Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for phylogenetic 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 plastid genes of 107 published plastid genomes based on various sequence-derived properties and their tree distance to plastid genome phylogenies and found 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.
Zhan SH, Shi CC, and Liu SL. Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era. Evol Ecol 10(3): 1299-1310.
Maintainer: Shing Hei Zhan (Dept. of Zoology & Biodiversity Research Centre, the University of British Columbia)