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Abstract Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation. 

Abstract For centuries, fossils from the Maastrichtian type locality and adjacent quarries have provided key evidence of vertebrate diversity during the latest Cretaceous, yet until recently the Maastrichtian type area had revealed no important insights into the evolutionary history of birds, one of the world’s most conspicuous groups of extant tetrapods. With the benefit of high-resolution micro-CT scanning, two important avian fossils from the Maastrichtian type area have now been examined in detail, offering profound, complementary insights into the evolutionary history of birds. The holotype specimens of these new taxa,Janavis finalidensBenito, Kuo, Widrig, Jagt and Field, 2022, andAsteriornis maastrichtensisField, Benito, Chen, Jagt and Ksepka, 2020, were originally collected in the late 1990s, but were only investigated in detail more than twenty years later. Collectively,JanavisandAsteriornisprovide some of the best evidence worldwide regarding the factors that influenced stem bird extinction and crown bird survivorship through the Cretaceous-Palaeogene transition, as well as insights into the origins of key anatomical features of birds such as an extensively pneumatised postcranial skeleton, a kinetic palate, and a toothless beak.Asteriornisalso provides scarce evidence of a Cretaceous-aged divergence time calibration within the avian crown group, while together,JanavisandAsteriornisconstitute the only documented co-occurrence of crown birds and non-neornithine avialans. Here, we review key insights into avian evolutionary history provided by these discoveries from the Maastrichtian stratotype, document undescribed and newly discovered Maastrichtian fossils potentially attributable to Avialae and provide the first histological data for the holotype ofAsteriornis, illustrating its skeletal maturity at the time of its death. 

Abstract Spatial models show that genetic differentiation between populations can be explained by factors ranging from geographic distance to environmental resistance across the landscape. However, genomes exhibit a landscape of differentiation, indicating that multiple processes may mediate divergence in different portions of the genome. We tested this idea by comparing alternative geographic predctors of differentiation in ten bird species that co-occur in Sonoran and Chihuahuan Deserts of North America. Using population-level genomic data, we described the genomic landscapes across species and modeled conditions that represented historical and contemporary mechanisms. The characteristics of genomic landscapes differed across species, influenced by varying levels of population structuring and admixture between deserts, and the best-fit models contrasted between the whole genome and partitions along the genome. Both historical and contemporary mechanisms were important in explaining genetic distance, but particularly past and current environments, suggesting that genomic evolution was modulated by climate and habitat There were also different best-ftit models across genomic partitions of the data, indicating that these regions capture different evolutionary histories. These results show that the genomic landscape of differentiation can be associated with alternative geographic factors operating on different portions of the genome, which reflect how heterogeneous patterns of genetic differentiation can evolve across species and genomes. 

Abstract Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within data sets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade’s species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of the genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower-quality samples. Most instances of topological conflict and nonmonophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, the noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many data sets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology. [Historical DNA; machine learning; museomics; Psittaciformes; species tree.] 

Humans did not arrive on most of the world’s islands until relatively recently, making islands favorable places for disentangling the timing and magnitude of natural and anthropogenic impacts on species diversity and distributions. Here, we focus onAmazonaparrots in the Caribbean, which have close relationships with humans (e.g., as pets as well as sources of meat and colorful feathers). Caribbean parrots also have substantial fossil and archaeological records that span the Holocene. We leverage this exemplary record to showcase how combining ancient and modern DNA, along with radiometric dating, can shed light on diversification and extinction dynamics and answer long-standing questions about the magnitude of human impacts in the region. Our results reveal a striking loss of parrot diversity, much of which took place during human occupation of the islands. The most widespread species, the Cuban Parrot, exhibits interisland divergences throughout the Pleistocene. Within this radiation, we identified an extinct, genetically distinct lineage that survived on the Turks and Caicos until Indigenous human settlement of the islands. We also found that the narrowly distributed Hispaniolan Parrot had a natural range that once included The Bahamas; it thus became “endemic” to Hispaniola during the late Holocene. The Hispaniolan Parrot also likely was introduced by Indigenous people to Grand Turk and Montserrat, two islands where it is now also extirpated. Our research demonstrates that genetic information spanning paleontological, archaeological, and modern contexts is essential to understand the role of humans in altering the diversity and distribution of biota. 

Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in adaptive evolution, in particular the extent to which similar genetic mechanisms drive adaptation to common selective forces. Here, we investigated the genomics of local adaptation in two nonsister woodpeckers that are codistributed across an entire continent and exhibit remarkably convergent patterns of geographic variation. We sequenced the genomes of 140 individuals of Downy (Dryobates pubescens) and Hairy (Dryobates villosus) woodpeckers and used a suite of genomic approaches to identify loci under selection. We showed evidence that convergent genes have been targeted by selection in response to shared environmental pressures, such as temperature and precipitation. Among candidates, we found multiple genes putatively linked to key phenotypic adaptations to climate, including differences in body size (e.g., IGFPB) and plumage (e.g., MREG). These results are consistent with genetic constraints limiting the pathways of adaptation to broad climatic gradients, even after genetic backgrounds diverge. 

Abstract Tetraoninae (grouse) and Meleagridinae (turkeys) are conspicuous representatives of the modern North American avifauna. The pre-Pleistocene fossil record of these clades has historically been limited to fragmentary remains, in some cases contributing to confusion rather than improving our understanding of how these charismatic landfowl evolved. We report an exquisitely preserved partial skeleton representing a new species of Late Miocene phasianid from the Ash Hollow Formation of Nebraska. Centuriavis lioae n. gen. n. sp. is a phasianid species close in size to modern sage-grouse that diverged prior to the grouse-turkey split, and thus offers insight into the early history of this radiation. The cranial endocast resembles other North American phasianids and differs from odontophorids in exhibiting a strongly projected Wulst bordered by a well-defined vallecula. Phylogenetic analyses indicate that Centuriavis lioae forms a clade with Tetraoninae, Meleagridinae, and Pucrasia macrolopha (Koklass pheasant). The new fossil species provides a Late Miocene minimum calibration for the divergence of these extant taxa from other Galliformes and supports the hypothesis of a single dispersal from Asia to North America by a lineage that later gave rise to grouse and turkeys. UUID: https://zoobank.org/34ecda2f-f2f2-4c92-a82f-292e23cf2da1