Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies.

The identification of genetic mechanisms underlying evolutionary change is critical to our understanding of natural diversity, but is presently limited by the lack of genetic and genomic resources for most species. Here, we present a new comparative genomic approach that can be applied to a broad taxonomic sampling of nonmodel species to investigate the genetic basis of evolutionary change. Using our analysis pipeline, we show that duplication and divergence of fgfr1a is correlated with the reduction of scales within fishes of the genus Phoxinellus. As a parallel genetic mechanism is observed in scale-reduction within independent lineages of cypriniforms, our finding exposes significant developmental constraint guiding morphological evolution. In addition, we identified fixed variation in fgf20a within Phoxinellus and demonstrated that combinatorial loss-of-function of fgfr1a and fgf20a within zebrafish phenocopies the evolved scalation pattern. Together, these findings reveal epistatic interactions between fgfr1a and fgf20a as a developmental mechanism regulating skeletal variation among fishes.

The development of the cucullaris muscle and the branchial musculature in the Longnose Gar, (Lepisosteus osseus, Lepisosteiformes, Actinopterygii) and its implications for the evolution and development of the head/trunk interface in vertebrates.

The vertebrate head/trunk interface is the region of the body where the different developmental programs of the head and trunk come in contact. Many anatomical structures that develop in this transition zone differ from similar structures in the head or the trunk. This is best exemplified by the cucullaris/trapezius muscle, spanning the head/trunk interface by connecting the head to the pectoral girdle. The source of this muscle has been claimed to be either the unsegmented head mesoderm or the somites of the trunk. However most recent data on the development of the cucullaris muscle are derived from tetrapods and information from actinopterygian taxa is scarce. We used classical histology in combination with fluorescent whole-mount antibody staining and micro-computed tomography to investigate the developmental pattern of the cucullaris and the branchial muscles in a basal actinopterygian, the Longnose gar (Lepisosteus osseus). Our results show (1) that the cucullaris has been misidentified in earlier studies on its development in Lepisosteus. (2) Cucullaris development is delayed compared to other head and trunk muscles. (3) This developmental pattern of the cucullaris is similar to that reported from some tetrapod taxa. (4) That the retractor dorsalis muscle of L. osseus shows a delayed developmental pattern similar to the cucullaris. Our data are in agreement with an explanatory scenario for the cucullaris development in tetrapods, suggesting that these mechanisms are conserved throughout the Osteichthyes. Furthermore the developmental pattern of the retractor dorsalis, also spanning the head/trunk interface, seems to be controlled by similar mechanisms.

Genetic lineage labeling in zebrafish uncovers novel neural crest contributions to the head, including gill pillar cells.

At the protochordate-vertebrate transition, a new predatory lifestyle and increased body size coincided with the appearance of a true head. Characteristic innovations of this head are a skull protecting and accommodating a centralized nervous system, a jaw for prey capture and gills as respiratory organs. The neural crest (NC) is a major ontogenetic source for the 'new head' of vertebrates and its contribution to the cranial skeleton has been intensively studied in different model organisms. However, the role of NC in the expansion of the respiratory surface of the gills has been neglected. Here, we use genetic lineage labeling to address the contribution of NC to specific head structures, in particular to the gills of adult zebrafish. We generated a sox10:ER(T2)-Cre line and labeled NC cells by inducing Cre/loxP recombination with tamoxifen at embryonic stages. In juvenile and adult fish, we identified numerous established NC derivatives and, in the cranium, we precisely defined the crest/mesoderm interface of the skull roof. We show the NC origin of the opercular bones and of multiple cell types contributing to the barbels, chemosensory organs located in the mouth region. In the gills, we observed labeled primary and secondary lamellae. Clonal analysis reveals that pillar cells, a craniate innovation that mechanically supports the filaments and forms gill-specific capillaries, have a NC origin. Our data point to a crucial role for the NC in enabling more efficient gas exchange, thus uncovering a novel, direct involvement of this embryonic tissue in the evolution of respiratory systems at the protochordate-vertebrate transition.

Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA.

Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.

Zebrafish eda and edar mutants reveal conserved and ancestral roles of ectodysplasin signaling in vertebrates.

The genetic basis of the development and variation of adult form of vertebrates is not well understood. To address this problem, we performed a mutant screen to identify genes essential for the formation of adult skeletal structures of the zebrafish. Here, we describe the phenotypic and molecular characterization of a set of mutants showing loss of adult structures of the dermal skeleton, such as the rays of the fins and the scales, as well as the pharyngeal teeth. The mutations represent adult-viable, loss of function alleles in the ectodysplasin (eda) and ectodysplasin receptor (edar) genes. These genes are frequently mutated in the human hereditary disease hypohidrotic ectodermal dysplasia (HED; OMIM 224900, 305100) that affects the development of integumentary appendages such as hair and teeth. We find mutations in zebrafish edar that affect similar residues as mutated in human cases of HED and show similar phenotypic consequences. eda and edar are not required for early zebrafish development, but are rather specific for the development of adult skeletal and dental structures. We find that the defects of the fins and scales are due to the role of Eda signaling in organizing epidermal cells into discrete signaling centers of the scale epidermal placode and fin fold. Our genetic analysis demonstrates dose-sensitive and organ-specific response to alteration in levels of Eda signaling. In addition, we show substantial buffering of the effect of loss of edar function in different genetic backgrounds, suggesting canalization of this developmental system. We uncover a previously unknown role of Eda signaling in teleosts and show conservation of the developmental mechanisms involved in the formation and variation of both integumentary appendages and limbs. Lastly, our findings point to the utility of adult genetic screens in the zebrafish in identifying essential developmental processes involved in human disease and in morphological evolution.

Convergent evolution in mechanical design of lamnid sharks and tunas.

The evolution of 'thunniform' body shapes in several different groups of vertebrates, including whales, ichthyosaurs and several species of large pelagic fishes supports the view that physical and hydromechanical demands provided important selection pressures to optimize body design for locomotion during vertebrate evolution. Recognition of morphological similarities between lamnid sharks (the most well known being the great white and the mako) and tunas has led to a general expectation that they also have converged in their functional design; however, no quantitative data exist on the mechanical performance of the locomotor system in lamnid sharks. Here we examine the swimming kinematics, in vivo muscle dynamics and functional morphology of the force-transmission system in a lamnid shark, and show that the evolutionary convergence in body shape and mechanical design between the distantly related lamnids and tunas is much more than skin deep; it extends to the depths of the myotendinous architecture and the mechanical basis for propulsive movements. We demonstrate that not only have lamnids and tunas converged to a much greater extent than previously known, but they have also developed morphological and functional adaptations in their locomotor systems that are unlike virtually all other fishes.

Larval development and osteology of Callanthias platei (Teleostei: Callanthiidae) from Desventuradas Islands, South Pacific.

Larvae of the Juan Fernández Splendid Perch, Callanthias platei Steindachner, 1898 (Teleostei: Callanthiidae), are described for the first time. The five available specimens, ranging from 3 mm notochord length (NL) to 6.1 mm standard length (SL), were collected with plankton nets near Desventuradas Islands, Southeast Pacific, during the austral spring of 2015 and 2016. The larvae are deep bodied with a narrow caudal peduncle, a large head and a triangular, coiled gut. The pigmentation is scarce in preflexion larvae but increases after flexion. All individuals have several groups of head spines: anterior and posterior preopercular, interopercular, subopercular, opercular and supracleithral. The formation of all fins occurs early in development, with the pectoral fins appearing first and the pelvic fins last. The osteological development of the skull, vertebral column, fins, and scales are described.

Development of the muscles associated with the mandibular and hyoid arches in the Siberian sturgeon, Acipenser baerii (Acipenseriformes: Acipenseridae).

The skeleton of the jaws and neurocranium of sturgeons (Acipenseridae) are connected only through the hyoid arch. This arrangement allows considerable protrusion and retraction of the jaws and is highly specialized among ray-finned fishes (Actinopterygii). To better understand the unique morphology and the evolution of the jaw apparatus in Acipenseridae, we investigated the development of the muscles of the mandibular and hyoid arches of the Siberian sturgeon, Acipenser baerii. We used a combination of antibody staining and formalin-induced fluorescence of tissues imaged with confocal microscopy and subsequent three-dimensional reconstruction. These data were analyzed to address the identity of previously controversial and newly discovered muscle portions. Our results indicate that the anlagen of the muscles in A. baerii develop similarly to those of other actinopterygians, although they differ by not differentiating into distinct muscles. This is exemplified by the subpartitioning of the m. adductor mandibulae as well as the massive m. protractor hyomandibulae, for which we found a previously undescribed portion in each. The importance of paedomorphosis for the evolution of Acipenseriformes has been discussed before and our results indicate that the muscles of the mandibular and the hyoid may be another example for heterochronic evolution.

Development of the skull and pectoral girdle in Siberian sturgeon, Acipenser baerii, and Russian sturgeon, Acipenser gueldenstaedtii (Acipenseriformes: Acipenseridae).

The head is considered the major novelty of the vertebrates and directly linked to their evolutionary success. Its form and development as well as its function, for example in feeding, is of major interest for evolutionary biologists. In this study, we describe the skeletal development of the cranium and pectoral girdle in Siberian (Acipenser baerii) and Russian sturgeon (A. gueldenstaedtii), two species that are commonly farmed in aquaculture and increasingly important in developmental studies. This study comprises the development of the neuro-, viscero- and dermatocranium and the dermal and chondral components of the pectoral girdle, from first condensation of chondrocytes in prehatchlings to the early juvenile stage and reveals a clear pattern in formation. The otic capsules, the parachordal cartilages, and the trabeculae cranii are the first centers of chondrification, at 8.4mm TL. These are followed by the mandibular, then the hyoid, and later the branchial arches. Teeth form early on the dentary, dermopalatine, and palatopterygoid, and then appear later in the buccal cavity as dorsal and ventral toothplates. With ongoing chondrification in the neurocranium a capsule around the brain and a strong rostrum are formed. Dermal ossifications start to form before closure of the dorsal neurocranial fenestrae. Perichondral ossification of cartilage bones occurs much later in ontogeny. Our results contribute data bearing on the homology of elements such as the lateral rostral canal bone that we regard homologous to the antorbital of other actinopterygians based on its sequence of formation, position and form. We further raise doubts on the homology of the posterior ceratobranchial among Actinopteri based on the formation of the hyoid arch elements. We also investigate the basibranchials and the closely associated unidentified gill-arch elements and show that they are not homologous. J. Morphol. 278:418-442, 2017. © 2017 Wiley Periodicals, Inc.

Evolution of high-performance swimming in sharks: transformations of the musculotendinous system from subcarangiform to thunniform swimmers.

In contrast to all other sharks, lamnid sharks perform a specialized fast and continuous "thunniform" type of locomotion, more similar to that of tunas than to any other known shark or bony fish. Within sharks, it has evolved from a subcarangiform mode. Experimental data show that the two swimming modes in sharks differ remarkably in kinematic patterns as well as in muscle activation patterns, but the morphology of the underlying musculotendinous system (red muscles and myosepta) that drives continuous locomotion remains largely unknown. The goal of this study was to identify differences in the musculotendinous system of the two swimming types and to evaluate these differences in an evolutionary context. Three subcarangiform sharks (the velvet belly lantern shark, Etmopterus spinax, the smallspotted catshark, Scyliorhinus canicula, and the blackmouth catshark, Galeus melanostomus) from the two major clades (two galeans, one squalean) and one lamnid shark, the shortfin mako, Isurus oxyrhinchus, were compared with respect to 1) the 3D shape of myomeres and myosepta of different body positions; 2) the tendinous architecture (collagenous fiber pathways) of myosepta from different body positions; and 3) the association of red muscles with myoseptal tendons. Results show that the three subcarangiform sharks are morphologically similar but differ remarkably from the lamnid condition. Moreover, the "subcarangiform" morphology is similar to the condition known from teleostomes. Thus, major features of the "subcarangiform" condition in sharks have evolved early in gnathostome history: Myosepta have one main anterior-pointing cone and two posterior-pointing cones that project into the musculature. Within a single myoseptum cones are connected by longitudinally oriented tendons (the hypaxial and epaxial lateral and myorhabdoid tendons). Mediolaterally oriented tendons (epineural and epipleural tendons; mediolateral fibers) connect vertebral axis and skin. An individual lateral tendon spans only a short distance along the body (a fraction between 0.05 and 0.075 of total length, L, of the shark). This span is similar in all tendons along the body. Red muscles insert into the midregion of the lateral tendons. The shortfin mako differs substantially from this condition in several respects: Red muscles are internalized and separated from white muscles by a sheath of lubricative connective tissue. They insert into the anterior part of the hypaxial lateral tendon. Rostrocaudally, this tendon becomes very distinct and its span increases threefold (0.06L anteriorly to 0.19L posteriorly). Mediolateral fibers do not form distinct epineural/epipleural tendons in the mako. Since our morphological findings are in good accordance with experimental data it seems likely that the thunniform swimming mode has evolved along with the described morphological specializations.

The median-fin skeleton of the Eastern Atlantic and Mediterranean clingfishes Lepadogaster lepadogaster (Bonnaterre) and Gouania wildenowi (Risso) (Teleostei: Gobiesocidae).

Previous research on the osteology of the Gobiesocidae focused mostly on the neurocranium and the thoracic sucking disc (formed by the paired-fin girdles). Little attention has been paid to the skeleton of the median fins. The dorsal- and anal-fin skeleton of Lepadogaster lepadogaster and other gobiesocids (excluding Alabes, which lacks these fins) are characterized by the absence of spines, branched fin-rays, and middle radials. In gobiesocids, the distal radials never ossify and consist of elastic hyaline-cell cartilage. Gouania wildenowi is unique among gobiesocids in having further reductions of the dorsal- and anal-fin skeleton, including a notable decrease in the size of the proximal-middle radials in an anterior-posterior direction. Unlike L. lepadogaster, which exhibits a one-to-one relationship between the dorsal- and anal-fin rays and proximal-middle radials, G. wildenowi has a higher number of proximal-middle radials than distal radial cartilages and fin rays in the dorsal and anal fins. In G. wildenowi, the dorsal- and anal-fin rays do not articulate with the distal tip of the proximal-middle radials but are instead positioned between proximal-middle radials, which is unusual for teleosts. Previously unrecognized dorsal and ventral pads of elastic hyaline-cell cartilage are also present in the caudal skeleton of L. lepadogaster, G. wildenowi, and all other gobiesocids examined.

Patterns of red muscle strain/activation and body kinematics during steady swimming in a lamnid shark, the shortfin mako (Isurus oxyrinchus).

The dynamics of steady swimming were examined in the shortfin mako (Isurus oxyrinchus), a member of the cartilaginous fish family Lamnidae, a family known for their morphological adaptations for high-performance locomotion and their similarity in hydromechanical design to tunas. Patterns of red muscle (RM) strain (i.e. relative length change) and activation were quantified at two axial positions ( approximately 0.4 and 0.6L, where L is total body length), using sonomicrometry and electromyography (EMG), and correlated with simultaneous measurements of dorsal midline kinematics during steady swimming ( approximately 0.5-1 L s(-1)). RM strain varied longitudinally with strain amplitudes ranging from 5.5+/-1.1% (s.e.m.) in the anterior to 8.7+/-0.9% in the posterior. We found no significant longitudinal variation in patterns of RM activation, with mean onset of activation occurring at 83-84 degrees (90 degrees is peak length) and offset at 200-210 degrees at both body positions. Likewise, duty cycles were similar: 35.5+/-1.0% in the anterior and 32.2+/-1.6% in the posterior. Comparison of the timing of waves of dorsal midline curvature and predicted strain relative to measured RM strain revealed a phase shift between RM shortening and local body bending. Furthermore, when the body is bent passively, RM shortens synchronously with the surrounding white muscle (WM) and skin, as expected. During active swimming, peaks in RM strain were delayed relative to peaks in WM strain by a mean of approximately 10% of the tailbeat cycle, with one individual as high as approximately 17% in the anterior and nearly 50% in the posterior. The longitudinal consistency in the EMG/strain phase relationship in the mako is similar to that in the leopard shark, suggesting a consistent trend among sharks using different locomotor modes. However, unlike in the leopard shark, RM shortening in the mako is physically uncoupled from deformation of the surrounding body during steady swimming, a characteristic shared between the mako and tunas.