Anatomical network analysis of the musculoskeletal system reveals integration loss and parcellation boost during the fins-to-limbs transition

Exploring the Influence of Neomorphic Gekkotan Paraphalanges on Limb Modularity and Integration

Digital specializations of geckos are widely associated with their climbing abilities. A recurring feature that has independently emerged within the sister families Gekkonidae and Phyllodactylidae is the presence of neomorphic paraphalanges (PPEs), usually paired, paraxial skeletal structures lying adjacent to interphalangeal and metapodial-phalangeal joints. The incorporation of PPEs into gekkotan autopodia has the potential to modify the modularity and integration of the ancestral limb pattern by affecting information flow among skeletal limb parts. Here we explore the influence of PPEs on limb organization using anatomical networks. We modeled the fore- and hindlimbs in species ancestrally devoid of PPEs (Iguana iguana and Gekko gecko) and paraphalanx-bearing species (Hemidactylus mabouia and Uroplatus fimbriatus). To further clarify the impact of PPEs we also expunged PPEs from paraphalanx-bearing network models. We found that PPEs significantly increase modularity, giving rise to tightly integrated sub-modules along the digits, suggesting functional specialization. Species-specific singularities also emerged, such as the trade-off between the presence of PPEs favoring modularity (along the proximodistal axis) and the interdigital webbing favoring integration (across the lateromedial axis) in the limbs of U. fimbriatus. The PPEs are characterized by low connectivity compared with other skeletal elements; nevertheless, this varies based on their specific location and seemingly reflects developmental constraints. Our results also highlight the importance of the fifth metatarsal in generating a shift in lepidosaurian hindlimb polarity that contrasts with the more symmetrical bauplan of tetrapods. Our findings support extensive modification of the autopodial system in association with the addition of the neomorphic and intriguing PPEs.

Modularity and community detection in human brain morphology

Humans possess morphologically complex brains, which are spatially constrained by their many intrinsic and extrinsic physical interactions. Anatomical network analysis can be used to study these constraints and their implications. Modularity is a key issue in this framework, namely, the presence of groups of elements that undergo morphological evolution in a concerted way. An array of community detection algorithms was tested on a previously designed anatomical network model of the human brain in order to provide a detailed assessment of modularity in this context. The algorithms that provide the highest quality partitions also reveal general phenotypic patterns underlying the topology of human brain morphology. Taken together, the community detection algorithms highlight the simultaneous presence of a longitudinal and a vertical modular partition of the brain's topology, the combination of which matches the organization of the enveloping braincase. Specifically, the longitudinal organization is in line with the different morphogenetic environments of the three endocranial fossae, while the vertical arrangement corresponds to the distinct developmental processes associated with the cranial base and vault, respectively. The results are robust and have the potential to be compared with equivalent network models of other species. Furthermore, they suggest a degree of concerted topological reciprocity in the spatial organization of brain and skull elements, and posit questions about the extent to which geometrical constraints of the cranial base and the modular partition of the corresponding brain regions may channel both evolutionary and developmental trajectories.

Deep-time invention and hydrodynamic convergences through amniote flipper evolution

The diapsid plesiosaurs were pelagic and inhabited the oceans from the Triassic to the Cretaceous. A key evolutionary character of plesiosaurs is the four wing-like flippers. While it is mostly accepted that plesiosaurs were underwater fliers like marine turtles, penguins, and maybe whales, other swimming styles have been suggested in the past. These are rowing and a combination of rowing and underwater flight (e.g., pig-nosed turtle, sea lion). Underwater fliers use lift in contrast to rowers that employ drag. For efficiently profiting of lift during underwater flying, it is necessary that plesiosaurs twisted their flippers by muscular activity. To research the evolution of flipper twisting in plesiosaurs and functionally analogous taxa, including turtles, we used anatomical network analysis (AnNA) and reassessed distal flipper muscle functions. We coded bone-to-bone and additionally muscle-to-bone contacts in N × N matrices for foreflippers of the plesiosaur, the loggerhead sea turtle, the pig-nosed turtle, the African penguin, the California sea lion, and the humpback whale based on literature data. In "R," "igraph" was run by using a walktrap algorithm to obtain morphofunctional modules. AnNA revealed that muscle-to-bone contacts are needed to detect contributions of modules to flipper motions, whereas only-bone matrices are not informative for that. Furthermore, the plesiosaur, the marine turtles, the seal, and the penguin flipper twisting mechanisms, but the penguin cannot actively twist the flipper trailing edge. Finally, the foreflipper of the pig-nosed turtle and of the whale is not actively twisted during swimming.

Convergence, divergence, and macroevolutionary constraint as revealed by anatomical network analysis of the squamate skull, with an emphasis on snakes

Traditionally considered the earliest-diverging group of snakes, scolecophidians are central to major evolutionary paradigms regarding squamate feeding mechanisms and the ecological origins of snakes. However, quantitative analyses of these phenomena remain scarce. Herein, we therefore assess skull modularity in squamates via anatomical network analysis, focusing on the interplay between 'microstomy' (small-gaped feeding), fossoriality, and miniaturization in scolecophidians. Our analyses reveal distinctive patterns of jaw connectivity across purported 'microstomatans', thus supporting a more complex scenario of jaw evolution than traditionally portrayed. We also find that fossoriality and miniaturization each define a similar region of topospace (i.e., connectivity-based morphospace), with their combined influence imposing further evolutionary constraint on skull architecture. These results ultimately indicate convergence among scolecophidians, refuting widespread perspectives of these snakes as fundamentally plesiomorphic and morphologically homogeneous. This network-based examination of skull modularity-the first of its kind for snakes, and one of the first to analyze squamates-thus provides key insights into macroevolutionary trends among squamates, with particular implications for snake origins and evolution.

Redefining the simplicity of the craniomandibular complex of nightjars: The case of Systellura longirostris (Aves: Caprimulgidae) by means of anatomical network analysis

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.

Breaking the mold: telescoping drives the evolution of more integrated and heterogeneous skulls in cetaceans

Background

Along with the transition to the aquatic environment, cetaceans experienced profound changes in their skeletal anatomy, especially in the skull, including the posterodorsal migration of the external bony nares, the reorganization of skull bones (= telescoping) and the development of an extreme cranial asymmetry (in odontocetes). Telescoping represents an important anatomical shift in the topological organization of cranial bones and their sutural contacts; however, the impact of these changes in the connectivity pattern and integration of the skull has never been addressed.

Methods

Here, we apply the novel framework provided by the Anatomical Network Analysis to quantify the organization and integration of cetacean skulls, and the impact of the telescoping process in the connectivity pattern of the skull. We built anatomical networks for 21 cetacean skulls (three stem cetaceans, three extinct and 10 extant mysticetes, and three extinct and two extant odontocetes) and estimated network parameters related to their anatomical integration, complexity, heterogeneity, and modularity. This dataset was analyzed in the context of a broader tetrapod skull sample as well (43 species of 13 taxonomic groups).

Results

The skulls of crown cetaceans (Neoceti) occupy a new tetrapod skull morphospace, with better integrated, more heterogeneous and simpler skulls in comparison to other tetrapods. Telescoping adds connections and improves the integration of those bones involved in the telescoping process (e.g., maxilla, supraoccipital) as well as other ones (e.g., vomer) not directly affected by telescoping. Other underlying evolutionary processes (such as basicranial specializations linked with hearing/breathing adaptations) could also be responsible for the changes in the connectivity and integration of palatal bones. We also find prograde telescoped skulls of mysticetes distinct from odontocetes by an increased heterogeneity and modularity, whereas retrograde telescoped skulls of odontocetes are characterized by higher complexity. In mysticetes, as expected, the supraoccipital gains importance and centrality in comparison to odontocetes, increasing the heterogeneity of the skull network. In odontocetes, an increase in the number of connections and complexity is probably linked with the dominant movement of paired bones, such as the maxilla, in retrograde telescoping. Crown mysticetes (Eubalaena, Caperea, Piscobalaena, and Balaenoptera)are distinguished by having more integrated skulls in comparison to stem mysticetes (Aetiocetus and Yamatocetus), whereas crown odontocetes (Waipatia, Notocetus, Physeter, and Tursiops) have more complex skulls than stem forms (Albertocetus). Telescoping along with feeding, hearing and echolocation specializations could have driven the evolution of the different connectivity patterns of living lineages.

Cranial Anatomical Integration and Disparity Among Bones Discriminate Between Primates and Non-primate Mammals

The primate skull hosts a unique combination of anatomical features among mammals, such as a short face, wide orbits, and big braincase. Together with a trend to fuse bones in late development, these features define the anatomical organization of the skull of primates—which bones articulate to each other and the pattern this creates. Here, I quantified the anatomical organization of the skull of 17 primates and 15 non-primate mammals using anatomical network analysis to assess how the skulls of primates have diverged from those of other mammals, and whether their anatomical differences coevolved with brain size. Results show that primates have a greater anatomical integration of their skulls and a greater disparity among bones than other non-primate mammals. Brain size seems to contribute in part to this difference, but its true effect could not be conclusively proven. This supports the hypothesis that primates have a distinct anatomical organization of the skull, but whether this is related to their larger brains remains an open question.

Reduction, reorganization and stasis in the evolution of turtle shell elements

Novel phenotypic configurations can profoundly alter the evolutionary trajectories of species. Although innovation can precede lengthy periods of evolutionary stasis, the potential for species to diversify further can be realized via modular changes across distinct levels of hierarchical organization. To test this expectation, we undertook anatomical network analyses to model the organization and composition of the turtle’s shell. Our results suggest that stem turtles featured the greatest diversity in the number of skeletal (bones) and epidermal (scutes) shell elements. The shell subsequently underwent numerical simplification. Thus, the sum of potential connections (links) in shell networks has diminished in modern turtles. Some network system descriptors of complexity, integration and modularity covaried with the number of network components (nodes), which has remained evolutionarily stable since the Jurassic. We also demonstrated that shell reorganization might be feasible within modular subdivisions, particularly in modern turtles with simplified and less integrated network structures. We discuss how these findings align with previous studies on numerical simplification with enhanced skeletal specialization in the tetrapod skull. Altogether, our analyses expose the evolvability of the turtle’s shell and bolster the foundation for further macroevolutionary comparisons of ancient and modern species.

A node-based informed modularity strategy to identify organizational modules in anatomical networks

The study of morphological modularity using anatomical networks is growing in recent years. A common strategy to find the best network partition uses community detection algorithms that optimize the modularity Q function. Because anatomical networks and their modules tend to be small, this strategy often produces two problems. One is that some algorithms find inexplicable different modules when one inputs slightly different networks. The other is that algorithms find asymmetric modules in otherwise symmetric networks. These problems have discouraged researchers to use anatomical network analysis and boost criticisms to this methodology. Here, I propose a node-based informed modularity strategy (NIMS) to identify modules in anatomical networks that bypass resolution and sensitivity limitations by using a bottom-up approach. Starting with the local modularity around every individual node, NIMS returns the modular organization of the network by merging non-redundant modules and assessing their intersection statistically using combinatorial theory. Instead of acting as a black box, NIMS allows researchers to make informed decisions about whether to merge non-redundant modules. NIMS returns network modules that are robust to minor variation and does not require optimization of a global modularity function. NIMS may prove useful to identify modules also in small ecological and social networks.

Summary: A new method to identify modules in anatomical networks without optimization and statistically assess their degree of overlap. This method will assist researchers in identifying meaningful biological modules.

Fingers zipped up or baby mittens? Two main tetrapod strategies to return to the sea

The application of network methodology in anatomical structures offers new insights on the connectivity pattern of skull bones, skeletal elements and their muscles. Anatomical networks helped to improve our understanding of the water-to-land transition and how the pectoral fins were transformed into limbs via their modular disintegration. Here, we apply the same methodology to tetrapods secondarily adapted to the marine environment. We find that these animals achieved their return to the sea with four types of morphological changes, which can be grouped into two different main strategies. In all marine mammals and the majority of the reptiles, the fin is formed by the persistence of superficial and interdigital connective tissues, like a 'baby mitten', whereas the underlying connectivity pattern of the bones does not influence the formation of the forefin. On the contrary, ichthyosaurs 'zipped up' their fingers and transformed their digits into carpal-like elements, forming a homogeneous and better-integrated forefin. These strategies led these vertebrates into three different macroevolutionary paths exploring the possible spectrum of morphological adaptations.

Birds have peramorphic skulls, too: anatomical network analyses reveal oppositional heterochronies in avian skull evolution

In contrast to the vast majority of reptiles, the skulls of adult crown birds are characterized by a high degree of integration due to bone fusion, e.g., an ontogenetic event generating a net reduction in the number of bones. To understand this process in an evolutionary context, we investigate postnatal ontogenetic changes in the skulls of crown bird and non-avian theropods using anatomical network analysis (AnNA). Due to the greater number of bones and bone contacts, early juvenile crown birds have less integrated skulls, resembling their non-avian theropod ancestors, including Archaeopteryx lithographica and Ichthyornis dispars. Phylogenetic comparisons indicate that skull bone fusion and the resulting modular integration represent a peramorphosis (developmental exaggeration of the ancestral adult trait) that evolved late during avialan evolution, at the origin of crown-birds. Succeeding the general paedomorphic shape trend, the occurrence of an additional peramorphosis reflects the mosaic complexity of the avian skull evolution.

Plateau and Foth use anatomical network analysis to study the evolution of avian skull anatomy. They report that the ontogenetic changes in the morphology and modularity of the avian skulls is comparable to evolutionary transformations from non-avian theropods to modern birds. Their work highlights the complexity of avian skull evolution.

Evolutionary parallelisms of pectoral and pelvic network-anatomy from fins to limbs

Lobe-fins transformed into limbs during the Devonian period, facilitating the water-to-land transition in tetrapods. We traced the evolution of well-articulated skeletons across the fins-to-limbs transition, using a network-based approach to quantify and compare topological features of fins and limbs. We show that the topological arrangement of bones in pectoral and pelvic appendages evolved in parallel during the fins-to-limbs transition, occupying overlapping regions of the morphospace, following a directional trend, and decreasing their disparity over time. We identify the presence of digits as the morphological novelty triggering topological changes that discriminated limbs from fins. The origin of digits caused an evolutionary shift toward appendages that were less densely and heterogeneously connected, but more assortative and modular. Disparity likewise decreased for both appendages, more markedly until a time concomitant with the earliest-known tetrapod tracks. Last, we rejected the presence of a pectoral-pelvic similarity bottleneck at the origin of tetrapods.