The sequence data from the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) gene and 18S ribosomal DNA (small subunit) of taxa in the freshwater rhodophyte order Batrachospermales were used to construct phylogenetic hypotheses. Taxa examined in this study represent four families, eight genera, and six sections of the genus Batrachospermum. In addition, Rhododraparnaldia oregonica Sheath, Whittick et Cole, was included in the analysis because it shares particular ultrastructural, reproductive, and morphological characteristics with members of the Batrachospermales and Acrochaetiales. The trees generated from each gene, as well as a combined data set, were largely congruent. Rhododraparnaldia consistently occurs on an early branch within the Acrochaetiales-Palmariales clade and does not appear to be a member of the Batrachospermales. In addition,Thorea violacea Bory de St. Vincent was not closely related to the other taxa of the Batrachospermales in all trees and hence the family Thoreaceae does not appear to be a natural grouping within this order. All other taxa analyzed, which are presently classified within this order, formed a monophyletic clade in most analyses. Psilosiphon scoparium Entwisle was not closely allied with the taxa of the Lemaneaceae, lending support to the newly proposed family Psilosiphonaceae. Sequence data from the remaining taxa of the Lemaneaceae support the concept of a derived monophyletic clade. The genus Batrachospermum appears to comprise many morphologically similar but distantly related taxa, which will need further investigation to resolve their taxonomic status. Tuomeya, Sirodotia and Nothocladus are retained at the generic level until further data are obtained.

Recent molecular and morphological data necessitate a major taxonomic revision of the Batrachospermales, an order of red algae, distributed in freshwater habitats throughout the world. This article is a synthesis of available information with some targeted additional sequence data, resulting in a few relatively conservative taxonomic changes to begin the process of creating a natural taxonomy for the Batrachospermales. To increase the information content of our taxonomic categories, and in particular to reduce paraphyly, we describe one new genus (Kumanoa) and a new section in Batrachospermum (section Macrospora), and we amend the circumscriptions of the family Batrachospermaceae (to include Lemaneaceae and Psilosiphonaceae), the genus Batrachospermum (to exclude the sections Contorta and Hybrida, raised to genus level as Kumanoa), and the sections Aristata, Helminthoidea, and Batrachospermum of Batrachospermum. We also provide a new name, B. montagnei, for the illegitimate B. guyanense, and recognize an informal paraphyletic grouping of taxa within Batrachospermum, the "Australasica Group." This taxonomic synthesis increases the level of monophyly within the Batrachospermales but minimizes taxonomic change where data are still inadequate.

River regulation can cause various downstream changes to the physical environment of stream channels. Here, we examined whether disturbance of the stream bed and/or degree of emergence of large substrata affect the diversity and abundances of bryophytes and macroalgae in three regulated and three unregulated upland streams. We marked and mapped randomly selected rocks in situ for each stream and measured the rates at which these substrata disappeared. We recorded percentage covers of bryophytes and macroalgae in each stream on rocks of differing sizes ('small' <10 cm, 'medium' = 10-20 cm, 'large' >20 cm maximum top dimension) and lying either loosely on top of the bed or packed into it; we also recorded when rocks were emergent. We found strong positive associations between plant cover (mostly bryophytes) and substrate size, consistent with the hypothesis that substratum stability primarily drives bryophyte abundance. Nevertheless, highest covers of bryophytes in unregulated streams were found on emergent rocks, which tended to be large, meaning that disturbance and emergence effects were difficult to discriminate. Regulated streams did not have lower disturbance frequencies than unregulated systems. Percentage covers of plants, primarily bryophytes, were lower in regulated systems because of reduced cover on large substrata, but not small or medium ones. Together, these two pieces of evidence suggest that effects of river regulation on bryophytes were not caused by altered disturbance frequencies. A more likely explanation is that regulated streams have little of the daily or weekly rises and falls in discharge that occur in unregulated streams because of small rainfall events. Consequently, large rocks in regulated streams have only narrow zones that are subject to a variety of wetted conditions, which may be more suitable for bryophyte growth and colonization than constant submergence. Distinguishing between disturbance and emergence effects is important for setting environmental flows: alleviating the former requires more flushing flows whilst the latter requires greater temporal variability in non-flood flows.

Sixty-five accessions of the species-rich freshwater red algal order Batrachospermales were characterized through DNA sequencing of two regions: the mitochondrial cox1 gene (664 bp), which is proposed as the DNA barcode for red algae, and the UPA (universal plastid amplicon) marker (370 bp), which has been recently identified as a universally amplifying region of the plastid genome. UPGMA phenograms of both markers were consistent in their species-level relationships, although levels of sequence divergence were very different. Intraspecific variation of morphologically identified accessions for the cox1 gene ranged from 0 to 67 bp (divergences were highest for the two taxa with the greatest number of accessions; Batrachospermum helminthosum and Batrachospermum macrosporum); while in contrast, the more conserved universal plastid amplicon exhibited much lower intraspecific variation (generally 0-3 bp). Comparisons to previously published mitochondrial cox2-3 spacer sequences for B. helminthosum indicated that the cox1 gene and cox2-3 spacer were characterized by similar levels of sequence divergence, and phylogeographic patterns based on these two markers were consistent. The two taxa represented by the largest numbers of specimens (B. helminthosum and B. macrosporum) have cox1 intraspecific divergence values that are substantially higher than previously reported, but no morphological differences can be discerned at this time among the intraspecific groups revealed in the analyses. DNA barcode data, which are based on a short fragment of an organellar genome, need to be interpreted in conjunction with other taxonomic characters, and additional batrachospermalean taxa need to be analyzed in detail to be able to draw generalities regarding intraspecific variation in this order. Nevertheless, these analyses reveal a number of batrachospermalean taxa worthy of more detailed DNA barcode study, and it is predicted that such research will have a substantial effect on the taxonomy of species within the Batrachospermales in the future.

The creation of Australia’s Virtual Herbarium forced the Australian plant systematics community to find a mechanism for deciding between alternative taxonomies. Following a workshop on the Orchidaceae and the publication of some simple draft guidelines, a set of ‘rules of thumb’ are presented here that we believe represent the view of most practising systematists. Not everyone will agree, and we have provided alternative views where possible. We include the need for monophyletic taxa, minimising taxonomic change, understanding that some taxa have strong ‘interest groups’, making it clear that ‘preferred name’ does not necessarily imply ‘best name’ on all criteria, avoiding epithets used in possible congeners, and the concept of ‘majority rules’ when states and territories have differing views.