The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives. The dataset contains 85 fastq files. Each file contains reads of amplicons from five MHC loci (DQA, DQB, DRA, DRB, and class I genes) combined across separate sequencing runs from a single cetacean. Details on individual cetacean sample abbreviations can be found in the manuscript. Reads are paired and merged with the Illumina adapter removed. It also contains one fastq file with all class I alleles found and one fastq file with non-functional DRB alleles found. Alleles are labeled with four letter species abbreviation followed by locus designation (DRB or N for class I) and are numbered in the order they were discovered. Further details are provided at: Heimeier, D., Garland, E. C., Eichenberger, F., Garrigue, C., Vella, A., Baker, C. S., & Carroll, E. L. (2024). A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies. Molecular Ecology Resources, 00, e13955. https://doi.org/10.1111/1755-0998.13955 GET DATA: https://doi.org/10.5061/dryad.wh70rxwvb

The New Zealand Terrestrial Antarctic Biocomplexity Survey (nzTABS) is the largest and most comprehensive interdisciplinary landscape-scale study of terrestrial biology ever undertaken in Antarctica, incorporating fieldwork of 1500+ person days in 6 of the Dry Valleys (total area of 6500 km2), strategic sampling of over 1200 sites designed to encompass the landscape heterogeneities in the ecosystem, and a range of high-resolution remote sensing data. All samples were collected during the month of January in each sampling year. Initially a 220 km2 study area, consisting of Miers, Marshall, and Garwood Valleys as well as Shangri-La, was divided into more than 600 geographically and geologically distinct ice-free sectors (hereinafter “tiles”) using remote-sensing data and published soil maps. Tile boundaries were delineated where the combination of geographical and geological variables changed, and on-the-ground assessments were carried out in November 2008 to confirm the reliability of delineations. 554 tiles were chosen for sampling to encompass the entire range of geographical and geological heterogeneity. Sampling of soils and biological communities was carried out over two successive austral summers (January 2009 and January 2010). Surveys were conducted for vegetation (i.e., mosses, lichens, algal and cyanobacterial mats), lithic microbial communities, and invertebrates at each sampling site (verified by GPS to be inside its respective tile), followed by collection of bulk soil samples for additional analyses, including molecular analyses of bacteria (total and cyanobacteria-only) and fungi. In addition, a number of key variables were derived from satellite imagery, including surface soil temperature, a topographically derived ‘wetness index’, and distance to the coast. After quality control, data for 490 samples were included in the analysis. These data represent geochemistry and geomorphology to population genetics and microbial ecology parameters. Further details are provided at https://doi.org/10.1038/s42003-018-0274-5. Please cite the data with the following citation: Lee, C.K., Laughlin, D.C., Bottos, E.M. et al. Biotic interactions are an unexpected yet critical control on the complexity of an abiotically driven polar ecosystem. Commun Biol 2, 62 (2019). https://doi.org/10.1038/s42003-018-0274-5