Species delimitation has been divided by two approaches: DNA barcoding that focuses on standardization of the genetic marker and multilocus methods that place a premium on genomic coverage and conceptual rigor in modeling the divergence process. Most multilocus methods fail as barcodes, however, because few assay the same marker set and are therefore not readily comparable across studies and databases. We introduce ultraconserved elements (UCEs) as potential genomic barcodes that allow rigorous species delimitation and a bridge to DNA barcoding database to allow both rigorous species delimitation and standardized identification of delimited taxa. UCEs query thousands of loci across the nuclear genome in way that is replicable across broad taxonomic groups (i.e., vertebrates). We apply UCEs to species delimitation in a species complex of frogs found in the Mexican Highlands. Sarcohyla contains 24 described species, many of which are critically endangered and known only from their type localities. Evidence suggests that one broadly distributed member of the genus, S. bistincta, might contain multiple species. We generated data from 1,891 UCEs, which contained 1,742 informative SNPs for S. bistincta and closely related species. We also captured mitochondrial genomes for most samples as off-target bycatch of the UCE enrichment process. Phylogenies from UCEs and mtDNA agreed in many ways, but differed in that mtDNA suggested a more complex evolutionary history perhaps influenced by reticulate processes. The species delimitation method we used identified eight putative species (which we call lineages pending further study) within S. bistincta. Being able to compare linked mtDNA data to existing sequences on Genbank allowed us to identify one of these lineages nested within S. bistincta as an already-described species, S. pentheter. Another lineage nested within S. bistincta is currently being described as a new species (referred to here as sp. nov.). The remaining six lineages fell into two non-sister clades, one containing the core S. bistincta mostly in Oaxaca and Guerrero, and another in the Transvolcanic Belt. The latter clade, at 10% divergence in mtDNA and paraphyletic with respect to other S. bistincta, is a clear candidate for species status. Our study demonstrates not only that UCEs can be used as effective genomic DNA barcodes, but that combining multilocus genomic data with mtDNA is a powerful approach for both delimiting species and identifying them in poorly described and phenotypically challenging groups.

Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: (1) Tocantinia and Hippeastrum with 2n = 22, and (2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n = 12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade.

The sinipercids are freshwater fishes endemic to East Asia, mainly in China. Phylogenetic studies on the sinipercids have made great progress in the last decades, but interspecific relationships and evolutionary history of the sinipercids remain unresolved. Lack of distinctive morphological characters leads to problems in validating of some species, such as Siniperca loona. Moreover, genetic data are needed to delimitate species pairs with explicit hypothesis testing, such as in S. chuatsi vs. S. kneri and Coreoperca whiteheadi vs. C. liui. Here we reconstructed phylogeny of the sinipercids with an unprecedented scale of data, 16,943 loci of single-copy coding sequence data from nine sinipercid species, eight putative sister taxa and two outgroups. Targeted sequences were collected using gene enrichment and Illumina sequencing, yielding thousands of protein coding sequences and single nucleotide polymorphisms (SNPs) data. Maximum likelihood and coalescent species tree analyses resulted in identical and highly supported trees. We confirmed that the centrarchids are sister to the sinipercids. A monophyletic Sinipercidae with two genera, Siniperca and Coreoperca was also supported. Different from most previous studies, S. scherzeri was found as the most basal taxon to other species of Siniperca, which consists of two clades: a clade having S. roulei sister to S. chuatsi and S. kneri, and a clade consisting S. loona sister to S. obscura and S. undulata. We found that both S. loona and C. liui are valid species using Bayes factor delimitation (BFD∗) based on SNPs data. Species delimitation also provided decisive support for S. chuatsi and S. kneri being two distinct species. We calibrated a chronogram of the sinipercids based on 100 loci and three fossil calibration points using BEAST, and reconstructed ancestral ranges of the sinipercids using Lagrange Analysis (DEC model) and Statistical Dispersal-Vicariance Analysis (S-DIVA) implemented in RASP. Divergence time estimates and ancestral habitat reconstruction suggested a wide-ranging distribution of the common ancestor of the sinipercids in southern China at 53.1 million years ago (CI: 30.4–85.8Ma). The calibrated time tree is consistent with historical climate changes and geological events that might have shaped the current distribution of the sinipercids.