Biology subjects

Keddell, P.

Publications and source records attributed to Keddell, P..

3 recordsLinked to original sources

bioRxiv2026

OrthoGLMM: Phylogenetic Association Testing for Gene Content and Trait Evolution

1MotivationComparative genome projects can now assemble and annotate hundreds of species, creating an opportunity to test whether species-level traits are associated with repeated changes in gene content. These tests must account for shared ancestry, sparse orthogroups, rare trait origins, and thousands of simultaneous associations. ResultsWe present OrthoGLMM, a phylogenetically informed framework for the association of traits and orthogroup presence/absence or copy number across species. OrthoGLMM combines deterministic GLMM scans with solver-rerun empirical calibration and calibrated FDR estimation. In three benchmark datasets, OrthoGLMM recovered expected signals for bacterial diazotrophy, plant nodulation, and marine mammals. Availability and ImplementationSource code, documentation, example data, and reproducibility scripts will be available at http://github.com/jguhlin/OrthoGLMM. Contactjoseph.guhlin@gmail.com

bioinformatics↗

bioRxiv2025

The genome of Doleromyrma darwiniana and annotations for five additional Dolichoderinae species

Darwins ant, Doleromyrma darwiniana, is a native ant to Australia that has established invasive populations in nearby Aotearoa, New Zealand. Darwins ant belongs to the Dolichoderinae subfamily of the Formicidae family, which contains species with a broad range of invasion histories, including the internationally prolific Argentine ant (Linepithema humile). The genome of Darwins ant, Doleromyrma darwiniana, is presented here, created from a combined sample of 10 female workers. Generated using Oxford Nanopore Technologies PromethION 2 sequencing data, the assembly has a total length of 238.80 Mb and an N50 of 14.23 Mb. The assembly is compared to that of L. humile and four additional species from the same subfamily, the Dolichoderinae. Annotations were generated for all six Dolichoderinae species and sorted into orthogroups to assess the diversity and conservation of the Dolichoderinae genomic repertoire.

genomics↗

bioRxiv2024

Rapid and cost-effective production of high-quality insect genome sequences

Insects are the most diverse group of animals on earth, with nearly 1 million species described to date, yet this variation is not reflected within the ranks of genomes currently available. In the current age of genetics, the generation of high-quality reference genomes is invaluable, often necessary and expensive. We prove that insect genomes do not need to come at a large cost. We demonstrate a cost-efficient method for producing high-quality insect genomes, with comparisons to current reference assemblies.

genomics↗