Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era.

Shing Hei Zhan,Shao-Lun Liu,Chun-Chi Shih

doi:10.1002/ece3.5984

Shing Hei Zhan, Shao-Lun Liu + Show 1 more

Open Access

https://doi.org/10.1002/ece3.5984

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Abstract

Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of phycologists has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). In this proof‐of‐concept study, we leveraged this resource by developing and applying a phylogenomic strategy to seek candidate plastid markers suitable for phylogenetic community analysis. We ranked the core genes of 107 published plastid genomes based on various sequence‐derived properties and their tree distance to plastid genome phylogenies. The resulting ranking revealed that the most widely used marker, rbcL, is not necessarily the optimal marker, while other promising markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of them, rpoC1, in a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the rpoC1 primers will be useful to the phycological community for investigating the biodiversity and community ecology of the red algae.

Highlights

Integration of phylogenetic information into community ecology has enjoyed an upsurge of interest in the past decade (e.g., CavenderBares, Kozak, Fine, & Kembel, 2009; Webb, Ackerly, McPeek, & Donoghue, 2002; Weber, Wagner, Best, Harmon, & Matthews, 2017)
We developed a bioinformatics strategy to select phylogenetic markers informed by an analysis of 107 published plastid genomes, using these to assemble the AA and NT alignments and the gene trees of 120 single-copy core plastid gene families
In both sets of the normalized Robinson–Foulds distance (nRF) rankings of the AA and NT gene trees (Table S2 in Dryad), we found that psaA and psaB approximate the plastid genome trees better than rbcL and psbA

Summary

| INTRODUCTION

Integration of phylogenetic information into community ecology has enjoyed an upsurge of interest in the past decade (e.g., CavenderBares, Kozak, Fine, & Kembel, 2009; Webb, Ackerly, McPeek, & Donoghue, 2002; Weber, Wagner, Best, Harmon, & Matthews, 2017). We applied normalized Robinson– Foulds distance, a notion of tree distance that measures the proportion of bipartitions unique to one of the two given phylogenetic trees (Robinson & Foulds, 1981); in our study, the greater the distance (i.e., closer to 1), the more the disagreement there is in pairwise tree comparisons, and the more poorly a gene tree approximates the target plastid genome tree This phylogenomics approach allowed us to assess the commonly used markers (e.g., psaA, psaB, psbA, and rbcL) in red algal studies (reviewed in Brodie & Lewis, 2007; Leliaert et al., 2014; Saunders & Moore, 2013), as well as less-studied markers, to identify better candidates for biodiversity surveys and phylogenetic community ecology

| MATERIALS AND METHODS

| RESULTS AND DISCUSSION

| CONCLUSIONS