Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen‐based phylogenomic approach in resolving species boundaries

Abstract

Species concept and delimitation are fundamental to taxonomic and evolutionary studies. Both inadequate informative sites in the molecular data and limited taxon sampling have often led to poor phylogenetic resolution and incorrect species delineation. Recently, the whole chloroplast genome sequences from extensive herbarium specimen samples have been shown to be effective to amend the problem. Stachyuraceae are a small family consisting of only one genus Stachyurus of six to 16 species. However, species delimitation in Stachyurus has been highly controversial because of few and generally unstable morphological characters used for classification. In this study, we sampled 69 individuals of seven species (each with at least three individuals) covering the entire taxonomic diversity, geographic range, and morphological variation of Stachyurus from herbarium specimens for genome‐wide plastid gene sequencing to address species delineation in the genus. We obtained high‐quality DNAs from specimens using a recently developed DNA reconstruction technique. We first assembled four whole chloroplast genome sequences. Based on the chloroplast genome and one nuclear ribosomal DNA sequence of Stachyurus, we designed primers for multiplex polymerase chain reaction and high throughput sequencing of 44 plastid loci for species of Stachyurus. Data of these chloroplast DNA and nuclear ribosomal DNA internal transcribed spacer sequences were used for phylogenetic analyses. The phylogenetic results showed that the Japanese species Stachyurus praecox Siebold & Zucc. was sister to the rest in mainland China, which indicated a typical Sino‐Japanese distribution pattern. Based on diagnostic morphological characters, distinct distributional range, and monophyly of each clade, we redefined seven species for Stachyurus following an integrative species concept, and revised the taxonomy of the family based on previous reports and specimens, in particular the type specimens. Furthermore, our divergence time estimation results suggested that Stachyuraceae split from its sister group Crossosomataceae from the New World at ca. 54.29 Mya, but extant species of Stachyuraceae started their diversification only recently at ca. 6.85 Mya. Diversification time of Stachyurus in mainland China was estimated to be ca. 4.45 Mya. This research has provided an example of using the herbarium specimen‐based phylogenomic approach in resolving species boundaries in a taxonomically difficult genus.

Herbarium phylogenomics: Resolving the generic status of the enigmatic Pseudobartsia (Orobanchaceae)

“…Similarly, four and five plastid regions failed to amplify from DNAs obtained from herbarium collections of Phtheirospermum muliense C. Y. Wu & D. D. Tao and Phtheirospermum parishii Hook.f., respectively (Dong et al, 2013). In contrast, fragmented DNA can be successfully sequenced by a high‐throughput short‐read sequencing approach (Besnard et al, 2014; Bakker et al, 2016; Zeng et al, 2018; Su et al, 2020). Such an approach allows recovery of whole plastomes or other genomic data from the degraded herbarium material (Zeng et al, 2018).…”

“…Genomic DNA has been successfully isolated from old herbarium specimens (Staats et al, 2011(Staats et al, , 2013Xu et al, 2015;Zeng et al, 2018;Alsos et al, 2020;Su et al, 2020), some as old as 200 years (Andreasen et al, 2009;Weiss et al, 2016). However, genomic DNA from such collections is often degraded with time (Gutaker & Burbano, 2017;Zeng et al, 2018), or by low-quality curation (Särkinen et al, 2012;Shen et al, 2017).…”

“…These collections preserve rare and endangered local endemics, including specimens from places that are difficult to access or have been so altered that little of the original flora remains. With the development of DNA isolation methods and sequencing techniques from ancient tissues (Weiss et al, 2016; Zeng et al, 2018), herbarium specimens now provide genetic and genomic data for investigations of phylogeny, DNA barcoding, and evolutionary biology (Bakker et al, 2016; Gutaker & Burbano, 2017; Kuzmina et al, 2017; Mikheyev et al, 2017; Su et al, 2020).…”

In memory of Professor Tang Yan‐Cheng: New perspectives in systematic and evolutionary biology

“…Such studies enable simultaneous study of morphologically distinguishing characteristics for resolved clades in the phylogeny (Willis et al, 2017). All three studies (Hu et al, 2020;Su et al, 2020;Ye et al, 2020) clarified previous taxonomic debates in these taxa and enabled the authors to propose revised taxonomic treatments based on a large amount of molecular phylogenetic data. Furthermore, the phylogeny of Magnolia, in particular, provides a comprehensive framework that may prove useful in breeding programs in this horticulturally important genus.…”

Phylogeny and Species Delimitation of Chinese Medicago (Leguminosae) and Its Relatives Based on Molecular and Morphological Evidence

“…It may rather be more appropriate to use integrative species concepts ( Liu, 2016 ; Hong, 2020 ), which reconciles different sources of data and meets multiple criteria of the diverse species concepts. Recent studies based on statistical analysis of morphological variation within and between species, combined with molecular evidence, mostly DNA barcodes (e.g., psbA-trnH , trnL-F , and ITS) at the population level, have provided strong power and new insights in delimiting species boundaries in many taxa, such as Orinus ( Su et al, 2015 ), Orychophargmus ( Hu et al, 2015 ), Ostrya ( Lu et al, 2016 ), and Stachyuraceae ( Su et al, 2020 ). Here, we apply such an integrative approach to facilitate species delimitation in Medicago L. and its two related genera.…”