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Understanding the genetic basis of convergence at broad phylogenetic scales remains a key challenge in biology. Kingfishers (Aves: Alcedinidae) are a cosmopolitan avian radiation with diverse colors, diets, and feeding behaviors—including the archetypal plunge-dive into water. Given the sensory and locomotor challenges associated with air-water transitions, kingfishers offer a powerful opportunity to explore the effects of convergent behaviors on the evolution of genomes and phenotypes, as well as direct comparisons between continental and island lineages. Here, we use whole-genome sequencing of 30 diverse kingfisher species to identify the genomic signatures associated with convergent feeding behaviors. We show that species with smaller ranges (i.e., on islands) have experienced stronger demographic fluctuations than those on continents, and that these differences have influenced the dynamics of molecular evolution. Comparative genomic analyses reveal positive selection and genomic convergence in brain and dietary genes in plunge-divers. These findings enhance our understanding of the connections between genotype and phenotype in a diverse avian radiation.

 

Birds are among the most colorful animals on Earth. The different patterns and colors displayed on their feathers help them to identify their own species, attract mates or hide from predators. The bright plumages of birds are achieved through either pigments (such as reds and yellows) or structures (such as blues, greens or ultraviolet) inside feathers, or through a combination of both pigments and structures. Variation in the diversity of color patterns over time can give a helpful insight into the rate of evolution of a species. For example, structural colors evolve more quickly than pigment-based ones and can therefore be a key feature involved in species recognition or mate attraction. Studying the evolution of plumage patterns has been challenging due to differences in the vision of humans and birds. However, recent advances in technology have enabled researchers to map the exact wavelengths of the colors that make up the patterns, allowing for rigorous comparison of plumage color patterns across different individuals and species. To gain a greater understanding of how plumage color patterns evolve in birds, Eliason et al. studied kingfishers, a group of birds known for their complex and variable color patterns, and their worldwide distribution. The experiments analyzed the plumage color patterns of 72 kingfisher species (142 individual museum specimens) from both mainland and island populations by quantifying the amount of different wavelengths of light reflecting from a feather and accounting for relationships among species and among feather patches. The analyzes showed that having more complex patterns leads to a greater accumulation of plumage colors over time, supporting the idea that complex plumages provide more traits for natural or sexual selection to act upon. Moreover, in upper parts of the bodies, such as the back, the plumage varied more across the different species and evolved faster than in ventral parts, such as the belly or throat. This indicates that sexual selection may be the evolutionary force driving variation in more visible areas, such as the back, while patterns in the ventral part of the body are more important for kin recognition. Eliason et al. further found no differences in plumage complexity between kingfishers located in island or mainland habitats, suggesting that the isolation of the island and the different selection pressures this may bring does not impact the complexity of color patterns. However, kingfisher species located on islands did display higher rates of color evolution. This indicates that, regardless of the complexity of the plumage, island-specific pressures are driving rapid color diversification. Using a new multivariate approach, Eliason et al. have unearthed a pattern in plumage complexity that may otherwise have been missed and, for the first time, have linked differences in color pattern on individual birds with evolutionary differences across species. In doing so, they have provided a framework for future studies of color evolution. The next steps in this research would be to better understand why the island species are evolving more rapidly even though they do not have more complex plumage patterns and how the observed color differences relate to rapid rates of speciation. 

Abstract In this study, we infer genus-level relationships within shrikes (Laniidae), crows (Corvidae), and their allies using ultraconserved elements (UCEs). We confirm previous results of the Crested Shrikejay (Platylophus galericulatus) as comprising its own taxonomic family and find strong support for its sister relationship to laniid shrikes. We also find strong support that the African-endemic genus Eurocephalus, which comprises two allopatric species (E. ruppelli and E. anguitimens), are not “true-shrikes”. We propose elevating the white-crowned shrikes to their own family, Eurocephalidae. 

Islands are natural laboratories for studying patterns and processes of evolution. Research on island endemic birds has revealed elevated speciation rates and rapid phenotypic evolution in several groups (e.g. white-eyes, Darwin’s finches). However, understanding the evolutionary processes behind these patterns requires an understanding of how genotypes map to novel phenotypes. To date, there are few high-quality reference genomes for species found on islands. Here, we sequence the genome of one of Ernst Mayr’s “great speciators,” the collared kingfisher (Todiramphus chloris collaris). Utilizing high molecular weight DNA and linked-read sequencing technology, we assembled a draft high-quality genome with highly contiguous scaffolds (scaffold N50 = 19 Mb). Based on universal single-copy orthologs, we estimated a gene space completeness of 96.6% for the draft genome assembly. The population demographic history analyses reveal a distinct pattern of contraction and expansion in population size throughout the Pleistocene. Comparative genomic analysis of gene family evolution revealed that species-specific and rapidly expanding gene families in the collared kingfisher (relative to other Coraciiformes) are mainly involved in the ErbB signaling pathway and focal adhesion. Todiramphus kingfishers are a species-rich group that has become a focus of speciation research. This draft genome will be a platform for future taxonomic, phylogeographic, and speciation research in the group. For example, target genes will enable testing of changes in sensory structures associated with changes in vision and taste genes across kingfishers.

 

The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace’s Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers—specifically isolated island systems and Wallace’s Line—we investigated the tempo and mode of diversification in a diverse avian radiation, Corvides (Crows and Jays, Birds-of-paradise, Vangas, and allies). We combined a genus-level data set of thousands of ultraconserved elements (UCEs) and a species-level, 12-gene Sanger sequence matrix to produce a well-resolved supermatrix tree that we leveraged to explore the group’s historical biogeography and the effects of the biogeographic barriers on their macroevolutionary dynamics. The tree is well resolved and differs substantially from what has been used extensively for past comparative analyses within this group. We confirmed that Corvides, and its major constituent clades, arose in Australia and that a burst of dispersals west across Wallace’s Line occurred after the uplift of Wallacea during the mid-Miocene. We found that dispersal across this biogeographic barrier was generally rare, though westward dispersals were two times more frequent than eastward dispersals. Wallacea’s central position between Sundaland and Sahul no doubt acted as a bridge for island-hopping dispersal out of Australia, across Wallace’s Line, to colonize the rest of Earth. In addition, we found that the complex island archipelagoes east of Wallace’s Line harbor the highest rates of net diversification and are a substantial source of colonists to continental systems on both sides of this biogeographic barrier. Our results support emerging evidence that island systems, particularly the geologically complex archipelagoes of the Indo-pacific, are drivers of species diversification. [Historical biogeography; island biogeography; Melanesia; molecular phylogenetics; state-dependent diversification and extinction.]

 

Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately and may have unique and even conflicting evolutionary histories. Phylogenetic reconstructions from these discrete genomes can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance (i.e. discordant evolutionary histories between the nuclear and mitochondrial genomes) has been widely documented, but its causes are often considered idiosyncratic and inscrutable. We show that a case of mitonuclear discordance inTodiramphuskingfishers can be explained by extensive genome‐wide incomplete lineage sorting (ILS), likely a result of the explosive diversification history of this genus. For these kingfishers, quartet frequencies reveal that the nuclear genome is dominated by discordant topologies, with none of the internal branches in our consensus nuclear tree recovered in >50% of genome‐wide gene trees. Meanwhile, a lack of inter‐species shared ancestry, non‐significant pairwise tests for gene flow, and little evidence for meaningful migration edges between species, leads to the conclusion that gene flow cannot explain the mitonuclear discordance we observe. This lack of evidence for gene flow combined with evidence for extensive genome‐wide gene tree discordance, a hallmark of ILS, leads us to conclude that the mitonuclear discordance we observe likely results from ILS, specifically deep coalescence of the mitochondrial genome. Based on this case study, we hypothesize that similar demographic histories in other ‘great speciator’ taxa across the Indo‐Pacific likely predispose these groups to high levels of ILS and high likelihoods of mitonuclear discordance.

 

Hybridization, introgression, and reciprocal gene flow during speciation, specifically the generation of mitonuclear discordance, are increasingly observed as parts of the speciation process. Genomic approaches provide insight into where, when, and how adaptation operates during and after speciation and can measure historical and modern introgression. Whether adaptive or neutral in origin, hybridization can cause mitonuclear discordance by placing the mitochondrial genome of one species (or population) in the nuclear background of another species. The latter, introgressed species may eventually have its own mtDNA replaced or “captured” by other species across its entire geographical range. Intermediate stages in the capture process should be observable. Two nonsister species of Australasian monarch‐flycatchers, Spectacled Monarch (Symposiachrus trivirgatus) mostly of Australia and Indonesia and Spot‐winged Monarch (S. guttula) of New Guinea, present an opportunity to observe this process. We analysed thousands of single nucleotide polymorphisms (SNPs) derived from ultraconserved elements of all subspecies of both species. Mitochondrial DNA sequences of Australian populations ofS. trivirgatusform two paraphyletic clades, one being sister to and presumably introgressed byS. guttuladespite little nuclear signal of introgression. Population genetic analyses (e.g., tests for modern and historical gene flow and selection) support at least one historical gene flow event betweenS. guttulaand AustralianS. trivirgatus. We also uncovered introgression from the Maluku Islands subspecies ofS. trivirgatusinto an island population ofS. guttula, resulting in apparent nuclear paraphyly. We find that neutral demographic processes, not adaptive introgression, are the most likely cause of these complex population histories. We suggest that a Pleistocene extinction ofS. guttulafrom mainland Australia resulted from range expansion byS. trivirgatus.

 

Molecular systematics is bringing taxonomy into the 21st Century by updating our nomenclature to reflect phylogenetic relationships of taxa. This transformation is evidenced by massive changes in avian taxonomy, ranging from ordinal to subspecies changes. In this study, we employ target capture of ultraconserved elements to resolve genus‐level systematics of a problematic group of honeyeaters (Aves: Meliphagidae). With near complete species‐level taxon sampling of the Australo‐Papuan species within the traditionally recognizedMeliphagaandOreornis, we investigate generic limits using a genomic dataset. Likelihood and species tree methods confirm two clades within this group and found the New Guinea endemicOreornis chrysogenysembedded within one of these clades. Our study supports earlier recommendations thatMeliphagaLewin, 1808 should be restricted to three species,M. aruensis,M. lewiniiandM. notata. We make a case for recognizing three genera in the remaining species,Oreornisvan Oort, 1910,MicroptilotisMathews, 1912 andTerritornisMathews, 1924.