PREMISE The successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate the need for specific marker development, while retaining the benefits of full-gene sequences in population-level analyses. However, whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters is untested. METHODS Using herbarium specimens from a 50-year-old floristic survey in Texas, we sequenced 95 samples from 24 species using the Angiosperms353 probe set. Our data workflow calls variants within species and prepares data for population genetic analysis using standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations and displayed limited phylogenetic bias. RESULTS We identified over 1000 segregating variants with zero missing data for 92% of species and demonstrate that Angiosperms353 markers contain sufficient variation to estimate pairwise nucleotide diversity (π)—typically between 0.002 and 0.010, with most variation found in flanking non-coding regions. In a subset of variants that were filtered to reduce linkage, we uncovered high heterozygosity in many species, suggesting that denser sampling within species should permit estimation of gene flow and population dynamics. DISCUSSION Angiosperms353 should benefit conservation genetic studies by providing universal repeatable markers, low missing data, and haplotype information, while permitting inclusion of decades-old herbarium specimens.

Within tribe Gnaphalieae (Asteraceae), the Australasian clade is one of the four major clades. In Australia, the Gnaphalieae account for 488 species or approximately half of the native Asteraceae, encompassing wide ecological and morphological diversity including shrubs, everlasting paper daisies, cudweeds, alpine cushion plants, and ephemeral herbs in the arid zone. The evolution of the Australasian clade is still poorly understood. The most detailed previous infratribal classification of Gnaphalieae has recently been revised, resulting in the recognition of two subtribes, with all Australian species placed in subtribe Gnaphaliinae. The most comprehensive previous phylogeny of Australian Gnaphalieae used high-copy ribosomal and chloroplast markers but showed limited resolution and branch support. We used conserved ortholog set data produced with sequence capture and 53 chloroplast genes to infer nuclear and chloroplast likelihood phylogenies for Australian Gnaphalieae, generating data for at least one species each from 80 of the 86 native genera. Four major clades were resolved: the Euchiton clade of cudweed-like and alpine perennial species; the shrubby Cassinia clade; the predominantly perennial and eastern Australian Waitzia clade; and the predominantly ephemeral and western Australian to Eremaean Angianthus clade. The Cassinia, Waitzia, and Angianthus clades are largely congruent with “groups” in a previous morphological analysis and classification of Gnaphalieae. Analysis of ancestral ranges implied the temperate Southeast of Australia as the most likely area of origin for the Australian Gnaphalieae as a whole and for three of the four major clades. The Angianthus clade was implied to be ancestrally Eremaean, with a major secondary radiation originating in southwestern Australia. Our broadly sampled phylogeny provides a framework to inform sampling and design of future studies to test the circumscription of genera.

Premise Cunoniaceae are a family of shrubs and trees with 27 genera and ca. 335 species, mostly confined to tropical and wet temperate zones of the southern hemisphere. There are several known issues regarding generic limits, and the family also displays a number of intriguing long-range disjunctions. Methods We performed a phylogenomic study using the universal Angiosperms353 probe set for targeted sequence capture. We sampled 37 species covering all genera in the Cunoniaceae, and those in the three closely related families of the crown Oxalidales (Brunelliaceae, Cephalotaceae, and Elaeocarpaceae). We also performed analyses for molecular dating and ancestral area reconstruction. Results We recovered the topology (Cunoniaceae, (Cephalotaceae, (Brunelliaceae, Elaeocarpaceae))) and a well-resolved genus-level phylogeny of Cunoniaceae with strongly supported clades corresponding to all previously recognized tribes. As previously suspected, the genera Ackama and Weinmannia were recovered as paraphyletic. Australasia was inferred as the likely ancestral area for the family. Conclusions The current distribution of Cunoniaceae is best explained by long-distance dispersal with a few possible cases of Australasian–American vicariance events. Extinctions may have been important in determining the mostly Oceanian distribution of this family while some genera in the tribe Cunonieae and in New Caledonia have undergone recent bursts of diversification. New generic diagnoses, 80 new combinations, and one new name are provided for a recircumscribed Ackama (including Spiraeopsis), a much smaller Weinmannia (mostly New World), and a resurrected Pterophylla to accommodate Old World taxa previously in Weinmannia.

The evolutionary history of Ichneumoninae, the largest subfamily of ichneumonid wasps, is investigated using genomic ultraconserved elements (UCEs). The dataset includes 147 species in 130 genera of Ichneumoninae and 155 outgroup taxa from 19 subfamilies. Matrices with varying degrees of completeness were analysed with different partition schemes and the resulting topologies were found to be mostly congruent. All analyses recovered Ichneumoninae as a monophyletic group, sister to all other Ichneumoniformes except Agriotypinae. Almost no support was found for previous tribal classification schemes, except that the tribes Phaeogenini and Platylabini are largely monophyletic. A new tribal classification is proposed based on the relationships recovered, consisting of seven tribes: Alomyini Förster, Phaeogenini Förster, Notosemini Townes, Eurylabini Heinrich, Platylabini Berthoumieu, Ichneumonini Latreille and a new monogeneric tribe, Abzariini Santos & Wahl. As documented in other lineages of Ichneumonidae, pervasive morphological convergence poses a challenge to the establishment of higher-level groups that are both monophyletic and diagnosable. Extremely short branches at the base of the Ichneumoninae clade suggest that the group may have undergone a rapid radiation when it first diverged, potentially associated with its specialization on lepidopteran hosts. Multiple changes in the morphology of the female abdomen suggest that morphological convergence is associated with multiple transitions in the use of pupal versus larval hosts across the subfamily. The results demonstrate the power of phylogenomic approaches to resolve evolutionary relationships in hyper-diverse and poorly studied insect groups and to provide a framework for testing evolutionary hypotheses.