high gene flow

Introduction of Phylogeography: trends
and perspective
Fang DU
[email protected]
Beijing Forestry University
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
Population genetics: foundation of phylogeography
A brief history of Population genetics (1)
Alfred Russel Wallace
Charles Darwin
Gregor J. Mendel
(1809- 1882)
(1822 – 1884)
On the Origin of Species
“father of modern genetics”
Father of Biogeography
Population genetics: reconcile Mendel with
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 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
Random Genetic Drift
Gene 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.
Horizontal gene transfer
Phylogeny tree of life
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
As a subdiscipline of biogeography, it emphasizes historical aspects
of the contemporary spatial distributions of gene lineages (1996)
John C. Avise
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)
Founding father:
John C. Avise  mtDNA
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
1. infer the demographic history of important species
Evolutionary imprints
Genetic distribution
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)
Godfrey M Hewitt
(1940 - 2013)
The Global features, Last Glacial Maximum
Hewitt 2000 Nature
Godfrey M Hewitt
(1940 - 2013)
Inter glacial: Advance
Glacial: Retreat (glacial refugia)
Genetic consequence of postglacial colonization
Leading range expansion by long distance
Loss of alleles
Hewitt 1996
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
Medail & Katia Diadema J. Biogeogr 2009
Science 2003
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
(7) 中国、日本/朝鲜由于海洋变化形成的异域成种事件
Harrision 2001
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
均为单次起源但b, c,表现为
Nosil 2012
Speciation with in gene flow
No Contact (allopatry)
Geographical/Ecological Contact (Sympatric-Parapatric; Second Contact)
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
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) model
Jody 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
3. Identify different species
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
The introgression process
nuclear genome
Parent A
Parent B
F1 hybrid
Backcross 1 to A
Backcross 2...
Backcross 3...
Backcross 4...
The introgression process
maternally inherited genome
Parent A
Parent B
F1 hybrid
Backcross 1 to A
Backcross 2...
Backcross 3...
Backcross 4...
The introgression process
paternally inherited genome
Parent A
Parent B
F1 hybrid
Backcross 1 to A
Backcross 2...
Backcross 3...
Backcross 4...
Retention of ancestral polymorphism
Species X
Gene flow
Coalescent time
Hoelzer 1997, Wright 1943
 High gene
flow markers
better to
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”.
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
gene flow hinders differentiation
Research questions
• Which marker is better for species
- evidence from the Picea asperata complex
• If introgression occurs, can we predict in
which direction?
- evidence from the Picea likiangensis and Picea purpurea
Sigurgeirsson & Szmidt
Ran et al. (2006)
Du et al. unpublished
Wright (1955)
Florin (1963)
Farjon (1990)
Li (1995)
P. obovata
P. meyri
P. schrenkiana
P. koranensis
P. crassifolia
P. asperata
P. retroflexa
P. spinulosa
P. smithiana
P. neoveitchii
P. wilsonii
P. purpurea
P. likiangensis
P. brachytyra
P. jezoensis
P. crassifolia in the “holly” mountain in
P. crassifolia in the Qilian Mountain
Picea in XinJiang, Central Asia
The only Picea species distributed
in the desert of Inner Mongolia
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
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
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
mtDNA markers are not helpful to distinguish species!
 ‘Better’ species delimitation with cpDNA than with
mtDNA markers
Naciri et al., 2012
Future directions
• Ecological niche models (ENM)
• Studies of natural selection
• Ecological speciation
• Next- generation technique

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