Molecular phylogenetics of gnathostomous (jawed) fishes: old bones, new cartilage

Cartilaginous fishes (chondrichthyans) have traditionally been taken as an early offshoot among jawed vertebrates. To examine some crucial chondrichthyan relationships, we have sequenced the mitochondrial genomes of the holocephalan Chimaera monstrosa (ratfish) and the basal galeomorph species Heterodontus francisci (horn shark) and analysed them together with the corresponding data set of several other chondrichthyans, teleosts, the coelacanth, the African lungfish and the bichir. The rooting point of the tree was established using unequivocal outgroups, the sea lamprey , the sea lancelet or echinoderms. The phylogenetic analyses identified monophyletic Chondrichthyes in a terminal position in the piscine tree, lending no support to the traditionally accepted basal position of cartilaginous fishes among extant gnathostomes. The findings suggest that the cartilage characterizing extant chondrichthyans is a retention of an embryonic condition, thus representing a derived rather than a primitive phylogenetic and developmental stage. Similarly, the analyses suggest that the open gill slits of neoselachians (sharks and rays) constitute a derived state compared to the operculum (gill cover) characterizing bony fishes and holocephalans. The analyses did not support the so-called Squalea/Galea hypothesis which posits that batomorphs (sharks, rays) have arisen from recent selachians (sharks). Inconsistent with the common understanding of piscine and gnathostome evolution, the two taxa having lungs, the African lungfish and the bichir, had a basal position in the piscine tree. The findings put into question the phylogenetic validity of the taxonomic nomenclature attributed to various vertebrate, notably piscine, clades.     

The mitochondrial DNA molecule of the hagfish (myxine glutinosa) and vertebrate phylogeny

The vertebrates are traditionally classified into two distinct groups, Agnatha (jawless vertebrates) and Gnathostomata (jawed vertebrates). Extant agnathans are represented by hagfishes (Myxiniformes) and lampreys (Petromyzontiformes), frequently grouped together within the Cyclostomata. Whereas the recognition of the Gnathostomata as a clade is commonly acknowledged, a consensus has not been reached regarding whether or not Cyclostomata represents a clade. In the present study we have used newly established sequences of the protein-coding genes of the mitochondrial DNA molecule of the hagfish to explore agnathan and gnathostome relationships. The phylogenetic analysis of Pisces, using echinoderms as outgroup, placed the hagfish as a sister group of Vertebrata sensu stricto, i.e., the lamprey and the gnathostomes. The phylogenetic analysis of the Gnathostomata identified a basal divergence between gnathostome fishes and a branch leading to birds and mammals, i.e., between ``Anamnia' and Amniota. The lungfish has a basal position among gnathostome fishes with the teleosts as the most recently evolving lineage. The findings portray a hitherto unrecognized polarity in the evolution of bony fishes. The presently established relationships are incompatible with previous molecular studies. Received: 15 August 1997 / Accepted: 1 October 1997     

The phylogenetic placement of Chondrichthyes: inferences from analysis of multiple genes and implications for comparative studies

Elasmobranch fishes (sharks and rays) have proven valuable for inferring general and specific properties of molecular evolution through comparative studies with crown group vertebrates because they are the most ancient group of gnathostomes. Recent studies have questioned the conventional phylogenetic placement of sharks in the vertebrate tree, however. In this paper I review the importance of the basal position of Chondrichthyes for comparative biology and compile evidence from multiple, independent genes to evaluate the phylogenetic placement of sharks. The results suggests that alternative phylogenetic hypotheses of the relationships among the Chondrichthyes, Actinopterygii and Sarcopterygii can not be refuted with available data, implying that the assumption of the basal placement of sharks in the vertebrate tree is suspect. Resolving the phylogeny of basal vertebrates is important for testing hypotheses about the evolution of vertebrates, and the current lack of a robust phylogeny limits evolutionary inferences that can be gained from comparative studies that include sharks and rays.     

Phylogenetic Analysis of 18S rRNA and the Mitochondrial Genomes of the Wombat, <Emphasis Type="BoldItalic">Vombatus ursinus,</Emphasis> and the Spiny Anteater, <Emphasis Type="BoldItalic">Tachyglossus aculeatus:</Emphasis> Increased Support for the Marsupionta Hypothesis

The monotremes, the duck-billed platypus and the echidnas, are characterized by a number of unique morphological characteristics, which have led to the common belief that they represent the living survivors of an ancestral stock of mammals. Analysis of new data from the complete mitochondrial (mt) genomes of a second monotreme, the spiny anteater, and another marsupial, the wombat, yielded clear support for the Marsupionta hypothesis. According to this hypothesis marsupials are more closely related to monotremes than to eutherians, consistent with a basal split between eutherians and marsupials/monotremes among extant mammals. This finding was also supported by analysis of new sequences from a nuclear gene—18S rRNA. The mt genome of the wombat shares some unique features with previously described marsupial mtDNAs (tRNA rearrangement, a missing tRNA^Lys, and evidence for RNA editing of the tRNA^Asp). Molecular estimates of genetic divergence suggest that the divergence between the platypus and the spiny anteater took place ≈34 million years before present (MYBP), and that between South American and Australian marsupials ≈72 MYBP. Received: 28 October 2000 / Accepted: 23 March 2001     

Retroposition of the AFC Family of SINEs (Short Interspersed Repetitive Elements) Before and During the Adaptive Radiation of Cichlid Fishes in Lake Malawi and Related Inferences About Phylogeny

Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation. To clarify the phylogenetic relationships among these fish, we examined the presence and absence of SINEs (short interspersed repetitive elements) at orthologous loci. We identified six loci at which a SINE sequence had apparently been specifically inserted by retroposition in the common ancestor of all the investigated species of endemic cichlids in Lake Malawi. At another locus, unique sharing of a SINE sequence was evident among all the investigated species of endemic non-Mbuna cichlids with the exception of Rhamphochromis sp. The relationships were in good agreement with those deduced in previous studies with various different markers, demonstrating that the SINE method is useful for the elucidation of phylogenetic relationships among cichlids in Lake Malawi. We also characterized a locus that exhibited transspecies polymorphism with respect to the presence or absence of the SINE sequence among non-Mbuna species. This result suggests that incomplete lineage sorting and/or interspecific hybridization might have occurred or be occurring among the species in this group, which might potentially cause misinterpretation of phylogenetic data, in particular when a single-locus marker, such as a sequence in the mitochondrial DNA, is used for analysis. Received: 15 December 2000 / Accepted: 30 January 2001     

Anatomy and muscle activity of the dorsal fins in bamboo sharks and spiny dogfish during turning maneuvers

Stability and procured instability characterize two opposing types of swimming, steady and maneuvering, respectively. Fins can be used to manipulate flow to adjust stability during swimming maneuvers either actively using muscle control or passively by structural control. The function of the dorsal fins during turning maneuvering in two shark species with different swimming modes is investigated here using musculoskeletal anatomy and muscle function. White‐spotted bamboo sharks are a benthic species that inhabits complex reef habitats and thus have high requirements for maneuverability. Spiny dogfish occupy a variety of coastal and continental shelf habitats and spend relatively more time cruising in open water. These species differ in dorsal fin morphology and fin position along the body. Bamboo sharks have a larger second dorsal fin area and proportionally more muscle insertion into both dorsal fins. The basal and radial pterygiophores are plate‐like structures in spiny dogfish and are nearly indistinguishable from one another. In contrast, bamboo sharks lack basal pterygiophores, while the radial pterygiophores form two rows of elongated rectangular elements that articulate with one another. The dorsal fin muscles are composed of a large muscle mass that extends over the ceratotrichia overlying the radials in spiny dogfish. However, in bamboo sharks, the muscle mass is divided into multiple distinct muscles that insert onto the ceratotrichia. During turning maneuvers, the dorsal fin muscles are active in both species with no differences in onset between fin sides. Spiny dogfish have longer burst durations on the outer fin side, which is consistent with opposing resistance to the medium. In bamboo sharks, bilateral activation of the dorsal in muscles could also be stiffening the fin throughout the turn. Thus, dogfish sharks passively stiffen the dorsal fin structurally and functionally, while bamboo sharks have more flexible dorsal fins, which result from a steady swimming trade off. J. Morphol. 274:1288–1298, 2013. © 2013 Wiley Periodicals, Inc.     

Sperm Nuclear Basic Proteins (SNBPs) of Agnathans and Chondrichthyans: Variability and Evolution of Sperm Proteins in Fish

We have characterized for the first time SNBPs from the hagfish Eptatratus stouti (Myxini) and the lamprey Lampetra tridentatus (Cephalaspidomorphi) and have found that histones are the major protein components of the sperm of these agnathans. We have also conducted a systematic analysis of SNBPs from different groups of chondrichthyan fishes, including the skate Raja rhina and seven species of sharks. Together with our previous data showing the sporadic nature of SNBP evolution in bony fish (Saperas, N., Ausio, J., Lloris, D. and Chiva, M. [1994] J. Mol. Evol. 39: 282–295), the present study provides a unique insight into the overall evolutionary complexity and variability of the nuclear sperm proteins of fishes. It would appear that despite the discontinuous evolution of these proteins, the macroevolutionary pattern of histone (H type) → protamine-like (PL type) → protamine (P type) has been conserved in fish evolution, as it has in the evolution of other Deuterostomes. Received: 11 June 1996 / Accepted: 6 August 1996     

Monophyly of Lampreys and Hagfishes Supported by Nuclear DNA–Coded Genes

The phylogenetic position of hagfishes in vertebrate evolution is currently controversial. The 18S and 28S rRNA trees support the monophyly of hagfishes and lampreys. In contrast, the mitochondrial DNAs suggest the close association of lampreys and gnathostomes. To clarify this controversial issue, we have conducted cloning and sequencing of the four nuclear DNA–coded single-copy genes encoding the triose phosphate isomerase, calreticulin, and the largest subunit of RNA polymerase II and III. Based on these proteins, together with the Mn superoxide dismutase for which hagfish and lamprey sequences are available in database, phylogenetic trees have been inferred by the maximum likelihood (ML) method of protein phylogeny. It was shown that all the five proteins prefer the monophyletic tree of cyclostomes, and the total log-likelihood of the five proteins significantly supports the cyclostome monophyly at the level of ±1 SE. The ML trees of aldolase family comprising three nonallelic isoforms and the complement component group comprising C3, C4, and C5, both of which diverged during vertebrate evolution by gene duplications, also suggest the cyclostome monophyly. Received: 28 April 1999 / Accepted: 30 June 1999     

Multiple Protein Tyrosine Phosphatases in Sponges and Explosive Gene Duplication in the Early Evolution of Animals Before the Parazoan–Eumetazoan Split

Protein tyrosine phosphatases (PTPs) regulate various physiological events in animal cells. They comprise a diverse family which are classified into two categories, receptor type and nonreceptor type. From the domain organization and phylogenetic tree, we have classified known PTPs into 17 subtypes (9 receptor-type and 8 nonreceptor-type PTPs) which are characterized by different organization of functional domain and independent cluster in tree. The receptor type PTPs are thought to be implicated in cell–cell adhesion by association of cell adhesion molecules. Since sponges are the most primitive multicellular animals and are thought to be lacking cell cohesiveness and coordination typical of eumetazoans, cloning and sequencing of PTP cDNAs of Ephydatia fluviatilis (freshwater sponge) have been conducted by RT-PCR to determine whether or not sponges have PTP genes in their genomes. We have isolated nine PTPs, of which five are possibly receptor type. A phylogenetic tree including the sponge PTPs revealed that most of the gene duplications that gave rise to the 17 subtypes had been completed in the very early evolution of animals before the parazoan–eumetazoan split, the earliest branching among extant animal phyla. The family tree also revealed the rapid evolutionary rate of PTP subtypes in the early stage of animal evolution. Received: 22 October 1998 / Accepted: 27 November 1998     

Evolutionary Relationship Between Translation Initiation Factor eIF-2γ and Selenocysteine-Specific Elongation Factor SELB: Change of Function in Translation Factors

Eubacterial and eukaryotic translation initiation systems have very little in common, and therefore the evolutionary events that gave rise to these two disparate systems are difficult to ascertain. One common feature is the presence of initiation, elongation, and release factors belonging to a large GTPase superfamily. One of these initiation factors, the γ subunit of initiation factor 2 (eIF-2γ), is found only in eukaryotes and archaebacteria. We have sequenced eIF-2γ gene fragments from representative diplomonads, parabasalia, and microsporidia and used these new sequences together with new archaebacterial homologues to examine the phylogenetic position of eIF-2γ within the GTPase superfamily. The archaebacterial and eukaryotic eIF-2γ proteins are found to be very closely related, and are in turn related to SELB, the selenocysteine-specific elongation factor from eubacteria. The overall topology of the GTPase tree further suggests that the eIF-2γ/SELB group may represent an ancient subfamily of GTPases that diverged prior to the last common ancestor of extant life. Received: 2 January 1998 / Accepted: 1 June 1998     

Mitochondrial DNA Phylogeny of the Family Cichlidae: Monophyly and Fast Molecular Evolution of the Neotropical Assemblage

A mitochondrial DNA (mtDNA) phylogeny of cichlid fish is presented for the most taxonomically inclusive data set compiled to date (64 taxa). 16S rDNA data establish with confidence relationships among major lineages of cichlids, with a general pattern congruent with previous morphological studies and less inclusive molecular phylogenies based on nuclear genes. Cichlids from Madagascar and India are the most basal groups of the family Cichlidae and sister to African–Neotropical cichlids. The cichlid phylogeny suggests drift-vicariance events, consistent with the fragmentation of Gondwana, to explain current biogeographic distributions. Important phylogenetic findings include the placement of the controversial genus Heterochromis basal among African cichlids, the South American genus Retroculus as the most basal taxon of the Neotropical cichlid assemblage, and the close relationship of the Neotropical genera Cichla with Astronotus rather than with the crenicichlines. Based on a large number of South American genera, the Neotropical cichlids are defined as a monophyletic assemblage and shown to harbor significantly higher levels of genetic variation than their African counterparts. Relative rate tests suggest that Neotropical cichlids have experienced accelerated rates of molecular evolution. But these high evolutionary rates were significantly higher among geophagine cichlids. Received: 18 September 1998 / Accepted: 16 December 1998     

Biglycan-Like Extracellular Matrix Genes of Agnathans and Teleosts

Biglycan and decorin are two members of a family of small extracellular matrix proteoglycans characterized by the presence of 10 leucine-rich repeats and one or two attachment sites for glucosaminoglycans. Both have thus far been described only from tetrapod species, mainly mammals. Because the extracellular matrix has played an important part in the evolution of Metazoa, the phylogeny of its components is of considerable interest. In this study, biglycan-like (BGL) cDNA sequences have been obtained from two teleost (Oreochromis cichlid and zebrafish) and two lamprey species. The analysis of the sequences suggests that, like tetrapods, the lampreys possess two types of proteoglycans, both of which are biglycan-like; decorin-like proteoglycans could not be identified in these species. The genes specifying these two types apparently arose by duplication in the lamprey lineage after its divergence from gnathostomes. The two teleost species possess a BGL proteoglycan and a bona fide decorin. The BGL proteoglycan is highly divergent from the tetrapod biglycan and related to the BGL proteoglycans of the lamprey. Hence, although the duplication generating the ancestors of biglycan and decorin genes occurred after the divergence of agnathans but before the emergence of teleosts, only decorin acquired its characteristic properties in the bony fishes. The BGL gene presumably turned into a typical biglycan only in the tetrapod lineages. The presumed acquisitions of new functions appear to have been accompanied by changes in the evolutionary rate. Received: 13 April 2000 / Accepted: 4 July 2000     

The Complete Mitochondrial Genome of Rhea americana and Early Avian Divergences

The complete mitochondrial DNA, mtDNA, molecule of the greater rhea, Rhea americana, was sequenced. The size of the molecule is 16,710 nucleotides. The organization of the molecule conforms with that described for the chicken and the ostrich. It has been shown previously that relative to other vertebrates the NADH3 gene of the ostrich has an insertion of one nucleotide in position 174 of the gene. The same observation was made in the rhea and in the newly sequenced NADH3 gene of the emu, Dromaius novaehollandiae. Comparison with the NADH3 gene of the chicken and the rook suggests that the inserted nucleotide may be deleted by RNA editing. The divergence between the two struthioniform species, the ostrich and the rhea, was molecularly dated at ≈51 million years before present, MYBP. This dating is more recent than commonly acknowledged. Phylogenetic analysis of the complete cytochrome b genes of seven avian orders placed the Passeriformes basal in the avian tree with the Struthioniformes among the remaining Neognathae. These findings challenge the commonly accepted notion that the most basal avian divergence is that between the Palaeognathae and Neognathae. Received: 13 October 1997 / Accepted: 17 January 1998     

Timing of deep‐sea adaptation in dogfish sharks: insights from a supertree of extinct and extant taxa

Klug, S. & Kriwet, J. (2010). Timing of deep‐sea adaptation in dogfish sharks: insights from a supertree of extinct and extant taxa. —Zoologica Scripta, 39, 331–342. Dogfish sharks (Squaliformes) constitute a monophyletic group of predominantly deep‐water neoselachians, but the reasons and timing of their adaptation to this hostile environment remain ambiguous. Late Cretaceous dogfish sharks, which generally would be associated with deep‐water occur predominantly in shallow water environments. Did the end‐Cretaceous mass extinction event that eliminated large numbers of both terrestrial and aquatic taxa and clades including sharks trigger the evolutionary adaptation of present deep‐water dogfish sharks? Here, we construct, date, and analyse a genus‐level phylogeny of extinct and living dogfish sharks to bring a new perspective to this question. For this, eleven partial source trees of dogfish shark interrelationships were merged to create a comprehensive phylogenetic hypothesis. The resulting supertree is the most inclusive estimate of squaliform interrelationships that has been proposed to date containing 23 fossil and extant members of all major groups. ?Eoetmopterus represents the oldest dalatoid. ?Microetmopterus, ?Paraphorosoides, ?Proetmopterus and ?Squaliogaleus are stem‐group dalatoids in which bioluminescence most likely was not developed. According to our analyses, bioluminescence in dogfish sharks was already developed in the early Late Cretaceous indicating that these sharks adapted to deep‐water conditions most likely at about 100 Mya. The advantage of this reconstruction is that the fossil record is used directly for age node estimates rather than employing molecular clock approaches.     

Protein Tyrosine Kinase cDNAs from Amphioxus, Hagfish, and Lamprey: Isoform Duplications Around the Divergence of Cyclostomes and Gnathostomes

Animals evolved a variety of gene families involved in cell–cell communication and developmental control by gene duplication and domain shuffling. Each family is made up of several subtypes or subfamilies with distinct structures and functions, which diverged by gene duplications and domain shufflings before the divergence of parazoans and eumetazoans. Since the separation from protostomes, vertebrates expanded the multiplicity of members (isoforms) in the same subfamily by further gene duplications in their early evolution before the fish–tetrapod split. To know the dates of isoform duplications more closely, we have conducted isolation and sequencing cDNAs encoding the fibroblast growth factor receptor, Eph, src, and platelet-derived growth factor receptor subtypes belonging to the protein tyrosine kinase family from Branchiostoma belcheri, an amphioxus, Eptatretus burgeri, a hagfish, and Lampetra reissneri, a lamprey. From a phylogenetic tree of each subfamily inferred from a maximum likelihood (ML) method, together with a bootstrap analysis based on the ML method, we have shown that the isoform duplications frequently occurred in the early evolution of vertebrates around or just before the divergence of cyclostomes and gnathostomes by gene duplications and possibly chromosomal duplications. Received: 28 April 1998 / Accepted: 30 June 1999     

Phylogeny of Nematoda and Cephalorhyncha Derived from 18S rDNA

Phylogenetic relationships of nematodes, nematomorphs, kinorhynchs, priapulids, and some other major groups of invertebrates were studied by 18S rRNA gene sequencing. Kinorhynchs and priapulids form the monophyletic Cephalorhyncha clade that is the closest to the coelomate animals. When phylogenetic trees were generated by different methods, the position of nematomorphs appeared to be unstable. Inclusion of Enoplus brevis, a representative of a slowly evolving nematode lineage, in the set of analyzed species refutes the tree patterns, previously derived from molecular data, where the nematodes appear as a basal bilateral lineage. The nematodes seem to be closer to the coelomate animals than was speculated earlier. According to the results obtained, nematodes, nematomorphs, tardigrades, arthropods, and cephalorhynchs are a paraphyletic association of closely related taxa. Received: 1 December 1997 / Accepted: 9 April 1998     

Otx1 gene-controlled morphogenesis of the horizontal semicircular canal and the origin of the gnathostome characteristics

SUMMARY The horizontal semicircular canal of the inner ear is a unique feature of gnathostomes and is predated by the two vertical semicircular canals, which are already present in lampreys and some fossil, armored jawless vertebrates regarded as close relatives of gnathostomes. Inactivation in mice of the orthodenticle -related gene Otx1 results in the absence of this structure. In bony fishes and tetrapods (osteichthyans), this gene belongs to a small multigene family comprising at least two orthology classes, Otx1 and Otx2 . We report that, as in the mouse, xenopus and zebrafish, Otx1- and Otx2 -related genes are present in a chondrichthyan, the dogfish Scyliorhinus canicula , with an Otx1 expression domain in the otocyst very similar to those observed in osteichthyans. A strong correlation is thus observed in extant vertebrates between the distribution of the horizontal semicircular canal and the presence of an Otx1 ortholog expressed in the inner ear, which supports the hypothesis that the absence of this characteristic in Otx1 ^-/- mice may correspond to an atavism. The same conclusion applies to two other gnathostome-specific characteristics also deleted in Otx1 ^-/- mice, the utriculosaccular duct and the ciliary process. Together with functional analyses of Otx1 and Otx2 genes in mice and comparative analyses of the Otx gene families characterized in chordates, these discoveries lead to the hypothesis that some of the anatomic characteristics of gnathostomes have appeared quite suddenly and almost simultaneously in vertebrate evolution, possibly as a consequence of gene functional diversifications following duplications of an ancestral chordate gene.     

Evolution of the Mitochondrial Cytochrome Oxidase II Gene in Collembola

The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data. Received: 12 January 1996 / Accepted: 10 August 1996     

Fishery and Ontogenetic Driven Changes in the Diet of the Spiny Dogfish, Squalus acanthias, in Patagonian Waters, Argentina

The diet of the spiny dogfish in northern and central Patagonian waters was studied from the by-catch of the bottom trawling fisheries directed to Argentine hake Merluccius hubbsi and Argentine red shrimp Pleoticus muelleri between 1996 and 1998. Food habits were analyzed in relation to sex and maturity of sharks. Also, the relationship between diet and abundance of the main prey was explored. Intraspecific diet comparisons were performed. Differences in diet were found between immature individuals, mature males, and mature females. The Argentine shortfin squid Illex argentinus, the Argentine hake and ctenophores Pleurobrachia pileus were the most important prey for the spiny dogfish. Immature and small individuals were pelagic predators. After sexual maturity, the spiny dogfish shifted its diet. Mature and large individuals tended to reduce the consumption of ctenophores, and increase the consumption of demersal and benthic species. Previous diet studies on the spiny dogfish in 1984–1985 and 1994 indicated that the Argentine hake was the most important prey. In the present study, carried out in 1998, squid was the most important prey, followed by the hake. This diet change was related to the major decrease of hake due to overfishing and the increase of squid abundance between 1994 and 1999.