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Genome-wide analyses of admixture between two closely related and sympatric North American oriole species reveals longstanding barriers enforcing reproductive isolation.

Abstract We present comments on an article published by Confer et al. (Ecology and Evolution, 10, 2020). Confer et al. (2020) aggregate data from multiple studies of social pairing between Vermivora chrysoptera and V. cyanoptera, two wood warblers in the family Parulidae that hybridize extensively where they co‐occur. From analysis of these data, they conclude there is near‐complete reproductive isolation between these two species. In our reply, we show that this finding is not supported by other lines of evidence, and significant drawbacks of their study design preclude such strong conclusions. In our critique, we show that (a) coarse‐scale plumage classifications cannot be used to accurately estimate hybrid ancestry in Vermivora; (b) extra‐pair paternity is very high in Vermivora and is likely facilitating hybridization, yet was not considered by Confer et al. (2020), and we suggest this will have a substantial influence on the interpretation of reproductive isolation in the system; and (c) the central finding of strong total reproductive isolation is not compatible with the results of other long‐term studies, which demonstrate low isolation and high gene flow. We conclude with a more comprehensive interpretation of hybridization and reproductive isolation in Vermivora warblers.

The Horned Lark (Eremophila alpestris) is a small songbird that exhibits remarkable geographic variation in appearance and habitat across an expansive distribution. While E. alpestris has been the focus of many ecological and evolutionary studies, we still lack a highly contiguous genome assembly for the Horned Lark and related taxa (Alaudidae). Here, we present CLO_EAlp_1.0, a highly contiguous assembly for E. alpestris generated from a blood sample of a wild, male bird captured in the Altiplano Cundiboyacense of Colombia. By combining short-insert and mate-pair libraries with the ALLPATHS-LG genome assembly pipeline, we generated a 1.04 Gb assembly comprised of 2713 scaffolds, with a largest scaffold size of 31.81 Mb, a scaffold N50 of 9.42 Mb, and a scaffold L50 of 30. These scaffolds were assembled from 23685 contigs, with a largest contig size of 1.69 Mb, a contig N50 of 193.81 kb, and a contig L50 of 1429. Our assembly pipeline also produced a single mitochondrial DNA contig of 14.00 kb. After polishing the genome, we identified 94.5% of single-copy gene orthologs from an Aves data set and 97.7% of single-copy gene orthologs from a vertebrata data set, which further demonstrates the high quality of our assembly. We anticipate that this genomic resource will be useful to the broader ornithological community and those interested in studying the evolutionary history and ecological interactions of larks, which comprise a widespread, yet understudied lineage of songbirds.

Abstract Theory suggests that different taxa having colonized a similar, challenging environment will show parallel or lineage‐specific adaptations to shared selection pressures, but empirical examples of parallel evolution in independent taxa are exceedingly rare. We employed comparative genomics to identify parallel and lineage‐specific responses to selection within and among four species of North American sparrows that represent four independent, post‐Pleistocene colonization events by an ancestral, upland subspecies and a derived salt marsh specialist. We identified multiple cases of parallel adaptation in these independent comparisons following salt marsh colonization, including selection of 12 candidate genes linked to osmoregulation. In addition to detecting shared genetic targets of selection across multiple comparisons, we found many novel, species‐specific signatures of selection, including evidence of selection of loci associated with both physiological and behavioral mechanisms of osmoregulation. Demographic reconstructions of all four species highlighted their recent divergence and small effective population sizes, as expected given their rapid radiation into saline environments. Our results highlight the interplay of both shared and lineage‐specific selection pressures in the colonization of a biotically and abiotically challenging habitat and confirm theoretical expectations that steep environmental clines can drive repeated and rapid evolutionary diversification in birds.

Gouldian finches have a head colour polymorphism that is also associated with physiological and behavioural differentiation. Here, the authors map this colour polymorphism to a putative regulatory region for follistatin on the Z chromosome and suggest it is maintained by balancing selection.

Correlation ECE (CECE) is a diagnostic technique that allows measurement of small amplitude electron temperature, Te, fluctuations through standard cross-correlation analysis methods. In Alcator C-Mod, a new CECE diagnostic has been installed[Sung RSI 2012], and interesting phenomena have been observed in various plasma conditions. We find that local Te fluctuations near the edge (ρ ~ 0:8) decrease across the linearto- saturated ohmic confinement transition, with fluctuations decreasing with increasing plasma density[Sung NF 2013], which occurs simultaneously with rotation reversals[Rice NF 2011]. Te fluctuations are also reduced across core rotation reversals with an increase of plasma density in RF heated L-mode plasmas, which implies that the same physics related to the reduction of Te fluctuations may be applied to both ohmic and RF heated L-mode plasmas. In I-mode plasmas, we observe the reduction of core Te fluctuations, which indicates changes of turbulence occur not only in the pedestal region but also in the core across the L/I transition[White NF 2014]. The present CECE diagnostic system in C-Mod and these experimental results are described in this paper.

Widespread population declines of the Golden-winged Warbler (Vermivora chrysoptera) are thought to be due in part to hybridization with the expanding Blue-winged Warbler (V. pinus), which predictably replaces Golden-winged Warblers at breeding sites in which the two species come into contact. However, the mechanism by which this replacement occurs remains unresolved. Recent genetic work has indicated that, even in areas where the two species have been in contact for a short period, introgression of Blue-winged mitochondrial (mtDNA) and nuclear genes into Golden-winged individuals is common. To explore this process on a broader scale, we screened more than 750 individuals from nine U.S. states and three provinces to examine geographic patterns of mtDNA introgression. The only population in which all phenotypic Golden-winged Warblers had Golden-winged mtDNA haplotypes, and in which there are no breeding Blue-winged or hybrid individuals, was in the province of Manitoba, near the northwestern edge of the species' breeding distribution. The near ubiquity of mitochondrial introgression suggests that there are far fewer genetically pure populations of Golden-winged Warblers than previously believed, a finding with important implications for this threatened species.

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Student attrition is a persistent challenge in the life sciences, particularly among underrepresented minorities, first-generation students, and women. Experiential learning through short-term study abroad opportunities diversifies curricula by immersing students in nontraditional academic environments. However, most experiential learning and study abroad opportunities are primarily available to upper-division undergraduates. Here, we present a qualitative analysis of an experiential learning opportunity offered exclusively to first-year U.S. undergraduate students from underrepresented demographics. We performed ethnographic observations of a 10-day field component in the Galápagos Islands and analyzed self-reported survey results and field journals. Students consistently reported strong cognitive gains in their understanding of basic evolutionary concepts. Most students also benefited socially, although we observed higher variation in selfreported social gains. Our findings suggest that immersive field courses increase scientific literacy and promote social cohesion among students. We speculate that experiential learning opportunities may improve retention of underrepresented minorities in the life sciences, and we encourage future studies to further examine the short-term and long-term impacts of study abroad on student cognition and retention.

This article covers the in-vessel design of the SPARC interferometry diagnostic system, highlighting unique aspects of the systems design and port plug integration in preparation for "day-1" plasma operations as a critical diagnostic for density feedback control. An early decision for the diagnostic was to deploy two lasers in the infrared wavelength spectrum, allowing the system to have a higher optical throughput. The optimization of the in-vessel geometry for the diagnostic follows a similar approach, focusing on de-risking possible damage to the plasma facing optical components by moving them further from the plasma with an orientation that provides a greater possibility for protective features to be added. The inclusion of in-vessel optical assemblies requires detailed design efforts of custom all-metal parts, designed to remain functional when subjected to harsh operational conditions, in many cases for the entire SPARC lifetime. The details presented here were included in the design to ensure that the assemblies can not only withstand a major electromagnetic disruption or thermal event but also maintain good stability through normal operations. The design also addresses more nuanced effects, such as the transient heat loading of the plasma facing mirrors. Through the utilization of modeling and design tools, these effects were brought into the design and simulation workflow, further reducing uncertainty as the system moves toward system commissioning. [ABSTRACT FROM AUTHOR]

Planting date, row configuration, and seeding rate are three critical factors in obtaining maximum soybean [Glycine max (L.) Merr.] grain yield and can vary based on soil texture. Therefore, two studies were conducted at the Delta Research and Extension Center in Stoneville, MS. The first study was conducted from 2019 to 2021 and sought to determine the effects of planting date (optimal and delayed 21 days), and row configuration (single‐, twin‐, and triple‐row) on soybean growth, development, and grain yield. The second study was conducted in 2021 with three site‐years to determine the effects of seeding rate (130,000, 180,000, and 220,000 seeds acre−1) in a triple‐row configuration on soybean grain yield compared to a single‐row configuration at 130,000 seeds acre−1 on two soil textures (silt loam and clay). Both studies were repeated on silt loam and clay soil textures in every site‐year. In the first study, the optimal planting date increased soybean grain yield regardless of soil texture. On both soil textures, twin‐ and single‐row configuration yields were equivalent, but triple‐row configuration reduced soybean grain yield up to 9%. Similarly, triple‐row configuration reduced soybean density and height at R3 and R8 growth stages. In the second study, increasing triple‐row configuration soybean seeding rate by at least 38% provided similar soybean grain yields to a single‐row configuration at 130,000 seeds acre−1. These data indicate that triple‐row soybean planting configurations do have some benefits, but that future research should focus on equipment limitations experienced in the current research.Plain Language Summary: Planting date, row configuration, and seeding rate decisions do not occur in a vacuum and must be influenced by other variables such as soil texture and tillage practices. Therefore, two studies were conducted in Stoneville, MS, from 2019 to 2021 at Mississippi State University's Delta Research and Extension Center to evaluate the effects of planting date and row configuration (single, twin, or triple row on a single 40‐inch‐wide seedbed) on two soil textures (silt loam and clay) on soybean yield. Regardless of soil texture, single‐ and twin‐row configurations produced equivalent yields while triple‐row configurations reduced soybean grain yield at a standard seeding rate. When the seeding rate was increased at least 38% on clay soil, triple‐row configurations yielded greater than single‐row configurations. These data indicate that triple‐row configurations in a raised seedbed environment are a possibility, but more research is needed to overcome limitations associated with current equipment. [ABSTRACT FROM AUTHOR]

Trait polymorphisms are a perennially popular topic of study in ecology and evolutionary biology. Plumage polymorphisms occur broadly in birds, with a particularly high rate among the raptors. The regularity of this heritable, melanin-based trait in raptors has prompted research into its potential connections to aspects of life history such as immune response, foraging ecology, and mating systems. Because raptors are a non-monophyletic grouping of multiple orders, they can further be leveraged to explore the eco-evolutionary drivers of recurrent plumage polymorphism phenotypes. Here we characterize plumage polymorphism throughout the raptors and review the existing literature on factors involved in its development and maintenance. We identify patterns and trends in this past body of research and discuss the opportunity to strengthen our understanding of plumage polymorphism through a holistic research approach. Specifically, we detail the likely benefits of applying genomic tools to plumage polymorphism research in raptors while encouraging both a focus on unstudied polymorphic species and on the potential interactions among multiple hypotheses that might promote plumage polymorphism. [ABSTRACT FROM AUTHOR]

Nonlinear transfer processes between large-scale edge flows and the ambient broadband fluctuations have been shown to play a significant role in the dynamics of edge turbulence, including spreading power from coherent modes and suppressing turbulence at the formation of edge transport barriers. In order to predict thresholds of confinement regimes, both the transition dynamics and the parametric dependence of the nonlinear energy transfer must be studied. Since the expected flow damping terms depend on ion collision rates and local safety factors, recent experiments aimed also to explore the nonlinear drive at various values of the plasma current, density and amount of auxiliary heating. Nonlinear interactions between zonal flows and turbulence in L-mode are estimated using bispectral as well as time-resolved methods based on gas-puff-imaging in Alcator C-Mod [1].

Transitions of tokamak confinement regimes from low- to high-confinement are studied on Alcator C-Mod (Hutchinson et al 1994 Phys. Plasmas 1 1511) tokamak using gas-puff-imaging, with a focus on the interaction between the edge drift-turbulence and the local shear flow. Results show that the nonlinear turbulent kinetic energy transfer rate into the shear flow becomes comparable to the estimated value of the drift turbulence growth rate at the time the turbulent kinetic energy starts to drop, leading to a net energy transfer that is comparable to the observed turbulence losses. A corresponding growth is observed in the shear flow kinetic energy. The above behavior is demonstrated across a series of experiments. Thus both the drive of the edge zonal flow and the initial reduction of turbulence fluctuation power are shown to be consistent with a lossless kinetic energy conversion mechanism, which consequently mediates the transition into H-mode. The edge pressure gradient is then observed to build on a slower (1ms) timescale, locking in the H-mode state. These results unambiguously establish the time sequence of the transition as: first the peaking of the normalized Reynolds power, then the collapse of the turbulence, and finally the rise of the diamagnetic electric field shear as the L-H transition occurs. © 2014 IOP Publishing Ltd.