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 based taxonomic varieties, some of which are critical pollution indicators. Morphological differences among the varieties are subtle and phylogenetic studies 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. Subsequent 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 and a resulting putative recent hybrid. Our study shows that phylogenomic analyses of many 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

“…Light microscopy (LM) counts distinguished strains based on their length, width, and fibula density features (Additional file 1: Table S2). These features overlapped with the morphometric ranges provided by Çiftçi et al [41], except for TCC907 (Additional file 1: Table S3). This strain is reported to be a recent putative hybrid, and it had many morphological deformities due to culture conditions.…”

“…The number of total clusters that we obtained after the removal of TCC13903 and the clusters that passed all filtering steps are 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 [41].…”

“…Among the clusters filtered based on homology, nontarget mappings were most common between TCC523, TCC641, and TCC852 (Table 2, Additional file 1: Table S1), the members of a single clade based on the 183 nuclear gene phylogenies provided by Ciftci et al [41]. BLASTN filtering removed 1.48% of the clusters in the meta-reference.…”

“…Molecular data (rbcL, 28S rRNA, and cox1 genes) suggest no objective criteria to choose a precise molecular threshold for species boundaries in N. palea, although the complex does contain several lineages [12,39,40]. Ciftci et al [41] revealed three evolutionary lineages based on 183 genes and detected recent gene flow between clades with different morphologies and a resulting putative hybrid. It is important to identify and quantify the abundances of these intraspecific lineages to reveal any differences in their distribution and ecology.…”

Exploring diatom diversity through cultures - a case study from the Bow River, Canada

“…(Stelbrink et al, 2018). Cultures will help to discriminate such complexes Vanormelingen et al, 2013;Çiftçi et al, 2022), thereby improving their use as bio-indicators.…”