Eric W. Linton

Molecular phylogeny of Pholadoidea Lamarck, 1809 supports a single origin for xylotrophy (wood feeding) and xylotrophic bacterial endosymbiosis in Bivalvia

The ability to consume wood as food (xylotrophy) is unusual among animals. In terrestrial environments, termites and other xylotrophic insects are the principle wood consumers while in marine environments wood-boring bivalves fulfill this role. However, the evolutionary origin of wood feeding in bivalves has remained largely unexplored. Here we provide data indicating that xylotrophy has arisen just once in Bivalvia in a single wood-feeding bivalve lineage that subsequently diversified into distinct shallow- and deep-water branches, both of which have been broadly successful in colonizing the worlds oceans. These data also suggest that the appearance of this remarkable life habit was approximately coincident with the acquisition of bacterial endosymbionts. Here we generate a robust phylogeny for xylotrophic bivalves and related species based on sequences of small and large subunit nuclear rRNA genes. We then trace the distribution among the modern taxa of morphological characters and character states associated with xylotrophy and xylotrepesis (wood-boring) and use a parsimony-based method to infer their ancestral states. Based on these ancestral state reconstructions we propose a set of plausible hypotheses describing the evolution of symbiotic xylotrophy in Bivalvia. Within this context, we reinterpret one of the most remarkable progressions in bivalve evolution, the transformation of the typical myoid body plan to create a unique lineage of worm-like, tube-forming, wood-feeding clams. The well-supported phylogeny presented here is inconsistent with most taxonomic treatments for xylotrophic bivalves, indicating that the bivalve family Pholadidae and the subfamilies Teredininae and Bankiinae of the family Teredinidae are non-monophyletic, and that the principle traits used for their taxonomic diagnosis are phylogenetically misleading.

Reconstructing euglenoid evolutionary relationships using three genes: nuclear SSU and LSU, and chloroplast SSU rDNA sequences and the description of Euglenaria gen. nov. (Euglenophyta).

Using Maximum Likelihood and Bayesian analyses of three genes, nuclear SSU (nSSU) and LSU (nLSU) rDNA, and chloroplast SSU (cpSSU) rDNA, the relationships among 82 plastid-containing strains of euglenophytes were clarified. The resulting tree split into two major clades: clade one contained Euglena, Trachelomonas, Strombomonas, Colacium, Monomorphina, Cryptoglena and Euglenaria; clade two contained Lepocinclis, Phacus and Discoplastis. The majority of the members of Euglena were contained in clade A, but seven members were outside of this clade. Euglena limnophila grouped with, and was thus transferred to Phacus. Euglena proxima was a single taxon at the base of clade one and is unassociated with any subclade. Five members of Euglena grouped together within clade one and were transferred into the newly erected genus Euglenaria. The monophyly of the remaining genera was supported by Bayesian and Maximum Likelihood analyses. Combining datasets resolved the relationships among ten genera of photosynthetic euglenoids.

Taxon-rich multigene phylogeny of the photosynthetic euglenoids (Euglenophyceae)

To establish taxonomy and understand phylogenetic relationships among strains and species of the photosynthetic euglenoids, we performed phylogenetic analyses based on a four gene sequence dataset (nr SSU and LSU rDNA, and pt SSU and LSU rDNA) from 343 taxa (including three outgroup). The phylogenetic tree based on the combined dataset was split into two major clades: Euglenaceae and Phacaceae. The family Euglenaceae was a well-supported monophyletic group containing eight genera (Colacium, Cryptoglena, Euglena, Euglenaformis, Euglenaria, Monomorphina, Strombomonas, and Trachelomonas), each representing a monophyletic lineage, except for the genus Euglena. The genus Euglena was divided into three subclades (A1, A2, and A3) and was paraphyletic due to Euglena archeoplastidiata being grouped with the genus Euglenaria and E. cf. velata with the genus Colacium. The family Phacaceae was supported as a monophyletic group and contained three genera (Discoplastis, Lepocinclis, and Phacus). The genus Phacus contained traditionally defined members as well as the non-traditional P. warszewiczii and P. limnophila, which support the generic concept of Linton et al. (2010).

The chloroplast genome of Phacus orbicularis (Euglenophyceae): an initial datum point for the phacaceae.

The Euglenophyceae chloroplast was acquired when a heterotrophic euglenoid engulfed a green alga and subsequently retained the algal chloroplast, in a process known as secondary endosymbiosis. Since this event, Euglenophyceae have diverged widely and their chloroplast genomes (cpGenomes) have as well. Changes to the cpGenome include extensive gene rearrangement and the proliferation of introns, the analyses of which have proven to be useful in examining cpGenome changes throughout the Euglenophyceae. The Euglenales fall into two families, Euglenaceae and Phacaceae. Euglenaceae contains eight genera and at least one cpGenome has been published for each genus. Phacaceae, on the other hand, contains three genera, none of which have had a representative chloroplast genome sequenced. Members of this family have many small disk‐shaped chloroplasts that lack pyrenoids. We sequenced and annotated the cpGenome of Phacus orbicularis in order to fill in the large gap in our understanding of Euglenophyceae cpGenome evolution, especially in regard to intron number and gene order. We compared this cpGenome to those of species from both the Euglenaceae and Eutreptiales of the Euglenophyceae phylogenetic tree. The cpGenome showed characteristics that were more derived than that of the basal species Eutreptia viridis, with extensive gene rearrangements and nearly three times as many introns. In contrast, it contained fewer introns than all but one of the previously reported Euglenaceae cpGenomes, had a smaller estimated genome size, and shared greater synteny with two main branches of that family.

Genetic differentiation among isolates of Teredinibacter turnerae, a widely occurring intracellular endosymbiont of shipworms.

Teredinibacter turnerae is a cultivable intracellular endosymbiont of xylotrophic (wood‐feeding) bivalves of the Family Teredinidae (shipworms). Although T. turnerae has been isolated from many shipworm taxa collected in many locations, no systematic effort has been made to explore genetic diversity within this symbiont species across the taxonomic and geographical range of its hosts. The mode of symbiont transmission is unknown. Here, we examine sequence diversity in fragments of six genes (16S rRNA, gyrB, sseA, recA, rpoB and celAB) among 25 isolates of T. turnerae cultured from 13 shipworm species collected in 15 locations in the Atlantic, Pacific and Indian Oceans. While 16S rRNA sequences are nearly invariant between all examined isolates (maximum pairwise difference <0.26%), variation between examined protein‐coding loci is greater (mean pairwise difference 2.2–5.9%). Phylogenetic analyses based on each protein‐coding locus differentiate the 25 isolates into two distinct and well‐supported clades. With five exceptions, clade assignments for each isolate were supported by analysis of alleles of each of the five protein‐coding loci. These exceptions include (i) putative recombinant alleles of the celAB and gyrB loci in two isolates (PMS‐535T.S.1b.3 and T8510), suggesting homologous recombination between members of the two clades; and (ii) evidence for a putative lateral gene transfer event affecting a second locus (recA) in three isolates (T8412, T8503 and T8513). These results demonstrate that T. turnerae isolates do not represent a homogeneous global population. Instead, they indicate the emergence of two lineages that, although distinct, likely experience some level of genetic exchange with each other and with other bacterial species.

Identification of a new-to-science cyanobacterium, Toxifilum mysidocida gen. nov. & sp. nov. (Cyanobacteria, Cyanophyceae).

Cyanobacteria occupy many niches within terrestrial, planktonic, and benthic habitats. The diversity of habitats colonized, similarity of morphology, and phenotypic plasticity all contribute to the difficulty of cyanobacterial identification. An unknown marine filamentous cyanobacterium was isolated from an aquatic animal rearing facility having mysid mortality events. The cyanobacterium originated from Corpus Christi Bay, TX. Filaments are rarely solitary, benthic mat forming, unbranched, and narrowing at the ends. Cells are 2.1 × 3.1 μm (width × length). Thylakoids are peripherally arranged on the outer third of the cell; cyanophycin granules and polyphosphate bodies are present. Molecular phylogenetic analysis in addition to morphology (transmission electron microscopy and scanning electron microscopy) and chemical composition all confirm it as a new genus and species we name Toxifilum mysidocida. At least one identified Leptolyngbya appears (based on genetic evidence and TEM) to belong to this new genus.

Multiresolution Analysis of DNA Sequences

A wavelet based method for transforming DNA sequences is illustrated by using the small subunit of the ribosome. This paper discusses the application of multi resolution analysis on FASTA-formatted DNA sequences using biorthogonal wavelets. Once transformed, the data could be used for pairwise or multiple sequence alignments needed for studies of evolutionary relationships or for gene finding. Further studies of wavelet based methods are also mentioned.

Intrageneric chloroplast genome comparison in the genus Euglena (Phylum: Euglenophyta) with annotated chloroplast genomes of Euglena hiemalis and Euglena clara

The genus Euglena is composed of six subclades with a diversity of chloroplast morphologies, unlike that found in the other genera of Euglenaceae. This genus contains five published chloroplast genomes (cpGenome) and the colorless plastid genome (ptGenome) of the non-photosynthetic euglenoid Euglena longa within the same subclade as Euglena gracilis. Previous studies of cpGenomes revealed that Euglena viridis and E. gracilis, although in separate subclades, had few cpGenome differences, while Euglena mutabilis maintained the same gene order but was mirror-inverted except for the rRNA cluster. However, we expanded the number of cpGenomes available in Euglena by sequencing and annotating the cpGenomes of Euglena clara, the earliest diverging species in the E. gracilis and E. longa subclade and Euglena hiemalis, the putative sister species to E. longa. Analysis of these newly annotated cpGenomes showed them to be largely similar in gene content, conserved gene clusters (operons), and Gu2009+u2009C/Au2009+u2009T percentage to previously published Euglena cpGenomes. The only extensive gene rearrangements observed were between cpGenomes and the ptGenome in subclade B. However, a unique feature of the subclade was multi-copies of the rRNA operon. Also, homologous twintrons in psbD and psbF to E. gracilis were observed in E. hiemalis. Overall, these results revealed a conserved intrageneric cpGenome for Euglena species.