Why five fingers? Evolutionary constraints on digit numbers

The legacy and evolvability of Pere Alberch's ideas

Pere Alberch played a pivotal role in shaping the field of evolutionary developmental biology during the 1980s and 1990s. Whereas initially his contributions were sidelined by the empirical advancements of the molecular revolution in developmental and evolutionary biology, his theoretical insights have left a lasting impact on the discipline. This article provides a comprehensive review of the legacy and evolvability of Alberch's ideas in contemporary evo-devo, which included the study of morphogenesis as the proper level of developmental causation, the interplay between developmental constraints and natural selection, the epistemic role of teratologies, the origin of evolutionary novelties and the concept of evolvability.

The logic of monsters: development and morphological diversity in stem-cell-based embryo models

Organoids and stem-cell-based embryo models (SEMs) are imperfect organ or embryo representations that explore a much larger space of possible forms, or morphospace, compared to their in vivo counterparts. Here, we discuss SEM biology in light of seminal work by Pere Alberch, a leading figure in early evo-devo, interpreting SEMs as developmental 'monstrosities' in the Alberchian sense. Alberch suggested that ordered patterns in aberrant development-i.e. 'the logic of monsters'-reveal developmental constraints on possible morphologies. In the same vein, we detail how SEMs have begun to shed light on structural features of normal development, such as developmental variability, the relative importance of internal versus external constraints, boundary conditions and design principles governing robustness and canalization. We argue that SEMs represent a powerful experimental tool to explore and expand developmental morphospace and propose that the 'monstrosity' of SEMs can be leveraged to uncover the 'hidden' rules and developmental constraints that robustly shape and pattern the embryo.

Mammalian forelimb evolution is driven by uneven proximal-to-distal morphological diversity

Vertebrate limb morphology often reflects the environment due to variation in locomotor requirements. However, proximal and distal limb segments may evolve differently from one another, reflecting an anatomical gradient of functional specialization that has been suggested to be impacted by the timing of development. Here, we explore whether the temporal sequence of bone condensation predicts variation in the capacity of evolution to generate morphological diversity in proximal and distal forelimb segments across more than 600 species of mammals. Distal elements not only exhibit greater shape diversity, but also show stronger within-element integration and, on average, faster evolutionary responses than intermediate and upper limb segments. Results are consistent with the hypothesis that late developing distal bones display greater morphological variation than more proximal limb elements. However, the higher integration observed within the autopod deviates from such developmental predictions, suggesting that functional specialization plays an important role in driving within-element covariation. Proximal and distal limb segments also show different macroevolutionary patterns, albeit not showing a perfect proximo-distal gradient. The high disparity of the mammalian autopod, reported here, is consistent with the higher potential of development to generate variation in more distal limb structures, as well as functional specialization of the distal elements.

Rarity of congenital malformation and deformity in the fossil record of vertebrates - A non-human perspective

OBJECTIVE

A malformed pectoral joint of the middle Devonian antiarch fish Asterolepis ornata is described, and a survey of congenital malformations in the fossil record is provided.

MATERIALS

The specimen of A. ornata (MB.f.73) from Ehrman in Latvia, stored at the Museum für Naturkunde Berlin, Germany.

METHODS

A. ornata was macroscopically and radiologically investigated, and the overview on congenital malformation was based on an extensive literature survey.

RESULTS

In the deformed joint of A. ornata, the articular surfaces and muscle attachment sites are greatly reduced, indicating restricted mobility. Congenital malformations can be found since the middle Silurian and affect all groups of vertebrates, but they are rare. Teeth and the vertebral column are the most commonly affected anatomical regions, and the mechanisms causing these malformations probably remained the same through geological time.

CONCLUSIONS

Micro-CT of the deformed joint shows no disturbance of the normal trabecular pattern and no evidence of trauma or disease, suggesting a congenital hypoplasia, although an acquired deformity cannot be ruled out completely.

SIGNIFICANCE

Congenital malformations, even those that are rare, were part of the common history of vertebrates for more than 400 million years.

LIMITATIONS

Epidemiologic measures like incidence and prevalence usually cannot be applied to define rare diseases in the fossil record.

SUGGESTIONS FOR FURTHER RESEARCH

A broadly based analysis of species of fossil vertebrates with numerus recovered specimens (e.g. many bony fishes, amphibians, certain dinosaurs) might statistically affirm the occurrence of malformations and possible correlations with the paleoenvironment.

Digit ratio in the common toad Bufo bufo: the effects of reduced fingers and of age dependency

INTRODUCTION

Despite the growing number of studies describing digit ratio patterns in tetrapods, knowledge concerning certain basic issues is still scarce. In lower vertebrates such as tailless amphibians (Anura), the numbering of individual fingers on the forelimbs and their homology with the fingers of other vertebrates pose an unsolved problem. Based on reviewed data on anuran limb development, we argue that the correct finger numbering scheme should be based on the assumption that the first finger, not the fifth finger, was reduced on the forelimbs. We analyzed the digit ratio in the common toad (Bufo bufo, Bufonidae), a species characterized by well-developed sexual dimorphism whereby females are larger than males, using both numbering schemes present in the literature.

RESULTS

We found that the digit ratio on hindlimbs differed significantly between the sexes only in the cases of left 2D:3D, with lower digit ratios in females, and of left 3D:4D, with lower digit ratios in males. We found that sex was the only significant variable for forelimbs, differentiating 2D:3D on the left forelimb, with lower digit ratios in females; 2D:4D on the right forelimb, with lower digit ratios in males; and 3D:4D on both forelimbs, with lower digit ratios in males. These results relate to variant II reflecting the hypothesis that the first digit was reduced during phylogenesis. There was no relationship between the body size (SVL) of individuals and any digit ratio, excluding 2D:4D on the right forelimbs in models with age variables. Additionally, for a subset of data where individual age was known, the models indicated that age was linked to significant differences in 2D:4D and 3D:4D on the left hindlimbs, while age, SVL, and sex influenced 2D:4D on the right forelimbs.

CONCLUSION

We emphasize the importance of the problem of the correct numbering of forelimb digits in Anura and, under the assumption that it was the fifth digit that was reduced, argue that earlier results on digit ratio in this group should be interpreted with caution. The detected relationship between digit ratio and age in amphibians expands our knowledge, indicating that the age of individuals should be included in future digit ratio studies. This relationship may also apply to studies using digit ratio as a noninvasive indicator of endocrine disruption in amphibians.

A novel energy-motion model for continuous sEMG decoding: from muscle energy to motor pattern

At present, sEMG-based gesture recognition requires vast amounts of training data; otherwise it is limited to a few gestures. Objective. This paper presents a novel dynamic energy model that decodes continuous hand actions by training small amounts of sEMG data. Approach. The activation of forearm muscles can set the corresponding fingers in motion or state with movement trends. The moving fingers store kinetic energy, and the fingers with movement trends store potential energy. The kinetic energy and potential energy in each finger are dynamically allocated due to the adaptive-coupling mechanism of five-fingers in actual motion. Meanwhile, the sum of the two energies remains constant at a certain muscle activation. We regarded hand movements with the same direction of acceleration for five-finger as the same in energy mode and divided hand movements into ten energy modes. Independent component analysis and machine learning methods were used to model associations between sEMG signals and energy modes and expressed gestures by energy form adaptively. This theory imitates the self-adapting mechanism in actual tasks. Thus, ten healthy subjects were recruited, and three experiments mimicking activities of daily living were designed to evaluate the interface: (1) the expression of untrained gestures, (2) the decoding of the amount of single-finger energy, and (3) real-time control. Main results. (1) Participants completed the untrained hand movements (100/100, p < 0.0001). (2) The interface performed better than chance in the experiment where participants pricked balloons with a needle tip (779/1000, p < 0.0001). (3) In the experiment where participants punched a hole in the plasticine on the balloon, the success rate was over 95% (97.67 ± 5.04%, p < 0.01). Significance. The model can achieve continuous hand actions with speed or force information by training small amounts of sEMG data, which reduces learning task complexity.

Morphospace analysis leads to an evo-devo model of digit patterning

Biological forms occupy a constrained portion of theoretical morphospaces. Developmental models accounting for empirical morphospaces are necessary to achieve a better understanding of this phenomenon. We analyzed the phalangeal formulas (PFs) in lizards and relatives' hands by comparing them with a set of simulated PFs that compose a theoretical morphospace. We detected that: (1) the empirical morphospace is severely limited in size, (2) the PFs comply with two properties of phalangeal count per digit, namely the ordering rule (DI ≤ DII ≤ DIII ≤ DIV ≥ DV), and the contiguity relationship (neighbor digits differ on average in one phalanx), (3) the totality of the PFs can be categorized into four categories of hands aligned along a feasibility gradient. We also reconstructed the evolution of PFs and found a stepwise trajectory from the plesiomorphic PF towards reduced conditions. Finally, we propose a developmental model as the generative mechanism behind the PFs. It is consistent with the bulk of evidence managed and involves an ordered digit primordia initialization timed with periodic signals of joint formation coming from digit tips. Our approach is also useful to address the study of other meristic sequences in nature such as dental, floral, and branchial formulas.

A Logical Model of Homology for Comparative Biology

There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated structures within an organism). We explored how to most effectively represent historical and serial homology across anatomical structures to facilitate computational reasoning. We assembled a collection of homology assertions from the literature with a set of taxon phenotypes for the skeletal elements of vertebrate fins and limbs from the Phenoscape Knowledgebase. Using seven competency questions, we evaluated the reasoning ramifications of two logical models: the Reciprocal Existential Axioms (REA) homology model and the Ancestral Value Axioms (AVA) homology model. The AVA model returned all user-expected results in addition to the search term and any of its subclasses. The AVA model also returns any superclass of the query term in which a homology relationship has been asserted. The REA model returned the user-expected results for five out of seven queries. We identify some challenges of implementing complete homology queries due to limitations of OWL reasoning. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery. [Homology; ontology; anatomy; morphology; evolution; knowledgebase; phenoscape.].

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.

Sesamoids in tetrapods: the origin of new skeletal morphologies

Along with supernumerary bones, sesamoids, defined as any organized intratendinous/intraligamentous structure, including those composed of fibrocartilage, adjacent to an articulation or joint, have been frequently considered as enigmatic structures associated with the joints of the skeletal system of vertebrates. This review allows us to propose a dynamic model to account for part of skeletal phenotypic diversity: during evolution, sesamoids can become displaced, attaching to and detaching from the long bone epiphyses and diaphysis. Epiphyses, apophyses and detached sesamoids are able to transform into each other, contributing to the phenotypic variability of the tetrapod skeleton. This dynamic model is a new paradigm to delineate the contribution of sesamoids to skeletal diversity. Herein, we first present a historical approach to the study of sesamoids, discussing the genetic versus epigenetic theories of their genesis and growth. Second, we construct a dynamic model. Third, we present a summary of literature on sesamoids of the main groups of tetrapods, including veterinary and human clinical contributions, which are the best-studied aspects of sesamoids in recent decades. Finally, we discuss the identity of certain structures that have been labelled as sesamoids despite insufficient formal testing of homology. We also propose a new definition to help the identification of sesamoids in general. This review is particularly timely, given the recent increasing interest and research activity into the developmental biology and mechanics of sesamoids. With this updated and integrative discussion, we hope to pave the way to improve the understanding of sesamoid biology and evolution.

Terrestriality constrains salamander limb diversification: Implications for the evolution of pentadactyly

Patterns of phenotypic evolution can abruptly shift as species move between adaptive zones. Extant salamanders display three distinct life cycle strategies that range from aquatic to terrestrial (biphasic), to fully aquatic (paedomorphic) and to fully terrestrial (direct development). Life cycle variation is associated with changes in body form such as loss of digits, limb reduction or body elongation. However, the relationships among these traits and life cycle strategy remain unresolved. Here, we use a Bayesian modelling approach to test whether life cycle transitions by salamanders have influenced rates, optima and integration of primary locomotory structures (limbs and trunk). We show that paedomorphic salamanders have elevated rates of limb evolution with optima shifted towards smaller size and fewer digits compared to all other salamanders. Rate of hindlimb digit evolution is shown to decrease in a gradient as life cycles become more terrestrial. Paedomorphs have a higher correlation between hindlimb digit loss and increases in vertebral number, as well as reduced correlations between limb lengths. Our results support the idea that terrestrial plantigrade locomotion constrains limb evolution and, when lifted, leads to higher rates of trait diversification and shifts in optima and integration. The basic tetrapod body form of most salamanders and the independent losses of terrestrial life stages provide an important framework for understanding the evolutionary and developmental mechanisms behind major shifts in ecological zones as seen among early tetrapods during their transition from water to land.

Development and Evolutionary Constraints in Animals

We review the evolutionary importance of developmental mechanisms in constraining evolutionary changes in animals—in other words, developmental constraints. We focus on hard constraints that can act on macroevolutionary timescales. In particular, we discuss the causes and evolutionary consequences of the ancient metazoan constraint that differentiated cells cannot divide and constraints against changes of phylotypic stages in vertebrates and other higher taxa. We conclude that in all cases these constraints are caused by complex and highly controlled global interactivity of development, the disturbance of which has grave consequences. Mutations that affect such global interactivity almost unavoidably have many deleterious pleiotropic effects, which will be strongly selected against and will lead to long-term evolutionary stasis. The discussed developmental constraints have pervasive consequences for evolution and critically restrict regeneration capacity and body plan evolution.

Phenotypic disparity of the elbow joint in domestic dogs and wild carnivores

In this article, I use geometric morphometrics in 2D from a sample of 366 elbow joints to quantify phenotypic disparity in domestic dog breeds, in wild canids, and across the order Carnivora. The elbow joint is a well-established morphological indicator of forearm motion and, by extension, of functional adaptations toward locomotor or predatory behavior in living carnivores. The study of the elbow joint in domestic dogs allows the exploration of potential convergences between (i) pursuit predators and fast-running dogs, and (ii) ambush predators and fighting breeds. The results indicate that elbow shape disparity among domestic dogs exceeds than in wolves; it is comparable to the disparity of wild Caninae, but is significantly lower than the one observed throughout Canidae and Carnivora. Moreover, fast-running and fighting breeds are not convergent in elbow joint shape with extreme pursuit and ambush wild carnivores, respectively. The role of artificial selection and developmental constraints in shaping limb phenotypic disparity through the extremely fast evolution of the domestic dog is discussed in the light of this new evidence.

C7 vertebra homeotic transformation in domestic dogs - are Pug dogs breaking mammalian evolutionary constraints?

The number of cervical vertebrae in mammals is almost constant at seven, regardless of their neck length, implying that there is selection against variation in this number. Homebox (Hox) genes are involved in this evolutionary mammalian conservation, and homeotic transformation of cervical into thoracic vertebrae (cervical ribs) is a common phenotypic abnormality when Hox gene expression is altered. This relatively benign phenotypic change can be associated with fatal traits in humans. Mutations in genes upstream of Hox, inbreeding and stressors during organogenesis can also cause cervical ribs. The aim of this study was to describe the prevalence of cervical ribs in a large group of domestic dogs of different breeds, and explore a possible relation with other congenital vertebral malformations (CVMs) in the breed with the highest prevalence of cervical ribs. By phenotyping we hoped to give clues as to the underlying genetic causes. Twenty computed tomography studies from at least two breeds belonging to each of the nine groups recognized by the Federation Cynologique Internationale, including all the brachycephalic 'screw-tailed' breeds that are known to be overrepresented for CVMs, were reviewed. The Pug dog was more affected by cervical ribs than any other breed (46%; P < 0.001), and was selected for further analysis. No association was found between the presence of cervical ribs and vertebral body formation defect, bifid spinous process, caudal articular process hypoplasia/aplasia and an abnormal sacrum, which may infer they have a different aetiopathogenesis. However, Pug dogs with cervical ribs were more likely to have a transitional thoraco-lumbar vertebra (P = 0.041) and a pre-sacral vertebral count of 26 (P < 0.001). Higher C7/T1 dorsal spinous processes ratios were associated with the presence of cervical ribs (P < 0.001), supporting this is a true homeotic transformation. Relaxation of the stabilizing selection has likely occurred, and the Pug dog appears to be a good naturally occurring model to further investigate the aetiology of cervical ribs, other congenital vertebral anomalies and numerical alterations.

Early limb patterning in the direct-developing salamander Plethodon cinereus revealed by sox9 and col2a1

Direct-developing amphibians form limbs during early embryonic stages, as opposed to the later, often postembryonic limb formation of metamorphosing species. Limb patterning is dramatically altered in direct-developing frogs, but little attention has been given to direct-developing salamanders. We use expression patterns of two genes, sox9 and col2a1, to assess skeletal patterning during embryonic limb development in the direct-developing salamander Plethodon cinereus. Limb patterning in P. cinereus partially resembles that described in other urodele species, with early formation of digit II and a generally anterior-to-posterior formation of preaxial digits. Unlike other salamanders described to date, differentiation of preaxial zeugopodial cartilages (radius/tibia) is not accelerated in relation to the postaxial cartilages, and there is no early differentiation of autopodial elements in relation to more proximal cartilages. Instead, digit II forms in continuity with the ulnar/fibular arch. This amniote-like connectivity to the first digit that forms may be a consequence of the embryonic formation of limbs in this direct-developing species. Additionally, and contrary to recent models of amphibian digit identity, there is no evidence of vestigial digits. This is the first account of gene expression in a plethodontid salamander and only the second published account of embryonic limb patterning in a direct-developing salamander species.

Digging for known genetic mutations underlying inherited bone and cartilage characteristics and disorders in the dog and cat

Gene mapping projects for many traits in both dogs and cats have yielded new knowledge. Both researchers and the public alike have been fascinated by the inheritance of breed characteristic phenotypes and sporadic disorders. It has been proposed that selective breeding practices have on occasion generated alterations in structure that might be harmful. In this review, simply inherited disorders and characteristics affecting bone and cartilage for which a putative mutation is known are collected. A better understanding of the known inherited basis of skeletal conditions and disorders will assist veterinarians to improve their diagnoses and increase their effectiveness on advising clients on the prevention, management, prognosis and possible treatment of the conditions.

Timing the developmental origins of mammalian limb diversity

Mammals have highly diverse limbs that have contributed to their occupation of almost every niche. Researchers have long been investigating the development of these diverse limbs, with the goals of identifying developmental processes and potential biases that shape mammalian limb diversity. To date, researchers have used techniques ranging from the genomic to the anatomic to investigate the developmental processes shaping the limb morphology of mammals from five orders (Marsupialia, Chiroptera, Rodentia, Cetartiodactyla, and Perissodactyla). Results of these studies suggest that the differential expression of genes controlling diverse cellular processes underlies mammalian limb diversity. Results also suggest that the earliest development of the limb tends to be conserved among mammalian species, while later limb development tends to be more variable. This research has established the mammalian limb as a model system for evolutionary developmental biology, and set the stage for more in-depth, cross-disciplinary research into the genetic controls, tissue-level cellular behaviors, and selective pressures that have driven the developmental evolution of mammalian limbs. Ideally, these studies will be performed in a diverse suite of mammalian species within a comparative, phylogenetic framework.

Disentangling Timing of Admixture, Patterns of Introgression, and Phenotypic Indicators in a Hybridizing Wolf Population

Hybridization is a natural or anthropogenic process that can deeply affect the genetic make-up of populations, possibly decreasing individual fitness but sometimes favoring local adaptations. The population of Italian wolves (Canis lupus), after protracted demographic declines and isolation, is currently expanding in anthropic areas, with documented cases of hybridization with stray domestic dogs. However, identifying admixture patterns in deeply introgressed populations is far from trivial. In this study, we used a panel of 170,000 SNPs analyzed with multivariate, Bayesian and local ancestry reconstruction methods to identify hybrids, estimate their ancestry proportions and timing since admixture. Moreover, we carried out preliminary genotype-phenotype association analyses to identify the genetic bases of three phenotypic traits (black coat, white claws, and spur on the hind legs) putative indicators of hybridization. Results showed no sharp subdivisions between nonadmixed wolves and hybrids, indicating that recurrent hybridization and deep introgression might have started mostly at the beginning of the population reexpansion. In hybrids, we identified a number of genomic regions with excess of ancestry in one of the parental populations, and regions with excess or resistance to introgression compared with neutral expectations. The three morphological traits showed significant genotype-phenotype associations, with a single genomic region for black coats and white claws, and with multiple genomic regions for the spur. In all cases the associated haplotypes were likely derived from dogs. In conclusion, we show that the use of multiple genome-wide ancestry reconstructions allows clarifying the admixture dynamics even in highly introgressed populations, and supports their conservation management.

Genetic rescue of an endangered domestic animal through outcrossing with closely related breeds: A case study of the Norwegian Lundehund

Genetic rescue, outcrossing with individuals from a related population, is used to augment genetic diversity in populations threatened by severe inbreeding and extinction. The endangered Norwegian Lundehund dog underwent at least two severe bottlenecks in the 1940s and 1960s that each left only five inbred dogs, and the approximately 1500 dogs remaining world-wide today appear to descend from only two individuals. The Lundehund has a high prevalence of a gastrointestinal disease, to which all remaining dogs may be predisposed. Outcrossing is currently performed with three Nordic Spitz breeds: Norwegian Buhund, Icelandic Sheepdog, and Norrbottenspets. Examination of single nucleotide polymorphism (SNP) genotypes based on 165K loci in 48 dogs from the four breeds revealed substantially lower genetic diversity for the Lundehund (H_E 0.035) than for other breeds (H_E 0.209–0.284). Analyses of genetic structure with > 15K linkage disequilibrium-pruned SNPs showed four distinct genetic clusters. Pairwise F_ST values between Lundehund and the candidate breeds were highest for Icelandic Sheepdog, followed by Buhund and Norrbottenspets. We assessed the presence of outlier loci among candidate breeds and examined flanking genome regions (1 megabase) for genes under possible selection to identify potential adaptive differences among breeds; outliers were observed in flanking regions of genes associated with key functions including the immune system, metabolism, cognition and physical development. We suggest crossbreeding with multiple breeds as the best strategy to increase genetic diversity for the Lundehund and to reduce the incidence of health problems. For this project, the three candidate breeds were first selected based on phenotypes and then subjected to genetic investigation. Because phenotypes are often paramount for domestic breed owners, such a strategy could provide a helpful approach for genetic rescue and restoration of other domestic populations at risk, by ensuring the involvement of owners, breeders and managers at the start of the project.

Transcriptomic insights into the genetic basis of mammalian limb diversity

Background

From bat wings to whale flippers, limb diversification has been crucial to the evolutionary success of mammals. We performed the first transcriptome-wide study of limb development in multiple species to explore the hypothesis that mammalian limb diversification has proceeded through the differential expression of conserved shared genes, rather than by major changes to limb patterning. Specifically, we investigated the manner in which the expression of shared genes has evolved within and among mammalian species.

Results

We assembled and compared transcriptomes of bat, mouse, opossum, and pig fore- and hind limbs at the ridge, bud, and paddle stages of development. Results suggest that gene expression patterns exhibit larger variation among species during later than earlier stages of limb development, while within species results are more mixed. Consistent with the former, results also suggest that genes expressed at later developmental stages tend to have a younger evolutionary age than genes expressed at earlier stages. A suite of key limb-patterning genes was identified as being differentially expressed among the homologous limbs of all species. However, only a small subset of shared genes is differentially expressed in the fore- and hind limbs of all examined species. Similarly, a small subset of shared genes is differentially expressed within the fore- and hind limb of a single species and among the forelimbs of different species.

Conclusions

Taken together, results of this study do not support the existence of a phylotypic period of limb development ending at chondrogenesis, but do support the hypothesis that the hierarchical nature of development translates into increasing variation among species as development progresses.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0902-6) contains supplementary material, which is available to authorized users.

Forbidden phenotypes and the limits of evolution

Evolution has produced an astonishing array of organisms, but does it have limits and, if so, how are these overcome and how have they changed over the course of time? Here, I review models for describing and explaining existing diversity, and then explore parts of the evolutionary tree that remain empty. In an analysis of 32 forbidden states among eukaryotes, identified in major clades and in the three great habitat realms of water, land and air, I argue that no phenotypic constraint is absolute, that most constraints reflect a limited time-energy budget available to individual organisms, that natural selection is ultimately responsible for both imposing and overcoming constraints, including those normally ascribed to developmental patterns of construction and phylogenetic conservatism, and that increases in adaptive versatility in major clades together with accompanying new ecological opportunities have eliminated many constraints. Phenotypes that were inaccessible during the Early Palaeozoic era have evolved during later periods while very few adaptive states have disappeared. The filling of phenotypic space has proceeded cumulatively in three overlapping phases characterized by diversification at the biochemical, morphological and cultural levels.

What limits the morphological disparity of clades?

The morphological disparity of species within major clades shows a variety of trajectory patterns through evolutionary time. However, there is a significant tendency for groups to reach their maximum disparity relatively early in their histories, even while their species richness or diversity is comparatively low. This pattern of early high-disparity suggests that there are internal constraints (e.g. developmental pleiotropy) or external restrictions (e.g. ecological competition) upon the variety of morphologies that can subsequently evolve. It has also been demonstrated that the rate of evolution of new character states decreases in most clades through time (character saturation), as does the rate of origination of novel bodyplans and higher taxa. Here, we tested whether there was a simple relationship between the level or rate of character state exhaustion and the shape of a clade's disparity profile: specifically, its centre of gravity (CG). In a sample of 93 extinct major clades, most showed some degree of exhaustion, but all continued to evolve new states up until their extinction. Projection of states/steps curves suggested that clades realized an average of 60% of their inferred maximum numbers of states. Despite a weak but significant correlation between overall levels of homoplasy and the CG of clade disparity profiles, there were no significant relationships between any of our indices of exhaustion curve shape and the clade disparity CG. Clades showing early high-disparity were no more likely to have early character saturation than those with maximum disparity late in their evolution.

The phantoms of a high-seven - or - why do our thumbs stick out?

The earliest tetrapods had hands and feet with up to eight digits but this number was subsequently reduced during evolution. It was assumed that lineages with more than five digits no longer exist but investigations of clawed-frogs now indicate that they posses a rudimentary or atavistic sixth digit in their hindlimb. A recent reevaluation of the stem tetrapod Ichthyostega predicts that its seven digits evolved from two different types of ancestral fin radials, pre-axial and post-axial. In this context we now ask the question, should we consider a pre-axial origin of the thumb as reason for its unique genetic signature?

The Relationship between Gene Network Structure and Expression Variation among Individuals and Species

Variation among individuals is a prerequisite of evolution by natural selection. As such, identifying the origins of variation is a fundamental goal of biology. We investigated the link between gene interactions and variation in gene expression among individuals and species using the mammalian limb as a model system. We first built interaction networks for key genes regulating early (outgrowth; E9.5-11) and late (expansion and elongation; E11-13) limb development in mouse. This resulted in an Early (ESN) and Late (LSN) Stage Network. Computational perturbations of these networks suggest that the ESN is more robust. We then quantified levels of the same key genes among mouse individuals and found that they vary less at earlier limb stages and that variation in gene expression is heritable. Finally, we quantified variation in gene expression levels among four mammals with divergent limbs (bat, opossum, mouse and pig) and found that levels vary less among species at earlier limb stages. We also found that variation in gene expression levels among individuals and species are correlated for earlier and later limb development. In conclusion, results are consistent with the robustness of the ESN buffering among-individual variation in gene expression levels early in mammalian limb development, and constraining the evolution of early limb development among mammalian species.

Evidence for an amphibian sixth digit

INTRODUCTION

Despite the great diversity in digit morphology reflecting the adaptation of tetrapods to their lifestyle, the number of digits in extant tetrapod species is conservatively stabilized at five or less, which is known as the pentadactyl constraint.

RESULTS

We found that an anuran amphibian species, Xenopus tropicalis (western clawed frog), has a clawed protrusion anteroventral to digit I on the foot. To identify the nature of the anterior-most clawed protrusion, we examined its morphology, tissue composition, development, and gene expression. We demonstrated that the protrusion in the X. tropicalis hindlimb is the sixth digit, as is evident from anatomical features, development, and molecular marker expression.

CONCLUSION

Identification of the sixth digit in the X. tropicalis hindlimb strongly suggests that the prehallux in other Xenopus species with similar morphology and at the same position as the sixth digit is also a vestigial digit. We propose here that the prehallux seen in various species of amphibians generally represents a rudimentary sixth digit.

Molecular Genetics of Sex Identification, Breed Ancestry and Polydactyly in the Norwegian Lundehund Breed

The Norwegian Lundehund breed of dog has undergone a severe loss of genetic diversity as a result of inbreeding and epizootics of canine distemper. As a consequence, the breed is extremely homogeneous and accurate sex identification is not always possible by standard screening of X-chromosomal loci. To improve our genetic understanding of the breed we genotyped 17 individuals using a genome-wide array of 170 000 single nucleotide polymorphisms (SNPs). Standard analyses based on expected homozygosity of X-chromosomal loci failed in assigning individuals to the correct sex, as determined initially by physical examination and confirmed with the Y-chromosomal marker, amelogenin. This demonstrates that identification of sex using standard SNP assays can be erroneous in highly inbred individuals.

Epigenetics decouples mutational from environmental robustness. Did it also facilitate multicellularity?

The evolution of ever increasing complex life forms has required innovations at the molecular level in order to overcome existing barriers. For example, evolving processes for cell differentiation, such as epigenetic mechanisms, facilitated the transition to multicellularity. At the same time, studies using gene regulatory network models, and corroborated in single-celled model organisms, have shown that mutational robustness and environmental robustness are correlated. Such correlation may constitute a barrier to the evolution of multicellularity since cell differentiation requires sensitivity to cues in the internal environment during development. To investigate how this barrier might be overcome, we used a gene regulatory network model which includes epigenetic control based on the mechanism of histone modification via Polycomb Group Proteins, which evolved in tandem with the transition to multicellularity. Incorporating the Polycomb mechanism allowed decoupling of mutational and environmental robustness, thus allowing the system to be simultaneously robust to mutations while increasing sensitivity to the environment. In turn, this decoupling facilitated cell differentiation which we tested by evaluating the capacity of the system for producing novel output states in response to altered initial conditions. In the absence of the Polycomb mechanism, the system was frequently incapable of adding new states, whereas with the Polycomb mechanism successful addition of new states was nearly certain. The Polycomb mechanism, which dynamically reshapes the network structure during development as a function of expression dynamics, decouples mutational and environmental robustness, thus providing a necessary step in the evolution of multicellularity.

Constraints on Mammalian forelimb development: insights from developmental disparity

Tetrapod limb development has been studied extensively for decades, yet the strength and role of developmental constraints in this process remains unresolved. Mammals exhibit a particularly wide array of limb morphologies associated with various locomotion modes and behaviors, providing a useful system for identifying periods of developmental constraint and conserved developmental mechanisms or morphologies. In this study, landmark-based geometric morphometrics are used to investigate levels and patterns of morphological diversity (disparity) among the developing forelimbs of four mammals with diverse limb morphologies: mice, opossums, horses, and pigs. Results indicate that disparity among the forelimbs of these species slightly decreases or stays the same from the appearance of the limb ridge to the bud stage, and increases dramatically from the paddle through tissue regression stages. Heterochrony exhibited by the precocial opossum limb was not found to drive these patterns of morphological disparity, suggesting that the low disparity of the middle stages of limb development (e.g., paddle stage) is driven by processes operating within the limb and is likely not a result of embryo-wide constraint.

Tracing the evolution of avian wing digits

It is widely accepted that birds are a subgroup of dinosaurs, but there is an apparent conflict: modern birds have been thought to possess only the middle three fingers (digits II-III-IV) of an idealized five-digit tetrapod hand based on embryological data, but their Mesozoic tetanuran dinosaur ancestors are considered to have the first three digits (I-II-III) based on fossil evidence. How could such an evolutionary quirk arise? Various hypotheses have been proposed to resolve this paradox. Adding to the confusion, some recent developmental studies support a I-II-III designation for avian wing digits whereas some recent paleontological data are consistent with a II-III-IV identification of the Mesozoic tetanuran digits. A comprehensive analysis of both paleontological and developmental data suggests that the evolution of the avian wing digits may have been driven by homeotic transformations of digit identity, which are more likely to have occurred in a partial and piecemeal manner. Additionally, recent genetic studies in mouse models showing plausible mechanisms for central digit loss invite consideration of new alternative possibilities (I-II-IV or I-III-IV) for the homologies of avian wing digits. While much progress has been made, some advances point to the complexity of the problem and a final resolution to this ongoing debate demands additional work from both paleontological and developmental perspectives, which will surely yield new insights on mechanisms of evolutionary adaptation.

Metapodial or phalanx? An evolutionary and developmental perspective on the homology of the first ray's proximal segment

The first mammalian metapodial (MP1) has periodically been argued to actually be a phalanx, because the first ray has one less element than the four posterior rays, and because the MP1 growth plate is proximal like those of all phalanges, rather than distal as in metapodials 2-5. However, growth plates are formed at both ends in non-therian tetrapod metapodials, and phylogenetic analysis demonstrates that growth plate loss is a therian synapomorphy that postdates the establishment of the mammalian phalangeal formula. These data, along with results of developmental and morphological studies, suggest that the MP1 is not a phalanx. The singular, proximal growth plates in MPs 2-5 are likely to be an adaptation to dynamic erect quadrupedal gait which was characterized by conversion of the posterior metapodials into rigid struts with the carpus/tarsus. While the adaptive significance of the reversed ossification of MP1 is less clear, we present three functional/developmental hypotheses.

Low neutral genetic variability in a specialist puffin hunter: the Norwegian Lundehund

The genetic variability of 125 Norwegian Lundehund and 27 Nova Scotia Duck Tolling Retriever was analysed using a set of 26 microsatellite markers. In Lundehund, the average number of alleles per locus was 1.73, and average observed (H(O)) and expected (H(E)) heterozygosity were 0.07. In Toller, all measures of genetic diversity were much higher than in Lundehund and similar to studies on other dog breeds. The cluster analysis correctly assigned individuals to their respective breed. The low genetic variability in Lundehund was not surprising, given the two strong bottlenecks in the 1940s and the 1960s. The relatedness of Lundehund to other Nordic small spitzes should be investigated in the view of possible outcrossing.

Digits lost or gained? Evidence for pedal evolution in the dwarf salamander complex (Eurycea, Plethodontidae)

Change in digit number, particularly digit loss, has occurred repeatedly over the evolutionary history of tetrapods. Although digit loss has been documented among distantly related species of salamanders, it is relatively uncommon in this amphibian order. For example, reduction from five to four toes appears to have evolved just three times in the morphologically and ecologically diverse family Plethodontidae. Here we report a molecular phylogenetic analysis for one of these four-toed lineages--the Eurycea quadridigitata complex (dwarf salamanders)--emphasizing relationships to other species in the genus. A multilocus phylogeny reveals that dwarf salamanders are paraphyletic with respect to a complex of five-toed, paedomorphic Eurycea from the Edwards Plateau in Texas. We use this phylogeny to examine evolution of digit number within the dwarf-Edwards Plateau clade, testing contrasting hypotheses of digit loss (parallelism among dwarf salamanders) versus digit gain (re-evolution in the Edwards Plateau complex). Bayes factors analysis provides statistical support for a five-toed common ancestor at the dwarf-Edwards node, favoring, slightly, the parallelism hypothesis for digit loss. More importantly, our phylogenetic results pinpoint a rare event in the pedal evolution of plethodontid salamanders.

Circumventing the polydactyly 'constraint': the mole's 'thumb'

Talpid moles across all northern continents exhibit a remarkably large, sickle-like radial sesamoid bone anterior to their five digits, always coupled with a smaller tibial sesamoid bone. A possible developmental mechanism behind this phenomenon was revealed using molecular markers during limb development in the Iberian mole (Talpa occidentalis) and a shrew (Cryptotis parva), as shrews represent the closest relatives of moles but do not show these conspicuous elements. The mole's radial sesamoid develops later than true digits, as shown by Sox9, and extends into the digit area, developing in relation to an Msx2-domain at the anterior border of the digital plate. Fgf8 expression, marking the apical ectodermal ridge, is comparable in both species. Developmental peculiarities facilitated the inclusion of the mole's radial sesamoid into the digit series; talpid moles circumvent the almost universal pentadactyly constraint by recruiting wrist sesamoids into their digital region using a novel developmental pathway and timing.

From flat foot to fat foot: structure, ontogeny, function, and evolution of elephant "sixth toes"

Several groups of tetrapods have expanded sesamoid (small, tendon-anchoring) bones into digit-like structures ("predigits"), such as pandas' "thumbs." Elephants similarly have expanded structures in the fat pads of their fore- and hindfeet, but for three centuries these have been overlooked as mere cartilaginous curiosities. We show that these are indeed massive sesamoids that employ a patchy mode of ossification of a massive cartilaginous precursor and that the predigits act functionally like digits. Further, we reveal clear osteological correlates of predigit joint articulation with the carpals/tarsals that are visible in fossils. Our survey shows that basal proboscideans were relatively "flat-footed" (plantigrade), whereas early elephantiforms evolved the more derived "tip-toed" (subunguligrade) morphology, including the predigits and fat pad, of extant elephants. Thus, elephants co-opted sesamoid bones into a role as false digits and used them for support as they changed their foot posture.

Breaking evolutionary and pleiotropic constraints in mammals: On sloths, manatees and homeotic mutations

Background

Mammals as a rule have seven cervical vertebrae, except for sloths and manatees. Bateson proposed that the change in the number of cervical vertebrae in sloths is due to homeotic transformations. A recent hypothesis proposes that the number of cervical vertebrae in sloths is unchanged and that instead the derived pattern is due to abnormal primaxial/abaxial patterning.

Results

We test the detailed predictions derived from both hypotheses for the skeletal patterns in sloths and manatees for both hypotheses. We find strong support for Bateson's homeosis hypothesis. The observed vertebral and rib patterns cannot be explained by changes in primaxial/abaxial patterning. Vertebral patterns in sloths and manatees are similar to those in mice and humans with abnormal numbers of cervical vertebrae: incomplete and asymmetric homeotic transformations are common and associated with skeletal abnormalities. In sloths the homeotic vertebral shift involves a large part of the vertebral column. As such, similarity is greatest with mice mutant for genes upstream of Hox.

Conclusions

We found no skeletal abnormalities in specimens of sister taxa with a normal number of cervical vertebrae. However, we always found such abnormalities in conspecifics with an abnormal number, as in many of the investigated dugongs. These findings strongly support the hypothesis that the evolutionary constraints on changes of the number of cervical vertebrae in mammals is due to deleterious pleitropic effects. We hypothesize that in sloths and manatees low metabolic and activity rates severely reduce the usual stabilizing selection, allowing the breaking of the pleiotropic constraints. This probably also applies to dugongs, although to a lesser extent.

Identity of the avian wing digits: problems resolved and unsolved

Controversy over bird wing digit identity has been a touchstone for various ideas in the phylogeny of birds, homology, and developmental evolution. This review summarizes the past 10 years of progress toward understanding avian digit identity. We conclude that the sum of evidence supports the Frame Shift Hypothesis, indicating that the avian wing digits have changed anatomical location. Briefly, the derivation of birds from theropod dinosaurs and the positional identities of the avian wing digits as 2, 3, and 4¹ are no longer in question. Additionally, increasing evidence indicates that the developmental programs for identity of the wing digits are of digits I, II, and III. Therefore, the attention moves from whether the digit identity frame shift occurred, to what the mechanisms of the frame shift were, and when in evolution it happened. There is considerable uncertainty about these issues and we identify exciting new research directions to resolve them.

Dollo's law and the irreversibility of digit loss in Bachia

Several recent studies conclude that exceptions to Dollo's law are more common than used to be thought. If the claims are true this would change our view on the role of developmental constraints in the evolution of body plans. One study claims the reevolution of lost digits in the lizard genus Bachia (Kohlsdorf and Wagner 2006). We evaluate this claim. We conclude that the proposed molecular phylogenetic tree is in conflict with evolutionary mechanisms concerning the biogeography of lizards and with morphology-based phylogenies. A reanalysis of the molecular data does not support the topology of the published tree. Furthermore, two implicit assumptions, that digit numbers are fixed and that polydactyly evolves independently from other characters, are incorrect. We conclude that there is no convincing support for reevolution of digits in Bachia. We discuss our findings in the light of the current evidence for the reversal of losses of complex traits. We conclude that in metazoans, exceptions to Dollo's law are mainly found among meristic traits that originate relatively late during embryogenesis, when developmental systems are more compartmentalized. Finally, our study shows that phylogenetic analyses should incorporate evolutionary mechanisms including constraints, variation, and selection, not only for correct phylogenetic reconstruction, but also for correct evolutionary inference.