The increasing interest in studying DNA methylation to understand how traits or diseases develop requires new and flexible approaches for quantifying DNA methylation in a diversity of organisms. In particular, we need efficient yet cost-effective ways to measure CpG methylation states over large and complete regions of the genome. Here, we develop TEEM-Seq (target-enriched enzymatic methyl sequencing), a method that combines enzymatic methyl sequencing with a custom-designed hybridization capture bait set that can be scaled to reactions including large numbers of samples in any species for which a reference genome is available. Using DNA from a passerine bird, the superb starling ( Lamprotornis superbus ), we show that TEEM-Seq is able to quantify DNA methylation states similarly well to the more traditional approaches of whole-genome and reduced-representation sequencing. Moreover, we demonstrate its reliability and repeatability, as duplicate libraries from the same samples were highly correlated. Importantly, the downstream bioinformatic analysis for TEEM-Seq is the same as for any sequence-based approach to studying DNA methylation, making it simple to incorporate into a variety of workflows. We believe that TEEM-Seq could replace traditional approaches for studying DNA methylation in candidate genes and pathways, and be effectively paired with other whole-genome or reduced-representation sequencing approaches to increase project sample sizes. In addition, TEEM-Seq can be combined with mRNA sequencing to examine how DNA methylation in promoters or other regulatory regions is related to the expression of individual genes or gene networks. By maximizing the number of samples in the hybridization reaction, TEEM-Seq is an inexpensive and flexible sequence-based approach for quantifying DNA methylation in species where other capture-based methods are unavailable or too expensive, particularly for non-model organisms.

The order Hymenoptera (wasps, ants, sawflies, and bees) represents one of the most diverse animal lineages, but whether specific key innovations have contributed to its diversification is still unknown. We assembled the largest time-calibrated phylogeny of Hymenoptera to date and investigated the origin and possible correlation of particular morphological and behavioral innovations with diversification in the order: the wasp waist of Apocrita; the stinger of Aculeata; parasitoidism, a specialized form of carnivory; and secondary phytophagy, a reversal to plant-feeding. Here, we show that parasitoidism has been the dominant strategy since the Late Triassic in Hymenoptera, but was not an immediate driver of diversification. Instead, transitions to secondary phytophagy (from parasitoidism) had a major influence on diversification rate in Hymenoptera. Support for the stinger and the wasp waist as key innovations remains equivocal, but these traits may have laid the anatomical and behavioral foundations for adaptations more directly associated with diversification.

Chromatids of mitotic chromosomes were suggested to coil into a helix in early cytological studies and this assumption was recently supported by chromosome conformation capture (3C) sequencing. Still, direct differential visualization of a condensed chromatin fibre confirming the helical model was lacking. Here, we combined Hi-C analysis of purified metaphase chromosomes, biopolymer modelling and spatial structured illumination microscopy of large fluorescently labeled chromosome segments to reveal the chromonema – a helically-wound, 400 nm thick chromatin thread forming barley mitotic chromatids. Chromatin from adjacent turns of the helix intermingles due to the stochastic positioning of chromatin loops inside the chromonema. Helical turn size varies along chromosome length, correlating with chromatin density. Constraints on the observable dimensions of sister chromatid exchanges further supports the helical chromonema model.

The Great Barrier Reef (GBR) is the world’s largest coral ecosystem and is threatened by climate change. This study investigated the impact of the 2016 Marine Heatwave (MHW) on plankton associated microbial communities along a ∼800 km transect in the GBR. 16S rRNA gene metabarcoding of archived plankton samples collected from November 2014 to August 2016 in this region showed a significant increase in Planctomycetes and bacteria belonging to the genus Vibrio and Synechococcus during and after the heatwave. Notably, Droplet Digital PCR and targeted metagenomic analysis applied on samples collected four months after the MHW event revealed the presence of several potential pathogenic Vibrio species previously associated with diseases in aquatic animals. Overall, the 2016 MHW significantly impacted the surface picoplankton community and fostered the spread of potentially pathogenic bacteria across the GBR providing an additional threat for marine biodiversity in this area.

Hybridization is a known source of morphological, functional and communicative signal novelty in many organisms. Although diverse mechanisms of established novel ornamentation have been identified in natural populations, we lack an understanding of hybridization effects across levels of biological scales and upon phylogenies. Hummingbirds display diverse structural colours resulting from coherent light scattering by feather nanostructures. Given the complex relationship between feather nanostructures and the colours they produce, intermediate coloration does not necessarily imply intermediate nanostructures. Here, we characterize nanostructural, ecological and genetic inputs in a distinctive Heliodoxa hummingbird from the foothills of eastern Peru. Genetically, this individual is closely allied with Heliodoxa branickii and Heliodoxa gularis, but it is not identical to either when nuclear data are assessed. Elevated interspecific heterozygosity further suggests it is a hybrid backcross to H. branickii. Electron microscopy and spectrophotometry of this unique individual reveal key nanostructural differences underlying its distinct gorget colour, confirmed by optical modelling. Phylogenetic comparative analysis suggests that the observed gorget coloration divergence from both parentals to this individual would take 6.6–10 My to evolve at the current rate within a single hummingbird lineage. These results emphasize the mosaic nature of hybridization and suggest that hybridization may contribute to the structural colour diversity found across hummingbirds.

Etiology of vestibular schwannoma (VS) is unknown. Viruses can infect and reside in neural tissues for decades, and new viruses with unknown tumorigenic potential have been discovered. The presence of herpesvirus, polyomavirus, parvovirus, and anellovirus DNA was analyzed by quantitative PCR in 46 formalin-fixed paraffin-embedded VS samples. Five samples were analyzed by targeted next-generation sequencing. Viral DNA was detected altogether in 24/46 (52%) tumor samples, mostly representing anelloviruses (46%). Our findings show frequent persistence of anelloviruses, considered normal virome, in VS. None of the other viruses showed an extensive presence, thereby suggesting insignificant role in VS.

The systematics of Madagascar’s extinct elephant birds remains controversial due to large gaps in the fossil record and poor biomolecular preservation of skeletal specimens. Here, a molecular analysis of 1000-year-old fossil eggshells provides the first description of elephant bird phylogeography and offers insight into the ecology and evolution of these flightless giants. Mitochondrial genomes from across Madagascar reveal genetic variation that is correlated with eggshell morphology, stable isotope composition, and geographic distribution. The elephant bird crown is dated to ca. 30 Mya, when Madagascar is estimated to have become less arid as it moved northward. High levels of between-clade genetic variation support reclassifying Mullerornis into a separate family. Low levels of within-clade genetic variation suggest there were only two elephant bird genera existing in southern Madagascar during the Holocene. However, we find an eggshell collection from Madagascar’s far north that represents a unique lineage of Aepyornis. Furthermore, divergence within Aepyornis coincides with the aridification of Madagascar during the early Pleistocene ca. 1.5 Ma, and is consistent with the fragmentation of populations in the highlands driving diversification and the evolution of extreme gigantism over shorts timescales. We advocate for a revision of their taxonomy that integrates palaeogenomic and palaeoecological perspectives.

Kosovo has previously seen two bluetongue (BT) epizootics, each caused by a different serotype, BTV-9 in 2001 and BTV-4 in 2014. Since 2014, no clinical cases of BT have been reported in Kosovo. In September, 2020, clinical signs suggestive of BTV infection were observed in several sheep farms in Kosovo. Blood samples from sheep (n = 40) were collected and subjected to further molecular investigations. Molecular analyses confirmed BTV serotype 4 (BTV-4) infection in thirty-six sheep from five different farms across two different regions. Full genome sequence analyses indicated that the BTV-4 strains (KOS2020/01 and KOS2020/02) detected in Kosovo in 2020 had high sequence identity (99.9%-100%) with a strain responsible for an outbreak in North Macedonia in July, 2020, (MKD2020/06) and with previous isolates (≥99.3%) from Greece, Hungary, and France. The percent nucleotide sequence (nt%) identity and phylogenetic analyses suggest that the incursion of BTV-4 into Kosovo was a re-emergence of a previously seen strain and not a novel reassortant. This could be due to a reintroduction of the strain into the region or from subclinical circulation which had been ongoing and underreported for years. Surveillance across Kosovo and the Balkan region to monitor the circulation of BTV is crucial if outbreaks are to be brought under control.