Major Histocompatibility Complex (MHC) class II sequence polymorphism in long-finned pilot whale (Globicephala melas) from the North Atlantic

References

• Abollo E, Lopez A, Gestal C, Benavente P, Pascual S. 1998. Macroparasites in cetaceans stranded on the northwestern Spanish Atlantic coast. Diseases of Aquatic Organisms 32:227–31. doi:10.3354/dao032227
   PubMed Web of Science ®Google Scholar
• Arbanasic H, Đuras M, Podnar M, Gomercic T, Curkovic S, Galov A. 2014. Major histocompatibility complex class II variation in bottlenose dolphin from Adriatic Sea: inferences about the extent of balancing selection. Marine Biology 161:2407–22. doi:10.1007/s00227-014-2515-6
   Web of Science ®Google Scholar
• Babik W, Pabijan M, Radwan J. 2008. Contrasting patterns of variation in MHC loci in the Alpine newt. Molecular Ecology 17:2339–55. doi:10.1111/j.1365-294X.2008.03757.x
   PubMed Web of Science ®Google Scholar
• Baker CS, Vant MD, Dalebout ML, Lento GM, O’Brien SJ, Yuhki N. 2006. Diversity and duplication of DQB and DRB-like genes of the MHC in baleen whales (suborder: Mysticeti). Immunogenetics 58:283–96. doi:10.1007/s00251-006-0080-y
   PubMed Web of Science ®Google Scholar
• Ballard JWO, Whitlock MC. 2004. The incomplete natural history of mitochondria. Molecular Ecology 13:729–44. doi:10.1046/j.1365-294X.2003.02063.x
   PubMed Web of Science ®Google Scholar
• Ballingall KT, Rocchi MS, McKeever DJ, Wright F. 2010. Trans-species polymorphism and selection in the MHC class II DRA genes of domestic sheep. PLoS One 5(6):e11402. 10 pages. doi:10.1371/journal.pone.0011402
   Google Scholar
• Beatson EL, O’Shea S, Stone C, Shortland T. 2007. Notes on New Zealand mammals 6. Second report on the stomach contents of long-finned pilot whales, Globicephala melas. New Zealand Journal of Zoology 34:359–62. doi:10.1080/03014220709510095
   Web of Science ®Google Scholar
• Bos DH, Gopurenko D, Williams RN, DeWoody JA. 2008. Inferring population history and demography using microsatellites, mitochodrial DNA and Major Histocompatibility Complex (MHC) genes. Evolution 62:1458–68. doi:10.1111/j.1558-5646.2008.00364.x
   PubMed Web of Science ®Google Scholar
• Brown JH, Jardetzky TS, Gorga JC, Stern LJ, Urban RG, Strominger JL, et al. 1993. Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364:33–39. doi:10.1038/364033a0
   PubMed Web of Science ®Google Scholar
• Cutrera AP, Lacey EA. 2006. Major Histocompatibility Complex variation in Talas tuco-tucos: the influence of demography on selection. Journal of Mammalogy 87:706–16. doi:10.1644/05-MAMM-A-383R1.1
   Web of Science ®Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9:772. doi:10.1038/nmeth.2109
   PubMed Web of Science ®Google Scholar
• Desportes G, Mouritsen R. 1993. Preliminary results on the diet of long-finned pilot whales off the Faroe Islands. Report of International Whaling Commision (Special Issue) 14:305–24.
   Google Scholar
• Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10:564–67. doi:10.1111/j.1755-0998.2010.02847.x
   PubMed Web of Science ®Google Scholar
• Fullard KJ, Early G, Heide-Jorgensen MP, Bloch D, Rosing-Asvid A, Amos W. 2000. Population structure of long-finned pilot whales in the North Atlantic: a correlation with sea surface temperature? Molecular Ecology 9:949–58. doi:10.1046/j.1365-294x.2000.00957.x
   PubMed Web of Science ®Google Scholar
• Gannon DP, Read AJ, Craddock JE, Fristrup KM, Nicolas JR. 1997. Feeding ecology of long-finned pilot whales Globicephala melas in the western north Atlantic. Marine Ecology Progress Series 148:1–10. doi:10.3354/meps148001
   Web of Science ®Google Scholar
• Gaudieri S, Dawkins RL, Habara K, Kulski JK, Gojobori T. 2000. SNP profile within the human major histocompatibility complex reveals an extreme and interrupted level of nucleotide diversity. Genome Research 10:1579–86. doi:10.1101/gr.127200
   PubMed Web of Science ®Google Scholar
• Goudet J. 1995. FSTAT (Version 1.2): a computer program to calculate F-statistics. Journal of Heredity 86:485–86.
   Web of Science ®Google Scholar
• Hayashi K, Nishida S, Yoshida H, Goto M, Pastene LA, Koike H. 2003. Sequence variation of the DQB allele in the cetacean MHC. Mammal Study 28:89–96. doi:10.3106/mammalstudy.28.89
   Google Scholar
• Heimeier D. 2009. Comparative Diversity at the Major Histocompatibility Complex in Two Dolphin Species. PhD Thesis. University of Auckland.
   Google Scholar
• Heimeier D, Baker CS, Russell K, Duignan PJ, Hutt A, Stone GS. 2009. Confirmed expression of MHC class I and class II genes in the New Zealand endemic Hector's dolphin (Cephalorhynchus hectori). Marine Mammal Science 25: 68–90.
   Google Scholar
• Holderegger R, Kamm U, Gugerli F. 2006. Adaptive vs. neutral genetic diversity: implications for landscape genetics. Landscape Ecology 21:797–807. doi:10.1007/s10980-005-5245-9
   Web of Science ®Google Scholar
• Hughes AL, Nei M. 1989. Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proceedings of the National Academy of Sciences 86:958–62. doi:10.1073/pnas.86.3.958
   PubMed Web of Science ®Google Scholar
• Kennedy LJ, Ryvar RM, Gaskell R, Addie DD, Willoughby K, Carter SD, et al. 2002. Sequence analysis of MHC DRB alleles in domestic cats from the United Kingdom. Immunogenetics 54:348–52. doi:10.1007/s00251-002-0465-5
   PubMed Web of Science ®Google Scholar
• Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16:111–20. doi:10.1007/BF01731581
   PubMed Web of Science ®Google Scholar
• Klein J. 1980. Generation of diversity at MHC loci: Implications for T-cell receptor repertoires. In: Fougereau M, Dausset J, editors. Immunology. London: Academic Press, p 239–53.
   Google Scholar
• Klein J, Bontrop RE, Dawkins RL, Erlich HA, Gyllensten UB, Heise ER. et al. 1990. Nomenclature for the major histocompatibility complexes of different species: a proposal. Immunogenetics 31:217–19.
   PubMed Web of Science ®Google Scholar
• Kundu S, Faulkes CG. 2004. Patterns of MHC selection in African mole-rats, family Bathyergidae: the effects of sociality and habitat. Proceedings of the Royal Society of London B 271:273–78. doi:10.1098/rspb.2003.2584
   Web of Science ®Google Scholar
• Lambshead PJD, Brown CJ, Ferrero TJ, Mitchell NJ, Smith CR, Hawkins LE, et al. 2002. Latitudinal diversity patterns of deep-sea marine nematodes and organic fluxes: a test from the central equatorial Pacific. Marine Ecology Progress Series 236:129–35. doi:10.3354/meps236129
   Web of Science ®Google Scholar
• Luque JL, Poulin R. 2008. Linking ecology with parasite diversity in neotropical fishes. Journal of Fish Biology 72:189–204. doi:10.1111/j.1095-8649.2007.01695.x
   Web of Science ®Google Scholar
• McCallum HI, Kuris A, Harvell CD, Lafferty KD, Smith GW, Porter J. 2004. Does terrestrial epidemiology apply to marine systems? Trends in Ecology & Evolution 19(11):585–91. doi:10.1016/j.tree.2004.08.009
   Web of Science ®Google Scholar
• Merila J, Crnokrak P. 2001. Comparison of genetic differentiation at marker loci and quantitative traits. Journal of Evolutionary Biology 14:892–903. doi:10.1046/j.1420-9101.2001.00348.x
   Web of Science ®Google Scholar
• Monteiro SS, Méndez-Fernandez P, Piertney S, Moffat CF, Ferreira M, Vingada JV, et al. 2015a. Long-finned pilot whale population diversity and structure in Atlantic waters assessed through biogeochemical and genetic markers. Marine Ecology Progress Series 536:243–57. doi:10.3354/meps11455
   Web of Science ®Google Scholar
• Monteiro S, Ferreira M, Vingada JV, López A, Brownlow A, Méndez-Fernandez P. 2015b. Application of stable isotopes to assess the feeding ecology of long-finned pilot whale (Globicephala melas) in the Northeast Atlantic Ocean. Journal of Experimental Marine Biology and Ecology 465:56–63. doi:10.1016/j.jembe.2015.01.007
   Web of Science ®Google Scholar
• Morand S, Cribb TH, Kulbickis M, Rigby MC, Chauvet C, Dufour V, et al. 2000. Endoparasite species richness of New Caledonian butterfly fishes: host density and diet matter. Parasitology 121:65–73. doi:10.1017/S0031182099006058
   PubMed Web of Science ®Google Scholar
• Munguia-Vega A, Esquer-Garrigos Y, Rojas-Bracho L, Vazquez-Juarez R, Castro-Prieto A, Flores-Ramirez S. 2007. Genetic drift vs. natural selection in a long-term small isolated population: major histocompatibility complex class II variation in the Gulf of California endemic porpoise (Phocoena sinus). Molecular Ecology 16:4051–65. doi:10.1111/j.1365-294X.2007.03319.x
   PubMed Web of Science ®Google Scholar
• Murray BW, Malik S, White BN. 1995. Sequence variation at the Major Histocompatibility Complex locus DQB in beluga whales (Delphinapterus leucas). Molecular Biology and Evolution 12:582–93.
   PubMed Web of Science ®Google Scholar
• Neefjes J, Jongsma ML, Paul P, Bakke O. 2011. Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nature Reviews Immunology 11:823–36.
   PubMed Web of Science ®Google Scholar
• Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3:418–26.
   PubMed Web of Science ®Google Scholar
• Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. New York: Oxford University Press. 333 pages.
   Google Scholar
• Nei M, Tajima F. 1981. DNA polymorphism detectable by restriction endonucleases. Genetics 97:145–63.
   PubMed Web of Science ®Google Scholar
• Oliver MK, Piertney SB. 2012. Selection maintains MHC diversity through a natural population bottleneck. Molecular Biology and Evolution 29:1713–20. doi:10.1093/molbev/mss063
   PubMed Web of Science ®Google Scholar
• Oliver MK, Lambin X, Cornulier T, Piertney SB. 2009. Spatio-temporal variation in the strength and mode of selection acting on major histocompatibility complex diversity in water vole (Arvicola terrestris) metapopulations. Molecular Ecology 18:80–92.
   PubMed Web of Science ®Google Scholar
• Oremus M, Gales R, Dalebout ML, Funahashi N, Endo T, Kage T, et al. 2009. Worldwide mitochondrial DNA diversity and phylogeography of pilot whales (Globicephala spp.). Biological Journal of the Linnean Society 98:729–44. doi:10.1111/j.1095-8312.2009.01325.x
   Web of Science ®Google Scholar
• Oremus M, Gales R, Kettles H, Baker CS. 2013. Genetic evidence of multiple matrilines and spatial disruption of kinship bonds in mass strandings of long-finned pilot whales, Globicephala melas. Journal of Heredity 104:301–11. doi:10.1093/jhered/est007
   PubMed Web of Science ®Google Scholar
• Page RDM. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12:357–58.
   PubMedGoogle Scholar
• Piertney SB, Oliver MK. 2006. The evolutionary ecology of the major histocompatibility complex. Heredity 96(1):7–21.
   PubMed Web of Science ®Google Scholar
• Radwan J, Biedrzycka A, Babik W. 2010. Does reduced MHC diversity decrease viability of vertebrate populations? Biological Conservation 143:537–44. doi:10.1016/j.biocon.2009.07.026
   Web of Science ®Google Scholar
• Raga JA, Balbuena JA. 1993. Parasites of the long-finned pilot whale, Globicephala melas (Traill, 1809), in European waters. Report of International Whaling Commission (Special Issue) 14:391–406.
   Google Scholar
• Raymond M, Rousset F. 1995. GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. The Journal of Heredity 86:248–49.
   Web of Science ®Google Scholar
• Reid JB, Evans PGH, Northridge SP. 2003. Atlas of Cetacean Distribution in North-West European Waters. Peterborough, UK: Joint Nature Conservation Committee. 76 pages.
   Google Scholar
• Rohde K. 1978. Latitudinal differences in host-specificity of marine Monogenea and Digenea. Marine Biology 47:125–34. doi:10.1007/BF00395633
   Web of Science ®Google Scholar
• Rohde K. 1984. Zoogeography of marine parasites. Helgoländer Meeresunters 37:35–52. doi:10.1007/BF01989294
   Google Scholar
• Rohde K. 2010. Marine parasite diversity and environmental gradients. In: Morand S, Krasnov BR, editors. The Biogeography of Host–Parasite Interactions. Oxford: Oxford University Press, p 73–89.
   Google Scholar
• Rohde K, Heap M. 1998. Latitudinal differences in species and community richness and in community structure of metazoan endo- and ectoparasites of marine teleost fish. International Journal for Parasitology 28:461–74. doi:10.1016/S0020-7519(97)00209-9
   PubMed Web of Science ®Google Scholar
• Ronquist F, Teslenko M, Mark PVD, Ayres DL, Darling A, Höhna S, et al. 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61:539–42. doi:10.1093/sysbio/sys029
   PubMed Web of Science ®Google Scholar
• Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning – A Laboratory Manual, 2nd edition. New York: Cold Spring Habour Laboratory Press.
   Google Scholar
• Santos MB, Monteiro SS, Vingada JV, Ferreira M, López A, Martinez-Cedeira J, et al. 2014. Patterns and trends in the diet of long-finned pilot whales (Globicephala melas) in the northeast Atlantic. Marine Mammal Science 30:1–19. doi:10.1111/mms.12015
   Web of Science ®Google Scholar
• Slade RW. 1992. Limited MHC polymorphism in the southern elephant seal: implications for MHC evolution and marine mammal population biology. Proceedings of the Royal Society B 249:163–71. doi:10.1098/rspb.1992.0099
   PubMed Web of Science ®Google Scholar
• Spurgin LG, Richardson DS. 2010. How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proceedings of the Royal Society B 277:979–88. doi:10.1098/rspb.2009.2084
   PubMed Web of Science ®Google Scholar
• Swofford DL. 2003. PAUP*: Phylogenetic analysis using parsimony (* and other methods), version 4.0b 10. Sunderland, MA: Sinauer Associates. Computer program.
   Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30:2725–29. doi:10.1093/molbev/mst197
   PubMed Web of Science ®Google Scholar
• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24:4876–82. doi:10.1093/nar/25.24.4876
   Web of Science ®Google Scholar
• Vassilakos D, Natoli A, Dahlheim M, Hoelzel AR. 2009. Balancing and directional selection at exon-2 of the MHC DQB1 locus among populations of odontocete cetaceans. Molecular Biology and Evolution 26:681–89. doi:10.1093/molbev/msn296
   PubMed Web of Science ®Google Scholar
• Villanueva-Noriega MJ, Baker CS, Medrano-González L. 2013. Evolution of the MHC-DQB exon 2 in marine and terrestrial mammals. Immunogenetics 65:47–61. doi:10.1007/s00251-012-0647-8
   PubMed Web of Science ®Google Scholar
• Witteveen BH, Straley JM, Chenoweth E, Baker S, Barlow J, Matkin C, et al. 2011. Using movements, genetics and trophic ecology to differentiate inshore from offshore aggregations of humpback whales in the Gulf of Alaska. Endangered Species Research 14:217–25. doi:10.3354/esr00351
   Google Scholar
• Xu S, Sun P, Zhou K, Yang G. 2007. Sequence variability at three MHC loci of finless porpoises (Neophocaena phocaenoides). Immunogenetics 59:581–92. doi:10.1007/s00251-007-0223-9
   PubMed Web of Science ®Google Scholar
• Xu S, Chen B, Zhou K, Yang G. 2008. High similarity at three MHC loci between the baiji and finless porpoise: trans-species or convergent evolution? Molecular Phylogenetics and Evolution 47:36–44. doi:10.1016/j.ympev.2007.05.026
   PubMed Web of Science ®Google Scholar
• Xu SX, Ren WH, Li SZ, Wei FW, Zhou KY, Yang G. 2009. Sequence polymorphism and evolution of three cetacean MHC genes. Journal of Molecular Evolution 69:260–75. doi:10.1007/s00239-009-9272-z
   PubMed Web of Science ®Google Scholar
• Xu S, Ren W, Zhou X, Zhou K, Yang G. 2010. Sequence polymorphism and geographical variation at a positively selected MHC-DRB gene in the finless porpoise (Neophocaena phocaenoides): Implication for recent differentiation of the Yangtze finless porpoise? Journal of Molecular Evolution 71:6–22. doi:10.1007/s00239-010-9357-8
   PubMed Web of Science ®Google Scholar
• Xu S, Ju J, Zhou X, Wang L, Zhou K, Yang G. 2012. Considerable MHC diversity suggests that the functional extinction of Baiji is not related to population genetic collapse. PLoS One 7:e30423. 9 pages. doi:10.1371/journal.pone.0030423
   Google Scholar
• Yang G. 2005. Sequence variation and gene duplication at MHC DQB loci of baiji (Lipotes vexillifer), a Chinese river dolphin. Journal of Heredity 96:310–17. doi:10.1093/jhered/esi055
   PubMed Web of Science ®Google Scholar