Polyphyly of the mail-cheeked fishes (Teleostei: Scorpaeniformes): evidence from mitochondrial and nuclear sequence data

Mitochondrial and nuclear DNA sequence data for 105 acanthomorph taxa are analyzed to address questions of scorpaeniform monophyly and relationships. The combination of 3425 aligned base pairs from the mitochondrial small subunit rDNA (12S), large subunit rDNA (16S), and tRNA-Val and the nuclear large subunit rDNA (28S), histone H3, and TMO-4c4 loci are analyzed. Representatives of all scorpaeniform suborders and 32 of 36 scorpaeniform families are included with most suborders represented by multiple species. In addition to 69 scorpaeniform taxa, 36 outgroup taxa, including representatives of most families previously conjectured to be related to the Scorpaeniformes, are analyzed due to serious concerns of scorpaeniform monophyly. The traditionally recognized scorpaeniform fishes are recovered as polyphyletic. The 13 representatives of the Atheriniformes, Blennioidei, Gasterosteoidei, Grammatidae, Notothenioidei, Percidae, Trichodontidae, and Zoarcoidei included in the analysis are all nested within the least inclusive clade that includes all traditionally recognized scorpaeniforms. The scorpaenoid lineage is widely polyphyletic, and its intrarelationships differed significantly from previous hypotheses. The cottoid lineage is paraphyletic with only the presence of the Trichodontidae, as the sister-taxon of the Cottoidei, disrupting the traditional subordinal hypothesis of relationships.     

Monophyly of the Citharidae (Pleuronectoidei: Pleuronectiformes: Teleostei) with considerations of pleuronectoid phylogeny

The monophyly of Citharidae, the pleuronectoid family thought to be a transitional group between the Psettodoidei and other typical pleuronectoids, has been in question mainly because of the lack of recognized synapomorphies for the family. In this study, the citharid skeleton is described, and the monophyly of the family and its phylogenetic position within the Pleuronectoidei are reassessed following a phylogenetic analysis based on 45 osteological, myological, and external characters. The Citharidae was found to represent a monophyletic group, supported by six synapomorphies (e.g., first dorsal proximal radials firmly wedged into notch of blind side lateral ethmoid; anterior dorsal proximal radials tightly mutually attached; blind side posterior nostril considerably enlarged). Two previously recognized subfamilies, sinistral Citharinae and dextral Brachypleurinae, are invalid because of their nonmonophylies. Interrelationships of the pleuronectoids shown herein are discussed. Received: February 19, 2001 / Revised: July 10, 2001 / Accepted: July 23, 2001     

An alternative hypothesis on the phylogenetic position of the family dactylopteridae (pisces: Teleostei), with a proposed new classification

The phylogenetic position of the family Dactylopteridae is inferred cladistically. The family lacks a close relationship with the Scorpaeniformes, owing to the posterior extension of the infraorbital in the former not being homologous with the scorpaeniform suborbital stay. Monophyly of the Dactylopteridae and percoid family Malacanthidae is supported by 20 synapomorphies, the former having a sister relationship with the malacanthid genusHoplolatilus supported by three synapomorphies. The former Dactylopteridae plus Malacanthidae are redefined as a percoid family. Dactylopteridae. being subdivided into the following four subfamilies: Branchiosteginae (includingBranchiostegus andLopholatilus), Malacanthinae (Caulolatilus andMalacanthus), Hoplolatilinae subfam. nov. (Hoplolatilus) and Dactylopterinae (Dactylopterus andDactyloptena).     

Morphology‐based phylogenetic analysis and classification of the family Rhinocryptidae (Aves: Passeriformes)

The family Rhinocryptidae comprises an assemblage of 12 genera and 55 species confined to the Neotropical region. Here we present the first morphology‐based phylogenetic study of the Rhinocryptidae, using 90 anatomical characters (62 osteological, 28 syringeal) scored for all genera of the family and representatives of all families of the infraorder Furnariides. Parsimony analysis of this dataset recovered 7428 equally most‐parsimonious trees. The strict consensus of those trees was completely resolved at the genus level, with the topology (Liosceles (Psilorhamphus ((Eleoscytalopus + Merulaxis) (Acropternis ((Teledromas + Rhinocrypta) ((Pteroptochos + Scelorchilus) (Eugralla (Myornis + Scytalopus)))))))). The monophyly of the Rhinocryptidae as presently understood was recovered with strong support [eight synapomorphies and Bremer support (BS) = 6). Strongly supported internal arrangements included the basal position of the Amazonian genus Liosceles relative to the rest of the family (four synapomorphies, BS = 4), a clade containing Acropternis through Scytalopus (six synapomorphies, BS = 4), and other less inclusive nodes. The main points of congruence between the present morphological phylogeny and previous molecular phylogenetic work on the family were clades supported by six or more synapomorphies and Bremer values of 6–7: Eleoscytalopus + Merulaxis (eight synapomorphies, BS = 6), Scelorchilus + Pteroptochos (seven synapomorphies, BS = 7), Rhinocrypta + Teledromas (seven synapomorphies, BS = 7), and Eugralla + Myornis + Scytalopus (six synapomorphies, BS = 6). A classification derived from the morphological phylogeny is proposed, with new suprageneric taxa being named and diagnosed. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 377–432.     

Phylogenetic systematic evaluation of a classification of the Zoogonidae Odhner, 1902 (Cercomeria: Trematoda: Digenea: Plagiorchiiformes)

A recent systematic study of the digenean family Zoogonidae presented a series of cladograms, which are the product of phylogenetic systematic, or cladistic, analysis. However, one of the two subfamilies and nine of the 21 genera recognised in that study lacked putative synapomorphies, a requirement for phylogenetic systematic studies. This study presents a re-analysis of the database for the zoogonids, based on rigorous application of phylogenetic systematic methods. A new phylogenetic tree is presented, which better fits the original data than the published tree (with a consistency index of 52.3% vs. 46.3%). Four subfamilies, three monophyletic and one of uncertain status, and 10 genera could be recognised phylogenetically. This would affect the nomenclatorial status of one-third (26) of the species in the family. However, it is recommended that another analysis, based on more characters, be carried out before nomenclatorial changes are proposed.     

Hemoglobin structure/function and globin-gene evolution in the Arctic fish Liparis tunicatus

The importance of the Arctic, in contributing to the knowledge of the overall ensemble of adaptive processes influencing the evolution of marine organisms, calls for investigations on molecular adaptations in Arctic fish. Unlike the vast majority of Antarctic Notothenioidei, several Arctic species display high hemoglobin multiplicity. The blood of four species, the spotted wolffish of the family Anarhichadidae and three Gadidae, contains three functionally distinct major components. Similar to many Antarctic notothenioids, Arctic Liparis tunicatus (suborder Cottoidei, family Liparidae) has one major hemoglobin (Hb 1) accompanied by a minor component (Hb 2). This paper reports the structural and functional characterisation of Hb 1 of L. tunicatus. This hemoglobin shows low oxygen affinity, and pronounced Bohr and Root effects. The amino-acid sequence of the beta chain displays an unusual substitution in NA2 (beta2) at the phosphate-binding site, and the replacement of Val E11 (beta67) with Ile. Similar to some Antarctic fish Hbs, electron paramagnetic resonance spectra reveal the formation of a ferric penta-coordinated species even at physiological pH. The amino-acid sequences have also been used to gain insight into the evolutionary history of globins of polar fish. L. tunicatus globins appear close to the notothenioid clades as predicted by teleostean phylogenies. Close phylogenetic relationships between Cottoidei and Notothenioidei, together with their life style, seem to be the main factor driving the globin-sequence evolution.     

Reassignment of Lamanema from Nematodirinae to Molineinae (Nematoda: Trichostronglyloidea)

The monospecific Lamanema historically has been assigned to the Nematodirinae within the Molineidae. Inconsistencies in morphological characters, within a phylogenetic context for Nematodirinae, led to a re-evaluation of the putative relationships and taxonomic placement of Lamanema. Among 7 putative synapomorphies for Nematodirinae, Lamanema possesses only 1, large eggs. Large eggs, sporadically present in phylogenetically disparate taxa of trichostrongyles, are equivocal with respect to placement of Lamanema; it is considered that possession of this single homoplasious character alone is insufficient justification to retain the genus in Nematodirinae. Affinities with the Trichostrongylidae (Cooperiinae or Haemonchinae) have also been proposed; however, Lamanema possess neither of 2 synapomorphies that diagnose monophyly of the family. Lamanema is retained in the Molineidae and transferred to the Molineinae as it possesses all characters of the family as currently defined. The origin of Lamanema represents a secondary colonization of ruminants by molineids and provides no context for elucidating the history of the Nematodirinae and Nematodirus.     

Phylogenetic placement of the Spirosomaceae

Comparative analysis of 16S rRNA sequences shows that the family Spirosomaceae belongs within the eubacterial phylum defined by the flavobacteria and bacteriodes. Its constituent genera, Spirosoma, Flectobacillus, and Runella form a monophyletic grouping therein. The phylogenetic assignment is based not only upon evolutionary distance analysis, but also upon sequence signatures and higher order structural synapomorphies in 16S rRNA. Another genus peripherally associated with the Spirosomaceae, Ancylobacter ("Microcyclus"), does not cluster with the flavobacteria and their relatives, but rather belongs to the alpha subdivision of the purple bacteria.     

Comparative osteology of <Emphasis Type="Italic">Bathylutichthys balushkini</Emphasis> and relationship of the family Bathylutichthyidae (Cottoidei)

The structure of skeleton of Bathylutichthys balushkini was studied and comparative analysis of it with representatives of other families of the suborder Cottoidei was performed. It was found that Bathylutichthyidae are characterized by the presence of a great number of original characters supporting its family status. They include: absence of mesethmoideum; bony canals of seismosensory system on frontale, pteroticum, and parietale and their strong reduction on infraorbitale; and absence of pterosphenoideum, intercalare, pharyngobranchiale 2, and basihyale. At the same time, Bathylutichthyidae retain a considerable number of generalized specific features: location of parietalia laterally to supraoccipitale and absence of their joint between themselves, presence of mesoptergoideum and basibranchialia 2 and 3. Cladistic analysis based on osteological characters and characters of the seismosensory system of 11 families of Cottoidei demonstrates that Bathylutichthyidae are combined into one group with families Rhamphocottidae, Agonidae, Psychrolutidae, Cyclopteridae, and Liparidae occupying an intermediate position between Psychrolutidae and the two last families. The cladogram obtained does not support the point of view of existence in the suborder Cottoidei of an independent superfamily Cyclopteroidea, including families Liparidae and Cyclopteridae.     

Osteology and myology of the cephalic region and pectoral girdle of Erethistes pusillus, comparison with other erethistids, and comments on the synapomorphies and phylogenetic relationships of the Erethistidae (Teleostei: Siluriformes)

The cephalic and pectoral girdle structures of the erethistid Erethistes pusillus (Erethistinae) are described and compared with those of another species of the subfamily Erethistinae, namely Hara filamentosa , and of the single species of the subfamily Continae, Conta conta , as well as of several other catfishes, as the foundation for a discussion on the synapomorphies and phylogenetic position of the Erethistidae. The observations and comparisons support de Pinna's phylogenetic hypothesis, according to which the Erethistidae is the sister‐group of the Aspredinidae, with the clade formed by these two families being the sister‐group of the Sisoridae sensu stricto . In addition, the observations and comparisons pointed out a new, additional character to diagnose the family Erethistidae, namely: mesocoracoid arch deeply bifurcated dorsally.     

Comparative characteristic of feeding of three species of cottoidei in the littoral of southern Baikal (Cape Berezovyi)

Comparison of the diet and analysis of the size composition of food items in three species of Baikal Cottoidei that inhabit the littoral of southern Baikal (Cape Berezovyi) were performed. The food of the studied species is represented by a wide range of bottom organisms, among which bottom amphipods play a dominant role in all fish. A comprehensive analysis of food composition indicated that the divergence of trophic niches in Cottoidei results from the consumption of different size groups, and, correspondingly, of species of amphipods. The relation between the sizes of prey and the mouth apparatus of the predator is considered as one of the basic reasons of size selectivity. It is shown that the range of the size spectrum of prey in Cottoidei is determined by parameters of the mouth opening in the predator.     

Multi-gene analysis provides a well-supported phylogeny of Rosales

Despite many attempts to resolve evolutionary relationships among the major clades of Rosales, some nodes have been extremely problematic and have remained unresolved. In this study, we use two nuclear and 10 plastid loci to infer phylogenetic relationships among all nine families of Rosales. Rosales were strongly supported as monophyletic; within Rosales all family relationships are well-supported with Rosaceae sister to all other members of the order. Remaining Rosales can be divided into two subclades: (1) Ulmaceae are sister to Cannabaceae plus (Urticaceae+Moraceae); (2) Rhamnaceae are sister to Elaeagnaceae plus (Barbeyaceae+Dirachmaceae). One noteworthy result is that we recover the first strong support for a sister relationship between the enigmatic Dirachmaceae and Barbeyaceae. These two small families have distinct morphologies and potential synapomorphies remain unclear. Future studies should try to identify nonDNA synapomorphies uniting Barbeyaceae with Dirachmaceae.     

The monophyly of the Characidiinae, a Neotropical group of characiform fishes (Teleostei: Ostariophysi)

Although virtually no phylogenetic evidence (in the sense advocated by Hennig, 1966) had been previously presented to support the monophyly of the Characidiinae, and most 'diagnostic' characters used by previous authors were found to be unacceptable in a cladistic classification, i t is still possible to diagnose the Characidiinae in a phylogenetic sense. This study revealed the existence of 13 synapomorphies supporting the monophyly of the group. Several of these synapomorphies, such as the modifications associated with the mesethmoid, the jaw bones, and the ribs of the fifth vertebra, are unique to the Characidiinae, thus providing a solid basis for recognizing the group as a monophyletic unit of characiform fishes. Demonstration of characidiin monophyly provides a solid foundation for further phylogenetic analysis of characidiin interrelationships, and higher level relationships among characiform fishes.     

Underlying Synapomorphies and Anagenetic Analysis

Evaluations of holomorphological similarities are based on synapomorphies, symplesiomorphies, convergence, and parallelisms as results of parallel selection and of underlying synapomorphies respectively. Only synapomorphies and underlying synapomorphies can show genealogical relationships. Distinctions between parallel selections and underlying synapomorphies are of major phylogenetic importance, while distinctions between different evolutionary histories (eu-parallelisms and pseudo-parallelisms) are not. The circumstance when underlying synapomorphies are of special phylogenetic importance has been termed unique inside-parallelism. Three such unique inside-parallelisms are found in the female genitalia of the Chironomidae, where they are shown necessary for the understanding of subfamily relationships. — The first minimum criterion for recognizing synapomorphy (Schlee 1971) is corrected to: It should be present within the whole group or clearly secondarily reduced an apomorphic taxa. It should not be present in the same formation in any taxon outside the group which can be regarded as a possible sister group. — The anagenetic component of the evolutionary processes can, following a cladistic analysis, be calculated by means of the adjusted evolution index assigning the different recognizable steps of trends or morphocline number from 1 to 2 and calculating the arithmetic mean of all numbers. Examples from Chaoboridae and Chironomidae support the cladistic diagrams and point out that different stages belong to differing "grades". Methods of numerical taxonomy may give a finer gradation of anagenetic levels.     

Phylogenetic interrelationships of the eel families Derichthyidae and Colocongridae (Elopomorpha: Anguilliformes) based on the pectoral skeleton

A cladistic analysis of the eel families Derichthyidae and Colocongridae is herein proposed for the first time on the basis of morphological data. We discovered dozens of new phylogenetic characters derived from a detailed analysis of the pectoral skeleton, an anatomical system neglected by most previous studies. Our maximum parsimony analysis indicates that Colocongridae sensu lato is paraphyletic, with its two constituent genera Coloconger and Congriscus appearing as successive sister groups of derichthyids. Monophyly of the family Derichthyidae, which has been questioned by some studies, is herein strongly supported by 10 unambiguous synapomorphies. We also stress the importance of the appendicular skeleton as a useful source of phylogenetic information for the resolution of systematic problems within Anguilliformes.     

Redefinition and phylogenetic relationships of the family Pinguipedidae (Teleostei: Perciformes)

The phylogenetic relationships of the family Pinguipedidae plus the genus Cheimarrichthys von Haast, 1874, were studied to redefine the family. Based on a phylogenetic analysis using derived characters belonging to 21 transformation series, accepting the monophyly of Pinguipedidae plus Cheimarrichthys provisionally for the operational procedure of the analysis, it was hypothesized that Cheimarrichthys is not closely related to Parapercis Bleeker, 1863, although these genera had been considered as having a close affinity. Although the Pinguipedidae and Cheimarrichthys share nine derived characters, it was determined that these characters are also found in other trachinoid families. In addition, several families, such as the Leptoscopidae, Uranoscopidae, and Trichodontidae, have many more derived characters in common with Cheimarrichthys than the pinguipedids have with that genus. The conclusion drawn here is that it is not parsimonious to recognize the monophyly of the Pinguipedidae and Cheimarrichthys based on these nine derived characters, and that these characters are not compelling enough to link these groups. The redefined Pinguipedidae is proposed to include the following five genera: Parapercis, Prolatilus Gill, 1865, Pinguipes Cuvier, 1829, Pseudopercis de Miranda-Ribeiro, 1903, and Kochichthys Kamohara, 1960. Cheimarrichthys, excluded from the Pinguipedidae, is put into its own family, Cheimarrichthyidae.     

Osteology and myology of the cephalic region and pectoral girdle of Pimelodus blochii, comparison with other pimelodines, and comments on the synapomorphies and phylogenetic relationships of the Pimelodinae (Ostariophysi: Siluriformes)

The cephalic and pectoral girdle structures of the pimelodin Pimelodus blochii (Pimelodus group) are described and compared to those of representatives of the two other main pimelodin groups, namely Calophysus macropterus (Calophysus group) and Pseudoplatystoma fasciatum (Sorubim group), and of a representative of the peculiar pimelodin genus Hypophthalmus, H. edentatus, and several other catfishes, as the foundation for a discussion on the synapomorphies and phylogenetic relationships of the Pimelodinae. Three new, additional potential synapomorphies to support the monophyly of the Pimelodinae are pointed out: (1) presence of a 'muscle 1 of the mandibular barbels' running from the antero-ventro-mesial surface of the cartilaginous plates carrying these barbels to the dentaries; (2) presence of a muscle tensor tripodis running from the posterior surface of the neurocranium to the dorsal surface of the swimbladder near the tripus; and (3) presence of a 'drumming muscle of the swimbladder' running from the parapophyses of the fourth vertebra and, eventually, the posterior surface of the neurocranium, to the antero and antero-ventral surface of the swimbladder. The subfamilies Pimelodinae, Heptapterinae and Pseudopimelodinae seem to constitute a monophyletic assemblage, thus contradicting the commonly accepted idea that the family Pimelodidae is a polyphyletic clade.     

Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression

The Rhinella granulosa group consists of 13 species of toads distributed throughout open areas of South America and Panama. In this paper we perform a phylogenetic analysis considering all but one species of the group, employing five nuclear and four mitochondrial genes, for up to 7910 bp per specimen. Separate phylogenetic analyses under direct optimization (DO) of nuclear and mitochondrial sequences recovered the R. granulosa group as monophyletic and revealed topological incongruence that can be explained mainly by multiple events of hybridization and introgression, both mitochondrial and nuclear. The DO combined analysis, after the exclusion of putatively introgressed or heterozygous genomes, resulted in a phylogenetic hypothesis for the R. granulosa group in which most of the species are recovered as monophyletic, but with interspecific relationships poorly supported. The optimization of morphological (adult and larval), chromosomal, and behavioural characters resulted in 12 putative phenotypic synapomorphies for this species group and some other synapomorphies for internal clades. Our results indicate the need for additional population genetic studies on R. dorbignyi and R. fernandezae to corroborate the taxonomic status of both taxa. Finally, we discuss biological and genetic characteristics of Bufonidae, as possible explanations for the common occurrence of hybridization and introgression observed in some lineages of this family.