Methodology: MCMC phylogenetic tip length

ID: 70


  • We used the supertree method to reconstruct the phylogenetic topology of Scleractinia, comprising 842 reef and 705 non-reef species. The source trees were derived from a molecular phylogeny of 474 species (based on seven mitochondrial DNA markers), 13 morphological trees and a tree based on current taxonomy. We then used BEAST 1.8 to fit the DNA sequence data onto the supertree topology using fossil node calibrations (origins of Caryophyllia to the Oxfordian, Dendrophylliidae to the Barremian, and Flabellum to the Campanian). These were each treated as a lognormal distribution with hard lower bound (age of fossil) and soft upper bound described by log mean and standard deviation of 2.0 and 0.85, respectively. We carried out 10 separate Markov chain Monte Carlo (MCMC) analyses each with 30 million generations and a sampling interval of 1000. Runs were combined following rejection of the first one-third of all posterior trees. We then calculated the terminal edge length of each species using the APE package in R.

Used for traits:

Added by: Danwei Huang

Observations using this methodology

Acanthastrea brevis

Acanthastrea echinata

Acanthastrea hemprichi

Acanthastrea ishigakiensis

Acanthastrea regularis

Acanthastrea rotundoflora

Acanthastrea subechinata

Acropora abrolhosensis

Acropora abrotanoides

Acropora aculeus

Acropora acuminata

Acropora akajimensis

Acropora anthocercis

Acropora appressa

Acropora arabensis

Acropora aspera

Acropora austera

Acropora awi

Acropora batunai

Acropora bifurcata

Acropora branchi

Acropora bushyensis

Acropora cardenae

Acropora carduus

Acropora caroliniana