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Abstract Hybridization between organisms from evolutionarily distinct lineages can have profound consequences on organismal ecology, with cascading effects on fitness and evolution. Most studies of hybrid organisms have focused on organismal traits, for example, various aspects of morphology and physiology. However, with the recent emergence of holobiont theory, there has been growing interest in understanding how hybridization impacts and is impacted by host‐associated microbiomes. Better understanding of the interplay between host hybridization and host‐associated microbiomes has the potential to provide insight into both the roles of host‐associated microbiomes as dictators of host performance as well as the fundamental rules governing host‐associated microbiome assembly. Unfortunately, there is a current lack of frameworks for understanding the structure of host‐associated microbiomes of hybrid organisms.In this paper, we develop four conceptual models describing possible relationships between the host‐associated microbiomes of hybrids and their progenitor or ‘parent’ taxa. We then integrate these models into a quantitative ‘4H index’ and present a new R package for calculation, visualization and analysis of this index.We demonstrate how the 4H index can be used to compare hybrid microbiomes across disparate plant and animal systems. Our analyses of these data sets show variation in the 4H index across systems based on host taxonomy, host site and microbial taxonomic group.Our four conceptual models, paired with our 4H index and associated visualization tools, facilitate comparison across hybrid systems. This, in turn, allows for systematic exploration of how different aspects of host hybridization impact the host‐associated microbiomes of hybrid organisms. 

Transposable elements (TEs) are sequences that replicate and move throughout genomes, and they can be silenced through methylation of cytosines at CpG dinucleotides. TE abundance contributes to genome size, but TE silencing variation across genomes of different sizes remains underexplored. Salamanders include most of the largest C-values – 9 to 120 Gb. We measured CpG methylation levels in salamanders with genomes ranging from 2N = ∼58 Gb to 4N = ∼116 Gb. We compared these levels to results from endo- and ectothermic vertebrates with more typical genomes. Salamander methylation levels are approximately 90%, higher than all endotherms. However, salamander methylation does not differ from other ectotherms, despite an approximately 100-fold difference in nuclear DNA content. Because methylation affects the nucleotide compositional landscape through 5-methylcytosine deamination to thymine, we quantified salamander CpG dinucleotide levels and compared them to other vertebrates. Salamanders and other ectotherms have comparable CpG levels, and ectotherm levels are higher than endotherms. These data show no shift in global methylation at the base of salamanders, despite a dramatic increase in TE load and genome size. This result is reconcilable with previous studies that considered endothermy and ectothermy, which may be more important drivers of methylation in vertebrates than genome size. 

Abstract Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genusXenopus. Here we report a high-quality reference genome sequence for the western clawed frog,Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species,Eleutherodactylus coqui,Engystomops pustulosus, andHymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map forX. tropicalisand chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.