Genetic variability within seagrass of the north west of Western Australia: Report of Theme 5 - Project 5.2 prepared for the Dredging Science Node

The response of seagrass species to on-going pressures such as dredging can be strongly influenced by their ability to adapt to, resist or recover from these pressures. The ability of species to adapt to a pressure, over generations, is influenced by the amount of genetic variation in a population: greater genetic diversity can enhance resistance and higher levels of gene flow between populations can enhance the rate of recovery following complete habitat loss. As seagrass are clonal plants, genetic diversity in a meadow is dependent on both the number of unique clones within the meadow, and distribution of this variation within and among meadows. Understanding the genetic diversity of seagrass meadows can provide important fundamental knowledge for the prediction of dredging impacts, by providing insights into the likelihood of recovery and the processes that may drive that recovery (vegetative regrowth, seed bank recruitment or immigration of recruits). It can also inform management, for example by providing insights into relative vulnerability to pressures, sources of recruitment populations and the importance of maintaining seed banks. However, for most seagrasses and in most parts of the world, extremely little is known about the genetic diversity and connectivity of populations..

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

A Multi-Gene Region Targeted Capture Approach to Detect Plant DNA in Environmental Samples: A Case Study From Coastal Environments

Published: 25 October 2021Metabarcoding 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 utilised 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/mL 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 eDNA 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.Nicole R. Foster, Kor-jent van Dijk, Ed Biffin, Jennifer M. Young, Vicki A. Thomson, Bronwyn M. Gillanders, Alice R. Jones and Michelle Waycot

Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model Eukaryote species

Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.Emese Meglécz, Gabriel Nève, Ed Biffin and Michael G. Gardne

Anetholea anisata transferred to, and two new Australian taxa of, Syzygium (Myrtaceae)

The distinction between Anetholea and Syzygium is lessened due to the occurrence of epigeal germination and dry fruitedness in the latter genus also and it is concluded that Anetholea is better placed within Syzygium. Analysis of sequence data from nuclear ribosomal DNA and the chloroplast genome support this conclusion. The sole species of Anetholea, A. anisata, is transferred to Syzygium and the new combination, S. anisatum (Vickery) Craven & Biffin, made. Syzygium wilsonii subsp. cryptophlebium is reinstated at species rank, necessitating the new combination, S. cryptophlebium (F. Muell.) Craven & Biffin. Two new taxa of Syzygium are described from Australia, S. wilsonii subsp. epigaeum Craven & Biffin and S. maraca Craven & Biffin

An infrageneric classification of Syzygium (Myrtaceae)

An infrageneric classification of Syzygium based upon evolutionary relationships as inferred from analyses of nuclear and plastid DNA sequence data, and supported by morphological evidence, is presented. Six subgenera and seven sections are recognised. An identification key is provided and names proposed for two species newly transferred to Syzygium

Acmena, Acmenosperma, Cleistocalyx, Piliocalyx and Waterhousea formally transferred to Syzygium (Myrtaceae)

Based on morphological and molecular data, we have concluded that Acmena, Acmenosperma, Cleistocalyx, Piliocalyx and Waterhousea should be combined with Syzygium. The five genera are formally transferred to Syzygium and new names provided for those of their accepted representatives for which names are as yet not available in Syzygium, with the exception of the New Caledonian members of Piliocalyx as these currently are being revised