Presentation on theme: "Introduction of Phylogeography: trends and perspective"— Presentation transcript:
1 Introduction of Phylogeography: trends and perspective Fang DUBeijing Forestry University
2 OutlineConcept & DevelopmentThe main scientific questionsTo infer the demographic history of important speciesTo understand the mechanisms of speciationTo identify the different speciesPerspectives
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 1918Since 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 geneticsThe study of the amount and distribution of genetic variation in populations and speciesThe study of the underlying evolutionary processes that determine the patterns of genetic diversity…Natural selectionMigrationRandom Genetic DriftMutationRecombinationGene 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… speciesGene…/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:HomoplasyHorizontal gene transferSampling…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 Macroevolutionphylogeography
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
15 The Global features, Last Glacial Maximum Godfrey M Hewitt ( ) The Global features, Last Glacial MaximumHewitt 2000 Nature
16 Inter glacial: Advance Godfrey M Hewitt ( ) Inter glacial: AdvanceGlacial: Retreat (glacial refugia)Interglacial glacial interglacial glacial interglacial
17 Genetic consequence of postglacial colonization Leading range expansion by long distance dispersal Loss of allelesHewitt 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 colonistsFounder 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 NorthwestOf North America: five angiosperms and one fernSoltis 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
22 The highest values were observed in Corsica, Italy, and the Balkans, including Croatia and Romania, whereas average or below-average values werePatterns 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 SwedenScience 2003
27 understand the mechanisms of speciation Phylogeography 2：understand the mechanisms of speciationIncreasing 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 speciesAfter Darwin, recognizing that species change over time, the biological species definition (BSD) has become widely acceptedBSD: a group of a potentially interbreeding populations, with a common gene pool, which are reproductively isolated from other such groupsdifficulties with the BSD other species conceptsibling species are populations that cannot interbreed, but are morphologically indistinctBSD: some pairs of species are morphologically different, but do interbreedmany plant species form hybridssome species always reproduce asexuallyfossil species cannot be classified according to the biological species definition
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.
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.
41 How to distinguishspecies?-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 flowMayr (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
44 The introgression process nuclear genome ♀ ♂Parent AParent BF1 hybridBackcross 1 to ABackcross 2...Backcross 3...Backcross 4...
45 The introgression process maternally inherited genome ♀ ♂Parent AParent BF1 hybridBackcross 1 to ABackcross 2...Backcross 3...Backcross 4...
46 The introgression process paternally inherited genome ♀ ♂Parent AParent BF1 hybridBackcross 1 to ABackcross 2...Backcross 3...Backcross 4...
47 Retention of ancestral polymorphism Species XCoalescent timegeneticstructureHoelzer 1997, Wright 1943Gene flowstronglongerLowerlowM1highweakshorterM 2higherTaxonomic resolutionHigh gene flow markers better to delimitate species
48 IntrogressionIntrogression 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 placeHigh 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+mNFeST41gene flow hinders differentiation
50 Research questions Which marker is better for species delimitation? - evidence from the Picea asperata complexIf 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. unpublishedWright (1955)Florin (1963)Farjon (1990)Li (1995)
52 P. crassifolia P. asperata P. retroflexa P. obovata P. meyri 1 P. koranensisP. jezoensisP. meyri1P. crassifoliaP. asperataP. retroflexaP. obovataP. schrenkianaP. spinulosaP. smithianaP. neoveitchiiP. wilsoniiP. purpureaP. likiangensisP. brachytyraSpecies 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 yearP. crassifolia in the Qilian Mountain
55 The only Picea species distributed in the desert of Inner Mongolia
56 strong geographic pattern little relationship with taxonomy ResultsGST =0.90459 individuals from 46 populationsmtDNA: nad1 intron b/c and nad5 intron1 (1674bp) strong geographic pattern little relationship with taxonomyDu et al. Mol Ecol 2009
57 ResultsGST = 0.56cpDNA: trnL-F + trnS-G + ndhK-C (2051bp) divided into four groups on the basis of cpDNA variation in relation with species or species groupsDu et al. Mol Ecol 2009
58 ConclusionMore 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-specific8 of 11 conifer complex studied where mtDNA markers are not species-specificmtDNA markers are not helpful to distinguish species! ‘Better’ species delimitation with cpDNA than with mtDNA markers