The genetics underpinning phenotype can impact the evolution of a trait and, in turn, a species. Here, researchers use genome sequences to investigate the putative genetic basis of phenotypic variation in redpoll finches (Acanthis spp.). Variation in the redpoll phenotype appears to be dictated by a ~55-Mb chromosomal inversion. This inversion impacted multiple candidate genes with putative functions related to melanogenesis, carotenoid coloration, and bill shape. This finding suggests that the inversion may act as a supergene impacted multiple linked traits. A latitudinal gradient in ecotype distribution suggests supergene driven variation in color and bill morphology are likely under environmental selection, maintaining supergene haplotypes as a balanced polymorphism. Our results provide a mechanism for the maintenance of ecotype variation in redpolls despite a genome largely homogenized by gene flow. (Text adapted and/or taken from from Nat. Comm.)

Funk, E. R., Mason, N. A., Pálsson, S., Albrecht, T., Johnson, J. A., and Taylor, S. A. (2021). A supergene underlies linked variation in color and morphology in a Holarctic songbird. Nat. Commun. doi:10.1038/s41467-021-27173-z.

Fungi pose a serious threat to global biodiversity. The lack of fungal genomes impedes our ability to characterize epidemics and develop strategies to stop them. To address this, researchers sequenced nine isolates of Batrachochytrium salamandrivorans that were associated with fire salamander die-offs that also span the geographic and temporal range of the outbreak. Molecular evolution analyses reveal lineage-specific gene family acquisitions, losses, and expansions. Analyses also revealed horizontal gene transfer events that occurred after the divergence of major lineages. Together, these analyses reveal a multitude of evolutionary mechanisms contribute to genome diversity among B. salamandrivorans isolates. Examination of gene content and functions therein suggests B. salamandrivorans has a saprotrophic lifestyle, which was previously not observed. This finding suggests that a natural reservoir of pathogens can continually infect fire salamanders even after population decline, which can lead to extinction. These findings shed light on pathogen success and provide key insights to inform the design of mitigation strategies.

Kelly, M., Pasmans, F., Muñoz, J. F., Shea, T. P., Carranza, S., Cuomo, C. A., et al. (2021). Diversity, multifaceted evolution, and facultative saprotrophism in the European Batrachochytrium salamandrivorans epidemic. Nat. Commun. doi:10.1038/s41467-021-27005-0.

Ducks are a source of food (i.e., meat and eggs) and feather down. Similar to other domesticated organisms, human intervention has imposed a strong selective pressure on ducks used for human affairs resulting in diversity of body size, plumage, and reproduction and the rise of two major breeds: one used for egg laying (the Shaoxing breed) and another used for meat consumption (the Pekin breed). Researchers generated high-quality genome assemblies for the Mallard, Pekin, and Shaoxing ducks to illuminate the genetic underpinnings of duck domestication. Over 35 million variants such as single nucleotide polymorphisms, insertions and deletions, and large structural variants were identified among wild and domesticated ducks. Comparative transcriptomics revealed differential gene expression among several genes including NR2F2, which is involved in adipocyte differentiation in mice. After introducing mutations in NR2F2 in an immortalized chicken preadipocyte cell line revealed variation in mRNA expression lovels and adipogenic potential. These results implicate NR2F2 in adipocyte variation between wild and domestic ducks, but further analysis is required. Taken together, this study uncovers several mutations associated with duck domestication and identifies candidate genes that may be associated with phenotypic differences among wild and domestic ducks.

Zhu, F., Yin, Z.-T., Wang, Z., Smith, J., Zhang, F., Martin, F., et al. (2021). Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. Nat. Commun. doi:10.1038/s41467-021-26272-1.

Genome sequencing of bacteria has revealed that horizontal gene transfer—wherein individuals acquire genes from non-vertical processes such as phage-related bioprocesses—occurs frequently. Horizontally acquired genes can have functional consequences related to organismal ecology. These processes suggest that the bacterial tree of life is more like a network rather than a bifurcating tree. Furthermore, the rate of horizontal gene transfer among chromosomal genes can exceed the rate of transfer among genetic elements classified as "mobile genetic elements" such as plasmids. As a result, these observations call into question whether bacterial chromosomes should also be considered mobile genetic elements. This question is complicated by asymmetric rates of horizontal gene transfer across bacterial chromosomes; thus, should genomic islands in the bacterial chromosome be considered mobile genetic elements or the entire chromosome? Another question to be posed is whether microbiomes should be viewed through the lens of taxonomic composition or the functional genetic toolkit available to the community?Although answers are not readily available, this thought provoking question can inform diverse studies including organismal ecology and the microbiome.

Hall (2021). Is the bacterial chromosome a mobile genetic element? Nat. Commun. doi:10.1038/s41467-021-26758-y.

Understanding the evolution of animal complexity requires resolved evolutionary relationships among extant taxa. Sponges, which have a simple body plan, were thought to be sister to all other animals thereby suggesting animal evolution is marked by a gradual increase in body plan and cell type complexity. This view has been challenged by phylogenomics, which initially supported comb jellies as sister to all other animals. This observation suggests secondary loss or independent origins of complex traits. Researchers demonstrate that comb jellies as sister to all other animals likely stems from model misspecification due to the use of overly simplistic models. Instead, they utilize site-heterogeneous mixture models, which frequently had better model fit than site-homogeneous models, and character recoding into a partitioned phylogenomic workflow. This strategy diminished the impact of long branch attraction artifacts and provided support for sponges as sister to all animals. The efficacy of using mixture models in partitioned phylogenomics provides a mechanism for future studies to combat analytical artifacts in phylogenomic analyses. Text adapted from Nature Communications.

Redmond and McLysaght (2021). Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding. Nat. Commun. doi:10.1038/s41467-021-22074-7.

Mutation rates may vary across the genome and be impacted by selection. Intra-genomic mutation rate variation may be linked to epigenetic modifications but studies that directly link the two are sparse. Here, researchers unravel the impact of epigenetic modifications and temperature stress on mutation rates in a fungal pathogen. Deletion mutants that lack epigenetic modifications reveal that histone mark H3K27me3 increases mutation rates; in contrast, H3K9me3 decreases the mutation rate. Researchers also reveal two ways that intra-genomic mutation rate can vary: one, cytosine methylation in transposable elements (TE) increases mutation rate, which results in significantly less TE mobilization, and, two, accessory chromosomes have a significantly higher mutation rates. Environmental stressors, namely temperature stress, were found to increase mutation rates. These results reveal that epigenetic and environmental parameters can significantly impact genome-wide mutation rate thereby impacting the evolutionary trajectory of a species. Text adapted from Nature Communications.

Habig, M., Lorrain, C., Feurtey, A., Komluski, J., and Stukenbrock, E. H. (2021). Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus. Nat. Commun. doi:10.1038/s41467-021-26108-y.

Increased resistance to antifungal drugs among fungal pathogens is of growing medical concern. However, the processes leading to resistance are poorly understood. Researchers used experimental evolution to study the mutational signatures associated with the evolution of fluconazole and anidulafungin resistance in the major fungal pathogen Candida glabrata. Resistance to one or both drugs occurred rapidly and was associated with repeatedly observed mutations in a few genes as well as a moderate fitness costs. Mutations in ERG3 were associated with resistance to anidulafungin and cross-resistance to fluconazole. These results shed light on the evolution of resistance and cross-resistance to antifungal drugs. Text adapted from Current Biology.

Ksiezopolska, E., Schikora-Tamarit, M. À., Beyer, R., Nunez-Rodriguez, J. C., Schüller, C., and Gabaldón, T. (2021). Narrow mutational signatures drive acquisition of multidrug resistance in the fungal pathogen Candida glabrata. Curr. Biol. doi:10.1016/j.cub.2021.09.084.

Phylogenomic studies have improved our understanding of the tree of life. Despite the technologic and medical significance of fungi, the evolutionary relationships among major clades are poorly resolved. To evaluate poorly resolved relationships, researchers constructed a phylogenomic data matrix of 290 genes from over 1,600 species, which includes representatives from most major lineages. Researchers also implemented a rigorous subsampling strategy for identifying incongruence bipartitions. Analyses of these the full and subsampled data matrices using concatenation- and coalescent-based approaches yielded a robust phylogeny of the fungal kingdom. Support was observed for several poorly resolved relationships and episodes of ancient diversification. These results provide a framework to studying fungal evolution. Text adapted from Current Biology.

Li, Y., Steenwyk, J. L., Chang, Y., Wang, Y., James, T. Y., Stajich, J. E., et al. (2021). A genome-scale phylogeny of the kingdom Fungi. Curr. Biol. doi:10.1016/j.cub.2021.01.074.

Arbuscular mycorrhizal fungi (AMF) (subphylum Glomeromycotina) form a symbiotic relationship with over 70% of known land plants. This symbiosis enables plants to acquire poorly soluble soil nutrients and AMF to receive photosynthetically fixed carbohydrates. This plant-fungus symbiosis dates back more than 400 million years and is thought to have contributed to the colonization of land by plants. Genomic analyses of plant species has begun to unravel the mechanisms that facilitated the evolution of this symbiosis, however, how and when the plant-fungus symbiosis emerged in AMF remains unknown and research into this topic has been stymied by the dearth of genomic data among key AMF fungi. Geosiphon pyriformis (Archaeosporales) is a basal AMF fungus and the only one known to produce endosymbiosis with nitrogen-fixing cyanobacteria (Nostoc punctiforme), which is thought to be the ancestral AMF-state. Thus, G. pyriformis is ideal to glean insights into the evolutionary origins of AMS and the emergence of AMF symbiosis. To begin to address these questions by sequencing, researchers sequenced the genome of G. pyriformis. Text adapted from Current Biology.

Malar C, M., Krüger, M., Krüger, C., Wang, Y., Stajich, J. E., Keller, J., et al. (2021). The genome of Geosiphon pyriformis reveals ancestral traits linked to the emergence of the arbuscular mycorrhizal symbiosis. Curr. Biol. doi:10.1016/j.cub.2021.01.058.