Introduction of Phylogeography : trends and perspective

1. Introduction of Phylogeography: trends and perspective Fang DU dufang325@gmail.com 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) Gregor J. Mendel (1822 – 1884) “father of modern genetics” Charles Darwin (1809- 1882) On the Origin of Species (1859) Alfred RusselWallace (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. Populationgenetics 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 Mutation Recombination 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. Limitations: Homoplasy Horizontal gene transfer Sampling … Phylogeny tree of life

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, itemphasizes 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. Phylogeography Founding father: John C. Avise  mtDNA

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. ” ---- BeheregarayMolEco 2008

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

13. Evolutionary imprints Past Genetic distribution Present

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(110 -12ky)

15. Godfrey M Hewitt (1940 - 2013)  The Global features, Last Glacial Maximum Hewitt 2000 Nature

16. Godfrey M Hewitt (1940 - 2013)  Inter glacial: Advance Glacial: Retreat (glacial refugia) Interglacial glacial interglacial glacial interglacial

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

18. Evolutionary imprints: bottleneck

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

20. 阿拉斯加未被冰覆盖的区域 North America 夏洛特皇后群岛 First plant examples: the Pacific Northwest Of North America: five angiosperms and one fern Soltis et al. 1997 温哥华岛 中北部爱达荷州

21. Medail & Katia DiademaJ. Biogeogr2009

22. Science 2003

24. QTP 中日地区 喜马拉雅地区

25. 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 Present LGM Harrision 2001

27. Phylogeography2： 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 均为单次起源但b, c,表现为 多次起源，假象~ Nosil 2012

32. Speciation with in gene flow No Contact (allopatry) Geographical/Ecological Contact (Sympatric-Parapatric; Second Contact) Smadja & ButlinMolEco 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. The introgression processnuclear genome ♀ ♂ Parent A Parent B F1 hybrid Backcross 1 to A Backcross 2... Backcross 3... Backcross 4...

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

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

47. Species X strong longer low Lower M1 Gene flow geneticstructure Coalescent time Hoelzer 1997, Wright 1943 Retention of ancestral polymorphism high weak shorter higher M 2 Taxonomic resolution • High gene flow markers better to delimitate species

48. Introgression Introgression more frequent for low gene flow markers than for high gene flow markersIntrogression more likely from local species to the invading one • ‘no way out’ once introgression has taken place • High gene flow markers better to delimitate species “…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. 1 » F ST + 1 4 N m e gene flowhinders differentiation 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

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