New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict

Heredity

Volumn 104, Issue 1, 2010, Pages 3-14

  Chen, J ^a   Kallman T ^a   Gyllenstrand, N ^a,b   Lascoux, M ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA;

ALLOZYME; GENE FLOW; GENETIC VARIATION; HETEROZYGOSITY; PHYLOGENETICS; PHYLOGEOGRAPHY; POLYMORPHISM; POPULATION SIZE; SPECIATION (BIOLOGY); SYMPATRY;

ARTICLE; ASIA; BIOLOGICAL MODEL; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; EUROPE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; GROWTH, DEVELOPMENT AND AGING; NORTH AMERICA; PHYLOGENY; POPULATION DENSITY; SPECIES DIFFERENTIATION; SPRUCE; TIME;

ASIA; DNA, PLANT; EUROPE; GENETIC SPECIATION; GENETIC VARIATION; GEOGRAPHY; MODELS, GENETIC; NORTH AMERICA; PHYLOGENY; PICEA; POLYMORPHISM, GENETIC; POPULATION DENSITY; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

ABIES; PICEA; PICEA MARIANA;

EID: 73349130751     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2009.88     Document Type: Article

References (39)

1. Bazin E, Glémin S, Galtier N (2006). Population size does not influence mitochondrial genetic diversity in animals. Science 312: 570-572.
2. Becquet C (2007). Population genetic approaches to the study of speciation. PhD thesis, Department of Human Genetics, University of Chicago.
3. Becquet C, Przeworski M (2007). A new approach to estimate parameters of speciation models with application to apes. Genome Res 17: 1505-1519.
4. Bouillé M, Bousquet J (2005). Trans-species shared polymorphisms at orthologous nuclear gene loci among distant species in the conifer Picea (Pinaceae): Implications for the long-term maintenance of genetic diversity in trees. Am J Bot 92: 63-73.
5. De Vernal A, Hillaire-Marcel C (2008). Natural variability of Greenland climate, vegetation, and ice volume during the past million years. Science 320: 1622-1625.
6. Ewing B, Green P (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194. (Pubitemid 28177230)
7. Ewing B, Hillier L, Wendl MC, Green P (1998). Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185. (Pubitemid 28177229)
8. Haddrill P, Thornton KR, Charlesworth B, Andolfatto P (2005). Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res 15: 790-799.
9. Heuertz M, De Paoli E, Källman T, Larsson H, Jurman I, Morgante M et al. (2006). Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway Spruce [Picea abies (L.) Karst]. Genetics 174: 2095-2105.
10. Hey J, Nielsen R (2004). Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167: 747-760.
11. Hudson RR, Coyne JA (2002). Mathematical consequences of the genealogical species concept. Evolution 56: 1557-1565.
12. Gordon D, Abajian C, Green P (1998). Consed: A graphical tool for sequence finishing. Genome Res 8: 195-202.
13. Ingvarsson PK (2008). Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. Genetics 180: 329-340.
14. Innan H, Kim Y (2008). Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations. Genetics 179: 1713-1719.
15. Lagercrantz U, Ryman N (1990). Genetic structure of Norway spruce (Picea abies): Concordance of morphological and allozymic variation. Evolution 44: 38-53.
16. Ledig FT, Hodgskiss P, Johnson D (2005). Genetic diversity, genetic structure, and mating system of Brewer spruce (Pinaceae), a relict of the Arcto-Tertiary forest. Am J Bot 92: 1975-1986.
17. Ledig FT, Jacob-Cervantes V, Hodgkiss PD, Equiluz-Piedra T (1997). Recent evolution and divergence among populations of a rare Mexican endemic, Chihuahua spruce, following Holocene climatic warming. Evolution 51: 1815-1827.
18. Liu L, Pearl DK (2007). Species trees from gene tree: Reconstructing Bayesian posterior distribution of a species phylogeny using estimated gene tree distributions. Syst Biol 56: 504-514.
19. Major JE, Mosseler A, Johnsen KH, Rajora BP, Barci DC, Kim KH et al. (2005). Reproductive barriers and hybridity in two spruces, Picea rubens, Picea mariana, sympatric in eastern North America. Can J Bot 83: 163-175.
20. McVean G, Awadalla P, Fearnhead P (2002). A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
21. Mikkola L (1969). Observations on interspecific sterility in Picea. Ann Bot Fennici 6: 285-339.
22. Nielsen R, Wakeley J (2001). Distinguishing migration from isolation: A Markov chain Monte Carlo approach. Genetics 158: 885-896.
23. Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D (2006). Genetic evidence for complex speciation of humans and chimpanzee. Nature 441: 1103-1108.
24. Perron M, Bousquet J (1997). Natural hybridization between black spruce and red spruce. Mol Ecol 6: 725-734.
25. Perron M, Perry DJ, Andalo C, Bousquet J (2000). Evidence from sequence-tagged-site markers of a recent progenitorderivative species pair in conifers. Proc Natl Acad Sci USA 97: 11331-11336.
26. Pyhäjärvi T (2008). Roles of demography and natural selection in molecular evolution of trees, focus on Pinus sylvestris. PhD thesis, University of Oulu, Finland.
27. Pyhäjärvi T, García-Gil MR, Knürr T, Mikkonen M, Wachowiak W, Savolainen O (2007). Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics 177: 1713-1724.
28. Rajora O, Dancik BP (2000). Population genetic variation, structure, and evolution in Engelmann spruce, white spruce, and their natural hybrid complex in Alberta. Can J Bot 78: 768-780.
29. Ran JH, Wei XX, Wang XQ (2006). Molecular phylogeny and biogeography of Picea (Pinaceae): Implications for phylogeographical studies using cytoplasmic haplotypes. Mol Phylogenet Evol 41: 405-419.
30. Ronquist F, Huelsenbeck JP (2003). MRBAYES: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
31. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
32. Schierup MH, Hein J (2000). Consequences of recombination on traditional phylogenetic analysis. Genetics 156: 879-891.
33. Slotte T, Huang H, Lascoux M, Ceplitis A (2008). Polyploid speciation did not confer instant reproductive isolation in Capsella (Brassicaceae). Mol Biol Evol 25: 1472-1481.
34. Thornton K (2003). Libsequence: A C++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.
35. Tollefsrud MM, Kissling R, Gugerli F, Johnsen O, Skr-ppa T, Cheddadi R et al. (2008). Genetic consequences of glacial survival and postglacial colonization in Norway spruce: Combined analysis of mitochondrial DNA and fossil pollen. Mol Ecol 17: 4134-4150.
36. Wakeley J (2008). Coalescent theory - An introduction. Roberts and Company Publishers.
37. Wakeley J, Hey J (1997). Estimating ancestral population parameters. Genetics 145: 847-855.
38. Wright SJ, Charlesworth B (2004). The HKA test revisited: A maximum likelihood ratio test of the standard neutral model. Genetics 168: 1071-1076.
39. Zhai W, Nielsen R, Slatkin M (2009). An investigation of the statistical power of neutrality tests based on comparative and population genetic data. Mol Biol Evol 26: 273-283.