Abundant incongruence in a clade endemic to a biodiversity hotspot: Phylogenetics of the scrub mint clade (Lamiaceae)

The Scrub Mint clade(Lamiaceae) provides a unique system for investigating the evolutionary processes driving diversification in the North American Coastal Plain from both a systematic and biogeographic context. The clade comprisesDicerandra, Conradina, Piloblephis, Stachydeoma, and four species of the broadly defined genus Clinopodium(Mentheae; Lamiaceae), almost all of which are endemic to the North American Eastern Coastal Plain. Most species of this clade are threatened or endangered and restricted to sandhill or a mosaic of scrub habitats. We analyzed relationships in this clade to understand the evolution of the group and identify evolutionary mechanisms acting on the clade, with important implications for conservation. We used a target-capture method to sequence and analyze 238 nuclear loci across all species of scrub mints, reconstructed the phylogeny, and calculated gene tree concordance, gene tree estimation error, and reticulation indices for every node in the tree using ML methods. Phylogenetic networks were used to determine reticulation events. Our nuclear phylogenetic estimates were consistent with previous results, while greatly increasing the robustness of taxon sampling. The phylogeny resolved the full relationship between Dicerandra and Conradina and the less-studied members of the clade (Piloblephis, Stachydeoma, Clinopodium spp.). We found hotspots of gene tree discordance and reticulation throughout the tree, especially in perennial Dicerandra. Several instances of reticulation events were uncovered between annual and perennial Dicerandra, and within the Conradina + allies clade. Incomplete lineage sorting also likely contributed to phylogenetic discordance. These results clarify phylogenetic relationships in the clade and provide insight on important evolutionary drivers in the clade, such as hybridization. General relationships in the group were confirmed, while the large amount of gene tree discordance is likely due to reticulation across the phylogeny.

Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana)

Using FrogCap, a recently-developed sequence-capture protocol, we obtained >12,000 highly informative exons, introns, and ultraconserved elements (UCEs), which we used to illustrate variation in evolutionary histories of these classes of markers, and to resolve long-standing systematic problems in Southeast Asian Golden-backed frogs of the genus-complex Hylarana. We also performed a comprehensive suite of analyses to assess the relative performance of different genetic markers, data filtering strategies, tree inference methods, and different measures of branch support. To reduce gene tree estimation error, we filtered the data using different thresholds of taxon completeness (missing data) and parsimony informative sites (PIS). We then estimated species trees using concatenated datasets and Maximum Likelihood (IQ-TREE) in addition to summary (ASTRAL-III), distance-based (ASTRID), and site-based (SVDQuartets) multispecies coalescent methods. Topological congruence and branch support were examined using traditional bootstrap, local posterior probabilities, gene concordance factors, quartet frequencies, and quartet scores. Our results did not yield a single concordant topology. Instead, introns, exons, and UCEs clearly possessed different phylogenetic signals, resulting in conflicting, yet strongly-supported phylogenetic estimates. However, a combined analysis comprising the most informative introns, exons, and UCEs converged on a similar topology across all analyses, with the exception of SVDQuartets. Bootstrap values were consistently high despite high levels of incongruence and high proportions of gene trees supporting conflicting topologies. Although low bootstrap values did indicate low heuristic support, high bootstrap support did not necessarily reflect congruence or support for the correct topology. This study reiterates findings of some previous studies, which demonstrated that traditional bootstrap values can produce positively misleading measures of support in large phylogenomic datasets. We also showed a remarkably strong positive relationship between branch length and topological congruence across all datasets, implying that very short internodes remain a challenge to resolve, even with orders of magnitude more data than ever before. Overall, our results demonstrate that more data from unfiltered or combined datasets produced superior results. Although data filtering reduced gene tree incongruence, decreased amounts of data also biased phylogenetic estimation. A point of diminishing returns was evident, at which higher congruence (from more stringent filtering) at the expense of amount of data led to topological error as assessed by comparison to more complete datasets across different genomic markers. Additionally, we showed that applying a parameter-rich model to a partitioned analysis of concatenated data produces better results compared to unpartitioned, or even partitioned analysis using model selection. Despite some lingering uncertainties, a combined analysis of our genomic data and sequences supplemented from GenBank (on the basis of a few gene regions) revealed highly supported novel systematic arrangements. Based on these new findings, we transfer Amnirana nicobariensis into the genus Indosylvirana; and I. milleti and Hylarana celebensis to the genus Papurana. We also provisionally place H. attigua in the genus Papurana pending verification from positively identified (voucher substantiated) samples.