title: Divergent selection and local adaptation in disjunct populations of an endangered conifer, Keteleeria davidiana var. formosana (Pinaceae).
abstract: The present study investigated the genetic diversity, population structure, F ST outliers, and extent and pattern of linkage disequilibrium in five populations of Keteleeria davidiana var. formosana, which is listed as a critically endangered species by the Council of Agriculture, Taiwan. Twelve amplified fragment length polymorphism primer pairs generated a total of 465 markers, of which 83.74% on average were polymorphic across populations, with a mean Nei's genetic diversity of 0.233 and a low level of genetic differentiation (approximately 6%) based on the total dataset. Linkage disequilibrium and HICKORY analyses suggested recent population bottlenecks and inbreeding in K. davidiana var. formosana. Both STRUCTURE and BAPS observed extensive admixture of individual genotypes among populations based on the total dataset in various clustering scenarios, which probably resulted from incomplete lineage sorting of ancestral variation rather than a high rate of recent gene flow. Our results based on outlier analysis revealed generally high levels of genetic differentiation and suggest that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, and humidity. Identification of ecologically associated outliers among environmentally disparate populations further support divergent selection and potential local adaptation.
authors.affiliation: Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.
authors.forename: Jing-Yu
authors.initials: JY
authors.lastname: Fang
authors.forename: Jeng-Der
authors.initials: JD
authors.lastname: Chung
authors.forename: Yu-Chung
authors.initials: YC
authors.lastname: Chiang
authors.forename: Chung-Te
authors.initials: CT
authors.lastname: Chang
authors.forename: Chia-Ying
authors.initials: CY
authors.lastname: Chen
authors.forename: Shih-Ying
authors.initials: SY
authors.lastname: Hwang
mesh_terms: D000222:Adaptation, Physiological; D054458:Amplified Fragment Length Polymorphism Analysis; D056727:Endangered Species; D019143:Evolution, Molecular; D014644:Genetic Variation; D023281:Genomics; D015810:Linkage Disequilibrium; D016015:Logistic Models; D028201:Pinaceae / Q000235:genetics* / Q000502:physiology*; D012641:Selection, Genetic
references.citation: Mol Ecol. 2010 Sep;19(17):3760-72
references.pmid: 20723056
references.citation: Proc Natl Acad Sci U S A. 1973 Dec;70(12):3321-3
references.pmid: 4519626
references.citation: Mol Ecol. 2010 Sep;19(17):3789-805
references.pmid: 20723060
references.citation: Mol Ecol. 2005 Jul;14(8):2611-20
references.pmid: 15969739
references.citation: Mol Ecol. 2009 May;18(9):2050-62
references.pmid: 19434814
references.citation: Mol Biol Evol. 2006 Apr;23(4):773-83
references.pmid: 16396915
references.citation: Trends Ecol Evol. 2007 Mar;22(3):140-7
references.pmid: 17113679
references.citation: Genetics. 2008 Oct;180(2):977-93
references.pmid: 18780740
references.citation: Philos Trans R Soc Lond B Biol Sci. 2012 Feb 5;367(1587):451-60
references.pmid: 22201174
references.citation: Trends Ecol Evol. 2008 Jan;23(1):38-44
references.pmid: 18006185
references.citation: Nat Genet. 1999 Dec;23(4):397-404
references.pmid: 10581024
references.citation: Nat Rev Genet. 2011 Oct 18;12(11):767-80
references.pmid: 22005986
references.citation: Nat Rev Genet. 2003 Dec;4(12):981-94
references.pmid: 14631358
references.citation: Nucleic Acids Res. 1995 Nov 11;23(21):4407-14
references.pmid: 7501463
references.citation: Evolution. 2008 Feb;62(2):316-36
references.pmid: 17999721
references.citation: PLoS One. 2008;3(12):e4010
references.pmid: 19104660
references.citation: Genetica. 2008 May;133(1):21-30
references.pmid: 17661154
references.citation: Mol Ecol. 2007 Sep;16(18):3737-58
references.pmid: 17850542
references.citation: Mol Ecol. 2002 Jul;11(7):1157-64
references.pmid: 12074723
references.citation: Evolution. 1975 Mar;29(1):1-10
references.pmid: 28563291
references.citation: Trends Genet. 2012 Jul;28(7):342-50
references.pmid: 22520730
references.citation: Mol Ecol. 2004 Apr;13(4):969-80
references.pmid: 15012769
references.citation: Genetics. 2006 Dec;174(4):2095-105
references.pmid: 17057229
references.citation: Philos Trans R Soc Lond B Biol Sci. 2012 Feb 5;367(1587):395-408
references.pmid: 22201169
references.citation: Genetics. 1969 Sep;63(1):229-38
references.pmid: 5365295
references.citation: Mol Ecol Resour. 2008 Sep;8(5):957-60
references.pmid: 21585940
references.citation: Genetics. 1985 Nov;111(3):675-89
references.pmid: 4054612
references.citation: BMC Bioinformatics. 2008 Dec 16;9:539
references.pmid: 19087322
references.citation: Genetics. 2002 Mar;160(3):1179-89
references.pmid: 11901132
references.citation: Mol Ecol. 2002 Nov;11(11):2337-47
references.pmid: 12406244
references.citation: Mol Biol Evol. 2005 Apr;22(4):1067-76
references.pmid: 15689532
references.citation: Mol Ecol. 2005 Sep;14(10):2899-914
references.pmid: 16101761
references.citation: Proc Natl Acad Sci U S A. 2004 Oct 19;101(42):15255-60
references.pmid: 15477602
references.citation: Mol Phylogenet Evol. 2004 Dec;33(3):791-801
references.pmid: 15522804
references.citation: Trends Genet. 2007 Nov;23(11):568-77
references.pmid: 17959267
references.citation: Mol Ecol. 2004 Apr;13(4):887-94
references.pmid: 15012763
references.citation: Mol Ecol. 2005 Mar;14(3):885-90
references.pmid: 15723680
references.citation: Mol Ecol. 2010 Jul;19(14):2896-907
references.pmid: 20609082
references.citation: Genetics. 2003 Jan;163(1):367-74
references.pmid: 12586722
references.citation: Genetics. 1998 Dec;150(4):1341-8
references.pmid: 9832514
references.citation: Theor Appl Genet. 1968 Jun;38(6):226-31
references.pmid: 24442307
references.citation: Mol Ecol. 2007 Sep;16(18):3955-69
references.pmid: 17850556
references.citation: Mol Ecol Resour. 2010 May;10(3):564-7
references.pmid: 21565059
references.citation: Mol Ecol. 2012 Aug;21(15):3729-38
references.pmid: 22680783
references.citation: Mol Ecol. 2011 Jan;20(2):193-205
references.pmid: 21091562
references.citation: Bioinformatics. 2004 Oct 12;20(15):2363-9
references.pmid: 15073024
references.citation: Mol Ecol. 2006 Sep;15(10):2833-43
references.pmid: 16911204
references.citation: Trends Genet. 2003 Jan;19(1):32-8
references.pmid: 12493246
references.citation: Trends Ecol Evol. 2009 Mar;24(3):145-56
references.pmid: 19185951
references.citation: Mol Biol Evol. 2005 Mar;22(3):506-19
references.pmid: 15525701
references.citation: Mol Ecol. 2009 Jun;18(12):2602-14
references.pmid: 19457184
references.citation: Mol Ecol. 1999 Jun;8(6):907-13
references.pmid: 10434412
references.citation: Am J Bot. 2011 Apr;98(4):669-79
references.pmid: 21613166
references.citation: J Evol Biol. 2010 Oct;23(10):2267-76
references.pmid: 20796133
references.citation: Genetics. 2000 Jun;155(2):945-59
references.pmid: 10835412
references.citation: Proc Natl Acad Sci U S A. 1993 May 15;90(10):4384-8
references.pmid: 8506277
references.citation: Proc Natl Acad Sci U S A. 2009 Jun 16;106 Suppl 1:9939-46
references.pmid: 19528641
references.citation: Mol Ecol. 2004 May;13(5):1143-55
references.pmid: 15078452
references.citation: Genetics. 1980 Oct;96(2):523-36
references.pmid: 17249067
references.citation: Am Nat. 2007 Aug;170(2):297-304
references.pmid: 17874380
references.citation: Mol Ecol. 2006 Oct;15(11):3469-80
references.pmid: 16968284
references.citation: Genetics. 2002 Sep;162(1):203-16
references.pmid: 12242234
references.citation: Mol Ecol Notes. 2007 Jul 1;7(4):574-578
references.pmid: 18784791
references.citation: Philos Trans R Soc Lond B Biol Sci. 2010 Jun 12;365(1547):1717-33
references.pmid: 20439277
references.citation: Annu Rev Entomol. 2001;46:441-69
references.pmid: 11112176
references.citation: Mol Ecol. 2002 Jan;11(1):139-51
references.pmid: 11903911
references.citation: Ecol Lett. 2008 Jun;11(6):624-36
references.pmid: 18384363
references.citation: Mol Ecol. 2005 Mar;14(3):671-88
references.pmid: 15723660
references.citation: Am J Bot. 2008 Oct;95(10):1262-9
references.pmid: 21632331
references.citation: Mol Ecol. 2012 Mar;21(6):1311-29
references.pmid: 22269082