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Introduction of Phylogeography: trends and perspective

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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)
Darwin‘s Origin of Species, published in 1859, propounded 2 main theses: 1st, modern species were descended from common ancestors; 2, the process of natural selection was the major mechanism of evolutionary change. 在达尔文时代没有遗传的概念,因此困惑达尔文及达尔文反对者的主要问题是:受自然选择作用的个体必须具备种内多样性,若多样性一致则选择不能发生;但是达尔文的反对者认为在自然选择作用下有限的变异会很快消失,这种现象与现实不符合,现实上的进化事件,正如达尔文所述需要连续的变异在很多代发生作用。 孟德尔的主要贡献:豌豆杂交试验 ( ):发现有一些物质(注意,彼时还没有基因的概念)可以从亲本传递到子代,有一些物质控制的性状可在子代中观察到(显性基因),有一些则观察不到 (隐性基因)。但是这一发现一只被埋没(文章在之后的30年仅被引用3次!)。原因是:1)人们不接受个体中某一性状的遗传,人们认为遗传是一个整体事件,不能分开;2)即使在孟德尔的工作在1900年重新发现后,科学家还是不能接受他的观点,因为当时的遗传学家主要是一些生物统计学家,他们关注的主要是一些连续的性状,而不是孟德尔做豌豆实验的分离性状。 Gregor J. Mendel  (1822 – 1884) “father of modern genetics” Charles Darwin ( ) On the Origin of Species (1859) 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 Since the Darwinian process was widely believed to work best on continuously varying traits, showing that the distribution of such traits was compatible with Mendelism was an important step towards reconciling Darwin with Mendel. 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 Mutation Recombination Gene flow…. “The study of the amount and distribution of genetic variation in populations and species, and the dynamics of the underlying genetic processes that determine the extant patterns of diversity (Yeh, 2000).” Essentially, (i) determining how much and what kind of diversity present in a population; (ii) explaining the origin of the variation, organization and maintenance (both for organismal and economic significance) Hierarchy: Genes… genotypes (individuals)… populations… species 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 Homoplasy: Certain characters are more likely to evolve convergently than others; logically, such characters should be given less weight in the reconstruction of a tree. 避免方法:给不同的突变方式不同的权重:maximum likelihood and Bayesian 算法 Horizontal gene transfer:organisms can inherit genes in two ways: vertical gene transfer and horizontal gene transfer. Vertical gene transfer is the passage of genes from parent to offspring, and horizontal (also called lateral) gene transfer occurs when genes jump between unrelated organisms 避免方法:The only way to determine which genes have been acquired vertically and which horizontally is to parsimoniously assume that the largest set of genes that have been inherited together have been inherited vertically; this requires analyzing a large number of genes. ….指例如 missing data等 Phylogeny tree of life

8 phylogeography 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 Phylogeography Founding father: John C. Avise  mtDNA
To narrow things further, I will mostly describe what might be the contributions of genetics or if you prefer of molecular ecologists in this field. Molecular ecologists are those guys who are equally keen on using a binocular and a pipetman. A prototype would be for instance John Avise sampling material and reading a gel here… 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. ” Beheregaray MolEco 2008

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

13 Evolutionary imprints
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) 三次大规模的大冰期:震旦、晚古生代、第四纪 ;最严重次:60万年!

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

16 Inter glacial: Advance
Godfrey M Hewitt  ( )  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
the effective population size, Ne, sharply decreases to a small percentage of the original. The immediate effect of a population bottleneck is to decrease genetic diversity, promoting the effects of stochasticgenetic drift over natural selection. In the long-term, repeated population bottlenecks can severely decrease population fitness

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
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 4个可能的避难所:1)中北部爱达荷州 2)温哥华岛 3)夏洛特皇后群岛 4)阿拉斯加未被冰覆盖的区域 中北部爱达荷州

21 Medail & Katia Diadema J. Biogeogr 2009

22 The highest values were observed in Corsica, Italy, and the Balkans, including Croatia and Romania, whereas average or below-average values were Patterns of diversity across forests were very different; both mean number of haplotypes (Fig. 2) and gene diversity (table S2) were higher in Central France, southern Germany, and Slovakia, whereas the southern- and northernmost populations generally had low or average diversity, with the exception of southwestern Sweden Science 2003


24 3大植物区系:QTP;喜马拉雅地区;中日地区

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 understand the mechanisms of speciation
Phylogeography 2: understand the mechanisms of speciation Increasing climate change driven many range changes. It was necessary to move, adapt or go extinct, and present lineages had the ability and luck to survive such shifts. Each time they would colonize new territory, face new environments and meet new neighbors. These challenges would cause genomes to diverge, both through selection and chance, and ultimately speciate

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 sibling species are populations that cannot interbreed, but are morphologically indistinct BSD: some pairs of species are morphologically different, but do interbreed many plant species form hybrids some species always reproduce asexually fossil species cannot be classified according to the biological species definition

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 & 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. Week genetic differentiation between taxa could be caused by shared ancestral polymorphisms, gene flow, recent divergence or a combination of these. e.g. low level of gene flow occurred after strong reproductive isolation.

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

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

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

47 Retention of ancestral polymorphism
Species X Coalescent time geneticstructure Hoelzer 1997, Wright 1943 Gene flow strong longer Lower low M1 high weak shorter M 2 higher 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 markers Introgression 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 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 + m N F e ST 4 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 Sigurgeirsson & Szmidt (1993)
Ran et al. (2006) Du et al. unpublished Wright (1955) Florin (1963) Farjon (1990) Li (1995)

52 P. crassifolia P. asperata P. retroflexa P. obovata P. meyri 1
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 Species underlined: not very visible. Use heavy font?

53 P. crassifolia in the “holly” mountain in QTP
P. crassifolia which mainly distributed in the edge and inner of QTP is a endemic conifer in China, the highest population we found is 3510m! The clourful flag on the mountain in left top picture is “holy flags” of nomadic Tibeten, they printed the Classic religion characters on the flag to have good wishes, this mountain with “holly flags” is usually called “holly mountain”, that is why usually at this region the trees is protected well. The picture in the right down is in Qilian mountain, which was covered by snow all over the year 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
Results GST =0.90 459 individuals from 46 populations mtDNA: nad1 intron b/c and nad5 intron1 (1674bp)  strong geographic pattern  little relationship with taxonomy Du et al. Mol Ecol 2009

57 Results GST = 0.56 cpDNA: trnL-F + trnS-G + ndhK-C (2051bp)  divided into four groups on the basis of cpDNA variation in relation with species or species groups 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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