bošković
- Department for Hunting, Fishery and Beekeeping, Faculty of Agriculture in Osijek, Josip Juraj Strossmayer University of Osijek, Kralja Petra Svačića 1d, Osijek 31000, Croatia
| | - Marco Galaverni
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
| | - Ettore Randi
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
- Department 18/Section of Environmental Engineering, Aalborg University, Sohngårdsholmsvej 57, Aalborg 9000, Denmark
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Red Queen Processes Drive Positive Selection on Major Histocompatibility Complex (MHC) Genes. PLoS Comput Biol 2015; 11:e1004627. [PMID: 26599213 PMCID: PMC4658181 DOI: 10.1371/journal.pcbi.1004627] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/27/2015] [Indexed: 11/19/2022] Open
Abstract
Major Histocompatibility Complex (MHC) genes code for proteins involved in the incitation of the adaptive immune response in vertebrates, which is achieved through binding oligopeptides (antigens) of pathogenic origin. Across vertebrate species, substitutions of amino acids at sites responsible for the specificity of antigen binding (ABS) are positively selected. This is attributed to pathogen-driven balancing selection, which is also thought to maintain the high polymorphism of MHC genes, and to cause the sharing of allelic lineages between species. However, the nature of this selection remains controversial. We used individual-based computer simulations to investigate the roles of two phenomena capable of maintaining MHC polymorphism: heterozygote advantage and host-pathogen arms race (Red Queen process). Our simulations revealed that levels of MHC polymorphism were high and driven mostly by the Red Queen process at a high pathogen mutation rate, but were low and driven mostly by heterozygote advantage when the pathogen mutation rate was low. We found that novel mutations at ABSs are strongly favored by the Red Queen process, but not by heterozygote advantage, regardless of the pathogen mutation rate. However, while the strong advantage of novel alleles increased the allele turnover rate, under a high pathogen mutation rate, allelic lineages persisted for a comparable length of time under Red Queen and under heterozygote advantage. Thus, when pathogens evolve quickly, the Red Queen is capable of explaining both positive selection and long coalescence times, but the tension between the novel allele advantage and persistence of alleles deserves further investigation.
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Lack of Spatial Immunogenetic Structure among Wolverine (Gulo gulo) Populations Suggestive of Broad Scale Balancing Selection. PLoS One 2015; 10:e0140170. [PMID: 26448462 PMCID: PMC4598017 DOI: 10.1371/journal.pone.0140170] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/22/2015] [Indexed: 11/19/2022] Open
Abstract
Elucidating the adaptive genetic potential of wildlife populations to environmental selective pressures is fundamental for species conservation. Genes of the major histocompatibility complex (MHC) are highly polymorphic, and play a key role in the adaptive immune response against pathogens. MHC polymorphism has been linked to balancing selection or heterogeneous selection promoting local adaptation. However, spatial patterns of MHC polymorphism are also influenced by gene flow and drift. Wolverines are highly vagile, inhabiting varied ecoregions that include boreal forest, taiga, tundra, and high alpine ecosystems. Here, we investigated the immunogenetic variation of wolverines in Canada as a surrogate for identifying local adaptation by contrasting the genetic structure at MHC relative to the structure at 11 neutral microsatellites to account for gene flow and drift. Evidence of historical positive selection was detected at MHC using maximum likelihood codon-based methods. Bayesian and multivariate cluster analyses revealed weaker population genetic differentiation at MHC relative to the increasing microsatellite genetic structure towards the eastern wolverine distribution. Mantel correlations of MHC against geographical distances showed no pattern of isolation by distance (IBD: r = -0.03, p = 0.9), whereas for microsatellites we found a relatively strong and significant IBD (r = 0.54, p = 0.01). Moreover, we found a significant correlation between microsatellite allelic richness and the mean number of MHC alleles, but we did not observe low MHC diversity in small populations. Overall these results suggest that MHC polymorphism has been influenced primarily by balancing selection and to a lesser extent by neutral processes such as genetic drift, with no clear evidence for local adaptation. This study contributes to our understanding of how vulnerable populations of wolverines may respond to selective pressures across their range.
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40
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Fijarczyk A, Babik W. Detecting balancing selection in genomes: limits and prospects. Mol Ecol 2015; 24:3529-45. [DOI: 10.1111/mec.13226] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Wiesław Babik
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
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41
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Trans-Species Polymorphism in Immune Genes: General Pattern or MHC-Restricted Phenomenon? J Immunol Res 2015; 2015:838035. [PMID: 26090501 PMCID: PMC4458282 DOI: 10.1155/2015/838035] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/04/2015] [Indexed: 11/24/2022] Open
Abstract
Immunity exhibits extraordinarily high levels of variation. Evolution of the immune system in response to host-pathogen interactions in particular ecological contexts appears to be frequently associated with diversifying selection increasing the genetic variability. Many studies have documented that immunologically relevant polymorphism observed today may be tens of millions years old and may predate the emergence of present species. This pattern can be explained by the concept of trans-species polymorphism (TSP) predicting the maintenance and sharing of favourable functionally important alleles of immune-related genes between species due to ongoing balancing selection. Despite the generality of this concept explaining the long-lasting adaptive variation inherited from ancestors, current research in TSP has vastly focused only on major histocompatibility complex (MHC). In this review we summarise the evidence available on TSP in human and animal immune genes to reveal that TSP is not a MHC-specific evolutionary pattern. Further research should clearly pay more attention to the investigation of TSP in innate immune genes and especially pattern recognition receptors which are promising candidates for this type of evolution. More effort should also be made to distinguish TSP from convergent evolution and adaptive introgression. Identification of balanced TSP variants may represent an accurate approach in evolutionary medicine to recognise disease-resistance alleles.
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Tracy KE, Kiemnec-Tyburczy KM, DeWoody JA, Parra-Olea G, Zamudio KR. Positive selection drives the evolution of a major histocompatibility complex gene in an endangered Mexican salamander species complex. Immunogenetics 2015; 67:323-35. [PMID: 25846208 DOI: 10.1007/s00251-015-0835-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 03/12/2015] [Indexed: 11/30/2022]
Abstract
Immune gene evolution can be critical to species survival in the face of infectious disease. In particular, polymorphism in the genes of the major histocompatibility complex (MHC) helps vertebrates combat novel and diverse pathogens by increasing the number of pathogen-derived proteins that can initiate the host's acquired immune response. In this study, we used a combination of presumably adaptive and neutral markers to investigate MHC evolution in populations of five salamander species within the Ambystoma velasci complex, a group consisting of 15 recently diverged species, several of which are endangered. We isolated 31 unique MHC class II β alleles from 75 total individuals from five species in this complex. MHC heterozygosity was significantly lower than expected for all five species, and we found no clear relationship between number of MHC alleles and species range, life history, or level of heterozygosity. We inferred a phylogeny representing the evolutionary history of Ambystoma MHC, with which we found signatures of positive selection on the overall gene, putative peptide-binding residues, and allelic lineages. We identified several instances of trans-species polymorphism, a hallmark of balancing selection observed in other groups of closely related species. In contrast, we did not detect comparable allelic diversity or signatures of selection on neutral loci. Additionally, we identified 17 supertypes among the 44 unique Ambystoma alleles, indicating that these sequences may encode functionally distinct MHC variants. We therefore have strong evidence that positive selection is a major evolutionary force driving patterns of MHC polymorphism in this recently radiated species complex.
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Affiliation(s)
- Karen E Tracy
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA,
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43
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Jan Ejsmond M, Radwan J, Wilson AB. Sexual selection and the evolutionary dynamics of the major histocompatibility complex. Proc Biol Sci 2014; 281:20141662. [PMID: 25339723 PMCID: PMC4213641 DOI: 10.1098/rspb.2014.1662] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/22/2014] [Indexed: 12/27/2022] Open
Abstract
The genes of the major histocompatibility complex (MHC) are a key component of the adaptive immune system and among the most variable loci in the vertebrate genome. Pathogen-mediated natural selection and MHC-based disassortative mating are both thought to structure MHC polymorphism, but their effects have proven difficult to discriminate in natural systems. Using the first model of MHC dynamics incorporating both survival and reproduction, we demonstrate that natural and sexual selection produce distinctive signatures of MHC allelic diversity with critical implications for understanding host-pathogen dynamics. While natural selection produces the Red Queen dynamics characteristic of host-parasite interactions, disassortative mating stabilizes allele frequencies, damping major fluctuations in dominant alleles and protecting functional variants against drift. This subtle difference generates a complex interaction between MHC allelic diversity and population size. In small populations, the stabilizing effects of sexual selection moderate the effects of drift, whereas pathogen-mediated selection accelerates the loss of functionally important genetic diversity. Natural selection enhances MHC allelic variation in larger populations, with the highest levels of diversity generated by the combined action of pathogen-mediated selection and disassortative mating. MHC-based sexual selection may help to explain how functionally important genetic variation can be maintained in populations of conservation concern.
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Affiliation(s)
- Maciej Jan Ejsmond
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland Department of Arctic Biology, The University Centre in Svalbard, Box 156, 9171 Longyearbyen, Norway
| | - Jacek Radwan
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Anthony B Wilson
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland Department of Biology, Brooklyn College and The Graduate Center, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
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44
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Babik W, Dudek K, Fijarczyk A, Pabijan M, Stuglik M, Szkotak R, Zieliński P. Constraint and adaptation in newt toll-like receptor genes. Genome Biol Evol 2014; 7:81-95. [PMID: 25480684 PMCID: PMC4316619 DOI: 10.1093/gbe/evu266] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Acute die-offs of amphibian populations worldwide have been linked to the emergence of viral and fungal diseases. Inter and intraspecific immunogenetic differences may influence the outcome of infection. Toll-like receptors (TLRs) are an essential component of innate immunity and also prime acquired defenses. We report the first comprehensive assessment of TLR gene variation for urodele amphibians. The Lissotriton newt TLR repertoire includes representatives of 13 families and is compositionally most similar to that of the anuran Xenopus. Both ancient and recent gene duplications have occurred in urodeles, bringing the total number of TLR genes to at least 21. Purifying selection has predominated the evolution of newt TLRs in both long (∼70 Ma) and medium (∼18 Ma) timescales. However, we find evidence for both purifying and positive selection acting on TLRs in two recently diverged (2-5 Ma) allopatric evolutionary lineages (Lissotriton montandoni and L. vulgaris graecus). Overall, both forms of selection have been stronger in L. v. graecus, while constraint on most TLR genes in L. montandoni appears relaxed. The differences in selection regimes are unlikely to be biased by demographic effects because these were controlled by means of a historical demographic model derived from an independent data set of 62 loci. We infer that TLR genes undergo distinct trajectories of adaptive evolution in closely related amphibian lineages, highlight the potential of TLRs to capture the signatures of different assemblages of pathogenic microorganisms, and suggest differences between lineages in the relative roles of innate and acquired immunity.
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Affiliation(s)
- Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Maciej Pabijan
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Michał Stuglik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Rafał Szkotak
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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Real-Monroy MD, Martínez-Méndez N, Ortega J. MHC-DRB Exon 2 Diversity of the Jamaican Fruit-Eating Bat (Artibeus jamaicensis) from Mexico. ACTA CHIROPTEROLOGICA 2014. [DOI: 10.3161/150811014x687260] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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46
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Radwan J, Kuduk K, Levy E, LeBas N, Babik W. Parasite load and MHC diversity in undisturbed and agriculturally modified habitats of the ornate dragon lizard. Mol Ecol 2014; 23:5966-78. [PMID: 25355141 DOI: 10.1111/mec.12984] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 11/26/2022]
Abstract
Major histocompatibility complex (MHC) gene polymorphism is thought to be driven by host-parasite co-evolution, but the evidence for an association between the selective pressure from parasites and the number of MHC alleles segregating in a population is scarce and inconsistent. Here, we characterized MHC class I polymorphism in a lizard whose habitat preferences (rock outcrops) lead to the formation of well-defined and stable populations. We investigated the association between the load of ticks, which were used as a proxy for the load of pathogens they transmit, and MHC class I polymorphism across populations in two types of habitat: undisturbed reserves and agricultural land. We hypothesized that the association would be positive across undisturbed reserve populations, but across fragmented agricultural land populations, the relationship would be distorted by the loss of MHC variation due to drift. After controlling for habitat, MHC diversity was not associated with tick number, and the habitats did not differ in this respect. Neither did we detect a difference between habitats in the relationship between MHC and neutral diversity, which was positive across all populations. However, there was extensive variation in the number of MHC alleles per individual, and we found that tick number was positively associated with the average number of alleles carried by lizards across reserve populations, but not across populations from disturbed agricultural land. Our results thus indicate that local differences in selection from parasites may contribute to MHC copy number variation within species, but habitat degradation can distort this relationship.
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Affiliation(s)
- Jacek Radwan
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
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Herdegen M, Babik W, Radwan J. Selective pressures on MHC class II genes in the guppy (Poecilia reticulata) as inferred by hierarchical analysis of population structure. J Evol Biol 2014; 27:2347-59. [PMID: 25244157 DOI: 10.1111/jeb.12476] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 08/08/2014] [Accepted: 08/11/2014] [Indexed: 11/29/2022]
Abstract
Genes of the major histocompatibility complex, which are the most polymorphic of all vertebrate genes, are a pre-eminent system for the study of selective pressures that arise from host-pathogen interactions. Balancing selection capable of maintaining high polymorphism should lead to the homogenization of MHC allele frequencies among populations, but there is some evidence to suggest that diversifying selection also operates on the MHC. However, the pattern of population structure observed at MHC loci is likely to depend on the spatial and/or temporal scale examined. Here, we investigated selection acting on MHC genes at different geographic scales using Venezuelan guppy populations inhabiting four regions. We found a significant correlation between MHC and microsatellite allelic richness across populations, which suggests the role of genetic drift in shaping MHC diversity. However, compared to microsatellites, more MHC variation was explained by differences between populations within larger geographic regions and less by the differences between the regions. Furthermore, among proximate populations, variation in MHC allele frequencies was significantly higher compared to microsatellites, indicating that selection acting on MHC may increase population structure at small spatial scales. However, in populations that have significantly diverged at neutral markers, the population-genetic signature of diversifying selection may be eradicated in the long term by that of balancing selection, which acts to preserve rare alleles and thus maintain a common pool of MHC alleles.
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Affiliation(s)
- M Herdegen
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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Jones MR, Cheviron ZA, Carling MD. Variation in positively selected major histocompatibility complex class I loci in rufous-collared sparrows (Zonotrichia capensis). Immunogenetics 2014; 66:693-704. [DOI: 10.1007/s00251-014-0800-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/25/2014] [Indexed: 11/25/2022]
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49
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Lighten J, van Oosterhout C, Bentzen P. Critical review of NGS analyses for de novo genotyping multigene families. Mol Ecol 2014; 23:3957-72. [DOI: 10.1111/mec.12843] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/08/2014] [Accepted: 06/17/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Jackie Lighten
- Department of Biology; Marine Gene Probe Laboratory; Dalhousie University; Halifax Nova Scotia Canada
| | - Cock van Oosterhout
- School of Environmental Sciences; University of East Anglia; Norwich Research Park; Norwich UK
| | - Paul Bentzen
- Department of Biology; Marine Gene Probe Laboratory; Dalhousie University; Halifax Nova Scotia Canada
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Stutz WE, Bolnick DI. Stepwise threshold clustering: a new method for genotyping MHC loci using next-generation sequencing technology. PLoS One 2014; 9:e100587. [PMID: 25036866 PMCID: PMC4103772 DOI: 10.1371/journal.pone.0100587] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/26/2014] [Indexed: 12/26/2022] Open
Abstract
Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems:1) a "gray zone" where low frequency alleles and high frequency artifacts can be difficult to disentangle and 2) a similar sequence problem, where very similar alleles can be difficult to distinguish as two distinct alleles. Here were present a new method for genotyping MHC loci--Stepwise Threshold Clustering (STC)--that addresses these problems by taking full advantage of the increase in sequence data provided by NGS technologies. Unlike previous approaches for genotyping MHC with NGS data that attempt to classify individual sequences as alleles or artifacts, STC uses a quasi-Dirichlet clustering algorithm to cluster similar sequences at increasing levels of sequence similarity. By applying frequency and similarity based criteria to clusters rather than individual sequences, STC is able to successfully identify clusters of sequences that correspond to individual or similar alleles present in the genomes of individual samples. Furthermore, STC does not require duplicate runs of all samples, increasing the number of samples that can be genotyped in a given project. We show how the STC method works using a single sample library. We then apply STC to 295 threespine stickleback (Gasterosteus aculeatus) samples from four populations and show that neighboring populations differ significantly in MHC allele pools. We show that STC is a reliable, accurate, efficient, and flexible method for genotyping MHC that will be of use to biologists interested in a variety of downstream applications.
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Affiliation(s)
- William E. Stutz
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
| | - Daniel I. Bolnick
- Howard Hughes Medical Institute & Section of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
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