The application of molecular data to the phylogenetic delimitation of species in bryophytes: A note of caution

Abstract

Molecular phylogenetics has been of prime importance in revisiting traditional taxonomic hypotheses, and this is especially true in taxa with reduced morphologies like bryophytes. Sequence identity at one or a few loci, as well as evidence for species para-or polyphyly, have been increasingly used to lump species. While sequence identity at loci that are usually variable within the group of interest can provide some incentive for additional study of such species, it does by no means alone provide sufficient evidence for synonymization. Similarly, the strict requirement that all species must be demonstrably monophyletic is equivalent to adopting an uncompromsing view that reproductive isolation (i.e., the biological species concept) is the only valid evidence for species status, and that all species have to be 100% isolated. Some modes of speciation lead to paraphyletic species or even phylogenetic networks. We therefore encourage case by case evaluation of all available data rather than applying a single criterion such as monophyly. We make some suggestions about how to use molecular data in the circumscription of bryophyte species.

Taxonomic studies in the Miconieae (Melastomataceae). XIII. Systematics of Miconia subcompressa, a Hispaniolan endemic comprised of three eco-geographic subspecies

“…6C)and greenish white petals (see Judd 2007). Parapatric/peripheral isolate speciation mechanisms should inevitably lead to such patterns, i.e., nonmonophyletic and phylogenetically unresolved species should be common (see general discussion in Donoghue 1985, Olmstead 1995, Reiseberg & Brouillet 1994, Reiseberg & Brouillet 1994, Willman & Meier 2000, de Queiroz 2007, Vanderpoorten & Shaw 2010, and the specific examples in Crisp & Chandler 1996, Thulin et al 2012, Porter-Utley 2014. Thus, as stated by Vanderpoorten and Shaw (2010, p. 234), "evidence for paraphyly does not necessarily provide strong evidence for combining paraphyletic and nested species"-and we emphasize that it is not at all problematic that M. subcompressa, as here circumscribed, is non-monophyletic.…”

“…Thus, as stated by Vanderpoorten and Shaw (2010, p. 234), "evidence for paraphyly does not necessarily provide strong evidence for combining paraphyletic and nested species"-and we emphasize that it is not at all problematic that M. subcompressa, as here circumscribed, is non-monophyletic. Vanderpoorten and Shaw (2010) further note that nucleotide sequence data from one or a few loci are often insufficient at the species level. We agree, along with many others (e.g., Despres et al 2003, Hughes et al 2006, Fazekas et al 2009).…”

“…This morphological information was considered along with the phylogenetic insights provided by the DNA-based phylogenetic analysis, keeping in mind the phylogenetic species approach (Donoghue 1985, Mishler & Brandon 1987, Mishler & Theriot 2000. However, some speciation mechanisms (e.g., peripheral isolation, parapatric speciation) frequently lead to species non-monophyly (see extensive discussion in Rieseberg & Brouillet 1994, Olmstead 1995, Crisp & Chandler 1996, Vanderpoorten & Shaw 2010) and thus we acknowledge that evidence for paraphyly does not necessarily provide strong evidence for combining paraphyletic and nested species. Subspecies are considered to be entities evolutionarily comparable to species, but phenetically more similar, showing incomplete differentiation, and thus not as easily diagnosed.…”

A special issue of Phytotaxa dedicated to Bryophytes: The closest living relatives of early land plants

“…The compilation of citations alone makes the paper a useful resource for those researchers who are at the stage of marker choice. The commentary paper by Vanderpoorten & Shaw (2010) presents a valuable and noteworthy discussion on the application of molecular data to the phylogenetic delimitation of species in bryophytes. In their paper, they suggest that if species delimitation, and species differentiation, are the primary goals in a research program, nucleotide sequence data should be complemented with approaches that focus on larger numbers of unlinked loci that are more variable.…”

Radula subg. Radula in Australasia and the Pacific (Jungermanniopsida)

“…Radula across the Pacific, broad species hypotheses have been inferred inappropriately. The underestimation of lineage diversity by morphologically based species circumscriptions is now a common theme in bryophyte systematics (Shaw 2001;Heinrichs et al 2009Heinrichs et al , 2010Heinrichs et al , 2011Vanderpoorten & Shaw 2010). This may be due to the species being defined on the basis of gross, often qualitative and often single, morphological characters.…”