Anjali Goswami

Recent advances in shape quantification techniques have revolutionised the field of evolutionary morphology by providing a time‐efficient alternative to well‐established methods such as geometric morphometrics. In particular, landmark‐free methods are at the forefront of new developments in shape analysis, but concerns over their reproducibility and sensitivity to non‐biological variation have hindered more widespread adoption. A primary source of non‐biological bias in shape analysis is misalignment and incorrect scaling of specimens, which can result in capturing anatomically incongruent aspects of shape in otherwise homologous structures. Here, we compare methods for mesh alignment and scaling using a recently described landmark‐free approach, Deterministic Atlas Analysis (DAA). We find similarities between morphospaces derived from meshes aligned using most alignment protocols, but with large differences in variance structure. Surprisingly, the largest differences are not found between Procrustes‐based and non‐Procrustes‐based approaches, but between the Procrustes‐based method with internal scaling and all other alignment approaches. More broadly, scaling method has the greatest impact on shape variation captured by DAA. Based on these results, we make recommendations to ensure that alignment strategy maintains homology in landmark‐free morphometry. As in all morphometric analyses, violating principles of homology can result in spurious or inaccurate biological inferences in macroevolutionary studies of anatomy and must be explicitly considered in designing methodological frameworks.

Multivariate phylogenetic comparative methods for modeling high-dimensional traits such as 3D shapes or gene expression profiles have been recently developed. However, these approaches are impractical and almost impossible to use when the number of traits exceeds a few thousands, as they become computationally prohibitive. We overcome these limitations by proposing a new maximum likelihood approach based on the Empirical Bayes framework. This approach takes into account the information of the complete covariances (among species and traits) to infer parameters and compare trait evolution models for high-dimensional data sets. Through simulations, we demonstrate that the proposed approach can accurately estimate parameters of various trait evolution models, even when the number of traits is 10 times larger than the number of lineages; it requires less memory and is at least 10 times faster than currently available approaches. This efficient framework enabled us to extend the high-dimensional multivariate phylogenetic comparative toolkit by including an Ornstein–Uhlenbeck process with multiple optima to study adaptation to various selective regimes. Applying our approach to the evolution of jaw morphology in relation to dietary adaptation in mammals, we demonstrate morphological convergence in carnivorous and herbivorous lineages. The proposed Empirical Bayes approach, implemented in the R package mvMORPH, enables phylogenetic comparative methods to efficiently handle high-dimensional data sets and complex models of trait evolution.

Given the ever-increasing availability of highly detailed phenotypes, modelling trait evolution in a multivariate framework is becoming a challenging task. Current phylogenetic comparative methods often struggle with high-dimensional datasets because they suffer computational limitations and interpretability. Here, we propose a maximum likelihood-based approach called Probabilistic and Phylogenetic Principal Components Analysis (P3CA) to circumvent current limitations. This approach is based on a continuous latent variable model, whereby observed traits are explained by a smaller number of unobserved variables that evolve according to a given evolutionary model. We implement the approach under Pagel’s lambda model using an Expectation-Maximisation algorithm that makes it computationally efficient and allows missing values. Using simulations, we demonstrate that evolutionary parameters are accurately estimated, regardless of phylogenetic signal, the number of traits or the proportion of missing values. The reconstruction of the reduced space is more accurate than the one obtained using other dimensionality reduction approaches, such as phylogenetic and conventional PCA. Likewise, the estimated values for missing data are more accurate than those obtained using current phylogenetic data imputation approaches. We illustrate the approach on a 3D geometric morphometric dataset describing Crocodyliformes skull shapes and containing around 4% of missing data. Our P3CA method unlocks the possibility to analyse and more easily interpret the large-scale multivariate datasets generated in recent decades within a phylogenetic comparative framework.

Domestic dogs ( Canis familiaris ) display more morphological variation than any other mammal. Cranial morphology has been extensively studied, as have the relationships with function, development, genetics, veterinary medicine, and breed welfare. Postcrania remain comparatively understudied, despite well-documented breed-specific predispositions to musculoskeletal disease. Here, we apply three-dimensional landmark-free morphometrics to quantify the shape of 743 elements from 213 dogs, including the scapula, humerus, radius, ulna, pelvic girdle, femur, tibia, and fibula. We assess integration among limb elements and investigate drivers of shape variation within and between breeds. Across most breeds, limb bone shape is strikingly similar. Dachshunds, however, exhibit distinct morphology across all elements and one to two orders of magnitude greater variation than any other breed. Despite this disparity, integration remains high between all element pairs. Remarkably, we find no significant relationship between bone shape and body mass, age, or pathology, but comparison with historic specimens reveals marked changes in dachshund long bone shape over the past ∼150 years. These extreme differences are not shared by other sampled chondrodysplastic breeds, underscoring the need to understand morphological diversity beyond simple categorisation. These findings provide a quantitative framework for linking postcranial morphology with function, disease risk, and evidence-based improvements to canine welfare.

Multivariate phylogenetic comparative methods for modelling high-dimensional traits such as 3D shapes or gene expression proBiles have been recently developed. However, these approaches are impractical and almost impossible to use when the number of traits exceeds a few thousands, as they become computationally prohibitive. We overcome these limitations by proposing a new maximum likelihood approach based on the Empirical Bayes framework. This approach takes into account the information of the complete covariances (among species and traits) to infer parameters and compare models of trait evolution for high-dimensional datasets. Through simulations, we demonstrate that the proposed approach can accurately estimate parameters of various trait evolution models, even when the number of traits is ten times larger than the number of lineages; it requires less memory and is at least 10 times faster than currently available approaches. This fast, efBicient framework enabled us to extend the high-dimensional multivariate phylogenetic comparative toolkit by including an Ornstein-Uhlenbeck process with multiple optima to study adaptation to various selective regimes. Applying our approach to the evolution of jaw morphology in relation to dietary adaptation in mammals, we demonstrate morphological convergence in carnivorous and herbivorous lineages. The proposed Empirical Bayes framework, implemented in the R package mvMORPH, enables phylogenetic comparative methods to efBiciently handle high-dimensional datasets and complex models of trait evolution.

Mandibles represent a key evolutionary innovation that has enabled jawed vertebrates to adapt and diversify in response to a range of food sources, and changes in mandible shape are often linked with adaptive radiations into new ecological niches. Using a phylogenetic comparative approach, we explore the phenotypic disparity and mechanical properties of the lower jaw in Pelagiaria, a morphologically diverse but relatively small clade of open-ocean fishes which arose near the Cretaceous/Paleogene (K/Pg) mass extinction event. Using three-dimensional (3D) geometric morphometrics, we find that the high phenotypic disparity of the pelagiarian mandible was established very early in their evolutionary history, and high levels of disparity have been maintained over tens of millions of years; this is consistent with the hypothesis that Pelagiaria represents an ancient adaptive radiation. We test the correlation of mandible shape with potential drivers of shape evolution and find that mandible shape is correlated with habitat depth and tooth type but not with body elongation or diet. Moreover, mandible shape is significantly correlated with mechanical advantage (MA), with closing MA being most strongly correlated. Pelagiarian jaw shapes fall broadly into six morphotypes, of which two show significantly higher closing MA than other groups, despite differing substantially in shape. Our results demonstrate both the mechanical and morphological diversity of the pelagiarian mandible and support the hypothesis that Pelagiaria underwent rapid morphological diversification early in their evolution, likely due to adaptive radiation.

India, one of the world’s most biodiverse countries and now the most populous, stands at a critical intersection of ecological wealth and intense anthropogenic pressure. Its unique geological history, once part of Gondwana and later colliding with Asia, has profoundly shaped its biota, resulting in high levels of endemism and evolutionary distinctiveness. Despite a deep cultural reverence for nature, much of India’s biodiversity, its distribution, evolutionary origins, and future trajectory remain poorly understood. At the heart of shaping a resilient future for biodiversity science in India lies the urgent need for a modern, accessible, and integrated biodiversity research. Here, we assess the current state of biodiversity science in India, drawing from taxonomic and biogeographical studies that rely heavily on natural history collections. For many taxa and ecosystems, data remain scarce or outdated, often based on collections from the 19th and 20th centuries, with critical gaps in molecular, distributional, and phenotypic trait information. Existing data are frequently fragmented, inaccessible, or poorly integrated. These limitations hinder the ability to understand biogeographical patterns or monitor biodiversity change during the Anthropocene. We argue that a national institution dedicated to biodiversity research is urgently needed to coordinate the documentation, analysis, and conservation of India’s natural heritage for future generations.

Phenotypic integration has been shown to influence the degree and direction of organismal evolution in vertebrates. Comparatively fewer multivariate analyses of shape have been conducted in invertebrates, partly due to difficulties in identifying unambiguously homologous landmarks. We present the first landmark-free deterministic atlas analysis (DAA) of shape and integration between insect tagmata, characterizing intraspecific variation in the blowfly Calliphora vicina (Diptera: Calliphoridae). We recover sexual dimorphism in the shape of all three tagmata, even where differences are gradational or indistinguishable from visual inspection. Partial least square analysis reveals high integration between tagmata within females, but not males. In males, integration is low between the thorax and abdomen, and absent between the head and abdomen. This reflects independence in the mechanisms underlying shape variation, including the development of highly sexually dimorphic eye morphologies and of structures that house the genital apparatus. Furthermore, we find a relationship between within-segment integration and morphological variance suggesting within-tagma integration may be facilitating shape variation in C. vicina. These intraspecific insights highlight the potential for landmark-free studies investigating the influence of development on shape and integration between species and across clades. Moreover, these techniques may aid forensic entomology, where sex determination can assist with postmortem interval estimates.

Metamorphosis, a common and spectacular developmental process, involves major phenotypic changes often linked to environmental transitions. Understanding how these changes affect morphological evolution is crucial for examining metamorphosis's evolutionary impacts. In this study, we analysed the role of metamorphosis and life cycle variation on the morphological evolution of the mandible in Caudata (salamanders and newts), a clade that exhibits a great diversity of life cycles and ecologies. We focused on the mandible, a key component of the masticatory apparatus, to investigate how life cycle variation may influence the diversification of feeding modes. Using 3D geometric morphometrics on 317 extant species of Caudata, we found that both life cycle and size influence mandible shape, with complex interactions between these factors. The morphology of the mandibular bones evolved more independently in species undergoing complete metamorphosis compared to those with partial metamorphosis, likely facilitating feeding diversification in terrestrial adults. On the other hand, high morphological integration in species undergoing partial metamorphosis could promote the rapid evolution of traits, resulting in the differentiation of more disparate morphologies, potentially aiding paedomorphic species in adapting to challenging environments. This study highlights the interplay between metamorphosis and the environment in shaping morphological evolution among species and provides new insights into the role of heterochrony in the morphological diversification of organisms. Read the free Plain Language Summary for this article on the Journal blog.

Evolution of the mandibular structure has played a key role in the taxonomic diversification and niche exploration of tetrapods, from the initial water-to-land transition to the origin and radiation of mammals. While jaw evolution through these key transition points have long attracted attention, no studies of jaw evolution to date capture the breadth of tetrapod diversity and evolutionary history. Here, we reconstruct the compositional evolution of the tetrapod mandible with a comprehensive dataset of 36 traits scored in 3047 species. This sampling spans the earliest eotetrapodiforms to extant amphibians, mammals, and reptiles and birds, capturing immense ecological, developmental, and taxonomic diversity among a near-even split of extant and fossil tetrapods. We find that lower jaw morphology rapidly canalises at the base of each major clade, including, Eotetrapodiformes, Amniota, Synapsida, Sauropsida, and Amphibia, as well as subclades within those groups, and that, as a result, jaw compositional variation is highly phylogenetically structured. We estimate an average of over 100 shifts in three key traits: number of elements (dermal and endochondral bones), number of tooth-bearing elements, and total teeth per hemimandible, with symmetrical rates of gains and losses estimated for the number of elements, and correlated evolution between these three characters. Although novel elements arise occasionally, disparity in jaw composition overwhelmingly decreases as clades canalise rapidly, successively, and pervasively through tetrapod evolutionary history.