A sampling strategy for genome sequencing the British terrestrial arthropod fauna.

The Darwin Tree of Life (DToL) project aims to sequence and assemble high-quality genomes from all eukaryote species in Britain and Ireland, with the first phase of the project concentrating on family-level coverage plus species of particular ecological, biomedical or evolutionary interest. We summarise the processes involved in (1) assessing the UK arthropod fauna and the status of individual species on UK lists; (2) prioritising and collecting species for initial genome sequencing; (3) handling methods to ensure that high-quality genomic DNA is preserved; and (4) compiling standard operating procedures for processing specimens for genome sequencing, identification verification and voucher specimen curation. We briefly explore some lessons learned from the pilot phase of DToL and the impact of the Covid-19 pandemic.

The genome sequence of the King Ragworm, Alitta virens (Sars, 1835).

We present a genome assembly from an individual Alitta virens (the King Ragworm; Annelida; Polychaeta; Phyllodocida; Nereididae). The genome sequence is 671.2 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.83 kilobases in length.

Mayfly taxonomy (Arthropoda: Hexapoda: Ephemeroptera) during the first two decades of the twenty-first century and the concentration of taxonomic publishing.

The twentieth anniversary of the first issue of Zootaxa (De Moraes Freire, 2001) provides an appropriate opportunity to reflect on some trends in global Ephemeroptera taxonomy publishing over the last two decades, with a focus on the description of new species and the outsized role of the journals Zootaxa and ZooKeys, in particular. Detailed reviews of world Ephemeroptera knowledge up to about 2000 were collected in a series of nine papers from a symposium on the subject, published together in the proceedings of the ninth International Conference on Ephemeroptera (Domínguez 2001). Domínguez Dos Santos (2014) provided updates and analysis for South America up to the year 2012. More recent detailed accounts of regional and taxonomic diversity, and other aspects of mayfly biology and ecology, were reviewed by Jacobus et al. (2019), while Ogden et al. (2019) discussed current issues involving higher classification.

Habitat requirements affect genetic variation in three species of mayfly (Ephemeroptera, Baetidae) from South Africa.

This study investigates genetic diversity in three species of Ephemeroptera, one eurytopic and therefore widespread (Afroptilum sudafricanum) and two stenotopic and thus endemic (Demoreptus natalensis and Demoreptus capensis) species, all of which co-occur in the southern Great Escarpment, South Africa. Mitochondrial DNA was analysed to compare the genetic diversity between the habitat generalist and the two habitat specialists. Afroptilum sudafricanum showed no indication of population genetic structure due to geographic location, while both Demoreptus species revealed clear genetic differentiation between geographic localities and catchments, evident from phylogenetic analyses and high FST values from AMOVA. In addition, the phylogenetic analyses indicate some deeper haplotype divergences within A. sudafricanum and Demoreptus that merit taxonomic attention. These results give important insight into evolutionary processes occurring through habitat specialisation and population isolation. Further research and sampling across a wider geographic setting that includes both major mountain blocks of the Escarpment and lowland non-Escarpment sites will allow for refined understanding of biodiversity and associated habitat preferences, and illuminate comparative inferences into gene flow and cryptic speciation.

Redescription and lectotype designation of the endemic South African mayfly Lestagella penicillata (Barnard, 1932) (Ephemeroptera: Teloganodidae).

The imago and nymph of Lestagella penicillata are redescribed based on historic specimens and new material from Table Mountain slopes (Skeleton Gorge and Window Stream), Western Cape, South Africa. A male from Barnard's syntype series is designated as the lectotype. Wear-and-tear of mouthparts, particularly the mandibles, has led to errors in identification of diagnostic characters for the nymphs in earlier publications. Previous descriptions of the mandibles being atrophied, in terms of dentition, are erroneous. The generic diagnosis of Lestagella is modified to account for these errors and intraspecific variability. Adults are distinguished from other Teloganodidae by the combination of a short, detached iMP vein on the forewing, three caudal filaments and gill socket vestiges on segments II - IV. Nymphs are distinguished from other Teloganodidae by a conspicuous head fringe, lamellate gills on abdominal segments II-IV and a dorso-ventrally flattened body. 

Cryptic variation in an ecological indicator organism: mitochondrial and nuclear DNA sequence data confirm distinct lineages of Baetis harrisoni Barnard (Ephemeroptera: Baetidae) in southern Africa.

BACKGROUND: Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9-10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa. RESULTS: Four gene regions were examined, two mitochondrial (cytochrome c oxidase subunit I [COI] and small subunit ribosomal 16S rDNA [16S]) and two nuclear (elongation factor 1 alpha [EF1α] and phosphoenolpyruvate carboxykinase [PEPCK]). Bayesian and parsimony approaches to phylogeny reconstruction resulted in five well-supported major lineages, which were confirmed using a general mixed Yule-coalescent (GMYC) model. Results from the EF1α gene were significantly incongruent with both mitochondrial and nuclear (PEPCK) results, possibly due to incomplete lineage sorting of the EF1α gene. Mean between-clade distance estimated using the COI and PEPCK data was found to be an order of magnitude greater than the within-clade distance and comparable to that previously reported for other recognised Baetis species. Analysis of the Isolation by Distance (IBD) between all samples showed a small but significant effect of IBD. Within each lineage the contribution of IBD was minimal. Tentative dating analyses using an uncorrelated log-normal relaxed clock and two published estimates of COI mutation rates suggest that diversification within the group occurred throughout the Pliocene and mid-Miocene (~2.4-11.5 mya). CONCLUSIONS: The distinct lineages of B. harrisoni correspond to categorical environmental variation, with two lineages comprising samples from streams that flow through acidic Table Mountain Sandstone and three lineages with samples from neutral-to-alkaline streams found within eastern South Africa, Malawi and Zambia. The results of this study suggest that B. harrisoni as it is currently recognised is not a single species with a wide geographic range and pH-tolerance, but may comprise up to five species under the phylogenetic species concept, each with limited pH-tolerances, and that the B. harrisoni species group is thus in need of taxonomic review.