Molecular data do not support the traditional morphology-based groupings in the scorpion family Buthidae (Arachnida: Scorpiones).

The family Buthidae represents an early-diverging and most species-rich lineage of extant scorpions, but its internal phylogenetic relationships are still poorly understood. The family is traditionally divided into six morpho-groups; however, the monophyly of some of them remains unclear. We combined multilocus sequence data with extensive taxon sampling to reconstruct the phylogenetic relationships among Buthidae and assess the validity of the morphology-based groupings. We recovered a monophyletic Buthus group as a sister clade to all the remaining Buthidae. We also found support for the monophyly of the Tityus group, but the remaining morpho-groups were recovered as para-/polyphyletic. Our results also suggest that some genera are in need of a taxonomic revision.

Multilocus species tree analyses resolve the ancient radiation of the subtribe Zizaniinae (Poaceae).

The phylogeny of the subtribe Zizaniinae of rice tribe (Oryzeae) has not been well resolved, particularly for the monotypic Hygroryza whose systematic position was inconsistent in previous studies. Here, we used the concatenation approach and coalescent-based species tree methods to reconstruct the phylogeny of Zizaniinae based on sequences of 14 nuclear single-copy loci and concatenated chloroplast fragments. Despite the low resolution of the tree from concatenated data and substantial topological incongruence of individual gene trees, the species trees inferred from three coalescent-based methods were fully concordant and highly supported. Importantly, the genus Hygroryza was consistently recovered with strong support by all coalescent-based methods. Further various phylogenetic analyses indicated that incomplete lineage sorting was the most likely process that generated pervasive discordance among individual gene trees, although hybridization and introgression cannot be excluded completely. Our species tree inferences based on multilocus data successfully resolved the phylogenetic relationships of the Zizaniinae lineages and confirmed that ancient rapid radiation has taken place in the diversification history of Zizaniinae. This study demonstrates that coalescent-based species tree approaches outperformed the concatenation method and could effectively decipher ancient rapid radiations as long as well resolved individual gene trees were sufficiently sampled.

Effects of missing data on species tree estimation under the coalescent.

With recent advances in genomic sequencing, the importance of taking the effects of the processes that can cause discord between the speciation history and the individual gene histories into account has become evident. For multilocus datasets, it is difficult to achieve complete coverage of all sampled loci across all sample specimens, a problem that also arises when combining incompletely overlapping datasets. Here we examine how missing data affects the accuracy of species tree reconstruction. In our study, 10- and 100-locus sequence datasets were simulated under the coalescent model from shallow and deep speciation histories, and species trees were estimated using the maximum likelihood and Bayesian frameworks (with STEM and (*)BEAST, respectively). The accuracy of the estimated species trees was evaluated using the symmetric difference and the SPR distance. We examine the effects of sampling more than one individual per species, as well as the effects of different patterns of missing data (i.e., different amounts of missing data, which is represented among random taxa as opposed to being concentrated in specific taxa, as is often the case for empirical studies). Our general conclusion is that the species tree estimates are remarkably resilient to the effects of missing data. We find that for datasets with more limited numbers of loci, sampling more than one individual per species has the strongest effect on improving species tree accuracy when there is missing data, especially at higher degrees of missing data. For larger multilocus datasets (e.g., 25-100 loci), the amount of missing data has a negligible effect on species tree reconstruction, even at 50% missing data and a single sampled individual per species.

Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia).

Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross-contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of scleractinians in the future.