This repository contains data and code used for phylogenetic analysis in:
Giovanni Forcina, Miguel Camacho-Sanchez, Fred. Y. Y. Tuh, Sacramento Moreno & Jennifer. A. Leonard. Markers for Genetic Change. Heliyon. Volume 7, ISSUE 1, e05583.https://doi.org/10.1016/j.heliyon.2020.e05583
The goal of the manuscript was to test a panel of genetic markers to evaluate the genetic diversity across the mammal community in two different national parks: Doñana National Park (Spain) and Kinabalu National Park (Malaysia). We further used the genetic data for phylogenetic reconstructions of the Rattini.
The phylogenetic analysis were done using complete mitochondrial genomes and a panel of nuclear markers, mainly introns:
- mitochondrial genomes: fasta files are here. The code used for annotating the mitochondrial genomes and all the analysis is here. The analysis resulted in one tree for complete mitogenomes and another one for cytochrome b.
- nuclear markers: a species tree was reconstructed from gene trees using Astral. The fasta files are here. The code is in src, and scripts are numbered by order. Intermediate files are here, and final tree with Astral is here.
In its current version the repository might not fully reproducible due to changes in relative paths between version changes.