Geometric morphometrics is the statistical analysis of landmark-based shape variation and its covariation with other variables. Over the past two decades, the gold standard of landmark data acquisition has been manual detection by a single observer. This approach has proven accurate and reliable in small-scale investigations. However, big data initiatives are increasingly common in biology and morphometrics

The visualization of the molecular context of an amino acid mutation in a protein structure is crucial for the assessment of its functional impact and the understanding of its evolutionary implications. Currently, searches for fast evolving amino acid positions using codon substitution models like those implemented in PAML (Yang and Nielsen in Estimating synonymous and nonsynonymous substitution rates

Theoretical and experimental studies have provided evidence for a positive role of phenotype resistance to genetic mutation in enhancing long-term adaptation to novel environments. With the aim of contributing to an understanding of the origin and evolution of phenotypic robustness to genetic mutations in organismal systems, we adopted a theoretical approach, elaborating on a classical mathematical

The inclusion of fossil phenotypes as ancestral character values at nodes in phylogenetic trees is known to increase both the power and reliability of phylogenetic comparative methods (PCMs) applications. We implemented the R function RRphylo as to integrate fossil phenotypic information as ancestral character values. We tested the new implementation, named RRphylo-noder (which is available as part

Researchers using geometric morphometric methods can be confronted with a need to combine separate landmark configurations from the same research subjects as a more holistic description of organismal morphology. Combining configurations might be valid if single configurations represent separate anatomical structures that can change position with respect to each other or have been shown to be phenotypically

The page where the original version of this article is posted unfortunately contained an error. In that page, the supplementary material is not currently included along with the article and this problem has been corrected with this erratum.

Encapsulated within the temporal bone and comprising the smallest elements of the vertebrate skeleton, the ear is key to multiple senses: balance, posture control, gaze stabilization, and hearing. The transformation of the primary jaw joint into the mammalian ear ossicles is one of the most iconic transitions in vertebrate evolution, but the drivers of this complex evolutionary trajectory are not fully

Many authors have hypothesized an association between rates of morphological evolution and rates of species diversification, however, this association has yet to be empirically tested in the primate cranium. In this investigation, we used phylogeny-based approaches to examine the relationship between rates of species diversification, rates of cranial size and shape evolution, and observed cranial morphological

Manual landmark data collection on large samples takes a long time. Several options exist to speed the process, though each introduces problems or raises concerns of its own. For bilaterally symmetric structures (e.g., crania), some recent papers recommend limiting landmark collection to one side and the anatomical midline, then approximating the true bilateral configuration by merging the hemi-form

Abstract Facultative traits can provide phenotypic lability in dynamic environments, but it is unclear how weaving between disparate habitats impacts non-facultative traits that are carried along the way. The life cycles of salamanders are associated with distinct ontogenies, aquatic-to-terrestrial (biphasic), completely-terrestrial (direct development), and completely-aquatic (larval form paedomorphic)

Abstract Despite the considerable scientific interest in the variability and patterns of integration in the dog skull, how these patterns impact or are driven by function remains largely unexplored. Since the mandible is directly involved in mastication, it can be expected to be directly related to the development of the adductor and abductor muscles. Here, we explore whether variation in the architecture

Abstract The increasing availability of 3D-imaging technology provides new opportunities for measuring morphology. Photogrammetry enables easy 3D-data acquisition compared to conventional methods and here we assess its accuracy for measuring the size of deer antlers, a complex morphological structure. Using a proprietary photogrammetry software, we generated 3D images of antlers for 92 individuals

Abstract The neck connects the head and the trunk and is the key structure allowing all movements of the head. The neck morphology of birds is the most variable among living tetrapods, including significant differences in the number and shape of the cervical vertebrae. Despite these differences, according to the literature, three morphofunctional regions (i.e., modules) have been identified along the

Abstract The identification of mechanisms that have generated biodiversity is one of the major tasks in biogeography and evolutionary biology. Here, using a set of environmental variables and historical presence records, we assessed whether closely related allopatric lineages in the Arremon brunneinucha (Aves: Passerellidae) complex are either more ecologically similar or different throughout their

Abstract Between group PCA (bgPCA) has been developed to summarize group differences in high dimensional spaces like in geometric morphometrics and microarray data where the number of variables is often larger than sample size. However, it has been very recently shown that this technique inflates apparent differences as seen in scatterplots and, in extreme cases, can even create differences where there

Abstract Many organisms studied by evolutionary biologists have different sexes, and the evolution of separate sexes and sexual dimorphisms in morphology and behaviour are central questions in evolutionary biology. Considering scientists to be embedded in a social and cultural context, we are also subjected to the risk of gender-biased assumptions and stereotypical thinking to appear when working on

Abstract Evolutionary relationships among and across species are almost exclusively examined through phylogenetic analysis based on trees constructed using gene sequences. Such trees are not without their limitations. Here we show that sets of numbers representing the masses of peptide segments within proteins encoded by those genes can also be used to construct trees of life employing a phylonumerics

Abstract Evolutionary dynamics of covariation patterns in craniometric traits was studied for bats from the Myotis myotis–Myotis blythii species group (Mammalia, Chiroptera, Vespertilionidae) namely M.m.myotis, M.b.oxygnathus, M.b.omari, M.b.blythii, and M.b.altaicus. These species evolved towards increasing the size. One more species, M.dasycneme, which is phylogenetically, morphologically, and ecologically

Abstract The natural selection of metabolism and mass can explain inter-specific body mass allometries from prokaryotes to mammals (Witting in Theor Popul Biol 117:23–42, https://doi.org/10.1016/j.tpb.2017.08.005, 2017a), with allometric exponents that depend on the selected metabolism and the packing of home ranges in predominately one (1D), two (2D), or three (3D) spatial dimensions. The predicted

Abstract In this article, we present the central ideas of evolutionary psychology, and discuss how their assumptions can help ethnobiologists to understand the dynamic relationship between people and their environments. In this sense, investigating this relationship from an evolutionary perspective can bring new empirical evidence about human evolution, also contributing to both evolutionary psychology

Abstract Identifying the evolutionary processes that underlie morphological variation at the intraspecific level is cornerstone for understanding the drivers of phenotypic diversity at higher macro-evolutionary scales. The fire salamander, Salamandra salamandra, exhibits exceptional intraspecific variation in multiple phenotypic traits (i.e. body size, head shape, coloration, reproductive modes). Pueriparity

Abstract Sexual size dimorphism in orb-weaving spiders is a relatively well-studied phenomenon, and numerous works have documented evolutionary variation in interspecific size and degree of dimorphism. To date, these studies have been largely limited to assessing the evolution of a single or few linear measurements correlated with body size. While the descriptive and comparative literature is rich

Abstract Using sampling experiments, we found that, when there are fewer groups than variables, between-groups PCA (bgPCA) may suggest surprisingly distinct differences among groups for data in which none exist. While apparently not noticed before, the reasons for this problem are easy to understand. A bgPCA captures the g − 1 dimensions of variation among the g group means, but only a fraction of

Abstract Toothed whales (Odontoceti, Cetacea) are well-known for their ability to produce complex vocalizations, to use tools, to possess self-recognition, and for their extreme behavioural plasticity. The toothed whale intelligence is said to compete with that of primates, so does their extremely large brain to body size ratio. Common explanations for the acquisition of such large brains over the

Abstract Quantifying the inner structure of bones is central to various analyses dealing with the phenotypic evolution of animals with an ossified skeleton. Computed tomography allows to assess the repartition of bone tissue within an entire skeletal element. Two parameters of importance for such analyses are the global compactness (Cg) and total cross-sectional area (Tt.Ar). However, no open-source

Abstract Good empirical applications of geometric morphometrics (GMM) typically involve several times more variables than specimens, a situation the statistician refers to as “high p/n,” where p is the count of variables and n the count of specimens. This note calls your attention to two predictable catastrophic failures of one particular multivariate statistical technique, between-groups principal

Abstract Photogrammetry (PH) is relatively cheap, easy to use, flexible and portable but its power and limitations have not been fully explored for studies of small animals. Here we assessed the accuracy of PH for the reconstruction of 3D digital models of bat skulls by evaluating its potential for evolutionary morphology studies at interspecific (19 species) level. Its reliability was assessed against

Abstract The inhibitory cascade (IC) model is a widely used evolutionary developmental explanation of among-species differences in relative molar tooth size. The IC model posits that, as molars develop from front to back, the relative strength of activating and inhibiting influences establishes a “ratcheting” mechanism leading to predictable relative molar sizes. Such a constraint on molar covariation

Abstract The development of techniques for the acquisition of high-resolution 3D images, such as computed tomography and magnetic resonance imaging, has opened new avenues to the study of complex morphologies. Detailed descriptions of internal and external traits can be now obtained, allowing the intensive sampling of surface points. In this paper, we introduce a morphometric and statistical framework

The Williams' hypothesis is one of the most widely known ideas in life history evolution. It states that higher adult mortality should lead to faster and/or earlier senescence. Theoretically derived gradients, however, do not support this prediction. Increased awareness of this fact has caused a crisis of misinformation among theorists and empirical ecologists. We resolve this crisis by outlining key

The capacity to learn and reproduce vocal sounds has evolved in phylogenetically distant tetrapod lineages. Vocal learners in all these lineages express similar neural circuitry and genetic factors when perceiving, processing, and reproducing vocalization, suggesting that brain pathways for vocal learning evolved within strong constraints from a common ancestor, potentially fish. We hypothesize that

Chemical communication plays a pivotal role in shaping sexual and ecological interactions among animals. In lizards, fundamental mechanisms of sexual selection such as female mate choice have rarely been shown to be influenced by quantitative phenotypic traits (e.g., ornaments), while chemical signals have been found to potentially influence multiple forms of sexual and social interactions, including

For highly mobile species that nevertheless show fine-scale patterns of population genetic structure, the relevant evolutionary mechanisms determining structure remain poorly understood. The bottlenose dolphin (Tursiops truncatus) is one such species, exhibiting complex patterns of genetic structure associated with local habitat dependence in various geographic regions. Here we studied bottlenose dolphin

Within carnivorans, cats show comparatively little disparity in overall morphology, with species differing mainly in body size. However, detailed shape analyses of individual osteological structures, such as limbs or skulls, have shown that felids display significant morphological differences that correlate with their observed ecological and behavioural ranges. Recently, these shape analyses have been

The diet of organisms generally provides a sufficient supply of energy and building materials for healthy growth and development, but should also contain essential nutrients. Species differ in their exogenous requirements, but it is not clear why some species are able to synthesize essential nutrients, while others are not. The unsaturated fatty acid, linoleic acid (LA; 18:2n-6) plays an important

Recent calls for a revision of standard evolutionary theory (SET) are based partly on arguments about the reciprocal causation. Reciprocal causation means that cause-effect relationships are bi-directional, as a cause could later become an effect and vice versa. Such dynamic cause-effect relationships raise questions about the distinction between proximate and ultimate causes, as originally formulated

Approaches to macroevolution require integration of its two fundamental components, within a hierarchical framework. Following a companion paper on the origin of variation, I here discuss sorting within an evolutionary hierarchy. Species sorting-sometimes termed species selection in the broad sense, meaning differential origination and extinction owing to intrinsic biological properties-can be split

Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in

The maintenance of males and outcrossing is widespread, despite considerable costs of males. By enabling recombination between distinct genotypes, outcrossing may be advantageous during adaptation to novel environments and if so, it should be selected for under environmental challenge. However, a given environmental change may influence fitness of male, female, and hermaphrodite or asexual individuals

Predation is a significant cause of nest failure in passerine birds, and, thus, natural selection is expected to favor behavioral plasticity to allow birds to respond to perceived changes in predation risk. However, behavioral plasticity in response to perceived predation risk, and its potential fitness-related costs, are understudied. In a wild population of breeding house wrens (Troglodytes aedon)

How does new genetic information arise? Traditional thinking holds that mutation happens by accident and then spreads in the population by either natural selection or random genetic drift. There have been at least two fundamental conceptual problems with imagining an alternative. First, it seemed that the only alternative is a mutation that responds "smartly" to the immediate environment; but in complex

Females in a variety of taxa adjust offspring sex ratios to prevailing ecological conditions. However, little is known about whether conditions experienced during a female's early ontogeny influence the sex ratio of her offspring. We tested for past and present ecological predictors of offspring sex ratios among known-age females that were produced as offspring and bred as adults in a population of

The evolution of senescence is often explained by arguing that, in nature, few individuals survive to be old and hence it is evolutionarily unimportant what happens to organisms when they are old. A corollary to this idea is that extrinsically imposed mortality, because it reduces the chance of surviving to be old, favors the evolution of senescence. We show that these ideas, although widespread, are

Human cognitive uniqueness is often defined in terms of cognitive abilities such as introspection, imitation and cooperativeness. However, little is known about how those traits vary in populations or correlate across individuals. Here we test whether those three cognitive domains are correlated manifestations of an underlying factor, analogous to the psychometric 'g' factor, or independent 'behavioural

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution

The introduction of novel phenotypic structures is one of the most significant aspects of organismal evolution. Yet the concept of evolutionary novelty is used with drastically different connotations in various fields of research, and debate exists about whether novelties represent features that are distinct from standard forms of phenotypic variation. This article contrasts four separate uses for

Differences in thermal regimes are of paramount importance in insect development. However, experiments that examine trait development under constant temperature conditions may yield less evolutionarily relevant results than those that take naturally occurring temperature fluctuations into account. We investigated the effect of different temperature regimes (constant 30 °C, constant 35 °C, fluctuating

In today's geometric morphometrics the commonest multivariate statistical procedures, such as principal component analysis or regressions of Procrustes shape coordinates on Centroid Size, embody a tacit roster of symmetries-axioms concerning the homogeneity of the multiple spatial domains or descriptor vectors involved-that do not correspond to actual biological fact. These techniques are hence inappropriate

Maintenance of genetic variance in secondary sexual traits, including bizarre ornaments and elaborated courtship displays, is a central problem of sexual selection theory. Despite theoretical arguments predicting that strong sexual selection leads to a depletion of additive genetic variance, traits associated with mating success show relatively high heritability. Here we argue that because of trade-offs

The behavioral processes at the basis of hybridization and introgression are understudied in terrestrial mammals. We use a unique model to test the role of sexual signals as a reproductive barrier to introgression by investigating behavioral responses to male sexual calls in estrous females of two naturally allopatric but reproductively compatible deer species, red deer and sika deer. Previous studies

Species morphological changes can be mutually influenced by environmental or biotic factors, such as competition. South American canids represent a quite recent radiation of taxa that evolved forms very disparate in phenotype, ecology and behaviour. Today, in the central part of South America there is one dominant large species (the maned wolf, Chrysocyon brachyurus) that directly influence sympatric

Under inbreeding, heterozygosity at neutral genetic markers is likely to reflect genome-wide heterozygosity and, thus, is expected to correlate with fitness. There is, however, growing evidence that some of heterozygosity-fitness correlations (HFCs) can be explained by 'local effects', where noncoding loci are at linkage disequilibrium with functional genes. The aim of this study was to investigate

The biologist examining samples of multicellular organisms in anatomical detail must already have an intuitive concept of morphological integration. But quantifying that intuition has always been fraught with difficulties and paradoxes, especially for the anatomically labelled Cartesian coordinate data that drive today's toolkits of geometric morphometrics. Covariance analyses of interpoint distances

Quantitative analysis of gene expression domains and investigation of relationships between gene expression and developmental and phenotypic outcomes are central to advancing our understanding of the genotype-phenotype map. Gene expression domains typically have smooth but irregular shapes lacking homologous landmarks, making it difficult to analyze shape variation with the tools of landmark-based

Studies examining age-specific patterns in genetic variance have focussed primarily on changes in the genetic variance within cohorts. It remains unclear whether parental age may affect the genetic variance among offspring. To date, such an effect has been reported only in a single study performed in a wild bird population. Here, we provide experimental evidence that the additive genetic variance (VA)

Skin pigmentation lightened progressively to a variable extent, as modern humans emigrated out of Africa, but extreme lightening occurred only in northern Europeans. Yet, loss of pigmentation alone cannot suffice to sustain cutaneous vitamin D3 (VD3) formation at the high latitudes of northern Europe. We hypothesized that loss-of-function mutations in the epidermal structural protein, filaggrin (FLG)

The essay discusses whether biotic and abiotic environments differ in their ability to speed up or slow down morphological change and the generation of new lineages. Examples from the class Branchiopoda show that morphological conservatism is associated with enemy free space in species-poor habitats dominated by abiotic factors, while Red Queen mechanisms are predominant in larger systems with complex

Social selection and indirect genetic effects (IGEs) are established concepts in both behavioural ecology and evolutionary genetics. While IGEs describe effects of an individual's genotype on phenotypes of social partners (and may thus affect their fitness indirectly), the concept of social selection assumes that a given phenotype in one individual affects the fitness of other individuals directly

Evolutionary stasis (long-term stability of morphology in an evolving lineage) is a pattern for which explanations are usually elusive. The Triassic tetrapod Gerrothorax pulcherrimus, a gill-bearing temnospondyl, survived for 35 million years in the Germanic Basin of Central Europe persisting throughout the dinosaur-dominated Late Triassic period. This evolutionary stasis coincides with the occurrence

A nocturnal activity pattern is central to almost all hypotheses on the adaptive origins of primates. This enduring view has been challenged in recent years on the basis of variation in the opsin genes of nocturnal primates. A correspondence between the opsin genes and activity patterns of species in Euarchonta-the superordinal group that includes the orders Primates, Dermoptera (colugos), and Scandentia