Pervasive Adaptive Protein Evolution Apparent in Diversity Patterns around Amino Acid Substitutions in Drosophila simulans

In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence—in particular, conclusions about the rate and strength of beneficial substitutions—remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot), and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3%) that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis of adaptation

A computational framework for resolving the microbiome diversity conundrum

Abstract Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term ‘the microbial β- diversity conundrum’. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals’ microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host’s fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population

A possible evolutionary function of phenomenal conscious experience of pain

Evolutionary accounts of feelings, and in particular of negative affect and of pain, assume that creatures that feel and care about the outcomes of their behavior outperform those that do not in terms of their evolutionary fitness. Such accounts, however, can only work if feelings can be shown to contribute to fitness-influencing outcomes. Simply assuming that a learner that feels and cares about outcomes is more strongly motivated than one that doesn’t is not enough, if only because motivation can be tied directly to outcomes by incorporating an appropriate reward function, without leaving any apparent role to feelings (as it is done in state-of-the-art engineered systems based on reinforcement learning). Here, we propose a possible mechanism whereby pain contributes to fitness: an actor-critic functional architecture for reinforcement learning, in which pain reflects the costs imposed on actors in their bidding for control, so as to promote honest signaling and ultimately help the system optimize learning and future behavior

Learning a generative probabilistic grammar of experience: a process-level model of language acquisition

Abstract We introduce a set of biologically and computationally motivated design choices for modeling the learning of language, or of other types of sequential, hierarchically structured experience and behavior, and describe an implemented system that conforms to these choices and is capable of unsupervised learning from raw natural-language corpora. Given a stream of linguistic input, our model incrementally learns a grammar that captures its statistical patterns, which can then be used to parse or generate new data. The grammar constructed in this manner takes the form of a directed weighted graph, whose nodes are recursively (hierarchically) defined patterns over the elements of the input stream. We evaluated the model in seventeen experiments, grouped into five studies, which examined, respectively, (a) the generative ability of grammar learned from a corpus of natural language, (b) the characteristics of the learned representation, (c) sequence segmentation and chunking, (d) artificial grammar learning, and (e) certain types of structure dependence. The model's performance largely vindicates our design choices, suggesting that progress in modeling language acquisition can be made on a broad front-ranging from issues of generativity to the replication of human experimental findings-by bringing biological and computational considerations, as well as lessons from prior efforts, to bear on the modeling approach

Supplemental Figures from Cultural specialization as a double-edged sword: division into specialized guilds might promote cultural complexity at the cost of higher susceptibility to cultural loss

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From correlations to dynamics in the study of past human resilience to climate change: Code

There is a growing body of research on human resilience to extreme climatic episodes in the past. Most studies focus on comparing archaeological records prior to a perceived climatic episode to those after it, in order to investigate a causal relationship between the two. Although these comparisons are important, they are limited in their potential to facilitate a causal understanding of the factors that determine the human response to climate change. We assert that for such understanding, it is necessary to explicitly consider prior processes that could have made certain populations more resilient to extreme climatic episodes. This assertion calls for a new focus on the cultural and demographic dynamics in ancient populations, over the generations that preceded the climatic episode. In this article, we lay out several processes of cultural evolution that – together with the experienced climatic dynamics prior to extreme climatic episodes – may have determined populations’ abilities to cope with them. This endeavour allows us to outline alternative hypotheses regarding what determined the fate of different human groups. These, in turn, may help direct the collection and analysis of archaeological data and highlight modalities within it that may be helpful for inference of the processes that determined populations' resilience to extreme climatic episodes.An early version of the paper is available at bioRxiv: https://www.biorxiv.org/content/10.1101/2023.09.19.558513v1</p