PHYLOGEOGRAPHY

by Jorge Bardales Prez & John Rojas Pino.

Introduction
Phylogeography is a young, vigorous and
integrative field of study that uses genetic data to
understand the history of populations. This field
has recently expanded into many areas of biology
and into several historical disciplines of Earth
sciences.

What is the phylogeography?

biogeography

phylogeography

ecogeography

PHYLOGEOGRAPHY
Is the study of the historical processes that
governing the geographic distributions of
the genealogy lineages of the species,
especially those within and among closely
related species.

HISTORY
-

John Avise uses the term phylogeography for first time in

1987 in his work The Mitochondrial DNA Bridge between
Population Genetics and Systematics, which explains how
the process geological, climatic and ecological conditions
influenced in the current distribution of species.

In 2000, Published his first book Phylogeography: The

History and Formation of Species , this one recounts the
genesis and ontogeny of phylogeography.

Phylogeography and Conservation:

Phylogeography can help in the prioritization
of areas of high value for conservation. Using
phylogeographic analysis is possible determine
places with a wide distribution of species and
with a high level of evolutionary significant
units of genetic patterns, places that could be
prioritized to the conservation.

Model-based Methods in
Phylogeography

Descriptive Phylogeographic Inference:

This era of Phylogeography coincided with the increased use of the polymerase chain
reaction

What types of molecular markers (genes) are the most

suitable?

Neutral Evolution
High nucleotide substitution rate
lack of recombination

Operational taxonomic units (OTUs)

Problems?

Study conclusions were often directly based on qualitative interpretations of each

taxons single locus gene genealogy such that the shape of phylogenies, the
geographic distribution of lineages, and estimated dates of gene tree branching
events, could be used directly to infer the demographic history of each taxon.

it is also a sign that the field is becoming more statistically rigorous and the
empiricists are coming to recognize that equating genealogical pattern with
demographic and evolutionary processes can lead to over interpretation when
ignoring coalescent stochasticity in the data

Model-based Statistical Phylogeographic

Inference

the statistical phylogeography

Chamberlins epistemological strategy

dovetails with the statistical
phylogeographic approach whereby
coalescent theory is used to build statistical
models for hypothesis testing under a
Bayesian and/or likelihood-based
framework.

Coalescent theory: Formal mathematical

and statistical processing for gene
genealogies within and amog related species

All genes in one generation coalesce into a

single ancestral gene

What does it mean?

Under the Bayesian/likelihood-based stratagem each competing hypotheses can

be evaluated by fitting the data to each model relative to other models, by way of
different decision theoretical methods (e.g., Bayes factors or likelihood ratio
It could explain the
tests).
geographical distribution
of genetic variation
observed at present
It bases on all the data
that we have

Hypotesis

Test basing on explicit

models

Model

Coalescent
Model

Model

Model
You have to look for The
best model that dovetails
the observed data.

Model

Comparative Phylogeographic Inference

Methods for analysis are being developed that go beyond interpreting results from
multiple single taxon analyses:

One method statistically estimates levels of topological congruence across taxa

and then assembles the genetic datasets from different taxa into a single
supertree depicting geographic linkages.

Another method that is both coalescent model-based and combines intraspecific

data sets into a single analysis is an ABC (Approximate Bayesian computation)
methods that employs a hierarchical Bayesian model.

Comparative phylogeographic ABC methods are in their infancy, yet have so far
been used to test for simultaneous divergence times across codistributed taxa in a
variety of biogeographic settings

Intraspecific Phylogeography
Or Analysis from mtDNA
At first the intraspecific phylogeography began to
employing and studying the mtDNA from mammals
with molecular markers, by this process is obtained:

- Haplotypes, it could be used to infer a phylogeny, or

gene
tree,
which
reflects
the
evolutionary
relationships of the individuals and populations
sampled. By combining the resulting gene trees with
the geographical location from which each individual
was sampled, one can elucidate the geographical
distributions of major gene lineages (monophyletic
clades) that comprise the gene tree.

Comparative Phylogeography

CP seeks to explain the

mechanisms responsible for
the phylogenetic
relationships and distribution
of different species

Some examples of CP
A comparative phylogenetic
approach in the Australian
Wet Tropics indicates that
regional patterns of species
distribution and diversity are
largely determined by local
extinctions and subsequent
recolonizations corresponding
to climatic cycles

Phylogeographic analyses of
terrestrial vertebrates on the
Baja California peninsula and
marine fish on both the
Pacific and gulf sides of the
peninsula display genetic
signatures that suggest a
vicariance event affected
multiple taxa during the
Pleistocene or Pliocene

Drawing an analogy from

historical biogeography of a
specie could test whether codistributed taxa have congruent
phylogeographic patterns of
genetic variation, which might
be predicted if a given area has
but a single history.

Future directions for integrative

comparative phylogeography
Ecological niche models: Integrating phylogeography with species range distribution
models is showing enormous promise for elucidating how isolation, speciation, and
selection are directly or indirectly linked to abiotic factors If environmental factors are
implicated in divergence and speciation, such integration can aide in species
delineation and testing models of niche conservatism and niche divergence.
Studies of natural selection: As genomic data become available for non-model
organisms, comparative phylogeographic studies will allow identification of
different locus- specific divergent selection patterns between pairs of codistributed
taxa or taxa that co-occur along the same geographic gradient while also testing
various multi-taxa demographic historical scenarios.
Integrating comparative phylogeography with studies of community assembly:
original objectives was to resolve deep-seated questions about how climate change
drives community assembly and evolution within whole biotas. Although interspecific phylogenetic data is increasingly being used to address questions of
community assembly using comparative phylogeographic data for such purposes has
so far been handicapped because such studies rarely involve more than a handful of
codistributed taxa

REFERENCES
Avise, J.C., 2000. Phylogeography: The History and Formation of Species. Harvard
University Press, Cambridge.
Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC. 1987. Intraspecific
phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annual Review
of Ecology and Systematics
M.J. Hickerson a,B.C. Carstens, J. Cavender-Bares, K.A. Crandall, C.H. Graham, J.B. Johnson, L. Rissler, P.F.
Victoriano and A.D. Yoder, Phylogeographys past, present, and future: 10 years after Avise, 2000, pag.
Elsevier.com, Molecular Phylogenetics and Evolution, 2010.
Luciano B. Beheregaray, Twenty years of phylogeography: the state of the field and the challenges for the
Southern Hemisphere, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.

http://en.wikipedia.org/wiki/Phylogeography
http://en.wikipedia.org/wiki/Biogeography
http://en.wiktionary.org/wiki/ecogeography

THANK
YOU!