Patterning and post-patterning modes of evolutionary digit loss in mammals

Insights into digit evolution from a fate map study of the forearm using Chameleon, a new transgenic chicken line

The cellular and genetic networks that contribute to the development of the zeugopod (radius and ulna of the forearm, tibia and fibula of the leg) are not well understood, although these bones are susceptible to loss in congenital human syndromes and to the action of teratogens such as thalidomide. Using a new fate-mapping approach with the Chameleon transgenic chicken line, we show that there is a small contribution of SHH-expressing cells to the posterior ulna, posterior carpals and digit 3. We establish that although the majority of the ulna develops in response to paracrine SHH signalling in both the chicken and mouse, there are differences in the contribution of SHH-expressing cells between mouse and chicken as well as between the chicken ulna and fibula. This is evidence that, although zeugopod bones are clearly homologous according to the fossil record, the gene regulatory networks that contribute to their development and evolution are not fixed.

Resolving the mechanisms underlying epithelial-to-mesenchymal transition of the lateral plate mesoderm

Formation of the vertebrate limb buds begins with a localized epithelial-to-mesenchymal transition (EMT) of the somatic lateral plate mesoderm (LPM). While the processes that drive proliferation and outgrowth of the limb mesenchyme are well established, the fundamental mechanisms that precede this process and initiate EMT are less understood. In this review, we outline putative drivers of EMT of the LPM, drawing from analyses across a range of vertebrates and developmental models. We detail the expression patterns of key EMT transcriptional regulators in the somatic LPM of the presumptive limb fields, and their potential role in producing a mesenchymal cell fate. These include a putative cooperative role between the EMT inducers PRRX1 and TWIST1, supported by evidence in zebrafish and chicken models but unconfirmed data from mice. As such, additional functional data are required to definitively determine the mechanisms that initiate and drive EMT of the somatic LPM, a critical transition preceding formation of the limb bud mesenchyme.

Affinity-optimizing enhancer variants disrupt development

Enhancers control the location and timing of gene expression and contain the majority of variants associated with disease1-3. The ZRS is arguably the most well-studied vertebrate enhancer and mediates the expression of Shh in the developing limb4. Thirty-one human single-nucleotide variants (SNVs) within the ZRS are associated with polydactyly4-6. However, how this enhancer encodes tissue-specific activity, and the mechanisms by which SNVs alter the number of digits, are poorly understood. Here we show that the ETS sites within the ZRS are low affinity, and identify a functional ETS site, ETS-A, with extremely low affinity. Two human SNVs and a synthetic variant optimize the binding affinity of ETS-A subtly from 15% to around 25% relative to the strongest ETS binding sequence, and cause polydactyly with the same penetrance and severity. A greater increase in affinity results in phenotypes that are more penetrant and more severe. Affinity-optimizing SNVs in other ETS sites in the ZRS, as well as in ETS, interferon regulatory factor (IRF), HOX and activator protein 1 (AP-1) sites within a wide variety of enhancers, cause gain-of-function gene expression. The prevalence of binding sites with suboptimal affinity in enhancers creates a vulnerability in genomes whereby SNVs that optimize affinity, even slightly, can be pathogenic. Searching for affinity-optimizing SNVs in genomes could provide a mechanistic approach to identify causal variants that underlie enhanceropathies.

Perspectives on Principles of Cellular Behavior from the Biophysics of Protists

Cells are the fundamental unit of biological organization. Although it may be easy to think of them as little more than the simple building blocks of complex organisms such as animals, single cells are capable of behaviors of remarkable apparent sophistication. This is abundantly clear when considering the diversity of form and function among the microbial eukaryotes, the protists. How might we navigate this diversity in the search for general principles of cellular behavior? Here, we review cases in which the intensive study of protists from the perspective of cellular biophysics has driven insight into broad biological questions of morphogenesis, navigation and motility, and decision making. We argue that applying such approaches to questions of evolutionary cell biology presents rich, emerging opportunities. Integrating and expanding biophysical studies across protist diversity, exploiting the unique characteristics of each organism, will enrich our understanding of general underlying principles.

Trait Loss in Evolution: What Cavefish Have Taught Us about Mechanisms Underlying Eye Regression

Reduction or complete loss of traits is a common occurrence throughout evolutionary history. In spite of this, numerous questions remain about why and how trait loss has occurred. Cave animals are an excellent system in which these questions can be answered, as multiple traits, including eyes and pigmentation, have been repeatedly reduced or lost across populations of cave species. This review focuses on how the blind Mexican cavefish, Astyanax mexicanus, has been used as a model system for examining the developmental, genetic, and evolutionary mechanisms that underlie eye regression in cave animals. We focus on multiple aspects of how eye regression evolved in A. mexicanus, including the developmental and genetic pathways that contribute to eye regression, the effects of the evolution of eye regression on other traits that have also evolved in A. mexicanus, and the evolutionary forces contributing to eye regression. We also discuss what is known about the repeated evolution of eye regression, both across populations of A. mexicanus cavefish and across cave animals more generally. Finally, we offer perspectives on how cavefish can be used in the future to further elucidate mechanisms underlying trait loss using tools and resources that have recently become available.

Skeletal-Vascular Interactions in Bone Development, Homeostasis, and Pathological Destruction

Bone is a highly vascularized organ that not only plays multiple roles in supporting the body and organs but also endows the microstructure, enabling distinct cell lineages to reciprocally interact. Recent studies have uncovered relevant roles of the bone vasculature in bone patterning, morphogenesis, homeostasis, and pathological bone destruction, including osteoporosis and tumor metastasis. This review provides an overview of current topics in the interactive molecular events between endothelial cells and bone cells during bone ontogeny and discusses the future direction of this research area to find novel ways to treat bone diseases.

Hipparion tracks and horses' toes: the evolution of the equid single hoof

The traditional story of the evolution of the horse (family Equidae) has been in large part about the evolution of their feet. How did modern horses come to have a single toe (digit III), with the hoof bearing a characteristic V-shaped keratinous frog on the sole, and what happened to the other digits? While it has long been known that the proximal portions of digits II and IV are retained as the splint bones, a recent hypothesis suggested that the distal portion of these digits have also been retained as part of the frog, drawing upon the famous Laetoli footprints of the tridactyl (three-toed) equid Hipparion as part of the evidence. We show here that, while there is good anatomical and embryological evidence for the proximal portions of all the accessory digits (i.e. I and V, as well as II and IV) being retained in the feet of modern horses, evidence is lacking for the retention of any distal portions of these digits. There is also good ichnological evidence that many tridactyl equids possessed a frog, and that the frog has been part of the equid foot for much of equid evolutionary history.

Distinct patterning responses of wing and leg neuromuscular systems to different preaxial polydactylies

The tetrapod limb has long served as a paradigm to study vertebrate pattern formation and evolutionary diversification. The distal part of the limb, the so-called autopod, is of particular interest in this regard, given the numerous modifications in both its morphology and behavioral motor output. While the underlying alterations in skeletal form have received considerable attention, much less is known about the accompanying changes in the neuromuscular system. However, modifications in the skeleton need to be properly integrated with both muscle and nerve patterns, to result in a fully functional limb. This task is further complicated by the distinct embryonic origins of the three main tissue types involved-skeleton, muscles and nerves-and, accordingly, how they are patterned and connected with one another during development. To evaluate the degree of regulative crosstalk in this complex limb patterning process, here we analyze the developing limb neuromuscular system of Silkie breed chicken. These animals display a preaxial polydactyly, due to a polymorphism in the limb regulatory region of the Sonic Hedgehog gene. Using lightsheet microscopy and 3D-reconstructions, we investigate the neuromuscular patterns of extra digits in Silkie wings and legs, and compare our results to Retinoic Acid-induced polydactylies. Contrary to previous findings, Silkie autopod muscle patterns do not adjust to alterations in the underlying skeletal topology, while nerves show partial responsiveness. We discuss the implications of tissue-specific sensitivities to global limb patterning cues for our understanding of the evolution of novel forms and functions in the distal tetrapod limb.

A single-cell transcriptome atlas profiles early organogenesis in human embryos

The early window of human embryogenesis is largely a black box for developmental biologists. Here we probed the cellular diversity of 4-6 week human embryos when essentially all organs are just laid out. On the basis of over 180,000 single-cell transcriptomes, we generated a comprehensive atlas of 313 clusters in 18 developmental systems, which were annotated with a collection of ontology and markers from 157 publications. Together with spatial transcriptome on embryonic sections, we characterized the molecule and spatial architecture of previously unappreciated cell types. Combined with data from other vertebrates, the rich information shed light on spatial patterning of axes, systemic temporal regulation of developmental progression and potential human-specific regulation. Our study provides a compendium of early progenitor cells of human organs, which can serve as the root of lineage analysis in organogenesis.

Air-breathing behavior underlies the cell death in limbs of Rana pirica tadpoles

Amphibians shape their limbs by differential outgrowth of digits and interdigital regions. In contrast, amniotes employ cell death, an additional developmental system, to determine the final shape of limbs. Previous work has shown that high oxygen availability is correlated with the induction of cell death in developing limbs. Given the diversity of life histories of amphibians, it is conceivable that some amphibians are exposed to a high-oxygen environment during the tadpole phase and exhibit cell death in their limbs. Here, we examined whether air-breathing behavior underlies the cell death in limbs of aquatic tadpoles of the frog species Rana pirica. Our experimental approach revealed that R. pirica tadpoles exhibit cell death in their limbs that is likely to be induced by oxidative stress associated with their frequent air-breathing behavior.

TATTOO-seq delineates spatial and cell type-specific regulatory programs in the developing limb

The coordinated differentiation of progenitor cells into specialized cell types and their spatial organization into distinct domains is central to embryogenesis. Here, we developed and applied an unbiased spatially resolved single-cell transcriptomics method to identify the genetic programs underlying the emergence of specialized cell types during mouse limb development and their spatial integration. We identify multiple transcription factors whose expression patterns are predominantly associated with cell type specification or spatial position, suggesting two parallel yet highly interconnected regulatory systems. We demonstrate that the embryonic limb undergoes a complex multiscale reorganization upon perturbation of one of its spatial organizing centers, including the loss of specific cell populations, alterations of preexisting cell states' molecular identities, and changes in their relative spatial distribution. Our study shows how multidimensional single-cell, spatially resolved molecular atlases can allow the deconvolution of spatial identity and cell fate and reveal the interconnected genetic networks that regulate organogenesis and its reorganization upon genetic alterations.

Evolutionary genetics of flipper forelimb and hindlimb loss from limb development-related genes in cetaceans

Background

Cetacean hindlimbs were lost and their forelimb changed into flippers characterized by webbed digits and hyperphalangy, thus allowing them to adapt to a completely aquatic environment. However, the underlying molecular mechanism behind cetacean limb development remains poorly understood.

Results

In the present study, we explored the evolution of 16 limb-related genes and their cis-regulatory elements in cetaceans and compared them with that of other mammals. TBX5, a forelimb specific expression gene, was identified to have been under accelerated evolution in the ancestral branches of cetaceans. In addition, 32 cetacean-specific changes were examined in the SHH signaling network (SHH, PTCH1, TBX5, BMPs and SMO), within which mutations could yield webbed digits or an additional phalange. These findings thus suggest that the SHH signaling network regulates cetacean flipper formation. By contrast, the regulatory activity of the SHH gene enhancer—ZRS in cetaceans—was significantly lower than in mice, which is consistent with the cessation of SHH gene expression in the hindlimb bud during cetacean embryonic development. It was suggested that the decreased SHH activity regulated by enhancer ZRS might be one of the reasons for hindlimb degeneration in cetaceans. Interestingly, a parallel / convergent site (D42G) and a rapidly evolving CNE were identified in marine mammals in FGF10 and GREM1, respectively, and shown to be essential to restrict limb bud size; this is molecular evidence explaining the convergence of flipper-forelimb and shortening or degeneration of hindlimbs in marine mammals.

Conclusions

We did evolutionary analyses of 16 limb-related genes and their cis-regulatory elements in cetaceans and compared them with those of other mammals to provide novel insights into the molecular basis of flipper forelimb and hindlimb loss in cetaceans.

Gene expression changes during the evolution of the tetrapod limb

Major changes in the vertebrate anatomy have preceded the conquest of land by the members of this taxon, and continuous changes in limb shape and use have occurred during the later radiation of tetrapods. While the main, conserved mechanisms of limb development have been discerned over the past century using a combination of classical embryological and molecular methods, only recent advances made it possible to identify and study the regulatory changes that have contributed to the evolution of the tetrapod appendage. These advances include the expansion of the model repertoire from traditional genetic model species to non-conventional ones, a proliferation of predictive mathematical models that describe gene interactions, an explosion in genomic data and the development of high-throughput methodologies. These revolutionary innovations make it possible to identify specific mutations that are behind specific transitions in limb evolution. Also, as we continue to apply them to more and more extant species, we can expect to gain a fine-grained view of this evolutionary transition that has been so consequential for our species as well.

Altered developmental programs and oriented cell divisions lead to bulky bones during salamander limb regeneration

There are major differences in duration and scale at which limb development and regeneration proceed, raising the question to what extent regeneration is a recapitulation of development. We address this by analyzing skeletal elements using a combination of micro-CT imaging, molecular profiling and clonal cell tracing. We find that, in contrast to development, regenerative skeletal growth is accomplished based entirely on cartilage expansion prior to ossification, not limiting the transversal cartilage expansion and resulting in bulkier skeletal parts. The oriented extension of salamander cartilage and bone appear similar to the development of basicranial synchondroses in mammals, as we found no evidence for cartilage stem cell niches or growth plate-like structures during neither development nor regeneration. Both regenerative and developmental ossification in salamanders start from the cortical bone and proceeds inwards, showing the diversity of schemes for the synchrony of cortical and endochondral ossification among vertebrates.

THE FORELIMBS OF ALVAREZSAUROIDEA (DINOSAURIA: THEROPODA): INSIGHT FROM EVOLUTIONARY TERATOLOGY

Alvarezsauroidea (Tetanurae) are non-avian theropod dinosaurs whose forelimb evolution is characterised by overdevelopment of digit I, at the expense of the other two digits, complemented by a drastic forelimb shortening in derived species (Parvicursorinae). These variations are recognised as evolutionary developmental anomalies. Evolutionary teratology hence leads to a double diagnosis with 1) macrodactyly of digit I and microdactyly of digits II and III, plus 2) anterior micromelia. The teratological macrodactyly/microdactyly coupling evolved first. Developmental mechanisms disturbing limb proportion are thought to be convergent with those of other Tetanurae (Tyrannosauridae, Carcharodontosauridae). As for the manual anomalies, both are specific to Alvarezsauroidea (macrodactyly/microdactyly) and inherited (digit loss/reduction). While considering the frame-shift theory, posterior digits develop before the most anterior one. There would therefore be a decrease in the area devoted to digits II (condensation 3) and III (condensation 4), in connection with the Shh signalling pathway, interacting with other molecular players such as the GLI 3 protein and the Hox system. Developmental independence of digit I (condensation 2) would contribute to generate a particular morphology. Macrodactyly would be linked to a variation in Hoxd-13, impacting Gli3 activity, increasing cell proliferation. The loss/reduction of digital ray/phalanges (digits II and III), would be associated to Shh activity, a mechanism inherited from the theropodan ancestry. The macrodactyly/macrodactyly coupling, and then anterior micromelia, fundamentally changed the forelimb mechanical function, compared to the 'classical' grasping structure of basal representatives and other theropods. The distal ossification of the macrodactylian digit has been identified as physiological, implying the use of the structure. However, the debate of a particular 'adaptive' use is pointless since the ecology of an organism is interactively complex, being both at the scale of the individual and dependent on circumstances. Other anatomical features also allow for compensation and a different predation (cursorial hindlimbs). This article is protected by copyright. All rights reserved.

CNPY4 inhibits the Hedgehog pathway by modulating membrane sterol lipids

The Hedgehog (HH) pathway is critical for development and adult tissue homeostasis. Aberrant HH signaling can lead to congenital malformations and diseases including cancer. Although cholesterol and several oxysterol lipids have been shown to play crucial roles in HH activation, the molecular mechanisms governing their regulation remain unresolved. Here, we identify Canopy4 (CNPY4), a Saposin-like protein, as a regulator of the HH pathway that modulates levels of membrane sterol lipids. Cnpy4-/- embryos exhibit multiple defects consistent with HH signaling perturbations, most notably changes in digit number. Knockdown of Cnpy4 hyperactivates the HH pathway in vitro and elevates membrane levels of accessible sterol lipids, such as cholesterol, an endogenous ligand involved in HH activation. Our data demonstrate that CNPY4 is a negative regulator that fine-tunes HH signal transduction, revealing a previously undescribed facet of HH pathway regulation that operates through control of membrane composition.

Developmental evolution of the distal ankle in the dinosaur-bird transition

The adult ankle of early reptiles had five distal tarsal (dt) bones, but in Dinosauria, these were reduced to only two: dt3 and dt4, articulated to metatarsals (mt) mt3 and mt4. Birds have a single distal tarsal ossification center that fuses to the proximal metatarsals to form a new adult skeletal structure: the composite tarsometatarsus. This ossification center develops within a single large embryonic cartilage, but it is unclear if this cartilage results from fusion of earlier cartilages. We studied embryos in species from four different bird orders, an alligatorid, and an iguanid. In all embryos, cartilages dt2, dt3, and dt4 are formed. In the alligatorid and the iguanid, dt2 failed to ossify: only dt3 and dt4 develop into adult bones. In birds, dt2, dt3, and dt4 fuse to form the large distal tarsal cartilage; the ossification center then develops above mt3, in cartilage presumably derived from dt3. During the entire dinosaur-bird transition, a dt2 embryonic cartilage was always formed, as inferred from the embryology of extant birds and crocodilians. We propose that in the evolution of the avian ankle, fusion of cartilages dt3 and dt2 allowed ossification from dt3 to progress into dt2, which began to contribute bone medially, while fusion of dt3 to dt4 enabled the evolutionary loss of the dt4 ossification center. As a result, a single ossification center expands into a plate-like unit covering the proximal ends of the metatarsals, that is key to the development of an integrated tarsometatarsus.

Comparative development of limb musculature in phylogenetically and ecologically divergent lizards

BACKGROUND

Squamate reptiles (lizards, snakes, and amphisbaenians) exhibit incredible diversity in their locomotion, behavior, morphology, and ecological breadth. Although they often are used as models of locomotor diversity, surprisingly little attention has been given to muscle development in squamate reptiles. In fact, the most detailed examination was conducted almost 80 years ago and solely focused on the proximal limb regions. Herein, we present forelimb and hindlimb muscle morphogenesis data for three lizard species with different locomotion and feeding strategies: the desert grassland whiptail lizard, the central bearded dragon, and the veiled chameleon. This study fills critical gaps in our understanding of muscle morphogenesis in squamate reptiles and presents a comparative and temporospatial analysis of muscle development.

RESULTS

Our results reveal a conserved pattern of early muscle development among lizards with different adult morphologies and ecologies. The variations that exist are concentrated in distal regions, particularly the specialized autopodia of chameleons, where differentiation of muscles associated with the digits is delayed.

CONCLUSIONS

The chameleon autopod provides an example of major evolutionary modifications to the skeleton with only minor disruption of the conserved order and pattern of limb muscle development. This robustness of muscle patterning facilitates the evolution of extreme yet functional phenotypes.

Ossification pattern of the unusual pisiform in two-toed (Choloepus) and three-toed sloths (Bradypus)

Two-toed (Choloepus sp.) and three-toed (Bradypus sp.) sloths possess short, rounded pisiforms that are rare among mammals and differ from other members of Xenarthra like the giant anteater (Myrmecophaga tridactyla) which retain elongated, rod-like pisiforms in common with most mammals. Using photographs, radiographs, and μCT, we assessed ossification patterns in the pisiform and the paralogous tarsal, the calcaneus, for two-toed sloths, three-toed sloths, and giant anteaters to determine the process by which pisiform reduction occurs in sloths and compare it to other previously studied examples of pisiform reduction in humans and orangutans. Both extant sloth genera achieve pisiform reduction through the loss of a secondary ossification center and the likely disruption of the associated growth plate based on an unusually porous subchondral surface. This represents a third unique mechanism of pisiform reduction among mammals, along with primary ossification center loss in humans and retention of two ossification centers with likely reduced growth periods in orangutans. Given the remarkable similarities between two-toed and three-toed sloth pisiform ossification patterns and the presence of pisiform reduction in fossil sloths, extant sloth pisiform morphology does not appear to represent a recent convergent adaptation to suspensory locomotion, but instead is likely to be an ancestral trait of Folivora that emerged early in the radiation of extant and fossil sloths.

(Non)Parallel developmental mechanisms in vertebrate appendage reduction and loss

Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. The multiple routes to appendage reduction and loss suggest that adaptive loss of function phenotypes might arise routinely through changes in expression of key developmental genes.

Conserved and species-specific chromatin remodeling and regulatory dynamics during mouse and chicken limb bud development

Chromatin remodeling and genomic alterations impact spatio-temporal regulation of gene expression, which is central to embryonic development. The analysis of mouse and chicken limb development provides important insights into the morphoregulatory mechanisms, however little is known about the regulatory differences underlying their morphological divergence. Here, we identify the underlying shared and species-specific epigenomic and genomic variations. In mouse forelimb buds, we observe striking synchrony between the temporal dynamics of chromatin accessibility and gene expression, while their divergence in chicken wing buds uncovers species-specific regulatory heterochrony. In silico mapping of transcription factor binding sites and computational footprinting establishes the developmental time-restricted transcription factor-DNA interactions. Finally, the construction of target gene networks for HAND2 and GLI3 transcriptional regulators reveals both conserved and species-specific interactions. Our analysis reveals the impact of genome evolution on the regulatory interactions orchestrating vertebrate limb bud morphogenesis and provides a molecular framework for comparative Evo-Devo studies.

The vertebrate limb bud is a paradigm to uncover the fundamental mechanisms that govern embryogenesis and evolutionary diversification. Here the authors compare mouse and chicken limb bud development to study the impact of genome evolution on conserved and divergent gene regulatory interactions.

Spatial regulation by multiple Gremlin1 enhancers provides digit development with cis-regulatory robustness and evolutionary plasticity

Precise cis-regulatory control of gene expression is essential for normal embryogenesis and tissue development. The BMP antagonist Gremlin1 (Grem1) is a key node in the signalling system that coordinately controls limb bud development. Here, we use mouse reverse genetics to identify the enhancers in the Grem1 genomic landscape and the underlying cis-regulatory logics that orchestrate the spatio-temporal Grem1 expression dynamics during limb bud development. We establish that transcript levels are controlled in an additive manner while spatial regulation requires synergistic interactions among multiple enhancers. Disrupting these interactions shows that altered spatial regulation rather than reduced Grem1 transcript levels prefigures digit fusions and loss. Two of the enhancers are evolutionary ancient and highly conserved from basal fishes to mammals. Analysing these enhancers from different species reveal the substantial spatial plasticity in Grem1 regulation in tetrapods and basal fishes, which provides insights into the fin-to-limb transition and evolutionary diversification of pentadactyl limbs.

The BMP antagonist Gremlin1 balances BMP and SHH signalling, endowing limb bud development with robustness. Here, the authors identify enhancers controlling Grem1 levels in an additive, and spatial regulation in a synergistic manner, providing digit patterning with cis-regulatory robustness and evolutionary plasticity.

Primordial Germ Cell Specification in Vertebrate Embryos: Phylogenetic Distribution and Conserved Molecular Features of Preformation and Induction

The differentiation of primordial germ cells (PGCs) occurs during early embryonic development and is critical for the survival and fitness of sexually reproducing species. Here, we review the two main mechanisms of PGC specification, induction, and preformation, in the context of four model vertebrate species: mouse, axolotl, Xenopus frogs, and zebrafish. We additionally discuss some notable molecular characteristics shared across PGC specification pathways, including the shared expression of products from three conserved germline gene families, DAZ (Deleted in Azoospermia) genes, nanos-related genes, and DEAD-box RNA helicases. Then, we summarize the current state of knowledge of the distribution of germ cell determination systems across kingdom Animalia, with particular attention to vertebrate species, but include several categories of invertebrates - ranging from the "proto-vertebrate" cephalochordates to arthropods, cnidarians, and ctenophores. We also briefly highlight ongoing investigations and potential lines of inquiry that aim to understand the evolutionary relationships between these modes of specification.

Non-model systems in mammalian forelimb evo-devo

Mammal forelimbs are highly diverse, ranging from the elongated wing of a bat to the stout limb of the mole. The mammal forelimb has been a long-standing system for the study of early developmental patterning, proportional variation, shape change, and the reduction of elements. However, most of this work has been performed in mice, which neglects the wide variation present across mammal forelimbs. This review emphasizes the critical role of non-model systems in limb evo-devo and highlights new emerging models and their potential. We discuss the role of gene networks in limb evolution, and touch on functional analyses that lay the groundwork for further developmental studies. Mammal limb evo-devo is a rich field, and here we aim to synthesize the findings of key recent works and the questions to which they lead.

Selection on phalanx development in the evolution of the bird wing

The frameshift hypothesis is a widely-accepted model of bird wing evolution. This hypothesis postulates a shift in positional values, or molecular-developmental identity, that caused a change in digit phenotype. The hypothesis synthesised developmental and palaeontological data on wing digit homology. The 'most anterior digit' (MAD) hypothesis presents an alternative view based on changes in transcriptional regulation in the limb. The molecular evidence for both hypotheses is that the most anterior digit expresses Hoxd13 but not Hoxd11 and Hoxd12. This digit I 'signature' is thought to characterise all amniotes. Here, we studied Hoxd expression patterns in a phylogenetic sample of 18 amniotes. Instead of a conserved molecular signature in digit I, we find wide variation of Hoxd11, Hoxd12 and Hoxd13 expression in digit I. Patterns of apoptosis, and Sox9 expression, a marker of the phalanx-forming region, suggest that phalanges were lost from wing digit IV because of early arrest of the phalanx-forming region followed by cell death. Finally, we show that multiple amniote lineages lost phalanges with no frameshift. Our findings suggest that the bird wing evolved by targeted loss of phalanges under selection. Consistent with our view, some recent phylogenies based on dinosaur fossils eliminate the need to postulate a frameshift in the first place. We suggest that the phenotype of the Archaeopteryx lithographica wing is also consistent with phalanx loss. More broadly, our results support a gradualist model of evolution based on tinkering with developmental gene expression.

Gene Regulatory and Expression Differences between Mouse and Pig Limb Buds Provide Insights into the Evolutionary Emergence of Artiodactyl Traits

Digit loss/reductions are evolutionary adaptations in cursorial mammals such as pigs. To gain mechanistic insight into these processes, we performed a comparative molecular analysis of limb development in mouse and pig embryos, which revealed a loss of anterior-posterior polarity during distal progression of pig limb bud development. These alterations in pig limb buds are paralleled by changes in the mesenchymal response to Sonic hedgehog (SHH) signaling, which is altered upstream of the reduction and loss of Fgf8 expression in the ectoderm that overlaps the reduced and vestigial digit rudiments of the pig handplate, respectively. Furthermore, genome-wide open chromatin profiling using equivalent developmental stages of mouse and pig limb buds reveals the functional divergence of about one-third of the regulatory genome. This study uncovers widespread alterations in the regulatory landscapes of genes essential for limb development that likely contributed to the morphological diversion of artiodactyl limbs from the pentadactyl archetype of tetrapods.

The developmental hourglass model and recapitulation: An attempt to integrate the two models

Recapitulation is a hypothetical concept that assumes embryogenesis of an animal parallels its own phylogenetic history, sequentially developing from more ancestral features to more derived ones. This concept predicts that the earliest developmental stage of various animals should represent the most evolutionarily conserved patterns. Recent transcriptome‐based studies, on the other hand, have reported that mid‐embryonic, organogenetic periods show the highest level of conservation (the developmental hourglass model). This, however, does not rule out the possibility that recapitulation would still be detected after the mid‐embryonic period. In accordance with this, recapitulation‐like morphological features are enriched in late developmental stages. Moreover, our recent chromatin accessibility‐based study provided molecular evidence for recapitulation in the mid‐to‐late embryogenesis of vertebrates, as newly evolved gene regulatory elements tended to be activated at late embryonic stages. In this review, we revisit the recapitulation hypothesis, together with recent molecular‐based studies that support the developmental hourglass model. We contend that the recapitulation hypothesis does not entirely contradict the developmental hourglass model and that these two may even coexist in later embryonic stages of vertebrates. Finally, we review possible mechanisms underlying the recapitulation pattern of chromatin accessibility together with the hourglass‐like evolutionary conservation in vertebrate embryogenesis.

Recapitulation pattern has been reported for chromatin accessibility during the mid‐to‐late embryogenesis.

The observed recapitulation pattern and the developmental hourglass model may coexist.

The possible evolutionary mechanisms underlying tendencies of embryonic evolution were discussed.

Regulation of vertebrate forelimb development and wing reduction in the flightless emu

The vertebrate limb is a dynamic structure which has evolved into many diverse forms to facilitate complex behavioral adaptations. The principle molecular and cellular processes that underlie development of the vertebrate limb are well characterized. However, how these processes are altered to drive differential limb development between vertebrates is less well understood. Several vertebrate models are being utilized to determine the developmental basis of differential limb morphogenesis, though these typically focus on later patterning of the established limb bud and may not represent the complete developmental trajectory. Particularly, heterochronic limb development can occur prior to limb outgrowth and patterning but receives little attention. This review summarizes the genetic regulation of vertebrate forelimb diversity, with particular focus on wing reduction in the flightless emu as a model for examining limb heterochrony. These studies highlight that wing reduction is complex, with heterochronic cellular and genetic events influencing the major stages of limb development. Together, these studies provide a broader picture of how different limb morphologies may be established during development.

The five digits of the giraffe metatarsal

Evolution has shaped the limbs of hoofed animals in specific ways. In artiodactyls, it is the common assumption that the metatarsal is composed of the fusion of digits III and IV, whereas the other three digits have been lost or are highly reduced. However, evidence from the fossil record and internal morphology of the metatarsal challenges these assumptions. Furthermore, only a few taxonomic groups have been analysed. In giraffes, we discovered that all five digits are present in the adult metatarsal and are highly fused and modified rather than lost. We examined high-resolution micro-computed tomography scans of the metatarsals of two mid and late Miocene giraffid fossils and the extant giraffe and okapi. In all the Giraffidae analysed, we found a combination of four morphologies: (1) four articular facets; (2) four or, in most cases, five separate medullary cavities internally; (3) a clear, small digit I; and (4) in the two fossil taxa of unknown genus, the presence of external elongated grooves where the fusions of digits II and V have taken place. Giraffa and Okapia, the extant Giraffidae, show a difference from all the extinct taxa in having more flattened digits tightly packed together, suggesting convergent highly fused digits despite divergent ecologies and locomotion. These discoveries provide evidence that enhances our understanding of how bones fuse and call into question current hypotheses of digit loss.

Regulation of the limb shape during the development of the Chinese softshell turtles

Interdigital cell death is an important mechanism employed by amniotes to shape their limbs; inhibiting this process leads to the formation of webbed fingers, as seen in bats and ducks. The Chinese softshell turtle Pelodiscus sinensis (Reptilia: Testudines: Trionychidae) has a distinctive limb morphology: the anterior side of the limbs has partially webbed fingers with claw‐like protrusions, while the posterior fingers are completely enclosed in webbings. Here, P. sinensis embryos were investigated to gain insights on the evolution of limb‐shaping mechanisms in amniotes. We found cell death and cell senescence in their interdigital webbings. Spatial or temporal modulation of these processes were correlated with the appearance of indentations in the webbings, but not a complete regression of this tissue. No differences in interdigital cell proliferation were found. In subsequent stages, differential growth of the finger cartilages led to a major difference in limb shape. While no asymmetry in bone morphogenetic protein signaling was evident during interdigital cell death stages, some components of this pathway were expressed exclusively in the clawed digit tips, which also had earlier ossification. In addition, a delay and/or truncation in the chondrogenesis of the posterior digits was found in comparison with the anterior digits of P. sinensis, and also when compared with the previously published pattern of digit skeletogenesis of turtles without posterior webbings. In conclusion, modulation of cell death, as well as a heterochrony in digit chondrogenesis, may contribute to the formation of the unique limbs of the Chinese softshell turtles.

Cell death and senescence shape the interdigital webbings of Pelodiscus sinensis.

Delayed chondrogenesis/ossification and truncated tips are found in posterior digits, as well as differential expression of bone morphogenetic proteins and Msh homeobox 1 transcription factors.

Cell death in the developing vertebrate limb: A locally regulated mechanism contributing to musculoskeletal tissue morphogenesis and differentiation

Our aim is to critically review current knowledge of the function and regulation of cell death in the developing limb. We provide a detailed, but short, overview of the areas of cell death observed in the developing limb, establishing their function in morphogenesis and structural development of limb tissues. We will examine the functions of this process in the formation and growth of the limb primordia, formation of cartilaginous skeleton, formation of synovial joints, and establishment of muscle bellies, tendons, and entheses. We will analyze the plasticity of the cell death program by focusing on the developmental potential of progenitors prior to death. Considering the prolonged plasticity of progenitors to escape from the death process, we will discuss a new biological perspective that explains cell death: this process, rather than secondary to a specific genetic program, is a consequence of the tissue building strategy employed by the embryo based on the formation of scaffolds that disintegrate once their associated neighboring structures differentiate.

We examine the functions of cell death in the formation and growth of the limb primordia.

We analyze the plasticity of the cell death program by focusing on the developmental potential of progenitors prior to death.

Considering the prolonged plasticity of progenitors to escape from the death process and the absence of defined genetic program in their regulation we propose that cell death is a consequence of the tissue building strategy employed by the embryo regulated by epigenetic factors .

Hedgehog signaling controls segmentation dynamics and diversity via msx1 in a spider embryo

Hedgehog (Hh) signaling plays fundamental roles in animal body patterning. Understanding its mechanistic complexity requires simple tractable systems that can be used for these studies. In the early spider embryo, Hh signaling mediates the formation of overall anterior-posterior polarity, yet it remains unclear what mechanisms link the initial Hh signaling activity with body axis segmentation, in which distinct periodic stripe-forming dynamics occur depending on the body region. We performed genome-wide searches for genes that transcriptionally respond to altered states of Hh signaling. Characterization of genes negatively regulated by Hh signaling suggested that msx1, encoding a conserved transcription factor, functions as a key segmentation gene. Knockdown of msx1 prevented all dynamic processes causing spatial repetition of stripes, including temporally repetitive oscillations and bi-splitting, and temporally nonrepetitive tri-splitting. Thus, Hh signaling controls segmentation dynamics and diversity via msx1 These genome-wide data from an invertebrate illuminate novel mechanistic features of Hh-based patterning.

Osteomorphological features of the hind limb bones of Saiga antelope (Saiga tatarica)

The intralimb indices and calcaneal linear metrics are known as the reliable predictors of locomotor adaptation in artiodactyls. The osteological features of hindlimb in adult Saiga (Saiga tatarica) were described, and its correlation with cursoriality and habitat adaptation was discussed. Gross anatomy data showed Saiga owned the deep acetabulum as a broad lunate surface, the large acetabular anteversion, the well-developed ischiatic tuberosity and the prominent gluteal lines. It also presented the robust rough line and the strong gluteal tuberosity. A proximodistally elongated eminence located on the cranially distal tibia, which had not been found in goat. The tibial extensor groove was deep. The calcaneal tuberosity was robust. Digital anatomy data showed Saiga owned the higher metatarsal-femur ratio than forest musk deer and sheep. Comparing with wild bovids and sheep, Saiga presented a transitional variation in calcaneal form. The mean greatest length of the calcaneus (GLC) and the height of the sustentacular facet (HSF) in Saiga were shorter than that in sheep and longer than that in wild bovids respectively (F = 587.492; F = 10.264, p < .05). The wild bovids had longer cubonavicular facets than the other two groups (F = 18.587, p < .05). The great metatarsal-femur ratio of Saiga implied a superior cursorial ability and high conservation confronting the different habitats. The calcaneal linear metrics might shed light on lifestyle-related functional adaptation over decades of short-term evolution in the semi-free range environment.

Polydactyly Patient Carried a Mutation of PTCH1 Which Has Been Identified in Nevoid Basal Cell Nevus Syndrome

Polydactyly frequently exhibits autosomal dominant inheritance, which is characterized by supernumerary fingers or toes. The growth of the limb was controlled by three signaling pathways in three-dimensional axis. Sonic Hedgehog signaling, which controls the anterior to posterior (radial to ulnar) orientation has been suspected to be a main cause for polydactyly. To determine the pathogenesis of the patients with polydactyly, we recruited a polydactyly family with two patients. Taking advantage of next-generation sequencing technology, we applied whole-exome sequencing and Sanger sequencing to the proband and her daughter. The analysis of the whole-exome sequencing showed a heterozygous missense mutation c.3617G>A (p.R1206H) in the PTCH1 gene. The results of Sanger sequencing also verified this mutation. Our research discovered a candidate gene of polydactyly-PTCH1. We are the first to point out the relationship between polydactyly and PTCH1 mutation in human. As the PTCH1 gene mutations have been identified in nevoid basal cell nevus syndrome (NBCCS), and polydactyly is one phenotype of NBCCS, it may provide a new clue to the study of the genotype-phenotype correlations between the PTCH1 gene mutations and NBCCS.

Digit ratio and length asymmetry in calves' limbs

This study considered possible sexual dimorphism in the relative lengths of the second, third and fourth digits (digit ratio), in calves. Furthermore, a different length of the bone structures of the third (3D) and of the fourth (4D) digits has been examined as an evolutionary adaptation to locomotion on soft ground. The length of the digital bones of the right fore-limb of 33 females and 15 male calves was measured in vivo using a portable X-ray machine. The vestigial structure of the second digit (2D), and 3D and 4D, from metacarpus to the third phalanx were considered in a mixed model, as well as some ratios between 2D and different parts of 3D or 4D (2D:3D and 2D:4D). A covariate for the mean finger length was considered for digit ratios to control for possible biases due to shape allometry. Shorter first phalanx and trotter were found in 3D than in 4D, and the reverse for the third phalanx. The 2D was significantly shorter in females, as well as the second phalanges of 3D and 4D. Significant sex differences in 2D:3D and 2D:4D were found for some digit parts of 3D and 4D and for the first phalanges of 3D:4D. These ratios were always shorter in females, in contrast to that found in most mammals. The asymmetry between 3D and 4D could mean a functional adaptation for locomotion. Sex differences in 2D:4D and 3D:4D were found, but with a reverse pattern than in most mammal species (males > females rather than males < females). In this regard digit ratio in calves was similar to that of Old World monkeys. This study is the first investigation of digit ratio in Ungulates, whose limbs differ from the limbs of most mammals, maintaining five digits. The reverse pattern of sex differences (digit ratios: males> females) could be due to the peculiar nature of the vestigial dewclaw of 2D and to the hormone patterns acting on this digit during development, but further research is required around this topic.

Forelimb shortening of Carcharodontosauria (Dinosauria: Theropoda): an update on evolutionary anterior micromelias in non-avian theropods

Evolutionary teratology recognises certain anatomical modifications as developmental anomalies. Within non avian-theropod dinosaurs, the strong forelimb shortening of Tyrannosauridae, Carnotaurinae and Limusaurus - associated with a reduction or loss of autonomy - have been previously diagnosed as evolutionary anterior micromelias. The feature is here examined with Acrocanthosaurus atokensis (Carcharodontosauridae) and Gualicho shinyae (Neovenatoridae). The micromelic diagnosis is confirmed for Acrocanthosaurus, without supplementary malformations. Gualicho is considered as a borderline case, outside of the micromelic spectrum, but shows a total phalangeal loss on digit III. The reduction in the biomechanical range of Acrocanthosaurus' forelimbs was compensated by the skull and jaws as main predatory organs. The same is assumed for Gualicho, but its robust first digit and raptorial claw are to be underlined. Other gigantic-sized and derived representatives of Carcharodontosauridae probably shared the anterior micromelia condition, potentially due to developmental modifications involving differential forelimbs/hindlimbs embryological growth rates, secondarily associated with post-natal growth rates leading to large and gigantic sizes; a converging state with Tyrannosauridae. Nevertheless, whereas developmental growth rates are also considered in the shortened condition of Gualicho, there is no association with post-natal gigantism. Finally, the digit III reduction likely followed the same evolutionary pathways as Tyrannosauridae, potentially involving BMPs, Fgfs and Shh signalling.

Development of the chick wing and leg neuromuscular systems and their plasticity in response to changes in digit numbers

The tetrapod limb has long served as a paradigm to study vertebrate pattern formation. During limb morphogenesis, a number of distinct tissue types are patterned and subsequently must be integrated to form coherent functional units. For example, the musculoskeletal apparatus of the limb requires the coordinated development of the skeletal elements, connective tissues, muscles and nerves. Here, using light-sheet microscopy and 3D-reconstructions, we concomitantly follow the developmental emergence of nerve and muscle patterns in chicken wings and legs, two appendages with highly specialized locomotor outputs. Despite a comparable flexor/extensor-arrangement of their embryonic muscles, wings and legs show a rotated innervation pattern for their three main motor nerve branches. To test the functional implications of these distinct neuromuscular topologies, we challenge their ability to adapt and connect to an experimentally altered skeletal pattern in the distal limb, the autopod. Our results show that, unlike autopod muscle groups, motor nerves are unable to fully adjust to a changed peripheral organisation, potentially constrained by their original projection routes. As the autopod has undergone substantial morphological diversifications over the course of tetrapod evolution, our results have implications for the coordinated modification of the distal limb musculoskeletal apparatus, as well as for our understanding of the varying degrees of motor functionality associated with human hand and foot malformations.

Evidence of five digits in embryonic horses and developmental stabilization of tetrapod digit number

Previous work comparing the developmental mechanisms involved in digit reduction in horses with other mammals reported that horses have only a 'single digit', with two flanking metapodials identified as remnants of digit II and IV. Here we show that early Equus embryos go through a stage with five digit condensations, and that the flanking splint metapodials result from fusions of the two anterior digits I and II and the two posterior digits IV and V, in a striking parallel between ontogeny and phylogeny. Given that even this most extreme case of digit reduction exhibits primary pentadactyly, we re-examined the initial stages of digit condensation of all digit-reduced tetrapods where data are available and found that in all cases, five or four digits initiate (four with digit I missing). The persistent pentadactyl initiation in the horse and other digit-reduced modern taxa underscores a durable developmental stability at the initiation of digits. The digit evodevo model may help illuminate the biological circumstances under which organ systems become highly stabilized versus highly plastic.

The Evolution of a Single Toe in Horses: Causes, Consequences, and the Way Forward

Horses are a classic example of macroevolution in three major traits-large body size, tall-crowned teeth (hypsodonty), and a single toe (monodactyly)-but how and why monodactyly evolved is still poorly understood. Existing hypotheses usually connect digit reduction in horses to the spread and eventual dominance of open-habitat grasslands, which took over from forests during the Cenozoic; digit reduction has been argued to be an adaptation for speed, locomotor economy, stability, and/or increased body size. In this review, we assess the evidence for these (not necessarily mutually exclusive) hypotheses from a variety of related fields, including paleoecology, phylogenetic comparative methods, and biomechanics. Convergent evolution of digit reduction, including in litopterns and artiodactyls, is also considered. We find it unlikely that a single evolutionary driver was responsible for the evolution of monodactyly, because changes in body size, foot posture, habitat, and substrate are frequently found to influence one another (and to connect to broader potential drivers, such as changing climate). We conclude with suggestions for future research to help untangle the complex dynamics of this remarkable morphological change in extinct horses. A path forward should combine regional paleoecology studies, quantitative biomechanical work, and make use of convergence and modern analogs to estimate the relative contributions of potential evolutionary drivers for digit reduction.

Convergent metatarsal fusion in jerboas and chickens is mediated by similarities and differences in the patterns of osteoblast and osteoclast activities

In many vertebrate animals that run or leap, the metatarsals and/or metacarpals of the distal limb are fused into a single larger element, likely to resist fracture due to high ground-reaction forces during locomotion. Although metapodial fusion evolved independently in modern birds, ungulates, and jerboas, the developmental basis has only been explored in chickens, which diverged from the mammalian lineage approximately 300 million years ago. Here, we use a bipedal rodent, the lesser Egyptian jerboa (Jaculus jaculus), to understand the cellular processes of metatarsal fusion in a mammal, and we revisit the developing chicken to assess similarities and differences in the localization of osteoblast and osteoclast activities. In both species, adjacent metatarsals align along flat surfaces, osteoblasts cross the periosteal membrane to unite the three elements in a single circumference, and osteoclasts resorb bone at the interfaces leaving a single marrow cavity. However, the pattern of osteoclast activity differs in each species; osteoclasts are highly localized to resorb bone at the interfaces of neighboring jerboa metatarsals and are distributed throughout the endosteum of chicken metatarsals. Each species, therefore, provides an opportunity to understand mechanisms that pattern osteoblast and osteoclast activities to alter bone shape during development and evolution.

L-type voltage-gated Ca2+ channel CaV1.2 regulates chondrogenesis during limb development

All cells, including nonexcitable cells, maintain a discrete transmembrane potential (V _mem), and have the capacity to modulate V _mem and respond to their own and neighbors' changes in V _mem Spatiotemporal variations have been described in developing embryonic tissues and in some cases have been implicated in influencing developmental processes. Yet, how such changes in V _mem are converted into intracellular inputs that in turn regulate developmental gene expression and coordinate patterned tissue formation, has remained elusive. Here we document that the V _mem of limb mesenchyme switches from a hyperpolarized to depolarized state during early chondrocyte differentiation. This change in V _mem increases intracellular Ca²⁺ signaling through Ca²⁺ influx, via Ca_V1.2, 1 of L-type voltage-gated Ca²⁺ channels (VGCCs). We find that Ca_V1.2 activity is essential for chondrogenesis in the developing limbs. Pharmacological inhibition by an L-type VGCC specific blocker, or limb-specific deletion of Ca_V1.2, down-regulates expression of genes essential for chondrocyte differentiation, including Sox9, Col2a1, and Agc1, and thus disturbs proper cartilage formation. The Ca²⁺-dependent transcription factor NFATc1, which is a known major transducer of intracellular Ca²⁺ signaling, partly rescues Sox9 expression. These data reveal instructive roles of Ca_V1.2 in limb development, and more generally expand our understanding of how modulation of membrane potential is used as a mechanism of developmental regulation.

Environmental Oxygen Exposure Allows for the Evolution of Interdigital Cell Death in Limb Patterning

Amphibians form fingers without webbing by differential growth between digital and interdigital regions. Amniotes, however, employ interdigital cell death (ICD), an additional mechanism that contributes to a greater variation of limb shapes. Here, we investigate the role of environmental oxygen in the evolution of ICD in tetrapods. While cell death is restricted to the limb margin in amphibians with aquatic tadpoles, Eleutherodactylus coqui, a frog with terrestrial-direct-developing eggs, has cell death in the interdigital region. Chicken requires sufficient oxygen and reactive oxygen species to induce cell death, with the oxygen tension profile itself being distinct between the limbs of chicken and Xenopus laevis frogs. Notably, increasing blood vessel density in X. laevis limbs, as well as incubating tadpoles under high oxygen levels, induces ICD. We propose that the oxygen available to terrestrial eggs was an ecological feature crucial for the evolution of ICD, made possible by conserved autopod-patterning mechanisms.

Locomotor correlates of the scapholunar of living and extinct carnivorans

The relationship of carpal morphology to ecology and habitat is under studied in carnivorans and more generally in mammals. Here, we use 3D-scanning techniques to assess the usefulness of a carpal bone, the scapholunar, in carnivorans to reflect ecology and habitat, and to reconstruct the ecology of five extinct carnivorans from two fossil sites: Rancho La Brea and Natural Trap Cave. We 3D-scanned scapholunars and measured articular surface areas and angles between articular facets using GeoMagic and Rhino 3D-software. We analyzed the difference in these metrics using multivariate analysis of variance and discriminant function analysis. Results show that the scapholunar reflects ecological signal, with clear groupings of cursorial carnivorans and grappling/climbing carnivorans; however, phylogenetic signal was also present in the results with hyaenids, canids, and large felids in distinct morphospaces. Extinct species Miracinonyx trumani (American cheetah) and Smilodon fatalis (sabertooth cat) showed surprising results with M. trumani grouping with pantherines instead of Acinonyx or Puma, suggesting it runs but still retains the ability to grapple prey. S. fatalis groups with pantherines, but also shows some unique adaptations, suggesting it had a different range of wrist motion than living cats. Overall, the scapholunar is a good indicator of ecology and functional morphology and can be another tool to use in modern and fossil carnivorans to reconstruct extinct ecologies and locomotor behaviors.

Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (Lycaon pictus)

Within the Canidae, the African wild dog (Lycaon pictus) is the most specialized with regards to cursorial adaptations (specialized for running), having only four digits on their forefeet. In addition, this species is one of the few canids considered to be an obligate meat-eater, possessing a robust dentition for taking down large prey, and displays one of the most variable coat colorations amongst mammals. Here, we used comparative genomic analysis to investigate the evolutionary history and genetic basis for adaptations associated with cursoriality, hypercanivory, and coat color variation in African wild dogs. Genome-wide scans revealed unique amino acid deletions that suggest a mode of evolutionary digit loss through expanded apoptosis in the developing first digit. African wild dog-specific signals of positive selection also uncovered a putative mechanism of molar cusp modification through changes in genes associated with the sonic hedgehog (SHH) signaling pathway, required for spatial patterning of teeth, and three genes associated with pigmentation. Divergence time analyses suggest the suite of genomic changes we identified evolved ~1.7 Mya, coinciding with the diversification of large-bodied ungulates. Our results show that comparative genomics is a powerful tool for identifying the genetic basis of evolutionary changes in Canidae.