PHYLOGEOGRAPHY

by Jorge Bardales Pérez & 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?

phylogeographybiogeography

ecogeography

Is the study of the historical processes thatgoverning the geographic distributions ofthe genealogy lineages of the species,especially those within and among closelyrelated species.

PHYLOGEOGRAPHY

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 taxon’s 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 PhylogeographicInference

• the statistical phylogeography

• Chamberlin’s 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 tests).

CoalescentModel

You have to look for The best model that dovetails

the observed data.Hypotesis

Test basing on explicit models

It could explain the geographical distribution

of genetic variation observed at present

Model Model

ModelModel

It bases on all the data that we have

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 toemploying and studying the mtDNA from mammalswith molecular markers, by this process is obtained:

- Haplotypes, it could be used to infer a phylogeny, orgene tree, which reflects the evolutionaryrelationships of the individuals and populationssampled. By combining the resulting gene trees withthe geographical location from which each individualwas sampled, one can elucidate the geographicaldistributions of major gene lineages (monophyleticclades) 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 phylogeneticapproach in the AustralianWet Tropics indicates thatregional patterns of speciesdistribution and diversity arelargely determined by localextinctions and subsequentrecolonizations correspondingto climatic cycles

Phylogeographic analyses ofterrestrial vertebrates on theBaja California peninsula andmarine fish on both thePacific and gulf sides of thepeninsula display geneticsignatures that suggest avicariance event affectedmultiple taxa during thePleistocene or Pliocene

Drawing an analogy fromhistorical biogeography of aspecie could test whether co-distributed taxa have congruentphylogeographic patterns ofgenetic variation, which mightbe predicted if a given area hasbut 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-modelorganisms, comparative phylogeographic studies will allow identification ofdifferent locus- specific divergent selection patterns between pairs of codistributedtaxa or taxa that co-occur along the same geographic gradient while also testingvarious 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 inter-specific 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

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, Phylogeography’s past, present, and future: 10 years after Avise, 2000, pag.

Elsevier.com, Molecular Phylogenetics and Evolution, 2010.

Avise, J.C., 2000. Phylogeography: The History and Formation of Species. HarvardUniversity Press, Cambridge.

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

Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC. 1987. Intraspecificphylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annual Reviewof Ecology and Systematics

THANK

YOU!