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Tests of phenotypic convergence can provide evidence of adaptive evolution, and the popularity of such studies has grown in recent years due to the development of novel, quantitative methods for identifying and measuring convergence. These methods include the commonly applied C1-C4 measures of Stayton (2015a), which measure morphological distances between lineages, and Ornstein-Uhlenbeck (OU) model-fitting analyses, which test whether lineages converged on shared adaptive peaks. We test the performance of C-measures and other convergence measures under various evolutionary scenarios and reveal a critical issue with C-measures: they often misidentify divergent lineages as convergent. We address this issue by developing novel convergence measures-Ct1-Ct4-measures-that calculate distances between lineages at specific points in time, minimizing the possibility of misidentifying divergent taxa as convergent. Ct-measures are most appropriate when focal lineages are of the same or similar geologic ages (e.g., extant taxa), meaning that the lineages' evolutionary histories include considerable overlap in time. Beyond C-measures, we find that all convergence measures are influenced by the position of focal taxa in phenotypic space, with morphological outliers often statistically more likely to be measured as strongly convergent. Further, we mimic scenarios in which researchers assess convergence using OU models with a priori regime assignments (e.g., classifying taxa by ecological traits) and find that multiple-regime OU models with phenotypically divergent lineages assigned to a shared selective regime often outperform simpler models. This highlights that model support for these multiple-regime OU models should not be assumed to always reflect convergence among focal lineages of a shared regime. Our new Ct1-Ct4-measures provide researchers with an improved comparative tool, but we emphasize that all available convergence measures are imperfect, and researchers should recognize the limitations of these methods and use multiple lines of evidence to test convergence hypotheses.

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Exploring the phylogenetic signal of morphological traits using geometric morphometry represents a powerful approach to assess the relative weights of convergence and shared evolutionary history in shaping species' forms. We evaluated the phylogenetic signal in shape and size of ventral and dorsal haptoral anchors of 10 species of monogenoids (Hamatopeduncularia, Chauhanellus and Susanlimocotyle) occurring in marine catfish (Siluriformes: Ariidae) from the Atlantic coast of South America. The phylogenetic relationships among these species were mapped onto the morphospaces of shape and size of dorsal and ventral anchors. Two different tests (squared change-parsimony and Kmult) were applied to establish whether the spatial positions in the phylomorphospace were influenced by phylogenetic relationships. A significant phylogenetic signal was found between anchor form and parasite phylogeny. Allometric effects on anchor shape were non-significant. Phylogenetically distant species on the same host differed markedly in anchor morphology, suggesting little influence of host species on anchor form. A significantly higher level of shape variation among ventral anchors was also found, suggesting that the evolutionary forces shaping ventral anchor morphology may operate with differing intensities or exhibit distinct mechanisms compared to their dorsal counterparts. Our results suggest that phylogenetic relationships were a key driver of changes in shape (but not size) of anchors of monogenoids of South American ariids. However, it seems that the emergence of the digitiform haptor in Hamatopenducularia and in some species of Chauhanellus played an important role in the reduction in anchor size and may cause secondary losses of anchors in other groups of monogenoids.

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Symbiotic species, living within or on the surface of host organisms, may evolve a wide range of adaptations as a result of various selection pressures, host specificity of the symbiont and the nature of the symbiosis. In tropical marine coral reef ecosystems, palaemonid shrimps (Crustacea: Decapoda: Caridea) live in association with at least five different invertebrate phyla. Host switches between (distantly) related host groups, and the thereby associated selection pressures were found to play a major role in the diversification of these shrimp lineages, giving rise to various host-specific adaptations. Two lineages of palaemonid shrimp, which have switched from an ectosymbiotic association towards endosymbiosis, are studied for their morphological diversification and possible convergence. Special attention is given to the between-phyla host switches involving ascidian and bivalve hosts, which are characteristic for these lineages. Using landmark-based (phylo)morphospace analyses and Scanning Electron Microscopy, the walking leg dactylus shape and the microstructures on these dactyli are studied. No specific bivalve- or ascidian-associated morphotypes were found, but morphological convergence in dactylus morphology was found in various species within the two studied clades with similar host groups. In addition, multiple lineages of bivalve-associated species appear to be morphologically diverging more than their ascidian-associated relatives, with 'intermediate' morphotypes found near host-switching events.

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Morphological analyses are critical to quantify phenotypic variation, identify taxa, inform phylogenetic relationships, and shed light on evolutionary patterns. This work is particularly important in groups that display great morphological disparity. Such is the case in geomyoid rodents, a group that includes 2 of the most species-rich families of rodents in North America: the Geomyidae (pocket gophers) and the Heteromyidae (kangaroo rats, pocket mice, and their relatives). We assessed variation in skull morphology (including both shape and size) among geomyoids to test the hypothesis that there are statistically significant differences in skull measurements at the family, genus, and species levels. Our sample includes 886 specimens representing all geomyoid genera and 39 species. We used the geometric mean to compare size across taxa. We used 14 measurements of the cranium and lower jaw normalized for size to compare shape among and within taxa. Our results show that skull measurements enable the distinction of geomyoids at the family, genus, and species levels. There is a larger amount of size variation within Geomyidae than within Heteromyidae. Our phylomorphospace analysis shows that the skull shape of the common ancestor of all geomyoids was more similar to the common ancestor of heteromyids than that of geomyids. Geomyid skulls display negative allometry whereas heteromyid skulls display positive allometry. Within heteromyids, dipodomyines, and non-dipodomyines show significantly different allometric patterns. Future analyses including fossils will be necessary to test our evolutionary hypotheses.

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Incorporating morphological data into modern phylogenies allows integration of fossil evidence, facilitating divergence dating and macroevolutionary inferences. Improvements in the phylogenetic utility of morphological data have been sought via Procrustes-based geometric morphometrics (GMM), but with mixed success and little clarity over what anatomical areas are most suitable. Here, we assess GMM-based phylogenetic reconstructions in a heavily sampled source of discrete characters for mammalian phylogenetics-the basicranium-in 57 species of marsupial mammals, compared with the remainder of the cranium. We show less phylogenetic signal in the basicranium compared with a 'Rest of Cranium' partition, using diverse metrics of phylogenetic signal (Kmult, phylogenetically aligned principal components analysis, comparisons of UPGMA/neighbour-joining/parsimony trees and cophenetic distances to a reference phylogeny) for scaled, Procrustes-aligned landmarks and allometry-corrected residuals. Surprisingly, a similar pattern emerged from parsimony-based analyses of discrete cranial characters. The consistent results across methods suggest that easily computed metrics such as Kmult can provide good guidance on phylogenetic information in a landmarking configuration. In addition, GMM data may be less informative for intricate but conservative anatomical regions such as the basicranium, while better-but not necessarily novel-phylogenetic information can be expected for broadly characterized shapes such as entire bones. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

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Most members of the speciose pea crab family (Decapoda: Brachyura: Pinnotheridae) are characterized by their symbioses with marine invertebrates in various host phyla. The ecology of pea crabs is, however, understudied, and the degree of host dependency of most species is still unclear. With the exception of one lineage of ectosymbiotic echinoid-associated crabs, species within the subfamily Pinnotherinae are endosymbionts, living within the body cavities of mollusks, ascidians, echinoderms, and brachiopods. By contrast, most members of the two other subfamilies are considered to have an ectosymbiotic lifestyle, sharing burrows and tubes with various types of worms and burrowing crustaceans (inquilism). The body shapes within the family are extremely variable, mainly in the width and length of the carapace. The variation of carapace shapes in the family, focusing on pinnotherines, is mapped using landmark-based morphometrics. Mean carapace shapes of species groups (based on their host preference) are statistically compared. In addition, a phylomorphometric approach is used to study three different convergence events (across subfamilies; between three genera; and within one genus), and link these events with the associated hosts.

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Protists, the micro-eukaryotes that are neither plants, animals nor fungi build up the greatest part of eukaryotic diversity on Earth. Yet, their evolutionary histories and patterns are still mostly ignored, and their complexity overlooked. Protists are often assumed to keep stable morphologies for long periods of time (morphological stasis). In this work, we test this paradigm taking Arcellinida testate amoebae as a model. We build a taxon-rich phylogeny based on two mitochondrial (COI and NADH) and one nuclear (SSU) gene, and reconstruct morphological evolution among clades. In addition, we prove the existence of mitochondrial mRNA editing for the COI gene. The trees show a lack of conservatism of shell outlines within the main clades, as well as a widespread occurrence of morphological convergences between far-related taxa. Our results refute, therefore, a widespread morphological stasis, which may be an artefact resulting from low taxon coverage. As a corollary, we also revise the groups systematics, notably by emending the large and highly polyphyletic genus Difflugia. These results lead, amongst others, to the erection of a new infraorder Cylindrothecina, as well as two new genera Cylindrifflugia and Golemanskia.

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To study morphological evolution, it is necessary to combine information from multiple intersecting research fields. Here, we report on the structure of the bony and muscular elements of the craniomandibular complex of birds, highlighting its morphological architecture and complexity (or simplification) in the context of anatomical networks of the Band-winged Nightjar Systellura longirostris (Caprimulgiformes, Caprimulgidae). This species has skull osteology and jaw myology that departs from the general structural plan of the craniomandibular complex of Neornithes and is considered morphologically simple. Our goal is to test if its simplification is also reflected in its anatomical network, particularly in those parameters that measure complexity and to explore if the distribution of the networks in a phylomorphospace is conditioned by their evolutionary history or by convergence. Our results show that S. longirostris clusters with other Strisores and momotids and is segregated from the other bird species analyzed when plotted in the phylomorphospace, as a consequence of convergence in the network parameters. Systellura has a craniomandibular complex consisting of fewer muscles connecting more bones than the model species (e.g., the rock pigeon or the guira cuckoo). In this sense, Systellura is actually more complex regarding the number of integrative bony parts, while its craniomandibular complex is simpler. According to its anatomical network, Systellura also can be interpreted as less complex, particularly compared with other Strisores and taxa that reflect the general structure of the craniomandibular complex in Neornithes.

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Sauropodomorph dinosaurs include the largest terrestrial animals that ever lived on Earth. The early representatives of this clade were, however, relatively small and partially to totally bipedal, conversely to the gigantic and quadrupedal sauropods. Although the sauropod bauplan is well defined, notably by the acquisition of columnar limbs, the evolutionary sequence leading to its emergence remains debated. Here, we aim to tackle this evolutionary episode by investigating shape variation in the six limb long bones for the first time using three-dimensional geometric morphometrics. The morphological features of the forelimb zeugopod bones related to the sauropod bauplan tend to appear abruptly, whereas the pattern is more gradual for the hindlimb zeugopod bones. The stylopod bones tend to show the same pattern as their respective zeugopods. The abrupt emergence of the sauropod forelimb questions the locomotor abilities of non-sauropodan sauropodomorphs inferred as quadrupeds. Features characterizing sauropods tend to corroborate a view of their locomotion mainly based on stylopod retraction. An allometric investigation of the shape variation in accordance with size highlight differences in hindlimb bone allometries between the sauropods and the non-sauropodan sauropodomorphs. These differences notably correspond to an unexpected robustness decrease trend in the sauropod hindlimb zeugopod. In addition to forelimb bones that appear to be proportionally more gracile than in non-sauropodan sauropodomorphs, sauropods may have relied on limb architecture and features related to the size increase, rather than general robustness, to deal with the role of weight-bearing.

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The evolution of plant defenses is often constrained by phylogeny. Many of the differences between competing plant defense theories hinge upon the differences in the location of meristem damage (apical versus auxiliary) and the amount of tissue removed. We analyzed the growth and defense responses of 12 Quercus (oak) species from a well-resolved molecular phylogeny using phylogenetically independent contrasts. Access to light is paramount for forest-dwelling tree species, such as many members of the genus Quercus. We therefore predicted a greater investment in defense when apical meristem tissue was removed. We also predicted a greater investment in defense when large amounts of tissue were removed and a greater investment in growth when less tissues were removed. We conducted five simulated herbivory treatments including a control with no damage and alterations of the location of meristem damage (apical versus auxiliary shoots) and intensity (25% versus 75% tissue removal). We measured growth, defense, and nutrient re-allocation traits in response to simulated herbivory. Phylomorphospace models were used to demonstrate the phylogenetic nature of trade-offs between characteristics of growth, chemical defenses, and nutrient re-allocation. We found that growth-defense trade-offs in control treatments were under phylogenetic constraints, but phylogenetic constraints and growth-defense trade-offs were not common in the simulated herbivory treatments. Growth-defense constraints exist within the Quercus genus, although there are adaptations to herbivory that vary among species.

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BACKGROUND: Natural model systems are indispensable for exploring adaptations in response to environmental pressures. Sinocyclocheilus of China, the most diverse cavefish clade in the world (75 species), provide unique opportunities to understand recurrent evolution of stereotypic traits (such as eye loss and sensory expansion) in the context of a deep and diverse phylogenetic group. However, they remain poorly understood in terms of their morphological evolution. Therefore, we explore key patterns of morphological evolution, habitat utilization and geographic distribution in these fishes. RESULTS: We constructed phylogenies and categorized 49 species based on eye-related condition (Blind, Micro-eyed, and Normal-eyed), habitat types (Troglobitic-cave-restricted; Troglophilic-cave-associated; Surface-outside caves) and existence of horns. Geometric-morphometric analyses show Normal-eyed morphs with fusiform shapes segregating from Blind/Micro-eyed deeper bodied morphs along the first principal-component axis; second axis accounts for shape complexity related to horns. The body shapes showed a significant association with eye-related condition and horn, but not habitat types. Ancestral reconstructions suggest at least three independent origins of Blind morphs, each with different levels of modification in relation to their ancestral Normal-eyed morphs; Sinocyclocheilus are also pre-adapted for cave dwelling. Our geophylogeny shows an east-to-west diversification spanning Pliocene and Pleistocene, with early-diversifying Troglobitic species dominating subterranean habitats of karstic plains whereas predominantly Surface forms inhabit hills to the west. Evolutionary rates analyses suggest that lineages leading to Blind morphs were characterized by significant rate shifts, such as a slowdown in body size evolution and a 5-20 fold increase in rate of eye regression, possibly explained by limited resource availability. Body size and eye size have undergone reversals, but not horns, a trait entailing considerable time to form. CONCLUSIONS: Sinocyclocheilus occupied cave habitats in response to drying associated with aridification of China during late Miocene and the Pliocene. The prominent cave-adaptations (eye-regression, horn-evolution) occur in clades associated with the extensive subterranean cave system in Guangxi and Guizhou provinces. Integration of morphology, phylogeny, rate analyses, molecular-dating and distribution show not only several remarkable patterns of evolution, but also interesting exceptions to these patterns signifying the diversification of Sinocyclocheilus as an invaluable model system to explore evolutionary novelty.

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The size and shape of red blood cells (RBCs) provide key information on life-history strategies in vertebrates. However, little is known about how RBC shape evolved in response to environmental factors, body size and the role of evolutionary rate. Here, we analysed RBC morphometrics in a set of Teleostei (bony fishes) and Elasmobranchii (sharks and rays) species testing the hypothesis that phylogenetic relationship explains species occupation of morphospace. We collected data on cell and nucleus area and volume, nucleus:cytoplasm ratio and shape factor for 65 species belonging to 28 orders. Then, we built phylomorphospaces separately for bony fish and sharks and rays. To test whether phylogenetic relationships predicted phenotypic similarity, we calculated multivariate phylogenetic signal. We also estimated the evolutionary rate of RBC shape for each node and tip using ridge regression. Finally, we tested whether habitat and body size influenced RBC shape using a PGLS. We found a significant phylogenetic signal in RBC shape for bony fish, but not sharks and rays. Saltwater teleost species were more clustered than freshwater ones in the phylomorphospace, suggesting clade disparity. Accordingly, the rate of evolution was highly heterogeneous, with significant decrease in Acanthopterygii. Neither habitat nor body size influenced RBC shape. In conclusion, RBC shape seems to have evolved in fishes in response to multiple selective pressures independent of life-history characters.

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Waterfowl (Aves, Anseriformes) constitute an ancient global radiation, and understanding the pattern and timing of their evolution requires a well-corroborated phylogeny including extant species and fossils. Following the molecular advances in avian systematics, however, morphology has often been held as misleading, yet congruence with molecular data has been shown to vary considerably among different skeletal parts. Here, we explore phylogenetic signal in discrete characters of the lacrimal/ectethmoid region of waterfowl, which is highly variable among species and constitutes a rich source of data. We do so by combining cladistic and multivariate approaches, and using phylogenetic comparative methods. We quantitatively recognize three major morphological types among lacrimal bones, and discuss homoplasy and potential synapomorphies of major clades using a molecular backbone tree. Our results clearly indicate that the lacrimal bone carries substantial phylogenetic signal and could be of systematic value at different levels of the phylogeny of waterfowl, feeding the exploration of other regions of the skull with this combined approach.

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Quantifying morphological evolution is key to determining the patterns and processes underlying the origin of phyla. We constructed a hierarchical morphological character matrix to characterize the radiation and establishment of echinoderm body plans during the early Paleozoic. This showed that subphylum-level clades diverged gradually through the Cambrian, and the distinctiveness of the resulting body plans was amplified by the extinction of transitional forms and obscured by convergent evolution during the Ordovician. Higher-order characters that define these body plans were not fixed at the origin of the phylum, countering hypotheses regarding developmental processes governing the early evolution of animals. Instead, these burdened characters were flexible, enabling continued evolutionary innovation throughout the clades' history.

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In the present study we evaluated the putative cases of sympatric speciation in the genus Herichthys by studying the variation in head shape using principal component analysis, phylomorphospace and reconstructions of the ancestral states of feeding preferences. Herichthys includes both allopatric and sympatric sister species, as well as sympatric unrelated species and thus offers great potential for evolutionary studies of putatively sympatric speciation. Herichthys is the northernmost group of cichlids in America and one of the most ecologically disparate genera within Middle American cichlids. Fifteen anatomical points were recorded on the heads of 293 specimens of the 11 species recognized within the genus. The results show that in spite of having wide variation in consumed diets, most species of Herichthys are close in morphospace. However, morphological variation was great among the two pairs of sympatric sister species in agreement with the suggested sympatric model of speciation.

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A defining character of adaptive radiations is the evolution of a diversity of morphological forms that are associated with the use of different habitats, following the invasion of vacant niches. Island adaptive radiations have been thoroughly investigated but continental scale radiations are more poorly understood. Here, we use 52 species of Australian agamid lizards and their Asian relatives as a model group, and employ three-dimensional geometric morphometrics to characterize cranial morphology and investigate whether variation in cranial shape reflects patterns expected from the ecological process of adaptive radiation. Phylogenetic affinity, evolutionary allometry, and ecological life habit all play major roles in the evolution of cranial shape in the sampled lizards. We find a significant association between cranial shapes and life habit. Our results are in line with the expectations of an adaptive radiation, and this is the first time detailed geometric morphometric analyses have been used to understand the selective forces that drove an adaptive radiation at a continental scale.

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Previous investigations of the primate talo-crural joint (TCJ; specifically on the talus and distal tibia) have demonstrated that substrate preference significantly influences morphology, but this association is not necessarily found in subadults. This has been interpreted as the result of a plastic, behaviorally induced response of bone due to substrate use. In this investigation, we use geometric morphometric and phylogenetic comparative methods to investigate ontogenetic phenotypic plasticity in the catarrhine TCJ. Osteological specimens from four African hominoid and four cercopithecid species, divided into subadult and adult developmental stages based on molar eruption, formed the study group. We tested for phylogenetic signal in the shape of both the talar and tibial articular surfaces, at both developmental stages. We then used phylomorphospaces to examine the evolution of shape differences at each developmental stage for each element, and to determine if substrate usage is associated with shape in this phylogenetic context. A significant phylogenetic signal was found for both articular surfaces in subadults, but not adults. In phylomorphospace, both talar and tibial articular morphologies show an association with substrate preference in adults, but not in subadults. Our results provide confirmation of the significant effect of habitual substrate usage and the consequences of bone remodeling during ontogeny on the shape and presentation of the TCJ. These results also suggest caution when using adult talo-tibial shapes to evaluate phylogenetic relationships as TCJ morphology can be considered as a palimpsest, with substrate usage overwriting phylogenetic information in adult specimens. Anat Rec, 302:1977-1984, 2019. © 2019 American Association for Anatomy.

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BACKGROUND AND AIMS: Flowering plants show a high diversity of pollen morphology, assumed to reflect not only variations in the underlying design, but also stress imposed by ecological conditions related to pollen survival and germination. Both components are expected to constrain the accumulation of pollen disparity. However, this assumption has rarely been tested using empirical data. METHODS: This study is designed to test this hypothesis by inferring the accumulation of pollen disparity in Ericaceae, a large eudicot family with recent, ongoing radiations, with focus on three functionally significant pollen characters using a dated phylogeny. KEY RESULTS: Multiple lines of evidence supported the hypothesis that pollen disparity in Ericaceae did not evolve steadily but rather pulsed over time, clearly decoupling from the relative constant rate pattern of species diversification inferred. In a 3-D pollen morphospace, most major clades appear to occupy distinct neighbouring regions, whereas the subfamily Epacridoideae overlaps extensively with other subfamilies. No evidence for correlations was found between dimension of pollen disparity and species diversity at either the subfamily or generic level. Furthermore, the distribution of species in present pollen morphospace showed a strong central tendency, with the core compartment containing a large number of species from species-rich genera. CONCLUSIONS: The recovered evidence fits well with the expectations of limitations on available pollen morphological disparity, and suggests that innovation of pollen germination traits may have little effect on species diversification.

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Green microalgae of the Micrasterias lineage are unicellular microorganisms with modular morphology consisting of successively differentiated lobes. Due to their morphological diversity and peculiar morphogenesis, these species are important model systems for studies of cytomorphogenesis and cellular plasticity. Interestingly, the phylogenetic structure of the Micrasterias lineage and most other Desmidiales is poorly related to the traditional morphological characters used for delimitation of taxa. In this study, we focused on symmetry breaking between adjacent cellular lobes in relation to phylogeny of the studied species. While pronounced morphological asymmetry between the adjacent lobes is typical for some species, others have been characterized by the almost identical morphologies of these structures. We asked whether there is any detectable average shape asymmetry between the pairs of lobes and terminal lobules in 19 Micrasterias species representing all major clades of this desmidiacean lineage. Then, we evaluated whether the asymmetric patterns among species are phylogenetically structured. The analyses showed that the phylogeny was in fact strongly related to the patterns of morphological asymmetry between the adjacent cellular lobes. Thus, evolution of the asymmetric development between the adjacent lobes proved to be the key event differentiating cellular shape patterns of Micrasterias. Conversely, the phylogeny was only weakly related to asymmetry between the pairs of terminal lobules. The subsequent analyses of the phylogenetic morphological integration showed that individual hierarchical levels of cellular morphology were only weakly coordinated with regard to asymmetric variation among species. This finding indicates that evolutionary differentiation of morphogenetic processes leading to symmetry breaking may be relatively independent at different branching levels. Such modularity is probably the key to the evolvability of cellular shapes, leading to the extraordinary morphological diversity of these intriguing microalgae.

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While the analysis of ontogenetic trajectories is common in geometric morphometrics (GM), the simultaneous comparison of several trajectories can be unwieldy and is, in some cases, unable to make use of one of the main advantages of GM, visualization. Furthermore, due to the paucity of the paleontological record, analyses of trajectories are often limited to extant taxa. We address these issues by presenting a method for visualizing the similarities and differences of cranial ontogenetic trajectories among taxa and a method for reconstructing ancestral ontogenetic trajectories, so that these differences can be investigated in a phylogenetic context. We also tested for the presence of phylogenetic signal in the ontogenetic trajectories themselves. Using an ontogenetic series of 522 crania, representing 17 cercopithecine species from 8 genera, we first calculated ontogenetic trajectories of cranial shape change for each species, and then entered these trajectories into a principal components analysis to produce a developmental shape-change trajectory PCA (δPCA). Then, through an augmentation of the phylomorphospace approach, we projected a molecular phylogeny onto the major axes of trajectory shape variation from the δPCA to produce an 'ontophylomorphospace,' using squared-change parsimony to reconstruct interior nodes. Through these procedures, we were able to determine that the δPCAs illustrate patterns of variation in these developmental trajectories in a visually intuitive manner that allows for easier comparisons among taxa. Through examination of the ontophylomorphospace, we found that African papionins exhibit extensive homoplasy in the evolution of cranial ontogenetic trajectories, and that Asian species of Macaca show highly derived ontogenetic trajectories relative to other cercopithecines. Additionally, we found no support for the presence of a phylogenetic signal in cranial ontogenetic trajectories. The δPCA and the ontophylomorphospace are ways in which to visualize and compare complex, multivariate shape transformations, both among extant taxa and over evolutionary time, respectively.

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