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Topic 10: Phylogeography

� What is phylogeography?

� How does it differ from biogeography

� What are the key concepts of

phylogeography?

� Some herpetological examples

What is phylogeography?

� An offshoot of biogeography

� Originated with advent of ______________________

� A bridge between ______________ genetics and __________________

� A bridge between _________________ and _________________

� Originally looking at population interrelationships using mitochondrial DNA


� Has commonalities with biogeography

� Roles of vicariance and dispersal are important

� Interested in how ________ ____________ have shaped geographic distributions

� Focused on ___________ of divergences and events

� Ultimately goal is a ______________ approach

� Different taxa with similar distributions explained by similar phenomena

Avise 2000, Fig 1.1


� Phylogeography also has differences from biogeography

� __________________ or very closely related species studied

� Focus on population level processes

� Not reproductively isolated –__________________

� Phylogeny can be ________

� Generally uses genetic data

� Focus on mtDNA

� Haplotype networks and population genetic theories

Koblmuller et al. 2007

What are the key concepts of phylogeography?

� _______________________� Phylogeny with taxa replaced by ______________

� Can consider shifts in distribution during evolution

� Because OTUs are intraspecific, the focus is localities

Pough et al. 2004, Fig 5-22 Wiens and Penkrot 2002

Population-level phylogeny of Sceloporus

jarrovii sub-taxa

� Intraspecific focus� Gene flow

� Lots of breeding between individuals within a population

� Some interbreeding between individuals among populations

� Major implications

� A reticulate phylogeny

� Populations are not _________________

� Phylogeny can be _________________

What are the key concepts of

phylogeography?

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� ______________________

� Don’t need to force data into a dichotomous structure

� ______________ – a unique haploid genotype at a locus

� Single nucleotide polymorphism

� A haplotype network can show:

� Haplotype _____________

� Haplotype _____________

� Haplotype _____________

� Haplotype _____________

Rabemananjara et al. 2007


� Haplotype networks can be very complex!

� Numbers give number of nucleotide changes

� Colors correspond to _______________

� Keep in mind that this is intraspecific, so haplotypes tend to be quite similar


What are the key concepts

of phylogeography?

� Recent gene flow between species of Mantella cowani group



of phylogeography?

Pough et al. 2004, Fig. 5-14, 15


� _____________________� Typical pattern for populations with gene flow between them

� Less and less gene flow as the populations are ______ ______________________ ______________________

� Example: Cerberus rynchops

� MtDNA sequence divergence increases with geographic separation

� Phylogeography operates on the cusp of speciation

� The formation of __________ ________________ is a focus

� Species concepts are important

� ______________ is not instant

� __________________ Concept of species reconciles other species concepts

� Species concept vs. species criterion

� Sequential attainment of species criteria

De Queiroz 1998

Reproductive isolation

Morphologically distinct


of phylogeography?

� Phylogeography of Thecadactylus

Kronauer et al. 2005; Bergmann and Russell 2007

• No morphological synapomorphies

• ~25% cyt b divergence

• Split into:• T. rapicauda

• T. solimoensis


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� Stages of population differentiation and ultimately speciation from a population point of view

???

� When a geographic barrier divides a population:

� 2+ sub-populations

� ________________

� Multiple lineages in each

� So, what are they (A & B)??


� Lineages become extinct through time

� Subpopulations eventually become monophyletic

� _________________________________________________

??Time


1A 3A 3B2B1B 2A

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� Why mtDNA?� _______________________

� No recombination to give complex signal

� Can be biased by sexual differences (e.g. in dispersal)

� Can be biased by hybridization

� _______________________� Fast evolution� Appropriate for population-

level analyses

� _______ effective population size – faster to fixation

� Easy to amplify & sequence

De Queiroz 1998

What are the key concepts of phylogeography? Herp Phylogeography

� Eumeces fasciatus

� Longitudinal structuring of

haplotypes

� Consistent with hypothesis

of __________________

� During Pleistocene, North America experienced some glacial maxima

� Organismal distributions retreated south

� Sometimes, near the glacial maximum, little pockets of habitat

remained = refugia

Howes et al. 2006

Herp Phylogeography

� Eumeces fasciatus

� Haplotypes that radiated from these refugia are highly distinct

� Oklahoma and Wisconsin

� Deep divergences predate the Pleistocene

� Carolinas

� Lots of ___________ east of the Mississippi River

� River is a barrier to gene flow

� Poor genetic differentiation

Howes et al. 2006

Herp Phylogeography

� Ensatina eschscholtzi

(Plethodontidae)

� West coast USA, “______

__________” around

central valley, California

� Gene flow between neighboring subspecies

� How are they related?

� Where did they originate

from?

� How have they dispersed?

Vences and Wake 2007

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Herp Phylogeography

� Ensatina eschscholtzi (Plethodontidae)


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Herp Phylogeography

� Ensatina eschscholtzi(Plethodontidae)

� Patterns of genetic similarity

� Suggest _________

________________

� Circles indicate:

� Areas of secondary ____________

� ____________


Herp Phylogeography

� Comparative phylogeography

� Do we see concordant

patterns in multiple species?

� If yes:

� Strengthens hypotheses of common ______________ _________________

� That similar historical events shaped how many _____________________

� If no:

� Maybe factors unique to our species of interest


Herp Phylogeography

� Comparative phylogeography

Feldman & Spicer 2006

Charina bottae Lampropeltis zonataElgaria multicarinata

Herp Phylogeography

Leache et al. 2009; Photo © J Melli

� Phylogeography of the Phrynosoma coronatum complex

� One species, or as many as five!

� Much debated over the years

� Look at both morphological and DNA data

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Herp Phylogeography

Leache et al. 2009

� Each of the 5 hypothesized species forms a ____________

� Only one (red) is distinct from all the others with __________

Herp Phylogeography

Leache et al. 2009

� One (red) or two (orange) are distinct in head shape

� Two (red & orange) are distinct climatically

Herp Phylogeography

Leache et al. 2009

� Three valid species?

� P. blainvillii (blue, green, yellow)

� P. cerroense (orange)

� P. coronatum (red)

� But, what is wrong with doing this?

� ___________________________ ___________________________

___________________________

t10 phylogeography

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