Selection together with variation in floral traits can act to mold floral form, often driven by a plant’s predominant or most effective pollinators. To investigate the evolution of traits associated with pollination, we developed a phylogenetic framework for evaluating tempo and mode of pollination shifts across the genus Costus L., known for its evolutionary toggle between traits related to bee and bird pollination. Using a target enrichment approach, we obtained 957 loci for 171 accessions to expand the phylogenetic sampling of Neotropical Costus . In addition, we performed whole genome resequencing for a subset of 20 closely related species with contrasting pollination syndromes. For each of these 20 genomes, a high-quality assembled transcriptome was used as reference for consensus calling of candidate loci hypothesized to be associated with pollination-related traits of interest. To test for the role these candidate genes may play in evolutionary shifts in pollinators, signatures of selection were estimated as dN/dS across the identified candidate loci. We obtained a well-resolved phylogeny for Neotropical Costus despite conflict among gene trees that provide evidence of incomplete lineage sorting and/or reticulation. The overall topology and the network of genome-wide single nucleotide polymorphisms (SNPs) indicate that multiple shifts in pollination strategy have occurred across Costus , while also suggesting the presence of previously undetected signatures of hybridization between distantly related taxa. Traits related to pollination syndromes are strongly correlated and have been gained and lost in concert several times throughout the evolution of the genus. The presence of bract appendages is correlated with two traits associated with defenses against herbivory. Although labellum shape is strongly correlated with overall pollination syndrome, we found no significant impact of labellum shape on diversification rates. Evidence suggests an interplay of pollination success with other selective pressures shaping the evolution of the Costus inflorescence. Although most of the loci used for phylogenetic inference appear to be under purifying selection, many candidate genes associated with functional traits show evidence of being under positive selection. Together these results indicate an interplay of phylogenetic history with adaptive evolution leading to the diversification of pollination-associated traits in Neotropical Costus .

Abstract Panicum miliaceum L. was domesticated in northern China at least 7000 years ago and was subsequentially adopted in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, where vast quantities archaeobotanical material were well preserved via desiccation. The rich botanical material found at Areni-1 includes P. miliaceum grains that were identified morphologically and 14 C dated to the medieval period (873 ± 36 CE and 1118 ± 35 CE). To investigate the demographic and evolutionary history of the Areni-1 millet, we used ancient DNA extraction, hybridization capture enrichment, and high throughput sequencing to assemble three chloroplast genomes from the medieval grains and then compared these sequences to 50 modern P. miliaceum chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity with domesticated accessions separated by a maximum of 5 SNPs and little inference on demography could be made. However, in phylogenies the chloroplast genomes separated into two clades, similar to what has been reported for nuclear DNA from P. miliaceum . The chloroplast genomes of two wild (undomesticated) accessions of P. miliaceum contained a relatively large number of variants, 11 SNPs, not found in the domesticated accessions. These results demonstrate that P. miliaceum grains from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.

Biogeographic patterns in the Southern Hemisphere have largely been attributed to vicariant processes, but recent studies have challenged some of the classic examples of this paradigm. The parasitoid wasp subfamily Labeninae has been hypothesized to have a Gondwanan origin, but the lack of divergence dating analysis and the discovery of a putative labenine fossil in Europe pose a challenge to that idea. Here we used a combination of phylogenomics, divergence dating and event-based biogeographical inference to test whether Gondwanan vicariance may explain the distribution patterns of Labeninae. Data from genomic ultraconserved elements were used to infer the phylogeny of Labeninae with 54 species from 9 genera and a broad selection of 99 outgroup taxa. Total-evidence divergence dating places the origin of Labeninae at around 146 mya, which is consistent with a Gondwanan origin but predates the full separation of Africa and South America. The results suggest a path for biotic exchange between South America and Australia potentially through Antarctica, until at least 49 million years ago. Total-evidence analysis places the fossil Trigonator macrocheirus Spasojevic et al. firmly inside crown-group Labeninae, suggesting that labenine distribution range at some point during the Eocene surpassed the boundaries of Gondwanaland. Biogeographic inference also indicates that North American groups represent more recent range expansions that nonetheless occurred before the formation of the Isthmus of Panama land bridge. These conclusions point to a more complex scenario than previously expected for Labeninae biogeography.