Biology subjects

Biffin, E.

Publications and source records attributed to Biffin, E..

4 recordsLinked to original sources

bioRxiv2026

Phylogenomic analyses of the Austral podocarps (Podocarpus: Podocarpaceae) reveals unlikely hybrid ancestry of a New Zealand species

Hybridisation is ubiquitous amongst plants and has important evolutionary consequences ranging from the collapse of distinct lineages through to the generation of new species. Here, we develop a phylogenetic hypothesis for the Austral podocarps (Podocarpus), a monophyletic group of six species distributed in Tasmania, mainland Australia, New Zealand and New Caledonia, and identify a putative hybrid lineage. Using a targeted capture approach to generate DNA sequence data, we find discordance between nuclear and plastid derived phylogenetic estimates and in particular, the relationships of the New Zealand species Podocarpus nivalis and Australian P. lawrencei are significantly discordant. Species network analyses largely resolve this incongruence and indicate that P. nivalis is a hybrid lineage, with P. laetus (New Zealand) and P. lawrencei as parents. We hypothesise that P. nivalis has arisen following trans-Tasman dispersal of P. lawrencei, and shows eco-geographic divergence from P. laetus, which could facilitate reproductive isolation. We suggest that introgression from P. laetus to colonising P. lawrencei could significantly reduce founder effects while cold tolerance inherited from P. lawrencei has enabled P. nivalis to occupy alpine environments. Our findings highlight the importance of reticulate evolution in Southern Hemisphere conifers and demonstrate the value of phylogenomic network approaches for resolving recent and complex radiations.

evolutionary biology↗

bioRxiv2025

A comparison of two universal angiosperm bait sets and the phylogenomics of Alismatales

High throughput sequencing of hybridisation capture libraries provides an efficient approach for assembling large scale phylogenomic data. These include universal bait sets that aim to generate comparable data from any lineage within the taxon of interest. Here, we present the OzBaits v2 bait set, which targets a set of low copy nuclear loci for angiosperms. Using published genomic data, we design a set of RNA baits targeting a single exon in each of 98 putatively orthologous nuclear protein coding genes. We tested the efficiency of this bait set for a diverse range of angiosperms and recovered, on average, 93 (95%) genes per sample. We compared a common set of samples for the monocot order Alismatales enriched using OzBaits and the Angiosperms353 (A353) bait set, a widely used universal probe set targeting up to 353 nuclear genes in angiosperms. Gene recovery was, on average, c. 1.7 times higher for OzBaits relative to A353. Using proxies for signal and bias to rank gene alignments by their phylogenetic usefulness, we found that on average, the OzBaits data had higher phylogenetic utility. Both data sets resolved largely congruent, well-supported phylogenies for Alismatales although measures of internal discordance where higher for the A353 data. We discuss the implications of these findings for the design universal baits sets.

evolutionary biology↗

bioRxiv2021

A hybrid capture RNA bait set for resolving genetic and evolutionary relationships in angiosperms from deep phylogeny to intraspecific lineage hybridization

Novel multi-gene targeted capture probes have been developed with the objective of obtaining multi-locus high quality sequence reads across any angiosperm lineage. Using existing genomic and transcriptomic data, two independent single assay probe/bait sets have been developed, the first targeting conserved exons from 20 low copy nuclear genes (OzBaits_NR V1.0) and the second, 19 plastid gene regions (OZBaits_CP V1.0). These universal bait sets can efficiently generate DNA sequence data that are suitable for systematics and evolutionary studies of flowering plants. The bait sets can be ordered as Daicel-Arbor Sciences custom myBaits. We demonstrate the utility of the bait set in consistently recovering the targeted genomic regions across an evolutionarily broad range of angiosperm taxa.

evolutionary biology↗

bioRxiv2021

A multi-gene region targeted capture approach to detect plant DNA in environmental samples: A case study from coastal environments

Metabarcoding of plant DNA recovered from environmental samples, termed environmental DNA (eDNA), has been used to detect invasive species, track biodiversity changes and reconstruct past ecosystems. The P6 loop of the trnL intron is the most widely utilized gene region for metabarcoding plants due to the short fragment length and subsequent ease of recovery from degraded DNA, which is characteristic of environmental samples. However, the taxonomic resolution for this gene region is limited, often precluding species level identification. Additionally, targeting gene regions using universal primers can bias results as some taxa will amplify more effectively than others. To increase the ability of DNA metabarcoding to better resolve flowering plant species (angiosperms) within environmental samples, and reduce bias in amplification, we developed a multi-gene targeted capture method that simultaneously targets 20 chloroplast gene regions in a single assay across all flowering plant species. Using this approach, we effectively recovered multiple chloroplast gene regions for three species within artificial DNA mixtures down to 0.001 ng/{micro}L of DNA. We tested the detection level of this approach, successfully recovering target genes for 10 flowering plant species. Finally, we applied this approach to sediment samples containing unknown compositions of environmental DNA and confidently detected plant species that were later verified with observation data. Targeting multiple chloroplast gene regions in environmental samples enabled species-level information to be recovered from complex DNA mixtures. Thus, the method developed here, confers an improved level of data on community composition, which can be used to better understand flowering plant assemblages in environmental samples.

molecular biology↗