Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex

Abstract

In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse group of aquatic microalgae that includes important bioindicator species and many such lineages. One example is Nitzschia palea , a widespread species complex with several morphologically defined taxonomic varieties, some of which are critical pollution indicators. Morphological differences among the varieties are subtle and phylogenetic studies based on a few genes fail to resolve their evolutionary relationships. We conducted morphometric and transcriptome analyses of 10 Nitzschia palea strains to resolve the relationships among strains and taxonomic varieties. Nitzschia palea was resolved into three clades, one of which corresponds to a group of strains with narrow linear‐lanceolate valves. The other morphological group recovered in the shape outline analysis was not monophyletic and consisted of two clades. Gene‐tree concordance analyses and phylogenetic network estimations revealed patterns of incomplete lineage sorting and gene flow between intraspecific lineages. We detected reticulated evolutionary patterns among lineages with different morphologies, resulting in a putative recent hybrid. Our study shows that phylogenomic analyses of unlinked nuclear loci, complemented with morphometrics, can resolve complex evolutionary histories of recently diverged species complexes.

Genotyping by Sequencing for Estimating Relative Abundances of Diatom Taxa in Mock Communities

“…debilis) have considerable overlap in their morphological characteristics, making the species complex taxonomically challenging (12,37,38). Ciftci et al 39 recovered three strains analyzed in this study (TCC523, TCC641, and TCC852) in one molecular clade with lanceolate morphology. In contrast, two of the remaining three strains (TCC13901 and TCC13903) had narrower linear-lanceolate morphology.…”

“…The morphometric ranges measured with LM overlapped for three strains that were morphologically and phylogenetically closest (TCC523, TCC641, and TCC852) (39). These were smaller than the ranges indicated for the species due to size reduction in long-term cultures (41), and some of their valves had deformities due to culture conditions.…”

“…The number of total clusters that we obtained after the removal of TCC13903 and the clusters that passed all ltering steps is listed in Table 1. TCC907 had the lowest average number of reads per cluster in the meta-reference, probably due to the higher genetic polymorphism of its allopolyploid genome (39). Among the clusters ltered based on homology, non-target mappings were most common between TCC523, TCC641, and TCC852 (Table 2, Additional le 1: Table S1), the members of a single clade based on the 183 nuclear gene phylogenies provided by Ciftci et al 39 .…”

“…TCC907 had the lowest average number of reads per cluster in the meta-reference, probably due to the higher genetic polymorphism of its allopolyploid genome (39). Among the clusters ltered based on homology, non-target mappings were most common between TCC523, TCC641, and TCC852 (Table 2, Additional le 1: Table S1), the members of a single clade based on the 183 nuclear gene phylogenies provided by Ciftci et al 39 . BLASTN ltering removed 1.48% of the clusters in the meta-reference.…”

“…Morphological differences between these varieties are very subtle, and their differentiation using light microscopy is impossible (37,38). Ciftci et al 39 revealed several evolutionary lineages in this species complex with recent gene ow between clades with different morphologies and a resulting putative hybrid. Given that N. palea plays a prominent role in the biological monitoring for the WFD, being able to rapidly and quantitatively distinguish among different lineages is of crucial importance.…”