Evolutionary biologists commonly use landmark-based geometric morphometrics to characterize and compare biological shapes. Advances in three-dimensional imaging hold potential to catapult morphometric studies, but quantifying shape from 3D surfaces efficiently remains challenging. Several surface-only morphometric procedures have been proposed, which align surfaces to one another and use their differences as the basis of shape quantification and analysis. Comparisons of landmark-based and surface-only methods for specific datasets have revealed mixed results, but these studies utilized empirical datasets where the true patterns of shape differences are unknown. In this study we performed a simulation experiment where the true shape differences between objects were known, and evaluated the performance of two landmark-based and four surface-only methodologies under these conditions. Several procedures, including landmarks plus semilandmarks, as well as the surface-only method DAA (and to a lesser extent auto3d), most consistently recovered the known patterns of shape variation. Results from other surface-only procedures (GPSA and pseudoLM) were more variable. Notably, patterns in more complex shapes were better characterized than patterns in simpler shapes, implying that automated surface-only methods were challenged when presented with shapes whose principal axes were similar, or where structures contained few localized shape differences for these methods to properly orient the surfaces. Overall, our findings highlight that while biologically informed landmarking remains imperative as a foundation for morphometric analyses, some surface-only procedures do offer a powerful and efficient means of characterizing shape, and hold promise for morphometric studies.
The Extended Evolutionary Synthesis (EES) has been presented as an expansion of the Modern Synthesis (MS). A common and parsimonious view maintains that MS’s quantitative evolutionary biology remains both valid and central within the EES, insofar as the EES primarily introduces a more elaborate qualitative research agenda. This article examines the relationship between qualitative and quantitative approaches in the EES debate and argues for a more complex view of how the EES relates to the MS. Its guiding question is whether quantitative evolutionary biology itself might call for an EES. Although no specific answer is supported, the article analyzes the significance of this question and surveys the principal positions in the current literature. Two aims structure the discussion. First, by providing a detailed literature review, I show that, over the past two decades, quantitative research programs have increasingly contributed to modeling the phenomena at the core of the EES. The rationale for the EES is not confined to qualitative considerations; a growing body of work now (re)interprets population-level dynamics through the EES lens. Second, I present the problem of models: Is the mathematical framework of the MS sufficient to account for the phenomena emphasized by the EES, or must these models be extended? I identify and discuss four main positions: (1) strong accretionism—standard quantitative evolutionary biology is enough; (2) mild accretionism—the continuous historical expansion implies that current extensions do not constitute a substantive theoretical shift; (3) mild radicalism—population models require EES assumptions and novel applications; and (4) strong radicalism—some biological phenomena demand genuine modifications to the existing modeling framework.
Obligate endosymbionts such as Buchnera aphidicola are expected to evolve under strong genetic drift due to small effective population sizes and repeated transmission bottlenecks, which may limit the efficacy of natural selection. However, whether ecological differences among aphid host plants can impose detectable selection on these symbionts remains unclear. Here, we investigated the evolutionary dynamics of Buchnera in gall-forming aphids associated with two distinct primary host plants, Rhus and Pistacia. Using comparative genomics of 18 species, we reconstructed phylogenetic relationships and analyzed genome-wide patterns of selection. We found that Buchnera from aphids associated with Pistacia exhibited stronger purifying selection, whereas lineages associated with Rhus showed a progressive relaxation of selective constraints. This consistent directional pattern is unlikely to be explained by stochastic processes alone, suggesting a role for host plant-associated selection. To further assess short-term physiological responses, we compared transcriptomes of Schlechtendalia chinensis across its primary host plant (Rhus chinensis) and secondary overwintering host (the moss Plagiomnium maximoviczii). Genes involved in amino acid biosynthesis were downregulated during overwintering, whereas stress-response genes were upregulated, indicating transient physiological adjustments to environmental conditions. Together, these results demonstrate that ecological variation among aphid host plants can shape the long-term evolution of an obligate symbiont despite the strong influence of genetic drift, while seasonal host shifts primarily affect short-term gene expression rather than long-term selective regimes.
Human populations have undergone extensive migrations throughout history, shaping genetic diversity through admixture. Admixed individuals inherit mosaic genomes composed of ancestry tracts from multiple ancestral populations. The distribution of these ancestry tracts provides insights into historical migration patterns and gene flow, as well as implications for complex disease disparities in admixed populations. However, modeling these genomic patterns remains challenging. The goal of this study is to systematically validate the analytical predictions of the tracts model against stochastic coalescent simulations. Using the tracts software and the coalescent simulator msprime, we modeled time-dependent gene flow and analyzed the distribution of admixture tracts under simple and complex demographic scenarios. We compared TRACTS model accuracy across different scenarios, including 2-way, 3-way admixture, as well as single pulse and multiple pulse models. Additionally, we assessed the computational efficiency of tracts and msprime in a two-population pulse admixture model under varying chromosome sizes. We demonstrate that the TRACTS model captures the dynamics of admixture tracts comparably to the msprime simulator under both simple and complex demographic scenarios, while offering a significant computational speed advantage.
Reproductive Character Displacement (RCD) often occurs when species with mating-related polymorphism come into secondary contact, leading to divergence in reproductive traits. Ischnura elegans and Ischnura graellsii have formed two independent hybrid zones in Spain where reinforcement has strengthened a mechanical barrier, and RCD has shaped mating-related structures, although reinforcement is asymmetric only in gynochrome females. This study examines the link between asymmetric reinforcement and asymmetric RCD. Using geometric morphometrics, we analyze prothorax shape and size in both female morphs and males, and male caudal appendages, to assess morphological divergence, determine whether gynochrome females show stronger divergence, and evaluate how reproductive traits respond across morphs and sexes. Our results reveal consistent patterns of size and shape variation across species and zones: in I. elegans, androchromes are larger and resemble males in size, with clear shape differentiation between female morphs that diminishes in hybrid zones. In contrast, I. graellsii shows less consistent size differences between males and morphs, and weaker shape differentiation. Our results confirm RCD in prothorax shape in I. elegans females from both hybrid zones, but reveal that RCD in prothorax size is asymmetric, occurring only in gynochrome females from the NC hybrid zone. These findings indicate that different reproductive traits respond asymmetrically to hybridization across morphs and species. Our results show that female polymorphism shapes the evolutionary response to hybridization by promoting asymmetric patterns of RCD and reinforcement among morphs, highlighting its role in the evolution of reproductive isolation in polymorphic systems.
Geometric morphometrics has become a widely used toolkit for quantitative morphology across diverse biological fields. It relies on the precise placement of anatomical landmarks in 2D or 3D. However, manual landmarking, especially in 3D, is labour-intensive, time-consuming, prone to intra- and inter-observer variation and requires significant expertise. These limitations are increasingly incompatible with the demands of high-throughput imaging workflows. This bottleneck has spurred efforts to automate landmarking, often through deformable registration of 3D images, surfaces, or point clouds. While these methods can effectively capture overall shape, they may introduce biases in landmark localization and distort patterns of variances and covariances. Previous attempts to mitigate these issues with deep learning (DL) have generally focused on specific anatomical parts of certain species, most notably human faces and craniofacial anatomy in model-organisms. In this study, we introduce a DL-based pipeline for refining landmark placement. The pipeline begins with approximate landmark predictions derived from a simple rigid registration. These initial predictions define local 3D surface regions, which are then parametrized into 2D using least-squares conformal maps and enhanced with colorization informed by diverse geometry and ambient lighting. The resulting standardized representations are then used to train Transformer and Convolutional Neural Network (CNN) architectures. The approach was evaluated using an open-access dataset of 3D mouse skull models with manually digitized landmarks. Focusing on ten distinct landmarks, we compared our rigid + DL predictions with those from a mainstream global registration approach, ALPACA. We assessed both distance accuracy to the manual groundtruth and preservation of the shape variation patterns. We also examined the effects of various hyperparameter settings strategies, offering practical guidelines for future implementations. Our results demonstrate the feasibility of using 2D colored-enhanced local geometric representations for accurate landmark position refinement with DL. The proposed approach mitigates biases associated with the considered deformable registration method and establishes a methodological foundation for more generalizable, high-throughput morphometric analyses using DL.
The Navajini is a clade of Neotropical electric fishes specialized to inhabit deep river channels in the lowland Amazonian, with species that exhibit high craniofacial disparity and a highly conservative post-cranial body shape. This study investigates the morphological, ecological, and developmental factors contributing to phenotypic diversification in this clade. By integrating 3D geometric morphometrics, phylogenetic comparative methods, and ancestral state estimation within a robust phylogenetic framework, we examine the evolution of skull shape across the group. Our approach combines high-resolution micro-CT scanning with multivariate analyses to identify major axes of craniofacial disparity, and to assess how these patterns relate to ecology, sexual dimorphism, and phylogenetic history. Rather than being randomly distributed or purely environmentally plastic, key traits such as lower jaw elongation, opercle morphology, and maxilla orientation exhibit strong phylogenetic signal and structural consistency within genera. We explore how certain lineages have accessed distinct regions of craniofacial morphospace, likely by means of trophic specialization and developmental shifts. Sexual dimorphism emerges as a major contributor to morphological disparity in some but not all subclades. These results highlight repeated evolutionary trajectories among taxa that share similar ecological roles or mating strategies. Together, these findings provide new insights into the processes driving phenotypic evolution in one of the most morphologically diverse lineages of Neotropical freshwater fishes.
Robustness is a common feature of many developmental systems. This is perhaps best demonstrated by tolerance to heterozygous loss of function for many mutations. This non-linear interaction acts protectively, preventing major deleterious effects and preserving correct development. Critical cell signalling pathways that are reused throughout development, such as Hedgehog (Hh) signalling may tend to exhibit high degrees of robustness to variation in gene expression level due to selection against the widespread deleterious effects of their functional perturbation. Here, we investigate the robustness of Hh signalling in zebrafish by selectively inhibiting Hh signalling at a specific timepoint with varying concentrations of the small molecule inhibitor cyclopamine. Through increasing the concentration, we alter the amount of Hh signalling the embryo receives from low inhibition to complete inhibition. Using 3D geometric morphometrics, we uncovered a clear threshold at which Hh inhibition generates severe phenotypes and further defined a non-linear relationship between Hh signalling output and craniofacial morphology. Interestingly, this non-linear relationship also appears to allow for new directions of shape change that differ from the major “Hh loss” axis. This is particularly noticeable at below-threshold levels of inhibition, where the phenotypic changes are subtle and non-severe, but the direction is distinctly different. This change in covariance structure along the non-linear response curve suggests that the probing of limits of robustness for developmental processes may be a mechanism for overcoming developmentally constrained covariation structure to establish novel directions of evolutionary change.
Modern birds inhabit a remarkable breadth of ecological niches, a diversity that is in part attributable to the range of forms and functions that have evolved in the avian foot. Variation in the lengths, orientations, and internal proportions of their toes have enabled specialised grasping, climbing, and walking morphologies to evolve from a shared ancestral form. However, many individual elements of the foot are developmentally moderated in tandem. This integration of phenotypic traits can benefit the evolutionary process by coordinating traits to better maintain complex functions across generations, but may also inhibit adaptation in individual traits. Hence, trait integration has the capacity to constrain or enable evolution in certain directions. Here, we examine how adaptation for grasping (i.e., perching, climbing, and object manipulation) affects strength of integration in four common avian foot morphologies. Using measures of trait covariation and correlation, we conclude that grasping ability alone is likely an insufficient predictor of morphological integration. Overall, whole-foot integration strength and evolutionary potential are surprisingly consistent across the sampled morphologies, however, there exist differences in fine-scale integration patterns across species that merit further investigation. We find anisodactyl foot morphologies (e.g., fowl and songbirds) appear less integrated and more evolutionarily flexible than zygodactyl morphologies (e.g., parrots and woodpeckers), but that zygodactyl morphologies may be capable of a greater response to selection in certain directions. Such research helps to inform our understanding of both the evolutionary history of these taxa as well as how they may adapt to changing ecosystems in the future.
Differences in dentition between species relate to feeding specialisations, as examples of tetrapod dentition variation show clearly. The association of tooth traits and ecological opportunities in non-mammalian vertebrates is less studied. We examined variation in dental traits in four sympatric morphs of Arctic charr (Salvelinus alpinus) which differ in feeding specialisations, head and jaw bone morphology. We studied tooth numbers in six bones (dentary, maxilla, premaxilla, palatine, vomer and glossohyal) and tooth angles in one bone (maxilla). We found fluctuating asymmetry in tooth numbers and angles and that the allometry of tooth numbers varied by bone but not morphs. The premaxilla tooth numbers showed the least asymmetry, no difference between morphs and no allometry. Tooth numbers differed by morphs in four bones (dentary, palatine, vomer and glossohyal), with the morphs defined as pelagic having more teeth. There was also a difference in maxilla tooth angle, with benthic morphs having teeth which were angled more inwards. Previously we showed variation in bone shape and here we saw correlation between tooth number and bone shape. We hypothesize that tooth number differences are non-adaptive and are likely a correlated response to possible adaptive bone shape change. Maxilla tooth angle did not correlate with bone shape, we hypothesize tooth angle difference could be adaptive, not tested. While it is currently unknown what tooth characteristics are ancestral vs. derived in these populations, the marked differences in specific bones presents an opportunity to explore rapid evolution in dentition.
The Constrained Lever Model of vertebrate jaw biomechanics posits that the configuration of the triangle of support—demarcated by the bite point and the temporomandibular joints (TMJs)—limits muscle activity and thus feeding function. In particular, the resultant vector of the masticatory muscle forces must pass through the triangle or else the working-side mandibular condyle may be distracted out of the TMJ. We predict that the triangle acts as a functional module that is integrated with other aspects of mandibular morphology to facilitate coordinated evolution of the mandible as a whole. We tested whether skeletal traits in a triangle of support module facilitate mandibular evolution to a greater extent than random modules along a hypothetical selective trajectory. We applied viability selection modeling to simulate mandibular evolution from an ancestral population (common chimpanzees or Australopithecus afarensis) toward an adaptive peak representing modern humans. In these simulations, selection acts only on measurements assigned to the triangle of support or a random module, but other dimensions evolve via observed integration. The results demonstrated that selection on the triangle of support was more effective than expected by chance in producing a human-like mandible in a shorter amount of evolutionary time, when compared with randomly grouped sets of measurements.
Domestication is considered one of the most powerful evolutionary forces driving brain size reduction in animals, as observed when domestic species are compared with their wild conspecifics. This pattern is often attributed to the relaxed selective pressures associated with foraging and predator avoidance in domestic environments. In this study, we compared relative brain size between domestic and wild conspecific frogs, including the American bullfrog (Lithobates catesbeianus) and the black spotted frog (Pelophylax nigromaculatus), while controlling for body size. We found that domestic individuals exhibited significantly reduced brain sizes compared with their wild counterparts in both species. These findings align with domestication theory, which posits that reduced predation risk and human-provided resources in captive environments contribute to brain size reduction. We also found that domestic bullfrogs tended to show greater brain size reduction than domestic black spotted frogs. To our knowledge, this is the first empirical evidence demonstrating that domestication is a major factor driving brain reduction in frogs.
The insular golden lancehead Bothrops insularis presents several morphological features that diverge between sexes and closely related species such as body size, stoutness, and head traits. These differences are often attributed to specificities in reproductive or ecological requirements and frequently reflect microevolutionary patterns. In this study, we evaluated sexual dimorphism and ontogenetic allometry in B. insularis and compared head shape with two mainland populations of B. jararaca using linear and geometric morphometrics to understand the patterns involved in morphological divergence. Females were larger than males for almost all body parameters analyzed, except for tail traits, and also had a larger and wider head. We found no difference in model slopes for body and head shape ontogenetic trajectories, indicating that both sexes shared common trajectories in postnatal development. Interspecific comparisons revealed marked differences in males’ head shape and ontogenetic trajectories. The head of B. insularis was phenotypically closer to the highland B. jararaca population which is in accordance with the phylogenetic affinity of B. insularis with this population. On the other hand, B. insularis showed a snout size similar to that of the coastal population. The resemblance in snout shape to the coastal population may represent an evolutionary divergence from a shared ancestor with the highland population as a consequence of island isolation and diet consisting of birds.
Incorporating established models from biosemiotics, I propose five observable elements of living systems which are derived from current, established biological theory and empirical data. These identified elements suggest that species may evolve chaotically, not stochastically. One significant means by which it would be possible to examine whether the processes in an evolving living system are chaotic, is by calculating the system’s Lyapunov exponent (LE). The LE indicates the degree of observable chaos in a dynamic system, by determining the convergence or divergence of the system’s processes. It does this by comparing the rate at which two or more process trajectories within the dynamic system move and change. If the trajectories are moving away from each other in phase space, resulting in a positive Lyapunov exponent, it suggests the system is chaotic. Evolving species form process trajectories as their phenotypic characteristics change, whether the driving factors of evolution are external and selective, or internal and agential. Thus, the LE of an evolving system could be used in conjunction with molecular clock tree data to ascertain the degree of divergence, or chaos present in evolving living systems.
Talpids occupy a variety of ecological niches: terrestrial (shrew-like moles), semi-aquatic (desmans), semi-aquatic/fossorial (star-nosed mole), semi-fossorial (shrew moles) and fossorial (‘true moles’). Yet, the evolutionary steps underlying the niche differentiation in the Talpidae, starting in the mid-Tertiary, are not fully resolved. To address this, we constructed a phylogeny based on mitogenomes of 24 species, substantially expanding on previous mitogenome phylogenies of talpids. We provided the first mitogenome of the Russian desman Desmana moschata (Linnaeus, 1758), adding a third semi-aquatic talpid species to the analysis. Phylogenetic analyses with Maximum Likelihood and Bayesian Inference gave many congruent but some distinctive results. The Russian and Iberian desmans are closely related, and a time-calibrated Bayesian analysis suggests they diverged 16 million years ago. Considering wider relationships, the terrestrial shrew-like moles (subfamily Uropsilinae) are the sister group to other talpids (subfamily Talpinae), consistent with previous work. Within the Talpinae, the star-nosed mole (Condylura), with both semi-aquatic and fossorial adaptations, is sister to a clade comprising the rest of the subfamily in the Bayesian Inference mitogenome phylogenies (relationships are unresolved in the Maximum Likelihood phylogeny). Ancestral state reconstruction supports a terrestrial ancestry for the Talpidae but varied results for the ancestry of the Talpinae, and we discuss the possibility of ecological flexibility in that ancestor. We have generated the most detailed mitogenome phylogeny of the Talpidae to date, providing evolutionary scenarios into the origin of the different ecotypes in the family. Complementary studies with nuclear genomes will help confirm the sequence of acquisition of different traits.
