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Arbanasić H, Medrano-González L, Hrenar T, Mikelić A, Gomerčić T, Svetličić I, Pavlinec Ž, Đuras M, Galov A. Recent selection created distinctive variability patterns on MHC class II loci in three dolphin species from the Mediterranean Sea. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 150:105079. [PMID: 37832898 DOI: 10.1016/j.dci.2023.105079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
The major histocompatibility complex (MHC) includes highly polymorphic genes involved in antigen presentation, which is crucial for adaptive immune response. They represent fitness related genetic markers particularly informative for populations exposed to environmental challenges. Here we analyse the diversity and evolutionary traits of MHC class II DQA and DQB genes in the dolphins Stenella coeruleoalba and Grampus griseus from the Mediterranean Sea. We found substantial nucleotide and functional diversity, as well as strong evidence of balancing selection indicated by allele and supertype frequencies, Tajima's D statistics and dN/dS tests. The Risso's dolphin, considered the least abundant in the region, showed the effect of divergent allele advantage at the nucleotide and functional-peptide levels. An outstanding polymorphism was found in the striped dolphin, particularly intriguing in the DQA gene where the Ewens-Watterson test detected a selection sweep that occurred in recent history. We hypothesize that morbillivirus, which has recurrently invaded Mediterranean populations over the last decades, exerted the detected selective pressure.
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Affiliation(s)
- Haidi Arbanasić
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Luis Medrano-González
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.
| | - Tomica Hrenar
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Ana Mikelić
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Tomislav Gomerčić
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia.
| | - Ida Svetličić
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Željko Pavlinec
- Croatian Academy of Sciences and Arts, Trg Nikole Šubića Zrinskog 11, 10000, Zagreb, Croatia.
| | - Martina Đuras
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia.
| | - Ana Galov
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
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2
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Miyamae J, Okano M, Katakura F, Kulski JK, Moritomo T, Shiina T. Large-Scale Polymorphism Analysis of Dog Leukocyte Antigen Class I and Class II Genes ( DLA-88, DLA-12/88L and DLA-DRB1) and Comparison of the Haplotype Diversity between Breeds in Japan. Cells 2023; 12:cells12050809. [PMID: 36899945 PMCID: PMC10001263 DOI: 10.3390/cells12050809] [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: 11/28/2022] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Polymorphisms of canine leukocyte antigen (DLA) class I (DLA-88 and DLA-12/88L) and class II (DLA-DRB1) genes are important for disease susceptibility studies, but information on the genetic diversity among dog breeds is still lacking. To better elucidate the polymorphism and genetic diversity between breeds, we genotyped DLA-88, DLA-12/88L, and DLA-DRB1 loci using 829 dogs of 59 breeds in Japan. Genotyping by Sanger sequencing identified 89, 43, and 61 alleles in DLA-88, DLA-12/88L, and DLA-DRB1 loci, respectively, and a total of 131 DLA-88-DLA-12/88L-DLA-DRB1 haplotypes (88-12/88L-DRB1) were detected more than once. Of the 829 dogs, 198 were homozygotes for one of the 52 different 88-12/88L-DRB1 haplotypes (homozygosity rate: 23.8%). Statistical modeling suggests that 90% of the DLA homozygotes or heterozygotes with one or other of the 52 different 88-12/88L-DRB1 haplotypes within somatic stem cell lines would benefit graft outcome after 88-12/88L-DRB1-matched transplantation. As previously reported for DLA class II haplotypes, the diversity of 88-12/88L-DRB1 haplotypes varied remarkably between breeds but was relatively conserved within most breeds. Therefore, the genetic characteristics of high DLA homozygosity rate and poor DLA diversity within a breed are useful for transplantation therapy, but they may affect biological fitness as homozygosity progresses.
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Affiliation(s)
- Jiro Miyamae
- Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari 794-8555, Japan
- Correspondence: ; Tel.: +81-898-52-9126
| | - Masaharu Okano
- Department of Legal Medicine, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
| | - Fumihiko Katakura
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Jerzy K. Kulski
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara 259-1143, Japan
| | - Tadaaki Moritomo
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara 259-1143, Japan
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3
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Awadi A, Suchentrunk F, Knauer F, Smith S, Tolesa Z, Ben Slimen H. Spatial diversity of MHC class II DRB exon2 sequences in North African cape hares (Lepus capensis): positive selection and climatic adaptation signals. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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4
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Machuka EM, Muigai AWT, Amimo JO, Domelevo Entfellner JB, Lekolool I, Abworo EO, Pelle R. Comparative Analysis of SLA-1, SLA-2, and DQB1 Genetic Diversity in Locally-Adapted Kenyan Pigs and Their Wild Relatives, Warthogs. Vet Sci 2021; 8:180. [PMID: 34564574 PMCID: PMC8473215 DOI: 10.3390/vetsci8090180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discriminating self and foreign antigens and initiating an immune response. Studies on SLA polymorphism have demonstrated associations between SLA allelic variants, immune response, and disease resistance. The SLA polymorphism is due to host-pathogen co-evolution resulting in improved adaptation to diverse environments making SLA a crucial genomic region for comparative diversity studies. Although locally-adapted African pigs have small body sizes, they possess increased resilience under harsh environmental conditions and robust immune systems with reported tolerance to some diseases, including African swine fever. However, data on the SLA diversity in these pigs are not available. We characterized the SLA of unrelated locally-adapted domestic pigs from Homa Bay, Kenya, alongside exotic pigs and warthogs. We undertook SLA comparative diversity of the functionally expressed SLA class I (SLA-1, SLA-2) and II (DQB1) repertoires in these three suids using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. Our data revealed higher genetic diversity in the locally-adapted pigs and warthogs compared to the exotic pigs. The nucleotide substitution rates were higher in the peptide-binding regions of the SLA-1, SLA-2, and DQB1 loci, indicative of adaptive evolution. We obtained high allele frequencies in the three SLA loci, including some breed-specific private alleles, which could guide breeders to increase their frequency through selection if confirmed to be associated with enhanced resilience. Our study contributes to the growing body of knowledge on genetic diversity in free-ranging animal populations in their natural environment, availing the first DQB1 gene data from locally-adapted Kenyan pigs.
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Affiliation(s)
- Eunice Magoma Machuka
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya;
- Institute for Basic Sciences Technology and Innovation (PAUSTI), Pan African University, Nairobi P.O. Box 62000-00200, Kenya
| | - Anne W. Thairu Muigai
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya;
| | - Joshua Oluoch Amimo
- Center for Food Animal Health, Department of Animal Sciences, 1680 Madison Avenue, The Ohio State University, Wooster, OH 44691, USA;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya;
| | - Isaac Lekolool
- Kenya Wildlife Services, Nairobi P.O. Box 40241-00100, Kenya;
| | - Edward Okoth Abworo
- Animal and Human Health Program, International Livestock Research Institute, Nairobi P.O. Box 30709-00100, Kenya;
| | - Roger Pelle
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya;
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5
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Kloch A, Biedrzycka A, Szewczyk M, Nowak S, Niedźwiedzka N, Kłodawska M, Hájková A, Hulva P, Jędrzejewska B, Mysłajek R. High genetic diversity of immunity genes in an expanding population of a highly mobile carnivore, the grey wolf
Canis
lupus
, in Central Europe. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Agnieszka Kloch
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
| | | | - Maciej Szewczyk
- Department of Vertebrate Ecology and Zoology Faculty of Biology University of Gdańsk Gdańsk Poland
| | - Sabina Nowak
- Association for Nature “Wolf” Twardorzeczka Poland
| | | | - Monika Kłodawska
- Department of Zoology Faculty of Science Charles University Prague Czech Republic
| | - Andrea Hájková
- State Nature Conservancy of the Slovak Republic Spišská Nová Ves Slovakia
| | - Pavel Hulva
- Department of Zoology Faculty of Science Charles University Prague Czech Republic
- Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic
| | | | - Robert Mysłajek
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
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6
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Stefanović M, Ćirović D, Bogdanović N, Knauer F, Heltai M, Szabó L, Lanszki J, Zhelev CD, Schaschl H, Suchentrunk F. Positive selection on the MHC class II DLA-DQA1 gene in golden jackals (Canis aureus) from their recent expansion range in Europe and its effect on their body mass index. BMC Ecol Evol 2021; 21:122. [PMID: 34134625 PMCID: PMC8207625 DOI: 10.1186/s12862-021-01856-z] [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: 11/18/2020] [Accepted: 06/10/2021] [Indexed: 11/17/2022] Open
Abstract
Background In Europe, golden jackals (Canis aureus) have been expanding their range out of the southern and southeastern Balkans towards central Europe continually since the 1960s. Here, we investigated the level of functional diversity at the MHC class II DLA-DQA1 exon 2 in golden jackal populations from Bulgaria, Serbia, and Hungary. Specifically, we tested for positive selection on and geographic variation at that locus due to adaptation to supposedly regionally varying pathogenic landscapes. To test for potential fitness effects of different protein variants on individual body condition, we used linear modeling of individual body mass indexes (bmi) and accounted for possible age, sex, geographical, and climatic effects. The latter approach was performed, however, only on Serbian individuals with appropriate data. Results Only three different DLA-DQA1 alleles were detected, all coding for different amino-acid sequences. The neutrality tests revealed no significant but positive values; there was no signal of spatial structuring and no deviation from the Hardy–Weinberg equilibrium across the studied range of expansion. However, we found a signal of trans-species polymorphism and significant test results for positive selection on three codons. Our information-theory based linear modeling results indicated an effect of ambient temperature on the occurrence of individual DLA-DQA1 genotypes in individuals from across the studied expansion range, independent from geographical position. Our linear modeling results of individual bmi values indicated that yearlings homozygous for DLA-DQA1*03001 reached values typical for adults contrary to yearlings carrying other genotypes (protein combinations). This suggested better growth rates and thus a possible fitness advantage of yearlings homozygous for DLA-DQA1*03001. Conclusions Our results indicate a demographic (stochastic) signal of reduced DLA-DQA1 exon 2 variation, in line with the documented historical demographic bottleneck. At the same time, however, allelic variation was also affected by positive selection and adaptation to varying ambient temperature, supposedly reflecting geographic variation in the pathogenic landscape. Moreover, an allele effect on body mass index values of yearlings suggested differential fitness associated with growth rates. Overall, a combination of a stochastic effect and positive selection has shaped and is still shaping the variation at the studied MHC locus. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01856-z.
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Affiliation(s)
- Milomir Stefanović
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000, Novi Sad, Serbia.,Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
| | - Duško Ćirović
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia
| | - Neda Bogdanović
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia
| | - Felix Knauer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
| | - Miklós Heltai
- Institute for Wildlife Conservation, Szent István University, Páter Károly utca 1, Gödöllő, 2100, Hungary
| | - László Szabó
- Institute for Wildlife Conservation, Szent István University, Páter Károly utca 1, Gödöllő, 2100, Hungary
| | - József Lanszki
- Ecological Research Group, University of Kaposvár, PO Box 16, 7401, Kaposvár, Hungary
| | | | - Helmut Schaschl
- Department of Evolutionary Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
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7
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DeCandia AL, Schrom EC, Brandell EE, Stahler DR, vonHoldt BM. Sarcoptic mange severity is associated with reduced genomic variation and evidence of selection in Yellowstone National Park wolves ( Canis lupus). Evol Appl 2021; 14:429-445. [PMID: 33664786 PMCID: PMC7896714 DOI: 10.1111/eva.13127] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/28/2020] [Accepted: 08/25/2020] [Indexed: 01/25/2023] Open
Abstract
Population genetic theory posits that molecular variation buffers against disease risk. Although this "monoculture effect" is well supported in agricultural settings, its applicability to wildlife populations remains in question. In the present study, we examined the genomics underlying individual-level disease severity and population-level consequences of sarcoptic mange infection in a wild population of canids. Using gray wolves (Canis lupus) reintroduced to Yellowstone National Park (YNP) as our focal system, we leveraged 25 years of observational data and biobanked blood and tissue to genotype 76,859 loci in over 400 wolves. At the individual level, we reported an inverse relationship between host genomic variation and infection severity. We additionally identified 410 loci significantly associated with mange severity, with annotations related to inflammation, immunity, and skin barrier integrity and disorders. We contextualized results within environmental, demographic, and behavioral variables, and confirmed that genetic variation was predictive of infection severity. At the population level, we reported decreased genome-wide variation since the initial gray wolf reintroduction event and identified evidence of selection acting against alleles associated with mange infection severity. We concluded that genomic variation plays an important role in disease severity in YNP wolves. This role scales from individual to population levels, and includes patterns of genome-wide variation in support of the monoculture effect and specific loci associated with the complex mange phenotype. Results yielded system-specific insights, while also highlighting the relevance of genomic analyses to wildlife disease ecology, evolution, and conservation.
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Affiliation(s)
| | - Edward C. Schrom
- Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
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8
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Klumplerova M, Splichalova P, Oppelt J, Futas J, Kohutova A, Musilova P, Kubickova S, Vodicka R, Orlando L, Horin P. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae. BMC Genomics 2020; 21:677. [PMID: 32998693 PMCID: PMC7525986 DOI: 10.1186/s12864-020-07089-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/21/2020] [Indexed: 02/08/2023] Open
Abstract
Background The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. Results Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3. Conclusions The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae.
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Affiliation(s)
- Marie Klumplerova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Petra Splichalova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Jan Oppelt
- Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.,Ceitec MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Jan Futas
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Aneta Kohutova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Petra Musilova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Brno, Czech Republic.,Ceitec VRI, RG Animal Cytogenomics, Brno, Czech Republic
| | - Svatava Kubickova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Brno, Czech Republic.,Ceitec VRI, RG Animal Cytogenomics, Brno, Czech Republic
| | - Roman Vodicka
- Zoo Prague, U Trojského zámku 120/3, 171 00, Praha 7, Czech Republic
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, Toulouse, France.,Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark
| | - Petr Horin
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic. .,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.
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9
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Rocha RG, Magalhães V, López-Bao JV, van der Loo W, Llaneza L, Alvares F, Esteves PJ, Godinho R. Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore. BMC Evol Biol 2019; 19:90. [PMID: 30975084 PMCID: PMC6460805 DOI: 10.1186/s12862-019-1420-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/04/2019] [Indexed: 01/26/2023] Open
Abstract
Background Different population trajectories are expected to impact the signature of neutral and adaptive processes at multiple levels, challenging the assessment of the relative roles of different microevolutionary forces. Here, we integrate adaptive and neutral variability patterns to disentangle how adaptive diversity is driven under different demographic scenarios within the Iberian wolf (Canis lupus) range. We studied the persistent, the expanding and a small, isolated group within the Iberian wolf population, using 3 MHC class II genes (DRB1, DQA1, and DQB1), which diversity was compared with 39 microsatellite loci. Results Both the persistent and the expanding groups show evidence of balancing selection, revealed by a significant departure from neutrality at MHC loci, significant higher observed and expected heterozygosity and lower differentiation at MHC than at neutral loci, and signs of positive selection. However, despite exhibiting a significantly higher genetic diversity than the isolated group, the persistent group did not show significant excess of MHC heterozygotes. The expanding group, while showing a similar level of genetic diversity than the persistent group, displays by contrast a significant excess of MHC heterozygotes, which is compatible with the heterozygote advantage mechanism. Results are not clear regarding the role of drift and selection in the isolated group due to the small size of this population. Although diversity indices of MHC loci correspond to neutral expectations in the isolated group, accelerated MHC divergence, revealed by a higher differentiation at MHC than neutral loci, may indicate diversifying selection. Conclusion Different selective pressures were observed in the three different demographic scenarios, which are possibly driven by different selection mechanisms to maintain adaptive diversity. Electronic supplementary material The online version of this article (10.1186/s12862-019-1420-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rita G Rocha
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Vanessa Magalhães
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - José V López-Bao
- Research Unit of Biodiversity (UO/CSIC/PA), University of Oviedo, 33600, Mieres, Spain
| | - Wessel van der Loo
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Luis Llaneza
- A.RE.NA, S.L. Asesores en Recursos Naturales S.L., 27003, Lugo, Spain
| | - Francisco Alvares
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Raquel Godinho
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.
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10
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Arbanasić H, Konjević D, Vranković L, Bujanić M, Stipoljev S, Balažin M, Šprem N, Škorić D, Galov A. Evolution of MHC class II SLA-DRB1 locus in the Croatian wild boar (Sus scrofa) implies duplication and weak signals of positive selection. Anim Genet 2018; 50:33-41. [PMID: 30357873 DOI: 10.1111/age.12734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2018] [Indexed: 12/22/2022]
Abstract
The wild boar is an ancestor of the domestic pig and an important game species with the widest geographical range of all ungulates. Although a large amount of data are available on major histocompatibility complex (MHC) variability in domestic pigs, only a few studies have been performed on wild boars. Due to their crucial role in appropriate immune responses and extreme polymorphism, MHC genes represent some of the best candidates for studying the processes of adaptive evolution. Here, we present the results on the variability and evolution of the entire MHC class II SLA-DRB1 locus exon 2 in 133 wild boars from Croatia. Using direct sequencing and cloning methods, we identified 20 SLA-DRB1 alleles, including eight new variants, with notable divergence. In some individuals, we documented functional locus duplication, and SLA-DRB1*04:10 was identified as the allele involved in the duplication. The expression of a duplicated locus was confirmed by cloning and sequencing cDNA-derived amplicons. Based on individual genotypes, we were able to assume that alleles SLA-DRB1*04:10 and SLA-DRB1*06:07 are linked as an allelic combination that co-evolves as a two-locus haplotype. Our investigation of evolutionary processes at the SLA-DRB1 locus confirmed the role of intralocus recombination in generating allelic variability, whereas tests of positive selection based on the dN/dS (non-synonymous/synonymous substitution rate ratio) test revealed atypically weak and ambiguous signals.
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Affiliation(s)
- H Arbanasić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - D Konjević
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia
| | - L Vranković
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia
| | - M Bujanić
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia
| | - S Stipoljev
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - M Balažin
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - N Šprem
- Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - D Škorić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - A Galov
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
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11
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Liu G, Zhang H, Sun G, Zhao C, Shang S, Gao X, Xia T, Yang X. Characterization of the peripheral blood transcriptome and adaptive evolution of the MHC I and TLR gene families in the wolf (Canis lupus). BMC Genomics 2017; 18:584. [PMID: 28784091 PMCID: PMC5545864 DOI: 10.1186/s12864-017-3983-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 08/01/2017] [Indexed: 01/25/2023] Open
Abstract
Background The wolf (Canis lupus) is one of the most widely distributed terrestrial mammals, because it is well adapted to various ecological niches and their corresponding pathogen environments. Immunological competence is a crucial factor involved in adapting to a changing environment and fighting pathogen infection in animals. In this study, the peripheral blood transcriptome of wolves was generated via RNA-seq to advance understanding of the wolf immunome, with a special focus on the major histocompatibility complex class I (MHC I) and toll-like receptor (TLR) gene families, which are involved in pathogen recognition and defense. Results The blood transcriptomic libraries of eight wolves originating from Tibet and Inner Mongolia were sequenced, and approximately 383 million reads were generated. Using a genome-guided assembly strategy, we obtained 123,851 unigenes, with a mean length of 845 bp and an N50 length of 1121 bp. On the basis of BLAST searches against the NCBI non-redundant protein database (Nr), a total of 36,192 (29.22%) unigenes were annotated. For functional classification, 24,663 unigenes were assigned to 13,016 Gene Ontology (GO) terms belonging to 51 sub-categories of the three main GO categories. Additionally, 7682 unigenes were classified into 6 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories, in which the most represented functional sub-categories were signal transduction and the immune system, and 16,238 unigenes were functionally classified into 25 Eukaryotic Orthologous Groups (KOG) categories. We observed an overall higher ω (dN/dS) value at antigen-binding sites (ABSs) than at non-ABS regions as well as clear evidence of intergenic/intragenic recombination events at wolf MHC I loci. Additionally, our analysis revealed that carnivorous TLRs were dominated by purifying selection, with mean ω values at each TLR locus ranging from 0.173 to 0.527. However, we also found significant instances of positive selection that acted on several codons in pathogen recognition domains and were linked to species-specific differences in pathogen recognition. Conclusions This study represents the first attempt to characterize the blood transcriptome of the wolf and to highlight the value of investigating the immune system. Balancing selection and recombination have contributed to the historical evolution of wolf MHC I genes. Moreover, TLRs in carnivores have undergone adaptive evolution against the background of purifying selection, and a high level of adaptive evolution was detected in the wolf TLR system. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3983-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guangshuai Liu
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Honghai Zhang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China.
| | - Guolei Sun
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Chao Zhao
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Shuai Shang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Xiaodong Gao
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Tian Xia
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Xiufeng Yang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
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12
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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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13
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Hindrikson M, Remm J, Pilot M, Godinho R, Stronen AV, Baltrūnaité L, Czarnomska SD, Leonard JA, Randi E, Nowak C, Åkesson M, López-Bao JV, Álvares F, Llaneza L, Echegaray J, Vilà C, Ozolins J, Rungis D, Aspi J, Paule L, Skrbinšek T, Saarma U. Wolf population genetics in Europe: a systematic review, meta-analysis and suggestions for conservation and management. Biol Rev Camb Philos Soc 2016; 92:1601-1629. [PMID: 27682639 DOI: 10.1111/brv.12298] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 08/01/2016] [Accepted: 08/26/2016] [Indexed: 01/04/2023]
Abstract
The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human-carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the 'pre-genomic era' and the first insights of the 'genomics era'. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south-west (lowest genetic diversity) to north-east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650-850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we discuss the most pressing issues threatening wolf populations in Europe, highlight important gaps in current knowledge, suggest solutions to overcome these limitations, and provide recommendations for science-based wolf conservation and management at regional and Europe-wide scales.
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Affiliation(s)
- Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Jaanus Remm
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Malgorzata Pilot
- School of Life Sciences, University of Lincoln, Green Lane, LN6 7DL, Lincoln, UK
| | - Raquel Godinho
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Astrid Vik Stronen
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg Øst, Denmark
| | - Laima Baltrūnaité
- Laboratory of Mammalian Biology, Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Sylwia D Czarnomska
- Mammal Research Institute Polish Academy of Sciences, Waszkiewicza 1, 17-230, Białowieża, Poland
| | - Jennifer A Leonard
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Ettore Randi
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg Øst, Denmark
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), 40064, Ozzano dell'Emilia, Bologna, Italy
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - Mikael Åkesson
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | | | - Francisco Álvares
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Luis Llaneza
- ARENA Asesores en Recursos Naturales S.L. c/Perpetuo Socorro, n° 12 Entlo 2B, 27003, Lugo, Spain
| | - Jorge Echegaray
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Carles Vilà
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Janis Ozolins
- Latvian State Forest Research Institute "Silava", Rigas iela 111, LV-2169, Salaspils, Latvia
| | - Dainis Rungis
- Latvian State Forest Research Institute "Silava", Rigas iela 111, LV-2169, Salaspils, Latvia
| | - Jouni Aspi
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Ladislav Paule
- Department of Phytology, Faculty of Forestry, Technical University, T.G. Masaryk str. 24, SK-96053, Zvolen, Slovakia
| | - Tomaž Skrbinšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
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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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15
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Magalhães V, Abrantes J, Munõz-Pajares AJ, Esteves PJ. Genetic diversity comparison of the DQA gene in European rabbit (Oryctolagus cuniculus) populations. Immunogenetics 2015; 67:579-90. [PMID: 26307416 DOI: 10.1007/s00251-015-0866-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/13/2015] [Indexed: 10/23/2022]
Abstract
The European rabbit (Oryctolagus cuniculus) natural populations within the species native region, the Iberian Peninsula, are considered a reservoir of genetic diversity. Indeed, the Iberia was a Pleistocene refuge to the species and currently two subspecies are found in the peninsula (Oryctolagus cuniculus cuniculus and Oryctolagus cuniculus algirus). The genes of the major histocompatibility complex (MHC) have been substantially studied in wild populations due to their exceptional variability, believed to be pathogen driven. They play an important function as part of the adaptive immune system affecting the individual fitness and population viability. In this study, the MHC variability was assessed by analysing the exon 2 of the DQA gene in several European rabbit populations from Portugal, Spain and France and in domestic breeds. Twenty-eight DQA alleles were detected, among which 18 are described for the first time. The Iberian rabbit populations are well differentiated from the French population and domestic breeds. The Iberian populations retained the higher allelic diversity with the domestic breeds harbouring the lowest; in contrast, the DQA nucleotide diversity was higher in the French population. Signatures of positive selection were detected in four codons which are putative peptide-binding sites and have been previously detected in other mammals. The evolutionary relationships showed instances of trans-species polymorphism. Overall, our results suggest that the DQA in European rabbits is evolving under selection and genetic drift.
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Affiliation(s)
- Vanessa Magalhães
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Joana Abrantes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Antonio Jesús Munõz-Pajares
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal. .,Centro de Investigação em Tecnologias da Saúde (CITS), ISPN, CESPU, Gandra, Portugal.
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16
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Niskanen AK, Kennedy LJ, Ruokonen M, Kojola I, Lohi H, Isomursu M, Jansson E, Pyhäjärvi T, Aspi J. Balancing selection and heterozygote advantage in major histocompatibility complex loci of the bottlenecked Finnish wolf population. Mol Ecol 2014; 23:875-89. [DOI: 10.1111/mec.12647] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 12/19/2013] [Accepted: 12/20/2013] [Indexed: 02/03/2023]
Affiliation(s)
- A. K. Niskanen
- Department of Biology; University of Oulu; PO Box 3000 FI-90014 Oulu Finland
| | - L. J. Kennedy
- Centre for Integrated Genomic Medical Research; University of Manchester; Stopford Building Oxford Road Manchester M13 9PT UK
| | - M. Ruokonen
- Department of Biology; University of Oulu; PO Box 3000 FI-90014 Oulu Finland
| | - I. Kojola
- Finnish Game and Fisheries Research Institute; Paavo Havaksen tie 3 PO Box 413 FI-90014 Oulu Finland
| | - H. Lohi
- Department of Veterinary Biosciences; Research Programs Unit; Molecular Neurology; Folkhälsan Institute of Genetics; Biomedicum Helsinki; University of Helsinki; PO Box 63 FI-00014 Helsinki Finland
| | - M. Isomursu
- Fish and Wildlife Health Research Unit; Finnish Food Safety Authority Evira; PO Box 517 FI-90101 Oulu Finland
| | - E. Jansson
- Department of Biology; University of Oulu; PO Box 3000 FI-90014 Oulu Finland
| | - T. Pyhäjärvi
- Department of Biology; University of Oulu; PO Box 3000 FI-90014 Oulu Finland
| | - J. Aspi
- Department of Biology; University of Oulu; PO Box 3000 FI-90014 Oulu Finland
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17
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Galaverni M, Caniglia R, Fabbri E, Lapalombella S, Randi E. MHC variability in an isolated wolf population in Italy. J Hered 2013; 104:601-12. [PMID: 23885092 DOI: 10.1093/jhered/est045] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Small, isolated populations may experience increased extinction risk due to reduced genetic variability at important functional genes, thus decreasing the population's adaptive potential. The major histocompatibility complex (MHC), a key immunological gene cluster, usually shows high variability maintained by positive or balancing selection in response to challenges by pathogens. Here we investigated for the first time, the variability of 3 MHC class II genes (DRB1, DQA1, and DQB1) in 94 samples collected from Italian wolves. The Italian wolf population has been long isolated south of the Alps and is presently recovering from a recent bottleneck that decreased the population to less than 100 individuals. Despite the bottleneck, Italian wolves show remarkable MHC variability with 6-9 alleles per locus, including 2 recently described alleles at DRB1. MHC sequences show signatures of historical selective pressures (high d N/d S ratio, ω > 1.74) but no evidence of ongoing selection. Variation at the MHC genes and 12 background microsatellite loci were not apparently affected by the recent bottleneck. Although MHC alleles of domestic dog origin were detected in 8 genetically admixed individuals, these alleles were rare or absent in nonadmixed wolves. Thus, despite known hybridization events between domestic dogs and Italian wolves, the Italian wolf population does not appear affected by deep introgression of domestic dog MHC alleles.
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Affiliation(s)
- Marco Galaverni
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale, Ozzano dell’Emilia, Bologna, Italy.
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18
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Arbanasić H, Galov A, Ambriović-Ristov A, Grizelj J, Arsenos G, Marković B, Dovenski T, Vince S, Curik I. Extensive polymorphism of the major histocompatibility complex DRA gene in Balkan donkeys: perspectives on selection and genealogy. Anim Genet 2013; 44:711-6. [PMID: 23621397 DOI: 10.1111/age.12054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2013] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) contains genes important for immune response in mammals, and these genes exhibit high polymorphism and diversity. The DRA gene, a member of the MHC class II family, is highly conserved across a large number of mammalian species, but it displays exceptionally rich sequence variations in Equidae members. We analyzed allelic polymorphism of the DRA locus in 248 donkeys sampled across the Balkan Peninsula (Albania, Bulgaria, Croatia, Macedonia, Greece and Montenegro). Five known alleles and two new alleles were identified. The new allele Eqas-DRA*0601 was found to carry a synonymous mutation, and new allele Eqas-DRA*0701, a non-synonymous mutation. We further analyzed the historical selection and allele genealogy at the DRA locus in equids. Signals of positive selection obtained by various tests were ambiguous. A conservative conclusion is that DRA polymorphism occurred relatively recently and that positive selection has been acting on the DRA locus for a relatively brief period.
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Affiliation(s)
- Haidi Arbanasić
- Division of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
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