Introduction of Phylogeography: trends

and perspective

Fang DUdufang325@gmail.com

Beijing Forestry University

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

Population genetics: foundation of phylogeography

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

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

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…

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

…

Population genetics

Microevolution

PhylogenyMacroevolution

phylogeography

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

Founding father:John C. Avise mtDNA

Phylogeography

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

Phylogeography:

1. infer the demographic history of important species

Genetic distributionPresent

Evolutionary imprintsPast

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)

The Global features, Last Glacial Maximum Hewitt 2000 Nature

Godfrey M Hewitt (1940 - 2013) 

Interglacial glacial interglacial glacial interglacial

Inter glacial: Advance

Glacial: Retreat (glacial refugia)

Godfrey M Hewitt (1940 - 2013) 

Genetic consequence of postglacial colonization

Hewitt 1996

Leading range expansion by long distance dispersal Loss of alleles

Evolutionary imprints: bottleneck

Evolutionary imprints: founder effect

A new population is founded by a small group of colonists

Founder population

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

Medail & Katia Diadema J. Biogeogr 2009

Science 2003

QTP喜马拉雅地区

中日地区

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

Phylogeography 2 ： understand the mechanisms of speciation

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

Speciation process

Nosil et al. 2009

Speciation mode

Rundle & Nosil 2005

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 ~

No Contact (allopatry) Geographical/Ecological Contact (Sympatric-Parapatric; Second Contact)

Speciation with in gene flow

Smadja & Butlin MolEco 2011

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.

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.

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

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.

“Isolation with migration” (IM) modelJody Hey

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.

Nosil 2012

Phylogeography:

3. Identify different species

How to distinguishspecies?-the foremost question in biology

?

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

Two main reasons of shared polymorphisms

Parent B

F1 hybrid

Backcross 1 to A

Backcross 2...

Parent A

Backcross 3...

Backcross 4...

The introgression processnuclear genome♀ ♂

Parent B

F1 hybrid

Backcross 1 to A

Backcross 2...

Parent A

Backcross 3...

Backcross 4...

The introgression processmaternally inherited genome♀ ♂

Parent B

F1 hybrid

Backcross 1 to A

Backcross 2...

Parent A

Backcross 3...

Backcross 4...

The introgression processpaternally inherited genome♀ ♂

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

‘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”.

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

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

Wright (1955) Florin (1963)Farjon (1990)Li (1995)

Sigurgeirsson & Szmidt (1993)

Ran et al. (2006)

Du et al. unpublished

P. koranensis

P. jezoensis

P. meyri

1

P. crassifoliaP. asperataP. retroflexa

P. obovata

P. schrenkiana

P. spinulosaP. smithiana

P. neoveitchiiP. wilsoniiP. purpureaP. likiangensisP. brachytyra

P. crassifolia in the “holly” mountain in QTP

P. crassifolia in the Qilian Mountain

Picea in XinJiang, Central Asia

The only Picea species distributed

in the desert of Inner Mongolia

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

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

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

Naciri et al., 2012

Perspectives

Future directions

• Ecological niche models (ENM)

• Studies of natural selection

• Ecological speciation

• Next- generation technique