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Transcript of Introduction of Phylogeography: trends and perspective Fang DU [email protected] Beijing Forestry...
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Introduction of Phylogeography: trends
and perspective
Fang [email protected]
Beijing Forestry University
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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
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Population genetics: foundation of phylogeography
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A brief history of Population genetics (1)
Charles Darwin(1809- 1882)
On the Origin of Species (1859)
Gregor J. Mendel (1822 – 1884)
“father of modern genetics”
Alfred Russel Wallace (1823 - 1913)
Father of Biogeography
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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
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Population geneticsThe 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 selectionMigrationRandom Genetic DriftMutationRecombinationGene flow….
Gene…/Genotype (individual)…/populations…/Species…
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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
…
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Population genetics
Microevolution
PhylogenyMacroevolution
phylogeography
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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
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Founding father:John C. Avise mtDNA
Phylogeography
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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
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Phylogeography:
1. infer the demographic history of important species
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Genetic distributionPresent
Evolutionary imprintsPast
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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)
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The Global features, Last Glacial Maximum Hewitt 2000 Nature
Godfrey M Hewitt (1940 - 2013)
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Interglacial glacial interglacial glacial interglacial
Inter glacial: Advance
Glacial: Retreat (glacial refugia)
Godfrey M Hewitt (1940 - 2013)
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Genetic consequence of postglacial colonization
Hewitt 1996
Leading range expansion by long distance dispersal Loss of alleles
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Evolutionary imprints: bottleneck
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Evolutionary imprints: founder effect
A new population is founded by a small group of colonists
Founder population
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North America
First plant examples: the Pacific Northwest Of North America: five angiosperms and one fern Soltis et al. 1997
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
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Medail & Katia Diadema J. Biogeogr 2009
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Science 2003
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QTP喜马拉雅地区
中日地区
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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
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Phylogeography 2 : understand the mechanisms of speciation
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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
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Speciation process
Nosil et al. 2009
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Speciation mode
Rundle & Nosil 2005
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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 ~
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No Contact (allopatry) Geographical/Ecological Contact (Sympatric-Parapatric; Second Contact)
Speciation with in gene flow
Smadja & Butlin MolEco 2011
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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.
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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.
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Drawback: Requiring the existence of multiple population pairs for study, and ones that differ in their geographic arrangement.
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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.
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“Isolation with migration” (IM) modelJody Hey
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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.
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Nosil 2012
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Phylogeography:
3. Identify different species
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How to distinguishspecies?-the foremost question in biology
?
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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
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Two main reasons of shared polymorphisms
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Parent B
F1 hybrid
Backcross 1 to A
Backcross 2...
Parent A
Backcross 3...
Backcross 4...
The introgression processnuclear genome♀ ♂
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Parent B
F1 hybrid
Backcross 1 to A
Backcross 2...
Parent A
Backcross 3...
Backcross 4...
The introgression processmaternally inherited genome♀ ♂
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Parent B
F1 hybrid
Backcross 1 to A
Backcross 2...
Parent A
Backcross 3...
Backcross 4...
The introgression processpaternally inherited genome♀ ♂
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Retention of ancestral polymorphism
weak shorter higherhighM 2
Species X
Coalescent timegeneticstructure
Hoelzer 1997, Wright 1943
Gene flow
strong longer LowerlowM1
Taxonomic resolution
High gene flow markers better to delimitate species
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‘no way out’ once introgression has taken placeHigh 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”.
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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
+»
mNF
eST
41
1
gene flow hinders differentiation
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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
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Wright (1955) Florin (1963)Farjon (1990)Li (1995)
Sigurgeirsson & Szmidt (1993)
Ran et al. (2006)
Du et al. unpublished
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P. koranensis
P. jezoensis
P. meyri
1
P. crassifoliaP. asperataP. retroflexa
P. obovata
P. schrenkiana
P. spinulosaP. smithiana
P. neoveitchiiP. wilsoniiP. purpureaP. likiangensisP. brachytyra
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P. crassifolia in the “holly” mountain in QTP
P. crassifolia in the Qilian Mountain
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Picea in XinJiang, Central Asia
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The only Picea species distributed
in the desert of Inner Mongolia
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strong geographic pattern little relationship with taxonomy
mtDNA: nad1 intron b/c and nad5 intron1 (1674bp)
Du et al. Mol Ecol 2009
Results GST =0.90
459 individuals from 46 populations
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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)
GST = 0.56Results
Du et al. Mol Ecol 2009
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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
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Naciri et al., 2012
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Perspectives
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Future directions
• Ecological niche models (ENM)
• Studies of natural selection
• Ecological speciation
• Next- generation technique