Spatial phylogenetics of the native California flora

BMC Biology
Andrew H ThornhillBrent D Mishler

Abstract

California is a world floristic biodiversity hotspot where the terms neo- and paleo-endemism were first applied. Using spatial phylogenetics, it is now possible to evaluate biodiversity from an evolutionary standpoint, including discovering significant areas of neo- and paleo-endemism, by combining spatial information from museum collections and DNA-based phylogenies. Here we used a distributional dataset of 1.39 million herbarium specimens, a phylogeny of 1083 operational taxonomic units (OTUs) and 9 genes, and a spatial randomization test to identify regions of significant phylogenetic diversity, relative phylogenetic diversity, and phylogenetic endemism (PE), as well as to conduct a categorical analysis of neo- and paleo-endemism (CANAPE). We found (1) extensive phylogenetic clustering in the South Coast Ranges, southern Great Valley, and deserts of California; (2) significant concentrations of short branches in the Mojave and Great Basin Deserts and the South Coast Ranges and long branches in the northern Great Valley, Sierra Nevada foothills, and the northwestern and southwestern parts of the state; (3) significant concentrations of paleo-endemism in Northwestern California, the northern Great Valley, and western Sonoran D...Continue Reading

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Citations

Dec 23, 2017·Science·Thomas J Givnish
Nov 9, 2018·American Journal of Botany·Daniel SpalinkKenneth J Sytsma
Feb 20, 2020·Proceedings of the National Academy of Sciences of the United States of America·Susan HarrisonDaijiang Li
Jan 2, 2019·Nature Plants·Julie M AllenRobert P Guralnick
Nov 21, 2018·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Matthew M KlingDavid D Ackerly
Oct 31, 2019·The New Phytologist·Léo-Paul M J DagallierThomas L P Couvreur
Oct 29, 2020·American Journal of Botany·Rosa A SchersonTaryn Fuentes-Castillo
Jan 28, 2021·Biology·Konstantinos KougioumoutzisPanayotis Dimopoulos
Mar 16, 2021·Ecology and Evolution·Zhi-Xin ZhuHua-Feng Wang
Jun 12, 2021·Scientific Reports·Ángel DelsoJesús Muñoz
Jun 16, 2021·PloS One·Mayra Flores-TolentinoJosé Luis Villaseñor
Jun 29, 2021·American Journal of Botany·Ryan A Folk, Carolina M Siniscalchi
Nov 14, 2021·Journal of Integrative Plant Biology·Xiao-Xia ZhangZhi-Duan Chen

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Methods Mentioned

BETA
PCR

Software Mentioned

R
CANAPE
RAxML
Geneious
Matrix Maker
r8s
Biodiverse
Maxent
BLAST ( Basic Local Alignment Search Tool

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