Data from: out of chaos: phylogenomics of Asian Sonerileae

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.