Integration of morphological data sets for phylogenetic analysis of Amniota: the importance of integumentary characters and increased taxonomic sampling

Several mutually exclusive hypotheses have been advanced to explain the phylogenetic position of turtles among amniotes. Traditional morphology-based analyses place turtles among extinct anapsids (reptiles with a solid skull roof), whereas more recent studies of both morphological and molecular data support an origin of turtles from within Diapsida (reptiles with a doubly fenestrated skull roof). Evaluation of these conflicting hypotheses has been hampered by nonoverlapping taxonomic samples and the exclusion of significant taxa from published analyses. Furthermore, although data from soft tissues and anatomical systems such as the integument may be particularly relevant to this problem, they are often excluded from large-scale analyses of morphological systematics. Here, conflicting hypotheses of turtle relationships are tested by (1) combining published data into a supermatrix of morphological characters to address issues of character conflict and missing data; (2) increasing taxonomic sampling by more than doubling the number of operational taxonomic units to test internal relationships within suprageneric ingroup taxa; and (3) increasing character sampling by approximately 25% by adding new data on the osteology and histology of the integument, an anatomical system that has been historically underrepresented in morphological systematics. The morphological data set assembled here represents the largest yet compiled for Amniota. Reevaluation of character data from prior studies of amniote phylogeny favors the hypothesis that turtles indeed have diapsid affinities. Addition of new ingroup taxa alone leads to a decrease in overall phylogenetic resolution, indicating that existing characters used for amniote phylogeny are insufficient to explain the evolution of more highly nested taxa. Incorporation of new data from the soft and osseous components of the integument, however, helps resolve relationships among both basal and highly nested amniote taxa. Analysis of a data set compiled from published sources and data original to this study supports monophyly of Amniota, Synapsida, Reptilia, Parareptilia, Eureptilia, Eosuchia, Diapsida, Neodiapsida, Sauria, Lepidosauria, and Archosauriformes, as well as several more highly nested divisions within the latter two clades. Turtles are here resolved as the sister taxon to a monophyletic Lepidosauria (squamates + Sphenodon), a novel phylogenetic position that nevertheless is consistent with recent molecular and morphological studies that have hypothesized diapsid affinities for this clade.     

MicroRNAs support a turtle + lizard clade

Despite much interest in amniote systematics, the origin of turtles remains elusive. Traditional morphological phylogenetic analyses place turtles outside Diapsida-amniotes whose ancestor had two fenestrae in the temporal region of the skull (among the living forms the tuatara, lizards, birds and crocodilians)-and allied with some unfenestrate-skulled (anapsid) taxa. Nonetheless, some morphological analyses place turtles within Diapsida, allied with Lepidosauria (tuatara and lizards). Most molecular studies agree that turtles are diapsids, but rather than allying them with lepidosaurs, instead place turtles near or within Archosauria (crocodilians and birds). Thus, three basic phylogenetic positions for turtles with respect to extant Diapsida are currently debated: (i) sister to Diapsida, (ii) sister to Lepidosauria, or (iii) sister to, or within, Archosauria. Interestingly, although these three alternatives are consistent with a single unrooted four-taxon tree for extant reptiles, they differ with respect to the position of the root. Here, we apply a novel molecular dataset, the presence versus absence of specific microRNAs, to the problem of the phylogenetic position of turtles and the root of the reptilian tree, and find that this dataset unambiguously supports a turtle + lepidosaur group. We find that turtles and lizards share four unique miRNA gene families that are not found in any other organisms' genome or small RNA library, and no miRNAs are found in all diapsids but not turtles, or in turtles and archosaurs but not in lizards. The concordance between our result and some morphological analyses suggests that there have been numerous morphological convergences and reversals in reptile phylogeny, including the loss of temporal fenestrae.     

Turtle origins: insights from phylogenetic retrofitting and molecular scaffolds

Adding new taxa to morphological phylogenetic analyses without substantially revising the set of included characters is a common practice, with drawbacks (undersampling of relevant characters) and potential benefits (character selection is not biased by preconceptions over the affinities of the ‘retrofitted’ taxon). Retrofitting turtles (Testudines) and other taxa to recent reptile phylogenies consistently places turtles with anapsid‐grade parareptiles (especially Eunotosaurus and/or pareiasauromorphs), under both Bayesian and parsimony analyses. This morphological evidence for turtle–parareptile affinities appears to contradict the robust genomic evidence that extant (living) turtles are nested within diapsids as sister to extant archosaurs (birds and crocodilians). However, the morphological data are almost equally consistent with a turtle–archosaur clade: enforcing this molecular scaffold onto the morphological data does not greatly increase tree length (parsimony) or reduce likelihood (Bayesian inference). Moreover, under certain analytic conditions, Eunotosaurus groups with turtles and thus also falls within the turtle–archosaur clade. This result raises the possibility that turtles could simultaneously be most closely related to a taxon traditionally considered a parareptile (Eunotosaurus) and still have archosaurs as their closest extant sister group.     

The phylogenetic relationships among non-diplomystid catfishes as inferred from mitochondrial cytochrome b sequences; the search for the ictalurid sister taxon (Otophysi: Siluriformes)

The relationships among families of catfishes are poorly understood and have yet to be the subject of a comprehensive investigation with molecular data. Existing phylogenetic hypotheses are based on morphological data and incompletely resolved. This study analyzed complete sequences of mitochondrial gene cytochrome b for 170 species from 29 of 33 extant families, and focused on the relationships of Ictaluridae to other catfishes. In addition to previous phylogenetic studies, the fossil record, paleogeography, biogeography, and distribution of extant catfish families collectively suggest the location (if extant) of the ictalurid sister taxon to be Northern or Eastern Asia. Of the extant catfishes currently native to this area and included in this analysis, parsimony and Bayesian likelihood analyses recovered Cranoglanis bouderius as the most proximal sister taxon of Ictaluridae. Seemingly, ictalurids and cranoglanidids represent another biogeographic component linking freshwater fishes of North America and eastern Asia, e.g., catostomids and paddlefishes. The results coupled with present-day catfish distributions and inferences from the fossil record collectively suggest the ancestor of Ictaluridae to have invaded freshwaters of North America at the close of the Cretaceous through northeastern Asia and northwestern North America. Other superfamilial nodes supported the results of previous phylogenetic studies of narrower taxonomic scope. Several novel relationships were recovered (including a clade composed of Pimelodidae, Pseudopimelodidae, and Heptapteridae) and these along with sources of systematic error are discussed. A broad sampling of Bagridae permitted an examination of intergeneric relationships within this family and in light of recent morphological and molecular studies.     

A reevaluation of early amniote phylogeny

A new phylogenetic analysis of early amniotes based on 124 characters and 13 taxa (including three outgroups) indicates that synapsids are the sister-group of all other known amniotes. The sister-group of Synapsida is Sauropsida, including Mesosauridae and Reptilia as its two main subdivisions. Reptilia is divided into Parareptilia and Eureptilia. Parareptilia includes Testudines and its fossil relatives (Procolophonidae, Pareiasauria and Millerettidae), while Eureptilia includes Diapsida and its fossil relatives (Pakothyris and Captorhinidae). Parts of the phylogeny are robust, such as the sister-group relationship between procolophonids and testudines, and between pareiasaurs and the testudinomorphs (the clade including procolophonids and testudines). Other parts of the new tree are not so firmly established, such as the position of mesosaurs as the sister-group of reptiles. The new phylogeny indicates that three major clades of amniotes extend from the present to the Palaeozoic. These three clades are the Synapsida (including Mammalia), Parareptilia (including Testudines), and Eureptilia (including Sauria). In addition, the Procolophonidae, a group of Triassic parareptiles, are the sister-group of Testudines.     

The position of Cetacea within mammalia: phylogenetic analysis of morphological data from extinct and extant taxa

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.     

The emergence of cetaceans: phylogenetic analysis of male social behaviour supports the Cetartiodactyla clade

The phylogeny of cetaceans is still unresolved. Two hypotheses prevail for the position of cetaceans among ungulates. The first hypothesis shows that Artiodactyla is monophyletic and is sister taxon to a clade composed of cetaceans and mesonychians. The second one shows that Artiodactyla is paraphyletic and contains Cetacea that is sister taxon of Hippopotamida. These hypotheses are based on fossil records and molecular studies. The behaviour of extant species can provide as much phylogenetic information as other classical parameters. I considered the behaviour observed during male agonistic interactions in placental mammals in order to determine which of these hypotheses was supported by the behaviour of extant species. Headbutting was only observed in ruminants, hippopotamids and cetaceans, supporting the paraphyletic nature of Artiodactyla. Primitive ruminants (tragulids) and two genera of ruminants (Moschus and Oreamnos) were not observed headbutting. These secondary losses were only present in 6.25% of the 48 surveyed ruminant genera. Head-to-head attacks emerged in pigs, which have developed dermal protusions. Yet, these confrontations are not based on mutual blow delivery. The behavioural evidence supports the inclusion of cetaceans in Artiodactyla.     

Jaw musculature during the dawn of turtle evolution

Using a new approach to study muscle anatomy in vertebrates, the fully differentiated jaw musculature of 42 turtle species was studied and character mappings were performed. Soft tissue arrangements were correlated to the temporal openings (emarginations) of the skull and the trochlearis system of the jaw apparatus among turtle taxa. When compared to the cranial anatomy of stem Testudines, most characters detected as diagnostic of particular extant groups have to be considered as being evolved first within Testudines. Hence, jaw muscle anatomy of extant turtles is difficult to compare to that of other reptilian taxa. Moreover, the high number of apomorphic character changes speaks for a divergating turtle and saurian morphotype of jaw musculature, which could indicate either a position of turtles outside of Sauria or a highly derived, undetectable origin within that group. In general, a low direct correlation of most soft and hard tissue characters was detected. This finding could imply that both character complexes are more integrated to each other driven by functional morphology; i.e., the composition of muscle fibre types. That condition highlights the difficulty in using gross anatomy of jaw muscle characters to interpret temporal bone arrangements among amniotes in general.     

A new lizard-like reptile (Diapsida: Lepidosauromorpha) from the Middle Jurassic of England

The Middle Jurassic (Late Bathonian) Mammal Bed at Kirtlington, Oxfordshire, has yielded a rich assemblage of small vertebrates including mammals, frogs, salamanders and small reptiles. This paper describes the skull of a new diapsid reptile, Marmorelta oxoniensis, which was common within the fauna. The skull is gracile with large orbits and relatively long external nares. The frontals and parietals are single in the adult and almost separated on the roof of the skull by the postfrontals. The temporal region shows a mosaic of primitive and derived character states. The quadrate was firmly held to the skull by a large squamosal and a small, free, quadratojugal was retained. However, reduction of the anterior process of the quadratojugal and of the posterior process of the jugal left the lower temporal fenestra broadly open. Comparison with other diapsids leads to the conclusion that Marmoretta was a lepidosauromorph, most probably the sister taxon of Lepidosauria.     

Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa

Recent discoveries of new fossil hominid species have been accompanied by several phylogenetic hypotheses. All of these hypotheses are based on a consideration of hominid craniodental morphology. However, Collard and Wood (2000) suggested that cladograms derived from craniodental data are inconsistent with the prevailing hypothesis of ape phylogeny based on molecular data. The implication of their study is that craniodental characters are unreliable indicators of phylogeny in hominoids and fossil hominids but, notably, their analysis did not include extinct species. We report here on a cladistic analysis designed to test whether the inclusion of fossil taxa affects the ability of morphological characters to recover the molecular ape phylogeny. In the process of doing so, the study tests both Collard and Wood's (2000) hypothesis of character reliability, and the several recently proposed hypotheses of early hominid phylogeny. One hundred and ninety-eight craniodental characters were examined, including 109 traits that traditionally have been of interest in prior studies of hominoid and early hominid phylogeny, and 89 craniometric traits that represent size-corrected linear dimensions measured between standard cranial landmarks. The characters were partitioned into two data sets. One set contained all of the characters, and the other omitted the craniometric characters. Six parsimony analyses were performed; each data set was analyzed three times, once using an ingroup that consisted only of extant hominoids, a second time using an ingroup of extant hominoids and extinct early hominids, and a third time excluding Kenyanthropus platyops. Results suggest that the inclusion of fossil taxa can play a significant role in phylogenetic analysis. Analyses that examined only extant taxa produced most parsimonious cladograms that were inconsistent with the ape molecular tree. In contrast, analyses that included fossil hominids were consistent with that tree. This consistency refutes the basis for the hypothesis that craniodental characters are unreliable for reconstructing phylogenetic relationships. Regarding early hominids, the relationships of Sahelanthropus tchadensis and Ardipithecus ramidus were relatively unstable. However, there is tentative support for the hypotheses that S. tchadensis is the sister taxon of all other hominids. There is support for the hypothesis that A. anamensis is the sister taxon of all hominids except S. tchadensis and Ar. ramidus. There is no compelling support for the hypothesis that Kenyanthropus platyops shares especially close affinities with Homo rudolfensis. Rather, K. platyops is nested within the Homo + Paranthropus + Australopithecus africanus clade. If K. platyops is a valid species, these relationships suggest that Homo and Paranthropus are likely to have diverged from other hominids much earlier than previously supposed. There is no support for the hypothesis that A. garhi is either the sister taxon or direct ancestor of the genus Homo. Phylogenetic relationships indicate that Australopithecus is paraphyletic. Thus, A. anamensis and A. garhi should be allocated to new genera.     

Molecular paleobiological insights into the origin of the Brachiopoda

Most studies of brachiopod evolution have been based on their extensive fossil record, but molecular techniques, due to their independence from the rock record, can offer new insights into the evolution of a clade. Previous molecular phylogenetic hypotheses of brachiopod interrelationships place phoronids within the brachiopods as the sister group to the inarticulates, whereas morphological considerations suggest that Brachiopoda is a monophyletic group. Here, these hypotheses were tested with a molecular phylogenetic analysis of seven nuclear housekeeping genes combined with three ribosomal genes. The combined analysis finds brachiopods to be monophyletic, but with relatively weak support, and the craniid as the sister taxon of all other brachiopods. Phylogenetic-signal dissection suggests that the weak support is caused by the instability of the craniid, which is attracted to the phoronids. Analysis of slowly evolving sites results in a robustly supported monophyletic Brachiopoda and Inarticulata (Linguliformea+Craniiformea), which is regarded as the most likely topology for brachiopod interrelationships. The monophyly of Brachiopoda was further tested with microRNA-based phylogenetics, which are small, noncoding RNA genes whose presence and absence can be used to infer phylogenetic relationships. Two novel microRNAs were characterized supporting the monophyly of brachiopods. Congruence of the traditional molecular phylogenetic analysis, microRNAs, and morphological cladograms suggest that Brachiopoda is monophyletic with Phoronida as its likely sister group. Molecular clock analysis suggests that extant phoronids have a Paleozoic divergence despite their conservative morphology, and that the early brachiopod fossil record is robust, and is not affected by taphonomic factors relating to the late-Precambrian/early-Cambrian phosphogenic event.     

A phylogenetic hypothesis for Asilidae based on a total evidence analysis of morphological and DNA sequence data (Insecta: Diptera: Brachycera: Asiloidea)

An hypothesis of phylogenetic relationships of Asilidae and its constituent taxa is presented, combining morphological and DNA sequence data in a total evidence framework. It is based on 77 robber fly species, 11 Asiloidea outgroup species, 211 morphological characters of the adult fly, and approximately 7300 bp of nuclear DNA from five genes (18S and 28S rDNA, AATS, CAD, and EF-1α protein-encoding DNA). The equally weighted, simultaneous parsimony analysis under dynamic homology in POY resulted in a single most parsimonious cladogram with a cost of 27,582 (iterative pass optimization; 27,703 under regular direct optimization). Six of the 12 included subfamily taxa are recovered as monophyletic. Trigonomiminae, previously always considered as monophyletic based on morphology, is shown to be non-monophyletic. Two of the three Trigonomiminae genera, Holcocephala Jaennicke, 1867 and Rhipidocephala Hermann, 1926, group unexpectedly as the sister taxon to all other Asilidae. Laphriinae, previously seen in the latter position, is the sister group of the remaining Asilidae. Five other subfamily taxa, i.e. Brachyrhopalinae, Dasypogoninae, Stenopogoninae, Tillobromatinae, and Willistonininae, are also shown to be non-monophyletic. The phylogenetic relationships among the higher-level taxa are partly at odds with findings of a recently published morphological study based on more extensive taxon sampling. The total evidence hypothesis is considered as the most informative one, but the respective topologies from the total-evidence, morphology-only, and molecular-only analyses are compared and contrasted in order to discuss the signals from morphological versus molecular data, and to analyze whether the molecular data outcompete the fewer morphological characters. A clade Apioceridae+Mydidae is corroborated as the sister taxon to Asilidae.     

Nuclear gene phylogeny of narrow-mouthed toads (Family: Microhylidae) and a discussion of competing hypotheses concerning their biogeographical origins

The family Microhylidae has a large circumtropic distribution and contains about 400 species in a highly subdivided taxonomy. Relationships among its constituent taxa remained controversial due to homoplasy in morphological characters, resulting in conflicting phylogenetic hypotheses. A phylogeny based on four nuclear genes (rag-1, rag-2, tyrosinase, BDNF) and one mitochondrial gene (CO1) of representatives of all currently recognized subfamilies uncovers a basal polytomy between several subfamilial clades. A sister group relationship between the cophylines and scaphiophrynines is resolved with moderate support, which unites these endemic Malagasy taxa for the first time. The American members of the subfamily Microhylinae are resolved to form a clade entirely separate from the Asian members of that subfamily. Otophryne is excluded from the subfamily Microhylinae, and resolved as a basal taxon. The placement of the Asian dyscophine Calluella nested within the Asian Microhyline clade rather than with the genus Dyscophus is corroborated by our data. Bayesian estimates of the divergence time of extant Microhylidae (47-90 Mya) and among the subclades within the family are discussed in frameworks of alternative possible biogeographic scenarios.     

Morphological evidence for sister group relationship between flamingos (Aves: Phoenicopteridae) and grebes (Podicipedidae)

A recent molecular analysis strongly supported sister group relationship between flamingos (Phoenicopteridae) and grebes (Podicipedidae), a hypothesis which has not been suggested before. Flamingos are long-legged filter-feeders whereas grebes are morphologically quite divergent foot-propelled diving birds, and sister group relationship between these two taxa would thus provide an interesting example of evolution of different feeding strategies in birds. To test monophyly of a clade including grebes and flamingos, I performed a cladistic analysis of 70 morphological characters which were scored for 17 taxa. Parsimony analysis of these data supported monophyly of the taxon (Podicipedidae + Phoenicopteridae) and the clade received high bootstrap support. Previously overlooked morphological, oological and parasitological evidence is recorded which supports this hypothesis, and which makes the taxon (Podicipedidae + Phoenicopteridae) one of the best supported higher-level clades within modern birds. The phylogenetic significance of some fossil flamingo-like birds is discussed. The Middle Eocene taxon Juncitarsus is most likely the sister taxon of the clade (Podicipedidae + (Palaelodidae + Phoenicopteridae)) although resolution of its exact systematic position awaits revision of the fossil material. Contrary to previous assumptions, it is more parsimonious to assume that flamingos evolved from a highly aquatic ancestor than from a shorebird-like ancestor.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 157–169.     

Deep molluscan phylogeny: synthesis of palaeontological and neontological data

The position of the earliest-derived living molluscs, the Polyplacophora (chitons) and shell-less vermiform Aplacophora, remains highly contentious despite many morphological, developmental and molecular studies of extant organisms. These two groups are thought to represent either a basal molluscan grade or a clade (Aculifera) sister to the 'higher' molluscs (Conchifera). These incompatible hypotheses result in very different predictions about the earliest molluscs. A new cladistic analysis incorporating both Palaeozoic and extant molluscs is presented here. Our results support the monophyly of Aculifera and suggest that extant aplacophorans and polyplacophorans both derive from a disparate group of multivalved molluscs in two major clades. Reanalysis of the critical Ordovician taxon 'Helminthochiton' thraivensis shows that this animal lacks a true foot despite bearing polyplacophoran-like valves. Its position within our phylogenetic reconstruction indicates that many fossil 'polyplacophorans' in the order Palaeoloricata are likely to represent footless stem-group aplacophorans. 'H.' thraivensis and similar forms such as Acaenoplax may be morphological stepping stones between chitons and the shell-less aplacophorans. Our results imply that crown-group molluscan synapomorphies include serial repetition, the presence of a foot, a mineralized scleritome and a creeping rather than worm-like mode of life.     

Classification and phylogeny of the diapsid reptiles

Reptiles with two temporal openings in the skull are generally divided into two groups–the Lepidosauria (lizards, snakes, Sphenodon , 'eosuchians') and the Archosauria (crocodiles, thecodontians, dinosaurs, pterosaurs). Recent suggestions that these two are not sister-groups are shown to be unproven, whereas there is strong evidence that they form a monophyletic group, the Diapsida, on the basis of several synapomorphies of living and fossil forms. A cladistic analysis of skull and skeletal characters of all described Permo-Triassic diapsid reptiles suggests some significant rearrangements to commonly held views. The genus Petrolacosaurus is the sister-group of all later diapsids which fall into two large groups–the Archosauromorpha (Pterosauria, Rhynchosauria, Prolacertiformes, Archosauria) and the Lepidosauromorpha (Younginiformes, Sphenodontia, Squamata). The pterosaurs are not archosaurs, but they are the sister-group of all other archosauromorphs. There is no close relationship between rhynchosaurs and sphenodontids, nor between Prolacerta or Tanystropheus and lizards. The terms 'Eosuchia', 'Rhynchocephalia' and 'Protorosauria' have become too wide in application and they are not used. A cladistic classification of the Diapsida is given, as well as a phylogenetic tree which uses cladistic and stratigraphic data.     

Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae)

Family level molecular phylogenetic analyses of cichlid fishes have generally suffered from a limited number of characters and/or poor taxonomic sampling across one or more major geographic assemblage, and therefore have not provided a robust test of early intrafamilial diversification. Herein we use both nuclear and mitochondrial nucleotide characters and direct optimization to reconstruct a phylogeny for cichlid fishes. Representatives of major cichlid lineages across all geographic assemblages are included, as well as nearly twice the number of characters as any prior family‐level study. In a strict consensus of 81 equally most‐parsimonious hypotheses, based on the simultaneous analysis of 2222 aligned nucleotide characters from two mitochondrial and two nuclear genes, four major subfamilial lineages are recovered with strong support. Etroplinae, endemic to Madagascar (Paretroplus) and southern Asia (Etroplus), is recovered as the sister taxon to the remainder of Cichlidae. Although the South Asian cichlids are monophyletic, the Malagasy plus South Asian lineages are not. The remaining Malagasy lineage, Ptychochrominae, is monophyletic and is recovered as the sister group to a clade comprising the African and Neotropical cichlids. The African (Pseudocrenilabrinae) and Neotropical (Cichlinae) lineages are each monophyletic in this reconstruction. The use of multiple molecular markers, from both mitochondrial and nuclear genes, results in a phylogeny that in general exhibits strong support, notably for early diversification events within Cichlidae. Results further indicate that Labroidei is not monophyletic, and that the sister group to Cichlidae may comprise a large and diverse assemblage of percomorph lineages. This hypothesis may at least partly explain why morphological studies that have attempted to place Cichlidae within Percomorpha, or that have tested cichlid monophyly using only “labroid” lineages, have met with only limited success. © The Willi Hennig Society 2004.     

Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks

Early morphological studies regarding the evolutionary history of elasmobranchs suggested sharks and batoids (skates and rays) were respectively monophyletic. More modern morphological cladistic studies, however, have tended to suggest that batoids are derived sharks, closely related to sawsharks and angelsharks, a phylogenetic arrangement known as the Hypnosqualea hypothesis. Very few molecular studies addressing interordinal relationships of elasmobranchs have been published; the few that do exist, are very limited in terms of both taxon representation and/or aligned sequence positions, and are insufficient to answer the question of whether batoids are derived sharks. The purpose of this study was to address this issue with more complete taxon representation, concomitant with a reasonable number of aligned sequence positions. The data set included a 2.4-kb segment of the mitochondrial 12S rRNA-tRNA valine-16S rRNA locus, and in terms of taxa, representatives of two orders of Batoidea, at least one representative of all orders of sharks, and as an outgroup, the widely recognized sister group to elasmobranchs-Holocephali. The results provide the first convincing molecular evidence for shark monophyly and the rejection of the Hypnosqualea hypothesis. Our phylogenetic placement of batoids as a basal elasmobranch lineage means that much of the current thinking regarding the evolution of morphological and life history characteristics in elasmobranchs needs to be re-evaluated.     

Phylogenetic interrelationships of the barbets (Aves: Capitonidae) and toucans (Aves: Ramphastidae) based on morphology with comparisons to DNA-DNA hybridization

A phylogenetic analysis of the interrelationships of the barbets (Capitonidae) and the toucans (Aves: Ramphastidae, Superfamily Ramphastoidea) is presented. Thirty-two morphological characters from the literature and independent osteological observations were analysed. Character polarity was determined by outgroup comparison to the Picidae, Indicatoridae, Galbulidae, Bucconidae and Coraciiformes. Four alternative phylogenetic hypotheses were compared: (1) the overall most parsimonious morphological phylogeny, (2) the most parsimonious morphological phylogeny in which the capitonids and ramphastids were hypothesized as monophyletic sister groups, and (3) and (4) the most parsimonious hypotheses for the evolution of the morphological characters within two proposed DNA-DNA hybridization phylogenies of the ramphastoids. The analysis focused on the higher level relationships of ramphastids and capitonids and interrelationships among capitonid genera. Two cladistic analyses were performed using 26 phylogenetically informative characters, and the PAUP and CONTREE computer alogorithms. The most parsimonious morphological phylogeny required fewer character changes and had a lower consistency index than any of the alternative hypotheses but congruence between the most parsimonious phylogeny and the second, revised DNA-DNA hybridization hypothesis was very high. Based on these results the monophyly of the Capitonidae is rejected. The ramphastids and the Neotropical capitonids form a well corroborated clade within the pantropical ramphastoid radiation. Neither the African, Asian nor New World capitonids is monophyletic. The genus Trachyphonus is the sister group to all other capitonids and ramphastids. The sister group to the ramphastids is the genus Semnornis. The interrelationships of the Old World capitonids excluding Trachyphonus are not completely resolved by these morphological data but one of the alternative phylogenetic resolutions is presented as a preliminary hypothesis. The clades in this resolved phylogeny are diagnosed and the palaeontology and biogeography of the ramphastoids arc-reviewed in light of this new evidence. A phylogenetic classification is proposed in which the Capitonidae is rejected and the capitonids and ramphastids are placed in seven subfamilies of the Ramphastidae.     

Early fossils illuminate character evolution and interrelationships of Lampridiformes (Teleostei,Acanthomorpha)

Lampridiformes is a peculiar clade of pelagic marine acanthomorph (spiny‐rayed) teleosts. Its phylogenetic position remains ambiguous, and varies depending on the type of data (morphological or molecular) used to infer interrelationships. Because the extreme morphological specializations of lampridiforms may have overwritten the ancestral features of the group with a bearing on its relationships, the inclusion of fossils that exhibit primitive character state combinations for the group as a whole is vital in establishing its phylogenetic position. Therefore, we present an osteological data set of extant (ten taxa) and fossil (14 taxa) acanthomorphs, including early Late Cretaceous taxa for which a close relationship with extant Lampridiformes has been suggested: ?Aipichthyoidea, ?Pharmacichthyidae, and ?Pycnosteroididae. We find that all three taxa plus Lampridiformes form a clade that we call Lampridomorpha. Under this hypothesis, ?Aipichthyoidea is paraphyletic. The inclusion of fossils in the analysis changes the topology, highlighting their critical importance in phylogenetic studies of morphological characters. When fossils are included, Lampridomorpha is sister to Euacanthomorpha (all other extant acanthomorphs), concurring with most previous anatomical studies, but conflicting with most molecular results. Lampridomorpha as a whole was a major component of the earliest acanthomorph faunas, notably in the Cenomanian. © 2014 The Linnean Society of London