Evolutionary Biology

Data on the shape of a group of organisms can be conceptualized as forming a point cloud in the multivariate space of measurement. This is literally true for traditional linear measures, while in a geometric morphometric context the cloud resides in Kendalls shape space, tangent to the true shape space. Regardless of the method of construction, the topology of this point cloud, or phenotypic (hyper)ellipse, is a beguiling target for evolutionary analysis. Reordination of the axes will not change the geometry of this phenotypic ellipse, and the notion that its geometry carries a meaningful biological signal is an old idea; but the character of this signal is often elusive. This paper explores the application of the most commonly used parameter designed to summarize differences in phenotypic ellipse geometry (relative eigenvalue variance, or Vrel), and demonstrates that it is incapable of differentiating between several plausible ways in which phenotypic ellipse geometry might differ among species, because it confounds three separate parameters necessary to describe the ellipse. Two example data sets are analyzed to illustrate variability in phenotypic ellipse geometry and draw conclusions about observed differences. The first case compares wolves to domestic dogs, and replicates previous findings of much greater variance yet tighter integration in dogs. This calls into question the simple model of a single peak in the fitness landscape of dogs. The second example comprises geometric morphometric landmarks from the jaws of a clade of sigmodontine rodents, and allows comparison of ellipse geometry in a phylogenetically controlled setting with qualitative ecological categories. Three parameters are found to vary in concert along a grade of most to least ecologically specialized: the phenotypic variance, the effective rank (dimensionality), and the degree of covariance (Vrel and related metrics). Use of all three of these quantities to characterize the geometry of the phenotypic ellipse is advocated, as all are necessary to characterize how variance is distributed in the ellipse in different taxa. The phenotypic ellipse geometries illustrated here appear to reflect something of the geometry of the adaptive peak upon which each taxon sits; or that they represent (aspects of) the mapping function of adaptive peak to phenotypic ellipse, in ways first predicted by Simpson in the twentieth century.

Dense semilandmarks describe 3D surfaces with hundreds to thousands of points, and sliding them by bending energy or Procrustes distance is a near-universal default. Three questions remain open: does dense sampling add shape beyond fixed landmarks, how many points are needed, and does sliding help or harm? Real specimens cannot answer them: the true correspondence is unknown. We tested two workflows, ALPACA (single-template registration) and DeCAL (landmark-anchored correspondence), on 496 mouse skulls at 250-1,000 points, with and without sliding, scored by surface reconstruction. We repeated it on 500 synthetic skulls with exact correspondence, measuring each point's distance to its true homologue. Dense semilandmarks lowered error for almost every specimen; the fixed landmarks added little but supplied anchoring the semilandmarks could not, and the anchored method was more accurate. The benefit saturated near 250 points for ALPACA but kept improving to 1,000 for DeCAL. Procrustes-distance sliding harmed every configuration; bending-energy sliding helped only a poor, landmark-free correspondence, vanishing once anatomical anchors spanned the form. Match the sliding decision to the correspondence in hand: relax a poor one, leave a good one alone, never slide toward the mean. Known-correspondence specimens offer a general test of landmarking and sliding against ground truth.

Statistical associations between two variables can arise via various causal mechanisms. For example, one variable may influence the other, or they may share common causes. Surprisingly little attention has been devoted to quantifying how such causal pathways contribute to the overall association between variables. Here, I present two methods for partitioning a covariance between variables X and Z into a causal component arising from the effect of X and Z and a spurious component arising via other pathways. Both methods rely on averaging causal decompositions over the distributions of the variables, but the decomposition and averaging are performed in different ways. The 'gradient' definition decomposes causal effects in the neighbourhood of naturally occurring values, making it relatively straightforward to estimate. It assumes that the cause variable X is normally distributed. In contrast, the 'two step' definition decomposes large ('step-wise') changes in values and makes no distributional assumptions. I describe applications of these methods to analysing natural selection and illustrate them using the covariance between body size and the number of eggs carried by pregnant male dusky pipefish, Syngnathus floridae. I partition this total covariance into a causal component due to the effect of body size on egg number and a spurious component arising from variation in body size and egg number among collection sites.

Sexual dimorphism is a well-studied phenomenon in which males and females of a species exhibit different phenotypic characteristics. However, the degree of sexual dimorphism within a species may vary among populations and may be influenced by geographic factors such as seasonality, prey availability, and population density. In this study, we examined the effects of sexual dimorphism and geographic region on the craniomandibular morphology of bobcats (Lynx rufus) in Washington State. Using digital calipers, we measured 13 craniomandibular traits from 35 males and 42 females. We found that the degree of skull dimorphism does not differ between the eastern and western side of the Cascade Mountains. However, we found significant effects of sex and geographic region on craniomandibular morphology. Across the geographic regions, males were significantly larger than females in most craniomandibular traits, excluding postorbital constriction breadth (POC). After correcting for expected size differences, only condylobasal length (CBL) was disproportionately longer in males, indicating subtle shape dimorphism within this trait, that is largely unexplained by allometry. Mechanical advantage (MA) of the temporalis and masseter muscles did not differ between the sexes at the canine or the molar bite points. Comparisons between populations east and west of the Cascade Range revealed that while sex remains the primary indicator of overall size, there is a small regional effect on size as western bobcats are slightly larger than eastern bobcats. These regional differences highlight how environmental pressures including local prey availability and severe winter conditions may influence functional skull design. Future ecological and behavioral studies are needed to further clarify how these localized environmental drivers shape phenotypic variation across populations.

Perceptual experiments show that listeners recognize female speakers with lower accuracy than male speakers. Automatic speaker recognition systems may also show performance bias against female speakers even when training data sets are gender balanced. The underlying reasons for this discrepancy are unclear. Here, we apply geometric morphometrics to quantify sex-related morphological vocal tract disparity -- the extent of shape variation -- across both resting and articulatory configurations. We find that male speakers exhibit greater disparity in both resting and articulatory configurations. This morphological idiosyncrasy may in turn generate more discriminable acoustic signatures and offer a biological explanation for higher recognition accuracies for male voices by humans and machines. Our results suggest that innate variation in vocal tract morphology may contribute to performance bias in voice technology and voice perception by human listeners.

Reconstructing ancestral morphologies on a phylogenetic tree is a central task in evolutionary morphometrics. Established reconstruction methods, including multivariate Brownian-motion approaches, rely on linear assumptions and do not directly model the correlations between landmarks within a shape, which can oversimplify the reconstructed morphology. The DICAROS method (Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes; Severinsen et al., 2026) instead fuses sibling shapes along branches with large-deformation diffeomorphic (LDDMM) landmark dynamics that model these correlations, so that ancestors remain on the shape manifold. DICAROS was shown to outperform ordinary least-squares, Brownian-motion, and penalized-likelihood reconstruction, particularly on non-symmetric trees. The dicaros package repackages that pipeline as a documented, pip-installable tool that runs on arbitrary landmark datasets from a single command. It handles 2D and 3D landmarks, Newick and NEXUS trees, a choice of Euclidean or Frechet species means, optional anchor-based alignment, and tips backed by a single specimen, and it returns the reconstructed shapes for all nodes together with the tree relabelled at its internal nodes. We demonstrate dicaros on two new datasets: a 2D leaf dataset (217 species) and a 3D guenon skull dataset (22 species).

Three-dimensional imaging is rapidly increasing the scale of biological morphometric datasets, but establishing automated anatomical correspondence remains a major bottleneck. Conventional point-cloud registration methods transfer landmarks efficiently, yet poor initialization or high morphological variation can produce geometrically plausible but biologically implausible deformations. Here, we developed a statistical-shape-model (SSM)-regularized coherent point drift (CPD) estimator for automated morphometric landmark transfer. It replaces the unconstrained non-rigid CPD update with optimization in SSM coefficient space and regularizes coefficients by inverse population covariance, so deformations along low-variance biological modes are penalized more strongly. We compared pose-matched conventional CPD, SSM-CPD, and SSM-CPD with refinement in leave-one-out atlas experiments on laboratory mouse skulls (N=249), primate molars (N=115), and squamate vertebrae (N=254) under aligned, mildly perturbed, and severely perturbed initialization. We evaluated these formulations in terms of landmark accuracy, failure-tail behavior, runtime, and preservation of morphometric structure. Under severe perturbation, we also evaluated an integrated recovery procedure that optimizes the starting template, recovers global pose, and then applies SSM-CPD with refinement. Severe misalignment produced widespread failures in pose-matched conventional CPD, whereas SSM regularization reduced median error from 13 - 21% to approximately 1 - 3% of the target bounding-box diagonal. This improvement was highly consistent for skulls and molars. In the morphologically complex vertebral dataset, however, low median error concealed a substantial minority of catastrophic failures (28% of vertebrae above a 6% error threshold), which integrated recovery reduced to 4%. Across datasets, automated landmarks preserved the major axes and pairwise relationships of morphometric shape space, and local CPD refinement improved covariance preservation. Embedding learned biological variation directly into registration broadens the range of starting conditions and anatomies for which automated landmark transfer remains reliable. Our results also show that failure tails and downstream morphometric fidelity must be assessed alongside median accuracy when automated landmarking methods are evaluated.

The human bony labyrinth has attracted increasing interest because of its taxonomic, evolutionary, and functional significance. Although sexual dimorphism has been reported in several aspects of the temporal bone, the extent to which sex, age, size, and allometry contribute to labyrinth shape variation remains poorly understood. Here, we investigated patterns of sexual shape variation in the human bony labyrinth using three-dimensional geometric morphometrics in a sample of 98 archaeological individuals from South America with known genomic sex. Centroid size and allometric effects were assessed in a subset of 90 individuals with comparable metric scaling. In addition to analysing the complete labyrinth, the cochlea and semicircular canals were examined separately to evaluate region-specific patterns of sexual shape variation. Principal Component Analysis showed extensive overlap between females and males, and overall labyrinth shape did not differ significantly between sexes. Males exhibited significantly larger labyrinths than females, and centroid size explained a small but significant proportion of overall shape variation. Regional analyses showed no evidence of significant sexual shape differences in the cochlea or in any individual semicircular canal when analysed separately. In contrast, the combined semicircular canal system exhibited subtle but significant sexual shape variation independent of centroid size, whereas morphological disparity did not differ between sexes. The geometric comparison of the female and male consensus configurations further showed that sexual shape variation was regionally heterogeneous. Whereas the cochlea exhibited a pattern of localized changes with low directional coherence, the semicircular canals displayed more coordinated regional shape changes. The male consensus also exhibited slightly higher canal circularity across all three semicircular canals, particularly the posterior canal, while differences in canal-plane orientation remained minimal. These findings demonstrate that sexual shape variation in the human bony labyrinth is subtle and anatomically partitioned among its components. Although significant sex differences in centroid size were detected across most anatomical regions, overall labyrinth shape and cochlear morphology were primarily influenced by allometry, whereas significant sex-related shape differences were detected only when the semicircular canals were considered as an integrated anatomical system. These findings demonstrate that sexual dimorphism in the human bony labyrinth is subtle but regionally heterogeneous, with the cochlea and semicircular canals exhibiting distinct patterns of shape variation, suggesting that these structures are influenced by different developmental, functional, and evolutionary processes.

The morphology of cranial sutures (i.e., joints that connect the bones of the skull, are sites of growth, and absorb biomechanical stresses) is highly variable, especially in mammals. Exposure to different strain regimes as a result of development, function, and ecology can drive disparity in suture complexity at both the individual and taxonomic levels. Although the relationships between diet, muscle mass, static loading, and certain behaviors (e.g., headbutting) and suture morphology are well studied, the effects of fossoriality, particularly the use of the craniodental apparatus during substrate excavation, remain largely unknown. We synthesize data using an ordinal ranking scheme for digging mode importance in 107 rodent species; premaxillofrontal and nasofrontal suture complexity as measured by sinuosity index, power spectrum density, and spectral entropy, the latter of which is a novel suture complexity metric; and Bayesian multilevel models to examine the fossoriality-suture phenotype relationship at the suborder level and above and predict digging mode usage in 11 cryptic extant species. Most fossorial rodents utilize multiple digging modes, often at varying levels of importance. Chisel-tooth digging importance is associated with reduced nasofrontal suture complexity in multiple suborders, whereas scratch digging importance is correlated with elevated complexity in the premaxillofrontal suture. Suture complexity poorly reflects head-lift digging importance. We demonstrate that fossorial function is a complex, multivariate trait and reveal new insights into the functional morphology of cranial sutures across the most diverse mammalian order.

The shell colour polymorphism in the land snail Cepaea nemoralis is maintained by environmentally variable light intensity and predation. Previous work showed that divergence in colour polymorphism between habitat pairs of open and closed areas increased with age of the habitat. However, that study was limited to a time span of 80 years (27 snail generations). Here, we investigate shell colour divergence over habitat pair ages of 95 to 325 years. We did find an increase in evolutionary divergence of colour polymorphism with increasing age, however equilibrium could not be determined. This is possibly due to the evolutionary effect of camouflage working in opposite direction to light intensity in certain locations, consequently clouding the results. Therefore, camouflage might also be an important factor to take into account in the search for the evolutionary equilibrium of colour polymorphism in Cepaea nemoralis.

A prominent developmental plasticity theory proposes that early life adversity accelerates life history trajectories so organisms can maximize fitness in challenging environments. Standard tests of this hypothesis rely on empirical predictions about observable life history variables (e.g., age at first birth), because the proposed internal processes cannot be directly measured. However, the observable proxies are themselves mechanically linked, and regressions that ignore this may conflate causal effects with mechanical relationships among proxies. Here, we develop theory that explicitly justifies some existing empirical tests but rejects others. We integrate an accounting model that incorporates age at first birth, interbirth intervals, and lifespan with an optimization model, to derive the mathematical form that tests of the hypothesis should take. We apply these tests to data from wild female baboons, using early life rainfall as an exogenous proxy for early adversity so that estimates can plausibly be interpreted causally. The accounting model explains >98% of the variation in lifetime reproductive success among females that reproduced. However, our theory-derived tests find no evidence for the reproductive acceleration hypothesis. Our study illustrates the value of formal theory for causal inference in developmental plasticity research, where intertwined measurable variables may be obscured by strictly verbal hypotheses.

The nautilus (Nautilus sp.) is an early-branching cephalopods. It retains several conchiferan synapomorphies, including an external planispiral biomineralized shell. The shells complex structure allows it to withstand hydrostatic pressure, control buoyancy, and protect against external hazards. In this study, we comprehensively examined shell microstructures across different shell components and regions representing various ontogenetic stages in two adult museum shell specimens. We found that the nautilus shell is composed of five microstructural types (spherulitic, prismatic, nacreous, semi-prismatic, and irregularly oriented prismatic structures) organized into layered architectures within individual shell components and coordinated across the shell as an integrated system. Our observations highlight transitions between distinct microstructures within and across shell components and local variation within individual components such as the dorsal and ventral shell walls, suggesting that these patterns may contribute to shell strength and overall mechanical performance. Variation in caecum morphology suggests that this structure may be developmentally plastic and subject to relatively relaxed structural constraints. These findings show that the Nautilus shell is an integrated biomineral system in which diverse microstructures are organized across shell components to meet functional demands and provide the mechanical strength needed for survival.

Gliding enables mammals to forage and escape from predators by moving between discontinuous forests. Its benefits depend not only on glide distance but also on the ability to decelerate and land safely. This study developed a theoretical framework linking glide distance, gliding velocity, aerodynamic braking, body mass, and braking distance. Twenty-two representative distance-velocity observations from eight studies and five species were compiled. Among distance-velocity models, log-distance and saturated with V0 models received nearly equivalent support. Both models predicted increasing velocity with glide distance, with the rate of increase declining at longer distances. For a 1 kg animal undergoing a 60% reduction in velocity, predicted kinetic energy remaining immediately before contact increased from 4.80-5.14J at 20 m to 8.13-8.90 J at 80 m. This velocity reduction corresponded to a dissipation of 84% of approach kinetic energy before contact. Over a braking distance of 1 m, the required mean deceleration increased from 2.57-2.75 g at 20 m to 4.35-4.77 g at 80 m. At 80 m, shortening the braking distance from 4 to 0.5 m increased the required deceleration from 1.09-1.19 to 8.70-9.53 g. These results indicate that the absolute energetic and deceleration requirements of landing increase with glide distance, even when velocity is close to an asymptote. These results provide a quantitative basis for considering aerodynamic braking and landing requirements alongside conventional measures of glide performance. Summary statementModels quantify how glide distance, aerodynamic braking, and braking distance affect pre-contact kinetic energy and deceleration requirements in gliding mammals.

Laboratory environments can induce rapid phenotypic changes, but the earliest responses of natural populations to laboratory conditions remain poorly understood. Using geometric morphometrics, we investigated changes in wing size and wing shape in the Neotropical drosophilid Drosophila sturtevanti. We compared field-collected males (G0) with descendants from 12 lines each established from a single female from the same native population in the first (F1) and tenth (F10) laboratory generations. Wing size showed heterogeneous responses in F1, followed by a consistent reduction by F10, possibly reflecting differences among founder females and larval density. Wing shape changed significantly in every line between G0 and F1 and between F1 and F10. Total shape variance increased significantly between G0 and F1. Within-line shape variation was not significantly lower in F1 or F10 than the variation observed in G0, while between-line variation increased as the lines diverged. These patterns are consistent with previously cryptic variation becoming expressed following environmental change, together with founder effects, drift and increasing homozygosity. Our results show that substantial morphological changes can arise within a single laboratory generation, challenging the assumption that F1 individuals provide an unaltered representation of natural populations.

Specialized suction discs are functional innovations that enable fishes to attach to diverse surfaces and resist hydrodynamic forces. The adhesive discs of clingfishes (Gobiesocidae) vary in size and shape, but it is unclear how ecological factors have influenced their morphological evolution. Here we analyzed the disc and skull shape of 74 clingfish species using micro-CT scanning and 3D geometric morphometrics to investigate the role of habitat and substrate use on patterns of diversification. We also present novel comparisons of adhesive performance for 10 clingfish species. Clingfish interface directly with their environment using their adhesive discs, but we found that the disc and skulls are evolutionary integrated and share similar responses to habitat. Transitions from coastal habitats to coral reefs promoted elevated rates of evolution and morphological disparity across the body, whereas transitions to freshwater did not. Concurrently, repeated shifts from living on hard substrates to softer substrates (i.e., macroalgae and seagrass) were associated with more constrained disc shapes, convergent morphologies, and differences in adhesive performance. We propose that habitat and substrate use make complementary contributions to skeletal diversification in clingfishes, but the adhesive system requires further investigation to disentangle the complex interactions between form and function.

Animal personality is the expression of consistent among-individual variation in a behavioural trait across time and context. The application of this theory to behavioural research provides a valuable framework to investigate the among- and within-individual variation in behaviour. The animal personality theory is particularly relevant to understand and diagnostic fish welfare. It can be integrated within the nature-based welfare framework, which emphasizes the expression of species-specific behaviours and the maintenance of consistent behavioural patterns over time. Because behavioural trait such as boldness may be closely linked to other functional phenotypes, such associations reflect the broader concept of animal personality, whereby a behavioural trait can covary with another phenotypic trait to support an adaptive responses to environmental conditions. Although these relationships are both species and context dependent, they are consistently shaped by environmental conditions and environmental complexity tend to promote species specific behaviours and reduce maladaptive traits. Here we examined how structural environmental complexity shapes personality in Arctic charr and their covarying functional phenotypes, specifically growth rate and brain size. We propose that environmental complexity promotes alternative behavioural and functional phenotypes through multivariate phenotypic plasticity. We found that environmental complexity did not influence mean boldness between both treatments, but repeatability of boldness in the complex environment was remarkably consistent over a longer-term period, while estimates collapse after seven days in the plain treatment. Our findings are a clear evidence that environmental complexity foster stable behavioural trait expression and that a plain environment may suppress personality. Our results provide compelling evidence that behavioural structure and dynamics are embedded within patterns of behavioural variance. Although we found no support for behavioural covariation or associations with growth rate and brain size, we suggest that the animal personality framework may offer a valuable approach for diagnosing fish welfare issues through the partitioning of behavioural variance.

Multifunctional anatomical structures must accommodate potentially competing performance demands, leading to functional tradeoffs. The mammal rostrum (snout) is involved in multiple functions, including feeding, respiratory conditioning, olfaction, and, in most bats, echolocation. Therefore, it serves as an ideal system to investigate whether and how functional tradeoffs promote or constrain morphological diversification. While the external morphology of the rostrum has been linked with mechanical demands of feeding in bats, the factors and processes influencing its internal morphology, including the turbinals in the nasal cavity, remain comparatively unexplored. Here we investigate how internal rostral morphology reflects specialization and tradeoffs among respiratory air conditioning, echolocation, and olfaction by quantifying turbinal morphological diversity in a phylogenetically and ecologically diverse sample of bat species. We find that echolocation mode predominantly influences both the ethmoturbinal complex (ETc) and maxilloturbinal (MT) systems, with nasal-emitting bats having reduced and less complex turbinals compared to oral and non-laryngeally echolocating bat species. MT complexity and surface area are not associated with bioclimatic variables representing thermal variability and aridity. However, the ETc exhibits higher complexity in plantivorous bats than faunivorous bats, suggesting higher olfactory reliance. While MT morphological disparity was predominantly explained by echolocation mode, ETc morphological disparity was associated with both echolocation mode and diet, suggesting potentially opposing demands favoring turbinal reduction for sound transmission and elaboration for olfaction. Among nasal emitters, which must accommodate both demands within the nasal cavity, ETc complexity exhibited higher relative disparity compared to MT complexity. These patterns suggest that competing functional demands may promote or maintain morphological diversity, possibly through ecological specialization and/or many-to-one mapping between morphology and performance.

This study investigates the impact temperature-induced vertebral anomalies have on the C-start escape response of Astyanax mexicanus, a model species in evolutionary developmental biology. Employing three temperature treatments to induce varying degrees of skeletal anomalies, we assessed their effects on key swimming performance metrics including, C-start time, curvature coefficient, head displacement distance, and displacement velocity. Through the use of linear mixed models and generalized linear mixed models, our results reveal that specific anomalies such as vertebral fusions and anomalous haemal and neural spines affected the curving ability of C-start escape responses. However, these did not negatively impact other performance parameters, with velocity, distance, and response time showing no significant impacts from any anomaly types, when assessed individually. This suggests a complex interplay between structural deformities and compensatory physiological mechanisms that maintain functional performance. Other variables measured had a stronger and significant impact on swimming performance, including standard length, vertebral number, and temperature treatment, which influenced escape speed, curving ability, and overall locomotor performance. Our findings challenge conventional perceptions about the debilitating impact of vertebral anomalies, indicating that many affected fish can still effectively perform escape maneuvers critical for survival.

Adult sex ratios in mammals are usually female-biased, but the northern mole vole (Ellobius talpinus) (Pallas, 1770), a cooperatively breeding subterranean rodent, shows a persistent male bias that increases with age. Combining four years of capture-mark-recapture data with radiographic age estimation and genetic parentage data, we modeled apparent survival and state transitions (young-of-the-year, breeder, non-breeder) separately by sex. Young individuals showed significantly lower apparent survival than adults in both sexes, consistent with dispersal occurring predominantly in the first year of life. Within each age class, females showed consistently lower apparent survival than males, and this pattern held within breeding and non-breeding status groups alike, with female breeders showing lower apparent survival than male breeders. These results point to female-biased natal dispersal, an atypical pattern for mammals. We propose that faster turnover of reproductive females than males, in combination with singular breeding, favor female dispersal in search of vacant breeding positions, while promoting male philopatry and facultative polyandry.

Phenotypic differences among populations can arise through heritable genetic divergence, phenotypic plasticity, or both, making it difficult to determine whether trait-environment correlations observed in nature reflect adaptive evolution. Within threespine stickleback (Gasterosteus aculeatus) studies, numerous document morphological differences among allopatric-, parapatric-, and even sympatric populations. These phenotypic differences among populations are often correlated with diet and lake habitat (e.g., lake size), suggesting an adaptive value to the population differences. However, many studies of ecomorphological divergence in stickleback use wild-caught stickleback, which may differ due to evolution or plasticity. Although common garden experiments have confirmed that population differences can be heritable, such experiments typically entail small numbers of populations. Consequently, we still do not know to what extent well-known trait-environment correlations in stickleback are a result of evolution. To address this gap, we reared stickleback embryos from 27 lake populations on Vancouver Island, in a laboratory environment. Morphological differences among populations persist in common-garden fish, confirming a large role for divergent evolution. These heritable differences were associated with environmental variation among lakes, implying an adaptive value. However, some well-known trait-environment relationships in stickleback did not persist in common-garden fish and may be primarily plastic.