Satellites can reveal global extent of forced labor in the world's fishing fleet.

While forced labor in the world's fishing fleet has been widely documented, its extent remains unknown. No methods previously existed for remotely identifying individual fishing vessels potentially engaged in these abuses on a global scale. By combining expertise from human rights practitioners and satellite vessel monitoring data, we show that vessels reported to use forced labor behave in systematically different ways from other vessels. We exploit this insight by using machine learning to identify high-risk vessels from among 16,000 industrial longliner, squid jigger, and trawler fishing vessels. Our model reveals that between 14% and 26% of vessels were high-risk, and also reveals patterns of where these vessels fished and which ports they visited. Between 57,000 and 100,000 individuals worked on these vessels, many of whom may have been forced labor victims. This information provides unprecedented opportunities for novel interventions to combat this humanitarian tragedy. More broadly, this research demonstrates a proof of concept for using remote sensing to detect forced labor abuses.

The blue paradox: Preemptive overfishing in marine reserves.

Most large-scale conservation policies are anticipated or announced in advance. This risks the possibility of preemptive resource extraction before the conservation intervention goes into force. We use a high-resolution dataset of satellite-based fishing activity to show that anticipation of an impending no-take marine reserve undermines the policy by triggering an unintended race-to-fish. We study one of the world's largest marine reserves, the Phoenix Islands Protected Area (PIPA), and find that fishers more than doubled their fishing effort once this area was earmarked for eventual protected status. The additional fishing effort resulted in an impoverished starting point for PIPA equivalent to 1.5 y of banned fishing. Extrapolating this behavior globally, we estimate that if other marine reserve announcements were to trigger similar preemptive fishing, this could temporarily increase the share of overextracted fisheries from 65% to 72%. Our findings have implications for general conservation efforts as well as the methods that scientists use to monitor and evaluate policy efficacy.

Catalyzing sustainable fisheries management through behavior change interventions.

Small-scale fisheries are an important livelihood and primary protein source for coastal communities in many of the poorest regions in the world, yet many are overfished and thus require effective and scalable management solutions. Positive ecological and socioeconomic responses to management typically lag behind immediate costs borne by fishers from fishing pressure reductions necessary for fisheries recovery. These short-term costs challenge the long-term success of these interventions. However, social marketing may increase perceptions of management benefits before ecological and socioeconomic benefits are fully realized, driving new social norms and ultimately long-term sustainable behavior change. By conducting underwater visual surveys to quantify ecological conditions and by conducting household surveys with community members to quantify their perceptions of management support and socioeconomic conditions, we assessed the impact of a standardized small-scale fisheries management intervention that was implemented across 41 sites in Brazil, Indonesia, and the Philippines. The intervention combines TURF reserves (community-based territorial use rights for fishing coupled with no-take marine reserves) with locally tailored social-marketing behavior change campaigns. Leveraging data across 22 indicators and 4 survey types, along with data from 3 control sites, we found that ecological and socioeconomic impacts varied and that communities supported the intervention and were already changing their fishing practices. These results suggest that communities were developing new social norms and fishing more sustainably before long-term ecological and socioeconomic benefits of fisheries management materialized.

Catalización del Manejo de Pesquerías Sustentables por medio de Intervenciones de Cambio de Comportamiento Resumen Las pesquerías a pequeña escala son un sustento importante y la principal fuente de proteína para las comunidades costeras en muchas de las regiones más pobres del mundo, sin embargo, muchas sufren de sobrepesca y por lo tanto requieren soluciones de manejo efectivas y escalables. Las respuestas ecológicas y socioeconómicas positivas al manejo generalmente se retrasan con respecto a los costos inmediatos asumidos por los pescadores a partir de las reducciones de la presión ocasionada por la pesca necesarias para la recuperación de la pesquería. Estos costos a corto plazo son un reto para el éxito a largo plazo de las intervenciones. Sin embargo, la mercadotecnia social puede incrementar las percepciones de los beneficios del manejo antes de que se conozcan por completo los beneficios ecológicos y socioeconómicos, lo que genera nuevas normas sociales y finalmente un cambio en el comportamiento a largo plazo. Realizamos censos submarinos visuales para cuantificar las condiciones ecológicas y censos domésticos a los miembros de la comunidad para cuantificar sus percepciones del apoyo al manejo y de las condiciones socioeconómicas. Con esto, evaluamos el impacto de la intervención de manejo para pesquerías estandarizadas a pequeña escala que fue implementada en 41 sitios de Brasil, Indonesia y las Filipinas. La intervención combina las reservas TURF (derechos de uso de pesca territorial basados en la comunidad acoplados con reservas marinas con restricción de pesca) con campañas de mercadotecnia social para el cambio de comportamiento ajustadas al contexto local. Con la movilización de datos a lo largo de 22 indicadores y cuatro tipos de censos, junto con los datos de tres sitios de control, encontramos que los impactos ecológicos y socioeconómicos variaron y que las comunidades apoyaban la intervención y ya se encontraban cambiando sus prácticas de pesca. Estos resultados sugieren que las comunidades ya estaban desarrollando nuevas normas sociales y pescando de manera más sustentable antes de que los beneficios ecológicos y socioeconómicos a largo plazo del manejo de las pesquerías se materializaran.

Multiple regions within 8q24 independently affect risk for prostate cancer.

After the recent discovery that common genetic variation in 8q24 influences inherited risk of prostate cancer, we genotyped 2,973 SNPs in up to 7,518 men with and without prostate cancer from five populations. We identified seven risk variants, five of them previously undescribed, spanning 430 kb and each independently predicting risk for prostate cancer (P = 7.9 x 10(-19) for the strongest association, and P < 1.5 x 10(-4) for five of the variants, after controlling for each of the others). The variants define common genotypes that span a more than fivefold range of susceptibility to cancer in some populations. None of the prostate cancer risk variants aligns to a known gene or alters the coding sequence of an encoded protein.

A whole-genome admixture scan finds a candidate locus for multiple sclerosis susceptibility.

Multiple sclerosis is a common disease with proven heritability, but, despite large-scale attempts, no underlying risk genes have been identified. Traditional linkage scans have so far identified only one risk haplotype for multiple sclerosis (at HLA on chromosome 6), which explains only a fraction of the increased risk to siblings. Association scans such as admixture mapping have much more power, in principle, to find the weak factors that must explain most of the disease risk. We describe here the first high-powered admixture scan, focusing on 605 African American cases and 1,043 African American controls, and report a locus on chromosome 1 that is significantly associated with multiple sclerosis.

Assessing the impact of population stratification on genetic association studies.

Population stratification refers to differences in allele frequencies between cases and controls due to systematic differences in ancestry rather than association of genes with disease. It has been proposed that false positive associations due to stratification can be controlled by genotyping a few dozen unlinked genetic markers. To assess stratification empirically, we analyzed data from 11 case-control and case-cohort association studies. We did not detect statistically significant evidence for stratification but did observe that assessments based on a few dozen markers lack power to rule out moderate levels of stratification that could cause false positive associations in studies designed to detect modest genetic risk factors. After increasing the number of markers and samples in a case-cohort study (the design most immune to stratification), we found that stratification was in fact present. Our results suggest that modest amounts of stratification can exist even in well designed studies.

A high-density admixture scan in 1,670 African Americans with hypertension.

Hypertension (HTN) is a devastating disease with a higher incidence in African Americans than European Americans, inspiring searches for genetic variants that contribute to this difference. We report the results of a large-scale admixture scan for genes contributing HTN risk, in which we screened 1,670 African Americans with HTN and 387 control individuals for regions of the genome with elevated proportion of African or European ancestry. No loci were identified that were significantly associated with HTN. We also searched for evidence of an admixture signal at 40 candidate genes and eight previously reported linkage peaks, but none appears to contribute substantially to the differential HTN risk between African and European Americans. Finally, we observed nominal association at one of the loci detected in the admixture scan of Zhu et al. 2005 (p = 0.016 at 6q24.3 correcting for four hypotheses tested), although we caution that the significance is marginal and the estimated odds ratio of 1.19 per African allele is less than what would be expected from the original report; thus, further work is needed to follow up this locus.

A funder-imposed data publication requirement seldom inspired data sharing.

Growth of the open science movement has drawn significant attention to data sharing and availability across the scientific community. In this study, we tested the ability to recover data collected under a particular funder-imposed requirement of public availability. We assessed overall data recovery success, tested whether characteristics of the data or data creator were indicators of recovery success, and identified hurdles to data recovery. Overall the majority of data were not recovered (26% recovery of 315 data projects), a similar result to journal-driven efforts to recover data. Field of research was the most important indicator of recovery success, but neither home agency sector nor age of data were determinants of recovery. While we did not find a relationship between recovery of data and age of data, age did predict whether we could find contact information for the grantee. The main hurdles to data recovery included those associated with communication with the researcher; loss of contact with the data creator accounted for half (50%) of unrecoverable datasets, and unavailability of contact information accounted for 35% of unrecoverable datasets. Overall, our results suggest that funding agencies and journals face similar challenges to enforcement of data requirements. We advocate that funding agencies could improve the availability of the data they fund by dedicating more resources to enforcing compliance with data requirements, providing data-sharing tools and technical support to awardees, and administering stricter consequences for those who ignore data sharing preconditions.

A user-friendly tool to evaluate the effectiveness of no-take marine reserves.

Marine reserves are implemented to achieve a variety of objectives, but are seldom rigorously evaluated to determine whether those objectives are met. In the rare cases when evaluations do take place, they typically focus on ecological indicators and ignore other relevant objectives such as socioeconomics and governance. And regardless of the objectives, the diversity of locations, monitoring protocols, and analysis approaches hinder the ability to compare results across case studies. Moreover, analysis and evaluation of reserves is generally conducted by outside researchers, not the reserve managers or users, plausibly thereby hindering effective local management and rapid response to change. We present a framework and tool, called "MAREA", to overcome these challenges. Its purpose is to evaluate the extent to which any given reserve has achieved its stated objectives. MAREA provides specific guidance on data collection and formatting, and then conducts rigorous causal inference analysis based on data input by the user, providing real-time outputs about the effectiveness of the reserve. MAREA's ease of use, standardization of state-of-the-art inference methods, and ability to analyze marine reserve effectiveness across ecological, socioeconomic, and governance objectives could dramatically further our understanding and support of effective marine reserve management.

A genomewide admixture map for Latino populations.

Admixture mapping is an economical and powerful approach for localizing disease genes in populations of recently mixed ancestry and has proven successful in African Americans. The method holds equal promise for Latinos, who typically inherit a mix of European, Native American, and African ancestry. However, admixture mapping in Latinos has not been practical because of the lack of a map of ancestry-informative markers validated in Native American and other populations. To address this, we screened multiple databases, containing millions of markers, to identify 4,186 markers that were putatively informative for determining the ancestry of chromosomal segments in Latino populations. We experimentally validated each of these markers in at least 232 new Latino, European, Native American, and African samples, and we selected a subset of 1,649 markers to form an admixture map. An advantage of our strategy is that we focused our map on markers distinguishing Native American from other ancestries and restricted it to markers with very similar frequencies in Europeans and Africans, which decreased the number of markers needed and minimized the possibility of false disease associations. We evaluated the effectiveness of our map for localizing disease genes in four Latino populations from both North and South America.

Admixture mapping of an allele affecting interleukin 6 soluble receptor and interleukin 6 levels.

Circulating levels of inflammatory markers can predict cardiovascular disease risk. To identify genes influencing the levels of these markers, we genotyped 1,343 single-nucleotide polymorphisms (SNPs) in 1,184 African Americans from the Health, Aging and Body Composition (Health ABC) Study. Using admixture mapping, we found a significant association of interleukin 6 soluble receptor (IL-6 SR) with European ancestry on chromosome 1 (LOD 4.59), in a region that includes the gene for this receptor (IL-6R). Genotyping 19 SNPs showed that the effect is largely explained by an allele at 4% frequency in West Africans and at 35% frequency in European Americans, first described as associated with IL-6 SR in a Japanese cohort. We replicate this association (P<<1.0x10-12) and also demonstrate a new association with circulating levels of a different molecule, IL-6 (P<3.4x10-5). After replication in 1,674 European Americans from Health ABC, the combined result is even more significant: P<<1.0x10-12 for IL-6 SR, and P<2.0x10-9 for IL-6. These results also serve as an important proof of principle, showing that admixture mapping can not only coarsely localize but can also fine map a phenotypically important variant.

Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men.

A whole-genome admixture scan in 1,597 African Americans identified a 3.8 Mb interval on chromosome 8q24 as significantly associated with susceptibility to prostate cancer [logarithm of odds (LOD) = 7.1]. The increased risk because of inheriting African ancestry is greater in men diagnosed before 72 years of age (P < 0.00032) and may contribute to the epidemiological observation that the higher risk for prostate cancer in African Americans is greatest in younger men (and attenuates with older age). The same region was recently identified through linkage analysis of prostate cancer, followed by fine-mapping. We strongly replicated this association (P < 4.2 x 10(-9)) but find that the previously described alleles do not explain more than a fraction of the admixture signal. Thus, admixture mapping indicates a major, still-unidentified risk gene for prostate cancer at 8q24, motivating intense work to find it.

Comparison of fine-scale recombination rates in humans and chimpanzees.

We compared fine-scale recombination rates at orthologous loci in humans and chimpanzees by analyzing polymorphism data in both species. Strong statistical evidence for hotspots of recombination was obtained in both species. Despite approximately 99% identity at the level of DNA sequence, however, recombination hotspots were found rarely (if at all) at the same positions in the two species, and no correlation was observed in estimates of fine-scale recombination rates. Thus, local patterns of recombination rate have evolved rapidly, in a manner disproportionate to the change in DNA sequence.

Detecting recent positive selection in the human genome from haplotype structure.

The ability to detect recent natural selection in the human population would have profound implications for the study of human history and for medicine. Here, we introduce a framework for detecting the genetic imprint of recent positive selection by analysing long-range haplotypes in human populations. We first identify haplotypes at a locus of interest (core haplotypes). We then assess the age of each core haplotype by the decay of its association to alleles at various distances from the locus, as measured by extended haplotype homozygosity (EHH). Core haplotypes that have unusually high EHH and a high population frequency indicate the presence of a mutation that rose to prominence in the human gene pool faster than expected under neutral evolution. We applied this approach to investigate selection at two genes carrying common variants implicated in resistance to malaria: G6PD and CD40 ligand. At both loci, the core haplotypes carrying the proposed protective mutation stand out and show significant evidence of selection. More generally, the method could be used to scan the entire genome for evidence of recent positive selection.

A high-density admixture map for disease gene discovery in african americans.

Admixture mapping (also known as "mapping by admixture linkage disequilibrium," or MALD) provides a way of localizing genes that cause disease, in admixed ethnic groups such as African Americans, with approximately 100 times fewer markers than are required for whole-genome haplotype scans. However, it has not been possible to perform powerful scans with admixture mapping because the method requires a dense map of validated markers known to have large frequency differences between Europeans and Africans. To create such a map, we screened through databases containing approximately 450000 single-nucleotide polymorphisms (SNPs) for which frequencies had been estimated in African and European population samples. We experimentally confirmed the frequencies of the most promising SNPs in a multiethnic panel of unrelated samples and identified 3011 as a MALD map (1.2 cM average spacing). We estimate that this map is approximately 70% informative in differentiating African versus European origins of chromosomal segments. This map provides a practical and powerful tool, which is freely available without restriction, for screening for disease genes in African American patient cohorts. The map is especially appropriate for those diseases that differ in incidence between the parental African and European populations.