Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation.

Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as 'isolation by adaptation' (IBA). IBA can be complementary to the well-known pattern of 'isolation by distance' (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies, where divergent sexual selection is associated with phenotypic differentiation among allopatric populations. To investigate the relative contributions of selection and geographic distance to genome-wide differentiation, we compared genotypic and phenotypic variation from 350 barn swallows sampled across eight populations (28 pairwise comparisons) from four different subspecies. We report a draft whole-genome sequence for H. rustica, to which we aligned a set of 9493 single nucleotide polymorphisms (SNPs). Using statistical approaches to control for spatial autocorrelation of phenotypic variables and geographic distance, we find that divergence in traits related to migratory behaviour and sexual signalling, as well as geographic distance, together explain over 70% of genome-wide divergence among populations. Controlling for IBD, we find 42% of genomewide divergence is attributable to IBA through pairwise differences in traits related to migratory behaviour and sexual signalling alone. By (i) combining these results with prior studies of how selection shapes morphological differentiation and (ii) accounting for spatial autocorrelation, we infer that morphological adaptation plays a large role in shaping population-level differentiation in this group of closely related populations.

The state of US health, 1990-2010: burden of diseases, injuries, and risk factors.

IMPORTANCE: Understanding the major health problems in the United States and how they are changing over time is critical for informing national health policy. OBJECTIVES: To measure the burden of diseases, injuries, and leading risk factors in the United States from 1990 to 2010 and to compare these measurements with those of the 34 countries in the Organisation for Economic Co-operation and Development (OECD) countries. DESIGN: We used the systematic analysis of descriptive epidemiology of 291 diseases and injuries, 1160 sequelae of these diseases and injuries, and 67 risk factors or clusters of risk factors from 1990 to 2010 for 187 countries developed for the Global Burden of Disease 2010 Study to describe the health status of the United States and to compare US health outcomes with those of 34 OECD countries. Years of life lost due to premature mortality (YLLs) were computed by multiplying the number of deaths at each age by a reference life expectancy at that age. Years lived with disability (YLDs) were calculated by multiplying prevalence (based on systematic reviews) by the disability weight (based on population-based surveys) for each sequela; disability in this study refers to any short- or long-term loss of health. Disability-adjusted life-years (DALYs) were estimated as the sum of YLDs and YLLs. Deaths and DALYs related to risk factors were based on systematic reviews and meta-analyses of exposure data and relative risks for risk-outcome pairs. Healthy life expectancy (HALE) was used to summarize overall population health, accounting for both length of life and levels of ill health experienced at different ages. RESULTS: US life expectancy for both sexes combined increased from 75.2 years in 1990 to 78.2 years in 2010; during the same period, HALE increased from 65.8 years to 68.1 years. The diseases and injuries with the largest number of YLLs in 2010 were ischemic heart disease, lung cancer, stroke, chronic obstructive pulmonary disease, and road injury. Age-standardized YLL rates increased for Alzheimer disease, drug use disorders, chronic kidney disease, kidney cancer, and falls. The diseases with the largest number of YLDs in 2010 were low back pain, major depressive disorder, other musculoskeletal disorders, neck pain, and anxiety disorders. As the US population has aged, YLDs have comprised a larger share of DALYs than have YLLs. The leading risk factors related to DALYs were dietary risks, tobacco smoking, high body mass index, high blood pressure, high fasting plasma glucose, physical inactivity, and alcohol use. Among 34 OECD countries between 1990 and 2010, the US rank for the age-standardized death rate changed from 18th to 27th, for the age-standardized YLL rate from 23rd to 28th, for the age-standardized YLD rate from 5th to 6th, for life expectancy at birth from 20th to 27th, and for HALE from 14th to 26th. CONCLUSIONS AND RELEVANCE: From 1990 to 2010, the United States made substantial progress in improving health. Life expectancy at birth and HALE increased, all-cause death rates at all ages decreased, and age-specific rates of years lived with disability remained stable. However, morbidity and chronic disability now account for nearly half of the US health burden, and improvements in population health in the United States have not kept pace with advances in population health in other wealthy nations.

Spatially explicit models of divergence and genome hitchhiking.

Strong barriers to genetic exchange can exist at divergently selected loci, whereas alleles at neutral loci flow more readily between populations, thus impeding divergence and speciation in the face of gene flow. However, 'divergence hitchhiking' theory posits that divergent selection can generate large regions of differentiation around selected loci. 'Genome hitchhiking' theory suggests that selection can also cause reductions in average genome-wide rates of gene flow, resulting in widespread genomic divergence (rather than divergence only around specific selected loci). Spatial heterogeneity is ubiquitous in nature, yet previous models of genetic barriers to gene flow have explored limited combinations of spatial and selective scenarios. Using simulations of secondary contact of populations, we explore barriers to gene flow in various selective and spatial contexts in continuous, two-dimensional, spatially explicit environments. In general, the effects of hitchhiking are strongest in environments with regular spatial patterning of starkly divergent habitat types. When divergent selection is very strong, the absence of intermediate habitat types increases the effects of hitchhiking. However, when selection is moderate or weak, regular (vs. random) spatial arrangement of habitat types becomes more important than the presence of intermediate habitats per se. We also document counterintuitive processes arising from the stochastic interplay between selection, gene flow and drift. Our results indicate that generalization of results from two-deme models requires caution and increase understanding of the genomic and geographic basis of population divergence.

Prevalence and causes of vision loss in Southeast Asia and Oceania: 1990-2010.

BACKGROUND: To assess prevalence and causes of vision impairment in Southeast Asia and Oceania in 1990 and 2010. METHODS: Based on a systematic review of medical literature, prevalence of moderate and severe vision impairment (MSVI; presenting visual acuity <6/18 but ≥3/60 in the better eye) and blindness (presenting visual acuity <3/60) was estimated for 1990 and 2010. RESULTS: In Oceania, the age-standardised prevalence of blindness and MSVI did not decrease significantly (1.3% to 0.8% and 6.6% to 5.1%) respectively, but in Southeast Asia, blindness decreased significantly from 1.4% to 0.8%, a 43% decrease. There were significantly more women blind (2.18 million) compared with men (1.28 million) in the Southeast Asian population in 2010, but no significant gender differences in MSVI in either subregion. Cataract was the most frequent cause of blindness in Southeast Asia and Oceania in 1990 and 2010. Uncorrected refractive error, followed by cataract, macular degeneration, glaucoma and diabetic retinopathy were the most common causes for MSVI in 1990 and 2010. With the increasing size of the older population, there have been relatively small increases in the number of blind (2%), and with MSVI (14%) in Southeast Asia, whereas increases have been greater in Oceania of 14% for blindness and of 31% for MSVI. CONCLUSIONS: The prevalence of blindness has reduced significantly from 1990 to 2010, with moderate but non-significant lowering of MSVI. Cataract and uncorrected refractive error are the main causes of vision impairment and blindness; cataract continues as the main cause of blindness, but at lower proportions.

Morning sickness: a mechanism for protecting mother and embryo.

Approximately two-thirds of women experience nausea or vomiting during the first trimester of pregnancy. These symptoms are commonly known as morning sickness. Hook (1976) and Profet (1988) hypothesized that morning sickness protects the embryo by causing pregnant women to physically expel and subsequently avoid foods that contain teratogenic and abortifacient chemicals, especially toxic chemicals in strong-tasting vegetables, caffeinated beverages and alcohol. We examined this hypothesis by comprehensively reviewing the relevant medical, psychological and anthropological literature. In its support, (i) symptoms peak when embryonic organogenesis is most susceptible to chemical disruption (weeks 6-18), (ii) women who experience morning sickness are significantly less likely to miscarry than women who do not (9 of 9 studies), (iii) women who vomit suffer fewer miscarriages than those who experience nausea alone, and (iv) many pregnant women have aversions to alcoholic and nonalcoholic (mostly caffeinated) beverages and strong-tasting vegetables, especially during the first trimester. Surprisingly, however, the greatest aversions are to meats, fish, poultry, and eggs. A cross-cultural analysis using the Human Relations Area Files revealed 20 traditional societies in which morning sickness has been observed and seven in which it has never been observed. The latter were significantly less likely to have animal products as dietary staples and significantly more likely to have only plants (primarily corn) as staples than the 20 societies in which morning sickness occurred. Animal products may be dangerous to pregnant women and their embryos because they often contain parasites and pathogens, especially when stored at room temperatures in warm climates. Avoiding foodborne microorganisms is particularly important to pregnant women because they are immunosuppressed, presumably to reduce the chances of rejecting tissues of their own offspring (Haig 1993). As a result, pregnant women are more vulnerable to serious, often deadly infections. We hypothesize that morning sickness causes women to avoid foods that might be dangerous to themselves or their embryos, especially foods that, prior to widespread refrigeration, were likely to be heavily laden with microorganisms and their toxins. The alternative hypotheses that morning sickness is (i) an epiphenomenon of mother-offspring genetic conflict or hormones associated with viable pregnancies, or (ii) an indicator to potential sexual partners and kin that the woman is pregnant, resulting in reduced sexual behavior and increased nepotistic aid, were not well supported. Available data are most consistent with the hypothesis that morning sickness serves an adaptive, prophylactic function.