Biology subjects

Oatley, G.

Publications and source records attributed to Oatley, G..

3 recordsLinked to original sources

bioRxiv2025

Multiple instances of river-lake introgression in the adaptive radiation of sailfin silversides in Wallace's Dreampond

While adaptive radiations significantly contribute to the worlds biodiversity, much is unknown about the genetic and ecological factors underlying these rapid successions of speciation. It has been suggested that hybridisation can facilitate the speciation process by generating genetic diversity on which diversifying selection can act. Sailfin silverside fishes (Telmatherinidae) in the Malili Lakes system in Sulawesi have diversified within the last 2 million years. We assembled and annotated a chromosome-scale reference genome of the riverine sailfin silverside Telmatherina bonti and generated whole genome sequences of all species of Telmatherina in Lake Matano, South Sulawesi, Indonesia, one of the worlds oldest and deepest lakes. We reconstructed the phylogenetic relationships within the adaptive radiation of sailfin silversides and inferred past and ongoing introgression patterns. Genome-wide tests confirmed two monophyletic clades, sharpfins and roundfins. However, within clades, we found mismatches between morphology-based taxonomic assignments and genome-wide genetic relationships. We found signs of both old and ongoing introgression between river-dwelling T. bonti and the lacustrine sharpfin group, as shown in elevated D-statistic, f4-ratio and f-branch statistic. Levels of excess allele sharing between riverine species and the three most common lacustrine species declined with increasing distance from the river-inlet, indicating ongoing introgression at the lake-river interface. This combination of past and ongoing hybridisation in a radiating species flock makes Lake Matano Telmatherina a particularly valuable system to study fundamental mechanisms driving rapid speciation under genomic exchange. The phylogenomic framework elaborated in this study provides the foundation for studies of the processes shaping this charismatic radiation.

evolutionary biology↗

bioRxiv2025

On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species

Since its inception in 2019, the Tree of Life programme at the Wellcome Sanger Institute has released high-quality, chromosomally-resolved reference genome assemblies for over 2000 species. Tree of Life has at its core multiple teams, each of which are responsible for key components of the genome engine. One of these teams is the Tree of Life core laboratory, which is responsible for processing tissues across a wide range of species into high quality, high molecular weight DNA and intact RNA, and preparing tissues for Hi-C. Here, we detail the different workflows we have developed to successfully process a wide variety of species, covering plants, fungi, chordates, protists, arthropods, meiofauna and other metazoa. We summarise our success rates and describe how to best apply and combine the suite of current protocols, which are all publicly available at protocols.io.

molecular biology↗

bioRxiv2023

Candidate gene length polymorphisms are linked to dispersive behaviour: searching for a mechanism behind the "paradox of the great speciators"

The "paradox of the great speciators" has puzzled evolutionary biologists for over half a century. A great speciator requires excellent dispersal ability to explain its occurrence on multiple islands, but reduced dispersal ability to explain its high number of subspecies. A rapid reduction in dispersal ability is often invoked to solve this apparent paradox, but a proximate mechanism has not been identified. Here, we explore the role of six genes linked to migration and animal personality differences (CREB1, CLOCK, ADCYAP1, NPAS2, DRD4, and SERT) in 20 South Pacific populations of silvereye (Zosterops lateralis) that range from highly sedentary to partially migratory, to determine if genetic variation is associated with dispersal propensity. We detected genetic associations in three of the six genes: i) in a partial migrant population, migrant individuals had longer microsatellite alleles at the CLOCK gene compared to resident individuals from the same population; ii) CREB1 displayed longer average microsatellite allele lengths in recently colonised island populations (< 200 years), compared to evolutionarily older populations. Bayesian broken stick regression models supported a reduction in CREB1 length with time since colonisation and decreasing dispersal propensity; and iii) like CREB1, DRD4 showed differences in polymorphisms between recent and old colonisations but a further sample size is needed to confirm. ADCYAP1, SERT, and NPAS2 were variable but that variation was not associated with dispersal propensity. The association of genetic variants at three genes with migration and dispersal ability in silvereyes provides the impetus for further exploration of genetic mechanisms underlying dispersal shifts, and the prospect of resolving a long-running evolutionary paradox through a genetic lens.

evolutionary biology↗