Accurate identification of environmental DNA with informatic sequence classification trees.
Selected Publications
aphid: an R package for analysis with profile hidden Markov models.
Hidden Markov models and profile HMMs form an integral part of biological sequence analysis, supporting an ever-growing list of applications. The aphid R package can be used to derive, train, plot, import and export HMMs and profile HMMs in the R environment. Computationally-intensive dynamic programming recursions such as the Viterbi, forward and backward algorithms are implemented in C++ and parallelized for increased speed and efficiency.
Bioinformatics (2019) DOI: 10.1093/bioinformatics/btz159.
Elevated Symbiodiniaceae richness at Atauro Island (Timor-Leste): a highly biodiverse reef system.
To persist in oligotrophic waters, reef-building corals rely on nutritional interactions with symbiotic dinoflagellates of the family Symbiodiniaceae, but the true diversity of this family remains poorly characterised. In this paper, we assess Symbiodiniaceae richness at Atauro Island (Timor-Leste) as well as on reefs of the neighbouring Timor mainland using next-generation DNA sequencing. Our results reveal a symbiont richness that reflects the high biodiversity of these reefs, but also potentially negative effects of proximal human populations on Symbiodiniaceae, even when previous studies have shown corals to be largely unaffected.
Coral Reefs (2019) DOI:10.1007/s00338-018-01762-9
Taxonomic identification of environmental DNA with informatic sequence classification trees.
High-throughput sequencing of environmental DNA (eDNA) offers a simple and cost-effective solution for aquatic biodiversity assessments. Yet several analytical challenges remain, including the incorporation of robust statistical inference in the assignment of taxonomic identities. We present a new supervised machine-learning algorithm that incorporates full probabistic models to classify eDNA with improved recall and strict control over false discovery rates.
PeerJ Preprints (2018) 6:e26812v1.
Intra-genomic variation in Symbiodinium correlates negatively with photosynthetic efficiency and coral host performance.
Reef-building corals are nutritionally dependent on the symbiotic alga Symbiodiniaceae, and may select for high-performing symbiont lineages. However, the effects of fine-scale genetic variation within symbiont populations on host performance are not well understood. We measured the relative abundance of intra-genomically variable (IGV) Symbiodinium cells and those with homogeneous rDNA sequence repeats, and analysed their physical status and photosynthetic performance under temperature stress. The comparatively poor performance of heterogeneous symbiont cells suggests either a direct deleterious effect of IGV or reduced performance associated with inter-species recombination.
Coral Reefs 37:691–701.
phylogram: an R package for phylogenetic analysis with nested lists
Evolutionary biologists are increasingly turning to R for building, editing and visualizing phylogenetic trees, yet the wide variety of the different tree formats remain poorly integrated. We developed the phylogram package as part of the rOpenSci project, providing functions for tree conversion, importing and exporting trees as parenthetic text, and manipulating dendrograms for phylogenetic applications.
Journal of Open Source Software 3:790.
The distribution of intra-genomically variable dinoflagellate symbionts at Lord Howe Island, Australia.
The symbiotic dinoflagellates of corals are essential to the development of shallow-water tropical reefs. Most genetic variation arises through the accumulation of somatic mutations that arise during asexual reproduction, but increasing evidence suggests a role of cryptic recombination in the Symbiodiniaceae family. We used quantitative PCR to estimate proportions of genetically homogeneous symbionts and intra-genomically variable Symbiodiniaceae in the reef-building coral Pocillopora damicornis. The abundance of IGV symbionts varied between colonies within and between sites, but remained stable within colonies through time. The local thermal maximum emerged as a negative predictor for IGV symbiont abundance, consistent with an increased susceptibility to thermal stress. This suggests that the evolutionary processes that generate IGV (such as inter-lineage recombination and the accumulation of somatic mutations at the ITS2 locus) may have important implications for the fitness of the symbiont and that of the coral host.
Coral Reefs 35:565–576.
Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?
Intra-genomic variation (IGV) at nuclear ribosomal loci has long frustrated efforts to genetically identify morphologically-indistinguishable species of symbiotic algae. This study investigates the origin of IGV in Symbiodiniaceae and considers the implications of potential inter-species hybridization in this family.
BMC Evolutionary Biology 15:46.