DOI: 10.5061/dryad.p2ngf1vs1
title: Data from: out of chaos: phylogenomics of Asian Sonerileae

description: Sonerileae is a diverse Melastomataceae lineage comprising ca. 1000
 species in 44 genera, with more than 70% of genera and species distributed
 in Asia. Asian Sonerileae are taxonomically intractable with obscure
 generic circumscriptions. The backbone phylogeny of this group remains
 poorly resolved, possibly due to complexity caused by rapid species
 radiation in early and middle Miocene, which hampers further systematic
 study. Here, we used genome resequencing data to reconstruct the phylogeny
 of Asian Sonerileae. Three parallel datasets, viz. single-copy ortholog
 (SCO), genomic SNPs, and whole plastome, were assembled from genome
 resequencing data of 205 species for this purpose. Based on these
 genome-scale data, we provided the first well resolved phylogeny of Asian
 Sonerileae, with 34 major clades identified and 74% of the interclade
 relationships consistently resolved by both SCO and genomic data.
 Meanwhile, widespread phylogenetic discordance was detected among SCO gene
 trees as well as species trees reconstructed using different tree
 estimation methods (concatenation/site-based coalescent method/summary
 method) or different datasets (SCO/genomic/plastome). We explored sources
 of discordance using multiple approaches and found that the observed
 discordance in Asian Sonerileae was mainly caused by a combination of
 biased distribution of missing data, random noise from uninformative
 genes, incomplete lineage sorting, and hybridization/introgression.
 Exploration of these sources can enable us to generate hypotheses for
 future testing, which is the first step towards understanding the
 evolution of Asian Sonerileae. We also detected high level of homoplasy
 for characters traditionally used in taxonomy, which explains current
 chaotic generic delimitation. The backbone phylogeny of Asian Sonerileae
 revealed in this study offers a solid basis for future taxonomic revision
 at the generic level.
description: # Data from: out of chaos: phylogenomics of Asian Sonerileae
 [https://doi.org/10.5061/dryad.p2ngf1vs1](https://doi.org/10.5061/dryad.p2ngf1vs1) ## Description of the data and file structure \### Plastome_alignment.fasta Description: Alignment of 223 whole chloroplast genomes \### genomic_dataset.vcf Description: vcf file of genomic dataset, generated by mapping whole genome resequencing data of 223 samples to **Tigridiopalma magnifica** reference genome, further filtered based on hard filtering by GATK and LD by Plink. \### SCO_dataset.vcf Description:  vcf file of single copy ortholog dataset, generated by mapping whole genome resequencing data of 223 samples to 332 reference single copy orthologs, further filtered based on hard filtering by GATK. \### reference_sequeces_of_332_SCO.fasta Description: 332 reference single copy orthologs assembled using Mitobim, based on 332 single copy genes identified by OrthoFinder. \### supplementary_appendix.docx Description: supplementary methods and results \### supplementary_tables.docx Description: supplementary tables \### supplementary_figures.pdf Description: supplementary figures