Fine-scale phylogeography of coastal fishes in the South China Sea: Possible roles of biological traits and geography

This dataset contains input files for a suite of phylogeographic analyses conducted on several coastal fishes in the South China Sea, results of which described in the paper "Fine-scale phylogeography of coastal fishes in the South China Sea: Possible roles of biological traits and geography", submitted to Journal of Biogeography.

Outline of each analysis is as follows:

arlequin: Estimations of genetic diversity indices and genetic differentiation using Arlequin.

BSP: Reconstruction of historical demography using a Bayesian skyline plot implemented in BEAST.

MSN: Construction of minimum spanning networks using PopART.

BMS: Testing association between genetic diversity indices and biological traits by Bayesian Model Averaging using the R package 'bms'. 

PCF: Testing association between phylogeographic patterns and bilogical traits using Phylogeographic Concordance Factors.

See readme.txt in the folder for each analysis for more detail.