Next-generation lineage discovery: A case study of tuberous Claytonia L

Species formation is an intuitive endpoint of reproductive isolation, but circumscribing taxa that arise during speciation can be difficult because of gene flow, morphological continuity, hybridization or polyploidization, and low sequence variation among newly diverged lineages. Nonetheless, species complexes are ubiquitous, and their classification is essential for understanding how diversity influences ecosystem function.

We used modern sequencing technology to identify lineages of perennial Claytonia L. and assessed correspondence between genetic lineages and morphological/ecological variation. Subsets of 18 taxa from 63 populations were used for (a) lineage discovery using network and coalescent analyses, (b) leaf shape analyses using elliptical Fourier analysis and ordination, and (c) ecological analyses (soil chemistry, climate) using ANOVA and ordination.

Samples mainly aggregated into groups representing each of the previously recognized species in each of the genetic data sets. Compared to the double-digest restriction-site-associated DNA sequencing data set, genome skimming data provided more resolution and further opportunity to probe into patterns of nuclear and chloroplast genome diversity. Morphological and ecological associations are significantly different (albeit intergrading) among the taxa investigated. A new species, Claytonia crawfordii, is described based on morphological data presented here.

Genetic data presented in this study provide some of the first insights into phylogenetic relationships among recently diverged perennial Claytonia and are suggestive of past hybridization among caudicose and tuberous species. Given prior difficulties in understanding species boundaries among newly diverged plant lineages, this case study demonstrates the revolutionary breakthrough for systematics research that high throughput sequencing represents.