Cryptic diversity in the model fern genus Ceratopteris (Pteridaceae)

• Published in: Molecular phylogenetics and evolution 2020-11, Vol.152, p.106938-106938, Article 106938
• Main Authors: Kinosian, Sylvia P., Pearse, William D., Wolf, Paul G.
• Format: Article
• Language: English
• Subjects: Base Sequence; C-fern; Chromosome Mapping; Genome, Plant - genetics; Genomics; Hybridization, Genetic; Phylogeny; Polyploid; Polyploidy; Pteridaceae - classification; Pteridaceae - genetics; RADseq; Species Specificity; Systematics
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2020.106938

[Display omitted] •We produce the first multi-locus dataset for the model fern genus Ceratopteris.•Phylogeny and population structure were examined with samples from its full range.•Our analyses support known species concepts, and reveal novel cryptic variation.•The species Ceratopteris thalictroides may contain two polyphyletic cryptic species.•Taxonomic revision of this polymorphic species, and genus, is warranted. Cryptic species are present throughout the tree of life. They are especially prevalent in ferns, because of processes such hybridization, polyploidy, and reticulate evolution. In addition, the simple morphology of ferns limits phenotypic variation and makes it difficult to detect cryptic species. The model fern genus Ceratopteris has long been suspected to harbor cryptic diversity, in particular within the highly polymorphic C. thalictroides. Yet no studies have included samples from throughout its pan-tropical range or utilized genomic sequencing, making it difficult to assess the full extent of cryptic variation within this genus. Here, we present the first multilocus phylogeny of the genus using reduced representation genomic sequencing (RADseq) and examine population structure, phylogenetic relationships, and ploidy level variation. We recover similar species relationships found in previous studies, find support for the cryptic species C. gaudichaudii as genetically distinct, and identify novel genomic variation within two of the mostly broadly distributed species in the genus, C. thalictroides and C. cornuta. Finally, we detail the utility of our approach for working on cryptic, reticulate groups of ferns. Specifically, it does not require a reference genome, of which there are very few available for ferns. RADseq is a cost-effective way to work with study groups lacking genomic resources, and to obtain the thousands of nuclear markers needed to untangle species complexes.