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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]

Muscicapa flycatchers and their allies ( Bradornis , Dioptornis , Empidornis , Fraseria , Myioparus , Namibornis , and Sigelus ) are widely distributed in Africa, Europe and Asia. This broad distribution and the wide variety of habitats occupied by the group, ranging from arid to tropical forests, presents an interesting opportunity to explore the evolution of biogeographic patterns and habitat associations. Sequence data (up to 3310 base pairs from two mitochondrial and two nuclear genes) were generated for 36 of 42 species which comprise the assemblage. Complementary data from an additional species was retrieved from GenBank, as was an additional gene which was available for 21 of our included taxa. Using model-based phylogenetic methods and molecular clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the lineage. Ancestral area reconstructions were performed on the phylogeny using LaGrange and BioGeoBEARS. Our results indicate that Bradornis , Fraseria , and Muscicapa are each non-monophyletic, with the latter being shown to comprise five separate clades each more closely related to other genera. Two new genera ( Chapinia and Ripleyia ) are erected to account for these results. Muscicapa and allies originated c. 7.4 Ma, most likely in Africa given that their sister lineage is almost entirely from there, and rapidly achieved a Eurasian distribution by c. 7.1 Ma. A second divergence at c. 6.1 Ma resulted in two clades. The first is a largely Eurasian clade that subsequently recolonized Africa, perhaps as the result of the loss of migration. The second is an African clade, and ancestral reconstructions suggest a Congolian (e.g. tropical forest) origin for this clade, with several subsequent diversifications into more arid habitats. This is a unique result, as most tropical forest lineages are confined to that habitat. As with other studies of African bird lineages, Afrotropical forest dynamics appear to have played a significant role in driving diversification in Muscicapa and allies, and our results include just the second recorded case of southern to northern African colonization patterns. [ABSTRACT FROM AUTHOR]

The lories and lorikeets (Aves: Loriinae: Loriini) are a readily recognizable, discrete group of nectarivorous parrots confined to the Indo-Pacific region between Wallace’s Line and the Pitcairn Island group in the central-east Pacific Ocean. We present the first phylogenetic analysis of all currently recognized genera in the group using two mitochondrial and five nuclear loci. Our analyses suggest a New Guinean origin for the group at about 10 million years ago (95% HPD 4.8–14.8) but this origin must be interpreted within the context of that island’s complicated, recent geological history. That is, the origin and early diversification of the group may have taken place as New Guinea’s Central Cordillera arose and the final constituent terranes that form present-day New Guinea were accreted. The latter activity may have promoted dispersal as a key element in the group’s history. We have detected several instances of dispersal out of New Guinea that we argue constitute instances of founder-event speciation. Some phenotypically cohesive genera are affirmed as monophyletic but other genera are clearly in need of taxonomic dismantlement and reclassification. We recognize Parvipsitta Mathews, 1916 for two species usually placed in Glossopsitta and we advocate transfer of Chalcopsitta cardinalis into Pseudeos Peters, 1935. Other non-monophyletic genera such as Charmosyna , Psitteuteles and, probably, Trichoglossus , require improved taxon sampling and further phylogenetic analysis before their systematics can be resolved. Cursory examination of trait mapping across the group suggests that many traits are ancestral and of little use in determining genus-level systematics. [ABSTRACT FROM AUTHOR]