Approximately 2-4% of genetic material in human populations outside Africa is derived from Neanderthals who interbred with anatomically modern humans. Recent studies have shown that this Neanderthal ...DNA is depleted around functional genomic regions; this has been suggested to be a consequence of harmful epistatic interactions between human and Neanderthal alleles. However, using published estimates of Neanderthal inbreeding and the distribution of mutational fitness effects, we infer that Neanderthals had at least 40% lower fitness than humans on average; this increased load predicts the reduction in Neanderthal introgression around genes without the need to invoke epistasis. We also predict a residual Neanderthal mutational load in non-Africans, leading to a fitness reduction of at least 0.5%. This effect of Neanderthal admixture has been left out of previous debate on mutation load differences between Africans and non-Africans. We also show that if many deleterious mutations are recessive, the Neanderthal admixture fraction could increase over time due to the protective effect of Neanderthal haplotypes against deleterious alleles that arose recently in the human population. This might partially explain why so many organisms retain gene flow from other species and appear to derive adaptive benefits from introgression.
The rise of digital intermediaries such as search engines and social media is profoundly changing our media environment. Here, we analyze how news media organizations handle their relations to these ...increasingly important intermediaries. Based on a strategic case study, we argue that relationships between publishers and platforms are characterized by a tension between (1) short-term, operational opportunities and (2) long-term strategic worries about becoming too dependent on intermediaries. We argue that these relationships are shaped by news media’s fear of missing out, the difficulties of evaluating the risk/reward ratios, and a sense of asymmetry. The implication is that news media that developed into an increasingly independent institution in the 20th century—in part enabled by news media organizations’ control over channels of communication—are becoming dependent upon new digital intermediaries that structure the media environment in ways that not only individual citizens but also large, resource-rich, powerful organizations have to adapt to.
High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples ...simultaneously.
We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods.
The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd . The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.
There is an increasing interest in detecting genes, or genomic regions, that have been targeted by natural selection. The interest stems from a basic desire to learn more about evolutionary processes ...in humans and other organisms, and from the realization that inferences regarding selection may provide important functional information. This review provides a nonmathematical description of the issues involved in detecting selection from DNA sequences and SNP data and is intended for readers who are not familiar with population genetic theory. Particular attention is placed on issues relating to the analysis of large-scale genomic data sets.
Admixture-the mixing of genomes from divergent populations-is increasingly appreciated as a central process in evolution. To characterize and quantify patterns of admixture across the genome, a ...number of methods have been developed for local ancestry inference. However, existing approaches have a number of shortcomings. First, all local ancestry inference methods require some prior assumption about the expected ancestry tract lengths. Second, existing methods generally require genotypes, which is not feasible to obtain for many next-generation sequencing projects. Third, many methods assume samples are diploid, however a wide variety of sequencing applications will fail to meet this assumption. To address these issues, we introduce a novel hidden Markov model for estimating local ancestry that models the read pileup data, rather than genotypes, is generalized to arbitrary ploidy, and can estimate the time since admixture during local ancestry inference. We demonstrate that our method can simultaneously estimate the time since admixture and local ancestry with good accuracy, and that it performs well on samples of high ploidy-i.e. 100 or more chromosomes. As this method is very general, we expect it will be useful for local ancestry inference in a wider variety of populations than what previously has been possible. We then applied our method to pooled sequencing data derived from populations of Drosophila melanogaster on an ancestry cline on the east coast of North America. We find that regions of local recombination rates are negatively correlated with the proportion of African ancestry, suggesting that selection against foreign ancestry is the least efficient in low recombination regions. Finally we show that clinal outlier loci are enriched for genes associated with gene regulatory functions, consistent with a role of regulatory evolution in ecological adaptation of admixed D. melanogaster populations. Our results illustrate the potential of local ancestry inference for elucidating fundamental evolutionary processes.
There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of ...divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and divergence times over a variety of ancient and recent time scales. Using the same technique, we analyze deeply sequenced trio parents from the 1000 Genomes project. The data show evidence of extensive gene flow between Africa and Europe after the time of divergence as well as substructure and gene flow among ancestral hominids. In particular, we infer that recent African-European gene flow and ancient ghost admixture into Europe are both necessary to explain the spectrum of IBS sharing in the trios, rejecting simpler models that contain less population structure.
The purpose of this paper is to investigate the potential gains from changing the existing regulatory framework for fresh water aquaculture production in Denmark. The regulatory framework is changed ...from an input regulation based on farm-specific feed quotas, to an individual transferable quota system on nitrogen pollution. The regulatory change is analyzed using Data Envelopment Analysis to model the underlying production structure. The effect of allowing trading of nitrogen quotas on production and profitability is analyzed in a joint production model with good and bad output under different behavioral and technical assumptions, whilst keeping the overall pollution level of nitrogen constant. Furthermore, the effect of a catchment area restriction on nitrogen is analyzed to comply with the EU Water Framework Directive. The paper quantifies the gains of a policy change from a command and control system to an incentive based system. The estimated results suggest that the changed regulation could increase Danish aquaculture production by 16 to 55%, whilst actual profitability could be increased 5 to 10 times.
► Introduction of an individual transferable quota system on nitrogen in aquaculture. ► Quantification of gains following a policy change from a command and control to an incentive based management system. ► Production and profitability increases without increasing pollution. ► The changes are modeled using DEA and a joint production model with good and bad output.
Scholars have questioned the potential for incidental exposure in high-choice media environments. We use online survey data to examine incidental exposure to news on social media (Facebook, YouTube, ...Twitter) in four countries (Italy, Australia, United Kingdom, United States). Leaving aside those who say they intentionally use social media for news, we compare the number of online news sources used by social media users who do not see it as a news platform, but may come across news while using it (the incidentally exposed), with people who do not use social media at all (non-users). We find that (a) the incidentally exposed users use significantly more online news sources than non-users, (b) the effect of incidental exposure is stronger for younger people and those with low interest in news and (c) stronger for users of YouTube and Twitter than for users of Facebook.
In 1988, Felsenstein described a framework for assessing the likelihood of a genetic data set in which all of the possible genealogical histories of the data are considered, each in proportion to ...their probability. Although not analytically solvable, several approaches, including Markov chain Monte Carlo methods, have been developed to find approximate solutions. Here, we describe an approach in which Markov chain Monte Carlo simulations are used to integrate over the space of genealogies, whereas other parameters are integrated out analytically. The result is an approximation to the full joint posterior density of the model parameters. For many purposes, this function can be treated as a likelihood, thereby permitting likelihood-based analyses, including likelihood ratio tests of nested models. Several examples, including an application to the divergence of chimpanzee subspecies, are provided.
Patellar and Achilles tendinopathy commonly affect runners. Developing algorithms to predict cumulative force in these structures may help prevent these injuries. Importantly, such algorithms should ...be fueled with data that are easily accessible while completing a running session outside a biomechanical laboratory. Therefore, the main objective of this study was to investigate whether algorithms can be developed for predicting patellar and Achilles tendon force and impulse during running using measures that can be easily collected by runners using commercially available devices. A secondary objective was to evaluate the predictive performance of the algorithms against the commonly used running distance. Trials of 24 recreational runners were collected with an Xsens suit and a Garmin Forerunner 735XT at three different intended running speeds. Data were analyzed using a mixed-effects multiple regression model, which was used to model the association between the estimated forces in anatomical structures and the training load variables during the fixed running speeds. This provides twelve algorithms for predicting patellar or Achilles tendon peak force and impulse per stride. The algorithms developed in the current study were always superior to the running distance algorithm.
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