| [1] | Kirk H, Freeland JR (2011) Applications and implications of neutral versus non-neutral markers in molecular ecology. Int J Mol Sci 12: 3966–3988.
|
| [2] | Piertney SB, Oliver MK (2006) The evolutionary ecology of the major histocompatibility complex. Heredity 96: 7–21.
|
| [3] | Hughes AL, Yeager M (1998) Natural selection at major histocompatibility complex loci of vertebrates. Annu Rev Genet 32: 415–435.
|
| [4] | Radwan J, Biedrzycka A, Babik W (2010) Does reduced MHC diversity decrease viability of vertebrate populations? Biol Conserv 143: 537–544.
|
| [5] | Alcaide M, Edwards SV, Cadahia L, Negro JJ (2009) MHC class I genes of birds of prey: isolation, polymorphism and diversifying selection. Conserv Genet 10: 1349–1355.
|
| [6] | Babik W (2010) Methods for MHC genotyping in non-model vertebrates. Mol Ecol 10: 237–251.
|
| [7] | Jepson A, Banya W, Sisay-Joof F, Hassan-King M, Nunes C, et al. (1997) Quantification of the relative contribution of major histocompatibility complex (MHC) and non-MHC genes to human immune responses to foreign antigens. Infect Immun 65: 872–876.
|
| [8] | Vinkler M, Albrecht T (2009) The question waiting to be asked: Innate immunity receptors in the perspective of zoological research. Folia Zool 58: 15–28.
|
| [9] | Acevedo-Whitehouse K, Cunningham AA (2006) Is MHC enough for understanding wildlife immunogenetics? Trends Ecol Evol 21: 433–438.
|
| [10] | Turner AK, Begon M, Jackson JA, Paterson S (2012) Evidence for selection at cytokine loci in a natural population of field voles (Microtus agrestis). Mol Ecol 21: 1632–1646.
|
| [11] | Pespeni MH, Garfield DA, Manier MK, Palumbi SR (2012) Genome-wide polymorphisms show unexpected targets of natural selection. Proc R Soc Lond B Biol Sci 279: 1412–1420.
|
| [12] | Iwasaki A, Medzhitov R (2010) Regulation of adaptive immunity by the innate immune system. Science 327: 291–295.
|
| [13] | Roach JC, Glusman G, Rowen L, Kaur A, Purcell MK, et al. (2005) The evolution of vertebrate Toll-like receptors. Proc Nat Acad Sci USA 102: 9577–9582.
|
| [14] | Brownlie R, Allan B (2011) Avian toll-like receptors. Cell Tissue Res 343: 121–130.
|
| [15] | Akira S, Uematsu S, Takeuchi O (2006) Pathogen recognition and innate immunity. Cell 124: 783–801.
|
| [16] | Akira S, Takeda K, Kaisho T (2001) Toll-like receptors: Critical proteins linking innate and acquired immunity. Nat Immunol 2: 675–680.
|
| [17] | Cormican P, Lloyd AT, Downing T, Connell SJ, Bradley D, et al. (2009) The avian toll-like receptor pathway - subtle differences amidst general conformity. Dev Comp Immunol 33: 967–973.
|
| [18] | Hoshino K, Takeuchi O, Kawai T, Sanjo H, Ogawa T, et al. (1999) Cutting edge: Toll-Like receptor 4 (TLR4)-deficient mice are hyporesponsive to lipopolysaccharide: evidence for TLR4 as the Lps gene product. J Immunol 162: 3749–3752.
|
| [19] | Takeuchi O, Hoshino K, Kawai T, Sanjo H, Takada H, et al. (1999) Differential roles of TLR2 and TLR4 in recognition of Gram-negative and Gram-positive bacterial cell wall components. Immunity 11: 443–451.
|
| [20] | Uematsu S, Akira S (2008) Toll-like receptors (TLRs) and their ligands. Handb Exp Pharmacol 183: 1–20.
|
| [21] | Huang Y, Temperley N, Ren L, Smith J, Li N, et al. (2011) Molecular evolution of the vertebrate TLR1 gene family - a complex history of gene duplication, gene conversion, positive selection and co-evolution. BMC Evol Biol 11: 149.
|
| [22] | Netea MG, Van der Graaf C, Van der Meer JWM, Kullberg BJ (2004) Recognition of fungal pathogens by Toll-like receptors. Eur J Clin Microbiol 23: 672–676.
|
| [23] | Alcaide M, Edwards SV (2011) Molecular evolution of the toll-like receptor multigene family in birds. Mol Biol Evol 28: 1703–1715.
|
| [24] | Higgs R, Cormican P, Cahalane S, Allan B, Lloyd AT, et al. (2006) Induction of a novel chicken Toll-like receptor following Salmonella enterica serovar Typhimurium infection. Infect Immun 74: 1692–1698.
|
| [25] | Ramasamy KT, Verma P, Reddy MR, Murugesan S (2011) Molecular characterization of coding sequence and mRNA expression pattern of toll-like receptor 15 in Japanese quail (Coturnix japonica) and Indigenous Chicken Breeds (Aseel and Kadaknath). J Poult Sci 48: 168–175.
|
| [26] | Andersen-Nissen E, Smith KD, Bonneau R, Strong RK, Aderem A (2007) A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin. J Exp Med 204: 393–403.
|
| [27] | Schr？der NWJ, Schumann RR (2005) Single nucleotide polymorphisms of Toll-like receptors and susceptibility to infectious disease. Lancet Infect Dis 5: 156–164.
|
| [28] | Villase？or-Cardoso MI, Ortega E (2011) Polymorphisms of innate immunity receptors in infection by parasites. Parasite Immunol 33: 643–653.
|
| [29] | Miller SI, Ernst RK, Bader MW (2005) LPS, TLR4 and infectious disease diversity. Nat Rev Immunol 3: 36–46.
|
| [30] | Tschirren B, Andersson M, Scherman K, Westerdahl H, R？berg L (2011) Contrasting patterns of diversity and population differentiation at the innate immunity gene toll-like receptor 2 (TLR2) in two sympatric rodent species. Evolution 66: 720–731.
|
| [31] | Downing T, Lloyd AT, O'Farrelly C, Bradley DG (2011) The differential evolutionary dynamics of avian cytokine and TLR gene classes. J Immunol 184: 6993–7000.
|
| [32] | Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, et al. (2006) Positive natural selection in the human lineage. Science 312: 1614–1620.
|
| [33] | Ferrer-Admetlla A, Bosch E, Sikora M, Marquès-Bonet T, Ramírez-Soriano A, et al. (2008) Balancing selection is the main force shaping the evolution of innate immunity genes. J Immunol 181: 1315–1322.
|
| [34] | Takaki A, Yamazaki A, Maekawa T, Shibata H, Hirayama K, et al. (2012) Positive selection of Toll-like receptor 2 polymorphisms in two closely related old world monkey species, rhesus and Japanese macaques. Immunogenetics 64: 15–29.
|
| [35] | Tschirren B, R？berg L, Westerdahl H (2011) Signatures of selection acting on the innate immunity gene Toll-like receptor 2 (TLR2) during the evolutionary history of rodents. J Evol Biol 24: 1232–1240.
|
| [36] | Zagalska-Neubauer M, Babik W, Stuglik M, Gustafsson L, Cichon M, et al. (2010) 454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher. BMC Evol Biol 10: 395.
|
| [37] | Bollmer JL, Dunn PO, Whittingham LA, Wimpee C (2010) Extensive MHC class II B gene duplication in a Passerine, the common yellowthroat (Geothlypis trichas). J Hered 101: 448–460.
|
| [38] | Balakrishnan C, Ekblom R, Volker M, Westerdahl H, Godinez R, et al. (2010) Gene duplication and fragmentation in the zebra finch major histocompatibility complex. BMC Biol 8: 29.
|
| [39] | Babik W, Taberlet P, Ejsmond MJ, Radwan J (2009) New generation sequencers as a tool for genotyping of highly polymorphic multilocus MHC system. Mol Ecol Resour 9: 713–719.
|
| [40] | Ruan W, Wu Y, Zheng S (2012) Different genetic patterns in avian Toll-like receptor (TLR) 5 genes. Mol Biol Rep 39: 3419–3426.
|
| [41] | Fleming CA (1950) New Zealand flycatchers of the genus Petroica Swainson (Aves), Part II. Trans R Soc NZ 78: 127–160.
|
| [42] | Harper GA (2009) The native forest birds of Stewart Island/Rakiura: patterns of declines and extinctions. Notornis 56: 63–81.
|
| [43] | Jamieson IG (2011) Founder effects, inbreeding, and loss of genetic diversity in four avian reintroduction programs. Conserv Biol 25: 115–123.
|
| [44] | Boessenkool S, Taylor SS, Tepolt CK, Komdeur J, Jamieson IG (2007) Large mainland populations of South Island robins retain greater genetic diversity than offshore island refuges. Conserv Genet 8: 705–714.
|
| [45] | Taylor SS, Jamieson IG, Wallis GP (2007) Historic and contemporary levels of genetic variation in two New Zealand passerines with different histories of decline. J Evol Biol 20: 2035–2047.
|
| [46] | Townsend SM, King TM, Jamieson IG (2012) Isolation and characterisation of microsatellite markers from the South Island robin (Petroica australis). Conserv Genet Resour 4: 633–636.
|
| [47] | Stow AJ, Sunnucks P (2004) Inbreeding avoidance in Cunningham's skinks (Egernia cunninghami) in natural and fragmented habitat. Mol Ecol 13: 443–447.
|
| [48] | Rozen S, Skaletsky HJ (1998) Primer3. Available: http://www-genome.wi.mit.edu/genome_soft？ware/other/primer3.html.
|
| [49] | Altschul SF, Madden TL, Sch？ffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402.
|
| [50] | Galan M, Guivier E, Caraux G, Charbonnel N, Cosson J-F (2010) A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies. BMC Genomics 11: 296.
|
| [51] | Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978–989.
|
| [52] | Stephens M, Donnelly P (2003) A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73: 1162–1169.
|
| [53] | Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452.
|
| [54] | Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10: 564–567.
|
| [55] | McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652–654.
|
| [56] | Hedrick PW (2000) Genetics of populations. Sudbury, MA: Jones and Bartlett Publishers. 553 p.
|
| [57] | Garrigan D, Hedrick PW (2003) Perspective: detecting adaptive molecular polymorphism: lessons from the MHC. Evolution 57: 1707–1722.
|
| [58] | Thompson JD, Higgins DG, Gibson TJ (1994) 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.
|
| [59] | Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739.
|
| [60] | Nielsen R (2005) Molecular signatures of natural selection. Annu Rev Genet 39: 197–218.
|
| [61] | Graur D, Li WH (2000) Fundamentals of molecular evolution. Sunderland: Sinauer Associates.
|
| [62] | Sauna ZE, Kimchi-Sarfaty C (2011) Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet 12: 683–691.
|
| [63] | Smyth RP, Schlub TE, Grimm A, Venturi V, Chopra A, et al. (2010) Reducing chimera formation during PCR amplification to ensure accurate genotyping. Gene 469: 45–51.
|
| [64] | Laws RJ, Jamieson IG (2010) Is lack of evidence of inbreeding depression in a threatened New Zealand robin indicative of reduced genetic load? Anim Cons 14: 47–55.
|
| [65] | Palermo S, Capra E, Torremorell M, Dolzan M, Davoli R, et al. (2009) Toll-like receptor 4 genetic diversity among pig populations. Anim Genet 40: 289–299.
|
| [66] | Bergman IM, Edman K, Ekdahl KN, Rosengren KJ, Edfors I (2012) Extensive polymorphism in the porcine Toll-like receptor 10 gene. Int J Immunol 39: 68–76.
|
| [67] | Wlasiuk G, Nachman MW (2010) Adaptation and constraint at Toll-like receptors in primates. Mol Biol Evol 27: 2172–2186.
|
| [68] | Sutton JT, Nakagawa S, Robertson BC, Jamieson IG (2011) Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes. Mol Ecol 20: 4408–4420.
|
| [69] | Bonneaud C, Balenger SL, Zhang J, Edwards SV, Hill GE (2012) Innate immunity and the evolution of resistance to an emerging infectious disease in a wild bird. Mol Ecol 21: 2628–2639.
|
| [70] | Volmer C, Soubies SM, Grenier B, Guerin JL, Volmer R (2011) Immune response in the duck intestine following infection with low-pathogenic avian influenza viruses or stimulation with a Toll-like receptor 7 agonist administered orally. J Gen Virol 92: 534–543.
|
| [71] | Moresco EMY, LaVine D, Beutler B (2011) Toll-like receptors. Curr Biol 21: R488–R493.
|
| [72] | Barker FK, Cibois A, Schikler P, Feinstein J, Cracraft J (2004) Phylogeny and diversification of the largest avian radiation. Proc Nat Acad Sci USA 101: 11040–11045.
|
