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Genetic origins and diversity of bushpigs from Madagascar (Potamochoerus larvatus, family Suidae)

  • 1.

    Hansford, J. et al. Early holocene human presence in Madagascar evidenced by exploitation of avian megafauna. Sci. Adv. 4, 1–7 (2018).

    Article  Google Scholar 

  • 2.

    Douglass, K. et al. A critical review of radiocarbon dates clarifies the human settlement of Madagascar. Quat. Sci. Rev. 221, 105878 (2019).

    Article  Google Scholar 

  • 3.

    Pierron, D. et al. Genomic landscape of human diversity across Madagascar. Proc. Natl. Acad. Sci. USA 114, E6498–E6506 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 4.

    Anderson, A. et al. New evidence of megafaunal bone damage indicates late colonization of Madagascar. PLoS ONE 13, 1–14 (2018).

    Google Scholar 

  • 5.

    Blench, R. New palaeozoogeographical evidence for the settlement of Madagascar. Azania Archaeol. Res. Afr. 42, 69–82 (2007).

    Google Scholar 

  • 6.

    Beaujard, P. The first migrants to Madagascar and their introduction of plants: Linguistic and ethnological evidence. Azania 46, 169–189 (2011).

    Article  Google Scholar 

  • 7.

    Rakotozafy, L. M. A. & Goodman, S. M. Contribution à l’étude zooarchéologique de la région du Sud-ouest et extrême Sud de Madagascar sur la base des collections de l’ICMAA de l’Université d’Antananarivo. Taloha 14–15 (2005).

  • 8.

    Boivin, N., Crowther, A., Helm, R. & Fuller, D. Q. East Africa and Madagascar in the Indian Ocean world. J. World Prehistory 26, 213–281 (2013).

    Article  Google Scholar 

  • 9.

    Wright, H. T. et al. Early Seafarers of the Comoro Islands: The Dembeni Phase of the IXth-Xth Centuries AD. Azania Archaeol. Res. Africa 19, 13–59 (1984).

    Google Scholar 

  • 10.

    Krause, D. W. et al. Late cretaceous terrestrial vertebrates from Madagascar: Implications for Latin American biogeography 1. Ann. Missouri Bot. Gard. 93, 178–208 (2006).

    Article  Google Scholar 

  • 11.

    Roger, F., Ratovonjato, J., Vola, P. & Uilenberg, G. Ornithodoros porcinus ticks, bushpigs, and African swine fever in Madagascar. Exp. Appl. Acarol. 25, 263–269 (2001).

    CAS  PubMed  Article  Google Scholar 

  • 12.

    Sommer, S. The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Front. Zool. 2, 16 (2005).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 13.

    Venter, J., Ehlers-Smith, Y. & Seydack, A. Potamochoerus larvatus—Bushpig. 1–5 (The Red List of Mammals of South Africa, Swaziland and Lesotho, 2016).

  • 14.

    Andrianjakarivelo, V. Artiodactyla: Potamochoerus larvatus, Bush Pig. In The Natural History of Madagascar (eds Goodman, S. M. & Benstead, J. B.) 1365–1367 (The University of Chicago Press, Chicago, 2003).

  • 15.

    Grubb, P. The Afrotropical Suids (Phacochoerus, Hylochoerus, and Potamochoerus). In Pigs, Peccaries, and Hippos: Status Survey and Conservation Action Plan (ed. William, L. R. O.) 66–101 (International Union for the Conservation of Nature, Gland, 1993).

    Google Scholar 

  • 16.

    Forsyth, C. I. 5. On the Species of Potamochœrus, the Bush-Pigs of the Ethiopian Region. Proc. Zool. Soc. London 65, 359–370 (2009).

    Article  Google Scholar 

  • 17.

    Vercammen, P., Seydack, A. & Oliver, W. The Bush Pigs (Potamochoerus larvatus and P. porcus). In Pigs, Peccaries, and Hippos: Status Survey and Conservation Action Plan (ed. William, L. R. O.) 93–101 (IUCN SSC Pigs and Peccaries Specialist Group and IUCN SSC Hippo Specialist Group, Gland, 1993).

    Google Scholar 

  • 18.

    Funaioli, U. & Simonetta, A. M. The mammalian fauna of the somali republic: Status and conservation problems. Monit. Zool. Ital. Suppl. 1, 285–347 (1966).

    Google Scholar 

  • 19.

    Stuart, C. & Stuart, T. Chris and Tilde Stuart’s field guide to the mammals of southern Africa (R. Curtis Books Pub., Sanibel Island, 1988).

    Google Scholar 

  • 20.

    Blench, R. M. Archaeology, Language, and the African Past (Altamira Press, Lanham, 2006).

    Google Scholar 

  • 21.

    Alpers, E. A. Littoral society in Mozambique. In Cross Currents and Community Networks: The History of the Indian Ocean World (eds Ray, H. P. & Alpers, E. A.) 123–141 (Oxford University Press, Oxford, 2007).

    Google Scholar 

  • 22.

    Oura, C. A. L., Powell, P. P. & Parkhouse, R. M. E. African swine fever: A disease characterized by apoptosis. J. Gen. Virol. 79, 1427–1438 (1998).

    CAS  PubMed  Article  Google Scholar 

  • 23.

    Ravaomanana, J. et al. Assessment of interactions between African swine fever virus, bushpigs (Potamochoerus larvatus), Ornithodoros ticks and domestic pigs in north-western Madagascar. Transbound. Emerg. Dis. 58, 247–254 (2011).

    CAS  PubMed  Article  Google Scholar 

  • 24.

    Cecchi, G. & Mattioli, R. C. Global geospatial datasets for African trypanosomiasis management: a review. Progr. Afr. Trypanos. Tech. Sci. Ser. 9, 1–39 (2009).

    Google Scholar 

  • 25.

    Munangandu, H. M., Siamudaala, V., Munyeme, M. & Nalubamba, K. S. A review of ecological factors associated with the epidemiology of wildlife Trypanosomiasis in the Luangwa and Zambezi Valley Ecosystems of Zambia. Interdiscip. Perspect. Infect. Dis. 2012, 1–13 (2012).

    Article  Google Scholar 

  • 26.

    Gibbs, E. P. The public health risks associated with wild and feral swine. Rev. Sci. Tech. 16, 594–598 (1997).

    CAS  PubMed  Article  Google Scholar 

  • 27.

    Patton, D. & Gu, H. China has culled more than 900,000 pigs due to African swine fever. Reuters (2018).

  • 28.

    Ploshnitsa, A. I., Goltsman, M. E., Macdonald, D. W., Kennedy, L. J. & Sommer, S. Impact of historical founder effects and a recent bottleneck on MHC variability in Commander Arctic foxes (Vulpes lagopus). Ecol. Evol. 2, 165–180 (2012).

    PubMed  PubMed Central  Article  Google Scholar 

  • 29.

    Klein, J. Origin of major histocompatibility complex polymorphism: The trans-species hypothesis. Hum. Immunol. 19, 155–162 (1987).

    CAS  PubMed  Article  Google Scholar 

  • 30.

    Ho, C. S. et al. Nomenclature for factors of the SLA system, update 2008. Tissue Antigens 73, 307–315 (2009).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 31.

    Renard, C. et al. The genomic sequence and analysis of the swine major histocompatibility complex. Genomics 88, 96–110 (2006).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 32.

    Ka, S. et al. HLAscan: Genotyping of the HLA region using next-generation sequencing data. BMC Bioinform. 18, 1–11 (2017).

    Article  CAS  Google Scholar 

  • 33.

    Fan, W. et al. Shared class II MHC polymorphisms between humans and chimpanzees. Hum. Immunol. 26, 107–121 (1989).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 34.

    Piertney, S. B. & Oliver, M. K. The evolutionary ecology of the major histocompatibility complex. Heredity (Edinb). 96, 7–21 (2006).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 35.

    Flajnik, M. F., Canel, C., Kramer, J. & Kasahara, M. Which came first, MHC class I or class II?. Immunogenetics 33, 295–300 (1991).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 36.

    Borghans, J. A. M., Beltman, J. B. & De Boer, R. J. MHC polymorphism under host-pathogen coevolution. Immunogenetics 55, 732–739 (2004).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 37.

    Spurgin, L. G. & Richardson, D. S. How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proc. Biol. Sci. 277, 979–988 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 38.

    Hughes, A. L. & Nei, M. Nucleotide substitution at major histocompatibility complex class II loci: Evidence for overdominant selection. Proc. Natl. Acad. Sci. 86, 958–962 (1989).

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 39.

    Hughes, A. L. & Nei, M. Evolution of the major histocompatibility complex: Independent origin of nonclassical class I genes in different groups of mammals. Mol. Biol. Evol. 6, 559–579 (1989).

    CAS  PubMed  Google Scholar 

  • 40.

    Penn, D. J. & Ilmonen, P. Major histocompatibility complex (MHC). in Encyclopedia of Life Sciences 1–7 (John Wiley & Sons, Ltd, 2001). https://doi.org/10.1038/npg.els.0000919.

  • 41.

    Bonneaud, C., Pérez-Tris, J., Federici, P., Chastel, O. & Sorci, G. Major histocompatibility alleles associated with local resistance to malaria in a passerine. Evolution (N. Y.). 60, 383 (2006).

    CAS  Google Scholar 

  • 42.

    Schatz, G. E. Endemism in the Malagasy flora. In Diversity and Endemism in Madagascar (eds Lourenço, W. R. & Goodman, S. M.) 1–10 (2000).

  • 43.

    Lowden, S. et al. Application of Sus scrofa microsatellite markers to wild suiformes. Conserv. Genet. 3, 347–350 (2002).

    CAS  Article  Google Scholar 

  • 44.

    Gongora, J., Morales, S., Bernal, J. E. & Moran, C. Phylogenetic divisions among Collared peccaries (Pecari tajacu) detected using mitochondrial and nuclear sequences. Mol. Phylogenet. Evol. 41, 1–11 (2006).

    CAS  PubMed  Article  Google Scholar 

  • 45.

    Lee, C. et al. Inferring the evolution of the major histocompatibility complex of wild pigs and peccaries using hybridisation DNA capture-based sequencing. Immunogenetics 70, 401–417 (2018).

    CAS  PubMed  Article  Google Scholar 

  • 46.

    Kim, K. I. et al. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism. Anim. Genet. 33, 19–25 (2002).

    CAS  PubMed  Article  Google Scholar 

  • 47.

    Irwin, D. M., Kocher, T. D. & Wilson, A. C. Evolution of the Cytochrome b gene of mammals. J. Mol. Evol. 32, 128–144 (1991).

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 48.

    Giuffra, E. et al. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 154, 1785–1791 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 49.

    Ishiguro, N., Naya, Y., Horiuchi, M. & Shinagawa, M. A Genetic method to distinguish crossbred inobuta from Japanese Wild Boars. Zool. Sci. 19, 1313–1319 (2002).

    CAS  Article  Google Scholar 

  • 50.

    Fajardo, V. et al. Differentiation of European wild boar (Sus scrofa scrofa) and domestic swine (Sus scrofa domestica) meats by PCR analysis targeting the mitochondrial D-loop and the nuclear melanocortin receptor 1 (MC1R) genes. Meat Sci. 78, 314–322 (2008).

    CAS  PubMed  Article  Google Scholar 

  • 51.

    Firestone, K. B. Phylogenetic relationships among quolls revisited: The mtDNA control region as a useful tool. J. Mamm. Evol. 7, 1–22 (2000).

    Article  Google Scholar 

  • 52.

    Randi, E. et al. Evolution of the mitochondrial DNA control region and cytochrome b genes and the inference of phylogenetic relationships in the avian genus Lophura (Galliformes). Mol. Phylogenet. Evol. 19, 187–201 (2001).

    CAS  PubMed  Article  Google Scholar 

  • 53.

    Jiang, J. et al. Mitochondrial genome and nuclear markers provide new insight into the evolutionary history of macaques. PLoS ONE 11, 1–19 (2016).

    Google Scholar 

  • 54.

    Chen, L. et al. Intraspecific mitochondrial genome comparison identified CYTB as a high-resolution population marker in a new pest Athetis lepigone. Genomics 111, 744–752 (2019).

    CAS  PubMed  Article  Google Scholar 

  • 55.

    Gongora, J. et al. Phylogenetic relationships of Australian and New Zealand feral pigs assessed by mitochondrial control region sequence and nuclear GPIP genotype. Mol. Phylogenet. Evol. 33, 339–348 (2004).

    CAS  PubMed  Article  Google Scholar 

  • 56.

    Wang, J. et al. Phylogenetic relationships of pig breeds from Shandong province of China and their influence by modern commercial breeds by analysis of mitochondrial DNA sequences. Ital. J. Anim. Sci. 9, 248–254 (2010).

  • 57.

    García, G., Vergara, J. & Lombardi, R. Genetic characterization and phylogeography of the wild boar Sus scrofa introduced into Uruguay. Genet. Mol. Biol. 34, 329–337 (2011).

    PubMed  PubMed Central  Article  Google Scholar 

  • 58.

    Lopez, J., Hurwood, D., Dryden, B. & Fuller, S. Feral pig populations are structured at fine spatial scales in tropical Queensland, Australia. PLoS One 9, e91657 (2014).

  • 59.

    Dun, G., Li, X., Cao, H., Zhou, R. & Li, L. Variations of melanocortin receptor 1 (MC1R) gene in three pig breeds. J. Genet. Genomics 34, 777–782 (2007).

    CAS  PubMed  Article  Google Scholar 

  • 60.

    Chang, A. C. Y. et al. Phenotype-based identification of host genes required for replication of African swine fever virus. J. Virol. 80, 8705–8717 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 61.

    Bitzer, A., Basler, M. & Groettrup, M. Chaperone BAG6 is dispensable for MHC class I antigen processing and presentation. Mol. Immunol. 69, 99–105 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 62.

    Stam, M. et al. Centromeric/pericentromeric junction within the MHC locus on chromosome 7 in pig. In XXXI Conference of the International Society for Animal Genetics, Amsterdam, Netherlands (2008).

  • 63.

    Groenen, M. A. M. et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491, 393–398 (2012).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 64.

    Stucky, B. J. SeqTrace: A graphical tool for rapidly processing DNA sequencing chromatograms. J. Biomol. Tech. 23, 90–93 (2012).

    PubMed  PubMed Central  Article  Google Scholar 

  • 65.

    Rozas, J. et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 34, 3299–3302 (2017).

    CAS  PubMed  Article  Google Scholar 

  • 66.

    Watanobe, T. et al. Genetic relationship and distribution of the Japanese wild boar (Sus scrofa leucomystax) and Ryukyu wild boar (Sus scrofa riukiuanus) analysed by mitochondrial DNA. Mol. Ecol. 8, 1509–1512 (1999).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 67.

    Gongora, J. et al. Rethinking the evolution of extant sub-Saharan African suids (Suidae, Artiodactyla). Zool. Scr. 40, 327–335 (2011).

    Article  Google Scholar 

  • 68.

    Larson, G. et al. Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania. Proc. Natl. Acad. Sci. 104, 4834–4839 (2007).

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 69.

    Mona, S., Randi, E. & Tommaseo-Ponzetta, M. Evolutionary history of the genus Sus inferred from Cytochrome b sequences. Mol. Phylogenet. Evol. 45, 757–762 (2007).

    CAS  PubMed  Article  Google Scholar 

  • 70.

    Niebert, M. & Tönjes, R. R. Evolutionary spread and recombination of porcine endogenous retroviruses in the suiformes. J. Virol. 79, 649–654 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 71.

    Gongora, J. & Moran, C. Nuclear and mitochondrial evolutionary analyses of Collared, White-lipped, and Chacoan peccaries (Tayassuidae). Mol. Phylogenet. Evol. 34, 181–189 (2005).

    CAS  PubMed  Article  Google Scholar 

  • 72.

    Hassanin, A. et al. Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C. R. Biol. 335, 32–50 (2012).

    PubMed  Article  Google Scholar 

  • 73.

    Wu, G. S. et al. Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia. Genome Biol. 8, R245 (2007).

  • 74.

    Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 75.

    Vaidya, G., Lohman, D. J. & Meier, R. SequenceMatrix: Concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 27, 171–180 (2011).

    Article  Google Scholar 

  • 76.

    Gadagkar, S. R., Rosenberg, M. S. & Kumar, S. Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree. J. Exp. Zool. B. Mol. Dev. Evol. 304, 64–74 (2005).

    PubMed  Article  CAS  Google Scholar 

  • 77.

    Tonini, J., Moore, A., Stern, D., Shcheglovitova, M. & Ortí, G. Concatenation and species tree methods exhibit Statistically indistinguishable accuracy under a range of simulated conditions. PLoS Curr. 7, 1–15 (2015).

    Google Scholar 

  • 78.

    Arcila, D., Petry, P. & Ortí, G. Phylogenetic relationships of the family Tarumaniidae (Characiformes) based on nuclear and mitochondrial data. Neotrop. Ichthyol. 16, 16–19 (2018).

    Article  Google Scholar 

  • 79.

    Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 80.

    Schwarz, G. Estimating the dimension of a model. Ann. Stat. 6, 461–464 (1978).

    MathSciNet  MATH  Article  Google Scholar 

  • 81.

    Keane, T. M., Creevey, C. J., Pentony, M. M., Naughton, T. J. & Mclnerney, J. O. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6, 29 (2006).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 82.

    Leigh, J. W. & Bryant, D. POPART: Full-feature software for haplotype network construction. Methods Ecol. Evol. 6, 1110–1116 (2015).

    Article  Google Scholar 

  • 83.

    Weaver, S. et al. Datamonkey 2.0: A modern web application for characterizing selective and other evolutionary processes. Mol. Biol. Evol. 35, 773–777 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 84.

    Nei, M. & Gojobori, T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418–426 (1986).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 85.

    Murrell, B. et al. Detecting individual sites subject to episodic diversifying selection. PLoS Genet. 8, e1002764 (2012).

  • 86.

    Pond, S. L. K. & Frost, S. D. W. Not so different after all: A comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 22, 1208–1222 (2005).

    CAS  Article  Google Scholar 

  • 87.

    Awadi, A. et al. Positive selection and climatic effects on MHC class II gene diversity in hares (Lepus capensis) from a steep ecological gradient. Sci. Rep. 8, 11514 (2018).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 88.

    Garrigan, D. & Hedrick, P. W. Perspective: Detecting adaptive molecular polymorphism: Lessons from the MHC. Evolution 57, 1707–1722 (2003).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 89.

    Kumar, S., Stecher, G. & Tamura, K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 90.

    Tamura, K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol. Biol. Evol. 9, 678–687 (1992).

    CAS  PubMed  Google Scholar 

  • 91.

    Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120 (1980).

    ADS  CAS  PubMed  Article  Google Scholar 

  • 92.

    Jukes, T. H. & Cantor, C. R. Evolution of protein molecules. In Mammalian Protein Metabolism, 21–132 (Elsevier, 1969). https://doi.org/10.1016/B978-1-4832-3211-9.50009-7.

  • 93.

    Bouckaert, R. et al. BEAST 2: A software platform for bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 94.

    Kearse, M. et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).

    PubMed  PubMed Central  Article  Google Scholar 

  • 95.

    Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T. & Calcott, B. PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 34, 772–773 (2016).

    Google Scholar 

  • 96.

    Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. https://doi.org/10.1093/molbev/mss075 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  • 97.

    Bouckaert, R. et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. https://doi.org/10.1371/journal.pcbi.1006650 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  • 98.

    Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using tracer 1.7. Syst. Biol. 67, 901–904 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 99.

    Rambaut, A. FigTree v1.4.3. Molecular evolution, phylogenetics and epidemiology (2016).

  • 100.

    Radimilahy, C. Mahilaka: An Archaeological Investigation of an Early Town in Northwestern Madagascar (PhD Dissertation) (Acta Universitatis Upsaliensis, Uppsala, 1998).

    Google Scholar 

  • 101.

    Walsh, M. T. Island subsistence: Hunting, trapping and the translocation of wildlife in the Western Indian Ocean. Azania Archaeol. Res. Africa 42, 83–113 (2007).

    Google Scholar 

  • 102.

    Li, J. et al. Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication. Heredity (Edinb). 105, 274–281 (2010).

    CAS  PubMed  Article  Google Scholar 

  • 103.

    Kijas, J. M. H. et al. Melanocortin receptor 1 (MC1R) mutations and coat color in pigs. Genetics 150, 1177–1185 (1998).

  • 104.

    Arauco-Shapiro, G., Schumacher, K. I., Boersma, D. & Bouzat, J. L. The role of demographic history and selection in shaping genetic diversity of the Galápagos penguin (Spheniscus mendiculus). PLoS ONE 15, 1–20 (2020).

    Article  CAS  Google Scholar 

  • 105.

    Beck, H. E. et al. Present and future Köppen-Geiger climate classification maps at 1-km resolution. Sci. Data 5, 180214 (2018).

    PubMed  PubMed Central  Article  Google Scholar 

  • 106.

    Froeschke, G. & Sommer, S. MHC Class II DRB variability and parasite load in the striped mouse (Rhabdomys pumilio) in the Southern Kalahari. Mol. Biol. Evol. 22, 1254–1259 (2005).

    CAS  PubMed  Article  Google Scholar 

  • 107.

    Froeschke, G. & Sommer, S. Insights into the complex associations between MHC Class II DRB polymorphism and multiple gastrointestinal parasite infestations in the striped mouse. PLoS ONE 7, e31820 (2012).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 108.

    Yanagida, T. et al. Genetics of the pig tapeworm in Madagascar reveal a history of human dispersal and colonization. PLoS One 9, e109002 (2014).

  • 109.

    Braae, U. C. et al. Taenia solium taeniosis/cysticercosis and the co-distribution with schistosomiasis in Africa. Parasites Vectors 8, 1–14 (2015).

    Article  Google Scholar 

  • 110.

    Macpherson, C. N. L. & Craig, P. S. Trichinella in Africa and the nelsoni affair. In Parasitic Helminths and Zoonoses in Africa (eds Macpherson, C. & Craig, P.) 83–100 (Springer, Netherlands, 1991). https://doi.org/10.1007/978-94-011-3054-7_4.

  • 111.

    Sarovich, D. S. et al. Phylogenomic analysis reveals an Asian origin for African Burkholderia pseudomallei and further supports Melioidosis Endemicity in Africa. mSphere 1, 1–12 (2016).

  • 112.

    Kaesler, E. et al. Shared evolutionary origin of major histocompatibility complex polymorphism in sympatric lemurs. Mol. Ecol. 26, 5629–5645 (2017).

    CAS  PubMed  Article  Google Scholar 

  • 113.

    Kloch, A., Babik, W., Bajer, A., Siński, E. & Radwan, J. Effects of an MHC-DRB genotype and allele number on the load of gut parasites in the bank vole Myodes glareolus. Mol. Ecol. 19(Suppl 1), 255–265 (2010).

    PubMed  Article  Google Scholar 

  • 114.

    Kusza, S. et al. Transcription specificity of the class Ib genes SLA-6, SLA-7 and SLA-8 of the swine major histocompatibility complex and comparison with class Ia genes. Anim. Genet. 42, 510–520 (2011).

    CAS  PubMed  Article  Google Scholar 

  • 115.

    Chardon, P. et al. Sequence of the swine major histocompatibility complex region containing all non-classical class I genes. Tissue Antigens 57, 55–65 (2001).

    CAS  PubMed  Article  Google Scholar 

  • 116.

    Le Gal, F. A. et al. HLA-G-mediated inhibition of antigen-specific cytotoxic T lymphocytes. Int. Immunol. 11, 1351–1356 (1999).

    PubMed  Article  Google Scholar 

  • 117.

    Fournel, S. et al. Cutting edge: Soluble HLA-G1 triggers CD95/CD95 ligand-mediated apoptosis in activated CD8+ cells by interacting with CD8. J. Immunol. 164, 6100–6104 (2000).

    CAS  PubMed  Article  Google Scholar 

  • 118.

    Hunt, J. S., Langat, D. K., McIntire, R. H. & Morales, P. J. The role of HLA-G in human pregnancy. Reprod. Biol. Endocrinol. 4, 1–8 (2006).

    Article  CAS  Google Scholar 

  • 119.

    Minami, R. et al. BAG-6 is essential for selective elimination of defective proteasomal substrates. J. Cell Biol. 190, 637–650 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 120.

    Jori, F. & Bastos, A. D. S. Role of wild suids in the epidemiology of African swine fever. EcoHealth 6, 296–310 (2009).

    PubMed  Article  PubMed Central  Google Scholar 

  • 121.

    Brown, V. R. & Bevins, S. N. A Review of African Swine fever and the potential for introduction into the United States and the possibility of subsequent establishment in feral swine and native ticks. Front. Vet. Sci. 5, 1–18 (2018).

    ADS  Article  Google Scholar 

  • 122.

    Fowler, M. E. Husbandry and diseases of captive wild swine and peccaries. Rev. Sci. Tech. 15, 141–154 (1996).

    CAS  PubMed  Article  PubMed Central  Google Scholar 


  • Source: Ecology - nature.com

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