An Unexpectedly Complex Architecture for Skin Pigmentation in Africans.

Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.

Polychotomous traits and evolution under conformity.

Conformist and anticonformist transmission of dichotomous cultural traits (i.e., traits with two variants) have been studied both experimentally, in many species, and theoretically, with mathematical models. Signatures of types of conformity to polychotomous traits (with more than two variants; e.g., baby names and syllables in bird song) have been inferred from population-level data, but there are few models that include individual-level biases among more than two discrete variants. We generalize the standard dichotomous trait conformity model by Boyd and Richerson to incorporate [Formula: see text] role models and [Formula: see text] variants. Our analysis shows that in the case of [Formula: see text] role models, under anticonformity, the central polymorphic equilibrium [Formula: see text] is globally stable, whereas under conformity, if initially the frequencies of [Formula: see text] variants are all equal to the maximum variant frequency in the population, there is global convergence to an equilibrium in which the frequencies of these variants are all [Formula: see text] and all other variants are absent. With a general number n of role models, the same result holds with conformity, whereas under anticonformity, global convergence is not guaranteed, and there may be stable frequency cycles or chaos. If both conformity and anticonformity occur for different configurations of variants among the n role models, a variety of novel polymorphic equilibria may exist and be stable. Future empirical studies may use this formulation to directly quantify an individual's level of (anti)conformist bias to a polychotomous trait.

On random conformity bias in cultural transmission of polychotomous traits.

Mathematical models of conformity and anti-conformity have commonly included a set of simplifying assumptions. For example, (1) there are m=2 cultural variants in the population, (2) naive individuals observe the cultural variants of n=3 adult "role models," and (3) individuals' levels of conformity or anti-conformity do not change over time. Three recent theoretical papers have shown that departures from each of these assumptions can produce new population dynamics. Here, we explore cases in which multiple, or all, of these assumptions are violated simultaneously: namely, in a population with m variants of a trait where conformity (or anti-conformity) occurs with respect to n role models, we study a model in which the conformity rates at each generation are random variables that are independent of the variant frequencies at that generation. For this model a class of symmetric constant equilibria exist, and it is possible that all of these equilibria are simultaneously stochastically locally stable. In such cases, the effect of initial conditions on subsequent evolutionary trajectories becomes very complicated.

Cultural transmission, competition for prey, and the evolution of cooperative hunting.

Although cooperative hunting is widespread among animals, its benefits are unclear. At low frequencies, cooperative hunting may allow predators to escape competition and access bigger prey that could not be caught by a lone cooperative predator. Cooperative hunting is a more successful strategy when it is common, but its spread can result in overhunting big prey, which may have a lower per-capita growth rate than small prey. We construct a one-predator species, two-prey species model in which predators either learn to hunt small prey alone or learn to hunt big prey cooperatively. Predators first learn vertically from parents, then horizontally (i.e. socially) from random individuals or siblings. After horizontal transmission, they hunt with their learning partner if both are cooperative, and otherwise they hunt alone. Cooperative hunting cannot evolve when initially rare unless predators (a) interact with siblings, or (b) horizontally transmit the cooperative behavior to potential hunting partners. Whereas competition for small prey favors cooperative hunting when this cooperation is initially rare, the frequency of cooperative hunting cannot reach 100% unless big prey is abundant. Furthermore, a mutant that increases horizontal learning can invade if cooperative hunting is present, but not at 100%, because horizontal learning allows pairs of predators to have the same strategy. Our results reveal that the interactions between prey availability, social learning, and degree of cooperation among predators may have important effects on ecosystems.

Age-differentiated incentives for adaptive behavior during epidemics produce oscillatory and chaotic dynamics.

Heterogeneity in contact patterns, mortality rates, and transmissibility among and between different age classes can have significant effects on epidemic outcomes. Adaptive behavior in response to the spread of an infectious pathogen may give rise to complex epidemiological dynamics. Here we model an infectious disease in which adaptive behavior incentives, and mortality rates, can vary between two and three age classes. The model indicates that age-dependent variability in infection aversion can produce more complex epidemic dynamics at lower levels of pathogen transmissibility and that those at less risk of infection can still drive complexity in the dynamics of those at higher risk of infection. Policymakers should consider the interdependence of such heterogeneous groups when making decisions.

On randomly changing conformity bias in cultural transmission.

Humans and nonhuman animals display conformist as well as anticonformist biases in cultural transmission. Whereas many previous mathematical models have incorporated constant conformity coefficients, empirical research suggests that the extent of (anti)conformity in populations can change over time. We incorporate stochastic time-varying conformity coefficients into a widely used conformity model, which assumes a fixed number n of "role models" sampled by each individual. We also allow the number of role models to vary over time ([Formula: see text]). Under anticonformity, nonconvergence can occur in deterministic and stochastic models with different parameter values. Even if strong anticonformity may occur, if conformity or random copying (i.e., neither conformity nor anticonformity) is expected, there is convergence to one of the three equilibria seen in previous deterministic models of conformity. Moreover, this result is robust to stochastic variation in [Formula: see text] However, dynamic properties of these equilibria may be different from those in deterministic models. For example, with random conformity coefficients, all equilibria can be stochastically locally stable simultaneously. Finally, we study the effect of randomly changing weak selection. Allowing the level of conformity, the number of role models, and selection to vary stochastically may produce a more realistic representation of the wide range of group-level properties that can emerge under (anti)conformist biases. This promises to make interpretation of the effect of conformity on differences between populations, for example those connected by migration, rather difficult. Future research incorporating finite population sizes and migration would contribute added realism to these models.

Designing gene drives to limit spillover to non-target populations.

The prospect of utilizing CRISPR-based gene-drive technology for controlling populations has generated much excitement. However, the potential for spillovers of gene-drive alleles from the target population to non-target populations has raised concerns. Here, using mathematical models, we investigate the possibility of limiting spillovers to non-target populations by designing differential-targeting gene drives, in which the expected equilibrium gene-drive allele frequencies are high in the target population but low in the non-target population. We find that achieving differential targeting is possible with certain configurations of gene-drive parameters, but, in most cases, only under relatively low migration rates between populations. Under high migration, differential targeting is possible only in a narrow region of the parameter space. Because fixation of the gene drive in the non-target population could severely disrupt ecosystems, we outline possible ways to avoid this outcome. We apply our model to two potential applications of gene drives-field trials for malaria-vector gene drives and control of invasive species on islands. We discuss theoretical predictions of key requirements for differential targeting and their practical implications.

Cultural transmission of move choice in chess.

The study of cultural evolution benefits from detailed analysis of cultural transmission in specific human domains. Chess provides a platform for understanding the transmission of knowledge due to its active community of players, precise behaviours and long-term records of high-quality data. In this paper, we perform an analysis of chess in the context of cultural evolution, describing multiple cultural factors that affect move choice. We then build a population-level statistical model of move choice in chess, based on the Dirichlet-multinomial likelihood, to analyse cultural transmission over decades of recorded games played by leading players. For moves made in specific positions, we evaluate the relative effects of frequency-dependent bias, success bias and prestige bias on the dynamics of move frequencies. We observe that negative frequency-dependent bias plays a role in the dynamics of certain moves, and that other moves are compatible with transmission under prestige bias or success bias. These apparent biases may reflect recent changes, namely the introduction of computer chess engines and online tournament broadcasts. Our analysis of chess provides insights into broader questions concerning how social learning biases affect cultural evolution.

Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia.

An unsolved archaeological puzzle of the East Asian Upper Palaeolithic is why the southward expansion of an innovative lithic technology represented by microblades stalled at the Qinling-Huaihe Line. It has been suggested that the southward migration of foragers with microblades stopped there, which is consistent with ancient DNA studies showing that populations to the north and south of this line had differentiated genetically by 19 000 years ago. Many infectious pathogens are believed to have been associated with hominins since the Palaeolithic, and zoonotic pathogens in particular are prevalent at lower latitudes, which may have produced a disease barrier. We propose a mathematical model to argue that mortality due to infectious diseases may have arrested the wave-of-advance of the technologically advantaged foragers from the north.

Cultural niche construction with application to fertility control: A model for education and social transmission of contraceptive use.

The evolution of a cultural trait may be affected by niche construction, or changes in the selective environment of that trait due to the inheritance of other cultural traits that make up a cultural background. This study investigates the evolution of a cultural trait, such as the acceptance of the idea of contraception, that is both vertically and horizontally transmitted within a homogeneous social network. Individuals may conform to the norm, and adopters of the trait have fewer progeny than others. In addition, adoption of this trait is affected by a vertically transmitted aspect of the cultural background, such as the preference for high or low levels of education. Our model shows that such cultural niche construction can facilitate the spread of traits with low Darwinian fitness while providing an environment that counteracts conformity to norms. In addition, niche construction can facilitate the 'demographic transition' by making reduced fertility socially accepted.

Conformity and anti-conformity in a finite population.

Conformist and anti-conformist cultural transmission have been studied both empirically, in several species, and theoretically, with population genetic models. Building upon standard, infinite-population models (IPMs) of conformity, we introduce finite-population models (FPMs) and study them via simulation and a diffusion approximation. In previous IPMs of conformity, offspring observe the variants of n adult role models, where n is often three. Numerical simulations show that while the short-term behavior of the FPM with n=3 role models is well approximated by the IPM, stable polymorphic equilibria of the IPM become effective equilibria of the FPM at which the variation persists prior to fixation or loss, and which produce plateaus in curves for fixation probabilities and expected times to absorption. In the FPM with n=5 role models, the population may switch between two effective equilibria, which is not possible in the IPM, or may cycle between frequencies that are not effective equilibria, which is possible in the IPM. In all observed cases of 'equilibrium switching' and 'cycling' in the FPM, model parameters exceed O(1/N), required for the diffusion approximation, resulting in an over-estimation of the actual times to absorption. However, in those cases with n=5 role models that have one effective equilibrium and stable fixation states, even if conformity coefficients exceed O(1/N), the diffusion approximation matches closely the numerical simulations of the FPM. This suggests that the robustness of the diffusion approximation depends not only on the magnitudes of coefficients, but also on the qualitative behavior of the conformity model.

How Does Migration Affect HIV Sexual Risk Behaviors Among Involuntary Bachelors? The Mediating Roles of Neighborhoods and Social Networks.

The sex ratio imbalance in China since the 1980s has resulted in a large number of involuntary bachelors in rural China. Previous studies have found an association between migration and HIV sexual risk behaviors among involuntary bachelors, but how migration affects these bachelors' HIV sexual risk behaviors remain poorly understood. Using data from a cross-sectional survey in 2017 (a sample of 740 male respondents who had rural household registration, had never been married, and were aged 28-49 years), we investigated the relationship between migration and HIV sexual risk behaviors. Logistic regressions show that migration, neighborhood characteristics, and social networks were significantly associated with commercial sex and multiple sex partners, whereas only neighborhood characteristics and social networks were positively correlated with sexual partnership concurrency. Neighborhood characteristics and social networks mediated the relationships of migration with commercial sex and migration with multiple sex partners. Social networks mediated the association between neighborhood characteristics and concurrency. Multiple-step mediation analysis showed that the indirect effect of migration on commercial sex and multiple sexual partners through neighborhood characteristics and social networks was significant. Our findings suggest that further interventions should address neighborhood characteristics and social networks together.

Genetic nurturing, missing heritability, and causal analysis in genetic statistics.

Genetic nurturing, the effect of parents' genotypes on offspring phenotypes through parental phenotypic transmission, can be modeled in terms of gene-culture interactions. This paper first uses a simple one-locus, two-phenotype gene-culture cotransmission model to compute the effect of genetic nurturing in terms of regression of children's phenotypes on transmitted and nontransmitted alleles. With genetic nurturing, interpreting heritability and hence the meaning of "missing heritability" becomes problematic. Other factors, for example, population subdivision and assortative mating, generate similar signals to those of genetic nurturing, namely, correlation between parents' nontransmitted alleles and children's phenotypes. Corrections must be made for these to isolate the signal of genetic nurturing. Finally, a unified causal framework is constructed for genetic nurturing, population subdivision, and assortative mating. Causal and noncausal paths from transmitted and nontransmitted alleles to children's phenotypes are identified and investigated in the presence of genetic nurturing, population subdivision, and assortative mating. Using causal analysis, assumptions made in inferring direct and indirect effects are then clarified and evaluated in a broader causal context.

Cultural evolution of conformity and anticonformity.

Conformist bias occurs when the probability of adopting a more common cultural variant in a population exceeds its frequency, and anticonformist bias occurs when the reverse is true. Conformist and anticonformist bias have been widely documented in humans, and conformist bias has also been observed in many nonhuman animals. Boyd and Richerson used models of conformist and anticonformist bias to explain the evolution of large-scale cooperation, and subsequent research has extended these models. We revisit Boyd and Richerson's original analysis and show that, with conformity based on more than three role models, the evolutionary dynamics can be more complex than previously assumed. For example, we show the presence of stable cycles and chaos under strong anticonformity and the presence of new equilibria when both conformity and anticonformity act at different variant frequencies, with and without selection. We also investigate the case of population subdivision with migration and find that the common claim that conformity can maintain between-group differences is not always true. Therefore, the effect of conformity on the evolution of cooperation by group selection may be more complicated than previously stated. Finally, using Feldman and Liberman's modifier approach, we investigate the conditions under which a rare modifier of the extent of conformity or the number of role models can invade a population. Understanding the dynamics of conformist- and anticonformist-biased transmission may have implications for research on human and nonhuman animal behavior, the evolution of cooperation, and frequency-dependent transmission in general.

Drowning in shallow causality.

It has been known for decades that inference concerning genetic causes of human behavioral phenotypes cannot be legitimately made from correlations among relatives. We claim that these inferential difficulties cannot be overcome by assigning different names to causes inferred from within-family and population-level genome-wide association studies (GWASs). For educational attainment, for example, unraveling gene-environment interactions requires more than new names for causes.

Success-biased social learning in a one-consumer, two-resource model.

Previous analyses have predicted that social learning should not evolve in a predator-prey system. Here we examine whether success-biased social learning, by which social learners copy successful demonstrators, allows social learning by foragers to evolve. We construct a one-predator, two-prey system in which foragers must learn how to feed on depletable prey populations in an environment where foraging information can be difficult to obtain individually. We analyze two models in which social learning is success-biased: in the first, individual learning does not depend on the resource dynamics, and in the second model it depends on the relative frequency of the resource. Unlike previous results, we find that social learning does not cause predators to over-harvest one type of prey over the other. Furthermore, increasing the probability of social learning increases the probability of learning a successful foraging behavior, especially when individually learned information tends to be inaccurate. Whereas social learning does not evolve among individual learners in the first model, the assumption of resource-dependent learning in the second model allows a mutant with an increased probability of social learning to spread through the forager population.

Conformity and content-biased cultural transmission in the evolution of altruism.

The evolution of altruism has been extensively modeled under the assumption of genetic transmission, whereas the dynamics under cultural transmission are less well understood. Previous research has shown that cultural transmission can facilitate the evolution of altruism by increasing (1) the probability of adopting the altruistic phenotype, and (2) assortment between altruists. We incorporate vertical and oblique transmission, which can be conformist or anti-conformist, into models of parental care, sibling altruism, and altruism between individuals that meet assortatively. If oblique transmission is conformist, it becomes easier for altruism to invade a population of non-altruists as the probability of vertical transmission increases. If oblique transmission is anti-conformist, decreasing vertical transmission facilitates invasion by altruism in the assortative meeting model, whereas in other models, there is a trade-off: greater vertical transmission produces greater assortment among genetically related altruists, but lowers the probability of adopting altruism via anti-conformity. Compared to conditions for invasion under genetic transmission, e.g., Hamilton's rule, we show that invasion can be easier with sufficiently strong anti-conformity, and in some models, with sufficiently high assortment even if oblique transmission is conformist. We also explore invasion by an allele A that increases individuals' content bias for altruism, in the absence of other forms of cultural transmission. If costs and benefits combine additively, A invades under previously known conditions. If costs and benefits combine multiplicatively, invasion by A and by altruism become more difficult than in the corresponding additive models.

Adaptive social contact rates induce complex dynamics during epidemics.

Epidemics may pose a significant dilemma for governments and individuals. The personal or public health consequences of inaction may be catastrophic; but the economic consequences of drastic response may likewise be catastrophic. In the face of these trade-offs, governments and individuals must therefore strike a balance between the economic and personal health costs of reducing social contacts and the public health costs of neglecting to do so. As risk of infection increases, potentially infectious contact between people is deliberately reduced either individually or by decree. This must be balanced against the social and economic costs of having fewer people in contact, and therefore active in the labor force or enrolled in school. Although the importance of adaptive social contact on epidemic outcomes has become increasingly recognized, the most important properties of coupled human-natural epidemic systems are still not well understood. We develop a theoretical model for adaptive, optimal control of the effective social contact rate using traditional epidemic modeling tools and a utility function with delayed information. This utility function trades off the population-wide contact rate with the expected cost and risk of increasing infections. Our analytical and computational analysis of this simple discrete-time deterministic strategic model reveals the existence of an endemic equilibrium, oscillatory dynamics around this equilibrium under some parametric conditions, and complex dynamic regimes that shift under small parameter perturbations. These results support the supposition that infectious disease dynamics under adaptive behavior change may have an indifference point, may produce oscillatory dynamics without other forcing, and constitute complex adaptive systems with associated dynamics. Implications for any epidemic in which adaptive behavior influences infectious disease dynamics include an expectation of fluctuations, for a considerable time, around a quasi-equilibrium that balances public health and economic priorities, that shows multiple peaks and surges in some scenarios, and that implies a high degree of uncertainty in mathematical projections.

Sexual network and condom use among male migrants in the context of China's gender imbalance.

In the context of China's gender imbalance, this study addresses the characteristics of sexual networks and their association with condom use in a sample of 713 male migrants (aged 28-64) who have rural hukou (household registration) in China. Descriptive statistics, univariate analyses, and multilevel random intercept models were used to investigate the characteristics of sexual networks and their associations with condom use. We found that age, marital status, type of sex partners, support (the main help given to each sex partner by the participant), type of sexual intercourse, and stability of sexual relationships were associated with condom use. The sexual networks were mainly composed of sex partners of similar age (58.46%), unmarried people (50.53%), and regular partners (49.38%). Married male migrants were more likely to use condoms with casual partners; unmarried male migrants were less likely to use condoms in emotional and stable relationships. Variation in individual factors, sex partners, and sexual relationship characteristics contribute to participation in condomless sex by male migrants. HIV prevention strategies should target unmarried male migrants and their casual sex partners by increasing their awareness of the risk of HIV transmission and the availability of free condoms.

Evolution of resilience in protein interactomes across the tree of life.

Phenotype robustness to environmental fluctuations is a common biological phenomenon. Although most phenotypes involve multiple proteins that interact with each other, the basic principles of how such interactome networks respond to environmental unpredictability and change during evolution are largely unknown. Here we study interactomes of 1,840 species across the tree of life involving a total of 8,762,166 protein-protein interactions. Our study focuses on the resilience of interactomes to network failures and finds that interactomes become more resilient during evolution, meaning that interactomes become more robust to network failures over time. In bacteria, we find that a more resilient interactome is in turn associated with the greater ability of the organism to survive in a more complex, variable, and competitive environment. We find that at the protein family level proteins exhibit a coordinated rewiring of interactions over time and that a resilient interactome arises through gradual change of the network topology. Our findings have implications for understanding molecular network structure in the context of both evolution and environment.