Kelley Thomas

The Dscam Homologue of the Crustacean Daphnia Is Diversified by Alternative Splicing Like in Insects

In insects, the homologue of the Down syndrome cell adhesion molecule (Dscam) is a unique case of a single-locus gene whose expression has extensive somatic diversification in both the nervous and immune systems. How this situation evolved is best understood through comparative studies. We describe structural, expression, and evolutionary aspects of a Dscam homolog in 2 species of the crustacean Daphnia. The Dscam of Daphnia generates up to 13,000 different transcripts by the alternative splicing of variable exons. This extends the taxonomic range of a highly diversified Dscam beyond the insects. Additionally, we have identified 4 alternative forms of the cytoplasmic tail that generate isoforms with or without inhibitory or activating immunoreceptor tyrosine-based motifs (ITIM and ITAM respectively), something not previously reported in insects Dscam. In Daphnia, we detected exon usage variability in both the brain and hemocytes (the effector cells of immunity), suggesting that Dscam plays a role in the nervous and immune systems of crustaceans, as it does in insects. Phylogenetic analysis shows a high degree of amino acid conservation between Daphnia and insects except in the alternative exons, which diverge greatly between these taxa. Our analysis shows that the variable exons diverged before the split of the 2 Daphnia species and is in agreement with the nearest-neighbor model for the evolution of the alternative exons. The genealogy of the Dscam gene family from vertebrates and invertebrates confirmed that the highly diversified form of the gene evolved from a nondiversified form before the split of insects and crustaceans.

Morphological and molecular analysis of six aphelenchoidoids from Australian conifers and their relationship to Bursaphelenchus (Fuchs, 1937)

Six isolates of Australian Aphelenchoidoidea, viz., Laimaphelenchus preissii from native coniferous Callitris preissii trees, L. australis from the common pine plantation trees of Pinus radiata and P. pinaster and L. heidelbergi and two morphospecies of Aphelenchoides (H1 and K1) and Cryptaphelenchus sp. (K2) from diseased P. radiata trees, were studied using light microscopy, scanning electron microscopy and phylogenetic analyses of nearly full length sequences of SSU, D2/D3 expansion segments of LSU rDNA and a fragment of cytochrome oxidase subunit I (COI). Bayesian phylogenetic analyses of SSU, LSU and COI of the six nematode species revealed that none of these Australian aphelenchoidoids was inferred to be closely related to Bursaphelenchus. The selected isolates of Aphelenchoides and Laimaphelenchus used in this study were paraphyletic in all molecular analyses. Cryptaphelenchus sp. (K2) was inferred to be sister to Seinura with SSU sequences.

Ficotylus congestae gen. n., sp. n. (Anguinata), from Ficus congesta (Moraceae) sycones in Australia.

A new monotypic genus of tylenchid nematode, Ficotylus n. gen., was recovered from sycones of Ficus congesta L. from Mourilyan, Mission Beach and Cairns, Queensland, Australia. The genus is characterised by having slender nematodes with a long stylet, a sub-cylindrical pharynx lacking a terminal bulb, pharyngeal glands overlapping the intestine for a short distance, secretory/excretory pore opening posterior to the nerve ring, female with a single gonad and post-vulval sac and male with slender, arcuate, cephalated spicules with the bursa arising near the proximal level of the retracted spicule and supported by a pair of papilla-like structures at its widest point. This is the first record of a tylenchid occurring within Ficus sycones. Ficotylus congestae gen. n., sp. n. is distinguished by possessing a long stylet (29-39 μm) with conus forming ca 40% of stylet length and three well developed bifid knobs at the base of the shaft, a degenerate pharynx with a vestigial metacorpus (no valve) and no basal bulb, females with a post-vulval uterine sac and males with a characteristic bursa supported by a pair of papilla-like structures at its widest point, then narrowing rapidly and just enveloping tail. Ficotylus congestae gen. n., sp. n. is a putative member of the Anguinata (sensu Siddiqi, 1985), based on molecular phylogeny of near full length SSU and D2/D3 expansion segments of the large subunit (LSU) rDNA. Morphologically, it has affinities with the superfamily Sphaerularioidea, family Neotylenchidae, where it is tentatively placed.

Acrostichus megaloptae n. sp. (Nematoda: Diplogastridae), a phoretic associate of Megalopta spp. (Hymenoptera: Halictidae) in Central America

Adults of the dusk-flying and rotting wood-nesting bees Megalopta genalis and/or M. ecuadoria were collected at Barro Colorado Island, The Smithsonian Tropical Research Institute (BCI, STRI), Panama and La Selva, Costa Rica, and examined for nematodes. Nematodes were recovered as dauer juveniles from the Dufours gland of female bees and aedeagus of male bees. Adult nematodes isolated from M. genalis (BCI and La Selva) and M. ecuadoria (BCI) were successfully cultured and kept in the laboratory. All three populations were used for morphological observations and molecular analyses and were identified as a new species that is described herein as Acrostichus megaloptae n. sp. It is characterised by its stomatal morphology, possession of six triangular cuticle flaps covering stomatal opening, duplicated cheilo- and gymnostomatal walls, large dorsal tooth and sclerotised ventral stegostomatal ridges, female with vulval flap, male spicule and gubernaculum morphology, i.e. , relatively straight spicule with oval-shaped manubrium, rounded flap-like rostrum and separated and strongly ventrally curved spicule with bifurcate tip, gubernaculum L-shaped in lateral view and anchor-shaped in ventral view, and filiform tail of both sexes. Sequences from the three A. megaloptae n. sp. geographical/host isolates were not significantly different and molecular phylogenetic analysis and biological and morphological comparisons place the new species close to A. halicti from Halictus ligatus and A. puri from Augochlora pura from North America, although the new species is distinguished from A. halicti and A. puri based upon its stomatal morphology of males and females, male spicule and gubernaculum morphology and female vulval structure.

The landscape of transcription errors in eukaryotic cells

This paper provides the first comprehensive analysis of the fidelity of transcription in eukaryotic cells. Accurate transcription is required for the faithful expression of genetic information. To understand the molecular mechanisms that control the fidelity of transcription, we used novel sequencing technology to provide the first comprehensive analysis of the fidelity of transcription in eukaryotic cells. Our results demonstrate that transcription errors can occur in any gene, at any location, and affect every aspect of protein structure and function. In addition, we show that multiple proteins safeguard the fidelity of transcription and provide evidence suggesting that errors that evade these layers of RNA quality control profoundly affect the physiology of living cells. Together, these observations demonstrate that there is an inherent limit to the faithful expression of the genome and suggest that the impact of mutagenesis on cellular health and fitness is substantially greater than currently appreciated.

Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure.

Studies monitoring changes in genetic diversity and composition through time allow a unique understanding of evolutionary dynamics and persistence of natural populations. However, such studies are often limited to species with short generation times that can be propagated in the laboratory or few exceptional cases in the wild. Species that produce dormant stages provide powerful models for the reconstruction of evolutionary dynamics in the natural environment. A remaining open question is to what extent dormant egg banks are an unbiased representation of populations and hence of the species’ evolutionary potential, especially in the presence of strong environmental selection. We address this key question using the water flea Daphnia magna, which produces dormant stages that accumulate in biological archives over time. We assess temporal genetic stability in three biological archives, previously used in resurrection ecology studies showing adaptive evolutionary responses to rapid environmental change. We show that neutral genetic diversity does not decline with the age of the population and it is maintained in the presence of strong selection. In addition, by comparing temporal genetic stability in hatched and unhatched populations from the same biological archive, we show that dormant egg banks can be consulted to obtain a reliable measure of genetic diversity over time, at least in the multidecadal time frame studied here. The stability of neutral genetic diversity through time is likely mediated by the buffering effect of the resting egg bank.

Divergent selection and drift shape the genomes of two avian sister species spanning a saline-freshwater ecotone

The role of species divergence due to ecologically-based divergent selection – or ecological speciation – in generating and maintaining biodiversity is a central question in evolutionary biology. Comparison of the genomes of phylogenetically related taxa spanning a selective habitat gradient enables discovery of divergent signatures of selection and thereby provides valuable insight into the role of divergent ecological selection in speciation. Tidal marsh ecosystems provide tractable opportunities for studying organisms’ adaptations to selective pressures that underlie ecological divergence. Sharp environmental gradients across the saline-freshwater ecotone within tidal marshes present extreme adaptive challenges to terrestrial vertebrates. Here we sequence 20 whole genomes of two avian sister species endemic to tidal marshes – the Saltmarsh Sparrow (Ammodramus caudacutus) and Nelson’s Sparrow (A. nelsoni) – to evaluate the influence of selective and demographic processes in shaping genome-wide patterns of divergence. Genome-wide divergence between these two recently diverged sister species was notably high (genome-wide FST = 0.32). Against a background of high genome-wide divergence, regions of elevated divergence were widespread throughout the genome, as opposed to focused within islands of differentiation. These patterns may be the result of genetic drift acting during past tidal march colonization events in addition to divergent selection to different environments. We identified several candidate genes that exhibited elevated divergence between Saltmarsh and Nelson’s sparrows, including genes linked to osmotic regulation, circadian rhythm, and plumage melanism – all putative candidates linked to adaptation to tidal marsh environments. These findings provide new insights into the roles of divergent selection and genetic drift in generating and maintaining biodiversity.