1 Evolution and Phylogeny

Over half of the world’s living vertebrates are fishes (more than 85 orders, 536 families, 5000 living genera, 34,000 species, and counting; Nelson et al. 2016). Fishes arose and began to radiate almost 500 million years ago and now exhibit incomparable diversity (Figure 1.1) in morphology, physiology, ecology, and behaviour.

FIGURE 1.1 Diversity among jawless fishes, chondrichthyans, and early-branching osteichthyans. See Figures 1.3, 1.4, and 1.6 for phylogenies.

To understand biotic diversity, we employ phylogenetic systematics. Phylogenies provide hypotheses of relationships among species to better understand character evolution within and between groups, visualized as phylogenetic trees or branching diagrams, and are the foundation for comparative studies, including comparative physiology.

The purpose of this chapter is to present an overview of the current hypotheses of fish phylogeny as a framework for understanding the remarkable diversity of fishes. We concentrate on the arrangement of large, important clades (Figure 1.2) to illustrate broad patterns. Information presented mainly follows Nelson et al. (2016). Another recent overview is that of Hastings et al. (2014). Phylogenetic studies based on molecular data include those of Near et al. (2012), Betancur-R. et al. (2013), Miya and Nishida (2015), and Hughes et al. (2018).

FIGURE 1.2 Phylogenetic relationships among craniates. Letters indicate the sequence of groups discussed in the text.

1.2 Jawless Vertebrates (Agnathans)

Only two orders (Myxiniformes or hagfishes and Petromyzontiformes or lampreys) remain today from what was a very diverse radiation of jawless fishes in the Early and Middle Paleozoic (Janvier 1996; Long 2012). Like Long (2012), we place hagfishes outside Vertebrata. Phylogenetic analyses of molecular sequence data, however, suggest that the two agnathan groups may belong in a single clade after all (e.g., Mallatt and Sullivan 1998). This controversy is far from settled, because placing them together requires massive reinterpretation of their very different anatomical and physiological features.

1.2.1 Order Myxiniformes (Hagfishes)

The hagfishes (Figure 1.2 clade A) are an eel-like marine group of about 78 species with many adaptations to their scavenging lifestyle (they emerge from burrows to scavenge on dead or dying animals) and many other apparently archaic traits (Jørgensen et al. 1998), such as one pair of semicircular canals (argued by some to be a fusion of two canals), one pair of maculae in the inner ear rather than two or three, no lateral-line system or neuromasts in adults, no rudimentary vertebral structures along the notochord, and body fluids isosmotic with seawater.

1.2.2 Order Petromyzontiformes (Lampreys)

The lampreys (Figure 1.2 clade B) are a group of about 43 species with anadromous or freshwater life histories (Renaud 2011). They have two semicircular canals in the inner ear, whereas hagfishes have one and jawed vertebrates have three. Lampreys pass through an “ammocoete,” filter-feeding larval stage before metamorphosis. There are seven pairs of external gill openings, a single nasohypophyseal opening and a pineal eye on top of the head, a spiral fold in the intestine, a notochord that is combined with rudimentary neural arches, and two dorsal fins but no paired fins. Lampreys have a simple electroreception system in their skin, whereas hagfishes do not. Petromyzon marinus is a model organism for spinal cord research (e.g., Herman et al. 2018; Hanslik et al. 2019).

1.3 Superclass Gnathostomata

All other vertebrates have jaws and are thus gnathostomes (Figure 1.2). The origin of the Gnathostomata was one of the most transformative events in vertebrate history, and the list of their novel features (e.g., Nelson et al. 2016) is long, including jaws possibly homologous with an anterior gill arch; hyomandibular supporting the jaw articulation; two or three inner ear maculae (saccular, lagenar, and utricular) and three semicircular canals; myelinated nerve fibers; and trunk muscles in epaxial and hypaxial blocks.

1.4 Class Chondrichthyes (Ratfishes, Sharks, and Rays)

The Chondrichthyes or cartilaginous fishes (Figure 1.2 clade C) collectively are the extant sister group to the Osteichthyes (including tetrapods). The roughly 1200 species of chondrichthyans live in all major oceans and seas but are rare in fresh waters (Lucifora et al. 2015) and virtually absent in the deepest parts of the ocean (Treberg and Speers-Roesch 2016). An important resource for information about chondrichthyans is Carrier et al. (2004).

The scales of chondrichthyans are denticles called placoid scales. The teeth are arranged in families or whorls, vary in shape, and are usually shed and replaced throughout life. Some sharks shed thousands of teeth in a lifetime.

All chondrichthyans have a well-developed electroreceptive system in the form of blind tubes called ampullae of Lorenzini, mostly on the head. An innervated ampulla at the inner end of each tube is filled with a jelly-like substance and opens externally via a pore. The tubes’ orientations permit sensing of the directions and intensities of weak electric fields generated by the heart or respiratory muscles of prey.

Chondrichthyans have internal fertilization, with males having intromittent organs in the form of pelvic-fin claspers. Females either retain young in their oviduct(s) until birth or lay large-yolked eggs enclosed in leathery egg capsules. In some sharks, the unborn young feed in utero by oophagy (eating of eggs) or by cannibalism (eating of unborn embryos). Gestation periods can be up to 2 years (e.g., Musick 2010).

Separate groups of chondrichthyans, including chimaeras, horn sharks, dogfish sharks, and stingrays, can deliver venom via dorsal spines or tail spines, primarily for defense (Smith et al. 2016).

1.4.1 Subclass Holocephali (Chimaeras)

The Holocephali (Figure 1.3) include three families, six genera, and nearly 50 species. They live mostly in deeper marine environments and have a dentition of flattened plates for crushing mollusks and crustaceans. Lateral-line canals on the head are in deep grooves. Paired fins are usually large; the first dorsal fin has an erectile spine, while the caudal fin is whip-shaped. Chimaeras are oviparous; males have a clasper on the head in addition to pelvic claspers. The chimaerid Callorhinchus milii, the elephant fish or Australian ghostshark, has a compact genome and has become a model organism for physiological and genomic studies (e.g., Hyodo et al. 2007; Venkatesh et al. 2014).

FIGURE 1.3 Phylogenetic relationships within Chondrichthyes. Holocephali are sister to Elasmobranchii, which in turn are divided into the Selachii (sharks) and the Batomorphi (skates and rays). Triangle sizes are correlated to species diversity.

1.4.2 Subclass Euselachii, Infraclass Elasmobranchii (Neoselachii)

The Elasmobranchii include all sharks (Selachii) and rays (Batomorphi). Today, we accept that sharks and rays are sister groups (Figure 1.3); their fossils are of about equal antiquity in the Early Jurassic (175–200 million years ago; Maisey et al. 2004).

1.4.2.1 Division Selachii (Sharks)

The extant sharks (Figure 1.3) include two superorders, nine orders, 34 families, 106 genera, and at least 561 species. In contrast to rays, sharks have gill slits that are mainly lateral, and the anterior margin of the pectoral fin is not attached to the side of the head. Left and right pectoral girdles are not joined dorsally. There are two main clades of selachians (Maisey et al. 2004): the Galeomorphi and the Squalomorphi.

1.4.2.1.1 Superorder Galeomorphi

Galeomorph sharks (Figure 1.3) comprise four orders, 23 families, 74 genera, and about 400 species (e.g., Compagno 2005). All have an anal fin and a closed lateral-line canal.

The four orders of galeomorphs include the Heterodontiformes (horn sharks), which are oviparous, and the Orectolobiformes (carpet sharks), which include the nurse sharks (Ginglymostomatidae), wobbegongs (Orectolobidae), and the whale shark (Rhincodontidae), the largest extant fish, a large-gape filter feeder that often swims near the surface.

Lamniformes (mackerel sharks) have a distinctively coiled intestinal spiral valve. Many embryos are nourished by oophagy (egg eating) or cannibalism of other embryos before birth. Lamnids can maintain elevated temperatures in their swimming muscles using a counter-current exchange system of blood vessels. Examples include the filter-feeding basking shark (Cetorhinidae) and megamouth shark (Megachasmidae) as well as the thresher sharks (Alopiidae), goblin shark (Mitsukurinidae), and sand tigers (Odontaspididae). The white shark (Lamnidae) is a top predator with a global marine distribution at temperate latitudes. It can travel thousands of kilometers in search of mates, food, or nursery grounds (Bonfil et al. 2005; Jorgensen et al. 2009).

Carcharhiniformes (ground sharks) have a variety of developmental modes, including oviparity and viviparity. Examples include cat sharks (Scyliorhinidae), hound sharks (Triakidae), requiem sharks (Carcharhinidae; some enter fresh water), and hammerhead sharks (Sphyrnidae) with hydrofoil-shaped heads that widely separate the eyes, nostrils, and ampullae of Lorenzini and might enable superior sensory abilities. It has been reported that embryonic yolk sacs of requiem and hammerhead sharks develop placenta-like attachments to the wall of the mother’s oviduct (Hamlett 1989).

1.4.2.1.2 Superorder Squalomorphi

The squalomorph sharks (Figure 1.3) share a unique jaw articulation (Maisey 1980) and lack an anal fin. The Hexanchiformes (six-gill sharks) have one spineless dorsal fin, a very elongate body, a large mouth, and six or seven gill slits. Eggs hatch from their egg cases inside the mother’s oviduct. The Chlamydoselachidae (frilled sharks) have six pairs of gill slits, and the Hexanchidae (cow sharks) have six or seven pairs.

Squaliformes (dogfish sharks) have two dorsal fins and retain spiracles. Examples include the Centrophoridae (gulper sharks), Etmopteridae (lantern sharks) known for their light-emitting organs, and Somniosidae (sleeper sharks). The Squalidae (dogfish sharks) include the usual comparative anatomy species, Squalus acanthias, which is viviparous and has a long gestation of up to 2 years.

Echinorhiniformes (bramble sharks) have unusually large, widely scattered scale denticles. Squatiniformes (angel sharks) are viviparous, benthic sharks with a body shape convergent with that of rays. They are ambush predators that use strong suction feeding. Pristiophoriformes (saw sharks) have a pair of long barbels on the ventral side of their elongate rostrum, which has laterally projecting “teeth” that are enlarged dermal denticles (Welten et al. 2015); the mouth is ventral. Prey are detected by ampullae of Lorenzini and/or by the barbels, exposed, and then killed or disabled by sideways slashing of the rostrum.

1.4.2.2 Division Batomorphi (Rays)

The Batomorphi (Figure 1.3) are the rays, with 632 species in four orders. They lack an anal fin. Pectoral fins are greatly enlarged and attached to the head dorsal to the gill slits but ventral to the eyes and spiracle. The pectoral girdles are joined ventrally as well as dorsal to the vertebral column. Rays are viviparous, except for skates (see later).

Torpediniformes (electric rays) have electric organs in the pectoral fins that can generate potentials with ventro-dorsal polarity of up to 220 volts or currents of up to 50 amperes for feeding or defense. Eyes are small and sometimes non-functional. The rays can ambush prey that swim near their head (Lowe et al. 1994). For defense, they can roll themselves up in a defensive posture.

Rajiformes (skates) are a single diverse family with 32 genera and about 288 species and a near-global marine distribution. Subfamilies divide hardnose skates from softnose skates. Unlike other rays, skates are oviparous, laying eggs in egg cases.

Pristiformes (guitarfishes and sawfishes) have a prominent elongate rostrum, which in sawfishes (family Pristidae) is a blade armed with socketed “teeth.” Like those of saw sharks, the rostral “teeth” of sawfishes are modified dermal denticles (e.g., Welten et al. 2015).

Myliobatiformes (stingrays, etc.) are a diverse group, most with a serrated and often venomous spine on their tail, which can inflict a painful and sometimes fatal wound. Examples are the Platyrhinidae (thornback rays), Zanobatidae (panrays), Dasyatidae (whiptail stingrays, including one that ranges into fresh water), Potamotrygonidae (river stingrays of South America), and Myliobatidae (eagle rays, cownose rays, devil rays, and manta rays).

1.5 Class Osteichthyes (Bony Fishes Including Tetrapods)

The Osteichthyes (Figure 1.2) comprise the remaining two monophyletic groups: Sarcopterygii, lobe-finned fishes plus tetrapods (Figure 1.2 clade D), and Actinopterygii, ray-finned fishes (Figure 1.2 clade E), all having well-ossified internal skeletons of endochondral or membrane bone. Lepidotrichia (bony fin rays) are now present and are formed as shafts of bone around bundles of collagen fibers called actinotrichia. In addition, a premaxilla is present, and the skull has sutures. Lungs, functioning as either air-breathing organs or as a buoyancy-controlling swimbladder, are present in all osteichthyans unless secondarily lost.

1.5.1 Subclass Sarcopterygii (Lobe-Finned Fishes and Tetrapods)

Notable within Sarcopterygii are the coelacanths (e.g., Latimeriidae, with one extant genus Latimeria and two species) and the lungfishes (Dipnoi) containing the Neoceratodontidae (Australian lungfish), Lepidosirenidae (South American lungfish), and Protopteridae (African lungfishes), the latter two families sometimes placed together in Lepidosireniformes. Lungfishes have true lungs that develop from an evagination of the pharynx, a partially divided atrium and ventricle in the heart, and a separation of pulmonary and systemic blood vessels with newly evolved pulmonary arteries. Although Neoceratodus (Australian lungfish) possesses one lung positioned dorsal to the gut, it respires mostly through gills. Protopterus (African lungfishes) and Lepidosiren (South American lungfish), on the other hand, possess paired lungs and are essentially obligate airbreathers. They can also estivate (remain dormant) in burrows during periods of heat or desiccation.

1.5.2 Subclass Actinopterygii (Ray-Finned Fishes)

The remainder of this chapter concerns the Actinopterygii or ray-finned fishes (Figure 1.4). Basic features include dermal bones, a layer of ganoine on the dermal bones and scales, a peg-and-socket articulation between trunk scales, a well-developed endoskeleton, and fin muscles that do not extend into the paired fins but still precisely control the fin rays. Actinopterygii are divided among 67 orders, 469 families, over 4000 genera and 30,500 species (Nelson et al. 2016). Almost half of these species inhabit fresh water.

FIGURE 1.4 Phylogenetic relationships among early-branching actinopterygians. Polypteridae form the sistergroup to Chondrostei (sturgeons and paddlefishes) + Holostei (gars and bowfins) + Teleostei. Triangle sizes are correlated to species diversity.

1.5.2.1 Early-Branching Actinopterygii

The three earliest branches from the actinopterygian stem that still have extant members (Figure 1.4) are 1) the order Polypteriformes (bichirs) from fresh waters of Africa; 2) the infraclass Chondrostei, comprising the order Acipenseriformes (paddlefishes and sturgeons) from fresh waters of the Northern Hemisphere (Grande and Bemis 1998)—both paddlefishes and sturgeons possess ampullary electroreceptors concentrated in the rostrum and oral area; and 3) the infraclass Holostei, containing the order Lepisosteiformes (gars) of North and Central America plus Cuba, together with the order Amiiformes (only the bowfin Amia calva) of North America (Grande and Bemis 1998; Grande 2010).

1.5.2.2 Division Teleostei

All remaining extant actinopterygians are members of the Teleostei. Teleosts have a rich fossil record. They first appeared in the Late Triassic fossil record (201–237 million years before present) and radiated in the Jurassic, Cretaceous, and Cenozoic, eventually replacing most other clades of fishes (e.g., Long 2012). Their monophyly is strongly supported by both morphological and molecular data (e.g., de Pinna 1996; Near et al. 2012, 2013). The teleostean caudal fin primitively includes two ural centra, ural neural arches elongated to form paired, strap-like uroneurals, and an externally homocercal shape.

Teleosts are the most speciose and diversified group of all vertebrates (Figures 1.1 and 1.5). With about 30,000 extant species (95% of all extant fishes), they dominate the world’s lakes, rivers, and oceans (Nelson et al. 2016).

FIGURE 1.5 Diversity of fishes within Otocephala and Euteleostei (details are in all remaining phylogeny figures) representing over 96% of all extant fishes.

1.5.2.3 Cohort Elopomorpha (Tarpons, Tenpounders, Bonefishes, Eels)

Elopomorphs (Figure 1.6) are known for their unique leptocephalus (slim-headed, transparent, ribbon-like) pelagic larval stage. There are two major body types of elopomorphs: the “fish-like” bodies of Elopiformes (tarpons, ladyfishes) and Albuliformes (bonefishes) and the “eel-like” body types of Notacanthiformes (deep-sea spiny eels) and Anguilliformes (marine and freshwater eels). Among elopomorphs, Anguilliformes (eels) are by far the most diverse order, with at least 938 species. Species within the family Megalopidae (e.g., Tarpon, Megalops) exhibit coelomic extensions of the swimbladder that expand anteriorly into bullae. Although these bullae make no connection with the inner ear, hearing enhancement has been hypothesized (Braun and Grande 2008) but apparently not experimentally tested.

FIGURE 1.6 Phylogeny of Teleostei. Early-branching clades are Elopomorpha, Osteoglossomorpha, and Otocephala (Clupeomorpha + Alepocephali + Ostariophysi), the latter being sister to the Euteleostei. Triangle sizes are correlated to species diversity.

1.5.2.4 Cohort Osteoglossomorpha (Bony-Tongues)

Osteoglossomorphs (Figure 1.6) are known as the bony-tongues because of their unique feeding mechanism: teeth on the gill arches shear food against teeth on the parasphenoid bone in the roof of the mouth. Anterior extensions of the swimbladder that approach the inner ear are common among osteoglossomorph taxa (e.g., Hiodon, Notopterus; Braun and Grande 2008). All living species inhabit fresh water and are divided into two orders: Hiodontiformes (mooneyes, sister to all other osteoglossomorphs) and Osteoglossiformes, comprising Pantodontidae (butterflyfishes), Osteoglossidae (arowanas), Mormyridae (elephantfishes), Notopteridae (featherfin knifefishes), and Gymnarchidae (the aba, Gymnarchus). Arapaima gigas, native to the Amazon river basin, is an obligate airbreather and is among the largest of extant freshwater fishes, growing to about 3 meters in length and at least 200 kilograms in weight. Mormyrids exhibit electrosensory ability correlated with an enlarged cerebrum for processing electroreceptive information. Gymnarchus niloticus can both produce and detect electric fields. The electric fields can be used for navigation as well as for species and individual recognition (e.g., Arnegard et al. 2010).

1.5.2.5 Cohort Otocephala

The Otocephala and its sistergroup the Euteleostei comprise all remaining fishes (Figures 1.5 and 1.6). The cohort Otocephala contains fishes with an otophysic connection between the swimbladder and the inner ear (Braun and Grande 2008). The group contains three superorders: Clupeomorpha (herrings, sardines, and anchovies), Alepocephali (slickheads), and Ostariophysi (e.g., carp, minnows, characins, catfishes, and Neotropical knifefishes) (Lecointre and Nelson 1996; Nelson et al. 2016).

1.5.2.5.1 Superorder Clupeomorpha

Clupeomorpha (Figure 1.6) are diagnosed by a unique otophysic connection comprising a pair of diverticula extending from the swimbladder through the exoccipitals and expanding into bullae within the prootics and often the pterotics of the skull (Grande 1985). The prootic bullae are closely associated with the utriculus of the inner ear. This connection enhances hearing in these fishes. Taxa belonging to order Clupeiformes are diagnosed by the presence of a recessus lateralis.

Clupeiforms comprise over 405 species, with about 79 of them being primarily freshwater forms. Their diversity is concentrated in the Indo-Pacific and the western Atlantic. Members of the families Engraulidae (anchovies; 17 genera and about 146 species) and Clupeidae (herrings, sardines, shads; 64 genera and about 218 species) contain the majority of species and are of great economic value throughout the world.

1.5.2.5.2 Superorder Ostariophysi

Ostariophysans (Figure 1.6) are the largest clade of mostly freshwater fishes. Breeding tubercles composed of keratin are diagnostic. There are two monophyletic series: Anotophysi, consisting of the order Gonorynchiformes (extant members mostly marine), and Otophysi, with four primarily freshwater orders, all four of them having a Weberian apparatus, which is a unique series of modified pleural ribs, neural arches, and supraneurals of the anterior-most vertebrae that conduct sound vibrations from the swimbladder to the inner ear.

The anotophysan order Gonorynchiformes contains three families (Poyato-Ariza et al. 2010): Chanidae (milkfish) from marine waters of the Indian and Pacific Oceans; Gonorynchidae (beaked sandfish) from marine waters of the Indo-Pacific; and Kneriidae (knerias and snake mudheads), from fresh waters of tropical Africa.

The Otophysi total over 10,000 species (Nelson et al. 2016) and are divided into four orders: Cypriniformes (carps and minnows including the goldfish and zebrafish, loaches, and suckers), Characiformes (characins such as the tetras and piranhas), Siluriformes (catfishes), and Gymnotiformes (Neotropical knifefishes).

Cypriniformes are very diverse in novelties, ecologies, and taxa (Hernandez and Cohn 2019), with at least 4200 species (Nelson et al. 2016). Their Weberian apparatus is relatively unspecialized (Bird and Hernandez 2007). Many are important food and aquarium fishes (e.g., Cyprinus carpio, common carp). The goldfish (Carassius auratus) is an experimental animal for fish physiology, and the zebrafish (Danio rerio), of course, is the model organism for fish developmental biology.

Characiformes, according to most morphological studies, are the sistergroup to gymnotiforms and siluriforms. All extant characiforms are restricted to fresh waters; about 200 species occur in Africa, and the remainder of the 2300 species are found in North, Central, and South America.

Siluriphysi (catfishes—3725 species + Neotropical knifefishes—207 species) exhibit morphological and ecological specializations too numerous to list here. Novelties of some catfishes (Siluriformes) include venom glands (e.g., Heteropneustidae), electric organs (Malapteruridae—their giant electromotor neurons are of special interest), armor (Callichthyidae, Loricariidae), and dwarfism (Scoloplacidae). A few are parasitic (Trichomycteridae: Vandellia cirrhosa). The Gymnotiformes (knifefishes) are restricted to Neotropical regions. Many (e.g., Electrophorus electricus) have electric organs capable of potentials of up to 600 volts.

1.5.2.6 Cohort Euteleostei

The Euteleostei contain all the remaining teleost fishes (Figures 1.5 and 1.7). The monophyly of this group is unquestioned and is supported by a unique pattern of supraneural development, the presence of a stegural with an anterodorsal membrane outgrowth, and the presence of caudal median cartilages (Wiley and Johnson 2010).

FIGURE 1.7 Phylogeny of Euteleostei. Lepidogalaxiiformes are sister to Protacanthopterygii (salmon and pikes) + Zoroteleostei (Osmeromorpha and Neoteleostei). Triangle sizes are correlated to species diversity.

Within Euteleostei, Lepidogalaxias (salamanderfish) is the sistergroup to all other extant euteleosts (Li et al. 2010; Campbell et al. 2017). The Protacanthopterygii (Salmoniformes plus Esociformes) are the sistergroup to all the rest (Figure 1.7). Nelson et al. (2016) gave totals of 50 orders, 351 families, 3160 genera, and over 19,000 species for Euteleostei.

1.5.2.6.1 Superorder Protacanthopterygii

A very restricted membership of Protacanthopterygii is accepted here (Wilson and Williams 2010, Campbell et al. 2013; Hughes et al. 2018): Salmoniformes + Esociformes (Figure 1.7).

Salmoniformes (trout, salmon, whitefishes) contain only Salmonidae, with 10 genera and at least 225 species. They are of high economic importance because of their exploitation in commercial, sport, and subsistence fisheries. Species of Salmo and Oncorhyncus are intensively farmed and/or widely introduced. The 17 species of Oncorhyncus (Pacific salmon) are of particular interest for their long-distance, anadromous migrations and their homing ability to their natal streams for spawning. Many of them are also semelparous (dying after just one spawning episode).

Esociformes (pikes and mudminnows) contain two families, four genera, and about 12 species (Grande et al. 2004). Esocidae comprise three of the four genera (Novumbra, Dallia, and Esox). Species within the genus Esox are well known for their characteristic duck-billed snout, elongated body, mouth of sharp depressible teeth, and voracious feeding behaviour. Pikes have recently been advocated as model organisms for developmental studies (Pospisilova et al. 2019). Umbridae (mudminnows) contain only the genus Umbra (López et al. 2004). At least two species of Umbra are adapted to tolerate low oxygen levels (Currie et al. 2010). Umbra limi is known to breathe from bubbles trapped under ice in ice-covered lakes (Magnuson et al. 1983).

1.5.2.6.2 Unranked Clade Zoroteleostei

This clade (Figure 1.7) includes all remaining Euteleostei, united by a partially or completely unroofed preopercular sensory canal in primitive members (Wilson and Williams 2010; Nelson et al. 2016) and by genome-scale molecular phylogenetic analysis (Hughes et al. 2018).

1.5.2.6.3 Superorder Osmeromorpha

The first group of Zoroteleostei (Figure 1.7) includes the orders Argentiniformes (marine smelts), Galaxiiformes (galaxiiforms), Osmeriformes (Northern Hemisphere smelts), and Stomiiformes (dragonfishes) (Hughes et al. 2018).

Galaxiiforms of the Southern Hemisphere are predominantly in fresh waters, while osmeriforms mostly spawn in fresh waters of the Northern Hemisphere. Both groups contain anadromous members (Nelson et al. 2016). Termed dragonfishes for the nightmarish teeth on their premaxilla and maxilla, stomiiforms are of particular interest because of bioluminescent organs (photophores) and a mostly deep-sea lifestyle (Kenaley 2009; Davis et al. 2016). Stomiiforms undergo daily feeding migrations from deep waters during the day to surface waters around sunset, returning to deep waters at sunrise, a behaviour typical of organisms of the “deep scattering layer.”

1.5.2.7 Unranked Clade Neoteleostei

Neoteleostei (Figure 1.8) comprise the superorders Ateleopodomorpha (Ateleopodiformes: jellynose fishes), Cyclosquamata (Aulopiformes: lizardfishes), Scopelomorpha (Myctophiformes: lanternfishes), Lamprimorpha (Lampriformes: opahs), Paracanthopterygii (five orders), and Acanthopterygii (the many spiny-finned fishes). The last three clades belong to the Acanthomorpha (spiny-rayed fishes discussed later). The clade Neoteleostei is strongly supported by numerous molecular studies (Davis 2010; Betancur-R. et al. 2013; Hughes et al. 2018) and is diagnosed by the presence of a retractor dorsalis muscle (RAB) (also found in stomiiforms), type 4 tooth attachment, insertion of the third levator on the fifth upper pharyngeal toothplate, and presence of a transverse epibranchial (Wiley and Johnson 2010).

FIGURE 1.8 Phylogeny of Neoteleostei. Included as early branches are the jellynoses, lizardfishes, and lanternfishes, the last being sister to the Acanthomorpha (spiny-rayed fishes). Triangle sizes are correlated to species diversity.

Several interesting groups of fishes branch from the stem of the neoteleost tree (Figure 1.8). The Ateleopodiformes (jellynoses) of circumtropical seas are a small group of deep-water bottom dwellers. Although they are teleosts, their skeletons are mostly cartilaginous, and their bulbous snouts are filled with a jelly-like substance of unknown function.

The order Aulopiformes (lizardfishes) includes about 260 mostly benthic species, many of which are hermaphroditic. Extinct forms were very diverse and important in Mesozoic Era seas (Davis and Fielitz 2010). Telescopefishes (family Giganturidae) are two species known for their bizarre tubular eyes with large lenses. They undergo an amazing developmental transformation in which the larval stage is so different that it was described as a completely separate fish, Rosaura rotunda, in the family Rosauridae (Konstantinidis and Johnson 2016).

The order Myctophiformes (lanternfishes), of two families, about 36 genera, and at least 2534 species, is an essential part of the marine ecosystem (Bray 2019). It accounts for more than half of all deep-sea biomass and is the main component of the “deep scattering layer.” The phylogeny of lanternfishes was studied by Martin et al. (2018).

1.5.2.8 Unranked Clade Acanthomorpha (Spiny-Rayed Fishes)

Acanthomorpha (Figure 1.8) have undergone an explosion of morphological diversity and body plans since the mid-Cretaceous, 100 million years ago (Friedman 2010). The group was originally recognized by Rosen (1973) to include teleosts with true spines in the dorsal, anal, and pelvic fins. The group has since been supported as monophyletic by both morphological and molecular studies (e.g., Wiley et al. 2000; Chen et al. 2014; Hughes et al. 2018).

1.5.2.8.1 Superorder Lamprimorpha

The sole order Lampriformes, sister to all other acanthomorphs (Figure 1.8), contains six families and about 22 species. These fishes have one of two body types, the deep-bodied members (Veliferidae and Lampridae) and the long, ribbon-bodied members (Lophotidae, Radiicephalidae, Trachipteridae, and Regalecidae). The amazing Regalecidae (oarfishes) are scaleless fishes with no anal fin and elongated pelvics that are reduced to only one ray. The extremely long dorsal fin has 260–412 rays. Regalecus glesne reaches a length of about 8 meters, the longest of all bony fishes, and dead oarfish are sometimes mistaken for sea serpents. For relationships within this group, see Olney et al. (1993) and Davesne et al. (2014).

1.5.2.8.2 Superorder Paracanthopterygii

The superorder Paracanthopterygii (Figure 1.8) was first proposed by Greenwood et al. (1966) as a morphologically equivalent group to Acanthopterygii. Currently included within Paracanthopterygii are Polymixiiformes (beardfishes), Percopsiformes (trout-perches), Gadiformes (cods), Stylephorus, and Zeiformes (dories) (Miya et al. 2007; Grande et al. 2013; Borden et al. 2013, 2019; Davesne et al. 2014; Hughes et al. 2018). We follow Nelson et al. (2016) and Borden et al. (2019) in placing Polymixia (beardfishes) as sister to all other members, and percopsiforms as sister to the clade Zeiformes + [Stylephorus + Gadiformes]. See Tyler et al. (2003) and Grande et al. (2018) for relationships among Zeiformes and Borden et al. (2019) for relationships within Polymixiiformes.

The Gadiformes are of particular interest and include over 600 species. A recent molecular phylogenetic analysis was done by Roa-Varón and Ortí (2009). Examples of gadiforms include Steindachneriidae (luminous hakes), Macrouridae (rattails), and Moridae (deep-sea cods) in the Antarctic, Arctic, North Pacific, and North Atlantic oceans (Cohen 1984; Dunn 1989; Borden et al. 2013). The circumpolar Lota lota (burbot) is the only one that inhabits fresh waters. The cold-water cods are of immense historical importance and still contribute over one-quarter of the world’s marine fish catch; however, the Atlantic cod Gadus morhua has been over-fished in the Western North Atlantic almost to extinction, and a cod-fishing moratorium has now lasted over 20 years. Cod populations, now challenged by global climate change and warming ocean waters, are projected to move farther north in coming decades (Morley et al. 2018).

1.5.2.8.3 Superorder Acanthopterygii

Acanthopterygii (Figures 1.8 and 1.9) comprise all remaining fish species. Their diversity in terms of morphology, ecology, physiology, and distribution patterns is greater than that of any other group. At least 15,000 species are recognized (Nelson et al. 2016), divided among 34 orders, 287 or more families, and at least 2433 genera. About a quarter of these fishes inhabit fresh waters.

FIGURE 1.9 Phylogeny of higher Percomorpha. Scombrimorpharia (seahorses and tunas) are sister to Ovalentaria (e.g., cichlids, killifishes, livebearers), Carangaria (e.g., jacks, remoras, barracudas, flatfishes), and Eupercaria (e.g., wrasses, perches, butterflyfishes, scorpionfishes, anglerfishes, boxfishes, puffers, molas). Triangle sizes are correlated to species diversity.

Three orders are early-branching clades (Figure 1.8): (1) Beryciformes (e.g., Rondeletiidae, whalefishes; Berycidae, alfonsinos); (2) Trachichthyiformes (e.g., Anomalopidae, flashlight fishes, which have luminous organs with symbiotic bacteria beneath the eye; Monocentridae, the heavily armored pinecone fishes; Trachichthyidae, including the slow-growing and easily over-fished orange roughy); and (3) Holocentriformes (squirrelfishes). These orders are sometimes grouped as series Berycida (Nelson et al. 2016).

1.5.2.9 Series Percomorpha

Percomorphs are the most diverse and derived fishes within Acanthopterygii. Here, we divide percomorphs into groups whose sequence of taxa suggests phylogenetic hierarchy. However, the relationships are far from settled. Groups recognized here (Figures 1.8 and 1.9) are Ophidiida, Batrachoidida, Gobiida, Scombrimorpharia, Ovalentaria, Carangaria, and Eupercaria (Betancur-R. et al. 2013; Nelson et al. 2016; Hughes et al. 2018).

1.5.2.9.1 Subseries Ophidiida

This sistergroup to all other Percomorpha (Figure 1.8) contains the cusk-eels (Ophidiiae), pearlfishes (Carapidae), viviparous brotulas (Bythitidae), blind cusk-eels (Aphyonidae), and false brotulas (Parabrotulidae).

1.5.2.9.2 Subseries Batrachoidida

This group contains the toadfishes in the single family Batrachoididae. Most are drab and can survive out of water for several hours. Males make nests or dig dens and then produce humming sounds with their swimbladder to attract females, which attach their eggs to the walls of the nest to be defended by the male. Their sound-producing “superfast” swimbladder muscles can operate at over 200 Hz (Rome 2006). Members of the subfamily Thalassophryninae have hollow dorsal and opercular spines connected to venom glands.

1.5.2.9.3 Subseries Gobiida

The Gobiida (Figure 1.8) contain two orders; Kurtiformes (nurseryfishes and cardinalfishes) and Gobiiformes (gobies). Male nurseryfishes have occipital hooks for carrying eggs on the head (Berra and Neira 2003). The cardinalfishes are mouth-brooders; a few have luminous organs. The gobies number over 2000 species, including freshwater, cave-dwelling, and marine forms with diverse ecological and life-history traits.

1.5.2.9.4 Subseries Scombrimorpharia

This group (Figure 1.9) includes Syngnathiformes (seamoths, pipefishes, and seahorses), Scombriformes (tunas, mackerels), and three other orders (Nelson et al. 2016). Evidence for grouping these orders is accumulating from molecular sequence studies (e.g., Near et al. 2012; Wainwright et al. 2012; Betancur-R. et al. 2013; Hughes et al. 2018), but the full membership of this clade has not been settled, and its unifying novelties remain unknown.

1.5.2.9.5 Subseries Ovalentaria

This diverse group (Figure 1.9), named by Smith and Near in Wainwright et al. (2012), includes Mugiliformes (mullets), Cichliformes (cichlids), Blenniiformes (blennies), Gobiesociformes (clingfishes), Atheriniformes (silversides), Beloniformes (needlefishes, flyingfishes, halfbeaks), and Cyprinodontiformes (killifishes and livebearers). These fishes are mostly small and have sticky demersal eggs. Reproductive strategies include substrate brooding, mouth brooding, and live bearing. The Japanese ricefish Oryzias latipes (medaka) is used in reproductive biology and toxicology. Nothobranchius furzeri (turquoise killifish) is used in studies of ageing because of its very short lifespan (Platzer and Englert 2016). Fundulus heteroclitus (mummichog) is used extensively in genomic, osmoregulatory, and toxicological studies (Reid and Whitehead 2016; Reid et al. 2017). Cichlids (about 1700 species), so familiar to aquarists, behaviourists, and evolutionary biologists, employ mouth brooding and provide notable examples of adaptive radiations, rapid evolution, and species flocks, especially in African rift lakes.

1.5.2.9.6 Subseries Carangaria

This sistergroup to Ovalentaria was suggested by Near et al. (2012), Wainwright et al. (2012), and Betancur-R. et al. (2013). Its members (Figure 1.9) include Synbranchiformes (swamp eels), Anabantiformes (labyrinth fishes, gouramies, fighting fishes), Carangiformes (jacks, dolphinfishes, remoras), Istiophoriformes (barracudas, billfishes, swordfishes), and Pleuronectiformes (flatfishes).

1.5.2.9.7 Subseries Eupercaria

The sister to the preceding two orders contains all remaining fish diversity. Included are Labriformes (wrasses and parrotfishes), Perciformes (perches and darters, freshwater sunfishes, sea basses, butterflyfishes and angelfishes, snappers, icefishes), Scorpaeniformes (scorpionfishes, searobins, eelpouts, sticklebacks, sculpins), Acanthuriformes (drums, surgeon fishes), Caproiformes (boarfishes), Lophiiformes (anglerfishes), and Tetraodontiformes (puffers, boxfishes, triggerfishes, filefishes, porcupinefishes, and molas).

Notothenioids (icefishes) are famous for their antifreeze glycoproteins and their lack of glomeruli, red blood cells, and hemoglobin, allowing many of them to survive sub-zero (˚C) temperatures in Antarctic waters (Eastman 2004).

Of particular interest are the scorpionfishes (Scorpaeniformes), exhibiting many novelties, including armor, spines, and venom as anti-predator defenses. They include some of the most deadly marine fishes (Smith et al. 2016). The reef stonefish Synanceia verrucosa, for example, has 13 dorsal-fin spines, each of which has two venom sacs filled with a neurotoxin that can cause shock, paralysis, and tissue death (Smith et al. 2016). A new phylogeny by Smith et al. (2018) revises ideas about the evolution of viviparity via a transition from external to internal fertilization, with retention of developing eggs or embryos within the female.

Sticklebacks of the suborder Gasterosteoidei are important model organisms for developmental and behavioural biologists and for studying rapid evolution in changing environments (Ahmed et al. 2017).

Lophiiformes (anglerfishes) have large mouths, macrophagous habits, and a cephalic spinous dorsal fin modified into a lure to attract prey. A possible adaptation in some ceratioids to rare deep-sea encounters between small males and larger females is extreme reduction in the size of males, which become embedded as sexual attachments on the body of the female (Pietsch 2005).

Finally, the incredible Tetraodontiformes (pufferfishes, boxfishes, triggerfishes) have over 435 species, only 14 restricted to fresh water. They were reviewed by Santini and Tyler (2003), and molecular phylogenetic studies were done by Holcroft et al. (2008). The pufferfish genus Takifugu has an extremely small genome and is a model organism for genomics. Perhaps the most iconic tetraodontiform is the large-bodied ocean sunfish, Mola mola (e.g., Nelson et al. 2016).

1.6 Conclusion

The survey presented here of the phylogeny and diversity of fishes is a small fraction of what is known about these fascinating aquatic animals. The bibliography included with Nelson et al. (2016) contains a wealth of resources for learning more, planning comparative studies, and accessing specialist literature. Our understanding of the fish tree of life has improved rapidly in the last few decades, so that we are now more confident than ever about the relationships presented here. Nevertheless, much remains to be learned about the ecological, physiological, developmental, genetic, morphological, and behavioural traits that have allowed these remarkable animals to achieve such large numbers of species and often large populations of individuals.

Literature Cited

Ahmed, N. I., C. Thompson , S. I. Bolnick and Y. E. Stuart . 2017. Brain morphology of the threespine stickleback (Gasterosteus aculeatus) varies inconsistently with respect to habitat complexity: A test of the clever foraging hypothesis. Ecol Evol 7:3372–3380.
Arnegard, M. E., P. B. McIntyre , L. J. Harmon , M. L. Zelditch , W. G. R. Crampton , J. K. Davis , J. P. Sullivan , S. Lavoué and C. D. Hopkins . 2010. Sexual signal evolution outpaces ecological divergence during electric fish species radiation. Am Nat 176(3):335–356.
Berra, T. M. and F. J. Neira . 2003. Early life history of the nurseryfish, Kurtus gulliveri (Perciformes: Kurtidae) from northern Australia. Copeia 2003(2):384–390.
Betancur-R., R., R. E. Broughton , E. O. Wiley , K. Carpenter , J. A. López , C. Li , N. I. Holcroft , D. Arcila , M. Sanciangco , J. C. Cureton II , F. Zhang , T. Buser , M. A. Campbell , J. A. Ballesteros , A. Roa-Varon , S. Willis , W. C. Borden , T. Rowley , P. C. Reneau , D. J. Hough , G. Lu , T. Grande , G. Arratia and G. Ortí . 2013. The Tree of Life and a new classification of bony fishes. PLoS Curr 1–41.
Bird, N. C. and L. P. Hernandez . (2007). Morphological variation in the Weberian apparatus of Cypriniformes. J Morphol 268(9):739–757.
Bonfil, R., M. A. Meyer , M. C. Scholl , R. L. Johnson , S. O'Brian , H. Oosthuizen , S. Swanson , D. Kotze and M. Patterson . 2005. Transoceanic migration, spatial dynamics, and population linkages of white sharks. Science 310:100–103.
Borden, W. C., T. Grande and W. L. Smith . 2013. Comparative osteology and myology of the caudal fin in Paracanthoptergyii (Teleostei: Acanthomorpha). pp 419–455. In G. Arratia , H.-P. Schultze and M. V. H. Wilson (Eds.), Mesozoic Fishes 5–Global Diversity and Evolution. Verlag Dr. Friedrich Pfeil. München.
Borden, W. C., T. C. Grande and M. V. H. Wilson . 2019. Phylogenetic relationships within the primitive acanthomorph genus Polymixia, with changes to species composition and geographic distributions. PLoS ONE 14(3):e0212954:1–30.
Braun, C. and T. Grande . 2008. Evolution of peripheral mechanisms for the enhancement of sound reception. pp 99–144. In J. Webb , R. Fay and A. Popper . (Eds.), Fish Bioacoustics. New York, NY: Springer Science.
Bray, D. J. 2019. Lanternfishes, Myctophiformes in Fishes of Australia, accessed 08 Oct 2019, http://fishesofaustralia.net.au/home/order/27.
Campbell, M. A., J. A. López , T. Sado and M. Miya 2013. Pike and salmon as sister taxa: Detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences. Gene 530:57–65.
Campbell, M. A., M. E. Alfaro , M. Belasco and J. A. López . 2017. Early-branching euteleost relationships: Areas of congruence between concatenation and coalescent model inferences. PeerJ 5:e3548:1–17.
Carrier, J. C., J. A. Musick and M. R. Heithaus . 2004. Biology of Sharks and Their Relatives. 2nd Edition. Boca Raton, FL: CRC Press, 666 pp.
Chen, W. J., F. Santini , G. Carnevale , J.-N. Chen , S.-H. Liu , S. Lavoué and R. L. Mayden . 2014. New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha). Front Mar Sci 1:1–17.
Cohen, D. M. 1984. Gadiformes: Overview. pp 259–265. In H. G. Moser , W. J. Richards , D. M. Cohen , M. P. Fahay , A. W. Kendall and S. L. Richardson , S. L. (Eds.), Ontogeny and Systematics of Fishes. Lawrence, KS: Amer Soc Ichthyol Herpetol Spec Publ 1.
Compagno, L. J. V. 2005. Checklist of Chondrichthyes, pp 503–547. In W. C. Hamlett (Ed.), Reproductive Biology and Phylogeny of Chondrichthyes: Sharks, Batoids and Chimaeras. Enfield, NH: Science Publishers.
Currie, S., B. Bagatto , M. DeMille , A. Learner , D. LeBlanc , C. Marks , K. Ong , J. Parker , N. Templeman , B. L. Tufts and P. A. Wright . Metabolism, nitrogen excretion, and heat shock proteins in the Central Mudminnow (Umbra limi), a facultative air-breathing fish living in a variable environment. Can J Zool 88(1):43–58.
Davesne, D., M. Friedman , V. Barriel , G., Lecointre , P. Janvier , C. Gallut . 2014. Fossils illuminate character evolution and relationships of Lampridiformes (Teleostei, Acanthomorpha). Zool J Linn Soc 172(2):475–498.
Davis, M. P. 2010. Evolutionary relationships of the Aulopiformes (Euteleostei: Cyclosquamata): A molecular and total evidence approach. pp 431–470. In J. S. Nelson , H.-P Schultze and M. V. H. Wilson (Eds.), Origin and Phylogenetic Interrelationships of Teleosts. München: Verlag Dr. Friedrich Pfeil.
Davis, M. P. and C. Fielitz . 2010. Estimating divergence times of lizardfishes and their allies (Euteleostei: Aulopiformes) and the timing of deep-sea adaptations. Mol Phylogenet Evol 57(2010):1194–1208.
Davis, M. P., J. S. Sparks and W. L. Smith . (2016). Repeated and widespread evolution of bioluminescence in marine fishes. PLoS ONE 11(6):e0155154.
de Pinna, M. C. C. 1996. Teleostean monophyly. pp. 147–162. In P. H. Greenwood , R. S. Miles and C. Patterson . (Eds.), Interrelationships of Fishes. San Diego, CA: Academic Press.
Dunn, J. R. 1989. A provisional phylogeny of gadid fishes based on adult and early life-history characters. pp 209–236. In D. M. Cohen (Ed.), Papers on the Systematics of Gadiform Fishes. Sci Ser No. 32. Los Angeles, CA: Nat Hist Mus LA Co.
Eastman, J. T. The nature and the diversity of Antarctic fishes. Polar Biol 28(2):93–107.
Friedman, M. 2010. Explosive morphological diversification of spiny-finned teleost fishes in the aftermath of the end-Cretaceous extinction. Proc R Soc B 277:1675–1683.
Grande, L. 1985. Recent and fossil clupeomorph fishes with materials for revision of the subgroups of clupeoids. Bull Amer Mus Nat Hist 181(2):231–372.
Grande, L. and W. E. Bemis . 1998. A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy. Soc Vert Paleontol Mem 4:690.
Grande, L. 2010. An empirical synthetic pattern study of gars (Lepisosteiformes) and closely related species, based mostly on skeletal anatomy. The resurrection of Holostei. Amer Soc Ichthyol Herpetol Spec Publ 6, Copeia 10(2A suppl.):871.
Grande, T., H. Laten and A. Lopez . 2004. Phylogenetic relationships of extant esocid species (Teleostei: Salmoniformes) based on morphological and molecular characters. Copeia 2004(4):743–757.
Grande, T., W. C. Borden and W. L. Smith . 2013. Limits and relationships of Paracanthopterygii: A molecular framework for evaluating past morphological hypotheses. pp 385–418. In G. Arratia , H.-P. Schultze and M. V. H. Wilson (Eds.), Mesozoic Fishes 5–Global Diversity and Evolution. München: Verlag Dr. Friedrich Pfeil.
Grande, T. C., W. C. Borden , M. V. H. Wilson and L. Scarpitta . 2018. Phylogenetic relationships among fishes in the order Zeiformes based on molecular and morphological data. Copeia 106(1):20–48.
Greenwood, P. H., D. E. Rosen , S. H. Weitzman and G. S. Myers . 1966. Phyletic studies of teleostean fishes, with a provisional classification of living forms. Bull Amer Mus Natur Hist 131:339–456.
Hamlett, W. C. 1989. Evolution and morphogenesis of the placenta in sharks. J Exp Zool Suppl 2:35–52.
Hanslik, K. L., S. R. Allen , T. L. Harkenrider , S. M. Fogerson , E. Guadarrama and J. R. Morgan . 2019. Regenerative capacity in the lamprey spinal cord is not altered after a repeated transection. PLoS ONE 14(1):1–27.
Hastings, P. A., H. J. Walker and G. R. Galland . 2014. Fishes: A Guide to Their Diversity. Oakland, CA: Univ Calif Press, 311 pp.
Herman, P. E., A. Papatheodorou , S. A. Bryant , C. K. M. Waterbury , J. R. Herdy , A. A. Arcese , J. D. Buxbaum , J. J. Smith , J. R. Morgan and O. Bloom . 2018. Highly conserved molecular pathways, including Wnt signaling, promote functional recovery from spinal cord injury in lampreys. Sci Rep 8(742):1–15.
Hernandez, L. P. and K. Cohn . 2019. The role of developmental integration and historical contingency in the origin and evolution of cypriniform trophic novelties. Integr Comp Biol 59(2):473–488.
Holcroft, N. I. and E. O. Wiley . 2008. Acanthuroid relationships revisited: A new nuclear gene-based analysis that incorporates tetraodontiform representatives. Ichthyol Res 55(3):274–283.
Hughes, L. C., G. Ortí , Y. Huang , Y. Sun , C. C. Baldwin , A. P. Thompson , D. Arcila , R. Betancur-R , C. Li , L. Becker , N. Bellora , X. Zhao , X. Li , M. Wang , C. Fang, Xie Bing , Z. Zhou , H. Huang , S. Chen , B. Venkatesh and Q. Shi . 2018. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proc Nat Acad Sci 115(4):6249–6254.
Hyodo, S., J. D. Bell , J. M. Healy , T. Kaneko , S. Hasegawa , Y. Takei , J. A. Donald and T. Toop . 2007. Osmoregulation in elephant fish Callorhinchus milii (Holocephali), with special reference to the rectal gland. J Exp Biol 210:1303–1310.
Janvier, P. 1996. Early Vertebrates. Oxford: Oxford Monographs on Geology and Geophysics, 33. Oxford Univ. Press, 393 pp.
Jorgensen, S. J., C. A. Reeb , T. K. Chapple , S. Anderson , C. Perle , S. R. Van Sommeran , C. Fritz-Cope , A. C. Brown , A. P. Klimley and B. A. Block . 2009 (2010). Philopatry and migration of Pacific white sharks. Proc R Soc B 277(1682):679–688.
Jørgensen, J. M., J. P. Lomholt , R. E. Weber and H. Malte (eds.) 1998. The Biology of Hagfishes. New York: Chapman and Hall, 578 pp.
Kenaley, C. P. 2009. Comparative innervation of cephalic photophores of the loosejaw dragonfishes (Teleostei: Stomiiformes: Stomiidae): Evidence for parallel evolution of long-wave bioluminescence. J Morphol 271(4):418–437.
Konstantinidis, P. and G. D. Johnson . 2016. Osteology of the telescopefishes of the genus Gigantura (Brauer, 1901), Teleostei: Aulopiformes. Zool J Linn Soc 2016 (12469):1–16.
Lecointre, G. and G. Nelson . 1996. Clupeomorpha, sister-group of Ostariophysi. pp 193–207. In M. L. J. Stiassny , L. R. Parenti and G. D. Johnson (Eds.), Interrelationships of Fishes. San Diego, CA: Academic Press.
Li, J., R. Xia , R. M. McDowall , J. A. López , G. Lei and C. Fu . 2010. Phylogenetic position of the enigmatic Lepidogalaxias salamandroides with comment on the orders of lower euteleostean fishes. Mol Phylogenet Evol 57:932–936.
Long, J. A. 2012. The Rise of Fishes: 500 Million Years of Evolution. 2nd Edition. Baltimore, MD: Johns Hopkins Univ. Press, 287 pp.
López, J. A., W. J. Chen and G. Ortí . 2004. Esociform phylogeny. Copeia 2004(3):449–464.
Lowe, C. G., R. N. Bray and D. R. Nelson . 1994. Feeding and associated electrical behavior of the Pacific electric ray Torpedo californica in the field. Marine Biol 120(1):161–169.
Lucifora, L. O., M. R. de Carvalho , P. M. Kyne and W. T. White . 2015. Freshwater sharks and rays. Curr Biol 25(20):R971–R973.
Magnuson, J. J., J. W. Keller , A. L. Beckel and G. W. Gallepp . 1983. Breathing gas mixtures different from air: An adaptation for survival under the ice of a facultative air-breathing fish. Science 220(4594):312–314.
Maisey, J. G. 1980. An evaluation of jaw suspension in sharks. Amer Mu. Novit 2706:1–17.
Maisey, J. G., G. J. P. Naylor and D. J. Ward . 2004. Mesozoic elasmobranchs, neoselachian phylogeny, and the rise of modern neoselachian diversity. pp 17–56. In G. Arratia and A. Tintori (Eds.), Mesozoic Fishes 3—Systematics, Paleoenvironments and Biodiversity. München: Verlag Dr. Friedrich Pfeil.
Mallatt, J. and J. Sullivan . 1998. 28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes. Mol Biol Evol 15:1706–1718.
Martin, R. P., E. E. Olson , M. G. Girard , W. L. Smith and M. P. Davis . 2018. Light in the darkness: New perspective on lanternfish relationships and classification using genomic and morphological data. Mol Phylogenet Evol 212:71–85.
Miya, M., N. I. Holcroft , T. P. Satoh , M. Yamaguchi , M. Nishida and E. O. Wiley . 2007. Mitochondrial genome and a nuclear gene indicate a novel phylogenetic position of deep-sea tube-eye fish (Stylephoridae). Ichthyol Res 54(4):323–332.
Miya, M. and M. Nishida . 2015. The mitogenomic contributions to molecular phylogenetics and evolution of fishes—a 15-year retrospect. Ichthyol Res 62:29–71.
Morley, J. W., R. Selden . R. J. Latour , T. L. Frölicher , R. J. Seagraves and M. L. Pinsky . 2018. Projecting shifts in thermal habitat for 686 species on the North American continental shelf. PloS ONE 13(5)e0196927:1–28.
Musick, J. A. 2010. Chondrichthyan reproduction. pp. 3–20. In K. Cole (Ed.), Reproduction and Sexuality in Marine Fishes: Patterns and Processes. Berkeley, CA: Univ. Calif. Press.
Near, T. J., R. I. Eytan , A. Dornburg , K. L. Kuhn , J. A. Moore , M. P. Davis , P. C. Wainwright , M. Friedman and W. L. Smith . 2012. Resolution of ray-finned fish phylogeny and timing of diversification. Proc Nat Acad Sci 109(34):13698–13703.
Near, T. J., A. Dornburg , R. I. Eytan , B. P. Keck , W. L. Smith , K. L. Kuhn , J. A. Moore , S. A. Price , F. T. Burbrink , M. Friedman and P. C. Wainwright . 2013. Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proc Nat Acad Sci 110:12738–12743.
Nelson, J. S., T. C. Grande and M. V. H. Wilson . 2016. Fishes of the World. 5th Edition. John Wiley & Sons, Inc., pp. 707.
Olney, J. E., G. D. Johnson and C. C. Baldwin . 1993. Phylogeny of lampridiform fishes. Bull Mar Sci 52(1):137–169.
Pietsch, T. W. 2005. Dimorphism, parasitism, and sex revisited: Modes of reproduction among deep-sea ceratioid anglerfishes (Teleostei: Lophiiformes). Ichthyological Research 52(3):207–236.
Platzer, M. and C. Englert . 2016. Nothobranchius furzeri: A model for aging research and more. Trends in Genetics 32(9):P543–P552.
Pospisilova, A., J. Brejcha , V. Miller , R. Holcman , R. Šanda and J. Stundl . 2019. Embryonic and larval development of the northern pike: An emerging fish model system for evo-devo research. J Morphol 280(8):1–23.
Poyato-Ariza, F. J., T. Grande and R. Diogo . 2010. Gonorynchiform interrelationships: Historic overview, analysis and revised systematics of the group. pp 227–338. In T. Grande , F. J. Poyato-Ariza and R. Diogo (Eds.), Gonorynchiformes and Ostariophysan Relationships: A Comprehensive Review. NH: Scientific Publishers, Inc.
Reid, N. M. and A. Whitehead . (2016). Functional genomics to assess biological responses to marine pollution at physiological and evolutionary timescales: Toward a vision of predictive ecotoxicology. Briefings in Funct Genom 15(5):358–364.
Reid, N. M., C. E. Jackson , D. Gilbert , P. Minx , M. J. Montague , T. H. Hampton , L. W. Helfrich , B. L. King , D. Nacci , N. Aluru , S. I. Karchner , J. K. Colbourne , M. E. Hahn , J. R. Shaw , M. F. Oleksiak , D. L. Crawford , W. C. Warren and A. Whitehead . (2017). The Atlantic killifish (Fundulus heteroclitus) genome and the landscape of genome variation within a population. Genome Biol Evol 9(3):659–676.
Renaud, C. B. 2011. Lampreys of the world: An annotated and illustrated catalogue of lamprey species known to date. FAO Species Catalogue for Fishery Purposes. No. 5. Rome: FAO, 109 pp.
Roa-Varón, A. and G. Ortí . 2009. Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data. Mol Phylogenet Evol 52:688–704.
Rome, L. C. 2006. Design and function of superfast muscles: New insights into the physiology of skeletal muscle. Ann Rev Physiol 68:193–211.
Rosen, D. E. 1973. Interrelationships of higher euteleostean fishes. In P. H. Greenwood , S. Miles and C. Patterson (Eds.), Interrelationships of Fishes. Zool J Linn Soc (London) 53 Supplement 1:397–513; New York: Academic Press.
Santini, F. and J. C. Tyler . 2003. A phylogeny of the families of fossil and extant tetraodontiform fishes (Acanthomorpha, Tetraodontiformes), Upper Cretaceous to Recent. Zool J Linn Soc 139(4):565–617.
Smith, W. L., J. H. Stern , M. G. Girard and M. P. Davis . 2016. Evolution of venomous cartilaginous and ray-finned fishes. Integr Comp Biol 56(5):950–961.
Smith, W. L., E. Everman and C. Richardson . 2018. Phylogeny and taxonomy of flatheads, scorpionfishes, sea robins, and stonefishes (Percomorpha: Scorpaeniformes) and the evolution of the lachrymal saber. Copeia 106(1):94–119.
Treberg, J. R. and B. Speers-Roesch . 2016. Does the physiology of chondrichthyan fishes constrain their distribution in the deep sea? J Exp Biol 219:615–625.
Tyler, J. C., B. O’Toole and R. Winterbottom . 2003. Phylogeny of the genera and families of zeiform fishes, with comments on their relationships with tetraodontiforms and caproids. Smithson Contrib Zool 618:1–110.
Venkatesh, B., A. P. Lee , V. Ravi , A. K. Maurya , M. M. Lian , J. B. Swann , Y. Ohta , M. F. Flajnik , Y. Sutoh , M. Kasahara , S. Hoon , V. Gangu , S. W. Roy and twenty others . 2014. Elephant Shark genome provides unique insights into gnathostome evolution. Nature 505(12826):173–179.
Wainwright, P. C., W. L. Smith , S. A. Price , K. L. Tang , J. S. Sparks , L. A. Ferry , K. L. Kuhn , R. I. Eytan and T. J. Near . 2012. The evolution of pharyngognathy: A phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Syst Biol 61(6):1001–1027.
Welten, M., M. M. Smith , C. Underwood and Z. Johanson . 2015 Evolutionary origins and development of saw-teeth on the sawfish and sawshark rostrum (Elasmobranchii; Chondrichthyes). Roy Soc Open Sci 2:150189.
Wiley, E. O., G. D. Johnson and W. W. Dimmick . 2000. The interrelationships of acanthomorph fishes: A total evidence approach using molecular and morphological data. Biochem Syst Ecol 28:319–350.
Wiley, E. O. and G. D. Johnson . 2010. A teleost classification based on monophyletic groups. pp 123–182. In J. S. Nelson , H-P. Schultze , M. V. H. Wilson (Eds.), Origin and Phylogenetic Interrelationships of Teleosts. München: Verlag Dr. Friedrich Pfeil.
Wilson, M. V. H. and R. G. Williams . 2010. Salmoniform fishes: Key fossils, supertree, and possible morphological synapomorphies. pp 379–409. In J. S. Nelson , H-P. Schultze and M. V. H. Wilson (Eds.), Origin and Phylogenetic Interrelationships of Teleosts. München: Verlag Dr. Friedrich Pfeil.