Evolution of gastrulation in the ray-finned (actinopterygian) fishes

Sometime before or during the early Mesozoic era, new lineages of actinopterygian (ray-finned) fishes radically transformed their mode of gastrulation. During this evolutionary transformation, yolky endoderm was a hotspot for ontogenetic change. As holoblastic cleavage patterns were modified into meroblastic cleavage patterns, major changes in cell identity specification occurred within the mesendodermal marginal zone, as well as in the superficial epithelium of the embryo. These cellular identity changes resulted in the appearance of two novel extra-embryonic tissues within the embryos of teleostean fishes: the enveloping layer (EVL) and the yolk syncytial layer (YSL). The generation of these extra-embryonic tissues prompted major morphogenetic changes within the Organizer Region. As these evolutionary changes occurred, the outermost cell layer of the Organizer (the Organizer Epithelium) was apparently retained as a signaling center necessary for the establishment of left-right embryonic asymmetry in the embryo. Conserved and derived features of Organizer morphogenesis and gastrulation within ancient lineages of ray-finned fishes provide important insights into how the genetically encoded cell behaviors of early morphogenesis can be altered during the course of evolution. In particular, a highly divergent form of actinopterygian gastrulation, which is found in the annual fishes of South America, demonstrates that no aspect of vertebrate gastrulation is inherently immutable to evolutionary change.     

Patterns of genome size diversity in the ray-finned fishes

The ray-finned fishes make up about half of all vertebrate diversity and are by far the best represented group in the Animal Genome Size Database. However, they have traditionally been the least well investigated among vertebrates in terms of patterns and consequences of genome size diversity. This article synthesizes and expands upon existing information about genome size diversity in ray-finned fishes. Specifically, compiled data from the Animal Genome Size Database and FishBase are used to examine the potential patterns of interspecific genome size variability according to ecology, environment, morphology, growth, physiology, reproduction, longevity, and taxonomic diversity. Polyploidy and haploid genome sizes are considered separately, revealing differences in their respective consequences. This represents the most comprehensive summary of fish genome size diversity presented to date, and highlights areas of particular interest to investigate as more data become available.

Phylogenetic perspectives in the evolution of parental care in ray-finned fishes

Among major vertebrate groups, ray-finned fishes (Actinopterygii) collectively display a nearly unrivaled diversity of parental care activities. This fact, coupled with a growing body of phylogenetic data for Actinopterygii, makes these fishes a logical model system for analyzing the evolutionary histories of alternative parental care modes and associated reproductive behaviors. From an extensive literature review, we constructed a supertree for ray-finned fishes and used its phylogenetic topology to investigate the evolution of several key reproductive states including type of parental care (maternal, paternal, or biparental), internal versus external fertilization, internal versus external gestation, nest construction behavior, and presence versus absence of sexual dichromatism (as an indicator of sexual selection). Using a comparative phylogenetic approach, we critically evaluate several hypotheses regarding evolutionary pathways toward parental care. Results from maximum parsimony reconstructions indicate that all forms of parental care, including paternal, biparental, and maternal (both external and internal to the female reproductive tract) have arisen repeatedly and independently during ray-finned fish evolution. The most common evolutionary transitions were from external fertilization directly to paternal care and from external fertilization to maternal care via the intermediate step of internal fertilization. We also used maximum likelihood phylogenetic methods to test for statistical correlations and contingencies in the evolution of pairs of reproductive traits. Sexual dichromatism and nest construction proved to be positively correlated with the evolution of male parental care in species with external fertilization. Sexual dichromatism was also positively correlated with female-internal fertilization and gestation. No clear indication emerged that female-only care or biparental care were evolutionary outgrowths of male-only care, or that biparental care has been a common evolutionary stepping stone between paternal and maternal care. Results are discussed in the context of prior thought about the evolution of alternative parental care modes in vertebrates.     

Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes

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Evolution of dimorphisms of the proteasome subunit beta type 8 gene (PSMB8) in basal ray-finned fish

The proteasome subunit beta type 8 (PSMB8) gene encodes a catalytic subunit of immunoproteasome that plays a central role in the processing of antigenic peptides presented by major histocompatibility complex class I molecules. The A- and F-type alleles defined by the 31st amino acid residue determining cleaving specificity have been identified from ray-finned fish, amphibia, and reptiles. These two types show extremely long-term trans-species polymorphism in Polypteriformes, Cypriniformes, and Salmoniformes, suggesting the presence of very ancient lineages termed A and F. To elucidate the evolution of the PSMB8 dimorphism in basal ray-finned fish, we analyzed Pantodon buchholzi (Osteoglossiformes), seven species of Anguilliformes, and Hypomesus nipponensis (Osmeriformes). Both A and F lineage sequences were identified from P. buchholzi and H. nipponensis, confirming that these two lineages have been conserved by basal ray-finned fish. However, both the A- and F-type alleles found in Anguilliformes species belonged to the F lineage irrespective of their types. This apparently suggests that the A lineage was lost in the common ancestor of Anguilliformes, and recovery of the A type within the F lineage occurred in Anguilliformes. The apparent loss of the F lineage and recovery of the F type within the A lineage have already been reported from tetrapods and higher teleosts. However, this is the first report on the reverse situation and reveals the dynamic evolution of the PSMB8 dimorphism.     

Head size constrains forebrain development and evolution in ray-finned fishes

In ray-finned fishes, which comprise nearly half of all vertebrate species, the telencephalon does not evaginate, as it does in other vertebrates, but instead everts. No detailed explanation for this species difference has ever been offered. Here we propose that telencephalic eversion evolved because ray-finned fish embryos are so small that their telencephalon cannot evaginate but must, instead, squeeze into the space just dorsal to the developing nasal epithelia and rostral to the eyes-morphogenetic movements that amount to eversion. Evidence for this hypothesis derives from cladistic analyses, which show that early ray-finned fishes reduced their adult body size and adopted a novel reproductive strategy, based on the production of myriad minute young. Because body size tends to be inversely proportional to brain:body ratio, this phylogenetic reduction in body size implies that embryonic ray-finned fishes should have proportionately larger brains than embryos of species whose telencephalons evaginate. This prediction was confirmed by comparing serially sectioned heads of representative ray-finned and cartilaginous fish embryos at several stages of development. The brain, excluding its ventricles, occupies 36-46% of the cranial cavity in embryonic ray-finned fishes, but less than 20% in embryonic sharks. Moreover, three-dimensional reconstructions show that in embryonic ray-finned fishes the telencephalon has no room for a full-fledged evagination; instead, it spreads into the spaces just dorsal and caudal to the developing nasal epithelia. These morphogenetic movements, in conjunction with a thinning of the forebrain roof, generate telencephalic eversion.     

Comparative phylogenetic analysis of male alternative reproductive tactics in ray-finned fishes

Using comparative phylogenetic analysis, we analyzed the evolution of male alternative reproductive tactics (MARTs) in ray-finned fishes (Actinopterygii). Numerous independent origins for each type of MART (involving sneaker males, female mimics, pirates, and satellite males) indicate that these behaviors have been highly labile across actinopterygiian evolution, consistent with a previous notion that convergent selection in fishes can readily mold the underlying suites of reproductive hormones into similar behaviors. The evolutionary appearance of MARTs was significantly correlated with the presence of sexually selected traits in bourgeois males (P = 0.001) but not with the presence of male parental care. This suggests that MARTs often arise from selection on some males to circumvent bourgeois male investment in mate monopolization, rather than to avoid male brood care per se. We found parsimony evidence for an evolutionary progression of MARTs wherein sneaking is usually the evolutionary precursor to the presumably more complex MARTs of female mimicry and cooperative satellite behavior. Nest piracy appears not to be part of this evolutionary progression, possibly because its late onset in the life cycle of most ray-finned fishes reduces the effects of selection on this reproductive tactic.     

The facial musculature of the Suoidea

The facial musculature and rhinarial anatomy of a tayassuid, Dicotyles, and four suids, Sus, Hylochoerus, Phacochoerus and Babirussa, are described. Differences found include the lack of m. zygomaticus in Hylochoerus and Phacochoerus and several modifications of the rostral muscles, mm. levator rostri, dilator naris, and depressor rostri. These differences are related to behavioral characteristics of the animals, particularly the occurrence of toothbaring and rhinarial mobility. The missing m. zygomaticus and relatively small mouth of Hylochoerus and Phacochoerus are probably associated with behavioral patterns which do not necessitate a large gape. In these genera the canines are exposed even when the mouth is closed. The development of the rostral musculature is correlated with movements of the rhinarium. Similarly, the distribution of terminal tendons depends on the shape of the nostril. In Hylochoerus and Phacochoerus, mobility of the rhinarium, especially the dorsal part, is less than in other suoids because of the firmer attachment of the rostral bone to the skull and the weaker development of the rostral muscles.     

Dual motor innervation in the axial musculature of fishes

A systematic survey of motor innervation in the myotomal muscle fibres in several groups of fishes was conducted to observe the extent of dual innervation, a phenomenon found within those myotomal muscle fibres with terminal innervation. It is concluded that the dually innervated myotomal muscle fibre is a primitive vertebrate feature. Furthermore, it is suggested that this particular form of polyneuronal innervation is retained in the course of neural evolution within the homogeneous white myotomal muscle fibre region in these fish groups in order to insure synchrony of firing during sudden, rapid locomotion. The findings are examined in light of current ideas regarding the direct adrenergic innervation in addition to cholinergic innervation of striated muscle fibres.     

Mating preferences, sexual selection and patterns of cladogenesis in ray-finned fishes

Evolutionary theory predicts that sexual selection may increase taxonomic diversity when emergent mating preferences result in reproductive isolation and therefore speciation. This theory has been invoked to explain patterns of diversity in ray-finned fishes (most notably in the cichlids), but the theory has not been tested comparatively in fish. Additionally, several other unrelated factors have been identified as promoters of cladogenesis, so it is unclear how important sexual selection might be in diversification. Using sister-clade analysis, I tested the relationship between the presence of sexually selected traits and taxonomic diversification in actinopterygiian fishes, a large clade that shows substantial diversity in mating preferences and related sexually selected traits. In all identified sister-families that differed with regard to the proportion of species manifesting sexually selected traits, sexual selection was correlated with increased diversification, and this association was significant across all sister clades (P=0.02). This suggests that sexual selection, when present, is a substantial driver of diversification in the ray-finned fishes, and lends further empirical support to the theoretical link between mating preferences and accelerated cladogenesis.     

Restoration of the superficial facial musculature in nimravids

The size, shape and position of the mouth and sensory features such as the nose, eyes and ears in the nimravid barbourofelins are reconstructed. The earliest barbourofelin studied, Sansanosmilus , is the most similar to both pantherine and nonpantherine felids in sensory structure morphology. Through time, the species of the barbourofelin lineage diverge from felids with regard to facial features. Evolutionary trends include expansion of the nasal region, a more lateral orientation of the eyes and lowered position for the ears. Increased width and shortening of the muzzle accommodates the large oral opening required by the large gape of Barboumfelis , culminating in B. fricki with eyes oriented laterally enough to reduce stereoscopic vision. The ear position in this species is also significantly lower than in the earlier barbourofelins or felids. This may reflect an anatomic compromise between sensory structure position and changes in relative size, shape and position of other skull features. These changes correlate with increased canine tooth length and increased gape, exemplified by Barboumfelis fricki. Cranial soft tissue structures are restored through scars of attachment on the fossil bones, and the proportions of these features to one another determined. New observations provide criteria for reconstructing soft tissue anatomy in extinct animals.     

Sex chromosomes and male ornaments: a comparative evaluation in ray-finned fishes

Theory predicts that the mechanism of genetic sex determination can substantially influence the evolution of sexually selected traits. For example, female heterogamety (ZZ/ZW) can favour the evolution of extreme male traits under Fisher's runaway model of sexual selection. We empirically test whether the genetic system of sex determination has played a role in the evolution of exaggerated male ornaments in actinopterygiian fishes, a clade in which both female-heterogametic and male-heterogametic systems of sex determination have evolved multiple times. Using comparative methods both uncorrected and corrected for phylogenetic non-independence, we detected no significant correlation between sex-chromosome systems and sexually selected traits in males. Results suggest that sex-determination mechanism is at best a relatively minor factor affecting the outcomes of sexual selection in ray-finned fishes.     

Molecular analysis of neurogenic placode development in a basal ray-finned fish

Neurogenic placodes are transient, thickened patches of embryonic vertebrate head ectoderm that give rise to the paired peripheral sense organs and most neurons in cranial sensory ganglia. We present the first analysis of gene expression during neurogenic placode development in a basal actinopterygian (ray-finned fish), the North American paddlefish (Polyodon spathula). Pax3 expression in the profundal placode confirms its homology with the ophthalmic trigeminal placode of amniotes. We report the conservation of expression of Pax2 and Pax8 in the otic and/or epibranchial placodes, Phox2b in epibranchial placode-derived neurons, Sox3 during epibranchial and lateral line placode development, and NeuroD in developing cranial sensory ganglia. We identify Sox3 as a novel marker for developing fields of electrosensory ampullary organs and for ampullary organs themselves. Sox3 is also the first molecular marker for actinopterygian ampullary organs. This is consistent with, though does not prove, a lateral line placode origin for actinopterygian ampullary organs.     

The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes.

Cytological and organismal characteristics associated with cellular DNA content underpin most adaptionist interpretations of genome size variation. Since fishes are the only group of vertebrate for which relationships between genome size and key cellular parameters are uncertain, the cytological correlates of genome size were examined in this group. The cell and nuclear areas of erythrocytes showed a highly significant positive correlation with each other and with genome size across 22 cartilaginous and 201 ray-finned fishes. Regressions remained significant at all taxonomic levels, as well as among different fish lineages. However, the results revealed that cartilaginous fishes possess higher cytogenomic ratios than ray-finned fishes, as do cold-water fishes relative to their warm-water counterparts. Increases in genome size owing to ploidy shifts were found to influence cell and nucleus size in an immediate and causative manner, an effect that persists in ancient polyploid lineages. These correlations with cytological parameters known to have important influences on organismal phenotypes support an adaptive interpretation for genome size variation in fishes.     

Two patterns of differentiation in the jaw musculature of teleostean fishes

In its most generalized configuration among modern teleosts the M. adductor mandibulae comprises a single, almost continuous mass of musculature extending from the cheek to the inner surface of the mandible. In more advanced teleosts this muscle is usually divided into sections. Two basically different pathways of differentiation in the cheek part of the adductor mandibulae are dealt with here. One is that in the ostariophysine fishes. The other is represented in at least the great majority of acanthopterygians. Only certain of the differentiated sections are homologous in these two large groups of fishes.     

Evolution of body wall musculature

A body wall musculature comprising an outer layer of circularfibers and an inner layer of longitudinal fibers is generallyseen as the basic plan in Annelida. Additional muscles may bepresent such as oblique, parapodial, chaetal, and dorsoventralmuscles. The longitudinal muscle fibers do not form a continuouslayer but are arranged in distinct bands in polychaetes. Mostlythere are four to six bands, usually including prominent ventraland dorsal bands. However, other patterns of muscle band arrangementalso exist. The ventral nerve cord lies between the two ventralbands in certain polychaetes, and is covered by an additionallongitudinal muscle band of comparatively small size. In manypolychaetes with reduced parapodia and in Clitellata a moreor less continuous layer of longitudinal fibers is formed. Clitellatais the only group with a complete layer of longitudinal musculature.Circular fibers are usually less developed than the longitudinalmuscles. However, recent investigations employing phalloidinstaining in combination with confocal laser scanning microscopyrevealed that absence of circular muscles is much more widelydistributed within the polychaetes than was previously known.This necessitates thorough reinvestigations of polychaete musclesystems, and this feature has to be taken into account in furtherdiscussions of the phylogeny and evolution of Annelida.     

Aquatic prey capture in ray-finned fishes: a century of progress and new directions

The head of ray-finned fishes is structurally complex and is composed of numerous bony, muscular, and ligamentous elements capable of intricate movement. Nearly two centuries of research have been devoted to understanding the function of this cranial musculoskeletal system during prey capture in the dense and viscous aquatic medium. Most fishes generate some amount of inertial suction to capture prey in water. In this overview we trace the history of functional morphological analyses of suction feeding in ray-finned fishes, with a particular focus on the mechanisms by which suction is generated, and present new data using a novel flow imaging technique that enables quantification of the water flow field into the mouth. We begin with a brief overview of studies of cranial anatomy and then summarize progress on understanding function as new information was brought to light by the application of various forms of technology, including high-speed cinematography and video, pressure, impedance, and bone strain measurement. We also provide data from a new technique, digital particle image velocimetry (DPIV) that allows us to quantify patterns of flow into the mouth. We believe that there are three general areas in which future progress needs to occur. First, quantitative three-dimensional studies of buccal and opercular cavity dimensions during prey capture are needed; sonomicrometry and endoscopy are techniques likely to yield these data. Second, a thorough quantitative analysis of the flow field into the mouth during prey capture is necessary to understand the effect of head movement on water in the vicinity of the prey; three-dimensional DPIV analyses will help to provide these data. Third, a more precise understanding of the fitness effects of structural and functional variables in the head coupled with rigorous statistical analyses will allow us to better understand the evolutionary consequences of intra- and interspecific variation in cranial morphology and function.     

A Middle Triassic thoracopterid from China highlights the evolutionary origin of overwater gliding in early ray-finned fishes

Gliding adaptations in thoracopterid flying fishes represent a remarkable case of convergent evolution of overwater gliding strategy with modern exocoetid flying fishes, but the evolutionary origin of this strategy was poorly known in the thoracopterids because of lack of transitional forms. Until recently, all thoracopterids, from the Late Triassic of Austria and Italy and the Middle Triassic of South China, were highly specialized ‘four-winged’ gliders in having wing-like paired fins and an asymmetrical caudal fin with the lower caudal lobe notably larger than the upper lobe. Here, we show that the new genus Wushaichthys and the previously alleged ‘peltopleurid’ Peripeltopleurus, from the Middle Triassic (Ladinian, 235–242 Ma) of South China and near the Ladinian/Anisian boundary of southern Switzerland and northern Italy, respectively, represent the most primitive and oldest known thoracopterids. Wushaichthys, the most basal thoracopterid, shows certain derived features of this group in the skull. Peripeltopleurus shows a condition intermediate between Wushaichthys and Thoracopterus in having a slightly asymmetrical caudal fin but still lacking wing-like paired fins. Phylogenetic studies suggest that the evolution of overwater gliding of thoracopterids was gradual in nature; a four-stage adaption following the ‘cranial specialization–asymmetrical caudal fin–enlarged paired fins–scale reduction’ sequence has been recognized in thoracopterid evolution. Moreover, Wushaichthys and Peripeltopleurus bear hooklets on the anal fin of supposed males, resembling those of modern viviparious teleosts. Early thoracopterids probably had evolved a live-bearing reproductive strategy.     

Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes

With about 24,000 extant species, teleosts are the largest group of vertebrates. They constitute more than 99% of the ray-finned fishes (Actinopterygii) that diverged from the lobe-finned fish lineage (Sarcopterygii) about 450 MYA. Although the role of genome duplication in the evolution of vertebrates is now established, its role in structuring the teleost genomes has been controversial. At least two hypotheses have been proposed: a whole-genome duplication in an ancient ray-finned fish and independent gene duplications in different lineages. These hypotheses are, however, based on small data sets and lack adequate statistical and phylogenetic support. In this study, we have made a systematic comparison of the draft genome sequences of Fugu and humans to identify paralogous chromosomal regions ("paralogons") in the Fugu that arose in the ray-finned fish lineage ("fish-specific"). We identified duplicate genes in the Fugu by phylogenetic analyses of the Fugu, human, and invertebrate sequences. Our analyses provide evidence for 425 fish-specific duplicate genes in the Fugu and show that at least 6.6% of the genome is represented by fish-specific paralogons. We estimated the ages of Fugu duplicate genes and paralogons using the molecular clock. Remarkably, the ages of duplicate genes and paralogons are clustered, with a peak around 350 MYA. These data strongly suggest a whole-genome duplication event early during the evolution of ray-finned fishes, probably before the origin of teleosts.