Evaluating the utility of organelle genes for the phylogeographic study of Halymeniales (Rhodophyta)

Abstract

Halymenialean species is one of the important red algal lineage in the marine biodiversity and phylogeography. Nowadays, sixteen organelle genomes (plastid and mitochondrion from eight species) of Halymeniales species are available Grateloupia angusta, Kintokiocolax aggregato-cerantha, Halymenia maculata, Polyopes affinis, P. lancifolious and Pachymenia lanciniata (in this study). Despite the increasing number of organelle genomes used for red algal researches, plastid rbcLand mitochondrial cox1 have been used in previous halymenialean red algal phylogeographic studies without screening or testing. The aim of the present study is to evaluate the utility of candidate genes and to suggest the alternative gene markers for halymenialean phylogeographic study. P-distance was considered as a proxy of gene evolution rate and their standard deviation (interquartile range, IQR) as differential rate across species. All mitochondrial and plastid genes (219) were sorted into five p-distance bins and three categories of relative IQR within each p-distance bin. A total 28 candidate genes were selected in high p-distance bins and low IQR among organelle genes. Nine plastid and five mitochondrial genes were selected as candidate genes under the criterion on total gene length.