Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects.

Fernando Faria Franco,Isabel A S Bonatelli,Monique Romeiro-Brito,Milena Cardoso Telhe,Evandro Marsola Moraes,Danilo Trabuco Amaral

doi:10.3390/genes13030452

Abstract

Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992–2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.

Highlights

Cactaceae (Caryophyllales, Angiosperms) is the major lineage of succulent plants, originating during the Eocene-Oligocene transition [1–3], and it is recognized by its remarkable diversity [4,5]
We retrieved 181 articles published from 1992 to 2021, of which 166 papers were mainly associated with phylogeny, population genetics, and phylogeography topics (Tables S1 and S2), while 27 papers were published since 2015 and were related to genomic and transcriptome assemblies (Table S3)
Protein electrophoresis, restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) were the primary markers used in evolutionary studies in cacti (26 studies), but they have lost their importance in the past decade

Summary

Introduction

Cactaceae (Caryophyllales, Angiosperms) is the major lineage of succulent plants, originating during the Eocene-Oligocene transition [1–3], and it is recognized by its remarkable diversity [4,5]. It is one of the most conspicuous examples of species radiation in the Americas, with intense diversification in the last 10 million years [1]. Cactus species have been traditionally studied by morphologists, and several taxonomic reorganizations have been proposed in the last century (e.g., [4,6–8]). As an emblematic and ecologically relevant group, many evolutionary studies using genetic-based markers have been published in recent decades (e.g., [9–15]). In several examples, classical molecular markers often lack sufficient information to resolve phylogenetic relationships (e.g., [16–19]) and genetic variation at intraspecific level (e.g., [20–22]). Considering the efforts undertaken so far in sampling traditional molecular markers for the family Cactaceae, and that the increasing accessibility to new sequencing technologies [23,24] has fostered genomic sampling in Cactaceae, we believe that a turning point has been reached and that this is the appropriate context for a review of current knowledge achieved using those molecular markers

Methods

Results

Discussion

Conclusion