Let’s talk about the (lady)birds and the bees: how insects can whisper a multitude of stories

If you have watched A Bug’s Life, you would have seen that insects come in an assortment of colours, shapes, and sizes. They are the perfect organism that could be used to describe the myriad diversity of all life on earth. These six-legged creatures are one of the most diverse groups of species, accounting for more than 80% of all documented living animals Ødegaard 2008. This huge diversity also makes it extremely time- and labour-intensive to carry out large-scale monitoring of insects. High-throughput sequencing technologies and the use of DNA barcodes for species identification have paved the way for the rapid biomonitoring of insects Hebert et al. 2003. However, millions of insect species are not well-represented in DNA reference databases, making species-level identification challenging for molecular research. Projects such as the Darwin Tree of Life (DToL) aim to cover this gap and generate DNA barcodes for all eukaryotic species found in the UK Blaxter et al. 2022. At the Wellcome Sanger Institute, the BIOSCAN UK for Flying Insects project has two main aims;Documenting the diversity of UK flying insectsDiscovering insect-cobiont interactionsTo meet these aims, we will be documenting the diversity of one million malaise-caught insects from 100 sites across the UK in the next five years. We will be using a non-destructive DNA extraction technique to preserve insect specimen integrity for museum collections or educational purposes Korlević et al. 2021. COI barcoding will be carried out using ONT and/or PacBio long-read technology to identify each insect specimen. To tease apart insect conbiont interactions, we will carry out mini barcoding using primers targeting microbes, parasites, vertebrates, invertebrates, and plants Fig. 1. Together, this molecular dataset consisting of one million specimens collected over space and time in the next five years will allow us to discover how insects interact with the ecosystem and advance insect biomonitoring research in the UK

Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Parallel evolution provides among the strongest evidence of the role of natural selection in shaping adaptation to the local environment. Yet, the chronology, mode and tempo of the process of parallel evolution remains broadly debated and discussed in the field of evolutionary biology. In this study, we harness the temporal resolution of paleogenomics to understand the tempo and independence of parallel coastal ecotype adaptation in common bottlenose dolphins (Tursiops truncatus). For this, we generated whole genome re-sequencing data from subfossil dolphins (8,610-5,626 years BP) originating from around the formation time of new coastal habitat and compared them with data from contemporary populations. Genomic data revealed a shift in genetic affinity, with the oldest ancient sample being closer to the pelagic populations, while the younger samples had intermediate ancestry that showed greater affinity with the local contemporary coastal populations. We found coastal-associated genotypes in the genome of our highest coverage ancient sample, SP1060, providing rare evidence of rapid adaptation from standing genetic variation. Lastly, using admixture graph analyses, we found a reticulate evolutionary history between pelagic and coastal populations. Ancestral gene flow from coastal populations was the probable source of standing genetic variation present in the pelagic populations that enabled rapid adaptation to newly emerged coastal habitat. The genetic response to past climatic warming provides an understanding of how bottlenose dolphins will respond to ongoing directional climate change and shifting coastlines

Genomic reconstruction of the SARS-CoV-2 epidemic in England

AbstractThe evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.</jats:p