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Introduction of Phylogeography: trends and perspective Fang DU Beijing Forestry University.

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Presentation on theme: "Introduction of Phylogeography: trends and perspective Fang DU Beijing Forestry University."— Presentation transcript:

1 Introduction of Phylogeography: trends and perspective Fang DU Beijing Forestry University

2 Outline Concept & Development The main scientific questions  To infer the demographic history of important species  To understand the mechanisms of speciation  To identify the different species Perspectives

3 Population genetics: foundation of phylogeography

4 A brief history of Population genetics (1) Charles Darwin ( ) On the Origin of Species (1859) Gregor J. Mendel (1822 – 1884) “father of modern genetics” Alfred Russel Wallace ( 1823 - 1913 ) Father of Biogeography

5 Population genetics: reconcile Mendel with Darwin In the 1920s to 1930s: R.A. Fisher, J.B.S. Haldane and Sewall Wright “if a given continuous trait, e.g. height, was affected by a large number of Mendelian factors, each of which made a small difference to the trait, then the trait would show an approximately normal distribution in a population. “ ---- R.A. Fisher 1918 R.A. Fisher

6 Population genetics The study of the amount and distribution of genetic variation in populations and species The study of the underlying evolutionary processes that determine the patterns of genetic diversity… Natural selection Migration Random Genetic Drift MutationRecombination Gene flow…. Gene…/Genotype (individual)…/populations…/Species…

7 Phylogeny : is the study of evolutionary relationships among groups of organisms (e.g. species, populations), which are discovered through molecular sequencing data and morphological data matrices. Phylogeny tree of life Limitations: Homoplasy Horizontal gene transfer Sampling…

8 Population genetics Microevolution Phylogeny Macroevolution phylogeography

9 Phylogeography: recent emergence and rapid development Phylogeography is a field of study concerned with the principles and processes governing the geographical distributions of genealogical lineages, especially those at the intraspecific level (1987) As a subdiscipline of biogeography, it emphasizes historical aspects of the contemporary spatial distributions of gene lineages (1996) Phylogeographic perspectives have consistently challenged conventional genetic and evolutionary paradigms, and they have forged empirical and conceptual bridges between the formerly separate disciplines of population genetics (microevolutionary analysis) and phylogenetic biology (in macroevolution). (2009) John C. Avise

10 Founding father: John C. Avise  mtDNA Phylogeography

11 Twenty years of Phylogeography: “Phylogeography has experienced explosive growth in recent years fulled by developments in DNA technology, theory and statistical analysis”…. “the intellectual maturation of the field will eventually depend not only on these recent developments, but also on syntheses of comparative information across different regions of the globe. ” ---- Beheregaray MolEco 2008

12 Phylogeography: 1. infer the demographic history of important species

13 Genetic distribution Present Evolutionary imprints Past

14 Evolutionary imprints: glacial refugia Three biggest glacial: 震旦、晚古生代、第四纪 Last glacial period: Pleistocene 更新世 后期 ( ky)

15 The Global features, Last Glacial Maximum Hewitt 2000 Nature Godfrey M Hewitt ( )

16 Interglacial glacial interglacial glacial interglacial Inter glacial: Advance Glacial: Retreat (glacial refugia) Godfrey M Hewitt ( )

17 Genetic consequence of postglacial colonization Hewitt 1996 Leading range expansion by long distance dispersal Loss of alleles

18 Evolutionary imprints: bottleneck

19 Evolutionary imprints: founder effect A new population is founded by a small group of colonists Founder population

20 North America First plant examples: the Pacific Northwest Of North America: five angiosperms and one fern Soltis et al 中北部爱达荷州 温哥华岛 夏洛特皇后群岛 阿拉斯加未被冰覆盖的区域

21 Medail & Katia Diadema J. Biogeogr 2009

22 Science 2003


24 QTP 喜马拉雅地区 中日地区

25 Present LGM Harrision 2001 Main scenarios: (1)QTP 东南部避难所冰期后回迁 (2) 中国西南部群体隔离和特有种物种形成 (3) 中国亚热带地区由于长期隔离造成的多个避难所 (4) QTP 台面在盛冰期也存在一些高山草本及森林树种 (5) 亚热带地区由于长期隔离造成的多个硬叶树种避难所 (6) 中国北方存在落叶林 “ 隐形避难所 ” (7) 中国、日本 / 朝鲜由于海洋变化形成的异域成种事件


27 Phylogeography 2 : understand the mechanisms of speciation

28 Species: A brief history Prior to Darwin, each species was regarded as a fixed entity, morphologically distinct from other species After Darwin, recognizing that species change over time, the biological species definition (BSD) has become widely accepted BSD: a group of a potentially interbreeding populations, with a common gene pool, which are reproductively isolated from other such groups difficulties with the BSD other species concept

29 Speciation process Nosil et al. 2009

30 Speciation mode Rundle & Nosil 2005

31 Limitation and caveats for testing parallel speciation Nosil 2012 均为单次起源但 b, c, 表现为 多次起源,假象 ~

32 No Contact (allopatry) Geographical/Ecological Contact (Sympatric-Parapatric; Second Contact) Speciation with in gene flow Smadja & Butlin MolEco 2011

33 Detecting divergence in the face of gene flow Difficult to infer confidently that gene flow occurred at any point in the speciation process. Difficult to infer timing of gene flow during divergence.

34 Detecting divergence in the face of gene flow: comparative geographic approaches Premise: Shared ancestral polymorphism affects both allopatric and sym/para-patric populations, whereas gene flow affects only sympatric populations. Thus, genetic divergence should be consistently greater for comparisons between allopatric populations.

35 Drawback: Requiring the existence of multiple population pairs for study, and ones that differ in their geographic arrangement.

36 Detecting divergence in the face of gene flow: coalescent approaches Premise: Gene flow varies widely across the genomic regions. In contrast, genetic drift might act more uniformly across the genome. Thus, a history of gene flow is generally indicated if some loci show little divergence and others show strong divergence, such that variation among loci is greater than expected under a model with no gene flow and divergence solely by drift.

37 “Isolation with migration” (IM) model Jody Hey

38 Detecting divergence in the face of gene flow: genomic approaches Premise: Using population genomic methods examining thousands of loci can infer “outliner loci” whose genetic differentiation statistically exceeds background neutral expectations. Thus, such outliner loci differentiate between populations more strongly, and introgress less freely, than neutrally evolving regions, and are putatively affected by divergent selection.

39 Nosil 2012

40 Phylogeography: 3. Identify different species

41 How to distinguish species?-the foremost question in biology ?

42 Gene flow & species definition Mayr (1942): species are 'groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups’  low interspecific gene flow Mayr (1963) '[t]he steady and high genetic input caused by gene flow is the main factor responsible for genetic cohesion among the populations of a species’  high intraspecific gene flow

43 Two main reasons of shared polymorphisms

44 Parent B F1 hybrid Backcross 1 to A Backcross 2... Parent A Backcross 3... Backcross 4... The introgression process nuclear genome ♀ ♂

45 Parent B F1 hybrid Backcross 1 to A Backcross 2... Parent A Backcross 3... Backcross 4... The introgression process maternally inherited genome ♀ ♂

46 Parent B F1 hybrid Backcross 1 to A Backcross 2... Parent A Backcross 3... Backcross 4... The introgression process paternally inherited genome ♀ ♂

47 Retention of ancestral polymorphism weakshorter higher high M 2 Species X Coalescent timegeneticstructure Hoelzer 1997, Wright 1943 Gene flow strong longer Lowerlow M1 Taxonomic resolution  High gene flow markers better to delimitate species

48  ‘no way out’ once introgression has taken place  High gene flow markers better to delimitate species Introgression Introgression more frequent for low gene flow markers than for high gene flow markers Introgression more likely from local species to the invading one “…we detect gene flow from Neandertals into modern humans but not reciprocal gene flow from modern humans into Neandertals gene flow from Neandertals into modern humans but not reciprocal gene flow from modern humans into Neandertals”.

49 In conifers, mtDNA is maternally inherited and transmitted by seeds only  low gene flow In conifers, cpDNA is paternally inherited and transmitted by pollen  high gene flow   mN F e ST 41 1 gene flow hinders differentiation

50 Research questions Which marker is better for species delimitation? - evidence from the Picea asperata complex If introgression occurs, can we predict in which direction? - evidence from the Picea likiangensis and Picea purpurea

51 Wright (1955) Florin (1963) Farjon (1990) Li (1995) Sigurgeirsson & Szmidt (1993) Ran et al. (2006) Du et al. unpublished

52 P. koranensis P. jezoensis P. meyri 1 P. crassifolia P. asperata P. retroflexa P. obovata P. schrenkiana P. spinulosa P. smithiana P. neoveitchii P. wilsonii P. purpurea P. likiangensis P. brachytyra

53 P. crassifolia in the “holly” mountain in QTP P. crassifolia in the Qilian Mountain

54 Picea in XinJiang, Central Asia

55 The only Picea species distributed in the desert of Inner Mongolia

56  strong geographic pattern  little relationship with taxonomy mtDNA: nad1 intron b/c and nad5 intron1 (1674bp) Du et al. Mol Ecol 2009 Results G ST = individuals from 46 populations

57  divided into four groups on the basis of cpDNA variation in relation with species or species groups cpDNA: trnL-F + trnS-G + ndhK-C (2051bp) G ST = 0.56 Results Du et al. Mol Ecol 2009

58 Conclusion More interspecific sharing for mtDNA than for cpDNA (also true in other conifers): 13 of 14 conifer complex studied where cpDNA markers are more or less species-specific 8 of 11 conifer complex studied where mtDNA markers are not species-specific  mtDNA markers are not helpful to distinguish species!  ‘Better’ species delimitation with cpDNA than with mtDNA markers

59 Naciri et al., 2012

60 Perspectives

61 Future directions Ecological niche models (ENM) Studies of natural selection Ecological speciation Next- generation technique

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