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During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, Sardinops sagax, form large shoals that migrate north-east towards the subtropical Indian Ocean. Recent studies have highlighted the role that genetic and environmental factors play in sardine run formation. In the present study, we used massively parallel sequencing to assemble and annotate the first reference transcriptome from the liver cells of South African sardines, and to investigate the functional content and transcriptomic diversity. A total of 1,310,530 transcripts with an N50 of 1578 bp were assembled de novo. Several genes and core biochemical pathways that modulate energy production, energy storage, digestion, secretory processes, immune responses, signaling, regulatory processes, and detoxification were identified. The functional content of the liver transcriptome from six individuals that participated in the 2019 sardine run demonstrated heterogeneous levels of variation. Data presented in the current study provide new insights into the complex function of the liver transcriptome in South African sardines.

Unravelling the taxonomy and distribution of two problematic small mammal genera in the Karoo biomeMain et al. Table S1: Location details for specimens sampled during this study. M. namaquensis Latitude: degrees South Longitude: degrees East Locations on map Marker RR1 −30.50666 21.34012 11 cytochrome b RR2 −30.50666 21.34012 11 cytochrome b RR3 −30.50666 21.34012 11 cytochrome b RR4 −30.50666 21.34012 11 cytochrome b RR5 −30.48179 21.35898 12 cytochrome b RR6 −30.48179 21.35898 12 cytochrome b RR7 −30.48179 21.35898 12 cytochrome b RR9 −30.48179 21.35898 12 cytochrome b RR10 −30.46297

A longstanding question in evolutionary biology is how natural selection and environmental pressures shape the mitochondrial genomic architectures of organisms. Mitochondria play a pivotal role in cellular respiration and aerobic metabolism, making their genomes functionally highly constrained. Evaluating selective pressures on mitochondrial genes can provide functional and ecological insights into the evolution of organisms. Collembola (springtails) are an ancient hexapod group that includes the oldest terrestrial arthropods in the fossil record, and that are closely associated with soil environments. Of interest is the diversity of habitat stratification preferences (life forms) exhibited by different species within the group. To understand whether signals of positive selection are linked to the evolution of life forms, we analysed 32 published Collembola mitogenomes in a phylomitogenomic framework. We found no evidence that signatures of selection are correlated with the evolution of novel life forms, but rather that mutations have accumulated as a function of time. Our results highlight the importance of nuclear-mitochondrial interactions in the evolution of collembolan life forms and that mitochondrial genomic data should be interpreted with caution, as complex selection signals may complicate evolutionary inferences.