Wyn A. Jones

A reassessment of the taxonomic status of Porphyra suborbiculata, Porphyra carolinensis and Porphyra lilliputiana (Bangiales, Rhodophyta) based on molecular and morphological data

We examined three species of diminutive Porphyra, Porphyra suborbiculata Kjellman from the North Pacific, Porphyra lilliputiana W. A. Nelson, G. A. Knight et M. W. Hawkes from the South Pacific, and Porphyra carolinensis Coll et J. Cox from the western North Atlantic. These taxa were compared in terms of morphology, habitat data and sequence haplotypes of nuclear small subunit rDNA (SSU) and internal transcribed spacers of the nuclear rDNA cistron (ITS). These three species have similar morphologies and growth habits, and share very similar type descriptions and habitat records. Haplotype variation was found within the 11 samples of P. lilliputiana we examined and within P. suborbiculata samples from two locations, but the single P. carolinensis haplotype (from collections from two separate locations) was identical to one found in several widespread P. lilliputiana samples. Unrooted phylogenetic trees based on sequence data do not support any of the three species as being a monophyletic group. We conclude that these three taxa represent a single species with the oldest name P. suborbiculata having nomenclatural priority. It is likely that P. suborbiculata has recently been introduced to the western Atlantic from the Pacific region.

Species recognition in New Zealand Porphyra using 18S rDNA sequencing

The long geographic isolation of New Zealand, an archipelago with a large latitudinal range (29°to 54°S) and an extensive coastline, has resulted in a high level of endemism in both land and coastal marine flora. The genus Porphyra in NZ is represented by 5 epiphytic species and a number of epilithic species, many of which are undescribed. Systematic studies aimed at understanding variation inmorphology and life history are underway, and have led to the description of a number of new species. The present study uses sequence data from the18S rDNA locus to investigate genetic variation in New Zealand Porphyra. Sequences have been fully determined for 10 epilithic species. A subset of these data has been shown to be sufficient to distinguish established taxa and to identify new entities. Our data indicate that New Zealand harbours at least 12 epilithic species of Porphyra, establishing the NZ coastline as a repository of diversity for this genus. Phylogenetic trees based on division in complete 18S rDNA sequence data show a deep division in the genus that is not obviously correlated with existing morphological characters, and indicate that representatives of the New Zealand flora have undergone long reproductive isolation.

Is gene deletion in eukaryotes sequence-dependent A study of nine deletion junctions and nineteen other deletion breakpoints in intron 7 of the human dystrophin gene

Although large deletions comprise 65% of the mutations that underlie most cases of Duchenne and Becker muscular dystrophies, the DNA sequence characteristics of the deletions and the molecular processes leading to their formation are largely unknown. Intron 7 of the human dystrophin gene is unusually large (110 kb) and a substantial number of deletions have been identified with endpoints within this intron. The distribution of 28 deletion endpoints was mapped to local sequence elements by PCR. The break points were distributed among unique sequence, LINE-1, Alu, MIR, MER and microsatellite sequences with frequencies expected from the frequency of those sequences in the intron. Thus, deletions in this intron are not associated primarily with any one of those sequences in the intron. Nine deletion junctions were amplified and sequenced. Eight were deletions between DNA sequences with minimal homology (0-4 bp) and are therefore unlikely to be products of homologous recombination. In the ninth case, a complex rearrangement was found to be consistent with unequal recombinational exchange between two Alu sequences coupled with a duplication. We have hypothesized that a paucity of matrix attachment regions in this very large intron expanded by the insertion of many mobile elements might provoke a chromatin structure that stimulates deletions (McNaughton et al., 1997, Genomics 40, 294-304). The data presented here are consistent with that idea and demonstrate that the deletion sequences are not usually produced by homologous DNA misalignments.

Phylogenetic diversity in South African Porphyra (Bangiales, Rhodophyta) determined by nuclear SSU sequence analyses

Specimens of Porphyra were collected at 10 sites along the western, southern and eastern Cape coasts of South Africa during late January to early February 2001. Sequence data from the variable V9 region of the nuclear small subunit rDNA (nSSU) locus were determined for 45 specimens. These data identified 11 distinct entities each with unique V9 sequences. Phylogenetic analyses incorporating sequences of Porphyra and Bangia from throughout the world revealed that eight of the entities examined in this study form a monophyletic group, apparently endemic to the southern African region. The other three entities exhibited no close phylogenetic relationship either with each other or with the other South African taxa. This survey indicates that the southern African coast is a repository of greater taxonomic diversity for this genus than has been previously reported.

Production of Recombinants after Protoplast Fusion in Clostridium acetobutylicum P262

Protoplast fusion of Clostridium acetobutylicum P262 auxotrophs produced stable recombinants and segregating biparentals at frequencies of 0.3-2.0% and 1.4-8.3% respectively. Two novel classes of biparentals, partially-complementing and zero non-complementing, were observed.

Sequence of a transposon identified as Tn1000 (γδ)

We report the complete sequence of a transposon found in a cosmid clone of a human DNA sequence. The transposon is identified as the Escherichia coli transposon Tn1000 (also known as gamma delta) on the basis of the identity of the restriction map of the new sequence with that previously recorded for Tn1000 and homology between parts of the new sequence and that of published fragments of Tn1000 sequence. The transposon, which comprises 5,981 nucleotides including two 35 bp inverted terminal repeat sequences (ITRs), contains three open reading frames. The sequence of the resolvase coding region (tnpR) is identical to that published by others. A second reading frame can be identified as the tnpA gene, coding for the transposase, on the grounds of its strong homology with the corresponding gene from transposon Tn3. The third reading frame has the potential to code for a protein of unknown function containing 698 amino acids.

The flora of Double Hill (Dunedin Volcanic Complex, Middle–Late Miocene) Otago, New Zealand

Plant fossils from a diatomaceous lake deposit at Double Hill within the Dunedin Volcanic Complex (Middle to Late Miocene) are described. Tentative affinities are assigned on the basis of leaf morphology, cuticle morphology and co-occurrence of micro- and megafossils. From an assemblage of more than 1000 fossil leaves, 35 different morphotypes can be discerned: four are assigned to Podocarpaceae, four to Monocotyledonae and 27 to Eudicotyledonae or Magnoliidae. All the possible plant families recognized from Double Hill as megafossils still occur in New Zealand today, but most could not tolerate the low temperatures or relatively low precipitation rates of the Dunedin area today.

Phylogenetic relationships among transposon-like elements in human and primate DNA

A THE-1 sequence in intron 7 of the human dystrophin gene has been found to represent a new subfamily of THE-1 elements. The sequence is closely related to the MstII family of repetitive sequences and is more like single-copy sequences found in the galago genome than any other THE-1 sequence previously reported. This new THE-1 sequence has been compared with two other complete THE-1 sequences and three related long-terminal repeat elements that we have previously found in intron 7 of the dystrophin gene, and with members of the same family from elsewhere in the primate genome. Parsimony and deletion analysis show that the cluster of THE-1 sequences in intron 7 of the dystrophin gene has arisen from at least three individual insertion events, rather than from the insertion and duplication of a single progenitor sequence.

Diverse and abundant insect herbivory on Miocene Nothofagaceae of the Dunedin Volcano, Otago, New Zealand

Terrigenous sediments occurring within the mid/upper Miocene Dunedin Volcanic Group in southern New Zealand contain well-preserved leaf-beds, commonly dominated by Nothofagaceae leaf fossils. Abundant insect herbivory traces occur on Nothofagaceae leaf fossils from the Double Hill and Kaikorai Valley localities, including 28 types of external foliage feeding traces, 8 types of galling and a possible fungal trace, several not described previously. Relatively high diversity of insect herbivory traces on broad-leaved Nothofagaceae suggests a high diversity of insect herbivores. The high abundance and diversity of trace fossils in combination with evidence for plicate vernation suggests that Nothofagaceae growing on the mid/late Miocene Dunedin Volcano had shorter leaf retention times than modern New Zealand Nothofagaceae. The loss of Nothofagaceae diversity from New Zealand due to cooling climate in the late Neogene could also have meant the demise of an arthropod community adapted to living on broad-leaved Nothofagaceae. Insect damage diversity and amount at Double Hill was significantly higher than at Kaikorai Valley, as well as the occurrence of plicate vernation and leaves with stunted growth forms. This suggests that there may have been some difference in the insect diversity of the two sites, relating to local palaeoenvironment, such as higher temperatures at Double Hill during the warm season and/or differences in forest density.

A new record of a marine macroalga from New Zealand ‐Giraudyopsis stellifera

Abstract The presence of the small brown‐gold alga Giraudyopsis stellifera in New Zealand is recorded for the first time. This alga was discovered in algal cultures initiated with material collected on Stewart Island. The comparison of 18S rDNA sequences enabled the confirmation of its identity. This species produces small basal discs from which erect uniseriate filaments develop. These erect filaments become pluriseriate and then produce many zoosporangia. Although this species is placed in the order Chrysomeridales the phylogenetic affinities of this order are unclear.