Search

Abstract Premise The HybPiper pipeline has become one of the most widely used tools for the assembly of target capture data for phylogenomic analysis. After the production of locus sequences and before phylogenetic analysis, the identification of paralogs is a critical step for ensuring the accurate inference of evolutionary relationships. Algorithmic approaches using gene tree topologies for the inference of ortholog groups are computationally efficient and broadly applicable to non‐model organisms, especially in the absence of a known species tree. Methods and Results We containerized and expanded the functionality of both HybPiper and a pipeline for the inference of ortholog groups, providing novel options for the treatment of target capture sequence data, and allowing seamless use of the outputs of the former as inputs for the latter. The Singularity container presented here includes all dependencies, and the corresponding pipelines (hybpiper‐nf and paragone‐nf, respectively) are implemented via two Nextflow scripts for easier deployment and to vastly reduce the number of commands required for their use. Conclusions The hybpiper‐nf and paragone‐nf pipelines are easily installed and provide a user‐friendly experience and robust results to the phylogenetic community. They are used by the Australian Angiosperm Tree of Life project. The pipelines are available at https://github.com/chrisjackson-pellicle/hybpiper-nf and https://github.com/chrisjackson-pellicle/paragone-nf.

While conducting phylogenetic analyses of sequence-capture data of Australian members of Asteraceae tribe Astereae, we found that Elachanthus pusillus F.Muell., Isoetopsis graminifolia Turcz. and Kippistia suaedifolia F.Muell. formed a clade with Minuria. We, therefore, conducted an analysis focused on this clade, but with replicate samples of the three smaller genera, and confirmed our results. Kippistia had been synonymised under Minuria between 1876 and 1980, when it was reinstated. Elachanthus and Isoetopsis had not previously been suggested to be part of Minuria , and, indeed, Isoetopsis had been considered so morphologically divergent that even its tribal affiliations were long controversial. However, on closer examination, Elachanthus and Isoetopsis are strikingly similar to Minuria , especially in cypsela and pappus morphology. The evolution of both genera from a common ancestor in Minuria appears plausible in the light of their overall similarity to annual species of that genus such as M. annua , their multiple uniform rows of herbaceous phyllaries with scarious margins, a pappus of scales v. the tendency of Minuria to form pappi with scale-like bases, female outer and male inner florets, and a cypsela indumentum shared with some species of Minuria. We propose the following three new combinations under Minuria : M. pusilla , M. glabra and M. graminifolia. We conducted a phylogenetic analysis of Minuria and related genera and found that Elachanthus , Isoetopsis , and Kippistia phylogenetically nested in Minuria. Before 1980, Kippistia had long been considered part of Minuria. Morphological examination showed many similarities between Eleachanthus , Isoetopsis , and annual species of Minuria. We publish new combinations for four species, synonymising the three smaller genera. (Image credit: Alexander Schmidt-Lebuhn.) This article belongs to the collection Genomics for Australian Plants. [ABSTRACT FROM AUTHOR]

Fires triggered by climate change threaten plant diversity in many biomes. Here the authors investigate how the catastrophic fires of 2019–2020 affected the vascular flora of SE Australia. They report that 816 species were highly impacted, including taxa of biogeographic and conservation interest.

Abstract Monitoring biodiversity is a growing and pressing challenge, particularly as climate change threatens species with extinction and leads to widespread shifts in plant distribution and phenology. Tracking changes via ground vegetation surveys is costly and time‐consuming, hence monitoring of complex and heterogenous communities remains an ongoing challenge. Molecular DNA methods are rapidly being developed to provide fast and reproducible results for environmental monitoring, including diet and ecosystem assessments. Here, we used DNA metabarcoding of pollen foraged by European honey bees (Apis mellifera) to investigate their floral resource use in an urban reserve. We collected three different pollen samples from hives: individual bees, raw honey and pollen traps, and identified plants using two metabarcoding markers (ITS2 and trnL). We then compared the results to a ground vegetation survey of surrounding flowering taxa. Pollen DNA metabarcoding detected 74 taxa (48.6% identified to species) across all pollen sources, compared to 44 taxa recorded by the survey (93% identified to species). Within the metabarcoding results, we identified 25% of the genera and 9% of the species found during the survey, with three of the top 10 flowering genera represented. While honey was the most taxon‐rich pollen source (mean = 8.5, SD = 3.5), followed by honey bees (mean = 5.8, SD = 6.1) and pollen traps (mean = 4.2, SD = 1.7), combining the results of six individual bees could detect similar taxa numbers to honey, while 20 bees were required to detect as many taxa as the survey. We demonstrate how DNA metabarcoding of the pollen foraged by honey bees can detect more flowering taxa than traditional survey methods, and how different pollen sources and genetic markers affect the level of detection of plant taxa. The foraging choices of honey bees matched few species detected by the vegetation survey, therefore pollen metabarcoding is recommended as a complementary approach to ground surveys. Rigorous validation and stringent filtering of metabarcoding results were also required to exclude potential false positives. Altogether, this molecular approach can be used to augment vegetation surveys, while tracking the floral resources used by bees.

PREMISE Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost‐efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 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, and reducing locus recovery. METHODS We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a ‘mega353’ target file, with each locus 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 data sets. RESULTS Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on‐target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%. DISCUSSION Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson‐pellicle/NewTargets.

The Senecio inaequidens – S. madagascariensis complex (Asteraceae: Senecioneae, subsequently "fireweed complex") is a group of six southern African species of Senecio, three of which are considered invasive in various parts of the world: S. madagascariensis in South America, Japan, Australia, and the Hawaiian Islands, S. skirrhodon in New Zealand, and S. inaequidens in Mexico and Europe. Morphological plasticity and historically limited access to reliable information in the introduced ranges have led to taxonomic confusion in many countries, where the weedy populations have been classified under changing names and sometimes erroneously considered to be native species. This confusion has hampered research into management options such as biological control. Recently, uncertainty has arisen about whether only one or two species of the fireweed complex are present in New Zealand. To resolve this question and test the utility of multi-locus sequence capture data for the understanding of the complex, we produced a first dataset of hundreds of genes for four of its species with a focus on S. madagascariensis and S. skirrhodon. Both species were found to be present in the North Island of New Zealand, with S. madagascariensis widespread in the Northland region and S. skirrhodon present at both sites sampled in the southern half of North Island. Our results show that sequence capture data provide high levels of confidence and resolution even at shallow phylogenetic levels, which will enable a greater understanding of the fireweed complex and its invasion history as the dataset is expanded. [ABSTRACT FROM AUTHOR]

Tribe Anthemideae (Asteraceae) is represented in Australia by only nine indigenous species of Cotula and Leptinella. The generic placement of Cotula alpina (Hook.f.) Hook.f. is considered problematic, because it shares the stoloniferous and scapose habit of Leptinella, but lacks corollas in female florets, a trait traditionally considered defining of Cotula. A previous phylogenetic analysis of Leptinella using ITS and chloroplast data showed that the species nested in that genus, but some uncertainty remained because of incomplete sequence data and missing cytological information, and no taxonomic change was made. Here, we use target-capture data from three different sequencing initiatives to reconstruct a phylogeny of Australian native and introduced Anthemideae to resolve this outstanding question. We confirm previous results with a high degree of support and formally transfer Cotula alpina to the genus Leptinella. A lectotype is selected for the basionym, Ctenosperma alpinum Hook.f. [ABSTRACT FROM AUTHOR]

Alpine plant–pollinator communities play an important role in the functioning of alpine ecosystems, which are highly threatened by climate change. However, we still have a poor understanding of how environmental factors and spatiotemporal variability shape these communities. Here, we investigate what drives structure and beta diversity in a plant–pollinator metacommunity from the Australian alpine region using two approaches: pollen DNA metabarcoding (MB) and observations. Individual pollinators often carry pollen from multiple plant species, and therefore we expected MB to reveal a more diverse and complex network structure. We used two gene regions (ITS2 and trnL) to identify plant species present in the pollen loads of 154 insect pollinator specimens from three alpine habitats and construct MB networks, and compared them to networks based on observations alone. We compared species and interaction turnover across space for both types of networks, and evaluated their differences for plant phylogenetic diversity and beta diversity. We found significant structural differences between the two types of networks; notably, MB networks were much less specialized but more diverse than observation networks, with MB detecting many cryptic plant species. Both approaches revealed that alpine pollination networks are very generalized, but we estimated a high spatial turnover of plant species (0.79) and interaction rewiring (0.6) as well as high plant phylogenetic diversity (0.68) driven by habitat differences based on the larger diversity of plant species and species interactions detected with MB. Overall, our findings show that habitat and microclimatic heterogeneity drives diversity and fine‐scale spatial turnover of alpine plant–pollinator networks. [ABSTRACT FROM AUTHOR]