An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae)

Abstract

What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question in Escallonia (Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist in Escallonia as an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species ($$< 20\%$$ < 20 % ) and that phenomic and genomic data seldom delimit congruent entities ($$< 20\%$$ < 20 % ). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.

Phylogenomics of the North American Desert RadiationLinanthus(Polemoniaceae) Reveals Mixed Trait Lability and No Single Geographic Mode of Speciation

“…We collected genomic data using two approaches, double-digest restriction-site associated sequencing (ddRADseq) and target capture (TC). RAD sequencing generates data that has been used to successfully address questions in both population genomics and phylogenetic relationships in closely related species (Rubin et al 2012; Eaton et al 2016, Jacobs et al 2021). We used a double-digest RAD approach which uses two-enzymes to better recover the same fragments of DNA across samples and reduce sequencing costs (Peterson et al 2012).…”

“…We collected genomic data using two approaches, double-digest restriction-site associated sequencing (ddRADseq) and target capture (TC). RAD sequencing generates data that has been used to successfully address questions in both population genomics and phylogenetic 10 relationships in closely related species (Rubin et al 2012;Eaton et al 2016, Jacobs et al 2021.…”

Draft genome assemblies for two species of Escallonia (Escalloniales)

“…Further, groups of closely related Escallonia species have diversified independently along elevational gradients in the tropical Andes, Southern Brazil, and the temperate Andes, suggesting that repeated ecological divergence may play an important role in Escallonia speciation [ 10 ]. Thus, Escallonia is emerging as a notable system to uncover the ecological and evolutionary processes underpinning tropical plant adaptation, speciation, and the nature of plant species [ 12 ]. To begin investigating the genomic substrate and biological processes underlying the radiations in Escallonia and Escalloniales, we hereby report the draft genomes of two Escallonia species.…”

Performance and physiological quality of Escallonia resinosa seeds: prospects for their use in reforestation and restoration

“…Escallonia Mutis ex L.f. (1781) (Escalloniaceae) is an ecologically and morphologically diverse neotropical genus that is widely distributed (7,000 km) mainly along the Andes, from Costa Rica (Cordillera de Talamanca) to southern Argentina and Chile (Tierra del Fuego) (Sede et al 2013; Sede & Denham 2018; Jacobs et al 2021). This genus comprises about 40 recognized species of small trees and shrubs (Sleumer 1968; Zapata & Villarroel 2019).…”