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Geographic isolation is considered essential to most speciation events, but our understanding of what controls the pace and degree of phenotypic divergence among allopatric populations remains poor. Why do some taxa exhibit phenotypic differentiation across barriers to dispersal, whereas others do not? To test factors controlling phenotypic divergence in allopatry, we employed a comparative phylogeographic approach consisting of replicates of ecologically similar Andean bird species isolated across a major biogeographic barrier, the Marañon Valley of Peru. Our study design leverages variation among codistributed taxa in their degree of plumage, morphometric, and vocal differentiation across the Marañon to examine the tempo of phenotypic evolution. We found that substantial plumage difference between populations required roughly two million years to evolve. In contrast, morphometric trait evolution showed greater idiosyncrasy and stasis. Our results demonstrate that despite a large degree of idiosyncrasy in the relationship between genetic and phenotypic divergence across taxa and environments, comparative studies within regions may reveal predictability in the pace of phenotypic divergence. Our results also suggest that social selection is important for driving differentiation of populations found in similar environments.

Millions of nocturnally migrating birds die each year from collisions with built structures, especially brightly illuminated buildings and communication towers. Reducing this source of mortality requires knowledge of important behavioral, meteorological, and anthropogenic factors, yet we lack an understanding of the interacting roles of migration, artificial lighting, and weather conditions in causing fatal bird collisions. Using two decades of collision surveys and concurrent weather and migration measures, we model numbers of collisions occurring at a large urban building in Chicago. We find that the magnitude of nocturnal bird migration, building light output, and wind conditions are the most important predictors of fatal collisions. The greatest mortality occurred when the building was brightly lit during large nocturnal migration events and when winds concentrated birds along the Chicago lakeshore. We estimate that halving lighted window area decreases collision counts by 11× in spring and 6× in fall. Bird mortality could be reduced by ∼60% at this site by decreasing lighted window area to minimum levels historically recorded. Our study provides strong support for a relationship between nocturnal migration magnitude and urban bird mortality, mediated by light pollution and local atmospheric conditions. Although our research focuses on a single site, our findings have global implications for reducing or eliminating a critically important cause of bird mortality.

On quantum nature Cavity quantum electrodynamics (QED) studies the interaction between a quantum emitter (for example an atom or a quantum dot) and a single mode from a radiation field. When the two are strongly coupled it is possible to realize key quantum information processing tasks. In the solid state this could be achieved by coupling semiconductor quantum dots to optical microcavities. However, validating the efficacy of quantum dots in quantum information applications requires confirmation of the quantum nature of the quantum-dot–cavity system in the strong coupling regime. A collaboration between labs at ETH Zurich and the University of California, Santa Barbara, now provides this sought-after confirmation. The experiments involve a photonic crystal nanocavity in which one, and only one, quantum dot is located precisely at the cavity electric field maximum. A series of experiments that provide confirmation of the quantum nature of the quantum–dot–cavity system in the strong coupling regime by studying a photonic crystal nanocavity in which one, and only one, quantum dot is located precisely at the cavity electric field maximum. Cavity quantum electrodynamics (QED) studies the interaction between a quantum emitter and a single radiation-field mode. When an atom is strongly coupled to a cavity mode 1 , 2 , it is possible to realize important quantum information processing tasks, such as controlled coherent coupling and entanglement of distinguishable quantum systems. Realizing these tasks in the solid state is clearly desirable, and coupling semiconductor self-assembled quantum dots to monolithic optical cavities is a promising route to this end. However, validating the efficacy of quantum dots in quantum information applications requires confirmation of the quantum nature of the quantum-dot–cavity system in the strong-coupling regime. Here we find such confirmation by observing quantum correlations in photoluminescence from a photonic crystal nanocavity 3 , 4 , 5 interacting with one, and only one, quantum dot located precisely at the cavity electric field maximum. When off-resonance, photon emission from the cavity mode and quantum-dot excitons is anticorrelated at the level of single quanta, proving that the mode is driven solely by the quantum dot despite an energy mismatch between cavity and excitons. When tuned to resonance, the exciton and cavity enter the strong-coupling regime of cavity QED and the quantum-dot exciton lifetime reduces by a factor of 145. The generated photon stream becomes antibunched, proving that the strongly coupled exciton/photon system is in the quantum regime. Our observations unequivocally show that quantum information tasks are achievable in solid-state cavity QED.

Migratory species exhibit seasonal variation in their geographic ranges, often inhabiting geographically and ecologically distinct breeding and nonbreeding areas. The complicated geography of seasonal migration has long posed a challenge for inferring the geographic origins of migratory species as well as evolutionary sequences of change in migratory behavior. To address this challenge, we developed a phylogenetic model of the joint evolution of breeding and nonbreeding (winter) ranges and applied it to the inference of biogeographic history in the emberizoid passerine birds. We found that seasonal migration between breeding ranges in North America and winter ranges in the Neotropics evolved primarily via shifts of winter ranges toward the tropics from ancestral ranges in North America. This result contrasts with a dominant paradigm that hypothesized migration evolving out of the tropics via shifts of the breeding ranges. We also show that major lineages of tropical, sedentary emberizoids are derived from northern, migratory ancestors. In these lineages, the winter ranges served as a biogeographic conduit for temperate-to-tropical colonization: winter-range shifts toward the tropics during the evolution of long-distance migration often preceded southward shifts of breeding ranges, the loss of migration, and in situ tropical diversification. Meanwhile, the evolution of long-distance migration enabled the persistence of old lineages in North America. These results illuminate how the evolution of seasonal migration has contributed to greater niche conservatism among tropical members of this diverse avian radiation.

Silicon film as basis for light-slowing device A phenomenon known as electromagnetically induced transparency has been the subject of much research in atomic systems, as it makes it possible to slow down and stop light. Electromagnetically induced transparency and tunable optical delays have now been demonstrated in a nanoscale optomechanical device, fabricated simply by etching holes into a thin film of silicon. This achievement is a significant step towards the goal of fabricating an integrated quantum optomechanical memory. It is also relevant to classical signal-processing applications: at room temperature, the system can be used for optical buffering, amplification and altering of microwave-over-optical signals. In atomic systems, electromagnetically induced transparency (EIT) has been the subject of much experimental research, as it enables light to be slowed and stopped. This study demonstrates EIT and tunable optical delays in a nanoscale optomechanical device, fabricated by simply etching holes into a thin film of silicon. These results indicate significant progress towards an integrated quantum optomechanical memory, and are also relevant to classical signal processing applications: at room temperature, the system can be used for optical buffering, amplification and filtering of microwave-over-optical signals. Controlling the interaction between localized optical and mechanical excitations has recently become possible following advances in micro- and nanofabrication techniques 1 , 2 . So far, most experimental studies of optomechanics have focused on measurement and control of the mechanical subsystem through its interaction with optics, and have led to the experimental demonstration of dynamical back-action cooling and optical rigidity of the mechanical system 1 , 3 . Conversely, the optical response of these systems is also modified in the presence of mechanical interactions, leading to effects such as electromagnetically induced transparency 4 (EIT) and parametric normal-mode splitting 5 . In atomic systems, studies 6 , 7 of slow and stopped light (applicable to modern optical networks 8 and future quantum networks 9 ) have thrust EIT to the forefront of experimental study during the past two decades. Here we demonstrate EIT and tunable optical delays in a nanoscale optomechanical crystal, using the optomechanical nonlinearity to control the velocity of light by way of engineered photon–phonon interactions. Our device is fabricated by simply etching holes into a thin film of silicon. At low temperature (8.7 kelvin), we report an optically tunable delay of 50 nanoseconds with near-unity optical transparency, and superluminal light with a 1.4 microsecond signal advance. These results, while indicating significant progress towards an integrated quantum optomechanical memory 10 , are also relevant to classical signal processing applications. Measurements at room temperature in the analogous regime of electromagnetically induced absorption show the utility of these chip-scale optomechanical systems for optical buffering, amplification, and filtering of microwave-over-optical signals.

The widespread application of high-throughput sequencing in studying evolutionary processes and patterns of diversification has led to many important discoveries. However, the barriers to utilizing these technologies and interpreting the resulting data can be daunting for first-time users. We provide an overview and a brief primer of relevant methods (e.g., whole-genome sequencing, reduced-representation sequencing, sequence-capture methods, and RNA sequencing), as well as important steps in the analysis pipelines (e.g., loci clustering, variant calling, whole-genome and transcriptome assembly). We also review a number of applications in which researchers have used these technologies to address questions related to avian systems. We highlight how genomic tools are advancing research by discussing their contributions to 3 important facets of avian evolutionary history. We focus on (1) general inferences about biogeography and biogeographic history, (2) patterns of gene flow and isolation upon secondary contact and hybridization, and (3) quantifying levels of genomic divergence between closely related taxa. We find that in many cases, high-throughput sequencing data confirms previous work from traditional molecular markers, although there are examples in which genome-wide genetic markers provide a different biological interpretation. We also discuss how these new data allow researchers to address entirely novel questions, and conclude by outlining a number of intellectual and methodological challenges as the genomics era moves forward.

Intraspecific genetic diversity across a species' geographic range is relevant to adaptive potential and long‐term population persistence, and identifying genetically distinct groups within species can direct management decisions focused on conserving species‐level genetic diversity. Comparative phylogeography using whole genome techniques allows for investigation of whether co‐distributed species exhibit shared spatial genetic differentiation at fine spatial scales, thereby facilitating a comparative approach to both landscape and conservation genetics. By sequencing over 900 low‐coverage whole genomes, we evaluated the concordance of genetic structure and diversity from 12 co‐occurring species of migratory birds whose breeding ranges span adjacent North American ecogeographic regions: the vast boreal forest belt and the temperate montane Appalachian forests. We detected concordant phylogeographic patterns in 11 of 12 species wherein populations from the southern Appalachians were genetically distinct from boreal belt populations. Our results reveal that small populations persisting in the southern Appalachian Mountains consistently harbor genetic diversity that is subtly distinct from much larger, widespread boreal populations of the same species. However, in most species, levels of standing genetic diversity were not significantly different between Appalachian and boreal populations despite the drastic difference in geographic extent of these populations. We found no evidence for shared signatures of selection across the genome, suggesting that the concordance of spatial genetic structure across species emerges from species‐specific patterns of molecular divergence across the genome rather than parallel patterns of selection. Conservation of the Appalachian ecosystem would likely support maintenance of distinct genetic diversity in several migratory avian species with widespread distributions.

Abstract Background Constrictive myelopathy (CM) involving a fibrous band around the spinal cord is a newly recognized disease in pug dogs. Objectives To identify the frequency of CM based on diagnostic imaging supplemented with necropsy; to determine whether a relationship exists between the sites of CM and other described T3-L3 myelopathies; and to determine the frequency of caudal articular process dysplasia (CAPD). Animals Thirty-two client-owned pug dogs diagnosed with a chronic, progressive T3-L3 myelopathy based on neurological examination performed by a board-certified neurologist. Methods This is a prospective study. All dogs underwent computed tomography (CT) and magnetic resonance imaging (MRI) reviewed by a board-certified radiologist. Magnetic resonance imaging abnormalities were categorized into diseases; CM only, CM plus other non-CM condition(s), or non-CM condition. Sites of CAPD were reported on CT. Nineteen dogs underwent necropsy. Results Magnetic resonance imaging revealed 3 dogs with CM only, 17 with CM plus at least 1 other myelopathy, 11 dogs with non-CM myelopathies only, and 1 with no MRI abnormalities. Nineteen of 32 dogs had >1 myelopathy diagnosis on MRI whereas 15/32 had >1 site of spinal cord compression. All dogs had CAPD at >1 site in the T3-L3 vertebral column on CT. Conclusions and Clinical Importance Constrictive myelopathy affected more than half of pug dogs presenting with chronic thoracolumbar myelopathies. Most had multilevel disease, concurrent myelopathies, or both. There was no apparent relationship between anatomic locations of CAPD and most severe myelopathy or myelopathy type.

Divergence with gene flow is well documented and reveals the influence of ecological adaptation on speciation. Yet, it remains intuitive that gene exchange inhibits speciation in many scenarios, particularly among ecologically similar populations. The influence of gene flow on the divergence of populations facing similar selection pressures has received less empirical attention than scenarios where differentiation is coupled with local environmental adaptation. I used a paired study design to test the influence of genomic divergence and introgression on plumage differentiation between ecologically similar allopatric replacements of Andean cloud forest birds. Through analyses of short-read genome-wide sequences from over 160 individuals in 16 codistributed lineages, I found that plumage divergence is associated with deep genetic divergence, implicating a prominent role of geographic isolation in speciation. By contrast, lineages that lack plumage divergence across the same geographic barrier are more recently isolated or exhibit a signature of secondary genetic introgression, indicating a negative relationship between gene flow and divergence in phenotypic traits important to speciation. My results suggest that the evolutionary outcomes of cycles of isolation and divergence in this important theatre of biotic diversification are sensitive to time spent in the absence of gene flow.

Understanding how co‐occurring species divide ecological space is a central issue in ecology. Functional traits have the potential to serve as a means for quantitatively assessing niche partitioning by different species based on their ecological attributes, such as morphology, behavior, or trophic habit. This enables testing ecological and evolutionary questions using functional traits at spatio‐temporal scales that are not feasible using traditional field methods. Both rapid evolutionary change and inter‐ and intraspecific competition, however, may limit the utility of morphological functional traits as indicators of how niches are partitioned. To address how behavior and morphology interact, we quantified foraging behavior of mixed‐species flocks of birds in the Solomon Islands to test whether behavior and morphology are correlated in these flocks. We find that foraging behavior is significantly correlated with morphological traits (p = .05), but this correlation breaks down after correcting for phylogenetic relatedness (p = .66). These results suggest that there are consistent correlations between aspects of behavior and morphology at large taxonomic scales (e.g., across genera), but the relationship between behavior and morphology depends largely on among‐clade differences and may be idiosyncratic at shallower scales (e.g., within genera). As a result, general relationships between behaviors and morphology may not be applicable when comparing close relatives. Understanding how co‐occurring species divide ecological space is a central issue in ecology. We demonstrate that morphology may reflect behavioral niche partitioning at large scales, but among islands in the Solomon Archipelago, shifts in avian morphology and behavior are decoupled. General relationships between behaviors and morphology may not be applicable when comparing close relatives.