Many traits in populations are well understood as being Mendelian effects at single loci or additive polygenic effects across numerous loci. However, there are important phenomena and traits that are ...intermediate between these two extremes and are known as oligogenic traits. Here we investigate digenic, or two-locus, traits and how their frequencies in populations are affected by non-random mating, specifically inbreeding, linkage disequilibrium, and selection. These effects are examined both separately and in combination to demonstrate how many digenic traits, especially double homozygous ones, can show significant, sometimes unexpected, changes in population frequency with inbreeding, linkage, and linkage disequilibrium. The effects of selection on deleterious digenic traits are also detailed. These results are applied to both digenic traits of medical significance as well as measuring inbreeding in natural populations.
•Digenic traits are influenced by linkage disequilibrium, linkage, and inbreeding.•Double homozygotes and double heterozygotes typically increase in inbreeding.•Linkage disequilibrium in recently admixed populations amplifies these effects.•Some genotypes increase frequency in consanguineous families in admixed populations.
The allele frequency dependence of the ranges of all measures of linkage disequilibrium is well-known. The maximum values of commonly used parameters such as r2 and D vary depending on the allele ...frequencies at each locus. However, though this phenomenon is recognized and accounted for in many studies, the comprehensive mathematical framework underlying the limits of linkage disequilibrium measures at various frequency combinations is often heuristic or empirical. Here, it is demonstrated that underlying this behavior is the fundamental shift between linear and nonlinear dependence in the linkage disequilibrium structure between loci. The proportion of linear and nonlinear dependence can be estimated and it demonstrates how even the same values of r2 can have different implications for the nature of the overall dependence. One result of this is the value of D′, when defined as only a positive number, has a minimum value of |r|. Understanding this dependence is crucial to making correct inferences about the relationships between two loci in linkage disequilibrium.
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•Linkage disequilibrium has nonlinear dependence with mismatched allele frequencies.•Linkage disequilibrium’s nonlinearity can be estimated with the ratio r2/D’2.•Nonlinearity distorts the conditional variance of a locus from the expectation of r2.•Nonlinearity is robust to recombination that affects linkage disequilibrium.
Abstract
The Drake equation has proven fertile ground for speculation about the abundance, or lack thereof, of communicating extraterrestrial intelligences (CETIs) for decades. It has been augmented ...by subsequent authors to include random variables in order to understand its probabilistic behaviour. However, in most cases, the emergence and lifetime of CETIs are assumed to be independent of each other. In this paper, we will derive several expressions that can demonstrate how CETIs may relate to each other in technological age as well as how the dynamics of the concurrent CETI population change under basic models of interaction, such as the Allee effect. By defining interaction as the change in the expected communication lifetime with respect to the density of CETI in a region of space, we can use models and simulation to understand how the CETI density can promote or inhibit the longevity and overall population of interstellar technological civilizations.
Summary Background Post-thrombotic syndrome (PTS) is a common and burdensome complication of deep venous thrombosis (DVT). Previous trials suggesting benefit of elastic compression stockings (ECS) to ...prevent PTS were small, single-centre studies without placebo control. We aimed to assess the efficacy of ECS, compared with placebo stockings, for the prevention of PTS. Methods We did a multicentre randomised placebo-controlled trial of active versus placebo ECS used for 2 years to prevent PTS after a first proximal DVT in centres in Canada and the USA. Patients were randomly assigned to study groups with a web-based randomisation system. Patients presenting with a first symptomatic, proximal DVT were potentially eligible to participate. They were excluded if the use of compression stockings was contraindicated, they had an expected lifespan of less than 6 months, geographical inaccessibility precluded return for follow-up visits, they were unable to apply stockings, or they received thrombolytic therapy for the initial treatment of acute DVT. The primary outcome was PTS diagnosed at 6 months or later using Ginsberg's criteria (leg pain and swelling of ≥1 month duration). We used a modified intention to treat Cox regression analysis, supplemented by a prespecified per-protocol analysis of patients who reported frequent use of their allocated treatment. This study is registered with ClinicalTrials.gov , number NCT00143598 , and Current Controlled Trials, number ISRCTN71334751. Findings From 2004 to 2010, 410 patients were randomly assigned to receive active ECS and 396 placebo ECS. The cumulative incidence of PTS was 14·2% in active ECS versus 12·7% in placebo ECS (hazard ratio adjusted for centre 1·13, 95% CI 0·73–1·76; p=0·58). Results were similar in a prespecified per-protocol analysis of patients who reported frequent use of stockings. Interpretation ECS did not prevent PTS after a first proximal DVT, hence our findings do not support routine wearing of ECS after DVT. Funding Canadian Institutes of Health Research.
Abstract Objective To present an approach, based on current evidence, for the diagnosis, treatment, and thromboprophylaxis of venous thromboembolism in pregnancy and postpartum. Evidence Published ...literature was retrieved through searches of PubMed, Medline, CINAHL, and The Cochrane Library from November 2011 to July 2013 using appropriate controlled vocabulary (e.g. pregnancy, venous thromboembolism, deep vein thrombosis, pulmonary embolism, pulmonary thrombosis) and key words (e.g., maternal morbidity, pregnancy complications, thromboprophylaxis, antithrombotic therapy). Results were restricted to systematic reviews, randomized control trials/controlled clinical trials, and observational studies published in English or French. There were no date restrictions. Grey (unpublished) literature was identified through searching the websites of clinical practice guideline collections, clinical trial registries, and national and international medical specialty societies. Values The quality of evidence in this document was rated using the criteria described in the Report of the Canadian Task Force on Preventative Health Care ( Table 1 ).
In this paper, new techniques that allow conditional entropy to estimate the combinatorics of symbols are applied to animal communication studies to estimate the communication's repertoire size. By ...using the conditional entropy estimates at multiple orders, the paper estimates the total repertoire sizes for animal communication across bottlenose dolphins, humpback whales and several species of birds for an N-gram length of one to three. In addition to discussing the impact of this method on studies of animal communication complexity, the reliability of these estimates is compared to other methods through simulation. While entropy does undercount the total repertoire size due to rare N-grams, it gives a more accurate picture of the most frequently used repertoire than just repertoire size alone.
The Internet is one of the largest and most complex communication and information exchange networks ever created. Therefore, its dynamics and traffic unsurprisingly take on a rich variety of complex ...dynamics, self-organization, and other phenomena that have been researched for years. This paper is a review of the complex dynamics of Internet traffic. Departing from normal treatises, we will take a view from both the network engineering and physics perspectives showing the strengths and weaknesses as well as insights of both. In addition, many less covered phenomena such as traffic oscillations, BGP storms, and comparisons of the Internet and biological models will be covered.
In a 1974 paper, Coale and Trussell described an empirical relationship between the age-specific fertility rate, the marital fertility rate, and the proportion of women with first marriages. However, ...their key assumption was no nonmarital fertility. This obscures the relationship between nonmarital fertility and overall fertility that distinguishes many modern Western societies from those of East Asia. Here, their equation is extended to incorporate nonmarital fertility and dual equations are derived relating age-specific fertility, marital or nonmarital fertility, proportion of women with first marriages, and the proportion of births within or outside of marriage. These equations are validated with multi-year data from countries in Europe, the USA (both African-Americans and White Americans) and Japan. They also help to illustrate the dilemma facing modern societies: between a relatively high marriage age, low nonmarital birth ratios, and high fertility, they can only accommodate two in combination.
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