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Low‐coverage whole‐genome sequencing (WGS) is increasingly used for the study of evolution and ecology in both model and non‐model organisms; however, effective application of low‐coverage WGS data requires the implementation of probabilistic frameworks to account for the uncertainties in genotype likelihoods.

Here, we present a probabilistic framework for using genotype likelihoods for standard population assignment applications. Additionally, we derive the Fisher information for allele frequency from genotype likelihoods and use that to describe a novel metric, theeffective sample size, which figures heavily in assignment accuracy. We make these developments available for application through WGSassign, an open‐source software package that is computationally efficient for working with whole‐genome data.

Using simulated and empirical data sets, we demonstrate the behaviour of our assignment method across a range of population structures, sample sizes and read depths. Through these results, we show that WGSassign can provide highly accurate assignment, even for samples with low average read depths (<0.01X) and among weakly differentiated populations.

Our simulation results highlight the importance of equalizing the effective sample sizes among source populations in order to achieve accurate population assignment with low‐coverage WGS data. We further provide study design recommendations for population assignment studies and discuss the broad utility of effective sample size for studies using low‐coverage WGS data.

 

Abstract The emergence of atomically thin van der Waals magnets provides a new platform for the studies of two-dimensional magnetism and its applications. However, the widely used measurement methods in recent studies cannot provide quantitative information of the magnetization nor achieve nanoscale spatial resolution. These capabilities are essential to explore the rich properties of magnetic domains and spin textures. Here, we employ cryogenic scanning magnetometry using a single-electron spin of a nitrogen-vacancy center in a diamond probe to unambiguously prove the existence of magnetic domains and study their dynamics in atomically thin CrBr 3 . By controlling the magnetic domain evolution as a function of magnetic field, we find that the pinning effect is a dominant coercivity mechanism and determine the magnetization of a CrBr 3 bilayer to be about 26 Bohr magnetons per square nanometer. The high spatial resolution of this technique enables imaging of magnetic domains and allows to locate the sites of defects that pin the domain walls and nucleate the reverse domains. Our work highlights scanning nitrogen-vacancy center magnetometry as a quantitative probe to explore nanoscale features in two-dimensional magnets. 

Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation‐by‐distance, and significantly elevated inbreeding. Among migratory breeding groups, on the other hand, we observed lower genetic differentiation, no isolation‐by‐distance, and substantially lower inbreeding. Using genotype–environment association analysis, we find significant evidence for relationships between migratory phenotypes (i.e., migrant versus resident) and environmental variation associated with cold temperatures during the winter and barren, open habitats. In the regions of the genome most differentiated between migrants and residents, we find significant enrichment for genes associated with the metabolism of fats. This may be linked to the increased pressure on migrants to process and store fats more efficiently in preparation for and during migration. Our results provide a significant contribution toward understanding the evolution of migratory behavior and vital insight into ongoing conservation and management efforts for the western burrowing owl.

 

Moiré superlattices of twisted nonmagnetic two-dimensional (2D) materials are highly controllable platforms for the engineering of exotic correlated and topological states. Here, we report emerging magnetic textures in small-angle twisted 2D magnet chromium triiodide (CrI 3 ). Using single-spin quantum magnetometry, we directly visualized nanoscale magnetic domains and periodic patterns, a signature of moiré magnetism, and measured domain size and magnetization. In twisted bilayer CrI 3 , we observed the coexistence of antiferromagnetic (AFM) and ferromagnetic (FM) domains with disorder-like spatial patterns. In twisted double-trilayer CrI 3 , AFM and FM domains with periodic patterns appear, which is in good agreement with the calculated spatial magnetic structures that arise from the local stacking-dependent interlayer exchange interactions in CrI 3 moiré superlattices. Our results highlight magnetic moiré superlattices as a platform for exploring nanomagnetism. 

Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low‐coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine‐scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population‐specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate‐Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.

 

Global loss of biodiversity has placed new urgency on the need to understand factors regulating species response to rapid environmental change. While specialists are often less resilient to rapid environmental change than generalists, species‐level analyses may obscure the extent of specialization when locally adapted populations vary in climate tolerances. Until recently, quantification of the degree of climate specialization in migratory birds below the species level was hindered by a lack of genomic and tracking information, but recent technological advances have helped to overcome these barriers. Here we take a genome‐wide genetic approach to mapping population‐specific migratory routes and quantifying niche breadth within genetically distinct populations of a migratory bird, the willow flycatcher (Empidonax traillii), which exhibits variation in the severity of population declines across its breeding range. While our sample size is restricted to the number of genetically distinct populations within the species, our results support the idea that locally adapted populations of the willow flycatcher with narrow climatic niches across seasons are already federally listed as endangered or in steep decline, while populations with broader climatic niches have remained stable in recent decades. Overall, this work highlights the value of quantifying niche breadth within genetically distinct groups across time and space when attempting to understand the factors that facilitate or constrain the response of locally adapted populations to rapid environmental change.