THE PLANT PRESS Department of Botany & the U.S. National Herbarium New Series - Vol. 23 - No. 2 April-June 2020 Prunus is a model clade for investigating tropical-to-temperate transitions By Richie Hodel or over a century, biologists have observed a latitudinal the northern hemisphere and in the tropics and subtropics. gradient in species diversity in many clades across the Phylogenetic studies of Prunus have used several chloroplast FTree of Life, with greater species richness near the and nuclear loci and produced key insights, but many ques- equator. However, we lack consensus about the cause of this tions remain. The phylogenetic position of Prunus within Ro- biogeographic pattern and several hypotheses have been pro- saceae is uncertain, and phylogenetic relationships within posed. The tropical conservatism hypothesis (TCH) is one ex- Prunus are not yet fully resolved. Discord among chloroplast, planation for the observed latitudinal gradient; the TCH states nuclear, and morphological phylogenies suggests ancient that the relatively high biodiversity of the tropics is explained polyploidy and/or hybridization may have impacted the evo- primarily by the geographic extent of tropical taxa during the lutionary history of Prunus, and more data are needed to re- past ~55 million years and the subsequent evolutionary conser- solve the phylogeny (see figure on page 2). vation of environmental niches. Continued on page 2 Recent large-scale phylogenetic studies using over 10,000 angiosperm species identified general trends describing how Because of its size, distribution, the latitudinal species gradient affects plant diversity. Notably, few lineages transitioned from tropical environments to tem- and an existing base of knowledge, perate ones, which may be explained by the difficulty of acquir- Prunus will be an ideal clade for ing the substantial adaptations necessary to tolerate the cooler testing the tropical conservatism conditions in temperate zones. One of the goals of my postdoc- toral work at the National Museum of Natural History hypothesis and investigating the (NMNH) is to use the genus Prunus (Rosaceae) to test the processes that shape the latitudinal TCH. species gradient once phylogenetic Prunus contains approximately 250-400 evergreen and de- ciduous species occurring throughout the temperate regions of relationships are resolved. Department of Botany & the U.S. National Herbarium Prunus Continued from page 1 A phylogenomic analysis of Prunus using hundreds of nuclear loci is needed to resolve uncertain relationships, address the role of ancient hybridization and/or allo- polyploidy in the evolution of Prunus, and serve as a framework for downstream analyses. One consequence of phylogenetic uncertainty is that the biogeographic his- tory of Prunus remains uncertain, and sub- sequent analyses, such as tests of the TCH, are challenging. Because of its size, distri- bution, and an existing base of knowledge, Prunus will be an ideal clade for testing the TCH and investigating the processes that shape the latitudinal species gradient once phylogenetic relationships are resolved. Moreover, because of three documented Figure 1. Cytonuclear discord in Prunus: the plastid phylogeny (left) infers a tropical-to-temperate transitions in Prunus monophyletic racemose group, but the nuclear phylogeny (right) yields a paraphyletic (solitary, corymbose, and racemose groups racemose group. ‘A’ represents taxa in the Prunus-Amygdalus group, ‘B’ shows taxa in – see specimen images below), this genus the Cerasus group, and ‘C’ depicts the polypoid racemose Prunus, which includes represents a model system for investigating Laurocerasus, Padus, Pygeum, and Maddenia. The question mark shows the location the dynamics and evolutionary implica- on the phylogeny where ancient allopolyploidy may have occurred, leading to uncertain tions of such transitions. phylogenetic relationships in the racemose Prunus. Figure modified from Chin et al. We are currently using targeted enrich- 2014 and Zhao et al. 2016. ment (Hyb-Seq) to generate hundreds of southeast Asia, tentatively planned for diversification rates within Prunus. Geo- nuclear loci and entire chloroplast ge- early Fall 2020. Obtaining a complete-as- referenced distributional data will be com- nomes for virtually all species in the genus. possible phylogeny of the genus is a critical bined with inferred diversification rates to Jun Wen and collaborators have an exten- first step. We will use the genomic data and investigate why tropical lineages diversify sive collection of tissue samples, which will the rich fossil record for this group to gen- more rapidly than temperate clades. be supplemented by field collections in erate a time-calibrated phylogeny and infer We will also reconstruct the biogeo- Herbarium sheets from the U.S. National Herbarium representing examples from (left to right) the solitary flower group ofPrunus (P. persica; peach), the corymbose group of Prunus (P. avium; sweet cherry), and the racemose group of Prunus (P. serotina; black cherry). Page 2 graphic history of Prunus, which will be Botanical research in the age of COVID-19 possible with a fully resolved phylogeny with complete taxon sampling. Next, we By Julia Beros can use the biogeographic results to define Life does not exist alone. It’s 12:30PM homes, the team continues working on a the patterns and processes of the tropical- and the only indication of my coworkers is backlog of specimen data (as we are still temperate transitions. Ecological niche how slow shared documents begin loading inundated with the roses and mustards), modeling analyses using geographic distri- in my remote desktop. During this time of checking for completeness and accuracy, bution data, phylogenomic data, and niche great uncertainty, misinformation, and uploading to the database, and making the models derived from bioclimatic variables vulnerability, it can be a challenge to nor- data searchable to expedite access to the will be used to trace niche evolution in malize and re-create the habitual, it can collections. Prunus to test if differences in niche con- even be an insult to the desire to be more Slightly inconvenienced by my new at- servatism among lineages determine their “useful.” But developing faith in our shared home workstation, I find myself still in current geographic distributions. and now virtual community necessitates awe, still inspired, and still feeling giddy as In some plants, key morphological that we keep on keepin’ on. The speed at I scan through the U.S. National Her- characters are typically associated with which the Smithsonian Institution reacted barium’s historic collections. Seeing an Al- tropical environments, such as entire leaf to the velocity of COVID-19’s approach in lium or Apiale specimen come up that margins; in contrast, temperate species preparing ourselves to transition from a happens to be the same kind that I tended often have toothed or lobed leaf margins. day-to-day routine working physically to in the garden this morning, or looking Tropical and temperate members of Pru- with specimens and collections to exclu- at a Rosaceae collected in 1800 and seeing nus have different leaf margin morphol- sively accessing them remotely and contin- a related species beginning to leaf and bud ogies and may represent an opportunity to uing research in the face of unknown along the fence in my yard in 2020, is like investigate how certain morphological challenges is not only impressive but admi- time-travel giving me a link to the past. characters facilitate tropical-to-temperate rable to see our passions overcome the im- Reading the names of women botanists transitions. We will leverage digitized her- mediate fight or flight reactionary instinct. like Emma Lucy Braun and Agnes Chase barium specimens from the U.S. National It is clear as well, that as we log in from our paving the way for plant research and dis- Herbarium for traditional morphological various homes to access the collections, Continued on page 4 analyses and a machine learning approach that the continued efforts of digitization at developed by other researchers in the the Smithsonian are a true asset to re- The Plant Press NMNH Botany Department to identify search and maintaining continuity with morphological characters important in key the ever-changing infrastructure of our New Series - Vol. 23 - No. 2 transitions in Prunus, including tropical- world. Chair of Botany to-temperate transitions, diversification Like much of the world right now, the Eric Schuettpelz rate shifts, and niche evolution. conveyor belt, photographing specimens ([email protected]) The COVID-19 pandemic has put and creating up to 4,000 images a day, has EDITORIAL STAFF some portions of this project into a hold- paused, and so have the dedicated contrac- ing pattern, such as lab work and collect- tors who facilitate the process. In this mo- Editor ing specimens in southeast Asia. I am ment of reflection we can see everything Gary Krupnick currently working on a phylogeny to re- ([email protected]) that the team accomplished thus far: of a solve the evolutionary history of cherries projected 5 million botanical specimens, Copy Editors (subgenus Cerasus) using publicly available 2.83 million have been imaged and or Robin Everly, Bernadette Gibbons, and genomic resources. I am also working to recorded in the database (not including Rose Gulledge assemble datasets of images from the U.S. those digitized by the Botany IT team pre- The Plant Press is a quarterly publication provided National Herbarium to be used in machine vious to the installation of the conveyor free of charge. To receive notification of when new learning analyses for identifying key char- belt, or historic photographs and other pdf issues are posted to the web, please subscribe acters associated with tropical-to-tem- media), making them available through to the listserve by sending a message to perate transitions. [email protected] containing only the the online catalog. With the effort of Open following in the body of the text: SUBSCRIBE Access the information of our specimen PLANTPRESS-NEWS Firstname Lastname.