Selection Regimes Research Articles

Experimental evolution under varying sex ratio and behavioral plasticity in response to perceived competitive environment independently affect calling effort in male crickets.

The operational sex ratio (OSR) is a key component influencing the magnitude of sexual selection driving the evolution of male sexual traits, but males often also retain the ability to plastically modulate trait expression depending on the current environment. Here we employed an experimental evolution approach to determine whether the OSR affects the evolution of male calling effort in decorated crickets, a costly sexual trait, and whether plasticity in calling effort is altered by the OSR under which males have evolved. Calling effort of males from 2 selection regimes maintained at different OSRs over 18-20 generations (male vs. female biased) was recorded at 2 different levels of perceived competition, in the absence of rivals or in the presence of an experimentally muted competitor. The effect of the OSR on the evolution of male calling effort was modest, and in the opposite direction predicted by theory. Instead, the immediate competitive environment strongly influenced male calling effort as males called more in the presence of a rival, revealing considerable plasticity in this trait. This increased calling effort came at a cost, however, as males confined with a muted rival experienced significantly higher mortality.

Universal and Selective Housing Regimes as Broad and Narrow Policy Fields. A Conceptual Proposal and its Application to Sweden

Universal and Selective Housing Regimes as Broad and Narrow Policy Fields. A Conceptual Proposal and its Application to Sweden

The effect of divergent and parallel selection on the genomic landscape of divergence.

While the role of selection in divergence along the speciation continuum is theoretically well understood, defining specific signatures of selection in the genomic landscape of divergence is empirically challenging. Modelling approaches can provide insight into the potential role of selection on the emergence of a heterogenous genomic landscape of divergence. Here, we extend and apply an individual-based approach that simulates the phenotypic and genotypic distributions of two populations under a variety of selection regimes, genotype-phenotype maps, modes of migration, and genotype-environment interactions. We show that genomic islands of high differentiation and genomic valleys of similarity may respectively form under divergent and parallel selection between populations. For both types of between-population selection, negative and positive frequency-dependent selection within populations generated genomic islands of higher magnitude and genomic valleys of similarity, respectively. Divergence rates decreased under strong dominance with divergent selection, as well as in models including genotype-environment interactions under parallel selection. For both divergent and parallel selection models, divergence rate was higher under an intermittent migration regime between populations, in contrast to a constant level of migration across generations, despite an equal number of total migrants. We highlight that interpreting a particular evolutionary history from an observed genomic pattern must be done cautiously, as similar patterns may be obtained from different combinations of evolutionary processes. Modelling approaches such as ours provide an opportunity to narrow the potential routes that generate the genomic patterns of specific evolutionary histories.

The relative size of the calcaneal tuber reflects heel strike plantigrady in African apes and humans.

The positional repertoire of the human-chimpanzee last common ancestor is critical for reconstructing the evolution of bipedalism. African apes and humans share a heel strike plantigrade foot posture associated with terrestriality. Previous research has established that modern humans have a relatively large and intrinsically robust calcaneal tuber equipped to withstand heel strike forces associated with bipedal walking and running. However, it is unclear whether African apes have a relatively larger calcaneal tuber than non-heel-striking primates, and how this trait might have evolved among anthropoids. Here, I test the hypothesis that heel-striking primates have a relatively larger calcaneal tuber than non-heel-striking primates. The comparative sample includes 331 individuals and 53 taxa representing hominoids, cercopithecoids, and platyrrhines. Evolutionary modeling was used to test for the effect of foot posture on the relative size of the calcaneal tuber in a phylogenetic framework that accounts for adaptation and inertia. Bayesian evolutionary modeling was used to identify selective regime shifts in the relative size of the calcaneal tuber among anthropoids. The best fitting evolutionary model was a Brownian motion model with regime-dependent trends characterized by relatively large calcaneal tubers among African apes and humans. Evolutionary modeling provided support for an evolutionary shift toward a larger calcaneal tuber at the base of the African ape and human clade. The results of this study support the view that African apes and humans share derived traits related to heel strike plantigrady, which implies that humans evolved from a semi-terrestrial quadrupedal ancestor.

Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians.

The genetic basis underlying adaptive physiological mechanisms has been extensively explored in mammals after colonizing the seas. However, independent lineages of aquatic mammals exhibit complex patterns of secondary colonization in freshwater environments. This change in habitat represents new osmotic challenges, and additional changes in key systems, such as the osmoregulatory system, are expected. Here, we studied the selective regime on coding and regulatory regions of 20 genes related to the osmoregulation system in strict aquatic mammals from independent evolutionary lineages, cetaceans, and sirenians, with representatives in marine and freshwater aquatic environments. We identified positive selection signals in genes encoding the protein vasopressin (AVP) in mammalian lineages with secondary colonization in the fluvial environment and in aquaporins for lineages inhabiting the marine and fluvial environments. A greater number of sites with positive selection signals were found for the dolphin species compared to the Amazonian manatee. Only the AQP5 and AVP genes showed selection signals in more than one independent lineage of these mammals. Furthermore, the vasopressin gene tree indicates greater similarity in river dolphin sequences despite the independence of their lineages based on the species tree. Patterns of distribution and enrichment of Transcription Factors in the promoter regions of target genes were analyzed and appear to be phylogenetically conserved among sister species. We found accelerated evolution signs in genes ACE, AQP1, AQP5, AQP7, AVP, NPP4, and NPR1 for the fluvial mammals. Together, these results allow a greater understanding of the molecular bases of the evolution of genes responsible for osmotic control in aquatic mammals.

Rapid evolution of phenotypic plasticity in patchy habitats

Phenotypic plasticity may evolve rapidly, enabling a population’s persistence in the face of sudden environmental change. Rapid evolution can occur when there is considerable genetic polymorphism at selected loci. We propose that balancing selection could be one of the mechanisms that sustain such polymorphism for plasticity. We use stochastic Monte Carlo simulations and deterministic analysis to investigate the evolution of a plasticity modifier locus in structured populations inhabiting favorable and adverse environments, i.e. patchy habitats. We survey a wide range of parameters including selective pressures on a target (structural) locus, plasticity effects, population sizes, and migration patterns between demes including periodic or continuous bidirectional and source-sink dynamics. We find that polymorphism in phenotypic plasticity can be maintained under a wide range of environmental scenarios in both favorable and adverse environments due to the balancing effect of population structure in patchy habitats. This effect offers a new plausible explanation for the rapid evolution of plasticity in nature: Phenotypic plasticity may rapidly evolve from genetic variation maintained by balancing selection if the population has experienced immigration from populations under different selection regimes.

Ergodicity of the Fisher infinitesimal model with quadratic selection

We study the convergence towards a unique equilibrium distribution of the solutions to a time-discrete model with non-overlapping generations arising in quantitative genetics. The model describes the dynamics of a phenotypic distribution with respect to a multi-dimensional trait, which is shaped by selection and Fisher’s infinitesimal model of sexual reproduction. We extend some previous works devoted to the time-continuous analogs, that followed a perturbative approach in the regime of weak selection, by exploiting the contractivity of the infinitesimal model operator in the Wasserstein metric. Here, we tackle the case of quadratic selection by a global approach. We establish uniqueness of the equilibrium distribution and exponential convergence of the renormalized profile. Our technique relies on an accurate control of the propagation of information across the large binary trees of ancestors (the pedigree chart), and reveals an ergodicity property, meaning that the shape of the initial datum is quickly forgotten across generations. We combine this information with appropriate estimates for the emergence of Gaussian tails and propagation of quadratic and exponential moments to derive quantitative convergence rates. Our result can be interpreted as a generalization of the Krein–Rutman theorem in a genuinely non-linear, and non-monotone setting.

Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion.

Bacteria commonly adhere to surfaces where they compete for both space and resources. Despite the importance of surface growth, it remains largely elusive how bacteria evolve on surfaces. We previously performed an evolution experiment where we evolved distinct Bacilli populations under a selective regime that favored colony spreading. In just a few weeks, colonies of Bacillus subtilis showed strongly advanced expansion rates, increasing their radius 2.5-fold relative to that of the ancestor. Here, we investigate what drives their rapid evolution by performing a uniquely detailed analysis of the evolutionary changes in colony development. We find mutations in diverse global regulators, RicT, RNAse Y, and LexA, with strikingly similar pleiotropic effects: They lower the rate of sporulation and simultaneously facilitate colony expansion by either reducing extracellular polysaccharide production or by promoting filamentous growth. Combining both high-throughput flow cytometry and gene expression profiling, we show that regulatory mutations lead to highly reproducible and parallel changes in global gene expression, affecting approximately 45% of all genes. This parallelism results from the coordinated manner by which regulators change activity both during colony development-in the transition from vegetative growth to dormancy-and over evolutionary time. This coordinated activity can however also break down, leading to evolutionary divergence. Altogether, we show how global regulators function as major pleiotropic hubs that drive rapid surface adaptation by mediating parallel changes in both colony composition and expansion, thereby massively reshaping gene expression.

Long-term effects on water chemistry and macroinvertebrates of selective thinning along small boreal forest streams

The maintenance of narrow strips of trees (forest buffers) along the shorelines of surface water bodies during logging is a common measure to protect freshwater habitats. The functionality of forest buffers may be improved by actively managing the streamside forest early in the rotation for their eventual function as buffers, including by increasing the proportion of broadleaf trees in spruce-dominated stands. In this study, long-term effects of different selective thinning regimes along two small forest streams were investigated in south-central Sweden. In a young coniferous forest, a c. 10 m-wide band along the streams was selectively thinned in 1998 to create a band with purely broadleaf trees along one of the streams and purely conifers along the other. Forest stand characteristics, water chemistry and benthic macroinvertebrates data were collected during 1996–2003 (before and after selective thinning). The streams were re-investigated 20–22 years after thinning, together with three streams representing operational forest management. The forest adjacent to all five streams was inventoried and litterfall, stream water chemistry, and benthic macroinvertebrates composition were monitored between spring and late autumn during 2018–2020. Twenty years after thinning, the thinned bands beside the streams were still dominated by either broadleaf trees or conifers, depending on the stream. Over the longer term, the differences in water chemistry between the streams with selective thinning were mainly related to lower pH, ANC, Tot-P and Tot-N concentrations in the stream bordered by mainly broadleaf trees. Analysis of benthic macroinvertebrates was based on environmental quality indices (ASPT and EPT), diversity and abundance metrics, and relative abundances of functional feeding groups. Streams with higher broadleaf litter inputs tended to score better on the ASPT and EPT indices than those with lower broadleaf inputs, as well as supporting higher relative abundances of one or more groups of invertebrate detritivores (leaf shredders, collector-gatherers and/or passive filter feeders). This suggests that management of the density of broadleaf trees beside these streams might support higher ecological status and will support a greater proportion of detritivores in benthic food webs.

Anthropogenic Change and the Process of Speciation.

Anthropogenic impacts on the environment alter speciation processes by affecting both geographical contexts and selection patterns on a worldwide scale. Here we review evidence of these effects. We find that human activities often generate spatial isolation between populations and thereby promote genetic divergence but also frequently cause sudden secondary contact and hybridization between diverging lineages. Human-caused environmental changes produce new ecological niches, altering selection in diverse ways that can drive diversification; but changes also often remove niches and cause extirpations. Human impacts that alter selection regimes are widespread and strong in magnitude, ranging from local changes in biotic and abiotic conditions to direct harvesting to global climate change. Altered selection, and evolutionary responses to it, impacts early-stage divergence of lineages, but does not necessarily lead toward speciation and persistence of separate species. Altogether, humans both promote and hinder speciation, although new species would form very slowly relative to anthropogenic hybridization, which can be nearly instantaneous. Speculating about the future of speciation, we highlight two key conclusions: (1) Humans will have a large influence on extinction and "despeciation" dynamics in the short term and on early-stage lineage divergence, and thus potentially speciation in the longer term, and (2) long-term monitoring combined with easily dated anthropogenic changes will improve our understanding of the processes of speciation. We can use this knowledge to preserve and restore ecosystems in ways that promote (re-)diversification, increasing future opportunities of speciation and enhancing biodiversity.

Copulatory mechanics of ghost spiders reveals a new self-bracing mechanism in entelegyne spiders.

Spiders evolved a distinctive sperm transfer system, with the male copulatory organs located on the tarsus of the pedipalps. In entelegyne spiders, these organs are usually very complex and consist of various sclerites that not only allow the transfer of the sperm themselves but also provide a mechanical interlock between the male and female genitalia. This interlocking can also involve elements that are not part of the copulatory organ such as the retrolateral tibial apophysis (RTA)-a characteristic of the most diverse group of spiders (RTA clade). The RTA is frequently used for primary locking i.e., the first mechanical engagement between male and female genitalia. Despite its functional importance, some diverse spider lineages have lost the RTA, but evolved an apophysis on the femur instead. It can be hypothesized that this femoral apophysis is a functional surrogate of the RTA during primary locking or possibly serves another function, such as self-bracing, which involves mechanical interaction between male genital structures themselves to stabilize the inserted pedipalp. We tested these hypotheses using ghost spiders of the genus Josa (Anyphaenidae). Our micro-computed tomography data of cryofixed mating pairs show that the primary locking occurs through elements of the copulatory organ itself and that the femoral apophysis does not contact the female genitalia, but hooks to a projection of the copulatory bulb, representing a newly documented self-bracing mechanism for entelegyne spiders. Additionally, we show that the femoral self-bracing apophysis is rather uniform within the genus Josa. This is in contrast to the male genital structures that interact with the female, indicating that the male genital structures of Josa are subject to different selective regimes.

Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes).

Some species are able to hybridize despite being exceptionally diverged. The causes of this variation in accumulation of reproductive isolation remain poorly understood, and domestication as an impetus or hindrance to reproductive isolation remains to be characterized. In this study, we investigated the role of divergence time, domestication, and mismatches in morphology, habitat, and clutch size among hybridizing species on reproductive isolation in the bird order Galliformes. We compiled and analyzed hybridization occurrences from literature and recorded measures of postzygotic reproductive isolation. We used a text-mining approach leveraging a historical aviculture magazine to quantify the degree of domestication across species. We obtained divergence time, morphology, habitat, and clutch size data from open sources. We found 123 species pairs (involving 77 species) with known offspring fertility (sterile, only males fertile, or both sexes fertile). We found that divergence time and clutch size were significant predictors of reproductive isolation (McFadden's Pseudo-R2 = 0.59), but not habitat or morphological mismatch. Perhaps most interesting, we found a significant relationship between domestication and reproductive compatibility after correcting for phylogeny, removing extreme values, and addressing potential biases (F1,74 = 5.43, R2 = 0.06, P-value = 0.02). We speculate that the genetic architecture and disruption in selective reproductive regimes associated with domestication may impact reproductive isolation, causing domesticated species to be more reproductively labile.

An argument for global realism about the units of selection

This paper defends global realism about the units of selection, the view that there is always (or nearly always) an objective fact of the matter concerning the level at which natural selection acts. The argument proceeds in two stages. First, it is argued that global conventionalist-pluralism is false. This is established by identifying plausible sufficient conditions for irreducible selection at a particular level, and showing that these conditions are sometimes satisfied in nature. Second, it is argued that local pluralism – the view that while realism is true of some selection regimes, pluralist conventionalism holds for others – should also be rejected. I show that the main arguments for local pluralism are consistent with global realism. I also suggest that local pluralism offers an unacceptably disunified view of the metaphysics of selection. It follows that we should accept global realism. But this leaves open the question of how to classify so called ‘multi-level selection type 1’ (MLS1) processes, such as Wilson’s classic trait-group model for the evolution of altruism: should they be interpreted as particle selection or collective selection? On the assumption of global realism, at most one of these is correct. I argue, against global realists such as Sober, that MLS1 processes should be understood as particle, not collective, selection, due to three features of MLS1: the reducibility of collective fitness, the absence of collective reproduction, and the dispensable role of collectives.

The evolution of multispecies populations: a multilevel selection perspective

Two or more independent species lineages can fuse through an evolutionary transition to form a single lineage, such as in the case of eukaryotic cells, lichens, and coral. The fusion of two or more independent lineages requires intermediary steps of increasing selective interdependence between these lineages. We argue a precursory selective regime of such a transition can be Multilevel Selection 1 (MLS1). We propose that intraspecies MLS1 can be extended to ecological multispecies arrangements. We develop a trait group selection (MLS1) model applicable to multispecies mutualistic interactions. We then explore conditions under which such a model could apply to mutualistic relationships between pollinators and plants. We propose that MLS1 could drive transitions towards higher interdependency between mutualists and stabilise obligate mutualisms in the face of invasion by cheater variants. This represents a radical extension of multilevel selection theory, applying it to the evolution of multispecies populations, and indicating new avenues for researching ecological community evolution.

Urbanisation-induced changes in the morphology of birds from a tropical city

ABSTRACT Urbanisation is accompanied by major environmental changes that impact the structure and functioning of communities and ecosystems, bringing new selective regimes for animal species and for eco-evolutionary dynamics. We aimed to evaluate whether urban intensification promotes ecomorphological changes in birds from a large city in Central Brazil. Analyses were performed on a set of 1314 individuals of 35 species, captured along a gradient of urban intensification. We found significant morphological changes associated with urban intensification by evaluating ten ecomorphological traits and body mass of the species assemblage. Beak length showed the most dramatic changes, and was significantly shorter as a function of urban intensification, mainly in individuals of insectivorous and omnivorous species. These results reinforce the notion that environmental changes caused by human activities in dense urban environments promote new selective pressures in resident bird species.

Alien plant fitness is limited by functional trade-offs rather than a long-term increase in competitive effects of native communities.

Alien plants experience novel abiotic conditions and interactions with native communities in the introduced area. Intra- and interspecific selection on functional traits in the new environment may lead to increased population growth with time since introduction (residence time). However, selection regimes might differ depending on the invaded habitat. Additionally, in high-competition habitats, a build-up of biotic resistance of native species due to accumulation of eco-evolutionary experience to aliens over time may limit invasion success. We tested if the effect of functional traits and the population dynamics of aliens depends on interspecific competition with native plant communities. We conducted a multi-species experiment with 40 annual Asteraceae that differ in residence time in Germany. We followed their population growth in monocultures and in interspecific competition with an experienced native community (varying co-existence times between focals and community). To more robustly test our findings, we used a naïve community that never co-existed with the focals. We found that high seed mass decreased population growth in monocultures but tended to increase population growth under high interspecific competition. We found no evidence for a build-up of competition-mediated biotic resistance by the experienced community over time. Instead, population growth of the focal species was similarly inhibited by the experienced and naïve community. By comparing the effect of experienced and naïve communities on population dynamics over 2 years across a large set of species with a high variation in functional traits and residence time, this study advances the understanding of the long-term dynamics of plant invasions. In our study system, population growth of alien species was not limited by an increase of competitive effects by native communities (one aspect of biotic resistance) over time. Instead, invasion success of alien plants may be limited because initial spread in low-competition habitats requires different traits than establishment in high-competition habitats.

Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae)

Gene tree discordance is a significant legacy of biological evolution. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss. Resolving the background of gene tree discordance is a critical way to uncover the process of species diversification. Camellia, the largest genus in Theaceae, has controversial taxonomy and systematics due in part to a complex evolutionary history. We used 60 transcriptomes of 55 species, which represented 15 sections of Camellia to investigate its phylogeny and the possible causes of gene tree discordance. We conducted gene tree discordance analysis based on 1,617 orthologous low-copy nuclear genes, primarily using coalescent species trees and polytomy tests to distinguish hard and soft conflict. A selective pressure analysis was also performed to assess the impact of selection on phylogenetic topology reconstruction. Our results detected different levels of gene tree discordance in the backbone of Camellia, and recovered rapid diversification as one of the possible causes of gene tree discordance. Furthermore, we confirmed that none of the currently proposed sections of Camellia was monophyletic. Comparisons among datasets partitioned under different selective pressure regimes showed that integrating all orthologous genes provided the best phylogenetic resolution of the species tree of Camellia. The findings of this study reveal rapid diversification as a major source of gene tree discordance in Camellia and will facilitate future investigation of reticulate relationships at the species level in this important plant genus.

Population differences in multimodal lizard communication are not well explained by habitat or history

AbstractAnimals evolve in complex selective regimes, where a suite of different factors can shape signal use. We might predict that more closely related species will exhibit more similar behavior than those more distantly related; however, sometimes signals are shaped more profoundly by the environment or other forces. Lizards in the genus Sceloporus communicate with conspecifics with multimodal signals that combine species‐typical push‐up and headbob displays and chemical signals in the form of femoral gland secretions. Here, we examine behavioral activity and signal use across three closely related populations of the Sceloporus undulatus species complex from diverse habitats across the United States, to test the relative roles of habitat and phylogeography in shaping communicative behavior. We filmed undisturbed levels of activity for free‐ranging males of S. consobrinus, syn. S. u. erythrocheilus, in Colorado, S. undulatus hyacinthinus in Indiana and S. u. undulatus in Georgia, and scored frequency and rates of behavior important for communication. We found that populations differed in their use of communicative signals in a way that deviates from expectations based solely on phylogeographic proximity or habitat, suggesting that plasticity or adaptation to conditions that vary among populations may be especially important. Specifically, canonical discriminant analyses found the largest differences in movement patterns. Sceloporus u. hyacinthinus was the most behaviorally different out of the three: males in this population had lower movement rates and particularly low levels of chemosensory behavior while male S. consobrinus and S. u. undulatus showed similar rates of chemosensory acts and headbob/push‐up displays. Phenotypic and environmental variation among closely related populations, in combination with phylogeographic knowledge can help us untangle the processes responsible for the origin and maintenance of organismal diversity in communicative behavior.

A persistent major mutation in canonical jasmonate signaling is embedded in an herbivory-elicited gene network

When insect herbivores attack plants, elicitors from oral secretions and regurgitants (OS) enter wounds during feeding, eliciting defense responses. These generally require plant jasmonate (JA) signaling, specifically, a jasmonoyl-L-isoleucine (JA-Ile) burst, for their activation and are well studied in the native tobacco Nicotiana attenuata. We used intraspecific diversity captured in a 26-parent MAGIC population planted in nature and an updated genome assembly to impute natural variation in the OS-elicited JA-Ile burst linked to a mutation in the JA-Ile biosynthetic gene NaJAR4. Experiments revealed that NaJAR4 variants were associated with higher fitness in the absence of herbivores but compromised foliar defenses, with two NaJAR homologues (4 and 6) complementing each other spatially and temporally. From decade-long seed collections of natural populations, we uncovered enzymatically inactive variants occurring at variable frequencies, consistent with a balancing selection regime maintaining variants. Integrative analyses of OS-induced transcriptomes and metabolomes of natural accessions revealed that NaJAR4 is embedded in a nonlinear complex gene coexpression network orchestrating responses to OS, which we tested by silencing four hub genes in two connected coexpressed networks and examining their OS-elicited metabolic responses. Lines silenced in two hub genes (NaGLR and NaFB67) co-occurring in the NaJAR4/6 module showed responses proportional to JA-Ile accumulations; two from an adjacent module (NaERF and NaFB61) had constitutively expressed defenses with high resistance. We infer that mutations with large fitness consequences can persist in natural populations due to compensatory responses from gene networks, which allow for diversification in conserved signaling pathways and are generally consistent with predictions of an omnigene model.

Improvement of selective laser melting regimes for the fabrication of Ti–6Al–4V porous structures for medical applications

This article describes approaches to the optimization of regimes of selective laser melting (SLM) used in the fabrication of porous materials from medical grade Ti–6Al–4V alloy with thin structural elements and a low level of defect porosity. Improved fusion of thin elements based on SLM regimes is achieved due to a significant decrease in the distance between laser passes (from 0.11 to 0.04–0.05 mm). Moreover, the balance between the laser energy density and building rate is compensated by changing the laser speed and laser power. The results of the study of defect porosity and hardness of samples fabricated according to experimental SLM regimes allowed three promising sets of parameters to be defined. One was selected for studying mechanical properties in comparison with the reference SLM regime. In the aims of this study, the samples were developed and fabricated using the structures of rhombic dodecahedron and Voronoi types with a porosity of 70–75 %. The decrease in defect porosity was established at ≈1.8 % to 0.6 %, depending on the SLM regime. This promotes a significant increase in strength properties of the material, including an increase in the yield strength of rhombic dodecahedron from 76 to 132 MPa and the Voronoi structure from 66 to 86 MPa. The low Young module (1–2 GPa) remains, corresponding to the rigidity level of spongy bone tissue.