Epigenetics and the environment: emerging patterns and implications

Complexity myths and the misappropriation of evolutionary theory

Recent papers by physicists, chemists, and geologists lay claim to the discovery of new principles of evolution that have somehow eluded over a century of work by evolutionary biologists, going so far as to elevate their ideas to the same stature as the fundamental laws of physics. These claims have been made in the apparent absence of any awareness of the theoretical framework of evolutionary biology that has existed for decades. The numerical indices being promoted suffer from numerous conceptual and quantitative problems, to the point of being devoid of meaning, with the authors even failing to recognize the distinction between mutation and selection. Moreover, the promulgators of these new laws base their arguments on the idea that natural selection is in relentless pursuit of increasing organismal complexity, despite the absence of any evidence in support of this and plenty pointing in the opposite direction. Evolutionary biology embraces interdisciplinary thinking, but there is no fundamental reason why the field of evolution should be subject to levels of unsubstantiated speculation that would be unacceptable in any other area of science.

A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide

The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales, multiple alleles are maintained in populations. In this study, we focus on the Drosophila AMP Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab-reared and wild-caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.

Dinucleotide preferences underlie apparent codon preference reversals in the Drosophila melanogaster lineage

We employ fine-scale population genetic analyses to reveal dynamics among interacting forces that act at synonymous sites and introns among closely related Drosophila species. Synonymous codon usage bias has proven to be well suited for population genetic inference. Under major codon preference (MCP), translationally superior "major" codons confer fitness benefits relative to their less efficiently and/or accurately decoded synonymous counterparts. Our codon family and lineage-specific analyses expand on previous findings in the Drosophila simulans lineage; patterns in naturally occurring polymorphism demonstrate fixation biases toward GC-ending codons that are consistent in direction, but heterogeneous in magnitude, among synonymous families. These forces are generally stronger than fixation biases in intron sequences. In contrast, population genetic analyses reveal unexpected evidence of codon preference reversals in the Drosophila melanogaster lineage. Codon family-specific polymorphism patterns support reduced efficacy of natural selection in most synonymous families but indicate reversals of favored states in the four codon families encoded by NAY. Accelerated synonymous fixations in favor of NAT and greater differences for both allele frequencies and fixation rates among X-linked, relative to autosomal, loci bolster support for fitness effect reversals. The specificity of preference reversals to codons whose cognate tRNAs undergo wobble position queuosine modification is intriguing. However, our analyses reveal prevalent dinucleotide preferences for ApT over ApC that act in opposition to GC-favoring forces in both coding and intron regions. We present evidence that changes in the relative efficacy of translational selection and dinucleotide preference underlie apparent codon preference reversals.

Reduced Parallel Gene Expression Evolution With Increasing Genetic Divergence-A Hallmark of Polygenic Adaptation

Parallel evolution, the repeated evolution of similar traits in independent lineages, is a topic of considerable interest in evolutionary biology. Although previous studies have focused on the parallelism of phenotypic traits and their underlying genetic basis, the extent of parallelism at the level of gene expression across different levels of genetic divergence is not yet fully understood. This study investigates the evolution of gene expression in replicate Drosophila populations exposed to the same novel environment at three divergence levels: within a population, between populations and between species. We show that adaptive gene expression changes are more heterogeneous with increasing genetic divergence between the compared groups. This finding suggests that the adaptive architecture-comprising factors such as allele frequencies and the effect size of contributing loci-becomes more distinct with increasing divergence. As a result, this leads to a reduction in parallel gene expression evolution. This result implies that redundancy is a crucial factor in both genetic selection responses and gene expression evolution. Hence, our findings are consistent with the omnigenic model, which posits that selection acts on higher-order phenotypes. This work contributes to our understanding of phenotypic evolution and the complex interplay between genomic and molecular responses.

Juvenile and total reproductive values for sexual reproduction under any genetic system

Reproductive value (RV) is the expected contribution of genes by an individual or class of individuals to the gene pool in the distant future, and it plays a crucial role in understanding adaptation in long-term evolution. Class RVs are linked to the genetic system and to life history: for diploid genetics, Grafen derived expressions for relative RVs of female and male juveniles and for the absolute RVs of all females and of all males. Subsequently, Gardner presented a derivation for relative RVs of juvenile females and males under haplodiploidy. Here, we generalize these results to any genetic system for biparental sexual reproduction, such that RV is explicitly linked to parameters of the genetic system and life history. The earlier results by Grafen and Gardner arise as special cases. Finally, we derive expressions for absolute juvenile and total RVs of both sexes under any genetic system.

Geometric Insights into evolutionary rescue dynamics in a two-deme model

Understanding evolutionary rescue mechanisms in fragmented populations is crucial in the context of rapidly changing environments. This study employs analytical derivations and simulations within a two-deme metapopulation model using Fisher's geometric model framework. We explore the impacts of abrupt environmental changes on two subpopulations that lead to distinct phenotypic optima. We determine the probability density of distances between these optima through analytical derivations. This enables us to calculate the intersection volume of the rescue domains of two subpopulations in the phenotypic space. This approach also allows us to assess the fixation probability of mutations that concurrently rescue both subpopulations and identify the domain of one-step rescue mutations. Our findings reveal that the likelihood of joint evolutionary rescue diminishes with increasing dimensionality of the phenotypic space, posing significant challenges for species with complex trait configurations. The study underscores the importance of genetic variation due to de novo mutations, local adaptation, and migration rates. These insights enhance our understanding of the factors that govern the adaptive potential of fragmented populations in response to severe environmental disturbances.

Recombinant inbred line panels inform the genetic architecture and interactions of adaptive traits in Drosophila melanogaster

The distribution of allelic effects on traits, along with their gene-by-gene and gene-by-environment interactions, contributes to the phenotypes available for selection and the trajectories of adaptive variants. Nonetheless, uncertainty persists regarding the effect sizes underlying adaptations and the importance of genetic interactions. Herein, we aimed to investigate the genetic architecture and the epistatic and environmental interactions involving loci that contribute to multiple adaptive traits using 2 new panels of Drosophila melanogaster recombinant inbred lines (RILs). To better fit our data, we re-implemented functions from R/qtl using additive genetic models. We found 14 quantitative trait loci (QTLs) underlying melanism, wing size, song pattern, and ethanol resistance. By combining our mapping results with population genetic statistics, we identified potential new genes related to these traits. None of the detected QTLs showed clear evidence of epistasis, and our power analysis indicated that we should have seen at least 1 significant interaction if sign epistasis or strong positive epistasis played a pervasive role in trait evolution. In contrast, we did find roles for gene-by-environment interactions involving pigmentation traits. Overall, our data suggest that the genetic architecture of adaptive traits often involves alleles of detectable effect, that strong epistasis does not always play a role in adaptation, and that environmental interactions can modulate the effect size of adaptive alleles.

Genetic monitoring in ex situ populations of the endangered primate Leontopithecus chrysopygus and integrative analyses with the wild founder population

Captive breeding programs have been used as a relevant strategy to maintain self-sustainable and demographically stable populations with the goal of safeguarding threatened species from their imminent risk of EXTINCTION. Thus, monitoring genetic diversity becomes essential to avoid the loss of genetic diversity and inbreeding depression throughout ex situ generations. Furthermore, such programs must carry out adequate metapopulation management to retain genetic diversity from the wild, minimizing eventual harmful effects associated with adaptation in captivity and sub-structuring. In this study, we analyzed ex situ populations of the endangered black lion tamarin (BLT), Leontopithecus chrysopygus, a primate endemic to the Brazilian Atlantic Forest. We monitored genetic diversity and structure in the three main ex situ groups for conservation purposes, before (2014) and after (2020) the transfer of five captive animals from Brazilian to European institutions. We also analyzed data from the whole studbook of the species to access life-history information about the ex situ populations. In addition, we performed an integrative ex situ/in situ analysis by including extant wild individuals from the same area of the founder population. Finally, we evaluated population viability based on genetic diversity trends predicted for the next 100 years. Our findings showed that the captive breeding program of BLT has been efficient in preventing the loss of heterozygosity despite significant reductions in allelic richness. This reduction is likely due to the loss of private and/or rare alleles resulting from the death of some individuals. The extant ex situ metapopulation and the wild population evidenced significant genetic differentiation and overall low levels of genetic diversity. The predictive analysis indicated that the loss of genetic diversity will be critical for the captive groups. However, the wild population demonstrated a greater capacity to retain genetic diversity over the next 100 years. These findings provide relevant information on the BLT's captive breeding program and its founder-related wild population, as well as insights for further integrated ex situ/in situ management actions.

Costs of reproduction in flowering plants

Costs of reproduction arise when investments into current reproduction reduce future reproductive fitness. Studies on reproductive costs use diverse approaches, including the analysis of gene expression, physiology, trade-offs between reproduction and growth/survival, and the impact of reproductive investments on population growth. These studies demonstrate that reproductive trade-offs have far-reaching effects on plants, affect their fitness, and are therefore important for shaping the evolution of life histories. However, not all studies have detected costs of reproduction, and c. 90% of these were conducted in natural populations, where controlling for variation in plant resource status is challenging. For dioecious plants, there is a common perception that fruit production should result in greater costs of reproduction for females than males, but divergent reproductive costs between the sexes are not supported by studies of reproductive trade-offs in dioecious plants. Other aspects of reproductive costs remain poorly understood, including ecological costs of reproduction, the fitness effects of reproductive trade-offs involving growth or physiological processes, and how the male sex role influences reproductive costs. Progress will be enabled by the use of measurements that allow for easier comparisons across studies and by more clearly distinguishing between the processes that contribute to current vs future reproductive fitness.

Strong genetic differentiation and low genetic diversity in a habitat-forming fucoid seaweed (Cystophora racemosa) across 850 km of its range

Temperate seaweed forests are among the most productive and widespread habitats in coastal waters. However, they are under threat from climate change and other anthropogenic stressors. To effectively conserve and manage these ecosystems under these rising pressures, an understanding of the genetic diversity and structure of habitat-forming seaweeds will be necessary. Australia's Great Southern Reef, a global hotspot of endemic diversity, is home to one of the world's most speciose habitat-forming seaweed genera, Cystophora (order Fucales). Despite severe declines in some species, genomic data on this genus remain limited. We used a reduced representation genomic approach (DaRTSeq) to investigate the genetic diversity and structure of Cystophora racemosa, a dominant canopy-forming species, across ~850 km of its range. Our sequencing captured 4741 high-quality single nucleotide polymorphisms (SNPs), and we distinguished neutral loci from those under natural selection (i.e., outlier loci). We identified strong population structure and high genetic differentiation for both neutral (mean FST = 0.404) and outlier loci (mean FST = 0.901). Across populations, genetic diversity was low (neutral: mean HE = 0.046; outlier: HE = 0.042), with high inferred inbreeding (neutral loci mean FIS = 0.531) and no evidence of isolation-by-distance. Several SNPs (n = 70) were observed to be putatively adaptive, with most (97%) correlated with annual maximum sea surface temperature (SST, °C), indicating local adaptation to this key ocean variable. Our results show that C. racemosa populations have low genetic diversity and high differentiation, both of which may increase the vulnerability of this important foundation species to global change.

Demographics of genetic admixture and expansion

We explore the dynamics of genetic admixture and expansion, as well as language assimilation, through mathematical-demographic modeling. Our primary goal is to address the population-genetics 'paradox' wherein autosomes and allosomes present markedly different, if not contradictory, pictures of past migrations. We demonstrate that this paradox may find a purely demographic explanation, as single-sex and two-sex reproduction models exhibit markedly distinct dynamics. We illustrate that the three processes-allosomal expansion, autosomal admixture, and language assimilation-occur at significantly different modes, potentially explaining the varied outcomes of these processes upon the completion of ethnogenetic transitions. Our research offers valuable insights into the intricate interplay between demography, genetics, and social organization, providing implications for historical scenarios and enhancing our understanding of the long-term consequences of migration and social cohesion.

Mate copying in Drosophila simulans

To find a suitable mate, many animals across taxa use social information. Mate copying is a form of social learning in which individuals use information regarding potential mates by observing and copying the mate choices of other individuals. While mate copying in Drosophila melanogaster has been extensively documented in the laboratory and its potential for cultural evolution has been demonstrated, little is known about mate copying in other Drosophila species. Here, we report the first evidence that Drosophila simulans females also copy the mate choice of their conspecifics. We used the well-established protocol developed for D. melanogaster: a naive, unmated female first observes a conspecific's mate choice between one artificially coloured green and one artificially coloured pink male and is afterwards allowed to choose between two males of the same phenotypes herself. Just as with D. melanogaster, D. simulans females were more likely to choose the same type of male as in the demonstration. This finding underscores the capacity of D. simulans females to engage in rapid social observational learning, a process that may play a significant role in the evolution of reproductive isolation.

Seeking consensus on the domestication concept

The domestication of plants and animals permitted the development of cities and social hierarchies, as well as fostering cultural changes that ultimately led humanity into the modern world. Despite the importance of this set of related evolutionary phenomena, scholars have not reached a consensus on what the earliest steps in the domestication process looked like, how long the seminal portions of the process took to unfold, or whether humans played a conscious role in parts or all of it. Likewise, many scholars find it difficult to disentangle the cultural processes of cultivation from the biological processes of domestication. Over the past decade, the prevailing views among scholars have begun to shift towards unconscious and protracted models of early domestication; however, the nomenclature used to discuss these changes has been stagnant. Discussions of early domestication remain bound up in prevailing definitions and preconceived ideas of what the process looked like. In this paper, we seek to break down definitions of domestication and to construct a definition that serves equal utility regardless of the views that researchers hold about the process.This article is part of the theme issue 'Unravelling domestication: multi-disciplinary perspectives on human and non-human relationships in the past, present and future'.

How animals discriminate between stimulus magnitudes: a meta-analysis

To maximize their fitness, animals must often discriminate between stimuli differing in magnitude (such as size, intensity, or number). Weber's Law of proportional processing states that stimuli are compared based on the proportional difference in magnitude, rather than the absolute difference. Weber's Law implies that when stimulus magnitudes are higher, it becomes harder to discriminate small differences between stimuli, leading to more discrimination errors. More generally, we can refer to a correlation between stimulus magnitude and discrimination error frequency as a magnitude effect, with Weber's law being a special case of the magnitude effect. However, the strength and prevalence of the magnitude effect across species have never previously been examined. Here, we conducted a meta-analysis to quantify the strength of the magnitude effect across studies, finding that, on average, perception followed Weber's Law. However, the strength of the magnitude effect varied widely, and this variation was not explained by any biological or methodological differences between studies that we examined. Our findings suggest that although its strength varies considerably, the magnitude effect is commonplace, and this sensory bias is therefore likely to affect signal evolution across diverse systems. Better discrimination at lower magnitudes might result in signalers evolving lower magnitude signals when being discriminated is beneficial, and higher magnitude signals when being discriminated is costly. Furthermore, selection for higher magnitude signals (eg sexual ornaments) may be weakened, because receivers are less able to discriminate as signal magnitudes increase.

A Comparison of Image Statistics of Peacock Jumping Spider Colour Patterns and Natural Scenes

The form of arbitrary sexual signals may be driven by the need to be detectable against the background or, alternatively, by selection for efficient processing by the nervous system. This latter alternative is a prediction of the sensory drive hypothesis extended to include efficient coding as a driver of the form of sexual signals. This hypothesis posits that animal visual systems are adapted to process the visual statistics of natural scenes, and that easily processed stimuli induce a sensation of pleasure in the viewer. In support of this, natural scene statistics have been found to be preferred not only by humans, but by the peacock spider Maratus spicatus. Here we test if male peacock spiders of the highly sexually dimorphic Maratus genus generally (a) evolve colour patterns with image statistics that contrast with the natural background or (b) exploit a potential processing bias by evolving colour patterns with visual statistics similar to those of natural scenes. We analyse and compare multispectral images of male and female spiders of 21 Maratus species and of natural scenes similar to the spiders' habitat. We find that the image statistics of male patterns diverge from those of natural scenes, whereas the statistics of female patterns do not. Our results support the idea that colour patterns evolve contrasting image statistics to increase conspicuousness and matching image statistics to be camouflaged. Any processing bias for natural scene image statistics in Maratus thus appears to play little role in the evolution of their sexual signals.

Natural averaging may complement known biological constraints in sexual reproduction's advantages over asexual in conserving species quantitative traits

Commonly recognized effects of sexual reproduction include increased diversity, improved adaptability, enabling of DNA repair, constrained accumulation of deleterious mutations, and species genotype homogenization. Additionally, there are studies that show how sexual reproduction slows down certain evolutionary responses, offering advantages in population cumulative growth and stability over time and other metrics. Here, we contribute an observation of another distinct effect of sexual reproduction, focusing on retaining a species's key traits. In an initial mathematical analysis and simulation, we show that in an environment where copying is prone to error, quantitative polygenic traits that are shared within a parents' generation are transmitted to future generations under sexual reproduction with less deviation than under asexual reproduction. Furthermore, the model shows that this retention of common traits (abbr. RoCT), is driven by the very nature of mixing of parental traits, and occurs even before adding effects like trait-specific reproductive advantages, DNA repair, or the raising of reproductive barriers. Since survival of ecosystems depends on the ability of individuals to replace the networked interactions and interdependencies associated with failing, dying, or absent members of the same species, RoCT helps sustain species and ecosystems.

Sweeps in space: leveraging geographic data to identify beneficial alleles in Anopheles gambiae

As organisms adapt to environmental changes, natural selection modifies the frequency of non-neutral alleles. For beneficial mutations, the outcome of this process may be a selective sweep, in which an allele rapidly increases in frequency and perhaps reaches fixation within a population. Selective sweeps have well-studied effects on patterns of local genetic variation in panmictic populations, but much less is known about the dynamics of sweeps in continuous space. In particular, because limited movement across a landscape leads to unique patterns of population structure, spatial dynamics may influence the trajectory of selected mutations. Here, we use forward-in-time, individual-based simulations in continuous space to study the impact of space on beneficial mutations as they sweep through a population. In particular, we show that selection changes the joint distribution of allele frequency and geographic range occupied by a focal allele and demonstrate that this signal can be used to identify selective sweeps. We then leverage this signal to identify in-progress selective sweeps within the malaria vector Anopheles gambiae , a species under strong selection pressure from vector control measures. By considering space, we identify multiple previously undescribed variants with potential phenotypic consequences, including mutations impacting known IR-associated genes and altering protein structure and properties. Our results demonstrate a novel signal for detecting selection in spatial population genetic data that may have implications for genomic surveillance and understanding geographic patterns of genetic variation.

Ex-situ avian sex skews: determinants and implications for conservation

With over half of all avian species in decline globally, zoo-based recovery programs are increasingly relied upon to save species from extinction. The success of such programs not only rests with political will, but also in our understanding of species' breeding biology and how individuals and populations respond to changes in their environment. Sex skews, that is, an imbalance in the optimal number of males to females, is an underlying mechanism of population decline in some threatened species. Ex-situ (i.e., zoo-based) management practices will need to become more efficient to support the growing number of conservation reliant species and manage sex skews to amend, repair and restore population stability both in- and ex-situ. In this article, we analysed data from over 182,000 birds in global ex-situ collections. We interpreted sex ratio variation by observing the proportion of males within and between orders, International Union for Conservation of Nature (IUCN) threat status and housing inside and outside of a species' natural range. Overall, our results showed that male-biased sex skews are more prevalent ex-situ than they are in the wild and although they vary greatly at the institutional level, were closer to parity at a global level. The variation amongst threat status and housing outside of range were less significant. These findings have implications for the conservation management of threatened birds and the potential of ex-situ populations to function with maximum effect in an integrated management system.

The divergence of mean phenotypes under persistent Gaussian selection

Although multigenic traits are often assumed to be under some form of stabilizing selection, numerous aspects of the population-genetic environment can cause mean phenotypes to deviate from presumed optima, often in ways that effectively transform the fitness landscape to one of directional selection. Focusing on an asexual population, we consider the ways in which such deviations scale with the relative power of selection and genetic drift, the number of linked genomic sites, the magnitude of mutation bias, and the location of optima with respect to possible genotypic space. Even in the absence of mutation bias, mutation will influence evolved mean phenotypes unless the optimum happens to coincide exactly with the mean expected under neutrality. In the case of directional mutation bias and large numbers of selected sites, effective population sizes (Ne) can be dramatically reduced by selective interference effects, leading to further mismatches between phenotypic means and optima. Situations in which the optimum is outside or near the limits of possible genotypic space (e.g. a half-Gaussian fitness function) can lead to particularly pronounced gradients of phenotypic means with respect to Ne, but such gradients can also occur when optima are well within the bounds of attainable phenotypes. These results help clarify the degree to which mean phenotypes can vary among populations experiencing identical mutation and selection pressures but differing in Ne, and yield insight into how the expected scaling relationships depend on the underlying features of the genetic system.

Substitution load revisited: a high proportion of deaths can be selective

Haldane's Dilemma refers to the concern that the need for many "selective deaths" to complete a substitution (i.e. selective sweep) creates a speed limit to adaptation. However, discussion of this concern has been marked by confusion, especially with respect to the term "substitution load". Here, we distinguish different historical lines of reasoning, and identify one, focused on finite reproductive excess and the proportion of deaths that are "selective" (i.e. causally contribute to adaptive allele frequency changes), that has not yet been fully addressed. We develop this into a more general theoretical model that can apply to populations with any life history, even those for which a generation or even an individual are not well defined. The actual speed of adaptive evolution is coupled to the proportion of deaths that are selective. The degree to which reproductive excess enables a high proportion of selective deaths depends on the details of when selection takes place relative to density regulation, and there is therefore no general expression for a speed limit. To make these concepts concrete, we estimate both reproductive excess, and the proportion of deaths that are selective, from a dataset measuring survival of 517 different genotypes of Arabidopsis thaliana grown in 8 different environmental conditions. In this dataset, a much higher proportion of deaths contribute to adaptation, in all environmental conditions, than the 10% cap that was anticipated as substantially restricting adaptation during historical discussions of speed limits.

Why humans evolved blue eyes

A surprising number of humans are equipped with a subpar eye model-featuring pale, colorful irides that are nowhere as good as the original dark ones at guarding the retina from sunlight and do, in fact, raise one's risk of eye disease. Here I apply evolutionary theory to understand why. I propose that the allele for human blue eyes, which arose just once, managed to spread from one individual to millions at an astonishing speed because it is a greenbeard. "Greenbeards"-imaginary genes, or groups of genes, that produce both a green beard and a behavior that favors other bearers of a green beard-have been deemed exceedingly unlikely to show up in the real world. And yet, as individuals who prefer blue eyes are more inclined to mate with blue-eyed partners and invest in blue-eyed offspring, any blue-eye preference (whether random or arising from the bias for colorful stimuli shared by all recognition systems) becomes rapidly linked to the blue-eye trait. Thus, blue eyes gain an edge by working like a peacock's colorful tail and a nestling's colorful mouth: twice self-reinforcing, "double runaway" evolution via sexual and parental selection. The blue-eye ornament gene, by binding to a behavior that favors other bearers of the blue-eye ornament gene, is ultimately recognizing and helping copies of itself in both kin and strangers-and greatly prospering, just like theory predicts.

Pleiotropy increases parallel selection signatures during adaptation from standing genetic variation

The phenomenon of parallel evolution, whereby similar genomic and phenotypic changes occur across replicated pairs of populations or species, is widely studied. Nevertheless, the determining factors of parallel evolution remain poorly understood. Theoretical studies have proposed that pleiotropy, the influence of a single gene on multiple traits, is an important factor. In order to gain a deeper insight into the role of pleiotropy for parallel evolution from standing genetic variation, we characterized the interplay between parallelism, polymorphism, and pleiotropy. The present study examined the parallel gene expression evolution in 10 replicated populations of Drosophila simulans, which were adapted from standing variation to the same new temperature regime. The data demonstrate that the parallel evolution of gene expression from standing genetic variation is positively correlated with the strength of pleiotropic effects. The ancestral variation in gene expression is, however, negatively correlated with parallelism. Given that pleiotropy is also negatively correlated with gene expression variation, we conducted a causal analysis to distinguish cause and correlation and evaluate the role of pleiotropy. The causal analysis indicated that both direct (causative) and indirect (correlational) effects of pleiotropy contribute to parallel evolution. The indirect effect is mediated by historic selective constraint in response to pleiotropy. This results in parallel selection responses due to the reduced standing variation of pleiotropic genes. The direct effect of pleiotropy is likely to reflect a genetic correlation among adaptive traits, which in turn gives rise to synergistic effects and higher parallelism.

Trade-offs in modeling context dependency in complex trait genetics

Genetic effects on complex traits may depend on context, such as age, sex, environmental exposures, or social settings. However, it remains often unclear if the extent of context dependency, or gene-by-environment interaction (GxE), merits more involved models than the additive model typically used to analyze data from genome-wide association studies (GWAS). Here, we suggest considering the utility of GxE models in GWAS as a trade-off between bias and variance parameters. In particular, we derive a decision rule for choosing between competing models for the estimation of allelic effects. The rule weighs the increased estimation noise when context is considered against the potential bias when context dependency is ignored. In the empirical example of GxSex in human physiology, the increased noise of context-specific estimation often outweighs the bias reduction, rendering GxE models less useful when variants are considered independently. However, for complex traits, we argue that the joint consideration of context dependency across many variants mitigates both noise and bias. As a result, polygenic GxE models can improve both estimation and trait prediction. Finally, we exemplify (using GxDiet effects on longevity in fruit flies) how analyses based on independently ascertained 'top hits' alone can be misleading, and that considering polygenic patterns of GxE can improve interpretation.

Low-dimensional genotype-fitness mapping across divergent environments suggests a limiting functions model of fitness

A central goal in evolutionary biology is to be able to predict the effect of a genetic mutation on fitness. This is a major challenge because fitness depends both on phenotypic changes due to the mutation, and how these phenotypes map onto fitness in a particular environment. Genotype, phenotype, and environment spaces are all extremely complex, rendering bottom-up prediction unlikely. Here we show, using a large collection of adaptive yeast mutants, that fitness across a set of lab environments can be well-captured by top-down, low-dimensional linear models that generate abstract genotype-phenotype-fitness maps. We find that these maps are low-dimensional not only in the environment where the adaptive mutants evolved, but also in more divergent environments. We further find that the genotype-phenotype-fitness spaces implied by these maps overlap only partially across environments. We argue that these patterns are consistent with a "limiting functions" model of fitness, whereby only a small number of limiting functions can be modified to affect fitness in any given environment. The pleiotropic side-effects on non-limiting functions are effectively hidden from natural selection locally, but can be revealed globally. These results combine to emphasize the importance of environmental context in genotype-phenotype-fitness mapping, and have implications for the predictability and trajectory of evolution in complex environments.

Reconciling ecology and evolutionary game theory or "When not to think cooperation"

Evolutionary game theory (EGT)-overwhelmingly employed today for the study of cooperation in various systems, from microbes to cancer and from insect to human societies-started with the seminal 1973 paper by Maynard Smith and Price showing that limited animal conflict can be selected at the individual level. Owing to the explanatory potential of this paper and enabled by the powerful machinery of the soon-to-be-developed replicator dynamics, EGT took off at an accelerated pace and began to shape expectations across systems and scales. But, even as EGT has expanded its reach, and even as its mathematical foundations expanded with the development of adaptive dynamics and inclusion of stochastic processes, the replicator equation remains, half a century later, its most widely used equation. Owing to its early development and its staying power, the replicator dynamics has helped set both the baseline expectations and the terminology of the field. However, much like the original 1973 paper, replicator dynamics rests on the assumption that individual differences in reproduction are determined only by the payoff from the game (i.e., in isolation, all individuals, regardless of their strategy, have identical intrinsic growth rates). Here, we argue that this assumption limits the scope of replicator dynamics to such an extent as to warrant not just a more deliberative application process, but also a reconsideration of the broad predictions and terminology that it has generated. Simultaneously, we reestablish a dialog with ecology that can be mutually fruitful, e.g., by providing an explanation for how diverse ecological communities can assemble evolutionarily.

Common variation in meiosis genes shapes human recombination phenotypes and aneuploidy risk

The leading cause of human pregnancy loss is aneuploidy, often tracing to errors in chromosome segregation during female meiosis. While abnormal crossover recombination is known to confer risk for aneuploidy, limited data have hindered understanding of the potential shared genetic basis of these key molecular phenotypes. To address this gap, we performed retrospective analysis of preimplantation genetic testing data from 139,416 in vitro fertilized embryos from 22,850 sets of biological parents. By tracing transmission of haplotypes, we identified 3,656,198 crossovers, as well as 92,485 aneuploid chromosomes. Counts of crossovers were lower in aneuploid versus euploid embryos, consistent with their role in chromosome pairing and segregation. Our analyses further revealed that a common haplotype spanning the meiotic cohesin SMC1B is significantly associated with both crossover count and maternal meiotic aneuploidy, with evidence supporting a non-coding cis-regulatory mechanism. Transcriptome- and phenome-wide association tests also implicated variation in the synaptonemal complex component C14orf39 and crossover-regulating ubiquitin ligases CCNB1IP1 and RNF212 in meiotic aneuploidy risk. More broadly, recombination and aneuploidy possess a partially shared genetic basis that also overlaps with reproductive aging traits. Our findings highlight the dual role of recombination in generating genetic diversity, while ensuring meiotic fidelity.

The Hallmarks of Cancer as Eco-Evolutionary Processes

SIGNIFICANCE

Viewing the hallmarks as a sequence of adaptations captures the "why" behind the "how" of the molecular changes driving cancer. This eco-evolutionary view distils the complexity of cancer progression into logical steps, providing a framework for understanding all existing and emerging hallmarks of cancer and developing therapeutic interventions.

Post-senescence reproductive rebound in Daphnia associated with reversal of age-related transcriptional changes

A long-lived species of zooplankton microcrustaceans, Daphnia magna, sometimes exhibits late-life rebound of reproduction, briefly reversing reproductive senescence. Such events are often interpreted as terminal investments in anticipation of imminent mortality. We demonstrate that such post-senescence reproductive events (PSREs) neither cause nor anticipate increased mortality. We analyze an RNAseq experiment comparing young, old reproductively senescent, and old PSRE Daphnia females. We first show that overall age-related transcriptional changes are dominated by the increased transcription of guanidine monophosphate synthases and guanylate cyclases, as well as two groups of presumed transposon-encoded proteins, and by a drop in transcription of protein synthesis-related genes. We then focus on gene families and functional groups in which full or partial reversal of age-related transcriptional changes occur. This analysis reveals a reversal, in the PSRE individuals, of age-related up-regulation of apolipoproteins D, lysosomal lipases, and peptidases as well as several proteins related to mitochondrial and muscle functions. While it is not certain which of these changes enable reproductive rejuvenation, and which are by-products of processes that lead to it, we present some evidence that post-senescence reproductive events are associated with the reversal of age-related protein and lipid aggregates removal and apoptosis.

Mutations in the albinism gene oca2 alter vision-dependent prey capture behavior in the Mexican tetra

Understanding the phenotypic consequences of naturally occurring genetic changes, as well as their impact on fitness, is fundamental to understanding how organisms adapt to an environment. This is critical when genetic variants have pleiotropic effects, as determining how each phenotype impacted by a gene contributes to fitness is essential to understand how and why traits have evolved. Here, we characterized the effects of mutations in the oca2 gene, which underlie albinism and reductions of sleep in the blind Mexican cavefish Astyanax mexicanus, on larval prey capture. We found that when surface A. mexicanus with engineered mutations in oca2 are hunting, they use cave-like, wide-angle strikes to capture prey. However, unlike cavefish or surface fish in the dark, which utilize the lateral line when hunting, oca2 mutant (oca2Δ2bp/Δ2bp) surface fish can use vision when striking at prey from wide angles. We found that when raised under lighted conditions, pigmented surface fish outcompete albino oca2Δ2bp/Δ2bp surface fish when hunting in lighted conditions. In contrast, when surface fish are reared in darkness, oca2Δ2bp/Δ2bp surface fish outcompete their wild type siblings in the dark. This raises the possibility that albinism is detrimental to larval feeding in a surface-like lighted environment, but may confer an advantage to fish in cave-like, dark environments. Together, these results demonstrate that oca2 plays a role in larval feeding behavior in A. mexicanus, and expand our understanding of the pleiotropic phenotypic consequences of oca2 in cavefish evolution.

Sexual differences in defensive strategies: investigating chemical defences and visual signals in a wasp moth Amata nigriceps

Aposematic animals use conspicuous warning signals to advertise their chemical defences to predators. Selection by predators can favour conspicuousness and large pattern elements, which enhance predator avoidance learning. In aposematic species, conspicuousness often varies among individuals. This variation can be explained if conspicuousness reflects the levels of chemical defences, if signal production or defence acquisition is costly, and if physiological trade-offs and opposing selection pressures impose constraints. To understand the link between conspicuousness and chemical defences, we need to quantify the variability in warning signals and identify the chemical compounds involved. Here, we examined the warning signal variability and chemical composition of the red-necked wasp moth (Amata nigriceps). We photographed the wings and abdomens of male and female moths and analysed their chemical composition using ultra-performance liquid chromatography. Females displayed more orange on their wings, a trait known to enhance protection against predators. While we ruled out the presence of pyrrolizidine alkaloids in adult moths, an untargeted metabolomics approach suggests that they sequester other compounds, such as steroidal alkaloids and alkylbenzenes, which may serve as chemical defences. Females had higher concentrations of these compounds than males but ecotoxicology assays with Daphnia showed that male and female moths exhibited similar levels of toxicity.

Secondary Sympatry as a Sorting Process

A much remarked-upon pattern in nature is elevated trait disparity in sympatric relative to allopatric populations or species. Early explanations focused on secondary contact between allopatrically speciating taxa and emphasised adaptive divergence driven by costly interactions in sympatry (i.e., 'character displacement'). Here we consider a related hypothesis, 'species sorting', which describes a bias in the outcome of secondary contact wherein lineages are unlikely to establish sympatry unless and until they evolve sufficient trait differences in allopatry. Sorting-like processes are prevalent in community assembly theory but are more seldom discussed in the context of speciation and secondary sympatry. We first define ecological and reproductive species sorting as analogous to ecological and reproductive character displacement, and we synthesise 'differential fusion' and the 'Templeton effect' within this framework. Through the logic of coexistence and assembly theories, we distinguish the types of allopatry-derived trait differences that will likely promote sympatry from those that likely will not, and we discuss biogeographic consequences of the latter. We then highlight new empirical approaches to distinguish sorting from displacement and survey the mixed evidence to-date. We finally suggest key priorities for future research into the hypothesized role of species sorting as a generator of major biodiversity patterns.

Polymorphic transposable elements contribute to variation in recombination landscapes

Meiotic recombination is a prominent force shaping genome evolution, and understanding why recombination rates vary within and between species has remained a central, though challenging, question. Variation in recombination is widely thought to influence the efficacy of selection in purging transposable elements (TEs), prevalent selfish genetic elements, leading to widely observed negative correlations between TE abundance and recombination rates across taxa. However, accumulating evidence suggests that TEs could instead be the cause rather than the consequence of this relationship. To test this prediction, we formally investigated the influence of polymorphic, putatively active TEs on recombination rates. We developed and benchmarked an approach that uses PacBio long-read sequencing to efficiently, accurately, and cost-effectively identify crossovers (COs), a key recombination product, among large numbers of pooled recombinant individuals. By applying this approach to Drosophila strains with distinct TE insertion profiles, we found that polymorphic TEs, especially RNA-based TEs and TEs with local enrichment of repressive marks, reduce the occurrence of COs. Such an effect leads to different CO frequencies between homologous sequences with and without TEs, contributing to varying CO maps between individuals. The suppressive effect of TEs on CO is further supported by two orthogonal approaches-analyzing the distributions of COs in panels of recombinant inbred lines in relation to TE polymorphism and applying marker-assisted estimations of CO frequencies to isogenic strains with and without transgenically inserted TEs. Our investigations reveal how the constantly changing TE landscape can actively modify recombination, shaping genome evolution within and between species.

Human deleterious mutation rate slows adaptation and implies high fitness variance

Each new human has an expectedU d = 2 - 10 new deleterious mutations. Using a novel approach to capture complex linkage disequilibria from highU d using genome-wide simulations, we confirm that fitness decline due to the fixation of many slightly deleterious mutations can be compensated by rarer beneficial mutations of larger effect. The evolution of increased genome size and complexity have previously been attributed to a similarly asymmetric pattern of fixations, but we propose that the cause might be highU d rather than the small population size posited as causal by drift barrier theory. High within-population variance in relative fitness is an inevitable consequence of highU d ∼ 2 - 10 combined with inferred human deleterious effect sizes; two individuals will typically differ in fitness by 15-40%. The need to compensate for the deluge of deleterious mutations slows net adaptation (i.e. to the external environment) by ~13%-55%. The rate of beneficial fixations is more sensitive to changes in the mutation rate than the rate of deleterious fixations is. As a surprising consequence of this, an increase (e.g. 10%) in overall mutation rate leads to faster adaptation; this puts to rest dysgenic fears about increasing mutation rates due to rising paternal age.

CTCF-anchored chromatin loop dynamics during human meiosis

BACKGROUND

During meiosis, the mammalian genome is organised within chromatin loops, which facilitate synapsis, crossing over and chromosome segregation, setting the stage for recombination events and the generation of genetic diversity. Chromatin looping is thought to play a major role in the establishment of cross overs during prophase I of meiosis, in diploid early primary spermatocytes. However, chromatin conformation dynamics during human meiosis are difficult to study experimentally, due to the transience of each cell division and the difficulty of obtaining stage-resolved cell populations. Here, we employed a machine learning framework trained on single cell ATAC-seq and RNA-seq data to predict CTCF-anchored looping during spermatogenesis, including cell types at different stages of meiosis.

RESULTS

We find dramatic changes in genome-wide looping patterns throughout meiosis: compared to pre-and-post meiotic germline cell types, loops in meiotic early primary spermatocytes are more abundant, more variable between individual cells, and more evenly spread throughout the genome. In preparation for the first meiotic division, loops also include longer stretches of DNA, encompassing more than half of the total genome. These loop structures then influence the rate of recombination initiation and resolution as cross overs. In contrast, in later mature sperm stages, we find evidence of genome compaction, with loops being confined to the telomeric ends of the chromosomes.

CONCLUSION

Overall, we find that chromatin loops do not orchestrate the gene expression dynamics seen during spermatogenesis, but loops do play important roles in recombination, influencing the positions of DNA breakage and cross over events.

Allele ages provide limited information about the strength of negative selection

For many problems in population genetics, it is useful to characterize the distribution of fitness effects (DFE) of de novo mutations among a certain class of sites. A DFE is typically estimated by fitting an observed site frequency spectrum (SFS) to an expected SFS given a hypothesized distribution of selection coefficients and demographic history. The development of tools to infer gene trees from haplotype alignments, along with ancient DNA resources, provides us with additional information about the frequency trajectories of segregating mutations. Here, we ask how useful this additional information is for learning about the DFE, using the joint distribution on allele frequency and age to summarize information about the trajectory. To this end, we introduce an accurate and efficient numerical method for computing the density on the age of a segregating variant found at a given sample frequency, given the strength of selection and an arbitrarily complex population size history. We then use this framework to show that the unconditional age distribution of negatively selected alleles is very closely approximated by reweighting the neutral age distribution in terms of the negatively selected SFS, suggesting that allele ages provide little information about the DFE beyond that already contained in the present day frequency. To confirm this prediction, we extended the standard Poisson random field method to incorporate the joint distribution of frequency and age in estimating selection coefficients, and test its performance using simulations. We find that when the full SFS is observed and the true allele ages are known, including ages in the estimation provides only small increases in the accuracy of estimated selection coefficients. However, if only sites with frequencies above a certain threshold are observed, then the true ages can provide substantial information about the selection coefficients, especially when the selection coefficient is large. When ages are estimated from haplotype data using state-of-the-art tools, uncertainty about the age abrogates most of the additional information in the fully observed SFS case, while the neutral prior assumed in these tools when estimating ages induces a downward bias in the case of the thresholded SFS.

Achromatic Markings as Male Quality Indicators in a Crepuscular Bird

Secondary sexual traits, such as specific body parts or colouration, play an important role in mating interactions. It has been proposed that they function as quality indicators driven by sexual selection. In birds, much attention has been paid to the study of feather pigmentation, especially in diurnal passerines. However, recent research demonstrates that structural achromatic colours are likely to be of similar importance for communication, especially for species inhabiting poorly lit environments and that are active at night. Using 15 years of capture-recapture data from a long-term study on adult European Nightjars (Caprimulgus europaeus), we investigated the role of males' white tail and wing markings as secondary sexual traits. We show that the inter-individual variation in marking size exceeds that of the other morphometric variables, suggesting that wing and tail markings could be subject to sexual selection. Older males, individuals with a higher body condition index, and long-term territory holders had larger markings, while these effects were particularly pronounced in terminal tail feather markings. The importance of markings for signalling is likely related to their observed use in social displays. Pronounced site differences in tail marking sizes and annual variation suggest environmental factors acting on the ornaments that remain to be further examined.

Towards a universal understanding of sex ratio in termites

Termites are eusocial cockroaches whose altruist caste is constituted of males and females. While sex ratio theory predicts a balanced investment between sexes in diploid organisms, extreme deviations are observed in termites, both in altruists and alate reproductives. Here, we expand the theoretical framework for the prediction of alate population sex ratio by considering partitioned sexual and parthenogenetic reproduction, and female/male relatedness asymmetries arising from their sex-linked chromosome complexes. We consider the viewpoint of either the primary reproductives or the altruists while accounting for the effect of caste developmental systems on the sex ratio. We compile all data on alate sex ratios available to date (97 species), and found the direction of the sex ratio bias to be consistent within major taxonomic groups. We test our models, along with models of intrasexual competition, on an exploratory set of 13 species with available demographic data. Our analyses indicate that the factors explaining bias in alate sex ratio are variable and include sexual dimorphism, sex-asymmetric inbreeding, imperfect use of sexual and parthenogenetic reproduction, sex-linked genomic inheritance, intrasexual competition and caste developmental constraints. Our study provides an integrative framework for sex ratio and conflicts in termites, and closes in on a universal theory.

Selective advantage of redirected helping in a viscous population

When a brood fails, the failed parent can help a neighbor rear its offspring. This behavior is known as redirected helping and occurs in various species. The advantage of redirected helping may seem obvious, provided the individual whose brood fails helps a related neighbor: The helper at least gains indirect fitness by redirecting its parental effort. However, complications arise when considering a viscous population, where individuals remain on or close to their natal site. In such a population, individuals compete with relatives, which dilutes the advantage of helping and may counteract it altogether. This raises a question: when can we expect redirected helping to evolve in a viscous population? We address this question with inclusive fitness models. We find that redirected helping can always be favored in a viscous population, provided the cost is sufficiently low. We also identify life-history features-like survival, dispersal, and brood-failure rate-that promote redirected helping. The effect of these life-history features, in general, depends on which component of fitness (survival or fecundity) benefits from help and how brood failure varies among demes. Unlike previous authors, we find that helping can be more strongly promoted when it provides survival rather than fecundity benefits.

Oral Sex May Serve as Low Mate Value Compensation Among Men: Evidence from a Pre-registered Study

From the evolutionary perspective, maintaining a committed relationship is beneficial for reproductive success but involves risks such as losing a partner or infidelity. People typically prefer partners with similar mate value (MV) to avoid rejection. However, when a mate value discrepancy (MVD) arises, the partner with lower MV might employ mate retention strategies to maintain the relationship. This study investigated whether men with lower MV compared to their female partners used cunnilingus more often and whether this effect was mediated by their motivation to satisfy the partner. Additionally, it tested the moderating role of men's perceived vulnerability to disease (PVD), predicting that men less concerned about disease would show a stronger link between MVD and cunnilingus frequency, given the health risks associated with oral sex. Data from 540 men in committed heterosexual relationships confirmed that a higher MVD-where the man's MV was lower than his partner's-led to more frequent cunnilingus, and this relationship was mediated by a greater motivation to sexually satisfy the partner. However, the moderating role of PVD was not confirmed. We explore the evolutionary perspective that men may perform oral sex on their partners as a mate retention strategy. This behavior potentially serves as a benefit-provisioning mechanism, compensating for discrepancies in mate value.

Territorial-sneaker games with non-uniform interactions and female mate choice

Male territorial-sneaker polymorphisms are common in nature. To understand how these polymorphisms evolve, we developed a game theoretical model analogous to the classical Hawk-Dove model, but with two important differences. First, we allowed non-uniform interaction rates of strategies to account for the possibility that some interactions between male strategies are disproportionately more frequent than others. Second, we allowed females to exhibit a preference for one type of male and thereby choose mates adaptively. Selection dynamics were modeled using coupled replicator equations. The model confirms that there is a broad range of conditions under which a male polymorphism will arise. We applied the model to understand the genetic polymorphism in adult male Mnais damselflies (Zygoptera). Here, orange-winged adult males defend oviposition sites and mate with females when they arrive, while clear-winged 'sneaker' males are typically non-territorial and opportunistically mate with females. Intriguingly, in allopatry, the males of Mnais costalis and M. pruinosa both exhibit the same orange-clear winged polymorphism but where the species co-occur, males of M. costalis evolve orange wings while males of M. pruinosa tend to evolve clear wings. To understand this phenomenon and evaluate the importance of female choice in mediating it, we extended our game-theoretical model to two interacting species. While both competitive and reproductive interference can explain the male monomorphisms in sympatry, reproductive interference explains the phenomenon under a wider set of conditions. When females of the rarer species change their male preferences to facilitate species discrimination, it can generate runaway selection on male phenotypes.

Females with Attractive Mates Gain Environmental Benefits That Increase Lifetime and Multigenerational Fitness

AbstractResolving the degree to which environmental (direct) versus genetic (indirect) benefits shape female mate choice is a long-standing challenge, particularly for socially monogamous species where male environmental and genetic contributions are difficult to disentangle. This study combines long-term population monitoring with quantitative genetic analyses in a socially monogamous but sexually promiscuous Australian songbird to demonstrate that female mating preferences are driven by nongenetic environmental benefits that increase the fitness of both the female and her offspring. Male Red-backed Fairywrens (Malurus melanocephalus) flexibly breed in either ornamented or unornamented plumage, and females consistently prefer ornamented males. Females paired with ornamented males bred earlier and allocated more to current reproduction yet experienced higher survival and lifetime fitness. Furthermore, these females produced more grand-offspring because their early-born sons were more likely to be ornamented and to breed successfully than the later-born sons of females with unornamented partners. Quantitative genetic models showed lifetime fitness was best explained by parental environment rather than genetic effects. Mating preferences in this system are maintained by a combination of primary environmental benefits that increase the lifetime fitness of choosy females and secondary environmental benefits that increase the multigenerational fitness of those females through enhanced offspring quality and performance.

Long-term studies provide unique insights into evolution

From experimental evolution in the laboratory to sustained measurements of natural selection in the wild, long-term studies have revolutionized our understanding of evolution. By directly investigating evolutionary dynamics in real time, these approaches have provided unparallelled insights into the complex interplay between evolutionary process and pattern. These approaches can reveal oscillations, stochastic fluctuations and systematic trends that unfold over extended periods, expose critical time lags between environmental shifts and population responses, and illuminate how subtle effects may accumulate into significant evolutionary patterns. Long-term studies can also reveal otherwise cryptic trends that unfold over extended periods, and offer the potential for serendipity: observing rare events that spur new evolutionary hypotheses and research directions. Despite the challenges of conducting long-term research, exacerbated by modern funding landscapes favouring short-term projects, the contributions of long-term studies to evolutionary biology are indispensable. This is particularly true in our rapidly changing, human-dominated world, where such studies offer a crucial window into how environmental changes and altered species interactions shape evolutionary trajectories. In this Review article, we showcase the groundbreaking discoveries of long-term evolutionary studies, underscoring their crucial role in advancing our understanding of the complex nature of evolution across multiple systems and timescales.

Synergistic effects of elevated temperature with pesticides on reproduction, development and survival of dung beetles

In times of global change, high temperatures can increase the negative effects of pesticides and other stressors. The goal of this study was to evaluate, under controlled laboratory conditions, the effect of a moderate increase in temperature in combination with ivermectin (an antiparasitic medication used in cattle that is excreted in dung), an herbicide, and parasitic pressure, on the reproductive success, development time and adult survival of dung beetles Euoniticellus intermedius. Whereas high temperature increased the number and proportion of emerged offspring, it had synergistic negative effects in combination with the ivermectin, herbicide and parasite treatments. Moreover, high temperature in combination with ivermectin and with parasitism caused a synergistic increase of adult offspring mortality and, in combination with the herbicide, it synergistically accelerated development. These results indicate that high temperatures can enhance the negative effects of other stressors and act synergistically with them, harming dung beetles, a group with high ecological and economic value in natural and productive ecosystems. Although adult sex ratio was not affected by experimental treatments, contrasting responses were found between males and females, supporting the idea that both sexes use different physiological mechanisms to cope with the same environmental challenges. The effects that combined stressors have on insects deepen our understanding of why we are losing beneficial species and their functions in times of drastic environmental changes.

Tradeoffs in Modeling Context Dependency in Complex Trait Genetics

Genetic effects on complex traits may depend on context, such as age, sex, environmental exposures or social settings. However, it is often unclear if the extent of context dependency, or Gene-by-Environment interaction (GxE), merits more involved models than the additive model typically used to analyze data from genome-wide association studies (GWAS). Here, we suggest considering the utility of GxE models in GWAS as a tradeoff between bias and variance parameters. In particular, We derive a decision rule for choosing between competing models for the estimation of allelic effects. The rule weighs the increased estimation noise when context is considered against the potential bias when context dependency is ignored. In the empirical example of GxSex in human physiology, the increased noise of context-specific estimation often outweighs the bias reduction, rendering GxE models less useful when variants are considered independently. However, we argue that for complex traits, the joint consideration of context dependency across many variants mitigates both noise and bias. As a result, polygenic GxE models can improve both estimation and trait prediction. Finally, we exemplify (using GxDiet effects on longevity in fruit flies) how analyses based on independently ascertained "top hits" alone can be misleading, and that considering polygenic patterns of GxE can improve interpretation.

A long tail of truth and beauty: A zigzag pattern of feather formation determines the symmetry, complexity, and beauty of the peacock's tail

Background

Darwin assumed that the peacock's long train was maladaptive and was the indirect effect of selection by female mate choice based on the train's beauty. While a relationship between the feathers' elaborate features and mating success has been shown in some studies, what features of the train females are attracted to remains controversial.

Methods

We used museum specimens to examine the anatomical plan underlying feather development responsible for the train's symmetry. We developed a model based on an alternate arrangement of primordial feather buds during development and locations of concentric circles of eyespot distribution using the pattern on the train as a template.

Results

We observed a zigzag pattern of feather follicles that determined both the number and the arrangement of eyespots on the train. Our model explains the bilateral symmetry of train feathers, the hexagonal arrangement of eyespots on the train, and the concentric color rings of the eyespots. While the zigzag pattern explains the symmetry, complexity, and (structural) beauty of the peacock's train, it also precludes variation in eyespot number except by annual addition of new feathers as a function of age.

Conclusions

We propose a multimodal model of mate choice which holds that (1) eyespot number and feather length are developmentally correlated and females see them not as separate traits but as one complex trait combining both, (2) females may not always choose males with the largest number of eyespots, as old males may lack vigor, and (3) females may choose mates on the basis of train size, vigor, and beauty. The maladaptation of the long tail is a byproduct of the adaptation of the tall train. Who would have thought that zigzag arrangement, the densest form of spherical packing, when applied to the living world would produce such profound effects on phenotypic diversity.

Recombinant inbred line panels inform the genetic architecture and interactions of adaptive traits in Drosophila melanogaster

The distribution of allelic effects on traits, along with their gene-by-gene and gene-by-environment interactions, contributes to the phenotypes available for selection and the trajectories of adaptive variants. Nonetheless, uncertainty persists regarding the effect sizes underlying adaptations and the importance of genetic interactions. Herein, we aimed to investigate the genetic architecture and the epistatic and environmental interactions involving loci that contribute to multiple adaptive traits using two new panels of Drosophila melanogaster recombinant inbred lines (RILs). To better fit our data, we re-implemented functions from R/qtl (Broman et al. 2003) using additive genetic models. We found 14 quantitative trait loci (QTL) underlying melanism, wing size, song pattern, and ethanol resistance. By combining our mapping results with population genetic statistics, we identified potential new genes related to these traits. None of the detected QTLs showed clear evidence of epistasis, and our power analysis indicated that we should have seen at least one significant interaction if sign epistasis or strong positive epistasis played a pervasive role in trait evolution. In contrast, we did find roles for gene-by-environment interactions involving pigmentation traits. Overall, our data suggest that the genetic architecture of adaptive traits often involves alleles of detectable effect, that strong epistasis does not always play a role in adaptation, and that environmental interactions can modulate the effect size of adaptive alleles.

Understanding mechanisms of avian flight by integrating observations with tests of competing hypotheses

A long-standing problem in the study of avian flight is determining how biomechanics and physiology are associated with behaviour, ecological interactions and evolution. In some avian clades, flight mechanisms are strongly linked to ecology. Hummingbirds, for example, exhibit traits that support both hovering flight and nectar foraging. In most avian clades, however, features such as wing shape are highly variable among taxa without clear relationships to biomechanics, energetics or ecology. In this Commentary, we discuss challenges to understanding associations between phenotype and performance in avian flight. A potential pitfall in studies that attempt to link trait specialization with performance is that the most relevant traits and environments are not being considered. Additionally, a large number of studies of the mechanisms of avian flight are highly phenomenological. Although observations are essential for hypothesis development, we argue that for our discipline to make progress, we will need much more integration of the observational phase with developing crucial tests of competing hypotheses. Direct comparison of alternative hypotheses can be accomplished through analytical frameworks as well as through experimentation.

ADAM-multi: software to simulate complex breeding programs for animals and plants with different ploidy levels and generalized genotypic effect models to account for multiple alleles

Stochastic simulation software, ADAM, has been developed for the purpose of breeding optimization in animals and plants, and for validation of statistical models used in genetic evaluations. Just like other common simulation programs, ADAM assumed the bi-allelic state of quantitative trait locus (QTL). While the bi-allelic state of marker loci is due to the common choice of genotyping technology of single nucleotide polymorphism (SNP) chip, the assumption may not hold for the linked QTL. In the version of ADAM-Multi, we employ a novel simulation model capable of simulating additive, dominance, and epistatic genotypic effects for species with different levels of ploidy, providing with a more realistic assumption of multiple allelism for QTL variants. When assuming bi-allelic QTL, our proposed model becomes identical to the model assumption in common simulation programs, and in genetic textbooks. Along with the description of the updated simulation model in ADAM-Multi, this paper shows two small-scale studies that investigate the effects of multi-allelic versus bi-allelic assumptions in simulation and the use of different prediction models in a single-population breeding program for potatoes. We found that genomic models using dense bi-allelic markers could effectively predicted breeding values of individuals in a well-structure population despite the presence of multi-allelic QTL. Additionally, the small-scale study indicated that including non-additive genetic effects in the prediction model for selection did not lead to an improvement in the rate of genetic gains of the breeding program.

Linking molecular mechanisms to their evolutionary consequences: a primer

A major obstacle to predictive understanding of evolution stems from the complexity of biological systems, which prevents detailed characterization of key evolutionary properties. Here, we highlight some of the major sources of complexity that arise when relating molecular mechanisms to their evolutionary consequences and ask whether accounting for every mechanistic detail is important to accurately predict evolutionary outcomes. To do this, we developed a mechanistic model of a bacterial promoter regulated by 2 proteins, allowing us to connect any promoter genotype to 6 phenotypes that capture the dynamics of gene expression following an environmental switch. Accounting for the mechanisms that govern how this system works enabled us to provide an in-depth picture of how regulated bacterial promoters might evolve. More importantly, we used the model to explore which factors that contribute to the complexity of this system are essential for understanding its evolution, and which can be simplified without information loss. We found that several key evolutionary properties-the distribution of phenotypic and fitness effects of mutations, the evolutionary trajectories during selection for regulation-can be accurately captured without accounting for all, or even most, parameters of the system. Our findings point to the need for a mechanistic approach to studying evolution, as it enables tackling biological complexity and in doing so improves the ability to predict evolutionary outcomes.

Counting chicks before they hatch: extending the observed lifetime to better characterize evolutionary processes in the wild

Evolutionary theorists have emphasized for over half a century that population sampling must be conducted at the intergenerational boundary if the distinct effects of selection and inheritance are to be reliably quantified, with individuals recognized at the point of conception and lifetime reproductive success (LRS) defined as the total number of zygotic offspring produced per zygote. However, in those species whose ecology is otherwise well-suited to individual-level population studies, the prenatal part of an individual's life is often difficult to observe. While uncertainty has long surrounded the fertilization status of unhatched bird eggs-hatching failure can arise through fertilization failure or prenatal mortality-2 recent studies show fertilization failure to be extremely rare within 2 of the most popular avian study species. As such, unhatched eggs are highly reliable indicators of prenatal mortality. Although the generality of these results remains unclear, they demonstrate that prenatality can be incorporated into the observable lifespan of free-living animals. This allows zygotic LRS to be retrospectively quantified using historical nest observations and facilitates a more complete characterization of the evolutionary dynamics of wild populations.