Data from: Current geography masks dynamic history of gene flow during speciation in northern Australian birds

Genome divergence is greatly influenced by gene flow during early stages of speciation. As populations differentiate, geographical 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 biogeographic 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.ND2_alignmentsND2 alignments separated by different species or species complex.SDM_data.tarSpecies distribution modeling data including occurrence points, R output, and historical climate layers.Entomyzon_cyanotis_ddRADSorted bam files of ddRAD reads mapped onto a reference.Gerygone_magnirostris_ddRADSorted bam files of ddRAD reads mapped onto a reference.Lichmera_indistincta_ddRADSorted bam files of ddRAD reads mapped onto a reference.Melithreptus_albogularis_ddRADSorted bam files of ddRAD reads mapped onto a reference.Myzomela_obscura_ddRADSorted bam files of ddRAD reads mapped onto a reference.Philemon_buceroides_ddRADSorted bam files of ddRAD reads mapped onto a reference.Philemon_citreogularis_ddRADSorted bam files of ddRAD reads mapped onto a reference.Ptilotula_flavescens_fuscus_ddRADSorted bam files of ddRAD reads mapped onto a reference