Abstract
The family of pantropical spiral gingers (Costaceae Nakai; c. 125 spp.) can be used as a model to enhance our understanding of the mechanisms underlying Neotropical diversity. Costaceae has higher taxonomic diversity in South and Central America (c. 72 Neotropical species, c. 30 African, c. 23 Southeast Asian), particularly due to a radiation of Neotropical species of the genus Costus L. (c. 57 spp.). However, a well-supported phylogeny of the Neotropical spiral gingers including thorough sampling of proposed species encompassing their full morphologic and geographic variation is lacking, partly due to poor resolution recovered in previous analyses using a small sampling of loci. Here we use a phylogenomic approach to estimate the phylogeny of a sample of Neotropical Costus species using a targeted enrichment approach. Baits were designed to capture conserved elements’ variable at the species level using available genomic sequences of Costus species and relatives. We obtained 832 loci (generating 791,954 aligned base pairs and 31,142 parsimony informative sites) for samples that encompassed the geographical and/or morphological diversity of some recognized species. Higher support values that improve the results of previous studies were obtained when including all the available loci, even those producing unresolved gene trees and having a low proportion of variable sites. Concatenation and coalescent-based species trees methods converge in almost the same topology suggesting a robust estimation of the relationships, even under the high levels of gene tree conflict presented here. The bait set design here presented made inferring a robust phylogeny to test taxonomic hypotheses possible and will improve our understanding of the origins of the charismatic diversity of the Neotropical spiral gingers.
Highlights
One of the most widely recognized patterns in ecology and biogeography is that lineages tend toward species richness in tropical regions (Kreft and Jetz, 2007); the mechanisms that originate such patterns of diversity are still poorly understood
Phylogenetic signal recovered for the sampling of Neotropical Costus demonstrates the efficacy of using a targeted enrichment approach to estimate phylogenies in challenging plant lineages with large genomes, especially those involving rapid radiations, putative hybrids, and/or high levels of incomplete lineage sorting
Normalized quartet score of the coalescent-based species tree topology indicates high levels of gene tree discordance, a result expected when incomplete lineage sorting is prevalent in the history of the group
Summary
One of the most widely recognized patterns in ecology and biogeography is that lineages tend toward species richness in tropical regions (Kreft and Jetz, 2007); the mechanisms that originate such patterns of diversity are still poorly understood. Richness is not uniform across the tropical regions; the Neotropics stand as the most diverse with around 90,000–110,000 species of seed plants that could exceed the numbers of tropical Africa with 30,000–35,000 spp. and tropical Asia and Oceania with 40,000–82,000 spp., combined (Antonelli and Sanmartıń , 2011; Hughes et al, 2013). Possibilities for prezygotic reproductive isolation driven by shifts in pollination syndromes (Serrano-Serrano et al, 2017), adaptation to local conditions leading to ecological speciation (Antonelli et al, 2018), or the effects of polyploidization on diversification rates (Soltis and Soltis, 2009; Landis et al, 2018) of Neotropical lineages are additional mechanisms that could explain the relatively higher diversity of Neotropical plant lineages compared to their Paleotropical congeners. The importance of extinction has been discussed to understand lower species richness in Africa compared to the Neotropics and South-East Asia (Couvreur, 2015)
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