Phylogeography

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Phylogeography

• Phylogenetics
• Understanding phylogenetic trees
• Major approaches to determining phylogenies
• Phylogeography

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Phylogenetics

• Study of the evolutionary relationships among
  individuals, groups, or species
• Relationships often represented as dichotomous
  branching tree
• Extremely common approach for detecting and
  displaying relationships among genotypes
• Important in evolution, systematics, and ecology
  (phylogeography)

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Evolution
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What is a phylogeny?

• Homology similarity that is the result of
  inheritance from a common ancestor

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Phylogenetic Tree Terms
A
B
C
D
E
F
G
H
I
J

ROOT
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Tree Topology
(Bacteria1,(Bacteria2,Bacteria3),(Eukaryote1,((Euk
aryote2,Eukaryote3),Eukaryote4)))
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Rooted versus Unrooted Trees
archaea
archaea
Unrooted tree
archaea
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Rooting with D as outgroup
G
F
E
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Now with C as outgroup
G
F
E
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Which of these four trees is different?
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Phenetics (distance) vs Cladistics (character
state based)
Lowe, Harris, and Ashton 2004
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Choosing Phylogenetic Trees

• MANY possible trees can be built for a given set
  of taxa
• Very computationally intensive to choose among
  these

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Choosing Phylogenetic Trees

• Many algorithms exist for searching tree space
• Local optima are problem need to traverse
  valleys to get to other peaks
• Heuristic search cut trees up systematically and
  reassemble
• Branch and bound search for optimal path through
  tree space

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Phylogeography

• The study of evolutionary relationships among
  individuals based on phylogenetic analysis of DNA
  sequences in geographic context
• Can be used to infer evolutionary history of
  populations
• Migrations
• Population subdivisions
• Bottlenecks/Founder Effects
• Can provide insights on current relationships
  among populations
• Connectedness of populations
• Effects of landscape features on gene flow

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Phylogeography

• Topology of tree provides clues about
  evolutionary and ecological history of a set of
  populations
• Dispersal creates poor correspondence between
  geography and tree topology
• Vicariance (division of populations preventing
  gene flow among subpopulations) results in neat
  mapping of geography onto haplotypes

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Example Pocket gophers (Geomys pinetis)

• Fossorial rodent that inhabits 3-state area in
  the U.S.
• RFLP for mtDNA of 87 individuals revealed 23
  haplotypes
• Parsimony network reveals geographic
  relationships among haplotypes
• Haplotypes generally confined to single
  populations
• Major east-west split in distribution revealed

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Example Brown Bears (Ursus arctos)

• Reduced to lt1 of original range in North America
• Sequence mtDNA control region of bears from
  worldwide distribution
• Notice unique haplotype F in ABC islands of
  Alaska
• Notice position of polar bear

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Brown Bear Surprise

• Subsequent study of samples from ice cores
  (36,000-43,000 years old) found all four
  haplotypes
• How do you explain the modern distribution?

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Brown Bears in North America (Ursus arctos)

• Diversity assessed based on 8 microsatellite loci
• Reduced diversity for more isolated sites
  (Kodiak, Yellowstone)

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Brown Bear Nuclear Differentiation

• Assessed differentiation based on 17 nuclear
  microsatellite loci
• Strong differentiation between Kodiak and
  Admiralty islands

Lowe, Harris, and Ashton 2004
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Brown Bear Nuclear Differentiation

• Less differentiation for nuclear than
  mitochondrial markers
• Degree of differentiation driven by distances
  between islands Admiralty much more divergent
  than Chicagof or Baranof
• Why?

Lowe, Harris, and Ashton 2004

• Also, maternal inheritance of mitochondrion
• Smaller effective population size of
  mitochondrion
• Mitochondrion is one locus selective sweeps!

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Ursus arctos in Europe

• Highly degraded populations, low genetic
  diversity
• Haplotypes reveal 3 refugia during glaciation
• Migration and admixture following deglaciation
  (suture zones in Scandinavia and central Europe)

Taberlet et al. 1998 Molecular Ecology 7453
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Human Phylogeography

• Most evidence points to origins in Africa and
  subsequent migrations

Cavalli-Sforza 2003 Nature Genetics 33266
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Human Phylogeography mtDNA

• Most ancient and diverse haplotypes in Africa
  (dots)
• Migration and admixture is evident from presence
  of African haplotypes in other clades

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Human Phylogeography X-chromosome genes

• Pyruvate dehydrogenase E1 alpha subunit sequence
• 25 polymorphic sites, 23 of which were in African
  sample
• African ?6.9, non-African ?0.57
• Using chimp sequence as outgroup, estimated that
  divergence occurred 1.9 million years ago

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Complexities to Human Phylogeography

• Some genes show evidence of Asian origin
• Sequence of X-linked ribonucleotide reductase M2
  pseudogene 4
• Suggests single origin model is too simple
  admixture and selection?

Garrigan 2007 Nature Reviews Genetics 7669
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Evidence of Admixture in Ancient Eurasians
Garrigan 2007 Nature Reviews Genetics 7669
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Evidence for Ancient Population Structure in
Nuclear but not Mitochondrial Trees
Garrigan 2007 Nature Reviews Genetics 7669
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Evidence for Ancient Population Structure in
Nuclear but not Mitochondrial Trees
Garrigan 2007 Nature Reviews Genetics 7669
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Alternative Models to Single Origin
Garrigan 2007 Nature Reviews Genetics 7669
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Human Phylogeography with SNP

• Assayed 500,000 SNP genotypes for 3,192
  Europeans
• Used Principal Components Analysis to ordinate
  samples in space
• High correspondence betweeen sample ordination
  and geographic origin of samples

• Individuals assigned to populations of origin
  with high accuracy

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Nested Clade Analysis

• Combines spatial and temporal tests of
  association
• Can be used to distinguish ongoing population
  processes from historical events

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Branco et al 2002 Evolution 56792803
Dc Clade distance (measures geographic range of
a particular clade) Dn Nested clade distance
(geographic relationship to other same level
categories) I-T average distance between
interior and tip clades within nested group
Use random permutation testing to test
significance of associations
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Templeton AR 1998 Molecular Ecology 7381-397
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Nested Clade Analysis - critique and summary
(reflections of a colleague)

• Hardly anyone believes in it anyway (ie Wayne
  Maddison is strongly against it, because it is
  too conjectural - not statistically sound)
• All you need to know is that people use it to
  make conclusions about range expansions and
  historical vicariant events, based on molecular
  data
• The method replies on this inference key, which
  ultimately tells you nothing in the end