Biology subjects

Fraser, C. J.

Publications and source records attributed to Fraser, C. J..

3 recordsLinked to original sources

bioRxiv2022

The chromodomain proteins, Cbx1 and Cbx2 have distinct roles in the regulation of heterochromatin and virulence in the fungal wheat pathogen, Zymoseptoria tritici.

Heterochromatin is characterized by specific histone post-translational modifications such as the di- and tri-methylation of histone H3 on lysine 9 (H3K9me2/3), which direct the recruitment of reader proteins to chromatin. In the fungal phytopathogen, Zymoseptoria tritici, deletion of the H3K9 methyltransferase gene kmt1, results in a global increase in the expression of transposable elements (TEs), genome instability and loss of virulence. Here we have identified two Z. tritici chromodomain proteins, Cbx1 and Cbx2, that recognise H3K9me modifications. Cbx1 is a Heterochromatin Protein 1 homolog that binds H3K9me2/3 in vitro and associates with heterochromatic loci in vivo. Transcriptomic analysis also indicates that Cbx1 and Kmt1 regulate overlapping sets of protein-encoding genes. However, unlike {Delta}kmt1 mutants, {Delta}cbx1 strains do not exhibit a global increase in TE expression and have only a partial reduction in virulence, suggesting the existence of additional H3K9me reader proteins. Accordingly, we have identified a fungal-specific chromodomain protein, Cbx2, that binds H3K9me3 in vitro. Strikingly, the growth defects of {Delta}cbx1 {Delta}cbx2 double mutants closely resemble those of {Delta}kmt1 consistent with Cbx1 and Cbx2 playing redundant roles in gene silencing. Overall, the data suggest that key functions of H3K9me modifications are mediated by a combination of Cbx1 and Cbx2.

microbiology↗

bioRxiv2022

Geological drivers of diversification in Papuan microhylid frogs

AO_SCPLOWBSTRACTC_SCPLOWStudies of the Papuan region have provided fundamental insights into both the evolutionary processes generating its exceptional biodiversity, as well support for alternative hypotheses of geological history. Lying at the junction of five tectonic plates, this region has experienced a turbulent geological history that has not only produced towering mountains allowing elevational specialization, and island archipelagos of varying distance promoting vicariance, but also active margins where land masses have collided and been subsequently rifted apart creating a mosaic of intermixed terranes with vastly different geological histories which may influence the evolutionary history of its biota. Asterophryine frogs are a hyperdiverse clade representing half the worlds microhylid diversity (over 360 species) centered on New Guinea and its satellite islands. We show that vicariance facilitated by geological history, and not elevational specialization best explain this far and wide distribution of a clade that should have poor dispersal abilities. Thus, some of the predictions of island biogeography theory are supported if informed by geological history. We recovered a mainland tectonic unit, the East Papua Composite Terrane (EPCT), as the center of origin for Asterophryinae and no fewer than 71 instances of what appear to be long-distance dispersal events, 29 of which are between mainland regions, with 42 from the mainland to the islands, some presently as far as 200 km away from source populations over open ocean. Furthermore, we find strong support for a "Slow and Steady" hypothesis for the formation of the northern margin of New Guinea by many separate accretion events during the Miocene, over other major geological alternatives, consistent with the 20 M year age of the clade and arrival via the EPCT. In addition, the historical biogeography of our frogs strongly support an affiliation of the Louisiade Archipelago and Woodlark Island with the Owen Stanley Mountain range on the EPCT, and the recent proximity of the large New Britain island. Our results show that Asterophryinae did not have to repeatedly and independently disperse across and large ocean barriers to the offshore islands, but that the current distribution can be explained through vicariance and short-distance oceanic dispersal as historical land connections disappeared and islands slowly became separated from each other. We show that islands have a life history, undergoing changes in area through island-building and erosion, but also change in distance from other land masses, with consequent opportunities for dispersal, isolation, and cladogenesis of their biotas. More broadly, we can begin to see how the geological history of the Papuan region can result in the rapid accumulation and staggering number of extant species.

evolutionary biology↗

bioRxiv2022

A large nuclear and mitochondrial sequence dataset for phylogenetic analysis of the hyperdiverse Asterophryinae frogs of the New Guinea region with data on lifestyle, GPS coordinates, elevation, and multispecies communities with accompanying code

The data provided here is related to the article "Resolving the Deep Phylogeny: Implications for Early Adaptive Radiation, Cryptic, and Present-day Ecological Diversity of Papuan Microhylid Frogs" [1]. The dataset is based on 233 tissue samples of the subfamily Asteroprhyinae, with representatives from all recognized genera, in addition to three outgroup taxa. The sequence dataset contains over 2400 characters per sample for five genes (three nuclear loci: BDNF, NXC-1, and SIA; and two mitochondrial loci: ND4 and CYTB) and is 99% complete. New primers were designed for all loci and accession numbers for the raw sequence data are provided. The sequences are used with geological time calibrations to produce time-calibrated Bayesian inference and Maximum Likelihood phylogenetic reconstructions using BEAST2 and IQTREE. Lifestyle data (arboreal, scansorial, terrestrial, fossorial, semi-aquatic) were collected from the literature and field notes and used to infer ancestral character states for each lineage. Collection location data (GPS and elevation data) were used to verify sites where multiple species or candidate species co-occur. All sequence data, alignments, and associated metadata (voucher specimen number, species identification, type locality status, GPS, elevation, site with species list, and lifestyle) as well as the code to produce all analyses and figures are provided.

evolutionary biology↗