Workshop 2017-----Biogeography 2017.1.8

biography geography biogeography What is biogeography? biography geography biogeography

Methods Dispersalism Panbiogeography Parsimony analysis of endemicity Cladistic biogeography Event-based methods Phylogeography ……

Phylogeography Evolution of species biogeographic pattern Population gene pedigree pattern Comparative phylogenetic biogeography Revealing key areas of biological protection from genetic

Common patterns and causes Populations of discontinuous gene lines. Populations of continuous gene lines.

Mitochondrial DNA markers The most common molecular markers The advantage The disadvantage

RASP—a tool for historical biogeography

Introduction RASP can make historical biogeographic using phylogenies more accessible , which provides a graphical user interface for existing popular historical biogeographic software packages In RASP 3.0 , the developers improved the implementation of S-DIVA , added the DEC and BayArea models , and written a S-DEC , and two additional tools.

Description Enhanced S-DIVA method DEC and S-DEC model BayArea method Two additional tools

Enhanced S-DIVA method Dispersal Vicariance Analysis Bayesian approach to DIVA S-DIVA

DIVA? What is DIVA The advantage of DIVA The disadvantage of DIVA

The original DIVA algorithm encodes four different types of biogeographic events : dispersal , extinction , vicariance , duplication. As DIVA optimizes reconstructions across a phylogenetic tree , the algorithm follows a rule set in which an optimal distribution of an ancestral node cannot contain a unit area not occupied by any descendant .

The outcome of this rule is extinction events will never appear in dispersal-vicariance optimizations . If some user-specified ranges are excluded , a null result may occur .

DEC and S-DEC model Dispersal-Extinction-Cladogenesis The additions to DEC model in RASP allow for a more comprehensive evaluation of degree of ancestral state uncertainty in biogeographic reconstructions .

BayArea method BayArea extends the application of biogeographic models to the analysis of realistic problems that involve a large number of areas .

Two additional tools The results combine tool The group remove tool

Summary While both S-DIVA and DEC assume a model where lineages bifurcate and never multifurcate , BayArea can accept trees with polytomies directly giving the researcher more flexibility in analysis . The output of all four methods can be displayed an exported as high quality graphics that are directly comparable .

A Rough Guide to RASP Preparation Check status Analysis

Perparation Trees data set Condensed tree (A sample trees data file:”[RASP folder]\Sample\Rubiaceae\RASP\1000_trees.trees”) Condensed tree (A sample condensed tree:”[RASP folder]\Sample\Rubiaceae\RASP\condensed.tre”) Distributions file ( not required )

Check status The total number of binary trees in your trees data set. The total number of trees in your trees data set. The number of trees that will be discarded from the beginning of the trees data set. Select random trees data setto run the S-DIVA and Bayes-Lagrange.

Analysis S-DIVA( will deal with both condensed tree and trees dateset)

Analysis Bayesian Binary MCMC (BBM) Method(only condensed tree)

Results

An example of RASP Inferences of biogeographical histories within subfamily Hyacinthoideae using S-DIVA and Bayesian binary MCMC analysis implemented in RASP.

The aim of this study was to reconstruct the biogeographical history of Hyacinthoideae based on phylogenetic analyses , to find the possible ancestral range of Hyacinthoideae and to identify factors responsible for the current disjunct distribution pattern.

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