• Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins

      Li, B; Lopes, JS; Foster, PG; Embley, TM; Cox, CJ (Oxford Academic, 2014-07)
      Archaeplastida (=Kingdom Plantae) are primary plastid-bearing organisms that evolved via the endosymbiotic association of a heterotrophic eukaryote host cell and a cyanobacterial endosymbiont approximately 1,400 Ma. Here, we present analyses of cyanobacterial and plastid genomes that show strongly conflicting phylogenies based on 75 plastid (or nuclear plastid-targeted) protein-coding genes and their direct translations to proteins. The conflict between genes and proteins is largely robust to the use of sophisticated data- and tree-heterogeneous composition models. However, by using nucleotide ambiguity codes to eliminate synonymous substitutions due to codon-degeneracy, we identify a composition bias, and dependent codon-usage bias, resulting from synonymous substitutions at all third codon positions and first codon positions of leucine and arginine, as the main cause for the conflicting phylogenetic signals. We argue that the protein-coding gene data analyses are likely misleading due to artifacts induced by convergent composition biases at first codon positions of leucine and arginine and at all third codon positions. Our analyses corroborate previous studies based on gene sequence analysis that suggest Cyanobacteria evolved by the early paraphyletic splitting of Gloeobacter and a specific Synechococcus strain (JA33Ab), with all other remaining cyanobacterial groups, including both unicellular and filamentous species, forming the sister-group to the Archaeplastida lineage. In addition, our analyses using better-fitting models suggest (but without statistically strong support) an early divergence of Glaucophyta within Archaeplastida, with the Rhodophyta (red algae), and Viridiplantae (green algae and land plants) forming a separate lineage.
    • Delegating sex: differential gene expression in stolonizing syllids uncovers the hormonal control of reproduction in Annelida

      Alvarez-Campos, P; Kenny, NJ; Verdes, A; Fernandez, RM; Novo, M; Giribet, G; Riesgo, A (Oxford Academic, 2018-12-11)
      Stolonization in syllid annelids is a unique mode of reproduction among animals. During the breeding season, a structure resembling the adult but containing only gametes, called stolon, is formed generally at the posterior end of the animal. When stolons mature, they detach from the adult and gametes are released into the water column. The process is synchronized within each species, and it has been reported to be under environmental and endogenous control, probably via endocrine regulation. To further understand reproduction in syllids and to elucidate the molecular toolkit underlying stolonization, we generated Illumina RNA-seq data from different tissues of reproductive and nonreproductive individuals of Syllis magdalena and characterized gene expression during the stolonization process. Several genes involved in gametogenesis (ovochymase, vitellogenin, testis-specific serine/threonine-kinase), immune response (complement receptor 2), neuronal development (tyrosine-protein kinase Src42A), cell proliferation (alpha-1D adrenergic receptor), and steroid metabolism (hydroxysteroid dehydrogenase 2) were found differentially expressed in the different tissues and conditions analyzed. In addition, our findings suggest that several neurohormones, such as methyl farnesoate, dopamine, and serotonin, might trigger stolon formation, the correct maturation of gametes and the detachment of stolons when gametogenesis ends. The process seems to be under circadian control, as indicated by the expression patterns of r-opsins. Overall, our results shed light into the genes that orchestrate the onset of gamete formation and improve our understanding of how some hormones, previously reported to be involved in reproduction and metamorphosis processes in other invertebrates, seem to also regulate reproduction via stolonization.
    • Measuring Biodiversity and Extinction-Present and Past

      Sigwart, JD; Bennett, KD; Edie, SM; Mander, L; Okamura, B; Padian, K; Wheeler, Q; Winston, JE; Yeung, NW (Oxford Academic, 2018-09-18)
      How biodiversity is changing in our time represents a major concern for all organismal biologists. Anthropogenic changes to our planet are decreasing species diversity through the negative effects of pollution, habitat destruction, direct extirpation of species, and climate change. But major biotic changes—including those that have both increased and decreased species diversity—have happened before in Earth’s history. Biodiversity dynamics in past eras provide important context to understand ecological responses to current environmental change. The work of assessing biodiversity is woven into ecology, environmental science, conservation, paleontology, phylogenetics, evolutionary and developmental biology, and many other disciplines; yet, the absolute foundation of how we measure species diversity depends on taxonomy and systematics. The aspiration of this symposium, and complementary contributed talks, was to promote better understanding of our common goals and encourage future interdisciplinary discussion of biodiversity dynamics. The contributions in this collection of papers bring together a diverse group of speakers to confront several important themes. How can biologists best respond to the urgent need to identify and conserve diversity? How can we better communicate the nature of species across scientific disciplines? Where are the major gaps in knowledge about the diversity of living animal and plant groups, and what are the implications for understanding potential diversity loss? How can we effectively use the fossil record of past diversity and extinction to understand current biodiversity loss?
    • Symbiosis, Selection, and Novelty: Freshwater Adaptation in the Unique Sponges of Lake Baikal

      Kenny, Nathan J.; Plese, Bruna; Riesgo, Ana; Itskovich, Valeria B. (Oxford Academic, 2019-06-27)
      Freshwater sponges (Spongillida) are a unique lineage of demosponges that secondarily colonized lakes and rivers and are now found ubiquitously in these ecosystems. They developed specific adaptations to freshwater systems, including the ability to survive extreme thermal ranges, long-lasting dessication, anoxia, and resistance to a variety of pollutants. Although spongillids have colonized all freshwater systems, the family Lubomirskiidae is endemic to Lake Baikal and plays a range of key roles in this ecosystem. Our work compares the genomic content and microbiome of individuals of three species of the Lubomirskiidae, providing hypotheses for how molecular evolution has allowed them to adapt to their unique environments. We have sequenced deep (>92% of the metazoan “Benchmarking Universal Single-Copy Orthologs” [BUSCO] set) transcriptomes from three species of Lubomirskiidae and a draft genome resource for Lubomirskia baikalensis. We note Baikal sponges contain unicellular algal and bacterial symbionts, as well as the dinoflagellate Gyrodinium. We investigated molecular evolution, gene duplication, and novelty in freshwater sponges compared with marine lineages. Sixty one orthogroups have consilient evidence of positive selection. Transporters (e.g., zinc transporter-2), transcription factors (aristaless-related homeobox), and structural proteins (e.g. actin-3), alongside other genes, are under strong evolutionary pressure in freshwater, with duplication driving novelty across the Spongillida, but especially in the Lubomirskiidae. This addition to knowledge of freshwater sponge genetics provides a range of tools for understanding the molecular biology and, in the future, the ecology (e.g., colonization and migration patterns) of these key species.
    • Uncovering the sub-lethal impacts of plastic ingestion by shearwaters using fatty acid analysis.

      Puskic, PS; Lavers, JL; Adams, LR; Grünenwald, M; Hutton, I; Bond, AL (Oxford Academic, 2019-05-16)
      Marine plastic pollution is increasing exponentially, impacting an expanding number of taxa each year across all trophic levels. Of all bird groups, seabirds display the highest plastic ingestion rates and are regarded as sentinels of pollution within their foraging regions. The consumption of plastic contributes to sub-lethal impacts (i.e. morbidity, starvation) in a handful of species. Additional data on these sub-lethal effects are needed urgently to better understand the scope and severity of the plastics issue. Here we explore the application of fatty acid (FA) analysis as a novel tool to investigate sub-lethal impacts of plastic ingestion on seabird body condition and health. Using gas chromatography-mass spectrometry, we identified 37 individual FAs within the adipose, breast muscle and liver of flesh-footed (Ardenna carneipes) and short-tailed (Ardenna tenuirostris) shearwaters. We found high amounts of FA 16:0, 18:0, 20:5n3 (eicosapentaenoic acid), 22:6n3 (docosahexaenoic acid) and 18:1n9 in both species; however, the overall FA composition of the two species differed significantly. In flesh-footed shearwaters, high amounts of saturated and mono-unsaturated FAs (needed for fast and slow release energy, respectively) in the adipose and muscle tissues were related to greater bird body mass. While total FAs were not related to the amount of plastic ingested in either species, these data are a valuable contribution to the limited literature on FAs in seabirds. We encourage studies to explore other analytical tools to detect these sub-lethal impacts of plastic.