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Abstract Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.] 

Abstract Hybrid zones are important windows into the evolutionary dynamics of populations, revealing how processes like introgression and adaptation structure population genomic variation. Importantly, they are useful for understanding speciation and how species respond to their environments. Here, we investigate two closely related sea star species, Asterias rubens and A. forbesi , distributed along rocky European and North American coastlines of the North Atlantic, and use genome‐wide molecular markers to infer the distribution of genomic variation within and between species in this group. Using genomic data and environmental niche modelling, we document hybridization occurring between northern New England and the southern Canadian Maritimes. We investigate the factors that maintain this hybrid zone, as well as the environmental variables that putatively drive selection within and between species. We find that the two species differ in their environmental niche breadth; Asterias forbesi displays a relatively narrow environmental niche while conversely, A. rubens has a wider niche breadth. Species distribution models accurately predict hybrids to occur within environmental niche overlap, thereby suggesting environmental selection plays an important role in the maintenance of the hybrid zone. Our results imply that the distribution of genomic variation in North Atlantic sea stars is influenced by the environment, which will be crucial to consider as the climate changes. 

Abstract We applied an integrative taxonomic framework to evaluate the systematics of the Neotropical Black-and-white Becard (Pachyramphus albogriseusSclater 1857). Combining phylogenomic (ultraconserved elements), morphological, and vocalization data, we confirmed that this species is polyphyletic; some individuals form a clade sister to P. polychopterus and should be afforded species rank as P. salviniRichmond 1899 (Slender-billed Becard), whereas the remaining subspecies of P. albogriseus (Broad-banded Becard) are sister to P. major. We found that P. salvini differs from P. albogriseus in song, color of the lores, wing-bar width, body size, and bill width. Whereas P. albogriseus occurs in montane forest in Costa Rica and Panama (ssp. ornatus) and along the eastern slope of the Andes from northern Venezuela to southern Peru (ssp. albogriseus), P. salvini is found in the lowlands from Pacific Colombia south to northwest Peru and in the Río Marañón drainage. The latter also occurs, possibly only seasonally, along the eastern slope of the Andes, where the two species’ ranges approach closely. We treat P. a. guayaquilensisZimmer 1936 as a junior synonym of P. salviniRichmond 1899, and P. a. coronatusPhelps and Phelps 1953 as a junior synonym of P. a. albogriseusSclater 1857. This study provides a striking example of a major problem for comparative biology: underestimated and mischaracterized diversity. We argue that there are likely many more cases like this awaiting discovery.