Biology subjects

Joyce, E. M.

Publications and source records attributed to Joyce, E. M..

2 recordsLinked to original sources

bioRxiv2025

The complex evolutionary history of Capparis L. (Capparaceae Juss.) in Australia, and the description of five new species and two new subspecies

Capparis comprises [~]145 species, of which [~]21 occur in Australia; however, the relationships and taxonomic status of Australian Capparis taxa remain to be tested. We present phylogenies of all Australian Capparis taxa by analysing Angiosperms353 loci using coalescent and concatenated approaches. All trees resolve Capparis as monophyletic, with a whole-genome duplication (WGD) event detected at the crown. Capparis sect. Capparis and sect. Busbeckea are monophyletic, but sect. Monostichocalyx is non-monophyletic. The relationships of species within sect. Busbeckea are poorly supported due to rapid radiation following ancient WGD. The relationships of taxa within sect. Capparis and the clades of sect. Monostichocalyx are well-supported, with some incomplete lineage sorting. Capparis spinosa is geographically, morphologically and phylogenetically structured across northern Australia. Based on these results, we describe five new species and two new subspecies of Capparis, bringing the total number of species in Australia to 26. Capparis xylocarpa, C. megacarpa, C. loxophleba and C. splendidissima are newly described. Capparis loranthifolia var. bancroftii is raised to species level as C. bancroftii. Capparis spinosa subsp. nummularia is split into three subspecies: subsp. formicosa, subsp. insularis, and subsp. nummularia. We provide a key for all Australian taxa.

evolutionary biology↗

bioRxiv2020

New targets acquired: improving locus recovery from the Angiosperms353 probe set

Universal target enrichment kits maximise utility across wide evolutionary breadth while minimising the number of baits required to create a cost-efficient kit. Locus assembly requires a target reference, but the taxonomic breadth of the kit means that target references files can be phylogenetically sparse. The Angiosperms353 kit has been successfully used to capture loci throughout angiosperms but includes sequence information from 6-18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, reducing locus recovery. We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a mega353 target file, with each gene represented by 17-373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene datasets. Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 31%, increased loci recovery at 75% length by 61.9%, and increased the total length of the concatenated loci by 30%. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets

bioinformatics↗