Skull morphology diverges between urban and rural populations of red foxes mirroring patterns of domestication and macroevolution

Shared reproductive disruption, not neural crest or tameness, explains the domestication syndrome

Altered neural crest cell (NCC) behaviour is an increasingly cited explanation for the domestication syndrome in animals. However, recent authors have questioned this explanation, while others cast doubt on whether domestication syndrome even exists. Here, we review published literature concerning this syndrome and the NCC hypothesis, together with recent critiques of both. We synthesize these contributions and propose a novel interpretation, arguing shared trait changes under ancient domestication resulted primarily from shared disruption of wild reproductive regimes. We detail four primary selective pathways for 'reproductive disruption' under domestication and contrast these succinct and demonstrable mechanisms with cryptic genetic associations posited by the NCC hypothesis. In support of our perspective, we illustrate numerous important ways in which NCCs contribute to vertebrate reproductive phenotypes, and argue it is not surprising that features derived from these cells would be coincidentally altered under major selective regime changes, as occur in domestication. We then illustrate several pertinent examples of Darwin's 'unconscious selection' in action, and compare applied selection and phenotypic responses in each case. Lastly, we explore the ramifications of reproductive disruption for wider evolutionary discourse, including links to wild 'self-domestication' and 'island effect', and discuss outstanding questions.

Addressing prey naivety in native mammals by accelerating selection for antipredator traits

Harnessing natural selection to improve conservation outcomes is a recent concept in ecology and evolutionary biology and a potentially powerful tool in species conservation. One possible application is the use of natural selection to improve antipredator responses of mammal species that are threatened by predation from novel predators. We investigated whether long-term exposure of an evolutionary naïve prey species to a novel predator would lead to phenotypic changes in a suite of physical and behavioral traits. We exposed a founder population of 353 burrowing bettongs (Bettongia lesueur) to feral cats (Felis catus) over 5 years and compared the physical and behavioral traits of this population (including offspring) to a control (non-predator exposed) population. We used selection analysis to investigate whether changes in the traits of bettongs were likely due to phenotypic plasticity or natural selection. We also quantified selection in both populations before and during major population crashes caused by drought (control) and high predation pressure (predator-exposed). Results showed that predator-exposed bettongs had longer flight initiation distances, larger hind feet, and larger heads than control bettongs. Trait divergence began soon after exposure and continued to intensify over time for flight initiation distance and hind foot length relative to control bettongs. Selection analysis found indicators of selection for larger hind feet and longer head length in predator-exposed populations. Results of a common garden experiment showed that the progeny of predator-exposed bettongs had larger feet than control bettongs. Results suggest that long-term, low-level exposure of naïve prey to novel predators can drive phenotypic changes that may assist with future conservation efforts.

Wild boar versus domestic pig-Deciphering of crown growth in porcine second molars

Based on the previously established periodicity of enamel growth marks, we reconstructed crown growth parameters of mandibular second molars from two wild boar and two domestic pigs of the Linderöd breed. Body weight gain and progression of dental development were markedly faster in the domestic pigs than the wild boar. While the final crown dimensions of the M₂ did not differ between domestic pigs and wild boar, mean crown formation time (CFT) of this tooth was considerably shorter in the domestic pigs (162 days) than in the wild boar (205 days). The difference in CFT was mainly attributable to a higher enamel extension rate (EER) in the domestic pig. Generally, EER was highest in the cuspalmost deciles of the length of the enamel-dentine-junction and markedly dropped in cervical direction, with lowest values occurring in the cervicalmost decile. In consequence, the cuspal half of the M₂ crown was formed about three times faster than the cervical half. In contrast to the EER, no marked difference in daily enamel secretion rate (DSR) was recorded between domestic pigs and wild boar. The duration of enamel matrix apposition as well as linear enamel thickness in corresponding crown portions was only slightly lower in the domestic pigs than the wild boar. Thus, the earlier completion of M₂ crown growth in the domestic pig was mainly achieved by a higher EER and not by an increased DSR. The more rapid recruitment of secretory ameloblasts in the course of molar crown formation of domestic pigs compared to wild boar is considered a side-effect of the selection for rapid body growth during pig domestication.

Domestication and the comparative embryology of birds

Studies of domesticated animals have greatly contributed to our understanding of avian embryology. Foundational questions in developmental biology were motivated by Aristotle's observations of chicken embryos. By the 19th century, the chicken embryo was at the center stage of developmental biology, but how closely does this model species mirror the ample taxonomic diversity that characterizes the avian tree of life? Here, we provide a brief overview of the taxonomic breadth of comparative embryological studies in birds. We particularly focused on staging tables and papers that attempted to document the timing of developmental transformations. We show that most of the current knowledge of avian embryology is based on Galliformes (chicken and quail) and Anseriformes (duck and goose). Nonetheless, data are available for some ecologically diverse avian subclades, including Struthioniformes (e.g., ostrich, emu) and Sphenisciformes (penguins). Thus far, there has only been a handful of descriptive embryological studies in the most speciose subclade of Aves, that is, the songbirds (Passeriniformes). Furthermore, we found that temporal variances for developmental events are generally uniform across a consensus chronological sequence for birds. Based on the available data, developmental trajectories for chicken and other model species appear to be highly similar. We discuss future avenues of research in comparative avian embryology in light of the currently available wealth of data on domesticated species and beyond.

The barley DIR gene family: An expanded gene family that is involved in stress responses

Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products. A total of 31,750 conserved orthologous groups (OGs) were identified using eight genomes/subgenomes, of which 1,113 and 6,739 were rapidly expanded and contracted OGs in barley, respectively. Five expanded OGs containing 20 barley dirigent genes (HvDIRs) were identified. HvDIRs from the same OG were phylogenetically clustered with similar gene structure and domain organization. In particular, 7 and 5 HvDIRs from OG0000960 and OG0001516, respectively, contributed greatly to the expansion of the DIR-c subfamily. Tandem duplication was the driving force for the expansion of the barley DIR gene family. Nucleotide diversity and haplotype network analysis revealed that the expanded HvDIRs experienced severe bottleneck events during barley domestication, and can thus be considered as potential domestication-related candidate genes. The expression profile and co-expression network analysis revealed the critical roles of the expanded HvDIRs in various biological processes, especially in stress responses. HvDIR18, HvDIR19, and HvDIR63 could serve as excellent candidates for further functional genomics studies to improve the production of barley products. Our study revealed that the HvDIR family was significantly expanded in barley and might be involved in different developmental processes and stress responses. Thus, besides providing a framework for future functional genomics and metabolomics studies, this study also identified HvDIRs as candidates for use in improving barley crop resistance to biotic and abiotic stresses.

Individual variation in feeding morphology, not diet, can facilitate the success of generalist species in urban ecosystems

Generalist species dominate urban ecosystems. The success of urban generalists is often related to a plastic diet and feeding traits that allow them to take advantage of a variety of food resources provided by humans in cities. The classification of a species as a generalist is commonly based on mean estimates of diet- and feeding-related traits. However, there is increasing evidence that a generalist population can consist of individual specialists. In such cases, estimates based on mean can hide important individual variation that can explain trophic ecology and the success of urban dwellers. Here, we focus on guppies, Poecilia reticulata, a widespread alien fish species which has invaded both urban and non-urban systems, to explore the effect of urbanization on individual diet and feeding morphology (cranium shape). Our results show that guppies in urban and non-urban populations are not individual specialists, having a similar generalist diet despite the high population density. However, there is important individual variation in cranium shape which allow urban guppies to feed more efficiently on highly nutritious food. Our data suggest that individual variation in feeding efficiency can be a critical overlooked trait that facilitates the success of urban generalists.

Pattern and pace of morphological change due to variable human impact: the case of Japanese macaques

Human impact influences morphological variation in animals, as documented in many captive and domestic animal populations. However, there are different levels of human impact, and their influence on the pattern and rate of morphological variation remains unclear. This study contributes to the ongoing debate via the examination of cranial and mandibular shape and size variation and pace of change in Japanese macaques (Macaca fuscata). This species is ideal for tackling such questions because different wild, wild-provisioned, and captive populations have been monitored and collected over seven decades. Linear measurements were taken on 70 skulls from five populations, grouped into three 'human impact groups' (wild, wild-provisioned, and captive). This made it possible to investigate the pattern and pace of skull form changes among the human impact groups as well as over time within the populations. It was found that the overall skull shape tends to differ among the human impact groups, with captive macaques having relatively longer rostra than wild ones. Whether these differences are a result of geographic variation or variable human impact, related to nutritional supply and mechanical properties of the diet, is unclear. However, this pattern of directed changes did not seem to hold when the single captive populations were examined in detail. Although environmental conditions have probably been similar for the two examined captive populations (same captive locality), skull shape changes over the first generations in captivity were mostly different. This varying pattern, together with a consistent decrease in body size in the captive populations over generations, points to genetic drift playing a role in shaping skull shape and body size in captivity. In the captive groups investigated here, the rates of change were found to be high compared to literature records from settings featuring different degrees of human impact in different species, although they still lie in the range of field studies in a natural context. This adds to the view that human impact might not necessarily lead to particularly fast rates of change.

Modularity patterns in mammalian domestication: Assessing developmental hypotheses for diversification

The neural crest hypothesis posits that selection for tameness resulted in mild alterations to neural crest cells during embryonic development, which directly or indirectly caused the appearance of traits associated with the "domestication syndrome" (DS). Although representing an appealing unitary explanation for the generation of domestic phenotypes, support for this hypothesis from morphological data and for the validity of the DS remains a topic of debate. This study used the frameworks of morphological integration and modularity to assess patterns that concern the embryonic origin of the skull and issues around the neural crest hypothesis. Geometric morphometric landmarks were used to quantify cranial trait interactions between six pairs of wild and domestic mammals, comprising representatives that express between five and 17 of the traits included in the DS, and examples from each of the pathways by which animals entered into relationships with humans. We predicted the presence of neural crest vs mesoderm modular structure to the cranium, and that elements in the neural crest module would show lower magnitudes of integration and higher disparity in domestic forms compared to wild forms. Our findings support modular structuring based on tissue origin (neural crest, mesoderm) modules, along with low module integration magnitudes for neural crest cell derived cranial elements, suggesting differential capacity for evolutionary response among those elements. Covariation between the neural crest and mesoderm modules accounted for major components of shape variation for most domestic/wild pairs. Contra to our predictions, however, we find domesticates share similar integration magnitudes to their wild progenitors, indicating that higher disparity in domesticates is not associated with magnitude changes to integration among either neural crest or mesoderm derived elements. Differences in integration magnitude among neural crest and mesoderm elements across species suggest that developmental evolution preserves a framework that promotes flexibility under the selection regimes of domestication.

Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe

Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.

Carnivoran intraspecific tooth-size variation shows heterogeneity along the tooth row and among species

Developing morphological diagnoses for fossil mammals requires an understanding of intraspecific variation in the anatomical elements under study. Dental traits along with tooth size can be informative of taxonomic identify for extinct species. However, it is unclear what selective or developmental processes are responsible for documented patterns in tooth-size variation making application to the fossil record difficult. We assessed combined species tooth-type variation and intraspecific tooth-size variation for 19 species to evaluate whether developmental controls or occlusion-driven functional demands influence carnivoran tooth-size variation. We also estimated phylogenetic signal for the coefficient of variation (CV). Combined species tooth-size variation separated by tooth type shows that canines are more variable than molars and lower premolars. We found intraspecific tooth-size variation patterns differ between species. However, comparisons of the CVs did not support the hypotheses that developmental controls or functional demands of occlusion constrain size variation in mammal teeth. Our results suggest that a combination of factors influence carnivoran tooth-size variation, such as differences in ontogeny, diet, sexual dimorphism, and evolutionary history. Patterns of carnivoran intraspecific tooth-size variation suggest a better understanding of dental size variation in extant species is essential for accurate morphological studies of fossil taxa.

Geometric morphometric investigation of craniofacial morphological change in domesticated silver foxes

To test the effects of domestication on craniofacial skeletal morphology, we used three-dimensional geometric morphometrics (GM) along with linear and endocranial measurements to compare selected (domesticated) and unselected foxes from the Russian Farm-Fox Experiment to wild foxes from the progenitor population from which the farmed foxes are derived. Contrary to previous findings, we find that domesticated and unselected foxes show minimal differences in craniofacial shape and size compared to the more substantial differences between the wild foxes and both populations of farmed foxes. GM analyses and linear measurements demonstrate that wild foxes differ from farmed foxes largely in terms of less cranial base flexion, relatively expanded cranial vaults, and increased endocranial volumes. These results challenge the assumption that the unselected population of foxes kept as part of the Russian Farm-Fox experiment are an appropriate proxy for ‘wild’ foxes in terms of craniofacial morphology and highlight the need to include wild populations in further studies of domestication syndrome to disentangle the phenotypic effects of multiple selection pressures. These findings also suggest that marked increases in docility cannot be reliably diagnosed from shape differences in craniofacial skeletal morphology.

Ecomorphological divergence and habitat lability in the context of robust patterns of modularity in the cichlid feeding apparatus

BACKGROUND

Adaptive radiations are characterized by extreme and/or iterative phenotypic divergence; however, such variation does not accumulate evenly across an organism. Instead, it is often partitioned into sub-units, or modules, which can differentially respond to selection. While it is recognized that changing the pattern of modularity or the strength of covariation (integration) can influence the range or rate of morphological evolution, the relationship between shape variation and covariation remains unclear. For example, it is possible that rapid phenotypic change requires concomitant changes to the underlying covariance structure. Alternatively, repeated shifts between phenotypic states may be facilitated by a conserved covariance structure. Distinguishing between these scenarios will contribute to a better understanding of the factors that shape biodiversity. Here, we explore these questions using a diverse Lake Malawi cichlid species complex, Tropheops, that appears to partition habitat by depth.

RESULTS

We construct a phylogeny of Tropheops populations and use 3D geometric morphometrics to assess the shape of four bones involved in feeding (mandible, pharyngeal jaw, maxilla, pre-maxilla) in populations that inhabit deep versus shallow habitats. We next test numerous modularity hypotheses to understand whether fish at different depths are characterized by conserved or divergent patterns of modularity. We further examine rates of morphological evolution and disparity between habitats and among modules. Finally, we raise a single Tropheops species in environments mimicking deep or shallow habitats to discover whether plasticity can replicate the pattern of morphology, disparity, or modularity observed in natural populations.

CONCLUSIONS

Our data support the hypothesis that conserved patterns of modularity permit the evolution of divergent morphologies and may facilitate the repeated transitions between habitats. In addition, we find the lab-reared populations replicate many trends in the natural populations, which suggests that plasticity may be an important force in initiating depth transitions, priming the feeding apparatus for evolutionary change.