Rui Diogo

Finding Our Way through Phenotypes

Imagine if we could compute across phenotype data as easily as genomic data; this article calls for efforts to realize this vision and discusses the potential benefits.

Muscles of vertebrates : comparative anatomy, evolution, homologies and development

Introduction and Aims Methodology and Material Muscles of Non-Osteichthyan Vertebrates Head and Neck Muscles of Actinopterygians and Basal Sarcopterygians From Sarcopterygian Fish to Modern Humans: Head and Neck Muscles Head and Neck Muscles of Amphibians Head and Neck Muscles of Reptiles Pectoral and Pectoral Fin Muscles of Actinopterygian and Sarcopterygian Fishes From Sarcopterygian Fish to Modern Humans: Pectoral and Forelimb Muscles Pectoral and Forelimb Muscles of Limbed Amphibians and Reptiles General Comments

A new heart for a new head in vertebrate cardiopharyngeal evolution

It has been more than 30 years since the publication of the new head hypothesis, which proposed that the vertebrate head is an evolutionary novelty resulting from the emergence of neural crest and cranial placodes. Neural crest generates the skull and associated connective tissues, whereas placodes produce sensory organs. However, neither crest nor placodes produce head muscles, which are a crucial component of the complex vertebrate head. We discuss emerging evidence for a surprising link between the evolution of head muscles and chambered hearts — both systems arise from a common pool of mesoderm progenitor cells within the cardiopharyngeal field of vertebrate embryos. We consider the origin of this field in non-vertebrate chordates and its evolution in vertebrates.

VIOLATION OF DOLLO'S LAW: EVIDENCE OF MUSCLE REVERSIONS IN PRIMATE PHYLOGENY AND THEIR IMPLICATIONS FOR THE UNDERSTANDING OF THE ONTOGENY, EVOLUTION, AND ANATOMICAL VARIATIONS OF MODERN HUMANS

According to Dollos law, once a complex structure is lost it is unlikely to be reacquired. In this article, we report new data obtained from our myology‐based cladistic analyses of primate phylogeny, which provide evidence of anatomical reversions violating Dollos law: of the 220 character state changes unambiguously optimized in the most parsimonious primate tree, 28 (13%) are evolutionary reversions, and of these 28 reversions six (21%) occurred in the nodes that lead to the origin of modern humans; nine (32%) violate Dollos law. In some of these nine cases, the structures that were lost in adults of the last common ancestor and are absent in adults of most subgroups of a clade are actually present in early ontogenetic stages of karyotypically normal individuals as well as in later ontogenetic stages of karyotypically abnormal members of those subgroups. Violations of Dollos law may thus result from the maintenance of ancestral developmental pathways during long periods of trait absence preceding the reacquisition of the trait through paedomorphic events. For instance, the presence of contrahentes and intermetacarpales in adult chimpanzees is likely due to a prolonged/delayed development of the hand musculature, that is, in this case chimpanzees are more neotenic than modern humans.

Comparative Anatomy, Evolution, and Homologies of Tetrapod Hindlimb Muscles, Comparison with Forelimb Muscles, and Deconstruction of the Forelimb‐Hindlimb Serial Homology Hypothesis

For more than two centuries, the idea that the forelimb and hindlimb are serially homologous structures has been accepted without serious question. This study presents the first detailed analysis of the evolution and homologies of all hindlimb muscles in representatives of each major tetrapod group and proposes a unifying nomenclature for these muscles. These data are compared with information obtained previously about the forelimb muscles of tetrapods and the muscles of other gnathostomes in order to address one of the most central and enigmatic questions in evolutionary and comparative anatomy: why are the pelvic and pectoral appendages of gnathostomes generally so similar to each other? An integrative analysis of the new myological data, combined with a review of recent paleontological, developmental, and genetic works and of older studies, does not support serial homology between the structures of these appendages. For instance, many of the strikingly similar forelimb and hindlimb muscles found in each major extant tetrapod taxon were acquired at different geological times and/or have different embryonic origins. These similar muscles are not serial homologues, but the result of evolutionary parallelism/convergence due to a complex interplay of ontogenetic, functional, topological, and phylogenetic constraints/factors. Anat Rec, 297:1047–1075, 2014.

Cranial Muscle Development in the Model Organism Ambystoma mexicanum: Implications for Tetrapod and Vertebrate Comparative and Evolutionary Morphology and Notes on Ontogeny and Phylogeny

There is still confusion about the homology of several cranial muscles in salamanders with those of other vertebrates. This is true, in part, because of the fact that many muscles present in early ontogeny of amphibians disappear during development and specifically during metamorphosis. Resolving this confusion is important for the understanding of the comparative and evolutionary morphology of vertebrates and tetrapods because amphibians are the phylogenetically most plesiomorphic tetrapods, concerning for example their myology, and include two often used model organisms, Xenopus laevis (anuran) and Ambystoma mexicanum (urodele). Here we provide the first detailed report of the cranial muscle development in axolotl from early ontogenetic stages to the adult stage. We describe different and complementary types of general muscle morphogenetic gradients in the head: from anterior to posterior, from lateral to medial, and from origin to insertion. Furthermore, even during the development of neotenic salamanders such as axolotls, various larval muscles become indistinct, contradicting the commonly accepted view that during ontogeny the tendency is mostly toward the differentiation of muscles. We provide an updated comparison between these muscles and the muscles of other vertebrates, a discussion of the homologies and evolution, and show that the order in which the muscles appear during axolotl ontogeny is in general similar to their appearance in phylogeny (e.g. differentiation of adductor mandibulae muscles from one anlage to four muscles), with only a few remarkable exceptions, as for example the dilatator laryngis that appears evolutionary later but in the development before the intermandibularis. Anat Rec, 296:1031–1048, 2013.

Anatomy of the pectoral and forelimb muscles of wildtype and green fluorescent protein-transgenic axolotls and comparison with other tetrapods including humans: a basis for regenerative, evolutionary and developmental studies.

The axolotl Ambystoma mexicanum is one of the most used model organisms in evolutionary, developmental and regenerative studies, particularly because it can reconstitute a fully functional and complete forelimb/hindlimb. Surprisingly, there is no publication that describes all the pectoral and forelimb muscles of this species or provides a comparative framework between these muscles and those of other model organisms and of modern humans. In the present paper we describe and illustrate all these muscles in A. mexicanum and provide the first report about the myology of adults of a model organism that is based on analyses and dissections of both wildtype animals and transgenic animals that express green fluorescent protein (GFP) in muscle fibers. On the one hand, the inclusion of GFP‐transgenic animals allows us to show the muscles as more commonly seen, and thus easier to understand, by current developmental and regenerative biologists. On the other hand, by including wildtype and GFP‐transgenic animals and by visualizing these latter animals with and without a simultaneous transmission laser light, we were able to obtain a more complete and clearer understanding of the exact limit of the fleshy and tendinous parts of the muscles and their specific connections with the skeletal elements. This in turn allowed us to settle some controversies in previous anatomical and comparative studies. As most developmental, regenerative and evolutionary biologists are interested in comparing their observations of A. mexicanum with observations in other model organisms, and ultimately in using this information to increase the understanding of human evolution and medicine, we also provide tables showing the homologies between the pectoral and forelimb muscles of axolotls, of model organisms such as mice, frogs and chicken, and of Homo sapiens. An example illustrating the outcomes of using our methodology and of our observations is that they revealed that, contrary to what is often stated in the literature, A. mexicanum has a muscle coracoradialis that has both a well developed proximal fleshy belly and a distal long and thin tendon, supporting the idea that this muscle very likely corresponds to at least part of the amniote biceps brachii. Our observations also: (i) confirmed that the flexores digitorum minimi, interphalangeus digiti 3, pronator quadratus and palmaris profundus 1 are present as distinct muscles in A. mexicanum, supporting the idea that the latter muscle does not correspond to the pronator accessorius of reptiles; (ii) confirmed that the so‐called extensor antebrachii radialis is present as a distinct muscle in this species and, importantly, indicated that this muscle corresponds to the supinator of other tetrapods; (iii) showed that, contrary to some other urodeles, including some other Ambystoma species, there is no distinct muscle epitrochleoanconeus in A. mexicanum and; (iv) showed that the ulnar and radial bundles of the abductor et extensor digiti 1 correspond to the abductor pollicis longus and extensor pollicis longus of other tetrapods, respectively.

Cranial muscle development in frogs with different developmental modes: direct development versus biphasic development.

Normal development in anurans includes a free swimming larva that goes through metamorphosis to develop into the adult frog. We have investigated cranial muscle development and adult cranial muscle morphology in three different anuran species. Xenopus laevis is obligate aquatic throughout lifetime, Rana (Lithobates) pipiens has an aquatic larvae and a terrestrial adult form, and Eleutherodactylus coqui has direct developing juveniles that hatch from eggs deposited on leaves (terrestrial). The adult morphology shows hardly any differences between the investigated species. Cranial muscle development of E. coqui shows many similarities and only few differences to the development of Rana (Lithobates) and Xenopus. The differences are missing muscles of the branchial arches (which disappear during metamorphosis of biphasic anurans) and a few heterochronic changes. The development of the mandibular arch (adductor mandibulae) and hyoid arch (depressor mandibulae) muscles is similar to that observed in Xenopus and Rana (Lithobates), although the first appearance of these muscles displays a midmetamorphic pattern in E. coqui. We show that the mix of characters observed in E. coqui indicates that the larval stage is not completely lost even without a free swimming larval stage. Cryptic metamorphosis is the process in which morphological changes in the larva/embryo take place that are not as obvious as in normal metamorphosing anurans with a clear biphasic lifestyle. During cryptic metamorphosis, a normal adult frog develops, indicating that the majority of developmental mechanisms towards the functional adult cranial muscles are preserved. J. Morphol. 275:398–413, 2014.

Muscles of Chondrichthyan Paired Appendages: Comparison With Osteichthyans, Deconstruction of the Fore–Hindlimb Serial Homology Dogma, and New Insights on the Evolution of the Vertebrate Neck

Here we present the first study comparing all the paired appendages muscles of representatives of each major extant gnathostome group. We address a crucial and enigmatic question in evolutionary and comparative anatomy: Why are the pelvic and pectoral appendages of gnathostomes, and particularly of tetrapods, in general so similar to each other? We argue that an integrative analysis of the new myological data and the information from the literature contradicts the idea that the forelimbs and hindlimbs are serial homologues. The data show that many of the strikingly similar fore‐ and hindlimb muscles of extant tetrapods evolved independently in each appendage because the ancestors of extant gnathostomes and osteichthyans only had an adductor and an abductor in each fin. Therefore, these data contradict the idea that at least some muscles present in the tetrapod fore‐ and hindlimbs were already present in some form in the first fishes with pectoral and pelvic appendages, as the result of an ancestral duplication of the paired appendages leading to a true serial homology. The origin of the pectoral girdle was instead likely related to head evolution, as illustrated by the cucullaris of gnathostomes such as chondrichthyans inserting onto both the branchial arches and pectoral girdle. Only later in evolution the cucullaris became differentiated into the levatores arcuum branchialium and protractor pectoralis, which gave rise to the amniote neck muscles trapezius and sternocleidomastoideus. These changes therefore contributed to an evolutionary trend toward a greater anatomical and functional independence of the pectoral girdle from head movements. Anat Rec, 298:513–530, 2015.

Is salamander limb regeneration really perfect? Anatomical and morphogenetic analysis of forelimb muscle regeneration in GFP-transgenic axolotls as a basis for regenerative, developmental, and evolutionary studies.

The axolotl Ambystoma mexicanum is one of the most commonly used model organisms in developmental and regenerative studies because it can reconstitute what is believed to be a completely normal anatomical and functional forelimb/hindlimb after amputation. However, to date it has not been confirmed whether each regenerated forelimb muscle is really a “perfect” copy of the original muscle. This study describes the regeneration of the arm, forearm, hand, and some pectoral muscles (e.g., coracoradialis) in transgenic axolotls that express green fluorescent protein (GFP) in muscle fibers. The observations found that: (1) there were muscle anomalies in 43% of the regenerated forelimbs; (2) however, on average in each regenerated forelimb there are anomalies in only 2.5% of the total number of muscles examined, and there were no significant differences observed in the specific insertion and origin of the other muscles analyzed; (3) one of the most notable and common anomalies (seen in 35% of the regenerated forelimbs) was the presence of a fleshy coracoradialis at the level of the arm; this is a particularly outstanding configuration because in axolotls and in urodeles in general this muscle only has a thin tendon at the level of the arm, and the additional fleshy belly in the regenerated arms is strikingly similar to the fleshy biceps brachii of amniotes, suggesting a remarkable parallel between a regeneration defect and a major phenotypic change that occurred during tetrapod limb evolution; (4) during forelimb muscle regeneration there was a clear proximo‐distal and radio‐ulnar morphogenetic gradient, as seen in normal development, but also a ventro‐dorsal gradient in the order of regeneration, which was not previously described in the literature. These results have broader implications for regenerative, evolutionary, developmental and morphogenetic studies. Anat Rec, 297:1076–1089, 2014.