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Genetic variation in Carpophyllum Greville and Cystophora J. Agardh (Fucales, Phaeophyceae) was investigated at a variety of scales. An extensive survey of mitochondrial spacer variation in Carpophyllum maschalocarpum from 32 populations around New Zealand shows strong population differentiation at relatively small scales (50–100 kilometres), but also pathways of long distance dispersal that connect populations over much greater distances. In addition, historical climate change appears to have restricted C. maschalocarpum to the northern North Island during the last glacial maximum, with subsequent southward range expansion revealed by low genetic diversity in southern populations. These results are consistent with limited dispersal at the gamete and zygote stage, expected in fucalean algae, but with occasional long distance dispersal by detached floating thalli. The genetic signature suggests these two modes of dispersal are decoupled. Internal Transcribed Spacers sequences show little differentiation between C. maschalocarpum and C. angustifolium, and hybridisation was found in several populations where these species are broadly sympatric. In the Bay of Plenty the two species had different ITS ribotypes, but most C. angustifolium specimens had a mitochondrial spacer haplotype that clustered with C. maschalocarpum haplotypes. This indicates mitochondrial introgression from C. maschalocarpum into C. angustifolium. In Northland species were difficult to separate by morphology or molecular markers, and some populations appear to be comprised entirely of hybrids. Genetic distances between different species of Cystophora are very variable, and in some cases intra-species distances are similar to interspecies distances. This is problematic for DNA barcoding methods that rely on thresholds between inter-species and intra-species genetic distances. In some (but not all) cases, the absence of molecular differentiation can be attributed to oversplitting of Cystophora species by morphological methods, and I synonymise C. congesta with C. retroflexa, and C. distenta with C. scalaris. These studies exemplify the difficulties of delimiting species in brown algae: Morphology is often misleading or uninformative; genetic differentiation of species is very variable and often low; and species’ histories show complex patterns of isolation and secondary contact. I argue for an explicitly historical concept of species, with species’ history included in species descriptions.

Molecular Studies of New Zealand Fucales: Phylogeography, Phylogeny and Taxonomy in Carpophyllum and Cystophora (Phaeophyceae)