African genomics and skin color: Skin color varies among human populations and is thought to be under selection, with light skin maximizing vitamin D production at higher latitudes and dark skin providing UV protection in equatorial zones. To identify the genes that give rise to the palette of human skin tones, Crawford et al. applied genome-wide analyses across diverse African populations (see the Perspective by Tang and Barsh). Genetic variants were identified with likely function in skin phenotypes. Comparison to model organisms verified a conserved function of MFSD12 in pigmentation. A global genetic panel was used to trace how alleles associated with skin color likely moved across the globe as humans migrated, both within and out of Africa. Science , this issue p. eaan8433 ; see also p. 867

How natural selection affects mouse coat color: Evolution, at its core, involves changes in the frequency of alleles subject to natural selection. But identifying the target of selection can be difficult. Barrett et al. investigated how allele frequencies affecting pigmentation change over time (see the Perspective by Pelletier). Wild-caught mice ( Peromyscus maniculatus ) were exposed to avian predators against naturally occurring dark or light backgrounds. Natural selection yielded shifts in coloration owing to genetic variants in the mouse coat color Agouti gene. Science , this issue p. 499 ; see also p. 452

Global and regional climate model simulations are frequently used for regional climate change assessments and in climate impact modeling studies. To reflect the inherent and methodological uncertainties in climate modeling, the assessment of regional climate change requires ensemble simulations from different global and regional climate model combinations. To interpret the spread of simulated results, it is useful to understand how the climate change signal is modified in the GCM-RCM modelmodelgeneral circulation model-regional climate model (GCM-RCM) chain. This kind of information can also be useful for impact modelers; for the process of experiment design and when interpreting model results. In this study, we investigate how the simulated historical and future climate of the Max-Planck-Institute earth system model (MPI-ESM) is modified by dynamic downscaling with the regional model REMO in different world regions. The historical climate simulations for 1950–2005 are driven by observed anthropogenic forcing. The climate projections are driven by projected anthropogenic forcing according to different Representative Concentration Pathways (RCPs). The global simulations are downscaled with REMO over the Coordinated Regional Climate Downscaling Experiment (CORDEX) domains Africa, Europe, South America and West Asia from 2006–2100. This unique set of simulations allows for climate type specific analysis across multiple world regions and for multi-scenarios. We used a classification of climate types by Köppen-Trewartha to define evaluation regions with certain climate conditions. A systematic comparison of near-surface temperature and precipitation simulated by the regional and the global model is done. In general, the historical time period is well represented by the GCM and the RCM. Some different biases occur in the RCM compared to the GCM as in the Amazon Basin, northern Africa and the West Asian domain. Both models project similar warming, although somewhat less so by the RCM for certain regions and climate types. A common feature in regions of tropical climate types is that REMO shows dryer climate conditions than forMax Planck Institute for Meteorology-Earth System Model (MPI-ESM) for RCP 4.5 and RCP 8.5, leading to an opposing sign in the climate change signal. With an increase in radiative forcing from RCP 2.6 to RCP 8.5 and towards the end of the 21st century, some of the detected differences between GCM and RCM are more pronounced.

In the past decade, several studies have estimated the human per-generation germline mutation rate using large pedigrees. More recently, estimates for various nonhuman species have been published. However, methodological differences among studies in detecting germline mutations and estimating mutation rates make direct comparisons difficult. Here, we describe the many different steps involved in estimating pedigree-based mutation rates, including sampling, sequencing, mapping, variant calling, filtering, and appropriately accounting for false-positive and false-negative rates. For each step, we review the different methods and parameter choices that have been used in the recent literature. Additionally, we present the results from a ‘Mutationathon,’ a competition organized among five research labs to compare germline mutation rate estimates for a single pedigree of rhesus macaques. We report almost a twofold variation in the final estimated rate among groups using different post-alignment processing, calling, and filtering criteria, and provide details into the sources of variation across studies. Though the difference among estimates is not statistically significant, this discrepancy emphasizes the need for standardized methods in mutation rate estimations and the difficulty in comparing rates from different studies. Finally, this work aims to provide guidelines for computational and statistical benchmarks for future studies interested in identifying germline mutations from pedigrees.

The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight. Yet, connecting theoretical results with empirical data has proven challenging, owing to a lack of information on the relationship between genotype, phenotype, and fitness. Here, we examine the demographic and selective history of deer mice in and around the Nebraska Sand Hills, a system in which variation at the Agouti locus affects cryptic coloration that in turn affects the survival of mice in their local habitat. We first genotyped 250 individuals from 11 sites along a transect spanning the Sand Hills at 660,000 single nucleotide polymorphisms across the genome. Using these genomic data, we found that deer mice first colonized the Sand Hills following the last glacial period. Subsequent high rates of gene flow have served to homogenize the majority of the genome between populations on and off the Sand Hills, with the exception of the Agouti pigmentation locus. Furthermore, mutations at this locus are strongly associated with the pigment traits that are strongly correlated with local soil coloration and thus responsible for cryptic coloration.