Given the problems of species delimitation in algae using morphology or sexual compatibility, molecular data are becoming the standard for delimiting species and testing their traditional boundaries. The idea that species are separately evolving metapopulation lineages, along with theoretical progress in phylogenetic and population genetic analyses, has led to the development of new methods of species delimitation. We review these recent developments in DNA-based species delimitation methods, and discuss how they have changed and continue to change our understanding of algal species boundaries. Although single-locus approaches have proven effective for a first rapid and large-scale assessment of species diversity, species delimitation based on single gene trees falls short due to gene tree-species tree incongruence, caused by confounding processes like incomplete lineage sorting, trans-species polymorphism, hybridization and introgression. Data from unlinked loci and multi-species coalescent methods, which combine principles from phylogenetics and population genetics, may now be able to account for these complicating factors. Several of these methods also provide statistical support regarding species boundaries, which is important because speciation is a process and therefore uncertainty about precise species boundaries is inevitable in recently diverged lineages.

Red algae of the Bostrychia radicans/B. moritziana complex are common in warm temperate areas of North America. Phylogenetic analysis of both plastid and mitochondrial DNA sequence data revealed seven distinct evolutionary lineages among worldwide samples. Although only two haplotypes (plastid and mitochondrial) were found in Pacific Mexico, four plastid and 11 mitochondrial haplotypes were found in a similar latitudinal spread along the Atlantic coast of the United States. On the U.S. Atlantic coast only one plastid haplotype was found in northern samples (Connecticut to North Carolina), whereas further south several plastid haplotypes were found. Phylogenetic analyses suggested that this single plastid haplotype found among northern samples could be the result of a northward range expansion possibly since the last glacial maximum. Crossing data of samples within the same evolutionary lineage showed that samples with the same plastid haplotypes were generally sexually compatible; samples with different plastid haplotypes were reproductively isolated. Samples from Pacific Mexico were partially reproductively compatible with some samples from the Atlantic USA (plastid haplotype C) and were more closely related to these samples than these U.S. samples were to other U.S. Atlantic samples. Compatible solute types mirrored the plastid haplotype, with plastid haplotype B having only sorbitol, whereas all other haplotypes also contained dulcitol. Samples from Atlantic USA, with different plastid haplotypes (e.g. B vs. C), but within the same evolutionary lineage, were reproductively isolated from each other. Data indicate that reproductive isolation occurs between and within supported evolutionary lineages and that the number of cryptic species is high.

The genus Caulerpa consists of about 75 species of tropical to subtropical siphonous green algae. To better understand the evolutionary history of the genus, a molecular phylogeny was inferred from chloroplast tufA sequences of 23 taxa. A sequence of Caulerpella ambigua was included as a potential outgroup. Results reveal that the latter taxon is, indeed, sister to all ingroup sequences. Caulerpa itself consists of a series of relatively ancient and species‐poor lineages and a relatively modern and rapidly diversifying clade, containing most of the diversity. The molecular phylogeny conflicts with the intrageneric sectional classification based on morphological characters and an evolutionary scheme based on chloroplast ultrastructure. High bootstrap values support monophyly of C. mexicana, C. sertularioides, C. taxifolia, C. webbiana, and C. prolifera, whereas most other Caulerpa species show para‐ or polyphyly.

Intraspecific studies of red algae have relied on nuclear or plastid markers rather than mitochondrial data to address questions of systematics, biogeography or population genetics. In this study, primers were developed that spanned the noncoding intergenic region between the mitochondrial cytochrome oxidase subunit 2 and cytochrome oxidase subunit 3 genes. These primers were demonstrated to be successful on a variety of red algae in different orders: Gracilariales, Bonnemaisoniales and Ceramiales (families: Delesseriaceae, Ceramiaceae and Rhodomelaceae). Amplification products were between 450 and 320 bp in length, with variation in length shown among geographically distant isolates within a species. The region was variable within a single species, as shown for Bostrychia moritziana and B. radicans, and within populations of Caloglossa leprieurii. In the latter species, four mitochondrial haplotypes were observed in isolates from a single locality in Woolooware Bay, New South Wales, Australia. Analysis of hybrids between different mitochondrial haplotypes of B. moritziana revealed that the mitochondria are maternally inherited in this species. This is the first report of a mitochondrial marker that is variable within red algal populations and may lead to a better understanding of the population ecology of these important marine organisms.

Red algal parasites are common and have a unique type of development in which parasite nuclei are transferred to host cells and “control” host cell development. Previous phylogenetic studies have concentrated on parasites closely related to their hosts, termed adelphoparasites. A second set of parasites, usually classified in a different family or tribe from their host, termed alloparasites, have not been studied phylogenetically. This study concentrates on the wholly parasitic family, the Choreocolacaceae (Gigartinales). Using small subunit rDNA sequence data, we found that all the parasites studied are within the same family as their host. Our data support the placement of Holmsella, species of which parasitize Gracilaria and Gracilariopsis, in the order Gracilariales and suggest that Holmsella is an old parasitic genus. Most other species of the Choreocolacaceae parasitize species of the Rhodomelaceae. The one exception is the hyperparasitism between Harveyella mirabilis (Reinsch) F. Schmitz et Reinke (Rhodomelaceae) and the parasite Gonimophyllum skottsbergii Setchell (Delesseriaceae). The parasites Bostrychiocolax australis Zuccarello et West and Dawsoniocolax bostrychiae (Joly et Yamaguishi‐Tomita) Joly et Yamaguishi‐Tomita are placed within the tribe Bostrychiae as are their hosts. Harveyella mirabilis has a single origin and has switched hosts several times during its passage between the Atlantic and Pacific Oceans. Evidence does not support the continued recognition of the family Choreocolacaceae. Our results also indicate that the distinction between adelphoparasites and alloparasites is unwarranted, with a continuum between newly evolved parasites closely related to their hosts and parasites less closely related to their hosts.