Transcriptome sequencing data provide a solid base to understand the phylogenetic relationships, biogeography and reticulated evolution of the genus Zamia L. (Cycadales: Zamiaceae)

Author:

Lindstrom Anders1,Habib Sadaf23,Dong Shanshan3,Gong Yiqing3,Liu Jian4,Calonje Michael5,Stevenson Dennis6,Zhang Shouzhou3

Affiliation:

1. Global Biodiversity Conservancy 144/124 Moo 3 , Soi Bua Thong, Bangsalae, Sattahip, Chonburi, 20250 , Thailand

2. Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences , Jiujiang 332900 , China

3. Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden Shenzhen & Chinese Academy of Sciences , Shenzhen, 518004 , China

4. Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, 650201 , China

5. Montgomery Botanical Center , Coral Gables, FL 33156 , USA

6. New York Botanical Garden , Bronx, NY 10458 , USA

Abstract

Abstract Background and Aims Cycads are a key lineage to understand the early evolution of seed plants and their response to past environmental changes. However, tracing the evolutionary trajectory of cycad species is challenging when the robust relationships at inter- or infrageneric level are not well resolved. Methods Here, using 2901 single-copy nuclear genes, we explored the species relationships and gene flow within the second largest genus of cycads, i.e. Zamia, based on phylotranscriptomic analyses of 90 % extant Zamia species. Based on a well-resolved phylogenetic framework, we performed gene flow analyses, molecular dating and biogeographical reconstruction to examine the spatiotemporal evolution of Zamia. We also performed ancestral state reconstruction of a total of 62 traits of the genus to comprehensively investigate its morphological evolution. Key Results Zamia comprises seven major clades corresponding to seven distinct distribution areas in the Americas, with at least three reticulation nodes revealed in this genus. Extant lineages of Zamia initially diversified around 18.4–32.6 (29.14) million years ago in Mega-Mexico, and then expanded eastward into the Caribbean and southward into Central and South America. Ancestral state reconstruction revealed homoplasy in most of the morphological characters. Conclusions This study revealed congruent phylogenetic relationships from comparative methods/datasets, with some conflicts being the result of incomplete lineage sorting and ancient/recent hybridization events. The strong association between the clades and the biogeographic areas suggested that ancient dispersal events shaped the modern distribution pattern, and regional climatic factors may have resulted in the following in situ diversification. Climate cooling starting during the mid-Miocene is associated with the global expansion of Zamia to tropical South America that has dramatically driven lineage diversification in the New World flora, as well as the extinction of cycad species in the nowadays cooler regions of both hemispheres, as indicated by the fossil records.

Funder

Scientific Foundation of Urban Management Bureau of Shenzhen

Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China

National Science Foundation

Publisher

Oxford University Press (OUP)

Reference105 articles.

1. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations;Abascal;Nucleic Acids Research,2010

2. New notes on the ecology of the epiphytic gymnosperm and Panamanian endemic Zamia pseudoparasitica;Bell-Doyon;Neotropical Naturalist,2020

3. Trimmomatic: a flexible trimmer for Illumina sequence data;Bolger;Bioinformatics,2014

4. Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data;Breinholt;Genome Biology and Evolution,2013

5. A time-calibrated species tree phylogeny of the New World cycad genus Zamia L. (Zamiaceae, Cycadales);Calonje;International Journal of Plant Sciences,2019

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