The Dasylirion genus is highly represented in the arid and semi-arid regions of Mexico and USA, playing important ecological and economical roles. Inferring the evolutionary patterns of this group will eventually facilitate understanding biological phenomena and outlining conservation and usage strategies. We performed a molecular phylogenetic analysis based on two chloroplast DNA regions: maturase-K gene (matK) and the large subunit of ribulose-1,5-bisphosphate carboxylase gene (rbcL). We constructed a phylogenetic tree by maximum likelihood with GTR as the sequence substitution model and a relaxed clock, inferred diversification patterns by lineage through time and explored the diversification rates of Dasylirion by the Yule model. The study included 11 species of the genus, which represent 50% of all its known species. We used two calibration points to date the tree, one based on fossil records of Acorus gramineus, and the other on the estimated stem age of the Yucca genus. The combined sequences of the two partial genes comprised 1455 bp and 18 polymorphic sites. We estimated an average substitution rate of 0.0005 nucleotide per million years for the concatenated DNA sequences. The molecular dating analysis estimated that the Dasylirion genus appeared more than 5.46 million years ago, with a rate of diversification of 0.0466 net speciation events per million years. The estimated age represents a lower bound, since not all Dasylirion species are included. These findings are consistent with other origin and diversification hypotheses for arid-land Asparagaceae in the Mexican highlands as a result of geomorphological events in North America.

Twelve hyper-β carotene-producing strains of algae assigned to the genus Dunaliella salina have been isolated from various hypersaline environments in Israel, South Africa, Namibia and Spain. Intron-sizing of the SSU rDNA and phylogenetic analysis of these isolates were undertaken using four commonly employed markers for genotyping, LSU rDNA, ITS, rbcL and tufA and their application to the study of Dunaliella evaluated. Novel isolates have been identified and phylogenetic analyses have shown the need for clarification on the taxonomy of Dunaliella salina. We propose the division of D. salina into four sub-clades as defined by a robust phylogeny based on the concatenation of four genes. This study further demonstrates the considerable genetic diversity within D. salina and the potential of genetic analyses for aiding in the selection of prospective economically important strains.

We developed a multiplex PCR DNA marker for quick and easy identification of the AAGG-genome timopheevii lineage, including Triticum timopheevii, Triticum araraticum and hexaploid Triticum zhukovskyi (AAAmAmGG), and the AABB-genome emmer wheat lineage, including Triticum durum, Triticum dicoccum and Triticum dicoccoides. Distinguishing between tetraploid AAGG- and AABB-genome wheat species based on morphology is known to be difficult. This multiplex PCR system is based on the simultaneous PCR amplification of two chloroplast regions, matK and rbcL. The matK region molecularly distinguishes the two lineages, whereas the rbcL region is a positive control amplicon. We also examined whether the simple sequence repeat is a fixed mutation within species, using genetic resources in the collection of KOMUGI, Kyoto University, which comprises accessioned species collected across diverse geographical areas. The multiplex PCR marker distinguished AAGG from AABB species with complete accuracy.

The green algal photobionts of 12 Xanthoria, seven Xanthomendoza, two Teloschistes species and Josefpoeltia parva (all Teloschistaceae) were analyzed. Xanthoria parietina was sampled on four continents. More than 300 photobiont isolates were brought into sterile culture. The nuclear ribosomal internal transcribed spacer region (nrITS; 101 sequences) and the large subunit of the RuBiSco gene (rbcL; 54 sequences) of either whole lichen DNA or photobiont isolates were phylogenetically analyzed. ITS and rbcL phylogenies were congruent, although some subclades had low bootstrap support. Trebouxia arboricola,T. decolorans and closely related, unnamed Trebouxia species, all belonging to clade A, were found as photobionts of Xanthoria species. Xanthomendoza species associated with either T. decolorans (clade A), T. impressa, T. gelatinosa (clade I) or with an unnamed Trebouxia species. Trebouxia gelatinosa genotypes (clade I) were the photobionts of Teloschistes chrysophthalmus,T. hosseusianus and Josefpoeltia parva. Only weak correlations between distribution patterns of algal genotypes and environmental conditions or geographical location were observed.

Grateloupia doryphora (Montagne) Howe, originally described from Peru, has repeatedly been reported as an invasive species in Atlantic and Mediterranean waters. Various attempts to explain this species’ route of introduction have been unsatisfactory. New evidence from comparative rbcL sequence analysis and morphology suggests that this adventive species in the NE and NW Atlantic corresponds with G. turuturu Yamada, originally described from Japan. This provenance follows a well-recognized trend of invasive marine organisms that have colonized the Atlantic Ocean and Mediterranean Sea from Pacific NE Asia.

Molecular and breeding studies on two pan-tropical marine red algae reveal vastly different levels of genetic variation and reproductive isolation. Sequenced DNA regions from the nuclear, mitochondrial and plastid genomes (partial LSU rRNA, cox2-3 spacer, RuBisCo spacer, respectively) revealed high genetic variation among individuals of Spyridia filamentosa. An rbcL analysis shows that Spyridia is a monophyletic genus distinct from other Ceramiaceae sampled, suggesting that the Ceramiaceae could be paraphyletic. There is complete congruence between all data sets of S. filamentosa, showing a well-supported phylogeographic pattern with samples from the Pacific distinct from Atlantic and Indian Ocean samples. One western Mediterranean sample is associated with Atlantic specimens, while an eastern Mediterranean sample has closer affinities to Pacific samples, possibly indicating a recent cryptic introduction into the eastern Mediterranean. Limited breeding studies imply that these samples are mostly reproductively isolated, whereas a successful cross demonstrated maternal inheritance of organellar DNA. These data indicate that S. filamentosa exists as several cryptic species. Murrayella periclados exhibits low levels of genetic variation and no phylogeographic structure, and almost complete reproductive compatibility between isolates. This suggests that all M. periclados samples share a recent common ancestor that may have dispersed relatively rapidly, or that rates of base pair substitution between these two species vary greatly. Rapid long-distance dispersal of M. periclados is not indicated by what is known of the biology of M. periclados, especially in comparison with S. filamentosa, which appears to be a much better candidate for long-distance dispersal. These data demonstrate that red algal morphospecies are not equivalent units of diversity, with implications for our view of red algal biodiversity and evolution.

Phylogenetic relationships within the Sphacelariales sensu stricto were investigated using both a molecular and a morphological approach. Twenty species were included, representing all three families (i.e. Cladostephaceae, Sphacelariaceae and Stypocaulaceae) and six of the eight genera. The outgroup consisted of six species representing the Syringodermatales, Dictyotales, Choristocarpaceae and Onslowiaceae. DNA sequences of partial rbcL [1255–1375 nucleotides (nt)] and the adjacent RUBISCO spacer (40–842 nt) were determined in order to assess the molecular phylogeny. Only the 3′-end of the spacer (112 nt positions) was alignable for the ingroup taxa. Partition homogeneity testing showed that rbcL and RUBISCO spacer sequences could be combined. However, analysis of rbcL alone or in combination with the RUBISCO spacer gave the same results with only slight differences in support (bootstrap, jackknife, decay). Support was low at the base of the ingroup. Four basal clades could be discerned: (1) Stypocaulaceae, (2) Sphacelaria radicans, (3) Sphacelaria caespitula and (4) all other included taxa: (Sphacella subtilissima+the Sphacelaria subgenus Propagulifera) and (Cladostephus spongiosus+Sphacelaria nana+the Sphacelaria subgenera Battersia+Pseudochaetopteris). The independent morphological analysis (using 23 unordered morphological characters) revealed high homoplasy and an almost completely unresolved tree in which only the subgenus Propagulifera was supported. The morphological characters were subsequently mapped onto the rbcL tree in order to identify diagnostic or phylogenetically informative characters. Blackening in response to bleach and the presence of secondary segments were found to be basal synapomorphies for the Sphacelariales; presence of propagules with a lenticular central apical cell defines the Propagulifera; and strict acroblastic branching mode and axillary zoidangia define the Stypocaulaceae. The remaining characters have been gained or lost multiple times. This study highlights the problem of extreme morphological convergence and/or plasticity. Four options for a new circumscription including nomenclatural changes are discussed. It is concluded that none of the options will lead to greater clarity with respect to either identification or classification.

Phylogenetic analyses of the Dasyaceae based on sequence analysis of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and 42 morphological characters are presented. Comparative sequence analysis confirms the general view of the Ceramiaceae as a primitive, paraphyletic group giving rise to the Rhodomelaceae, Delesseriaceae and Dasyaceae within the monophyletic Ceramiales. On the basis of both data sets, the Heterosiphonia-like genera (Heterosiphonia, Colacodasya and Dasyella) are the most primitive members of the Dasyaceae, whereas the Dasya-like genera (Dasya, Pogonophorella, Eupogodon and Rhodoptilum) and Thuretia and Dictyurus are of more recent origin. On the basis of morphological data only, Thuretia and Dictyurus form a sister group to Heterosiphonia, and Eupogodon is monophyletic whereas Dasya and Heterosiphonia are not. Primary radial symmetry has arisen once in the Dasya clade but is secondarily obscured in some species by heavy, asymmetrical cortication that gives the appearance of bilateral symmetry. This is illustrated by species of Eupogodon and Rhodoptilum.

Four populations of the newly described freshwater red algal species Batrachospermum spermatoinvolucrum were sampled from British Columbia on the west coast of North America and Labrador on the east. The rDNA internal transcribed spacer (ITS) 1 and 2 sequences, RUBISCO large subunit (rbcL) gene data for three of the populations and morphometric characteristics were compared with those of B. gelatinosum. In addition, the key feature distinguishing B. spermatoinvolucrum, spermatangia on the involucral filaments of the carpogonial branch, was investigated seasonally in one British Columbia population of this species. The ITS analysis suggested that the B. spermatoinvolucrum populations were more closely related to particular B. gelatinosum populations than to each other and did not form a monophyletic clade. Two populations of B. spermatoinvolucrum from Labrador and British Columbia had identical rbcL sequences that were distinct from that of B. gelatinosum. However, the rbcL sequence from the third population of B. spermatoinvolucrum differed by only one nucleotide substitution from the B. gelatinosum populations. The tree generated from the morphometric data showed two groupings, each containing populations of both taxa. The presence of spermatangia-bearing involucral filaments was a stable character throughout the year. On the basis of these findings, B. spermatoinvolucrum is reduced to a form of B. gelatinosum. This form would encompass variant populations with characteristic carpogonial involucral filaments bearing spermatangia.

Nucleotide gene sequences for both the nuclear-encoded small-subunit RNA (SSU) and plastid-encoded large subunit of RuBisCO (rbcL) were determined for 16 species classified in the red algal order Gelidiales. Sequence comparisons indicate that rbcL is evolving at a faster rate than SSU in these species and that there is a more even distribution of changes across the length of the rbcL gene compared with that observed for the SSU gene. The rbcL sequences also showed a marked anti-GC bias at synonymous third-codon base positions. Parsimony and maximum-likelihood analyses were used to generate phylogenetic trees from both separate and combined analyses of the two sequence data sets. Relationships among most taxa are resolved robustly; however, the relative order of branching for the Capreolia and Ptilophora clades remains uncertain. The molecular data provide unambiguous, independent support for recognition of the newly established genus Pterocladiella. Although the position of Pterocladiella within the Gelidiales was not resolved clearly by the rbcL data alone, analyses of both the SSU and combined data matrices indicate that this genus is one of the three earliest-diverging lineages within the order. These data also suggest that Gelidium as currently circumscribed is not monophyletic. Molecular and morphological evidence suggests that the origin and, perhaps, diversification of the major lineages of gelidialean algae is correlated with distinct, independently evolved nutritional strategies for the developing carposporophyte.