Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis, and extant cephalopods

Complete nucleotide sequences of mitochondrial (mt) genomes of the "living fossil" cephalopod Vampyroteuthis infernalis (Vampyromorpha) and the cuttlefish Sepia esculenta (Sepiida) were determined. The V. infernalis mt genome structure is identical to the incirrate octopod Octopus vulgaris mt genome structure, and is therefore more similar to that of the polyplacophoran Katharina tunicata, than to that of the other "living fossil" cephalopod Nautilus macromphalus. The mt genome structure of S. esculenta is identical to that of Sepia officinalis. Molecular phylogenetic analyses based on the mt protein genes from the completely sequenced cephalopod mt genomes suggested the monophyletic relationship of two myopsid squids Loligo bleekeri and Sepiotheuthis lessoniana, and the monophyletic relationship of two oegopsid squids Watasenia scintillans, and Todarodes pacificus. Sepiida appeared as the sister group of Teuthida (Myopsida + Oegopsida). The phylogenetic position of Vampyromorpha appeared as the sister group of Octopoda, although the monophyly of Vampyromorpha and Decapodiformes cannot be rejected outright by our phylogenetic analyses. The hypothesis that Vampyromorpha is basal among the coleoid cephalopods can be rejected because of low statistical support. Therefore, it is reasonable to recognize three major groups in Coleoidea--Vampyromorpha, Octopoda, and Decapodiformes.     

Of teeth and trees: A fossil tip‐dating approach to infer divergence times of extinct and extant squaliform sharks

Fossil tip‐dating allows for the inclusion of morphological data in divergence time estimates based on both extant and extinct taxa. Neoselachii have a cartilaginous skeleton, which is less prone to fossilization compared to skeletons of Osteichthyans. Therefore, the majority of the neoselachian fossil record is comprised of single teeth, which fossilize more easily. Neoselachian teeth can be found in large numbers as they are continuously replaced. Tooth morphologies are of major importance on multiple taxonomic levels for identification of shark and ray taxa. Here, we review dental morphological characters of squalomorph sharks and test these for their phylogenetic signal. Subsequently, we combine DNA sequence data (concatenated exon sequences) with dental morphological characters from 85 fossil and extant taxa to simultaneously infer the phylogeny and re‐estimate divergence times using information of 61 fossil tip‐dates as well as eight node age calibrations of squalomorph sharks. Our findings show that the phylogenetic placement of fossil taxa is mostly in accordance with their previous taxonomic allocation. An exception is the phylogenetic placement of the extinct genus ?Protospinax , which remains unclear. We conclude that the high number of fossil taxa as well as the comprehensive DNA sequence data for extant taxa may compensate for the limited number of morphological characters identifiable on teeth, serving as a backbone for reliably estimating the phylogeny of both extinct and extant taxa. In general, tip‐dating mostly estimates older node ages compared to previous studies based on calibrated molecular clocks.     

Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework

The resolution of higher level phylogeny of the coleoid cephalopods (octopuses, squids, and cuttlefishes) has been hindered by homoplasy among morphological characters in conjunction with a very poor fossil record. Initial molecular studies, based primarily on small fragments of single mitochondrial genes, have produced little resolution of the deep relationships amongst coleoid cephalopod families. The present study investigated this issue using 3415 base pairs (bp) from three nuclear genes (octopine dehydrogenase, pax-6, and rhodopsin) and three mitochondrial genes (12S rDNA, 16S rDNA, and cytochrome oxidase I) from a total of 35 species (including representatives of each of the higher level taxa). Bayesian analyses were conducted on mitochondrial and nuclear genes separately and also all six genes together. Separate analyses were conducted with the data partitioned by gene, codon/rDNA, gene+codon/rDNA or not partitioned at all. In the majority of analyses partitioning the data by gene+codon was the appropriate model with partitioning by codon the second most selected model. In some instances the topology varied according to the model used. Relatively high posterior probabilities and high levels of congruence were present between the topologies resulting from the analysis of all Octopodiform (octopuses and vampire "squid") taxa for all six genes, and independently for the datasets of mitochondrial and nuclear genes. In contrast, the highest levels of resolution within the Decapodiformes (squids and cuttlefishes) resulted from analysis of nuclear genes alone. Different higher level Decapodiform topologies were obtained through the analysis of only the 1st+2nd codon positions of nuclear genes and of all three codon positions. It is notable that there is strong evidence of saturation among the 3rd codon positions within the Decapodiformes and this may contribute spurious signal. The results suggest that the Decapodiformes may have radiated earlier and/or had faster rates of evolution than the Octopodiformes. The following taxonomic conclusions are drawn from our analyses: (1) the order Octopoda and suborders Cirrata, Incirrata, and Oegopsida are monophyletic groups; (2) the family Spirulidae (Ram's horn squids) are the sister taxon to the family Sepiidae (cuttlefishes); (3) the family Octopodidae, as currently defined, is paraphyletic; (4) the superfamily Argonautoidea are basal within the suborder Incirrata; and (5) the benthic octopus genera Benthoctopus and Enteroctopus are sister taxa.     

Molecules, morphology and fossils: a comprehensive approach to odonate phylogeny and the evolution of the odonate wing

We undertook a comprehensive morphological and molecular phylogenetic analysis of dragonfly phylogeny, examining both extant and fossil lineages in simultaneous analyses. The legitimacy of higher‐level family groups and the phylogenetic relationship between families were tested. Thirteen families were supported as monophyletic (Aeshnidae, Calopterygidae, Chlorocyphidae, Euphaeidae, Gomphidae, Isostictidae, Lestidae, Libellulidae, Petaluridae, Platystictidae, Polythoridae, Pseudostigmatidae and Synthemistidae) and eight as non‐monophyletic (Amphipterygidae, Coenagrionidae, Corduliidae, Megapodagrionidae, Protoneuridae and Synlestidae), although Perilestidae and Platycnemididae were recovered as monophyletic under Bayesian analyses. Nine families were represented by one species, thus monophyly was not tested (Epiophlebiidae, Austropetaliidae, Chlorogomphidae, Cordulegastridae, Macromiidae, Chorismagrionidae, Diphlebiidae, Lestoideidae and Pseudolestidae). Epiprocta and Zygoptera were recovered as monophyletic. Ditaxinerua is supported as the sister lineage to Odonata, Epiophlebiidae and the lestid‐like damselflies are sister to the Epiprocta and Zygoptera, respectively. Austropetaliidae + Aeshnidae is the sister lineage to the remaining Anisoptera. Tarsophlebia's placement as sister to Epiprocta or as sister to Epiprocta + Zygoptera was not resolved. Refinements are made to the current classification. Fossil taxa did not seem to provide signals crucial to recovering a robust phylogeny, but were critical to understanding the evolution of key morphological features associated with flight. Characters associated with wing structure were optimized revealing two wing character complexes: the pterostigma–nodal brace complex and the costal wing base & costal–ScP junction complex. In turn, these two complexes appear to be associated; the pterostigma–nodal brace complex allowing for further modification of the wing characters comprised within the costal wing base & costal–ScP junction complex leading the modern odonate wing. © The Willi Hennig Society 2008.     

Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia

Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.     

What can the mitochondrial genome reveal about higher‐level phylogeny of the molluscan class Cephalopoda?

We present the first analysis of cephalopod mitochondrial gene order and construct phylogenies based on gene order using Bayesian, distance, and parsimony analysis methods. Analyses included all species of cephalopod for which the whole mitochondrial genome has been sequenced. Where resolution was obtained, these analyses supported division of Neocoleoidea, in which all recent coleoid Cephalopoda can be placed, into Octopodiformes and Decapodiformes. For the same taxa, we also constructed a phylogeny in a maximum likelihood framework based on amino‐acid coded sequence data of all mitochondrial protein coding genes. As well as supporting Octopodiformes and Decapodiformes, amino‐acid analyses established support for Teuthoidea (Oegospida and Myopsida) to the exclusion of Sepiidae, and supported a monophyletic Oegopsida. Partial mitochondrial sequences of additional higher‐level taxa for which whole genome data were not available were subsequently included in the amino‐acid analysis to provide additional information on phylogeny. Spirulida was found to be basal amongst Decapodiformes. Mapping of morphological characters onto our phylogeny and consideration of palaeontological evidence suggests that our phylogeny reflects true evolutionary relationships. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 573–586.     

Cladistic analysis of the Cirripedia Thoracica

We present a cladistic analysis of the Cirripedia Thoracica using morphological characters and the Acrothoracica and Ascothoracida as outgroups. The list of characters comprised 32 shell and soft body features. The operational taxonomic units (OTUs) comprised 26 well-studied fossil and extant taxa, principally genera, since uncertainty about monophyly exists for most higher ranking taxonomic units. Parsimony analyses using PAUP 3.1.1 and Hennig86 produced 189 trees of assured minimal length. We also examined character evolution in the consensus trees using MacClade and Clados. The monophyly of the Balanomorpha and the Verrucomorpha sensu stricto is confirmed, and all trees featured a sister group relationship between the ‘living fossil Neoverruca and me Brachylepadomorpha. In the consensus trees the sequential progression of ‘pedunculate‘sister groups up to a node containing Neolepas also conforms to current views, but certain well-established taxa based solely on plesiomorphies stand out as paraphyletic, such as Pedunculata (= Lepadomorpha); Eolepadinae, Scalpellomorpha and Chthamaloidea. The 189 trees differed principally in the position of shell-less pedunculates, Neoverruca, the scalpelloid Capitulum, and the interrelationships within the Balanomorpha, although the 50% majority rule consensus tree almost fully resolved the latter. A monophyletic Sessilia comprising both Verrucomorpha and Balanomorpha appeared among the shortest trees, but not in the consensus. A tree with a monophyletic Verrucomorpha including Neoverruca had a tree length two steps longer than the consensus trees. Deletion of all extinct OTUs produced a radically different tree, which highlights the importance of fossils in estimating cirripede phylogeny. Mapping of our character set onto a manually constructed cladogram reflecting die most recent scenario of cirripede evolution resulted in a tree length five steps longer than any of our shortest trees. Our analysis reveals that several key questions in cirripede phylogeny remain unsolved, notably the position of shell-less forms and the transition from ‘pedunculate‘to ‘sessile‘barnacles. The inclusion of more fossil species at this point in our understanding of cirripede phylogeny will only result in even greater levels of uncertainty. When constructing the character list we also identified numerous uncertainties in the homology of traits commonly used in discussing cirripede evolution. Our study highlights larval ultrastructure, detailed studies of early ontogeny, and molecular data as the most promising areas for future research.     

Molecules, Morphology, Fossils, and the Relationship of Angiosperms and Gnetales

Morphological analyses of seed plant phylogeny agree that Gnetales are the closest living relatives of angiosperms, but some studies indicate that both groups are monophyletic, while others indicate that angiosperms are nested within Gnetales. Molecular analyses of several genes agree that both groups are monophyletic, but differ on whether they are related. Conflicts among morphological trees depend on the interpretation of certain characters; when these are analyzed critically, both groups are found to be monophyletic. Conflicts among molecular trees may reflect the rapid Paleozoic radiation of seed plant lines, aggravated by the long branches leading to extant taxa. Trees in which angiosperms are not related to Gnetales conflict more with the stratigraphic record. Even if molecular data resolve the relationships among living seed plant groups, understanding of the origin of angiosperm organs will require integration of fossil taxa, necessarily using morphology.     

Toward a Better Understanding of the Phylogeny of the Asplanchnidae (Rotifera)

We investigated the phylogenetic relationships of Family Asplanchnidae using both morphological and molecular data. The morphological database, comprising 23 characters from 19 taxa (15 Asplanchnidae and 4 outgroups), was compiled from a survey of the literature and our own observations; the molecular data (ITS and V4 region nuclear regions and mitochondrial cox1) was sequenced from specimens that we collected. Our analysis of the morphological data set (maximum parsimony) yielded 12 most-parsimonious trees with a tree length of 27 steps. From this analysis we conclude (1) Asplanchnidae is a monophyletic group as are the three genera comprising it, (2) there is no compelling support for the argument that Asplanchna should be separated into two discrete genera, and (3) there is some support for the proposal that Asplanchnidae and Synchaetidae are sister groups. Our analysis of the molecular data set supports the first two of these conclusions while the sister group of the family varied depending on the gene region analyzed and families and genera included. Current understanding of the phylogeny of Asplanchnidae is hampered by the need for additional informative morphological characters and a lack of molecular data for the genus Harringia and several other members of the Asplanchnidae.     

The systematics of right whales (Mysticeti: Balaenidae)

Balaenidae (right whales) are large, critically endangered baleen whales represented by four living species. The evolutionary relationships of balaenids are poorly known, with the number of genera, relationships to fossil taxa, and position within Mysticeti in contention. This study employs a comprehensive set of morphological characters to address aspects of balaenid phylogeny. A sister‐group relationship between neobalaenids and balaenids is strongly supported, although this conflicts with molecular evidence, which may be an artifact of long‐branch attraction (LBA). Monophyly of Balaenidae is supported, and three major clades are recognized: (1) extinct genus Balaenula, (2) extant and extinct species of the genus Eubalaena, and (3) extant and extinct species of the genus Balaena plus the extinct taxon, Balaenella. The relationships of these clades to one another, as well as to the early Miocene stem balaenid, Morenocetus parvus, remain unresolved. Pliocene taxa, Balaenula astensis and Balaenula balaenopsis, form a clade that is the sister group to the Japanese Pliocene Balaenula sp. Eubalaena glacialis and Pliocene Eubalaena belgica, are in an unresolved polytomy with a clade including E. japonica and E. australis. Extant and fossil species of Balaena form a monophyletic group that is sister group to the Dutch Pliocene Balaenella, although phylogenetic relationships within Balaena remain unresolved.     

Cladistics of the Spermatophyta

A cladistic interpretation of seed plant phylogeny is presented that supports the traditional morphological hypothesis: [Cycadales-(Ginkgoales-(Coniferales-(Gnetales-Angiosperms)))]. Gnetales and Angiosperms are supported as sister groups of theAnaspermae. A sister-group relationship between Coniferales and Ginkgoales represents a paraphyletic group, because Coniferales and Anaspermae share a common ancestry (Mesospermae). Ginkgoales and Mesospermae are sister groups of theCladospermae. Cycadales are supported as the most archaic Spermatophyta.A posteriori consideration of fossil taxa supports the conclusion that data from the fossil record are useful for confirming plesiomorphies of extant taxa. Fossil taxa with apomorphic character states are discussed as biasing for superficial accelerated transformations, which are probably unacceptable from the standpoint of morphological homology.     

Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets

It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.     

A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants

Flowering plants represent the most significant branch in the tree of land plants, with respect to the number of extant species, their impact on the shaping of modern ecosystems and their economic importance. However, unlike so many persistent phylogenetic problems that have yielded to insights from DNA sequence data, the mystery surrounding the origin of angiosperms has deepened with the advent and advance of molecular systematics. Strong statistical support for competing hypotheses and recent novel trees from molecular data suggest that the accuracy of current molecular trees requires further testing. Analyses of phytochrome amino acids using a duplicate gene-rooting approach yield trees that unite cycads and angiosperms in a clade that is sister to a clade in which Gingko and Cupressophyta are successive sister taxa to gnetophytes plus Pinaceae. Application of a cycads + angiosperms backbone constraint in analyses of a morphological dataset yields better resolved trees than do analyses in which extant gymnosperms are forced to be monophyletic. The results have implications both for our assessment of uncertainty in trees from sequence data and for our use of molecular constraints as a way to integrate insights from morphological and molecular evidence.     

On the phylogenetic position and systematics of extant and fossil Aclopinae (Coleoptera: Scarabaeidae)

The Aclopinae is a small subfamily within the family Scarabaeidae. It currently comprises five extant genera with 28 species, and eight fossil genera with 25 species. The systematic position of Aclopinae within the family Scarabaeidae is uncertain, particularly because representative species of Aclopinae have been absent in previous phylogenetic studies. Here we performed phylogenetic analyses using morphological and molecular data to investigate the phylogenetic position of fossil and extant Aclopinae. For this objective, we expanded and revised a former morphological data matrix (composed of 68 characters) including all extant genera of Aclopinae. We complemented our morphological investigations with a molecular phylogenetic analysis based on four genes of several extant taxa of Aclopinae and a wide sample of diverse Scarabaeoidea. Our phylogenetic analyses show that all the type species of the fossil genera formerly included within Aclopinae do not belong within the extant Aclopinae clade and support both the exclusion of those fossil taxa and the monophyly of the extant genera of Aclopinae: Aclopus Erichson, Desertaclopus Ocampo & Mondaca, Gracilaclopus Ocampo & Mondaca, Neophanaeognatha Allsopp and Phanaeognatha Hope. Our results also show that the fossil taxa Prophaenognatha robusta Bai et al. and Ceafornotensis archratiras Woolley are closely related to Ochodaeidae, while the remaining type species of fossils formerly included in Aclopinae (Cretaclopus longipes (Ponomarenko), Holcorobeus vittatus Nikritin, Juraclopus rodhendorfi Nikolajev, Mesaclopus mongolicus (Nikolajev), and Mongolrobeus zherikhini Nikolajev) belong to a distinct lineage closely related to Diphyllostomatidae. Based on these results, the subfamily Aclopinae appears monophyletic and sister to the ‘pleurostict’ lineage. Consequently, we propose the following changes to the current classification of the fossil taxa: Holcorobeus monreali (Gómez‐Pallerola) belongs to Carabidae (incertae sedis) as proposed by the original author, and we place Ceafornotensis Woolley, Cretaclopus Nikolajev, Holcorobeus Nikritin, Juraclopus Nikolajev, Mesaclopus Nikolajev, Mongolrobeus Nikolajev and Prophaenognatha Bai et al. in Scarabaeoidea (incertae sedis). Furthermore, we provide an identification key to, and diagnoses of, the genera, illustrations of diagnostic characters and checklists of their included species. The evolutionary perspective presented provides new insights into the evolution of the pleurostict condition in Scarabaeoidea and the biogeography of this group, which is now regarded as Gondwanan, probably evolving during the Cretaceous and not from the upper Jurassic as previously assumed.     

A Total Evidence Phylogeny of the Arctoidea (Carnivora: Mammalia): Relationships Among Basal Taxa

A total evidence phylogenetic analysis was performed for 14 extant and 18 fossil caniform genera using a data matrix of 5.6 kbp of concatenated sequence data from six independent loci and 80 morphological characters from the cranium and dentition. Maximum parsimony analysis recovered a single most parsimonious cladogram (MPC). The topology of the extant taxa in the MPC agreed with previous molecular phylogenies. Phylogenetic positions for fossil taxa indicate that several taxa previously described as early members of extant families (e.g., Bathygale and Plesictis) are likely stem taxa at the base of the Arctoidea. Taxa in the “Paleomustelidae” were found to be paraphyletic, but a monophyletic Oligobuninae was recovered within this set of taxa. This clade was closely related to the extant genera Gulo and Martes, therefore, nested within the extant radiation of the family Mustelidae. This analysis provides a resolution to several discrepancies between phylogenies considering either fossil taxa or extant taxa separately, and provides a framework for incorporating fossil and extant taxa into comprehensive combined evidence analyses.     

A phylogeny of the damselfly genus calopteryx (Odonata) using mitochondrial 16S rDNA markers

We seek to reconstruct the phylogenetic relationships of the damselfly genus Calopteryx, for which extensive behavioral and morphological knowledge already exists. To date, analyses of the evolutionary pathways of different life history traits have been hampered by the absence of a robust phylogeny based on morphological data. In this study, we concentrate on establishing phylogenetic information from parts of the 16S rDNA gene, which we sequenced for nine Calopteryx species and five outgroup species. The mt 16S rDNA data set did not show signs of saturated variation for ingroup taxa, and phylogenetic reconstructions were insensitive to variation of outgroup taxa. Parsimony, neighbor-joining, and maximum-likelihood reconstructions agreed on parts of the tree. A consensus tree summarizes the significant results and indicates problematic nodes. The 16S rDNA sequences support monophyly of the genera Mnais, Matrona, and Calopteryx. However, the genus Calopteryx may not be monophyletic, since Matrona basilaris and Calopteryx atrata are sister taxa under every parameter setting. The North American and European taxa each appear as monophyletic clades, while the Asian Calopteryx atrata and Calopteryx cornelia are not monophyletic. Our data implies a different paleobiogeographic history of the Eurasian and North American species, with extant Eurasian species complexes shaped by glacial periods, in contrast to extant North American species groups.     

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.     

More DNA support for a Cetacea/Hippopotamidae clade: the blood-clotting protein gene gamma-fibrinogen

Recent phylogenetic analyses of DNA sequences suggest that cetaceans (whales) and hippopotamid artiodactyls (hippos) are extant sister taxa. Consequently, the shared aquatic specializations of these taxa may be synapomorphies. This molecular view is contradicted by paleontological data that overwhelmingly support a monophyletic Artiodactyla (even-toed ungulates) and a close relationship between Cetacea and extinct mesonychian ungulates. According to the fossil evidence, molecular, behavioral, and anatomical resemblances between hippos and whales are interpreted as convergences or primitive retentions. In this report, competing interpretations of whale origins are tested through phylogenetic analyses of the blood-clotting protein gene gamma- fibrinogen from cetaceans, artiodactyls, perissodactyls (odd-toed ungulates), and carnivores (cats, dogs, and kin). In combination with published DNA sequences, the gamma-fibrinogen data unambiguously support a hippo/whale clade and are inconsistent with the paleontological perspective. If the phylogeny favored by fossil evidence is accepted, the convergence at the DNA level between Cetacea and Hippopotamidae is remarkable in its distribution across three genetic loci: gamma-fibrinogen, the linked milk casein genes, and mitochondrial cytochrome b.      

Problematica old and new

Problematica are taxa that defy robust phylogenetic placement. Traditionally the term was restricted to fossil forms, but it is clear that extant taxa may be just as difficult to place, whether using morphological or molecular (nucleotide, gene or genomic) markers for phylogeny reconstruction. We discuss the kinds and causes of Problematica within the Metazoa, as well as criteria for their recognition and possible solutions. The inclusive set of Problematica changes depending upon the nature and quality of (homologous) data available, the methods of phylogeny reconstruction and the sister taxa inferred by their placement or displacement. We address Problematica in the context of pre-cladistic phylogenetics, numerical morphological cladistics and molecular phylogenetics, and focus on general biological and methodological implications of Problematica, rather than presenting a review of individual taxa. Rather than excluding Problematica from phylogeny reconstruction, as has often been preferred, we conclude that the study of Problematica is crucial for both the resolution of metazoan phylogeny and the proper inference of body plan evolution.     

Phylogeny and evolution of Mesozoic and extant lineages of Histeridae (Coleoptera), with discovery of a new subfamily Antigracilinae from the Lower Cretaceous

In order to place a newly discovered species Antigracilus costatus gen. sp. n. from the Lower Cretaceous Yixian Formation (China) and to assess previously unplaced fossil taxa, we investigated the relationships of extant and extinct lineages of Histeridae based on three data sets: (i) 69 morphological characters belonging to 48 taxa (representing all 11 subfamilies and 15 of 17 tribes of modern Histeridae); (ii) partitioned alignment of 6030 bp from downloaded nucleotide sequences (28S, CAD, COI, 18S) of 50 taxa (representing 10 subfamilies and 15 of 17 tribes of modern Histeridae); and (iii) a combined morphological and molecular dataset for 75 taxa. Phylogenetic analyses of the morphology and combined matrices recovered the new Lower Cretaceous taxon as a sister group to remaining Histeridae and it is placed in †Antigracilinae subfam. n. †Antigracilinae constitutes the earliest record of Histeridae from the Lower Cretaceous Yixian Formation (∼125 Myr), backdating the minimum age of the family by 25 Myr from the earliest Cenomanian (~99 Myr) to the Barremian of the Cretaceous Period. Our molecular phylogeny supports Histeridae to be divided into seven different clades, with currently recognised subfamilies Abraeinae (sensu lato), Saprininae, Chlamydopsinae, and Histerinae (sensu lato) recovered as monophyletic, while Dendrophilinae, Onthophilinae, and Tribalinae are polyphyletic taxa. The Burmese amber species †Pantostictus burmanicus Poinar & Brown is placed as a sister group to the tribe Plegaderini (Abraeinae) and was assigned as a new tribe Pantostictini trib. n. Both molecular and combined phylogenies recovered the subfamilies Trypanaeinae and Trypeticinae deeply within the subfamily Abraeinae (sensu lato), and they are downgraded into Trypanaeini stat. n. and Trypeticini stat. n.