Aim Plant distributions are influenced by species’ ability to colonize new areas via long-distance dispersal and propensity to adapt to new environments via niche evolution. We use otobas, a clade of ecologically dominant trees found in low-to mid-elevation wet forests, as a system to understand the relative importance of these processes within the Neotropics. Location Neotropics and global. Taxon Otoba and entire Myristicaceae. Methods We resolve the first phylogeny of Otoba the Angiosperms353 loci and plastome sequences from 13 accessions representing seven species. We pair this with the most densely sampled phylogeny of Myristicaceae to date, inferred using publicly available plastid data. We then use environmental niche modelling, biogeographical reconstruction, phylogenetic principle components analysis and Ornstein–Uhlenbeck models to infer biogeography and examine patterns of niche evolution. Results Myristicaceae has an Old World origin, with a single expansion into the Americas. Divergence dates, fossil evidence and a notable lack of long-distance dispersal are consistent with a Boreotropical origin of Neotropical Myristicaceae. Mirroring the rarity of dispersal at the family level, Otoba’s biogeography is marked by few biogeographical events: two expansions into Central America from a South American ancestor and a single dispersal event across the Andes. This limited movement contrasts with rapid climatic niche evolution, typically occurring across geographically proximate habitats. Main conclusion Contrasting with previous studies, long-distance dispersal does not need to be invoked to explain the pantropical distribution of Myristicaceae, nor the biogeography of Otoba. This likely results from the family’s relatively large seeds that are dispersed by large-bodied vertebrates. Instead, rapid niche evolution in Otoba has facilitated its occurrence throughout mesic habitats of the northern Neotropics, including the Amazon rainforest and Andean montane forests. Otoba adds to a growing group of Neotropical plant clades in which climate adaptation following local migration is common, implying an important role of niche evolution in the assembly of the Neotropical flora.

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.