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Dong PP, Wang RR, Abduriyim S. Diversity and evolution of the MHC class II DRB gene in the Capra sibirica experienced a demographic fluctuation in China. Sci Rep 2023; 13:19352. [PMID: 37935954 PMCID: PMC10630338 DOI: 10.1038/s41598-023-46717-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
The major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, and their proteins play a critical role in adaptive immunity for defense against a variety of pathogens. MHC diversity was lost in many species after experiencing a decline in size. To understand the variation and evolution of MHC genes in the Siberian ibex, Capra sibirica, which has undergone a population decline, we analyzed the variation of the second exon of MHC class II DRB genes in samples collected from five geographic localities in Xinjiang, China, that belong to three diverged mitochondrial clades. Consequently, we identified a total of 26 putative functional alleles (PFAs) with 260 bp in length from 43 individuals, and found one (for 27 individuals) to three (for 5 individuals) PFAs per individual, indicating the presence of one or two DRB loci per haploid genome. The Casi-DRB1*16 was the most frequently occurring PFA, Casi-DRB1*22 was found in only seven individuals, 14 PFAs occurred once, 7 PFAs twice, implying high frequency of rare PFAs. Interestingly, more than half (15) of the PFAs were specific to clade I, only two and three PFAs were specific to clades II and III, respectively. So, we assume that the polygamy and sexual segregation nature of this species likely contributed to the allelic diversity of DRB genes. Genetic diversity indices showed that PFAs of clade II were lower in nucleotide, amino acid, and supertype diversity compared to those of the other two clades. The pattern of allele sharing and FST values between the three clades was to some extent in agreement with the pattern observed in mitochondrial DNA divergence. In addition, recombination analyses revealed no evidence for significant signatures of recombination events. Alleles shared by clades III and the other two clades diverged 6 million years ago, and systematic neighbor grids showed Trans-species polymorphism. Together with the PAML and MEME analyses, the results indicated that the DRB gene in C. sibirica evolved under balancing and positive selection. However, by comparison, it can be clearly seen that different populations were under different selective pressures. Our results are valuable in understanding the diversity and evolution of the DRB gene in a mountain living C. sibirica and in making decisions on future long-term protection strategies.
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Affiliation(s)
- Pei-Pei Dong
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Rui-Rui Wang
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Shamshidin Abduriyim
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University, Shihezi, 832003, Xinjiang, China.
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Zoologist, traveller and explorer: celebrating the 60th anniversary of Alexei Vladimirovich Abramov. RUSSIAN JOURNAL OF THERIOLOGY 2022. [DOI: 10.15298/rusjtheriol.21.2.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Diversity of the MHC class II DRB gene in the wolverine (Carnivora: Mustelidae: Gulo gulo) in Finland. PLoS One 2022; 17:e0267609. [PMID: 35536786 PMCID: PMC9089919 DOI: 10.1371/journal.pone.0267609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 11/19/2022] Open
Abstract
The wolverine (Gulo gulo) in Finland has undergone significant population declines in the past. Since major histocompatibility complex (MHC) genes encode proteins involved in pathogen recognition, the diversity of these genes provides insights into the immunological fitness of regional populations. We sequenced 862 amplicons (242 bp) of MHC class II DRB exon 2 from 32 Finnish wolverines and identified 11 functional alleles and three pseudogenes. A molecular phylogenetic analysis indicated trans-species polymorphism, and PAML and MEME analyses indicated positive selection, suggesting that the Finnish wolverine DRB genes have evolved under balancing and positive selection. In contrast to DRB gene analyses in other species, allele frequencies in the Finnish wolverines clearly indicated the existence of two regional subpopulations, congruent with previous studies based on neutral genetic markers. In the Finnish wolverine, rapid population declines in the past have promoted genetic drift, resulting in a lower genetic diversity of DRB loci, including fewer alleles and positively selected sites, than other mustelid species analyzed previously. Our data suggest that the MHC region in the Finnish wolverine population was likely affected by a recent bottleneck.
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Skorupski J. Fifty Years of Research on European Mink Mustela lutreola L., 1761 Genetics: Where Are We Now in Studies on One of the Most Endangered Mammals? Genes (Basel) 2020; 11:E1332. [PMID: 33187363 PMCID: PMC7696698 DOI: 10.3390/genes11111332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
The purpose of this review is to present the current state of knowledge about the genetics of European mink Mustela lutreola L., 1761, which is one of the most endangered mammalian species in the world. This article provides a comprehensive description of the studies undertaken over the last 50 years in terms of cytogenetics, molecular genetics, genomics (including mitogenomics), population genetics of wild populations and captive stocks, phylogenetics, phylogeography, and applied genetics (including identification by genetic methods, molecular ecology, and conservation genetics). An extensive and up-to-date review and critical analysis of the available specialist literature on the topic is provided, with special reference to conservation genetics. Unresolved issues are also described, such as the standard karyotype, systematic position, and whole-genome sequencing, and hotly debated issues are addressed, like the origin of the Southwestern population of the European mink and management approaches of the most distinct populations of the species. Finally, the most urgent directions of future research, based on the research questions arising from completed studies and the implementation of conservation measures to save and restore M. lutreola populations, are outlined. The importance of the popularization of research topics related to European mink genetics among scientists is highlighted.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-914-441-685
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
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Hosotani S, Nishita Y, Masuda R. Genetic diversity and evolution of the MHC class II DRB gene in the Japanese marten, Martes melampus (Carnivora: Mustelidae). MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00506-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Zhao B, Zhang X, Li B, Du P, Shi L, Dong Y, Gao X, Sha W, Zhang H. Evolution of major histocompatibility complex class I genes in the sable Martes zibellina (Carnivora, Mustelidae). Ecol Evol 2020; 10:3439-3449. [PMID: 32274000 PMCID: PMC7141072 DOI: 10.1002/ece3.6140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/31/2020] [Accepted: 02/04/2020] [Indexed: 11/10/2022] Open
Abstract
The molecules encoded by major histocompatibility complex (MHC) genes play an essential role in the adaptive immune response among vertebrates. We investigated the molecular evolution of MHC class I genes in the sable Martes zibellina. We isolated 26 MHC class I sequences, including 12 putatively functional sequences and 14 pseudogene sequences, from 24 individuals from two geographic areas of northeast China. The number of putatively functional sequences found in a single individual ranged from one to five, which might be at least 1-3 loci. We found that both balancing selection and recombination contribute to evolution of MHC class I genes in M. zibellina. In addition, we identified a candidate nonclassical MHC class I lineage in Carnivora, which may have preceded the divergence (about 52-57 Mya) of Caniformia and Feliformia. This may contribute to further understanding of the origin and evolution of nonclassical MHC class I genes. Our study provides important immune information of MHC for M. zibellina, as well as other carnivores.
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Affiliation(s)
- Baojun Zhao
- College of Life Science Qufu Normal University Qufu China
| | - Xue Zhang
- College of Life Science Qufu Normal University Qufu China
| | - Bo Li
- College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - Pengfei Du
- College of Life Science Qufu Normal University Qufu China
| | - Lupeng Shi
- College of Life Science Qufu Normal University Qufu China
| | - Yuehuan Dong
- College of Life Science Qufu Normal University Qufu China
| | - Xiaodong Gao
- College of Life Science Qufu Normal University Qufu China
| | - Weilai Sha
- College of Life Science Qufu Normal University Qufu China
| | - Honghai Zhang
- College of Life Science Qufu Normal University Qufu China
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Bartocillo AMF, Nishita Y, Abramov AV, Masuda R. Molecular evolution of MHC class II DRB exon 2 in Japanese and Russian raccoon dogs, Nyctereutes procyonoides (Carnivora: Canidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractRaccoon dogs, Nyctereutes procyonoides, are native to East Asia, but have been introduced into western Russia and eastern Europe. To determine allelic diversity and elucidate the evolution of major histocompatibility complex (MHC) class II genes in the raccoon dog, we analysed a 237-bp region of DRB exon 2 from 36 individuals of native and introduced populations from Japan and Russia. We detected 23 DRB alleles (Nypr-DRBs), 22 of which were novel. Some alleles were found across the species’ range, while others were geographically restricted. For both native and introduced populations, the ratio of non-synonymous to synonymous substitution rates for codons at predicted antigen-binding sites was significantly greater than 2, indicating that Nypr-DRBs have evolved under positive selection. Mixed effect model evolution analysis and an algorithm to detect recombination showed five positively selected codons and one recombination breakpoint, respectively. Overall, our results suggest that the diversity of MHC class II DRB in N. procyonoides was influenced and maintained by recombination, pathogen-driven positive selection, geographical barriers and the founder effect. A Bayesian phylogenetic tree revealed no evidence of trans-species polymorphism (TSP), but instead showed monophyly for the Nypr-DRB alleles within a larger clade of canid sequences. The lack of TSP may have been due to long-term divergence of raccoon dogs from other canids, or to their having encountered different sets of pathogens due to occupying a different ecological niche.
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Affiliation(s)
- Aye Mee F Bartocillo
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Kita-Ku, Sapporo, Japan
| | - Yoshinori Nishita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo, Japan
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. Saint Petersburg, Russia
| | - Ryuichi Masuda
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo, Japan
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Abduriyim S, Nishita Y, Kosintsev PA, Raichev E, Väinölä R, Kryukov AP, Abramov AV, Kaneko Y, Masuda R. Evolution of MHC class I genes in Eurasian badgers, genus Meles (Carnivora, Mustelidae). Heredity (Edinb) 2019; 122:205-218. [PMID: 29959426 PMCID: PMC6327056 DOI: 10.1038/s41437-018-0100-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 11/09/2022] Open
Abstract
Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7-21 putatively functional MHCI sequences in each of the badger species, and 2-7 sequences per individual, indicating the existence of 1-4 loci. MHCI exon 2 and 3 sequences encoding domains α1 and α2 exhibited different clade topologies in phylogenetic networks. Non-synonymous nucleotide substitutions at codons for antigen-binding sites exceeded synonymous substitutions for domain α1 but not for domain α2, suggesting that the domains α1 and α2 likely had different evolutionary histories in these species. Positive selection and recombination seem to have shaped the variation in domain α2, whereas positive selection was dominant in shaping the variation in domain α1. In the separate phylogenetic analyses for exon 2, exon 3, and intron 2, each showed three clades of Meles alleles, with rampant trans-species polymorphism, indicative of the long-term maintenance of ancestral MHCI polymorphism by balancing selection.
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Affiliation(s)
- Shamshidin Abduriyim
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yoshinori Nishita
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Pavel A Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Ekaterinburg, 620144, Russia
| | - Evgeniy Raichev
- Agricultural Faculty, Trakia University, 6000, Stara Zagora, Bulgaria
| | - Risto Väinölä
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, FI-00014, Helsinki, Finland
| | - Alexey P Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, 199034, Russia
| | - Yayoi Kaneko
- Carnivore Ecology and Conservation Research Group, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Ryuichi Masuda
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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Amaike Y, Nishita Y, Uraguchi K, Masuda R. Genetic Diversity of MHC Class II DRB1 Exon 2 in the Red Fox (Vulpes vulpes) on Hokkaido, Japan. Zoolog Sci 2018; 35:402-410. [DOI: 10.2108/zs170211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Yosuke Amaike
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Yoshinori Nishita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kohji Uraguchi
- Hokkaido Institute of Public Health, Kita 19, Nishi 12, Kita-ku, Sapporo 060-0819, Japan
| | - Ryuichi Masuda
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
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Nishita Y, Spassov N, Peeva S, Raichev EG, Kaneko Y, Masuda R. Genetic diversity of MHC class II DRB alleles in the marbled polecat, Vormela peregusna, in Bulgaria. ETHOL ECOL EVOL 2018. [DOI: 10.1080/03949370.2018.1486887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Yoshinori Nishita
- Department of Biological Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Nikolai Spassov
- National Museum of Natural History, Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Stanislava Peeva
- Department of Agricultural Science, Trakia University, Stara Zagora 6000, Bulgaria
| | - Evgeniy G. Raichev
- Department of Agricultural Science, Trakia University, Stara Zagora 6000, Bulgaria
| | - Yayoi Kaneko
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-0057, Japan
| | - Ryuichi Masuda
- Department of Biological Sciences, Hokkaido University, Sapporo 060-0810, Japan
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Nishita Y, Abramov AV, Murakami T, Masuda R. Genetic diversity of MHC class II DRB alleles in the continental and Japanese populations of the sable Martes zibellina (Mustelidae, Carnivora, Mammalia). MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0366-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Abduriyim S, Nishita Y, Kosintsev PA, Raichev E, Väinölä R, Kryukov AP, Abramov AV, Kaneko Y, Masuda R. Diversity and evolution of MHC class II DRB gene in the Eurasian badger genus Meles (Mammalia: Mustelidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Nishita Y, Kosintsev PA, Haukisalmi V, Väinölä R, Raichev EG, Murakami T, Abramov AV, Kaneko Y, Masuda R. Diversity of MHC class II DRB alleles in the Eurasian population of the least weasel, Mustela nivalis (Mustelidae: Mammalia). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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de Groot N, Stanbury K, de Vos-Rouweler AJM, de Groot NG, Poirier N, Blancho G, de Luna C, Doxiadis GGM, Bontrop RE. A quick and robust MHC typing method for free-ranging and captive primate species. Immunogenetics 2017; 69:231-240. [PMID: 28084496 PMCID: PMC5350218 DOI: 10.1007/s00251-016-0968-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/27/2016] [Indexed: 12/21/2022]
Abstract
Gene products of the major histocompatibility complex (MHC) of human and non-human primates play a crucial role in adaptive immunity, and most of the relevant genes not only show a high degree of variability (polymorphism) but also copy number variation (CNV) is observed. Due to this diversity, MHC proteins influence the capability of individuals to cope with various pathogens. MHC and/or MHC-linked gene products such as odorant receptor genes are thought to influence mate choice and reproductive success. Therefore, MHC typing of wild and captive primate populations is considered to be useful in conservation biology, which is, however, often hampered by the need of invasive and time-consuming methods. All intact Mhc-DRB genes in primates appear to possess a complex and highly divergent microsatellite, DRB-STR. A panel of 154 pedigreed olive baboons (Papio anubis) was examined for their DRB content by DRB-STR analysis of genomic DNA. Using the same methodology on DNA of feces samples, DRB variability of a silvery gibbon population (Hylobates moloch) (N = 24), an endangered species, could successfully be studied. In both species, length determination of the DRB-STR resulted in the definition of unique genotyping patterns that appeared to be specific for a certain chromosome. Moreover, the different STR lengths were shown to segregate with the allelic variation of the respective gene. The results obtained expand data gained previously on DRB-STR typing in macaques, great apes, and humans and strengthen the conclusion that this protocol is applicable in molecular ecology, conservation biology, and colony management, especially of endangered primate species.
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Affiliation(s)
- N de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - K Stanbury
- Writtle College, Essex University, Lordship Road, Writtle, Chelmsford, Essex, CM1 3RR, UK
| | - A J M de Vos-Rouweler
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - N G de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - N Poirier
- Institut National de la Sante et de la Recherche Medicale (INSERM) UMR1064, Institut de Transplantation-Urologie-Nephrologie (ITUN), 30 Bd Jean Monnet, 44093, Nantes, France
| | - G Blancho
- Institut National de la Sante et de la Recherche Medicale (INSERM) UMR1064, Institut de Transplantation-Urologie-Nephrologie (ITUN), 30 Bd Jean Monnet, 44093, Nantes, France
| | - C de Luna
- Writtle College, Essex University, Lordship Road, Writtle, Chelmsford, Essex, CM1 3RR, UK
| | - G G M Doxiadis
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.
| | - R E Bontrop
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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