Introduction of Phylogeography: trends
and perspective
Fang DU
dufang325@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)
Alfred Russel Wallace
Charles Darwin
Gregor J. Mendel
(1809- 1882)
(1822 – 1884)
On the Origin of Species
(1859)
“father of modern genetics”
(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 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….
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.
Limitations:
Homoplasy
Horizontal gene transfer
Sampling
…
Phylogeny tree of life
Population
genetics
Microevolution
phylogeography
Phylogeny
Macroevolution
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)
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)
Phylogeography
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
Phylogeography:
1. infer the demographic history of important species
Evolutionary imprints
Past
Genetic distribution
Present
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)
Interglacial
glacial
interglacial
glacial
interglacial
Genetic consequence of postglacial colonization
Leading range expansion by long distance
dispersal
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
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
中北部爱达荷州
Medail & Katia Diadema J. Biogeogr 2009
Science 2003
QTP
喜马拉雅地区
中日地区
Main scenarios:
(1)QTP 东南部避难所冰期后回迁
Present
(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
LGM
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
多次起源，假象~
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
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) 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
Phylogeography:
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
M1
low
strong
longer
Lower
M2
high
weak
shorter
higher
Gene flow
geneticstructure
Coalescent time
Hoelzer 1997, Wright 1943
Taxonomic
resolution
 High 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
‘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
FST 
1
1+4Nem
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
Sigurgeirsson & Szmidt
(1993)
Ran et al. (2006)
Du et al. unpublished
Wright (1955)
Florin (1963)
Farjon (1990)
Li (1995)
P. obovata
P. meyri
1
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
QTP
P. crassifolia in the Qilian Mountain
Picea in XinJiang, Central Asia
The only Picea species distributed
in the desert of Inner Mongolia
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
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
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