Advancing DNA barcoding and metabarcoding applications for plants requires systematic analysis of herbarium collections-an Australian perspective

Building DNA barcode databases for plants has historically been ad hoc, and often with a relatively narrow taxonomic focus. To realize the full potential of DNA barcoding for plants, and particularly its application to metabarcoding for mixed-species environmental samples, systematic sequencing of reference collections is required using an augmented set of DNA barcode loci, applied according to agreed data generation and analysis standards. The largest and most complete reference collections of plants are held in herbaria. Australia has a globally significant flora that is well sampled and expertly curated by its herbaria, coordinated through the Council of Heads of Australasian Herbaria. There exists a tremendous opportunity to provide a comprehensive and taxonomically robust reference database for plant DNA barcoding applications by undertaking coordinated and systematic sequencing of the entire flora of Australia utilizing existing herbarium material. In this paper, we review the development of DNA barcoding and metabarcoding and consider the requirements for a robust and comprehensive system. We analyzed the current availability of DNA barcode reference data for Australian plants, recommend priority taxa for database inclusion, and highlight future applications of a comprehensive metabarcoding system. We urge that large-scale and coordinated analysis of herbarium collections be undertaken to realize the promise of DNA barcoding and metabarcoding, and propose that the generation and curation of reference data should become a national investment priority

Rapid loss of self-incompatibility in experimental populations of the perennial outcrossing plant Linaria cavanillesii.

Transitions from self-incompatibility to self-compatibility in angiosperms may be frequently driven by selection for reproductive assurance when mates or pollinators are rare, and are often succeeded by loss of inbreeding depression by purging. Here, we use experimental evolution to investigate the spread of self-compatibility from one such population of the perennial plant Linaria cavanillesii into self-incompatible (SI) populations that still have high inbreeding depression. We introduced self-compatible (SC) individuals at different frequencies into replicate experimental populations of L. cavanillesii that varied in access to pollinators. Our experiment revealed a rapid shift to self-compatibility in all replicates, driven by both greater seed set and greater outcross siring success of SC individuals. We discuss our results in the light of computer simulations that confirm the tendency of self-compatibility to spread into SI populations under the observed conditions. Our study illustrates the ease with which self-compatibility can spread among populations, a requisite for species-wide transitions from self-incompatibility to self-compatibility

The loss of self-incompatibility in a range expansion.

It is commonly observed that plant species' range margins are enriched for increased selfing rates and, in otherwise self-incompatible species, for self-compatibility (SC). This has often been attributed to a response to selection under mate and/or pollinator limitation. However, range expansion can also cause reduced inbreeding depression, and this could facilitate the evolution of selfing in the absence of mate or pollinator limitation. Here, we explore this idea using spatially explicit individual-based simulations of a range expansion, in which inbreeding depression, variation in self-incompatibility (SI), and mate availability evolve. Under a wide range of conditions, the simulated range expansion brought about the evolution of selfing after the loss of SI in range-marginal populations. Under conditions of high recombination between the self-incompatibility locus (S-locus) and viability loci, SC remained marginal in the expanded metapopulation and could not invade the range core, which remained self-incompatible. In contrast, under low recombination and migration rates, SC was frequently able to displace SI in the range core by maintaining its association with a genomic background with purged genetic load. We conclude that the evolution of inbreeding depression during a range expansion promotes the evolution of SC at range margins, especially under high rates of recombination.‬

New insights from population genomics into the invasive Lantana camara L species complex

Extensive morphological diversity in the invasive L. camara species complex has resisted clear taxonomic characterisation, yet molecular studies to date have revealed minimal genetic structure. Analysis of thousands of genome-wide markers successfully detects differentiation among sub-lineages within the complex, revealing that two of the morphological variants in Australia comprise multiple, distinct lineages. The common pinkflowering morphotype appears to be monophyletic, whereas the pink-edged red flowering morphotype does not. Pending further investigation and expanded sampling, these findings hold promise for improving weed management through a deeper understanding of the systematics of the L. camara complex (e.g., by enabling selection of biological control agents that are best matched with target host populations)

Genetic diversity and structure of the Australian flora

AimTo investigate the relationships between species attributes and genetic parameters in Australian plant species and to determine the associations in relation to predictions from population theory and previous global analyses.LocationContinent of Australia.MethodsWe assembled a dataset of all known population genetic analyses of Australian plants based on neutral markers and catalogued them according to key species attributes, including range, abundance, range disjunction, biome and growth form; and genetic parameters, mean number of alleles per locus, observed and expected heterozygosity and population differentiation. We determined relationships between species attributes and genetic parameters using a maximum-likelihood, multimodel inference approach.ResultsWe found many associations that were consistent with predictions. Species attributes with greatest effect on genetic diversity were range size, growth form, abundance and biome. The most important attributes influencing genetic differentiation were range disjunction and abundance. We found unexpected results in the effects of biome and growth form on genetic diversity, with greater diversity in the eastern biome of Australia, and lower diversity in shrubs compared to trees.Main conclusionsOur analysis of genetic diversity of Australian plants showed associations consistent with predictions based on population genetics theory, with strong effects of range size, abundance and growth form. We identified a striking effect of range disjunction on population genetic differentiation, an effect that has received little attention in the literature. We also found some notable differences to global predictions, which were most likely explained by confounding effects across variables. This highlights that caution is needed when extrapolating trends from global analyses to regional floras. Identifying associations between species attributes and patterns of genetic diversity enables broadscale predictions to facilitate the inclusion of genetic considerations into conservation decision-making

A neonicotinoid impairs olfactory learning in Asian honey bees (Apis cerana) exposed as larvae or as adults

Xenobiotics such as the neonicotinoid pesticide, imidacloprid, are used globally, but their effects on native bee species are poorly understood. We studied the effects of sublethal doses of imidacloprid on olfactory learning in the native honey bee species, Apis cerana, an important pollinator of agricultural and native plants throughout Asia. We provide the first evidence that imidacloprid can impair learning in A. cerana workers exposed as adults or as larvae. Adults that ingested a single imidacloprid dose as low as 0.1 ng/bee had significantly reduced olfactory learning acquisition, which was 1.6-fold higher in control bees. Longer-term learning (1-17 h after the last learning trial) was also impaired. Bees exposed as larvae to a total dose of 0.24 ng/bee did not have reduced survival to adulthood. However, these larval-treated bees had significantly impaired olfactory learning when tested as adults: control bees exhibited up to 4.8-fold better short-term learning acquisition, though longer-term learning was not affected. Thus, sublethal cognitive deficits elicited by neonicotinoids on a broad range of native bee species deserve further study