Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans-Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds, and passerines) at population, subspecies, and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split-migration model (divergence with gene flow), three best fit a secondary-contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (FST), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed SNPs, and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.

As a dispersive lineage expands its distribution across a heterogeneous landscape, it leaves behind allopatric populations with varying degrees of geographic isolation that often differentiate rapidly. In the case of oceanic islands, even narrowly separated populations often differentiate, which seems contrary to the highly dispersive nature of the founding lineage. This pattern of highly dispersive lineages differentiating across narrow sea barriers has perplexed biologists for more than a century. We used two reduced-representation genomic datasets to examine the diversification of a recent, rapid geographic radiation, the white-eyes (Aves: Zosterops) of the Solomon Islands. We incorporated methods that targeted phylogenetic structure, population structure, and explicit tests for gene flow. Both data sets showed evidence of gene flow among species, but not involving the closely spaced islands in the New Georgia Group. Instead, gene flow has occurred among the larger islands in the archipelago, including those recently connected by land bridges as well as those isolated by large expanses of deep ocean. Populations separated by shallow seas, and connected by land bridges during glacial cycles, ranged from no differentiation to both phenotypic and genomic differentiation. These complex patterns of gene flow and divergence support a model of rapid geographic radiation in which lineages differentially evolve dispersal disparity and phenotypic differences. This article is protected by copyright. All rights reserved

Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (Rhincodon typus) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA-based population studies. The mitochondrial target capture successfully retrieved 235x (90x-352x per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant non-target species mackerel tuna (Euthynnus affinis), showing a clear relation between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrieved only few reads and polymorphic variants from the whale shark, but we successfully obtained millions of reads and thousands of polymorphic variants with different allele frequencies from E. affinis. We demonstrate that target capture of complete mitochondrial genomes and thousands of nuclear loci is possible from aquatic eDNA samples. Our results highlight that careful probe design, taking into account the range of divergence between target and non-target sequences as well as presence of non-target species at the sampling site, is crucial to consider. Environmental DNA sampling coupled with target capture approaches provide an efficient means with which to retrieve population genomic data from aggregating and spawning aquatic species.

Papillomaviruses infect the skin and mucosal surfaces of diverse animal hosts with consequences ranging from asymptomatic colonization to highly malignant epithelial cancers. Increasing evidence suggests a role for papillomaviruses in the most common cutaneous malignancy of domestic cats, squamous cell carcinoma (SCC). Using total DNA sequencing we identified a novel feline papillomavirus in a nasal biopsy taken from a cat presenting with both nasal cavity lymphoma and recurrent squamous cell carcinoma affecting the nasal planum. We designate this novel virus as Felis catus papillomavirus 6 (FcaPV6). The complete FcaPV6 7453 bp genome was similar to those of other feline papillomaviruses and phylogenetic analysis revealed that it was most closely related to FcaPV3, although was distinct enough to represent a new viral type. Classification of FcaPV6 in a new genus alongside FcaPVs 3, 4 and 5 is supported. Archived excisional biopsy of the SCC, taken 20 months prior to presentation, was intensely positive on p16 immunostaining. FcaPV6, amplified using virus-specific, but not consensus, PCR, was the only papillomavirus detected in DNA extracted from the SCC. Conversely, renal lymphoma, sampled at necropsy two months after presentation, tested negative on FcaPV6-specific PCR. In sum, using metagenomics we demonstrate the presence of a novel feline papillomavirus in association with cutaneous squamous cell carcinoma.

Premise Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well-documented phenomenon at shallow evolutionary levels but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes, but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome. Methods We present a phylogenomic examination of a major angiosperm clade (Asteridae) based on sequence data from the nuclear, plastid, and mitochondrial genomes as a means of evaluating currently accepted relationships inferred from the plastome and exploring potential sources of genomic conflict in this group. Results We recovered at least five instances of well-supported cytonuclear discordance concerning the placements of major asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis, and Icacinaceae). We attribute this conflict to a combination of incomplete lineage sorting and hybridization, the latter supported in part by previously inferred whole-genome duplications. Conclusions Our results challenge several long-standing hypotheses of asterid relationships and have implications for morphological character evolution and for the importance of ancient whole-genome duplications in early asterid evolution. These findings also highlight the value of reevaluating broad-scale angiosperm and green-plant phylogeny with nuclear genomic data.