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Phylogenomics in Cactaceae: A case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan and Sonoran deserts.

Authors
  • Majure, Lucas C1, 2
  • Baker, Marc A3
  • Cloud-Hughes, Michelle4
  • Salywon, Andrew2
  • Neubig, Kurt M5
  • 1 University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, Florida, 32611, USA.
  • 2 Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, Arizona, 85008, USA.
  • 3 College of Liberal Arts and Sciences, Arizona State University, Tempe, Arizona, 85287, USA.
  • 4 Desert Solitaire Botany and Ecological Restoration, San Diego, California, 92103, USA.
  • 5 School of Biological Sciences, Southern Illinois University, Carbondale, Illinois, 62901, USA.
Type
Published Article
Journal
American Journal of Botany
Publisher
Wiley (John Wiley & Sons)
Publication Date
Oct 01, 2019
Volume
106
Issue
10
Pages
1327–1345
Identifiers
DOI: 10.1002/ajb2.1364
PMID: 31545882
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Although numerous phylogenetic studies have been conducted in Cactaceae, whole-plastome datasets have not been employed. We used the chollas to develop a plastome dataset for phylogeny reconstruction to test species relationships, biogeography, clade age, and morphological evolution. We developed a plastome dataset for most known diploid members of the chollas (42 taxa) as well as for other members of Cylindropuntieae. Paired-end, raw reads from genome skimming were reference-mapped onto a de novo plastome assembly of one species of cholla, Cylindropuntia bigelovii, and were used to build our plastome dataset, which was analyzed using various methods. Our plastome dataset resolved the phylogeny of the chollas, including most interspecific and intraspecific relationships. Tribe Cylindropuntieae arose ~18 mya, during the early Miocene in southern South America, and is supported as sister to the South American clade Tephrocacteae. The (Micropuntia (Cylindropuntia + Grusonia)) clade most likely originated in the Chihuahuan Desert region around 16 mya and then migrated into other North American desert regions. Key morphological characters for recognizing traditional taxonomic series in Cylindropuntia (e.g., spiny fruit) are mostly homoplasious. This study provides the first comprehensive plastome phylogeny for any clade within Cactaceae. Although the chollas s.l. are widespread throughout western North American deserts, their most recent common ancestor likely arose in the Chihuahuan Desert region during the mid-Miocene, with much of their species diversity arising in the early to mid-Pliocene, a pattern strikingly similar to those found in other western North American desert groups. © 2019 Botanical Society of America.

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