The niche construction perspective: a critical appraisal

High Resolution Class I HLA -A, -B, and -C Diversity in Eastern and Southern African Populations

Africa remains significantly underrepresented in high-resolution Human Leukocyte Antigen (HLA) data, despite being one of the most genetically diverse regions in the world. This critical gap in genetic information poses a substantial barrier to HLA-based research on the continent. In this study, Class I HLA data from Eastern and Southern African populations were analysed to assess genetic diversity across the region. We examined allele and haplotype frequency distributions, deviations from Hardy-Weinberg Equilibrium (HWE), linkage disequilibrium (LD), and conducted neutrality tests of homozygosity across various populations. Additionally, the African HLA data were compared to those of Caucasian and African American populations using the Jaccard index and multidimensional scaling (MDS) methods. The study revealed that South African populations exhibited 50.4% more genetic diversity within the Class I HLA region compared to other African populations. Zambia showed an estimated 36.5% genetic diversity, with Kenya, Rwanda and Uganda showing 35.7%, 34.2%, and 31.1%, respectively. Furthermore, an analysis of in-country diversity among different tribes indicated an average Class I HLA diversity of 25.7% in Kenya, 17% in Rwanda, 2.8% in South Africa, 13.6% in Uganda, and 6.5% in Zambia. The study also highlighted the genetic distinctness of Caucasian and African American populations compared to African populations. Notably, the differential frequencies of disease-promoting and disease-preventing HLA alleles across these populations emphasize the urgent need to generate high-quality HLA data for all regions of Africa and its major ethnic groups. Such efforts will be crucial in enhancing healthcare outcomes across the continent.

Plasticity, symbionts and niche construction interact in shaping dung beetle development and evolution

Developmental plasticity is an important product of evolutionary processes, allowing organisms to maintain high fitness in the face of environmental perturbations. Once evolved, plasticity also has the potential to influence subsequent evolutionary outcomes, for example, by shaping phenotypic variation visible to selection and facilitating the emergence of novel trait variants. Furthermore, organisms may not just respond to environmental conditions through plasticity but may also actively modify the abiotic and (sym)biotic environments to which they themselves respond, causing plasticity to interact in complex ways with niche construction. Here, we explore developmental mechanisms and evolutionary consequences of plasticity in horned dung beetles. First, we discuss how post-invasion evolution of plasticity in an introduced Onthophagus species facilitated rapid range expansion and concurrent local adaptation of life history and morphology to novel climatic conditions. Second, we discuss how, in addition to plastically responding to variation in nutritional conditions, dung beetles engage in behaviors that modify the environment that they themselves respond to during later development. We document that these environment-modifying behaviors mask heritable variation for life history traits within populations, thereby shielding genetic variants from selection. Such cryptic genetic variation may be released and become selectable when these behaviors are compromised. Together, this work documents the complex interactions between plasticity, symbionts and niche construction, and highlights the usefulness of an integrative Eco-Evo-Devo framework to study the varied mechanisms and consequences of plasticity in development and evolution.

Niche construction and the environmental term of the price equation: How natural selection changes when organisms alter their environments

Organisms construct their own environments and phenotypes through the adaptive processes of habitat choice, habitat construction, and phenotypic plasticity. We examine how these processes affect the dynamics of mean fitness change through the environmental change term of the Price Equation. This tends to be ignored in evolutionary theory, owing to the emphasis on the first term describing the effect of natural selection on mean fitness (the additive genetic variance for fitness of Fisher's Fundamental Theorem). Using population genetic models and the Price Equation, we show how adaptive niche constructing traits favorably alter the distribution of environments that organisms encounter and thereby increase population mean fitness. Because niche-constructing traits increase the frequency of higher-fitness environments, selection favors their evolution. Furthermore, their alteration of the actual or experienced environmental distribution creates selective feedback between niche constructing traits and other traits, especially those with genotype-by-environment interaction for fitness. By altering the distribution of experienced environments, niche constructing traits can increase the additive genetic variance for such traits. This effect accelerates the process of overall adaption to the niche-constructed environmental distribution and can contribute to the rapid refinement of alternative phenotypic adaptations to different environments. Our findings suggest that evolutionary biologists revisit and reevaluate the environmental term of the Price Equation: owing to adaptive niche construction, it contributes directly to positive change in mean fitness; its magnitude can be comparable to that of natural selection; and, when there is fitness G × E, it increases the additive genetic variance for fitness, the much-celebrated first term.

Earthen mounds (heuweltjies) of South Africa and their termite occupants: applicability of concepts of the extended phenotype, ecosystem engineering and niche construction

Heuweltjies are earthen mounds found throughout the Succulent Karoo of South Africa and are inhabited by the termite Microhodotermes viator. Many have assumed that heuweltjies are constructed by the occupying termites. Consequently, heuweltjies have been used as an example of several important concepts in ecology and evolution: the extended phenotype, ecosystem engineering and niche construction. However, recent findings demonstrate that M. viator does not directly construct heuweltjies. Rather, termite colonies enrich the soil around their nests with plant nutrients, which promotes development of widely separated patches of denser vegetation. Eventual formation of heuweltjies represents a response of the physical environment to the windbreak effect of the denser vegetation patches (localized reduction of wind velocity and resultant deposition and accumulation of airborne sediment). Other structures constructed by the termites are justifiably regarded as extended phenotypes. Identification and investigation of a complex cascade of processes are required to more precisely assess the manner in which this termite species functions as an ecosystem engineer or niche constructor, thereby significantly influencing the availability of resources within local ecosystems. Environmental alterations that are either directly or indirectly generated by social animals that construct large, communal nests represent ecological processes that contribute significantly to local biodiversity. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.

Host manipulation by parasites through the lens of Niche Construction Theory

The effect of parasites on host behaviour is generally considered an example of the extended phenotype, implying that parasite genes alter host behaviour to benefit the parasite. While the extended phenotype is a valid perspective supported by empirical examples, this approach was proposed from an evolutionary perspective and it does not fully explain all processes that occur at ecological time scales. For instance, the roles of the ontogenetic environment, memory and learning in forming the host phenotype are not explicitly mentioned. Furthermore, the cumulative effect of diverse populations or communities of parasites on host phenotype cannot be attributed to a particular genotype, much less to a particular gene. Building on the idea that the behaviour of a host is the result of a complex process, which certainly goes beyond a specific parasite gene, we use Niche Construction Theory to describe certain systems that are not generally the main focus in the extended phenotype (EP) model. We introduce three niche construction models with corresponding empirical examples that capture the diversity and complexity of host-parasite interactions, providing predictions that simpler models cannot generate. We hope that this novel perspective will inspire further research on the topic, given the impact of ecological factors on both short-, and long-term effects of parasitism.

Evolutionary game theory of continuous traits from a causal perspective

Modern evolutionary game theory typically deals with the evolution of continuous, quantitative traits under weak selection, allowing the incorporation of rich biological detail and complicated nonlinear interactions. While these models are commonly used to find candidates for evolutionary endpoints and to approximate evolutionary trajectories, a less appreciated property is their potential to expose and clarify the causal structure of evolutionary processes. The mathematical step of differentiation breaks a nonlinear model into additive components which are more intuitive to interpret, and when combined with a proper causal hypothesis, partial derivatives in such models have a causal meaning. Such an approach has been used in the causal analysis of game-theoretical models in an informal manner. Here we formalize this approach by linking evolutionary game theory to concepts developed in causal modelling over the past century, from path coefficients to the recently proposed causal derivative. There is a direct correspondence between the causal derivative and the derivative used in evolutionary game theory. Some game theoretical models (e.g. kin selection) consist of multiple causal derivatives. Components of these derivatives correspond to components of the causal derivative, to path coefficients, and to edges on a causal graph, formally linking evolutionary game theory to causal modelling. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

Being ostensive (reply to commentaries on "Expression unleashed")

One of our main goals with "Expression unleashed" was to highlight the distinctive, ostensive nature of human communication, and the many roles that ostension can play in human behavior and society. The commentaries we received forced us to be more precise about several aspects of this thesis. At the same time, no commentary challenged the central idea that the manifest diversity of human expression is underpinned by a common cognitive unity. Our reply is organized around six issues: (1) languages and their cultural evolution; (2) the pervasiveness of expression in human behavior; (3) artificial intelligence and ostensive communication; (4) communication in other animals; (5) the ecology and evolution of ostensive communication; and (6) biolinguistics and pragmatics.

A generalised approach to the study and understanding of adaptive evolution

Evolutionary theory has made large impacts on our understanding and management of the world, in part because it has been able to incorporate new data and new insights successfully. Nonetheless, there is currently a tension between certain biological phenomena and mainstream evolutionary theory. For example, how does the inheritance of molecular epigenetic changes fit into mainstream evolutionary theory? Is niche construction an evolutionary process? Is local adaptation via habitat choice also adaptive evolution? These examples suggest there is scope (and perhaps even a need) to broaden our views on evolution. We identify three aspects whose incorporation into a single framework would enable a more generalised approach to the understanding and study of adaptive evolution: (i) a broadened view of extended phenotypes; (ii) that traits can respond to each other; and (iii) that inheritance can be non-genetic. We use causal modelling to integrate these three aspects with established views on the variables and mechanisms that drive and allow for adaptive evolution. Our causal model identifies natural selection and non-genetic inheritance of adaptive parental responses as two complementary yet distinct and independent drivers of adaptive evolution. Both drivers are compatible with the Price equation; specifically, non-genetic inheritance of parental responses is captured by an often-neglected component of the Price equation. Our causal model is general and simplified, but can be adjusted flexibly in terms of variables and causal connections, depending on the research question and/or biological system. By revisiting the three examples given above, we show how to use it as a heuristic tool to clarify conceptual issues and to help design empirical research. In contrast to a gene-centric view defining evolution only in terms of genetic change, our generalised approach allows us to see evolution as a change in the whole causal structure, consisting not just of genetic but also of phenotypic and environmental variables.

Teleonomy: Revisiting a Proposed Conceptual Replacement for Teleology

The concept of teleonomy has been attracting renewed attention recently. This is based on the idea that teleonomy provides a useful conceptual replacement for teleology, and even that it constitutes an indispensable resource for thinking biologically about purposes. However, both these claims are open to question. We review the history of teleological thinking from Greek antiquity to the modern period to illuminate the tensions and ambiguities that emerged when forms of teleological reasoning interacted with major developments in biological thought. This sets the stage for an examination of Pittendrigh's (Adaptation, natural selection, and behavior. In: Roe A, Simpson GG (eds) Behavior and evolution. Yale University Press, New Haven, pp 390-416, 1958) introduction of "teleonomy" and its early uptake in the work of prominent biologists. We then explore why teleonomy subsequently foundered and consider whether the term may yet have significance for discussions of goal-directedness in evolutionary biology and philosophy of science. This involves clarifying the relationship between teleonomy and teleological explanation, as well as asking how the concept of teleonomy impinges on research at the frontiers of evolutionary theory.

The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

BACKGROUND

The Ferula genus encompasses 180-185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China.

RESULTS

Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats.

CONCLUSION

Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.

Biological adaptation in light of the Lewontin-Williams (a)symmetry

Neo-Darwinism characterizes biological adaptation as a one-sided process, in which organisms adapt to their environment but not vice versa. This asymmetric relationship-here called Williams' asymmetry-is called into question by Niche Construction Theory, which emphasizes that organisms and their environments often mutually affect each other. Here, we clarify that Williams' asymmetry is specifically concerned with (quasi)-directed modifications toward phenotypes that increase individual fitness. This directedness-which drives the adaptive fit between organism and environment-entails far more than the mere presence of cause-effect relationships. We argue that difficulties with invoking fitness as the guiding principle of adaptive evolution are resolved with an appropriate definition of fitness and that objections against Williams' asymmetry reflect confusions about the nature of biological adaptation.

Niche construction in quantitative traits: heritability and response to selection

A central tenet of niche construction (NC) theory is that organisms can alter their environments in heritable and evolutionarily important ways, often altering selection pressures. We suggest that the physical changes niche constructors make to their environments may also alter trait heritability and the response of phenotypes to selection. This effect might change evolution, over and above the effect of NC acting via selection alone. We develop models of trait evolution that allow us to partition the effects of NC on trait heritability from those on selection to better investigate their distinct effects. We show that the response of a phenotype to selection and so the pace of phenotypic change can be considerably altered in the presence of NC and that this effect is compounded when trans-generational interactions are included. We argue that novel mathematical approaches are needed to describe the simultaneous effects of NC on trait evolution via selection and heritability. Just as indirect genetic effects have been shown to significantly increase trait heritability, the effects of NC on heritability in our model suggest a need for further theoretical development of the concept of heritability.

The ecology of wealth inequality in animal societies

Individuals vary in their access to resources, social connections and phenotypic traits, and a central goal of evolutionary biology is to understand how this variation arises and influences fitness. Parallel research on humans has focused on the causes and consequences of variation in material possessions, opportunity and health. Central to both fields of study is that unequal distribution of wealth is an important component of social structure that drives variation in relevant outcomes. Here, we advance a research framework and agenda for studying wealth inequality within an ecological and evolutionary context. This ecology of inequality approach presents the opportunity to reintegrate key evolutionary concepts as different dimensions of the link between wealth and fitness by (i) developing measures of wealth and inequality as taxonomically broad features of societies, (ii) considering how feedback loops link inequality to individual and societal outcomes, (iii) exploring the ecological and evolutionary underpinnings of what makes some societies more unequal than others, and (iv) studying the long-term dynamics of inequality as a central component of social evolution. We hope that this framework will facilitate a cohesive understanding of inequality as a widespread biological phenomenon and clarify the role of social systems as central to evolutionary biology.

A Dual Role for Behavior in Evolution and Shaping Organismal Selective Environments

The hypothesis that evolved behaviors play a determining role in facilitating and impeding the evolution of other traits has been discussed for more than 100 years with little consensus beyond an agreement that the ideas are theoretically plausible in accord with the Modern Synthesis. Many recent reviews of the genomic, epigenetic, and developmental mechanisms underpinning major behavioral transitions show how facultative expression of novel behaviors can lead to the evolution of obligate behaviors and structures that enhance behavioral function. Phylogenetic and genomic studies indicate that behavioral traits are generally evolutionarily more labile than other traits and that they help shape selective environments on the latter traits. Adaptive decision-making to encounter resources and avoid stress sources requires specific sensory inputs, which behaviorally shape selective environments by determining those features of the external world that are biologically relevant. These recent findings support the hypothesis of a dual role for behavior in evolution and are consistent with current evolutionary theory.

Bottom-up controls, ecological revolutions and diversification in the oceans through time

Animals originated in the oceans and evolved there for hundreds of millions of years before adapting to terrestrial environments. Today, oceans cover more than two-thirds of Earth and generate as much primary production as land. The path from the first macrobiota to modern marine biodiversity involved parallel increases in terrestrial nutrient input, marine primary production, species' abundance, metabolic rates, ecotypic diversity and taxonomic diversity. Bottom-up theories of ecosystem cascades arrange these changes in a causal sequence. At the base of marine food webs, nutrient fluxes and atmosphere-ocean chemistry interact with phytoplankton to regulate production. First-order consumers (e.g., zooplankton) might propagate changes in quantity and quality of phytoplankton to changes in abundance and diversity of larger predators (e.g., nekton). However, many uncertainties remain about the mechanisms and effect size of bottom-up control, particularly in oceans across the entire history of animal life. Here, we review modern and fossil evidence for hypothesized bottom-up pathways, and we assess the ramifications of these processes for four key intervals in marine ecosystems: the Ediacaran-Cambrian (635-485 million years ago), the Ordovician (485-444 million years ago), the Devonian (419-359 million years ago) and the Mesozoic (252-66 million years ago). We advocate for a clear articulation of bottom-up hypotheses to better understand causal relationships and proposed effects, combined with additional ecological experiments, paleontological documentation, isotope geochemistry and geophysical reconstructions. How small-scale ecological change transitions into large-scale evolutionary change remains an outstanding question for empirical and theoretical research.

Conformity to Bergmann's rule in birds depends on nest design and migration

Ecogeographical rules attempt to explain large-scale spatial patterns in biological traits. One of the most enduring examples is Bergmann's rule, which states that species should be larger in colder climates due to the thermoregulatory advantages of larger body size. Support for Bergmann's rule, however, is not consistent across taxonomic groups, raising questions about what factors may moderate its effect. Behavior may play a crucial, yet so far underexplored, role in mediating the extent to which species are subject to environmental selection pressures in colder climates. Here, we tested the hypothesis that nest design and migration influence conformity to Bergmann's rule in a phylogenetic comparative analysis of the birds of the Western Palearctic, a group encompassing dramatic variation in both climate and body mass. We predicted that migratory species and those with more protected nest designs would conform less to the rule than sedentary species and those with more exposed nests. We find that sedentary, but not short- or long-distance migrating, species are larger in colder climates. Among sedentary species, conformity to Bergmann's rule depends, further, on nest design: Species with open nests, in which parents and offspring are most exposed to adverse climatic conditions during breeding, conform most strongly to the rule. Our findings suggest that enclosed nests and migration enable small birds to breed in colder environments than their body size would otherwise allow. Therefore, we conclude that behavior can substantially modify species' responses to environmental selection pressures.

Theoretical plurality, the extended evolutionary synthesis, and archaeology

The study of cultural evolution now includes multiple theoretical frameworks. Despite common influence from Darwinian evolutionary theory, there is considerable diversity. Thus, we recognize those most influenced by the tenets of the Modern Synthesis (evolutionary archaeology, cultural transmission theory, and human behavioral ecology) and those most aligned more closely with concepts emerging in the Extended Evolutionary Synthesis (cultural macroevolution and evolutionary cognitive archaeology). There has been substantial debate between adherents of these schools of thought as to their appropriateness and priority for addressing the fundamentals of cultural evolution. I argue that theoretical diversity is necessary to address research questions arising from a complex archaeological record. Concepts associated with the Extended Evolutionary Synthesis may offer unique insights into the cultural evolutionary process.

What's Wrong with Evolutionary Causation?

This review essay reflects on recent discussions in evolutionary biology and philosophy of science on the central causes of evolution and the structure of causal explanations in evolutionary theory. In this debate, it has been argued that our view of evolutionary causation should be rethought by including more seriously developmental causes and causes of the individual acting organism. I use Tobias Uller's and Kevin Laland's volume Evolutionary Causation as well as recent reviews of it as a starting point to reflect on the causal role of agency, individuality, and the environment in evolution. In addition, I critically discuss classical philosophical frameworks of theory change (i.e. Popper's, Kuhn's and Lakatos') used in this debate to understand changing views of evolutionary causation.

Human behavioral ecology and niche construction

We examine the relationship between niche construction theory (NCT) and human behavioral ecology (HBE), two branches of evolutionary science that are important sources of theory in archeology. We distinguish between formal models of niche construction as an evolutionary process, and uses of niche construction to refer to a kind of human behavior. Formal models from NCT examine how environmental modification can change the selection pressures that organisms face. In contrast, formal models from HBE predict behavior assuming people behave adaptively in their local setting, and can be used to predict when and why people engage in niche construction. We emphasize that HBE as a field is much broader than foraging theory and can incorporate social and cultural influences on decision-making. We demonstrate how these approaches can be formally incorporated in a multi-inheritance framework for evolutionary research, and argue that archeologists can best contribute to evolutionary theory by building and testing models that flexibly incorporate HBE and NCT elements.

The challenges of documenting coevolution and niche construction: The example of domestic spaces

This essay delves into some of the challenges of studying the coevolution of humans and domestic spaces. These constructed arenas center on food preparation, and as part of the heritable niche they can shift the opportunities for, and constraints on, social interaction and cooperation in evolutionary time. Domestic spaces are widely evidenced in the archeological record, but investigators have made little progress in demonstrating causal links between proposed feedback spirals and constructed spaces of any sort. Bridging fine-scale and large-scale processes in coevolutionary systems is a complex problem that must engage higher levels of generative evolutionary theory. Archaeology nonetheless stands to offer a great deal to larger research programs by documenting and analyzing the pathways of change based on site formation processes along with evidence from subsistence refuse and technology. Choice models remain valuable tools for investigating aspects of the fine-scale feedback processes involved.

Genes, culture, and the human niche: An overview

The sharp distinction between biological traits and culturally based traits, which had long been standard in evolutionary approaches to behavior, was blurred in the early 1980s by mathematical models that allowed a co-dependent evolution of genetic transmission and cultural information. Niche-construction theory has since added another contrast to standard evolutionary theory, in that it views niche construction as a cause of evolutionary change rather than simply a product of selection. While offering a new understanding of the coevolution of genes, culture, and human behavior, niche-construction models also invoke multivariate causality, which require multiple time series to resolve. The empirical challenge lies in obtaining time-series data on causal pathways involved in the coevolution of genes, culture, and behavior. This is a significant issue in archeology, where time series are often sparse and causal behaviors are represented only by proxies in the material record.

Analysis of six chloroplast genomes provides insight into the evolution of Chrysosplenium (Saxifragaceae)

BACKGROUND

Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low light conditions. Although some progress has been made in the systematics and biogeography of Chrysosplenium, its chloroplast genome evolution remains to be investigated.

RESULTS

To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka) /synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene within Chrysosplenium. Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection.

CONCLUSION

This study provides genetic resources for exploring the phylogeny of Chrysosplenium and sheds light on plant adaptation to low light conditions. The lower average GC content and the lacking gene of rpl32 indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2) were under positive selection at sites in the coding region.

Ecomorphological diversification of some barbs and carps (Cyprininae, Cyprinidae) in the Lower Mekong Basin of Thailand

Morphological variation is fundamentally related to various aspects of fish ecology, including foraging, locomotion, and habitat utilisation. Twenty-six species of closely related cyprinid fish (n = 502) were analysed for patterns of morphological variations by using geometric morphometric methods. Ecological data of feeding and habitat preferences were determined by the observations in fields and laboratory together with the gathering of bibliographic information. The findings of major variation displayed in all parts of the fish body and correlated with ecological parameters. Variations of head shape especially form and position of mouthpart involved with feeding behaviours, whereas the variations of body depth and length which affected swimming patterns reflected responsiveness of water currents and habitat uses. Adaptation of head shape and body elongation was remarkably related to the feeding regime, swimming manoeuvrability and habitat utilisation of the species. Some convergent variation was observed between the tribes Smiliogastrini and Poropuntiini. Therefore, we propose that the morphological diversity of cyprinine fish is mainly affected by ecological gradients, while phylogenetic effects on morphology are minor.

The extended evolutionary synthesis and human origins: Archaeological perspectives

Recent developments in evolutionary biology have led to a call for an extension of standard evolutionary theory, with its emphasis on processes such as selection and drift, into a much larger theoretical framework that includes processes such as niche construction, developmental plasticity, inclusive inheritance, and developmental bias. Skeptics argue that these processes are already subsumed within the standard theory and thus an extension is not required. Here, we outline what this evolutionary "rethink" might mean for the study of human origins. Specifically, can paleoanthropologists benefit from an extended theoretical toolkit? The papers in this special issue suggest it can be useful but may not be necessary, depending on the kinds of questions that are being asked.

The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction

The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not. Interactions, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosters survival-of-the-fitted - those entities that resist entropic destruction - and not only of the fittest - the entities with the greatest reproductive success. The "unit" of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are "fit enough". We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.

The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction

The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not. Interactions, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosters survival-of-the-fitted - those entities that resist entropic destruction - and not only of the fittest - the entities with the greatest reproductive success. The "unit" of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are "fit enough". We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.

The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction

The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not. Interactions, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosters survival-of-the-fitted - those entities that resist entropic destruction - and not only of the fittest - the entities with the greatest reproductive success. The "unit" of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are "fit enough". We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.

Synthesising arguments and the extended evolutionary synthesis

Synthesising arguments motivate changes to the conceptual tools, theoretical structure, and evaluatory framework employed in a given scientific domain. Recently, a broad coalition of researchers has put forward a synthesising argument in favour of an Extended Evolutionary Synthesis ('EES'). Often this synthesising argument is evaluated using a virtue-based approach, which construes the EES as a wholesale alternative to prevailing practice. Here I argue this virtue-based approach is not fit for purpose. Taking the central concept of niche construction as a case study, I show that an agenda-based approach better captures the pragmatic and epistemological goals of the EES synthesising argument and diagnoses areas of empirical disagreement with prevailing practice.

Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689-150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796-82,919 bp), a small single copy region (SSC, 17,084-17,092 bp), and a pair of inverted repeat regions (IRs, 25,401-25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%-38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution

Recent advances in molecular phylogenetics provide us with information of Allium L. taxonomy and evolution, such as the subgenus Cyathophora, which is monophyletic and contains five species. However, previous studies detected distinct incongruence between the nrDNA and cpDNA phylogenies, and the interspecies relationships of this subgenus need to be furtherly resolved. In our study, we newly assembled the whole chloroplast genome of four species in subgenus Cyathophora and two allied Allium species. The complete cp genomes were found to possess a quadripartite structure, and the genome size ranged from 152,913 to 154,174 bp. Among these cp genomes, there were subtle differences in the gene order, gene content, and GC content. Seven hotspot regions (infA, rps16, rps15, ndhF, trnG-UCC, trnC-GCA, and trnK-UUU) with nucleotide diversity greater than 0.02 were discovered. The selection analysis showed that some genes have elevated Ka/Ks ratios. Phylogenetic analysis depended on the complete chloroplast genome (CCG), and the intergenic spacer regions (IGS) and coding DNA sequences (CDS) showed same topologies with high support, which revealed that subgenus Cyathophora was a monophyletic group, containing four species, and A. cyathophorum var. farreri was sister to A. spicatum with 100% bootstrap value. Our study revealed selective pressure may exert effect on several genes of the six Allium species, which may be useful for them to adapt to their specific living environment. We have well resolved the phylogenetic relationship of species in the subgenus Cyathophora, which will contribute to future evolutionary studies or phylogeographic analysis of Allium.

The Development of Cumulative Cultural Learning

Human culture is unique among animals in its complexity, variability, and cumulative quality. This article describes the development and diversity of cumulative cultural learning. Children inhabit cultural ecologies that consist of group-specific knowledge, practices, and technologies that are inherited and modified over generations. The learning processes that enable cultural acquisition and transmission are universal but are sufficiently flexible to accommodate the highly diverse cultural repertoires of human populations. Children learn culture in several complementary ways, including through exploration, observation, participation, imitation, and instruction. These methods of learning vary in frequency and kind within and between populations due to variation in socialization values and practices associated with specific educational institutions, skill sets, and knowledge systems. The processes by which children acquire and transmit the cumulative culture of their communities provide unique insight into the evolution and ontogeny of human cognition and culture.

Evolution evolving? Reflections on big questions

John Bonner managed a long and productive career that balanced specialized inquiry into cellular slime molds with general investigations of big questions in evolutionary biology, such as the origins of multicellular development and the evolution of complexity. This commentary engages with his final paper ("The evolution of evolution"), which argues that the evolutionary process has changed through the history of life. In particular, Bonner emphasizes the possibility that natural selection plays different roles at different size scales. I identify some underlying assumptions in his argument and evaluate its cogency to both foster future discussion and emulate the intellectual example set by Bonner over a lifetime. This endeavor is important beyond Bonner's own theoretical disposition because similar issues are visible in controversies about the possibility of an extended evolutionary synthesis.

The Extended Evolutionary Synthesis: what is the debate about, and what might success for the extenders look like?

Debate over the Extended Evolutionary Synthesis (EES) ranges over three quite different domains of enquiry. Protagonists are committed to substantive positions regarding (1) empirical questions concerning (for example) the properties and prevalence of systems of epigenetic inheritance; (2) historical characterizations of the modern synthesis; and (3) conceptual/philosophical matters concerning (among other things) the nature of evolutionary processes, and the relationship between selection and adaptation. With these different aspects of the debate in view, it is possible to demonstrate the range of cross-cutting positions on offer when well-informed evolutionists consider their stance on the EES. This overview of the multiple dimensions of debate also enables clarification of two philosophical elements of the EES debate, regarding the status of niche-construction and the role of selection in explaining adaptation. Finally, it points the way to a possible resolution of the EES debate, via a pragmatic approach to evolutionary enquiry.

Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome

The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.

Unraveling the biophysical underpinnings to the success of multispecies biofilms in porous environments

Biofilms regulate critical processes in porous ecosystems. However, the biophysical underpinnings of the ecological success of these biofilms are poorly understood. Combining experiments with fluidic devices, sequencing and modeling, we reveal that architectural plasticity enhances space exploitation by multispecies biofilms in porous environments. Biofilms consistently differentiated into an annular base biofilm coating the grains and into streamers protruding from the grains into the pore space. Although different flow-related processes governed the differentiation of these architectures, both BB and streamers were composed of similar bacterial assemblages. This is evidence for architectural plasticity. Architectural plasticity allowed for complementary use of the space provided by the grain–pore complexes, which increased biofilm carrying capacity at the larger scale of the porous system. This increase comes potentially at the cost of a tradeoff. Contrasting time scales of oxygen replenishment and consumption, we show that streamers locally inhibit the growth of the BB downstream from the grains. Our study provides first insights into the biophysical underpinnings to the success of multispecies biofilms in porous environments.

Indirect effects on fitness between individuals that have never met via an extended phenotype

Interactions between organisms are ubiquitous and have important consequences for phenotypes and fitness. Individuals can even influence those they never meet, if they have extended phenotypes that alter the environments others experience. North American red squirrels (Tamiasciurus hudsonicus) guard food hoards, an extended phenotype that typically outlives the individual and is usually subsequently acquired by non-relatives. Hoarding by previous owners can, therefore, influence subsequent owners. We found that red squirrels breed earlier and had higher lifetime fitness if the previous hoard owner was a male. This was driven by hoarding behaviour, as males and mid-aged squirrels had the largest hoards, and these effects persisted across owners, such that if the previous owner was male or died in mid-age, subsequent occupants had larger hoards. Individuals can, therefore, influence each other's resource-dependent traits and fitness without ever meeting, such that the past can influence contemporary population dynamics through extended phenotypes.

Why Gupta et al.'s critique of niche construction theory is off target

Gupta et al., in their article in this issue ('Niche construction in evolutionary theory: the construction of an academic niche?'. doi:10.1007/s12041-017-0787-6), lament 'serious problems with the way science is being done' and suggest that 'niche construction theory exemplifies this state of affairs.' However, their aggressively confrontational but superficial critique of niche construction theory (NCT) only contributes to these problems by attacking claims that NCT does not make. This is unfortunate, as their poor scholarship has done a disservice to the evolutionary biology community through propagating misinformation.We correct Gupta et al.'s misunderstandings, stressing that NCT does not suggest that the fact that organisms engage in niche construction is neglected, nor does it make strong claims on the basis of its formal theory. Moreover, the treatment of niche construction as an evolutionary process has been highly productive, and is both theoretically and empirically well-validated.We end by reflecting on the potentially deleterious implications of their publication for evolutionary science.

A variational approach to niche construction

In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields.

Affordances and Landscapes: Overcoming the Nature-Culture Dichotomy through Niche Construction Theory

In this paper we reject the nature-culture dichotomy by means of the idea of affordance or possibility for action, which has important implications for landscape theory. Our hypothesis is that, just as the idea of affordance can serve to overcome the subjective-objective dichotomy, the ideas of landscape and ecological niche, properly defined, would allow us to also transcend the nature-culture dichotomy. First, we introduce an overview of landscape theory, emphasizing processual landscape theory as the most suitable approach for satisfying both cultural and naturalist approaches. After that, we introduce the idea of affordance and we analyze a tension between sociocultural and transcultural affordances (affordances that depend on cultural conventions and affordances that depend on lawful information and bodily aspects of agents). This tension has various implications for landscape theory and ecological niches. Our proposal is that sociocultural and transcultural aspects of affordances could be systematically accommodated if we apply niche construction theory (the theory that explains the process by which organisms modify their selective environments) as a methodological framework for explaining the emergence of ecological niches. This approach will lead us to an integrative account of landscapes as the products of the interaction between human and environmental elements, making it a clear example of a concept that transcends the nature-culture dichotomy.