A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data.
BACKGROUND
The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools.


RESULTS
We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny.


CONCLUSIONS
With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean biogeography, and (iii) aid in incorporating evolutionary history into conservation planning.
Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York 10027, United States of America.
Robert
R
Muscarella
Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York 10027, United States of America.
María
M
Uriarte
Department of Botany, MRC-166, National Museum of Natural History Smithsonian Institution, P.O. Box 37012, Washington, D. C., 20013, United States of America.
David L
DL
Erickson
Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, United States of America.
Nathan G
NG
Swenson
Department of Environmental Science, University of Puerto Rico, San Juan, Puerto Rico 00925, United States of America.
Jess K
JK
Zimmerman
Department of Botany, MRC-166, National Museum of Natural History Smithsonian Institution, P.O. Box 37012, Washington, D. C., 20013, United States of America.
W John
WJ
Kress
D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D065928:Forests; D010802:Phylogeny; D011647:Puerto Rico; D014197:Trees / Q000145:classification / Q000235:genetics*