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Biodiversity loss has reached critical levels partly due to anthropogenic habitat loss and degradation. These landscape changes are damaging as they can fragment species distributions into small, isolated populations, resulting in limited gene flow, population declines and reduced adaptive potential. Genetic rescue, the translocation of individuals to increase genetic diversity and ultimately fitness, has produced promising results for fragmented populations but remains underutilized due to a lack of long‐term data and monitoring. To promote a better understanding of genetic rescue and its potential risks and benefits over the short‐term, we reviewed and analysed published genetic rescue attempts to identify whether genetic diversity increases following translocation, and if this change is associated with increased fitness. Our review identified 19 studies that provided genetic and fitness data from before and after the translocation; the majority of these were on mammals, and included experimental, natural and conservation‐motivated translocations. Using a Bayesian meta‐analytical approach, we found that on average, genetic diversity and fitness increased in populations post translocations, although there were some exceptions to this trend. Overall, genetic diversity was a positive predictor of population fitness, and in some cases this relationship extended three generations post‐rescue. These data suggest a single translocation can have lasting fitness benefits, and support translocation as another tool to facilitate conservation success. Given the limited number of studies with long‐term data, we echo the need for genetic monitoring of populations post‐translocation to understand whether genetic rescue can also limit the loss of adaptive potential in the long‐term. [ABSTRACT FROM AUTHOR]

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Summary: Systemic mastocytosis (SM) is a rare haematological neoplasm associated with the gain of function mutation KIT D816V in 90% of adult patients. Classically, cytogenetic aberrations are not common except in cases of SM associated with another haematological neoplasm. We highlight here an unusual clinical presentation of SM and demonstrate the utility of advanced cytogenetic analysis (optical genome mapping, OGM) in detecting a novel cytogenetic abnormality resulting in an unusual mechanism of DNMT3A and TET2 loss of function. [ABSTRACT FROM AUTHOR]

Background: Genome Mapping Technologies (optical and electronic) use ultra-high molecular weight DNA to detect structural variation and have application in constitutional genetic disorders, hematological neoplasms, and solid tumors. Genome mapping can detect balanced and unbalanced structural variation, copy number changes, and haplotypes. The technique is analogous to chromosomal microarray analysis, although genome mapping has the added benefit of being able to detect and ascertain the nature of more abnormalities in a single assay than array, karyotyping, or FISH alone. Key Messages: This paper describes a specific nomenclature for genome mapping that can be used by diagnostic and research centers to report their findings accurately. An international nomenclature is essential for patient results to be understood by different healthcare providers as well as for clear communication in publications and consistency in databases. Summary: Genome mapping can detect aneuploidy, balanced and unbalanced structural variation, as well as copy number changes. The Standing Committee for the International System for Human Cytogenomic Nomenclature (ISCN) recognised there was a need for a specific nomenclature for genome mapping that encompasses the range of abnormalities detected by this technique. This paper explains the general principles of the nomenclature as well as giving specific ISCN examples for the different types of numerical and structural rearrangements. [ABSTRACT FROM AUTHOR]

Simple Summary: Genetic rearrangements of the KMT2A gene are associated with diagnostic and prognostic outcomes in the context of myeloid neoplasms. While cytogenetically visible KMT2A rearrangements (e.g., translocations) are relatively straightforward to detect by conventional cytogenetics, KMT2A partial tandem duplications (KMT2A-PTD) are too small to be detected by karyotype or FISH. Our study compares the detection of the KMT2A-PTD using three technologies: next-generation sequencing, multiplex-ligation probe amplification, and optical genome mapping. Background: Gene rearrangements affecting KMT2A are frequent in acute myeloid leukemia (AML) and are often associated with a poor prognosis. KMT2A gene fusions are often detected by chromosome banding analysis and confirmed by fluorescence in situ hybridization. However, small intragenic insertions, termed KMT2A partial tandem duplication (KMT2A-PTD), are particularly challenging to detect using standard molecular and cytogenetic approaches. Methods: We have validated the use of a custom hybrid-capture-based next-generation sequencing (NGS) panel for comprehensive profiling of AML patients seen at our institution. This NGS panel targets the entire consensus coding DNA sequence of KMT2A. To deduce the presence of a KMT2A-PTD, we used the relative ratio of KMT2A exons coverage. We sought to corroborate the KMT2A-PTD NGS results using (1) multiplex-ligation probe amplification (MLPA) and (2) optical genome mapping (OGM). Results: We analyzed 932 AML cases and identified 41 individuals harboring a KMT2A-PTD. MLPA, NGS, and OGM confirmed the presence of a KMT2A-PTD in 22 of the cases analyzed where orthogonal testing was possible. The two false-positive KMT2A-PTD calls by NGS could be explained by the presence of cryptic structural variants impacting KMT2A and interfering with KMT2A-PTD analysis. OGM revealed the nature of these previously undetected gene rearrangements in KMT2A, while MLPA yielded inconclusive results. MLPA analysis for KMT2A-PTD is limited to exon 4, whereas NGS and OGM resolved KMT2A-PTD sizes and copy number levels. Conclusions: KMT2A-PTDs are complex gene rearrangements that cannot be fully ascertained using a single genomic platform. MLPA, NGS panels, and OGM are complementary technologies applied in standard-of-care testing for AML patients. MLPA and NGS panels are designed for targeted copy number analysis; however, our results showed that integration of concurrent genomic alterations is needed for accurate KMT2A-PTD identification. Unbalanced chromosomal rearrangements overlapping with KMT2A can interfere with the diagnostic sensitivity and specificity of copy-number-based KMT2A-PTD detection methodologies. [ABSTRACT FROM AUTHOR]

The practice of space-for-time substitution assumes that the responses of species or communities to land-use change over space represents how they will respond to that same change over time. Space-for-time substitution is commonly used in both ecology and conservation, but whether the assumption produces reliable insights remains inconclusive. Here, we tested space-for-time substitution using data from the North American Breeding Bird Survey (BBS) and Global Forest Change (GFC) to compare the effects of landscape-scale forest cover on bird richness and abundance over time and space, for 25 space-time comparisons. Each comparison consisted of a landscape that experienced at least 20% forest loss over 19 years (temporal site) and a set of 15-19 landscapes (spatial sites) that represented the same forest cover gradient over space in 2019 as experienced over time in their corresponding temporal site. Across the 25 comparisons, the observed responses of forest and open-habitat birds to forest cover over time generally aligned with their responses to forest cover over space, but with comparatively higher variability in the magnitude and direction of effect across the 25 temporal slopes than across the 25 spatial slopes. On average, the mean differences between the spatial and temporal slopes across the 25 space-time comparisons frequently overlapped with zero, suggesting that the spatial slopes are generally informative of the temporal slopes. However, we observed high variability around these mean differences, indicating that a single spatial slope is not strongly predictive of its corresponding temporal slope. We suggest that our results may be explained by annual variability in other relevant environmental factors that combine to produce complex effects on population abundances over time that are not easily captured by snapshots in space. While not being a 1:1 proxy, measuring bird responses to changes in habitat amount in space provides an idea on how birds might be expected to eventually equilibrate to similar changes in habitat amount over time. Further, analyses such as this could be potentially used to screen for cases of regional space-time mismatches where population-limiting factors other than habitat could be playing a more important role in the population trends observed there. [ABSTRACT FROM AUTHOR]

Population trend estimates form the core of avian conservation assessments in North America and indicate important changes in the state of the natural world. The models used to estimate these trends would be more efficient and informative for conservation if they explicitly considered the spatial locations of the monitoring data. We created spatially explicit versions of some standard status and trend models applied to long-term monitoring data for birds across North America. We compared the spatial models to simpler non-spatial versions of the same models, fitting them to simulated data and real data from 3 broad-scale monitoring programs: the North American Breeding Bird Survey (BBS), the Christmas Bird Count, and a collection of programs we refer to as Migrating Shorebird Surveys. All the models generally reproduced the simulated trends and population trajectories when there were many data, and the spatial models performed better when there were fewer data and in locations where the local trends differed from the range-wide means. When fit to real data, the spatial models revealed interesting spatial patterns in trend, such as recent population increases along the Appalachian Mountains for the Eastern Whip-poor-will (Antrostomus vociferus), that were much less apparent in results from the non-spatial versions. The spatial models also had higher out-of-sample predictive accuracy than the non-spatial models for a selection of species using BBS data. The spatially explicit sharing of information allows fitting the models with much smaller strata, allowing for finer-grained patterns in trends. Spatially informed trends will facilitate more locally relevant conservation, highlight areas of conservation successes and challenges, and help generate and test hypotheses about the spatially dependent drivers of population change. [ABSTRACT FROM AUTHOR]

Species declines and extinctions characterize the Anthropocene. Determining species vulnerability to decline, and where and how to mitigate threats, are paramount for effective conservation. We hypothesized that species with shared ecological traits also share threats, and therefore may experience similar population trends. Here, we used a Bayesian modeling framework to test whether phylogeny, geography, and 22 ecological traits predict regional population trends for 380 North American bird species. Groups like blackbirds, warblers, and shorebirds, as well as species occupying Bird Conservation Regions at more extreme latitudes in North America, exhibited negative population trends; whereas groups such as ducks, raptors, and waders, as well as species occupying more inland Bird Conservation Regions, exhibited positive trends. Specifically, we found that in addition to phylogeny and breeding geography, multiple ecological traits contributed to explaining variation in regional population trends for North American birds. Furthermore, we found that regional trends and the relative effects of migration distance, phylogeny, and geography differ between shorebirds, songbirds, and waterbirds. Our work provides evidence that multiple ecological traits correlate with North American bird population trends, but that the individual effects of these ecological traits in predicting population trends often vary between different groups of birds. Moreover, our results reinforce the notion that variation in avian population trends is controlled by more than phylogeny and geography, where closely related species within one region can show unique population trends due to differences in their ecological traits. We recommend that regional conservation plans, i.e. one-size-fits-all plans, be implemented only for bird groups with population trends under strong phylogenetic or geographic controls. We underscore the need to develop species-specific research and management strategies for other groups, like songbirds, that exhibit high variation in their population trends and are influenced by multiple ecological traits. [ABSTRACT FROM AUTHOR]

US law continues its historical trend of growing more permissive towards actors who engage in violent action in purported self-defense. We draw on some informal game theory to show why this is strategically irrational and suggest rolling back self-defense doctrines like stand your ground to earlier historical precedents like duty to retreat. [ABSTRACT FROM AUTHOR]

I. INTRODUCTION It should be no surprise to learn that humans behave in ways that are far from optimal. Be it from poor planning or untoward circumstance, we rarely, if [...], Behavioral economics has been employed in a number of policy applications over the last decade. From energy requirements to tax compliance to consumer finance, policymakers are increasingly operating under the assumption that people consistently fail to make rational choices. While the benefit of this policy trend remains an open debate, behavioral economists have long neglected a complementary examination of public decision-makers themselves. Comparison of two public agencies influenced by behavioral economics, the U.S. Consumer Financial Protection Bureau and U.K. Behavioural Insights Team, demonstrates how different institutions create divergent policy outcomes across the two agencies in a way that cannot be accounted for without incorporating public choice theory. I argue that improvement of private choice architecture must be accompanied by careful understanding of the public choice architecture in which policies are rendered if behavioral economics is to be a successful foundation for welfare-improving policies.

Introduction: Inherited DDX41 mutations cause familial predisposition to hematologic malignancies including acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), with the majority of DDX41 mutated MDS/AMLs described to date harboring germline DDX41 and co-occurring somatic DDX41 variants. DDX41-AMLs were shown to share distinguishing clinical features such as a late AML onset and an indolent disease associated with a favorable outcome. However, genotype-phenotype correlation in DDX41-MDS/AMLs remain poorly understood. Methods: Here, we studied the genetic profile, bone marrow morphology and immunophenotype of 51 patients with DDX41 mutations. We further assessed the functional impact of ten previously uncharacterized DDX41 variants of uncertain significance. Results: Our results demonstrate that MDS/AML cases harboring two DDX41 variants share specific clinicopathologic hallmarks that are not seen in other patients with monoallelic DDX41 related hematologic malignancies. We further showed that the features seen in these individuals with two DDX41 variants were concordant with biallelic DDX41 disruption. Discussion: Here, we expand on previous clinicopathologic findings on DDX41 mutated hematologic malignancies. Functional analyses conducted in this study unraveled previously uncharacterized DDX41 alleles and further illustrate the implication of biallelic disruption in the pathophysiology of this distinct AML entity. [ABSTRACT FROM AUTHOR]

Shorebirds are declining to a greater extent than many other avian taxa around the world. In North America, shorebirds, along with aerial insectivores and grassland birds, have some of the highest proportions of declining species of any group. Here, we apply a new hierarchical Bayesian model to analyze shorebird migration monitoring data from across North America, from 1980 to 2019, and present the most recent available estimates of trends for 28 species. Point estimates for survey-wide trends in abundance were negative for 26 of 28 species (93%). Despite challenges with low precision associated with migration count data, trends for 19 species had 95% credible intervals that were entirely negative. More than half of the species were estimated to have lost >50% of their abundance. Furthermore, estimated rates of decline have accelerated during the last three generations for most species. Point estimates of trend were more negative for 18 species (64%) during the most recent three-generation period in comparison to the previous three-generation period. Many species now exceed international criteria for threatened species listing. The analytic approach used here allows us to model regional variation in trends, although survey coverage and strength of inference were greatest in the eastern portions of North America (east of 100°W). We found the greatest declines at staging sites along the Atlantic Coast from North Carolina to Nova Scotia, and lesser declines along the Gulf Coast and in the midcontinental United States. The declines in shorebird populations reported here are worrisome and signal the urgent need for conservation action. In addition, it would be beneficial to validate these results through the collection and analysis of complementary data, and to initiate demographic studies throughout the annual cycle to determine where and when declines are most likely to originate. This improved information will allow for the development of more targeted efforts to reverse declines through conservation action. [ABSTRACT FROM AUTHOR]

Bird monitoring in North America over several decades has generated many open databases, housing millions of structured and semi‐structured bird observations. These provide the opportunity to estimate bird densities and population sizes, once variation in factors such as underlying field methods, timing, land cover, proximity to roads, and uneven spatial coverage are accounted for. To facilitate integration across databases, we introduce NA‐POPS: Point Count Offsets for Population Sizes of North American Landbirds. NA‐POPS is a large‐scale, multi‐agency project providing an open‐source database of detectability functions for all North American landbirds. These detectability functions allow the integration of data from across disparate survey methods using the QPAD approach, which considers the probability of detection (q) and availability (p) of birds in relation to area (a) and density (d). To date, NA‐POPS has compiled over 7.1 million data points spanning 292 projects from across North America, and produced detectability functions for 338 landbird species. Here, we describe the methods used to curate these data and generate these detectability functions, as well as the open‐access nature of the resulting database. [ABSTRACT FROM AUTHOR]

We argue that Madole & Harden's distinction between shallow versus deep genetic causes can bring some clarity to causal claims arising from genome-wide association studies (GWASs). However, the authors argue that GWAS only finds shallow genetic causes, making GWAS commensurate with the environmental studies they hope to supplant. We also assess whether their distinction applies best to explanations or causes. [ABSTRACT FROM AUTHOR]