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Abstract New study systems and tools are needed to understand how divergence and speciation occur between lineages with gene flow. Migratory birds often exhibit divergence despite seasonal migration, which brings populations into contact with one another. We studied divergence between 2 subspecies of Northern Saw-whet Owl (Aegolius acadicus), in which a sedentary population on the islands of Haida Gwaii, British Columbia (A. a. brooksi), exists in the presence of the other form (A. a. acadicus) during migration but not during the breeding season. Prior research showed fixed mtDNA divergence but left open the question of nuclear gene flow. We used 2,517 ultraconserved element loci to examine the demographic history of this young taxon pair. Although we did not observe fixed single nucleotide polymorphism differences between populations among our genotyped individuals, 100% of the birds were diagnosable and δaδI analyses suggested the demographic model best fitting the data was one of split-bidirectional-migration (i.e. speciation with gene flow). We dated the split between brooksi and acadicus to ~278 Kya, and our analyses suggested gene flow between groups was skewed, with ~0.7 individuals per generation coming from acadicus into brooksi and ~4.4 going the opposite direction. Coupled with an absence of evidence of phenotypic hybrids and the birds’ natural history, these data suggest brooksi may be a young biological species arising despite historic gene flow. 

Abstract Crocodilians are an economically, culturally, and biologically important group. To improve researchers’ ability to study genome structure, evolution, and gene regulation in the clade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus, from Illumina short read data from genomic libraries and in vitro proximity-ligation libraries. The assembled genome is 2,123.5 Mb, with N50 scaffold size of 17.7 Mb and N90 scaffold size of 3.8 Mb. We then annotated this new assembly, increasing the number of annotated genes by 74%. In total, 96% of 23,242 annotated genes were associated with a functional protein domain. Furthermore, multiple noncoding functional regions and mappable genetic markers were identified. Upon analysis and overlapping the results of branch length estimation and site selection tests for detecting potential selection, we found 16 putative genes under positive selection in crocodilians, 10 in C. porosus and 6 in Alligator mississippiensis. The annotated C. porosus genome will serve as an important platform for osmoregulatory, physiological, and sex determination studies, as well as an important reference in investigating the phylogenetic relationships of crocodilians, birds, and other tetrapods. 

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.