title: Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach.
abstract: Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology.
authors.affiliation: Department of Botany, Museum Routing Code-166, National Museum of Natural History, Smithsonian Institution Washington, DC, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Erickson
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA ; Smithsonian Tropical Research Institute, Panamá Panamá
authors.forename: Frank A
authors.initials: FA
authors.lastname: Jones
authors.affiliation: Department of Plant Biology, Michigan State University East Lansing, MI, USA.
authors.forename: Nathan G
authors.initials: NG
authors.lastname: Swenson
authors.affiliation: Forest Ecosystem Station of the Pearl River Delta, State Forestry Administration, Research Institute of Tropical Forestry, Chinese Academy of Forestry Guangzhou, China.
authors.forename: Nancai
authors.initials: N
authors.lastname: Pei
authors.affiliation: Conservation Ecology Center, Smithsonian Conservation Biology Institute, Smithsonian Institution Front Royal, VA, USA.
authors.forename: Norman A
authors.initials: NA
authors.lastname: Bourg
authors.affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences Guangzhou, China.
authors.forename: Wenna
authors.initials: W
authors.lastname: Chen
authors.affiliation: Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research Institute Washington, DC, USA.
authors.forename: Stuart J
authors.initials: SJ
authors.lastname: Davies
authors.affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences Guangzhou, China.
authors.forename: Xue-Jun
authors.initials: XJ
authors.lastname: Ge
authors.affiliation: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Science Shenyang, China.
authors.forename: Zhanqing
authors.initials: Z
authors.lastname: Hao
authors.affiliation: Department of Natural and Applied Sciences, Biology Program, University of Wisconsin-Green Bay Green Bay, WI, USA.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Howe
authors.affiliation: Laboratory of Molecular Phylogenetics, Department of Biology, National Museum of Natural Science Taichung, Taiwan.
authors.forename: Chun-Lin
authors.initials: CL
authors.lastname: Huang
authors.affiliation: Department of Forest Management, The University of Montana Missoula, MT, USA.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Larson
authors.affiliation: National Institute of Education, Nanyang Technological University, Singapore Singapore.
authors.forename: Shawn K Y
authors.initials: SK
authors.lastname: Lum
authors.affiliation: Wildland Resources, Utah State University Logan, UT, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Lutz
authors.affiliation: State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China.
authors.forename: Keping
authors.initials: K
authors.lastname: Ma
authors.affiliation: Department of Zoology, Faculty of Science, University of Peradeniya Peradeniya, Sri Lanka.
authors.forename: Madhava
authors.initials: M
authors.lastname: Meegaskumbura
authors.affiliation: State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China.
authors.forename: Xiangcheng
authors.initials: X
authors.lastname: Mi
authors.affiliation: Smithsonian Environmental Research Center, Smithsonian Institution Edgewater, MD, USA.
authors.forename: John D
authors.initials: JD
authors.lastname: Parker
authors.affiliation: Department of Natural Resources and Environmental Studies, National Dong Hwa University Hualien, Taiwan.
authors.forename: I
authors.initials: I
authors.lastname: Fang-Sun
authors.affiliation: Smithsonian Tropical Research Institute, Panamá Panamá
authors.forename: S Joseph
authors.initials: SJ
authors.lastname: Wright
authors.affiliation: Department of Natural and Applied Sciences, Biology Program, University of Wisconsin-Green Bay Green Bay, WI, USA.
authors.forename: Amy T
authors.initials: AT
authors.lastname: Wolf
authors.affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences Guangzhou, China.
authors.forename: W
authors.initials: W
authors.lastname: Ye
authors.affiliation: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Science Shenyang, China.
authors.forename: Dingliang
authors.initials: D
authors.lastname: Xing
authors.affiliation: Institute for Tropical Ecosystem Studies, University of Puerto Rico San Juan, PR, USA.
authors.forename: Jess K
authors.initials: JK
authors.lastname: Zimmerman
authors.affiliation: Department of Botany, Museum Routing Code-166, National Museum of Natural History, Smithsonian Institution Washington, DC, USA.
authors.forename: W John
authors.initials: WJ
authors.lastname: Kress
keywords: ForestGEO; barcode; community assembly; ecology; phylogenetic diversity; phylogeny