Search for: All records

Allopatric divergence is a fundamental component of most traditional models of biogeography and community assembly. Gene flow between allopatric populations should be influenced by the nature of geographic barriers and can have a profound impact on adaptation, the speciation process, and phylogenetic inference. Superspecies—monophyletic groups of taxa with species-level differences in phenotype or genotype that are found exclusively in allopatry or parapatry—present an opportunity to characterize the effects of gene flow on the divergence process. Here, we investigate patterns of gene flow, population structure, and inferred phylogenetic relationships for members of an avian superspecies, the Solomons Monarchs (Aves: Symposiachrus barbatus complex) occupying the Solomon Islands. We found that gene flow among allopatric species matches predictions based on geography, but phylogenetic relationships were not concordant with the most likely colonization history based on a stepping-stone colonization model. Notably, the most isolated island, Makira, has a species that was inferred to be sister to the taxa on all other islands in concatenated phylogenetic analyses, despite Makira being farthest from the presumed original source of immigrants. We use population genetic simulations to demonstrate that such a result could be driven by bias resulting from low levels of gene flow, reflecting a challenge in phylogeographic inference that results when one population is differentially isolated. These simulated findings demonstrate a distinguishability issue in phylogeographic inference, where gene flow and colonization history can be difficult to disentangle. 

Islands have long represented natural laboratories for studying many aspects of ecology and evolutionary biology, from speciation to community assembly. One aspect that has been well documented is the correlation between island size and taxonomic diversity, likely due to decreased complexity and population size on small islands. This same logic can apply to genetic diversity, which should predictably decrease with effective population size. The island size–diversity correlation has received support over the years but often focuses on single metrics of genetic diversity. Here, we useZosteropswhite-eyes in the Solomon Islands to study the correlation between island size and various metrics related to genetic diversity, including runs of homozygosity and fixation of transposable elements. We find that almost all these metrics strongly correlate with island size, and in turn with each other. We infer that island size is independently correlated with these different variables, demonstrating that population size impacts genomic metrics of diversity in a variety of ways across temporal and hierarchical scales. 

Abstract Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones—where reproductive isolation can further develop via reinforcement or phenotypic displacement—or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayr’s foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow. 

The flora and fauna of island systems, especially those in the Indo-Pacific, are renowned for their high diversification rates and outsized contribution to the development of evolutionary theories. The total diversity of geographic radiations of many Indo-Pacific fauna is often incompletely sampled in phylogenetic studies due to the difficulty in obtaining single island endemic forms across the Pacific and the relatively poor performance of degraded DNA when using museum specimens for inference of evolutionary relationships. New methods for production and analysis of genome-wide datasets sourced from degraded DNA are facilitating insights into the complex evolutionary histories of these influential island faunas. Here, we leverage whole genome resequencing (20X average coverage) and extensive sampling of all taxonomic diversity within Todiramphus kingfishers, a rapid radiation of largely island endemic Great Speciators. We find that whole genome datasets do not outright resolve the evolutionary relationships of this clade: four types of molecular markers (UCEs, BUSCOs, SNPs, and mtDNA) and tree building methods did not find a single well-supported and concordant species-level topology. We then uncover evidence of widespread incomplete lineage sorting and both ancient and contemporary gene flow and demonstrate how these factors contribute to conflicting evolutionary histories. Our complete taxonomic sampling allowed us to further identify a novel case of mitochondrial capture between two allopatric species, suggesting a potential historical (but since lost) hybrid zone as islands were successively colonized. Taken together, these results highlight how increased genomic and taxon sampling can reveal complex evolutionary patterns in rapid island radiations. 

N/A 

Abstract Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones—where reproductive isolation can further develop via reinforcement or phenotypic displacement—or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayr’s foundational work on allopatric speciation: the whistlers of Fiji (Aves:Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller, adjacent island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow. 

Abstract The exponential growth of molecular sequence data over the past decade has enabled the construction of numerous clade-specific phylogenies encompassing hundreds or thousands of taxa. These independent studies often include overlapping data, presenting a unique opportunity to build macrophylogenies (phylogenies sampling >1000 taxa) for entire classes across the Tree of Life. However, the inference of large trees remains constrained by logistical, computational, and methodological challenges. The Avian Tree of Life provides an ideal model for evaluating strategies to robustly infer macrophylogenies from intersecting data sets derived from smaller studies. In this study, we leveraged a comprehensive resource of sequence capture data sets to evaluate the phylogenetic accuracy and computational costs of four methodological approaches: (1) supermatrix approaches using concatenation, including the “fast” maximum likelihood (ML) methods, (2) filtering data sets to reduce heterogeneity, (3) supertree estimation based on published phylogenomic trees, and (4) a “divide-and-conquer” strategy, wherein smaller ML trees were estimated and subsequently combined using a supertree approach. Additionally, we examined the impact of these methods on divergence time estimation using a data set that includes newly vetted fossil calibrations for the Avian Tree of Life. Our findings highlight the advantages of recently developed fast tree search approaches initiated with parsimony starting trees, which offer a reasonable compromise between computational efficiency and phylogenetic accuracy, facilitating inference of macrophylogenies. 

Abstract The paradox of the great speciators describes a contradictory biogeographic pattern exhibited by numerous avian lineages in Oceania. Specifically, these lineages display broad geographic distributions across the region, implying strong over-water dispersal capabilities; yet, they also display repeated genetic and phenotypic divergence—even between geographically proximate islands—implying poor inter-island dispersal capabilities. One group originally cited as evidence for this paradox is the dwarf kingfishers of the genus Ceyx. Here, using genomic sequencing and comprehensive geographic sampling of the monophyletic Ceyx radiation from northern Melanesia, we find repeated, deep genetic divergence and no evidence for gene flow between lineages found on geographically proximate islands, providing an exceptionally clear example of the paradox of the great speciators. A dated phylogenetic reconstruction suggests a significant burst of diversification occurred rapidly after reaching northern Melanesia, between 3.9 and 2.9 MYA. This pattern supports a shift in net diversification rate, concordant with the expectations of the “colonization cycle” hypothesis, which implies a historical shift in dispersiveness among great speciator lineages during the evolutionary past. Here, we present a formalized framework that explains how repeated founder effects and shifting selection pressures on highly dispersive genotypes are the only ultimate causes needed to generate the paradox of the great speciators. Within this framework, we emphasize that lineage-specific traits and island-specific abiotic factors will result in varying levels of selection pressure against dispersiveness, caused by varying proximate eco-evolutionary mechanisms. Overall, we highlight how understanding patterns of diversification in the Ceyx dwarf kingfishers helped us generate a cohesive framework that provides a rigorous mechanistic explanation for patterns concordant with the paradox of the great speciators and the repeated emergence of geographic radiations in island archipelagoes across the globe.