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Plumage divergence can function as a strong premating barrier when species come into secondary contact. When it fails to do so, the results are often genome homogenization and phenotypic hybrids at the zone of contact. This is not the case in the largely sympatric masked woodswallow and white‐browed woodswallow species (Passeriformes: Artamidae: Artamus spp) complex in Australia where phenotypic integrity is sustained despite no discernible mitochondrial structure in earlier work. This lack of structure may suggest recent divergence, ongoing gene flow or both, and phenotypic hybrids are reported albeit rarely. Here, we further assessed the population structure and differentiation across the species' nuclear genomes using ddRAD‐seq. As found in the mitochondrial genome, no structure or divergence within or between the two species was detected in the nuclear genome. This coarse sampling of the genome nonetheless revealed peaks of differentiation around the genes SOX5 and AXIN1. Both are involved in the Wnt/β‐catenin signalling pathway, which regulates feather development. Reconstruction of demographic history and estimation of parameters supports a scenario of secondary contact. Our study informs how divergent plumage morphs may arise and be sustained despite whole‐genome homogenization and reveals new candidate genes potentially involved in plumage divergence. [ABSTRACT FROM AUTHOR]

Assignment of parentage with molecular markers is most difficult when the true parents have close relatives in the adult population. Here, we present an efficient solution to that problem by extending simple exclusion approaches to parentage analysis with single nucleotide polymorphic markers (SNPs). We augmented the previously published homozygote opposite test (hot), which counts mismatches due to the offspring and candidate parent having different homozygous genotypes, with an additional test. In this case, parents homozygous for the same SNP are incompatible with heterozygous offspring (i.e., "Homozygous Identical Parents, Heterozygous Offspring are Precluded": hiphop). We tested this approach in a cooperatively breeding bird, the superb fairy‐wren, Malurus cyaneus, where rates of extra‐pair paternity are exceptionally high, and where paternity assignment is challenging because breeding males typically have first‐order adult relatives in their neighbourhood. Combining the tests and conditioning on the maternal genotype with a set of 1376 autosomal SNPs always allowed us to distinguish a single most likely sire from his relatives, and also to identify cases where the true sire must have been unsampled. In contrast, if just the hot test was used, we failed to identify a single most‐likely sire in 2.5% of cases. Resampling enabled us to create guidelines for the number of SNPs required when first‐order relatives coexist in the mating pool. Our method, implemented in the R package hiphop, therefore provides unambiguous parentage assignments even in systems with complex social organisation. We also identified a suite of Z‐ and W‐linked SNPs that always identified sex correctly. [ABSTRACT FROM AUTHOR]

The superb fairy‐wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high‐quality reference. To rectify that, we present the first high‐quality genome assembly of a Meliphagides representative: the superb fairy‐wren. We combined Illumina shotgun and mate‐pair sequences, PacBio long‐reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07‐Gb genome, 975 Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11 Mb. This high‐quality bird genome assembly is one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree‐based bird genetic maps, we find that the fairy‐wren genetic map more closely resembles those of Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis map which more closely resembles that of Gallus gallus. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high‐quality, annotated genome assembly will be an invaluable resource not only regarding the superb fairy‐wren species and relatives but also broadly across the avian tree by providing a novel reference point for comparative genomic analyses. [ABSTRACT FROM AUTHOR]

Genome divergence is greatly influenced by gene flow during early stages of speciation. As populations differentiate, geographic barriers can constrain gene flow and so affect the dynamics of divergence and speciation. Current geography, specifically disjunction and continuity of ranges, is often used to predict the historical gene flow during the divergence process. We test this prediction in eight meliphagoid bird species complexes codistributed in four regions. These regions are separated by known biogeographical barriers across northern Australia and Papua New Guinea. We find that bird populations currently separated by terrestrial habitat barriers within Australia and marine barriers between Australia and Papua New Guinea have a range of divergence levels and probability of gene flow not associated with current range connectivity. Instead, geographic distance and historical range connectivity better predict divergence and probability of gene flow. In this dynamic environmental context, we also find support for a nonlinear decrease of the probability of gene flow during the divergence process. The probability of gene flow initially decreases gradually after a certain level of divergence is reached. Its decrease then accelerates until the probability is close to zero. This implies that although geographic connectivity may have more of an effect early in speciation, other factors associated with higher divergence may play a more important role in influencing gene flow midway through and later in speciation. Current geographic connectivity may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation. [ABSTRACT FROM AUTHOR]

Aim The diversification of the Australian avifauna has been greatly influenced by prominent historical and modern barriers to dispersal. The aims of this study were to characterize the patterns of divergence in population pairs of meliphagoid birds across adjacent transition zones and characterize how well morphometric divergence, habitat association and taxonomic or species ranking can predict genetic divergence. Location Northern Queensland, Australia. Methods Genetic divergence between parental populations on either side of the three biogeographical barriers corresponding to three clusters of hybrid zones was characterized in 27 species complexes of meliphagoid birds using one mitochondrial, 23 autosomal and 12 Z chromosome loci collected from a sequence capture system. Within each species, we characterized morphometric divergence using wing, bill and tail measurements from museum samples. Lastly, we evaluated the predictive power of these morphometric measurements on genetic divergence. Results Population pairs on either side of a transition zone depict a wide range of genomic and morphometric divergence. For some systems, species exhibiting morphometric divergence show little to no genomic divergence, while, conversely, other species exhibiting little to no morphometric divergence may show clear genomic divergence. Species rank is shown to be the strongest predictor for genetic divergence, habitat is the next strongest predictor and morphometric divergence is the weakest predictor. Main conclusions The variation in divergence levels of population pairs affirms that transition zones are ideal natural experiments to study the speciation process. In particular, transition zones allow understanding of how genomic divergence accumulates during speciation. Additionally, standing species rank classifications mostly prove to be robust after genetic characterization. Lastly, the discordance between morphometric and genetic divergence suggests other non-morphometric phenotypic traits used to designate species rank, such as song or plumage, may play a more important role in predicting genetic divergence. [ABSTRACT FROM AUTHOR]

Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of nonmodel organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes ( SCPP) protocol requires no specialized equipment, is highly flexible and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25-100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies. [ABSTRACT FROM AUTHOR]