Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

堐remise of the study: Just as Sanger sequencing did more than 20 years ago, next-generation sequencing (NGS) is poised to revolutionize plant systematics. By combining multiplexing approaches with NGS throughput, systematists may no longer need to choose between more taxa or more characters. Here we describe a genome skimming (shallow sequencing) approach for plant systematics. 堍ethods: Through simulations, we evaluated optimal sequencing depth and performance of single-end and paired-end short read sequences for assembly of nuclear ribosomal DNA (rDNA) and plastomes and addressed the effect of divergence on reference-guided plastome assembly. We also used simulations to identify potential phylogenetic markers from low-copy nuclear loci at different sequencing depths. We demonstrated the utility of genome skimming through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae). 堋ey results: Paired-end reads performed better than single-end reads. Minimum sequencing depths for high quality rDNA and plastome assemblies were 40נand 30׬ respectively. Divergence from the reference significantly affected plastome assembly, but relatively similar references are available for most seed plants. Deeper rDNA sequencing is necessary to characterize intragenomic polymorphism. The low-copy fraction of the nuclear genome was readily surveyed, even at low sequencing depths. Nearly 160000 bp of sequence from three organelles provided evidence of phylogenetic incongruence in the SDC. 堃onclusions: Adoption of NGS will facilitate progress in plant systematics, as whole plastome and rDNA cistrons, partial mitochondrial genomes, and low-copy nuclear markers can now be efficiently obtained for molecular phylogenetics studies.No Full Tex

Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy

We conducted phylogenetic analyses of the fern family Grammitidaceae using sequences from two cpDNA genes and from morphological characters. Data were obtained for 73 species from most recognized genera in the family. The genera Adenophorus, Ceradenia, Calymmodon, Cochlidium, Enterosora, and Melpomene were each strongly supported as being monophyletic. Other recognized genera that were not supported as monophyletic included Ctenopteris, Grammitis, Lellingeria, Micropolypodium, Prosaptia, and Terpsichore. Several previously unrecognized clades were identified, some of which are characterized by distinctive morphological features. Analyses of the distribution of morphological character states on our inferred phylogeny showed extremely high levels of homoplastic evolution for many different characters. Homoplasy for morphological characters was considerably greater than for molecular characters. Many of the characters that exhibited high levels of convergent or parallel evolution across the phylogeny are features that have been commonly used to circumscribe genera in this group (e.g., leaf blade dissection, various rhizome scale characters, and glandular paraphyses). Conversely, some of the characters that exhibited relatively low levels of homoplasy have either not been regarded as having taxonomic value or have been ignored (e.g., root insertion, rhizome scale sheen). Our data support a New World origin of Grammitidaceae, with Old World taxa generally being more evolutionarily derived. Several clades are either primarily Neotropical or primarily Paleotropical but also have a few members distributed in the opposite hemisphere. Thus, we postulate multiple, independent dispersal and colonization events in several lineages