A combined evidence phylogenetic analysis of Anguimorpha (Reptilia: Squamata)

Anguimorpha is a clade of limbed and limbless squamates with ca. 196 extant species and a known fossil record spanning the past 130 million years. Morphology‐based and molecule‐based phylogenetic analyses disagree on several key points. The analyses differ consistently in the placements of monstersaurs (e.g. Gila Monsters), shinisaurs (Crocodile Lizards), the anguid Anniella (American Legless Lizards), carusioids (Knobby Lizards), and the major clades within Varanus (Monitor Lizards). Given different data sources with such different phylogenetic hypotheses, Anguimorpha is an excellent candidate for a combined phylogenetic analysis. We constructed a data matrix consisting of 175 fossil and extant anguimorphs, and 2281 parsimony‐informative characters (315 morphological characters and 1969 molecular characters). We analysed these data using the computer program TNT using the “new technology search” with the ratchet. Our result is novel and shows similarities with both morphological and molecular trees, but is identical to neither. We find that a global combined evidence analysis (GCA) does not recover a holophyletic Varanoidea, but omission of fossil taxa reveals cryptic molecular support for that group. We describe these results and others from global morphological analysis, extant‐only morphological analysis, molecular data‐only analyses, combined evidence analysis of extant taxa, and GCA. © The Willi Hennig Society 2010.     

Slow molecular evolution in an ancient asexual ostracod

Genetic variability of the non-marine ostracod species Darwinula stevensoni was estimated by sequencing part of the nuclear and the mitochondrial genome. As Darwinulidae are believed to be ancient asexuals, accumulation of mutations should have occurred, both between alleles within lineages and between lineages, during the millions of years of parthenogenetic reproduction. However, our sequence data show the opposite: no variability in the nuclear ITS1 region was observed within or among individuals of D. stevensoni, despite sampling a geographical range from Finland to South Africa. Lack of allelic divergence might be explained by concerted evolution of rDNA repeats. Homogeneity among individuals may be caused either by slow molecular evolution in ITS1 or by a recent selective sweep. Variability of mitochondrial cytochrome oxidase (COI) was similar to intraspecific levels in other invertebrates, thus weakening the latter hypothesis. Calibrating interspecific, genetic divergences among D. stevensoni and other Darwinulidae using their fossil record enabled us to estimate rates of molecular evolution. Both COI and ITS1 evolve half as fast, at most, in darwinulids as in other invertebrates, and molecular evolution has significantly slowed down in ITS1 of D. stevensoni relative to other darwinulids. A reduced ITS1 mutation rate might explain this inconsistency between nuclear and mitochondrial evolution in D. stevensoni.     

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.     

Ecological strategies in the ancient asexual animal group Darwinulidae (Crustacea, Ostracoda)

• 1 We investigated the relationship between geographical distribution and ecological tolerance within the ancient asexual family Darwinulidae. Distribution maps were compiled based on data from the literature, the Non‐marine Ostracod Distribution in Europe database and personal collections. Ecological tolerance was assessed experimentally by exposing individual ostracods to a combination of eight different salinities (range from 0 to 30 g L^?1) and three different temperatures (10, 20 and 30 °C).
• 2 The type species of the family, Darwinula stevensoni, is ubiquitous and cosmopolitan; the two species Penthesilenula brasiliensis and Microdarwinula zimmeri also have an intercontinental distribution. Two other darwinulid species tested here (Vestalenula molopoensis and P. aotearoa) are known only from their type localities. The latter is also true for most extant darwinulids.
• 3 Darwinula stevensoni and P. brasiliensis had a broad salinity tolerance, tolerating distilled water and also salinity up to 25–30 g L^?1, whereas the maximum salinity tolerance of V. molopoensis was 12 g L^?1 and of P. aotearoa, 20 g L^?1.
• 4 The results indicate that both ecological specialists and generalists, as well as intermediate forms, exist in the Darwinulidae and that taxa with the broadest ecological tolerance also have the widest distribution.

     

Evaluation of the fossil fish‐specific diversity in a chadian continental assemblage: Exploration of morphological continuous variation in Synodontis (Ostariophysi,Siluriformes)

In the fossil record, the quantification of continuous morphological variation has become a central issue when dealing with species identification and speciation. In this context, fossil taxa with living representatives hold great promise, because of the potential to characterise patterns of intraspecific morphological variation in extant species prior to any interpretation in the fossil record. The vast majority of catfish families fulfil this prerequisite, as most of them are represented by extant genera. However, although they constitute a major fish group in terms of distribution, and ecological and taxonomic diversity, the quantitative study of their past morphological variation has been neglected, as fossil specimens are generally identified based on the scarcest remains, that is, complete neurocrania that bear discrete characters. Consequently, a part of freshwater catfish history is unprospected and unknown. In this study, we explored the morphological continuous variation of the humeral plate shape in Synodontis catfishes using Elliptic Fourier Analysis (EFA), and compared extant members and fossil counterparts. We analysed 153 extant specimens of 11 Synodontis species present in the Chad basin, in addition to 23 fossil specimens from the Chadian fossiliferous area of Toros Menalla which is dated around 7 Ma. This highly speciose genus, which is one of the most diversified in Africa, exhibits a rich fossil record with several hundred remains mostly identified as Synodontis sp. The analysis of the outline of the humeral plate reveals that some living morphological types were already represented in the Chad Basin 7 My ago, and allows for the discovery of extinct species. Beside illuminating the complex Neogene evolutionary history of Synodontis, these results underline the interest in the ability of isolated remains to reconstruct a past dynamic history and to validate the relevance of EFA as a tool to explore specific diversity through time. J. Morphol. 277:1486–1496, 2016. © 2016 Wiley Periodicals, Inc.     

MOLECULAR PHYLOGENY OF SELECTED SPECIES OF THE ORDER DINOPHYSIALES (DINOPHYCEAE)—TESTING THE HYPOTHESIS OF A DINOPHYSIOID RADIATION1

Almost 80 years ago, a radiation scheme based on structural resemblance was first outlined for the marine order Dinophysiales. This hypothetical radiation illustrated the relationship between the dinophysioid genera and included several independent, extant lineages. Subsequent studies have supplied additional information on morphology and ecology to these evolutionary lineages. We have for the first time combined morphological information with molecular phylogenies to test the dinophysioid radiation hypothesis in a modern context. Nuclear‐encoded LSU rDNA sequences including domains D1‐D6 from 27 species belonging to Dinophysis Ehrenb., Ornithocercus F. Stein, Phalacroma F. Stein, Amphisolenia F. Stein, Citharistes F. Stein, and Histioneis F. Stein were obtained from the Indian Ocean. Previously, LSU rDNA has only been determined from one of these. In Bayesian analyses, Amphisolenia formed a long basal clade to the other dinophysioids. These diverged into two separate lineages, the first comprised species with a classical Phalacroma outline, also including the type species P. porodictyum F. Stein. Thus, we propose to reinstate the genus Phalacroma. The relationship between the genera in the second lineage was not well resolved. However, the molecular phylogeny supported monophyly of Histioneis and Citharistes and showed the genus Dinophysis to be polyphyletic and in need of a taxonomic revision. Species of Ornithocercus grouped with Citharistes, but this relationship remained unresolved. The phylogenetic trees furthermore revealed convergent evolution of several morphological characters in the dinophysioids. According to the molecular data, the dinophysioids appeared to have evolved quite differently from the radiation schemes previously hypothesized. Four dinophysioid species had identical LSU rDNA sequences to other well‐established species.     

Evolution of fossil and living spider flies based on morphological and molecular data (Diptera,Acroceridae)

The phylogeny of spider flies is presented based on an analysis of DNA sequence data combined with morphological characters for both living and fossil species. We sampled 40 extant and extinct genera across all major lineages of Acroceridae, which were compared with outgroup taxa from various lower brachyceran families. In all, 81 morphological characters of 60 extant and 10 extinct ingroup species were combined with 7.1 kb of DNA sequences of two nuclear (CAD and 28S rDNA) and two mitochondrial genes (COI and 16S rDNA). Results strongly support the monophyly of Acroceridae, with major clades contained within classified here in five extant subfamilies (Acrocerinae, Cyrtinae stat. rev. , Ogcodinae stat. rev. , Panopinae and Philopotinae) and one extinct subfamily, Archocyrtinae. The evolution of important spider fly traits is discussed, including genitalia and wing venation. The status of the enigmatic Psilodera Gray and Pterodontia Gray as members of the Panopinae is confirmed based on both molecular and morphological data.     

Phylogeny,classification and divergence times of pygmy leaf‐mining moths (Lepidoptera: Nepticulidae): the earliest lepidopteran radiation on Angiosperms?

Nepticulidae represent one of the early diverging Lepidoptera lineages, and the family currently comprises over 850 described species. The larvae of the vast majority of the species are leaf miners on Angiosperms and highly monophagous, which has led to persistent ideas on coevolution with their plant hosts. We present here a molecular phylogeny based on eight gene fragments from 355 species, representing 20 out of 22 extant Nepticulidae genera. Using two fossil calibration points, we performed molecular dating to place the origin of the family in the Early Cretaceous, before the main Angiosperm diversification. Based on our results we propose a new classification, abandoning all ranks between family and genus, as well as subgenera to allow for a stable classification. The position of Enteucha Meyrick within Nepticulidae remains somewhat ambiguous, and the species‐rich cosmopolitan genus Stigmella Schrank, with nearly half of all described Nepticulidae, requires further study. Ectoedemia Busck, Zimmermannia Hering, Acalyptris Meyrick, Etainia Beirne, Parafomoria Borkowski, Muhabbetana Koçak & Kemal and Fomoria Beirne appear to have diversified in a relatively short evolutionary period, leading to short branches in the molecular phylogeny and unclear suprageneric relations. Otherwise support values throughout the phylogeny are mostly high and the species groups, genera and higher clades are discussed in respect of their supporting morphological and life‐history characters. Wing venation characters are confirmed to be mostly reliable and relevant for Nepticulidae classification, but some other previously used characters require reinterpretation. The species groups of most genera are recovered, but only partly so in the large genus Stigmella. The molecular dating results are compared with existing knowledge on the timing of the Angiosperm radiation and reveal that the diversification of Nepticulidae could largely have been contemporaneous with their hosts, although some of the genera restricted to a single plant family appear to have begun to diversify before their hosts.     

Morphology,molecules and the phylogeny of Characidae (Teleostei,Characiformes)

This is the most comprehensive phylogenetic analysis of the Characidae to date and the first large-scale hypothesis of the family, combining myriad morphological data with molecular information. A total of 520 morphological characters were analysed herein, of which 98 are newly defined. Among the analysed taxa, 259 species were coded by examining specimens, three fossil species were coded from the literature, one species was coded almost completely from published figures, 122 were partially coded from the literature, and 88 were analysed exclusively from molecular data. The total number of species in the analysed dataset is 473. Analyses were made by parsimony under equal and extended implied weighting with a broad range of parameters. The final hypothesis was selected using a stability criterion that chooses among the most parsimonious trees of all searches. It was found by weighting molecular characters with the average homoplasy of entire partitions (markers). The resulting hypothesis is congruent with previous molecular-based phylogenies of the family. The Characidae are monophyletic, with four main clades: the Spintherobolinae new subfamily; an expanded Stethaprioninae including the Grundulini, Gymnocharacini, Rhoadsiini and Stethaprionini; the Stevardiinae; and a clade composed of the Aphyocharacinae, Characinae, Cheirodontinae, Exodontinae and Tetragonopterinae. Also, a stem Characidae was found, as formed by the Eocene–Oligocene genera †Bryconetes and †Paleotetra as successive sister groups of extant members of the family. A subfamilial classification is proposed, but deep changes in the systematics that are beyond the scope of this study are still needed to classify the Characidae into monophyletic genera.     

Phylogenetic relationships of Microdontinae (Diptera: Syrphidae) based on molecular and morphological characters

The intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister‐group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k‐values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.     

Ancient DNA from an extinct Mediterranean micromammal—Hypnomys morpheus (Rodentia: Gliridae)—Provides insight into the biogeographic history of insular dormice

The dormice (Gliridae) are a family of rodents represented by relatively few extant species, though the family was much more species-rich during the Early Miocene. Intergeneric phylogenetic relationships among glirids in some cases remain unresolved, despite extensive molecular and morphological analyses. Uncertainty is greatest with respect to the relationships among fossil taxa and how extinct lineages are related to modern species. The fossil genus Hypnomys from the Balearic Islands (western Mediterranean Sea) includes the Late Pleistocene–Holocene species Hypnomys morpheus, which has variously been considered a close relative or subgenus of the extant Eliomys. In the present study, we sequenced ancient mitochondrial DNA from H. morpheus, which suggests a sister relationship with the extant members of Eliomys. In addition, the pairwise sequence variation between Hypnomys and Eliomys is higher than that observed between congeneric glirid species (e.g., many Graphiurus spp.), which allows us to reject the hypothesis that Hypnomys is a subgenus of Eliomys. Our molecular dating analyses suggest that Hypnomys and Eliomys diverged 13.67 million years ago (95% highest posterior density [HPD] = 7.39–20.07). The relatively early split between these genera together with the molar morphology of early representatives of Hypnomys points to a Middle-Late Miocene origin from a continental glirid with a complex molar pattern, such as Vasseuromys or a closely related genus.     

Phylogenetic classification of the Drosophilidae Rondani (Diptera): the role of morphology in the postgenomic era

Molecular sequences now overwhelm morphology in phylogenetic inference. Nonetheless, most molecular studies are conducted on a limited number of taxa, as DNA rarely can be analysed from old museum types or fossils. During the last 20 years, more than 150 molecular studies have challenged the current phylogenetic classification of the family Drosophilidae Rondani based on morphological characters. Most studies concerned a single genus, Drosophila Fallén, and included only few representative species from 17 out of the 78 genera of the family. Therefore, these molecular studies were unable to provide an alternative classification scheme. A supermatrix analysis of seven nuclear and one mitochondrial genes (8248 bp) for 33 genera was conducted using outgroups from one calyptrate and four ephydroid families. The Bayesian phylogeny was consistent with previous molecular studies including whole genome sequences and divided the Drosophilidae into four monophyletic clades. Morphological characters, mostly male genitalia, then were compared thoroughly between the four clades and homologous character states were identified. These states were then checked for 70 genera and a revised phylogenetic, family‐group classification for the Drosophilidae is proposed. Two genera –Cladochaeta Coquillett and Diathoneura Duda – of the tribe Cladochaetini Grimaldi are transferred to the family Ephydridae. The Drosophilidae is divided into two subfamilies: Steganinae Hendel (30 genera) and Drosophilinae Rondani (43 genera). A further two genera, Apacrochaeta Duda and Sphyrnoceps de Meijere, are incertae sedis, and Palmophila Grimaldi, is synonymized with Drosophila syn.n. The Drosophilinae is subdivided into two tribes: the re‐elevated Colocasiomyini Okada (nine genera) and Drosophilini Okada. The paraphyly of the genus Drosophila was not resolved to avoid affecting the binomina of important laboratory model species; however, its subgeneric classification was revised in light of molecular and morphological data. Three subgenera, namely Chusqueophila Brncic, Phloridosa Sturtevant and Psilodorha Okada, were synonymized with the subgenus Drosophila (Drosophila) Fallén syns.n. Among the 45 species groups and 5 species complexes of Drosophila (Drosophila), 22 groups and 1 complex were transferred to the subgenus Drosophila (Siphlodora) Patterson & Mainland and 6 groups, 2 species subgroups and 3 complexes are considered incertae sedis within the genus Drosophila. Different morphological characters provide different signals at different phylogenetic scales: thoracic characters (wing venation and presternal shape) discriminate families; grasping and erection‐related characters discriminate subfamilies to tribes; whereas phallic paraphyses, i.e. auxiliary intromittent organs, discriminate genera and Drosophila subgenera. The study shows the necessity of analysing morphological characters within a molecular phylogenetic framework to translate molecular phylogenies into taxonomically‐comprehensive classifications.     

A phylogeny of extant penguins (Aves: Sphenisciformes) combining morphology and mitochondrial sequences

The phylogenetic relationships among the penguins have received little attention, despite their well‐known anatomy and the conspicuous nature of the group. Previous attempts have included datasets limited to few, mostly osteological characters, and one study was based on integumentary and breeding characters. We developed a morphological matrix comprising 159 morphological characters of osteology (70 characters), myology (15), digestive tract (1), integument (66), and breeding (7 characters), scored in 18 extant forms (all currently recognized species plus one distinct subspecies). A gaviiform was placed at the root, and 11 species of representative procellariiform groups completed the outgroup. A heuristic parsimony analysis under equal weights was performed. We also compiled DNA sequences available in GenBank for the mitochondrial genes 12S rDNA and cytochrome b. We included the two data partitions in a combined analysis under direct optimization. Both analyses recovered the monophyly of Sphenisciformes and all the traditional polytypic genera. Morphological characters performed optimally at the ordinal and generic nodes, also providing resolution and varying degrees of support at supra‐ and intrageneric nodes. The comparison of molecular and morphological results indicated that the most significant problem in the phylogeny of extant penguins is rooting the ingroup. The mutual interaction of molecular and morphological data decreases the ambiguity regarding the placement of the root, and provides a resolved, relatively well‐supported phylogeny of extant penguins. Biogeographical patterns based on breeding ranges and derived from the combined analysis show that the major intercontinental vicariance events detected are consistent with cold marine current patterns of the Southern Hemisphere. © The Willi Hennig Society 2005.     

Phylogeny of the tribe Abrotrichini (Cricetidae,Sigmodontinae): integrating morphological and molecular evidence into a new classification

The tribe Abrotrichini (five genera and 14 living species) is a small clade within the speciose subfamily Sigmodontinae (Rodentia, Cricetidae), representing one of the extant successful radiations of mammals at southern high latitudes of the Neotropics. Its distribution is mostly Andean, reaching its greatest diversity in southern Argentina and Chile. We evaluate the phylogenetic relationships within this tribe through parsimony and Bayesian approaches based on 99 morphological characters (including 19 integumental characters, 38 skull characters, 31 dental characters, three postcranial skeletal characters, seven from the male accessory glands and phallus and one from the digestive system) and six molecular markers (one mitochondrial and five nuclear). We include representatives of all, except one, of the currently recognized species of living Abrotrichini plus one fossil form. Based on total evidence, we recovered a primary division between the genus Abrothrix and a group including the long‐clawed Abrotrichini, Chelemys, Geoxus, Notiomys and Pearsonomys. Both clades are recognized and named here as subtribes. The large degree of morphological variation observed within Abrothrix suggests that species in the genus fall into four groups, which we recognize as subgenera. In addition, the two known species of Chelemys do not form a monophyletic group, and Geoxus was recovered as paraphyletic with respect to Pearsonomys. To reconcile classification and phylogenetics, we describe a new genus for Chelemys macronyx and include Pearsonomys as a junior synonym of Geoxus. Our results highlight the importance of both morphology and molecules in resolving the phylogenetic relationships within this tribe. Based on biogeographical analyses, we hypothesize that Abrotrichini originated in south‐western South America by vicariance and then diversified mostly by successive dispersal events.     

Phylogenetic Position of Mammoth and Steller's Sea Cow Within Tethytheria Demonstrated by Mitochondrial DNA Sequences

Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Procavia capensis). These molecular data have allowed us to construct the phylogeny for the Tethytheria. Our molecular data resolve the trichotomy between the two species of living elephants and the mammoth and confirm that the mammoth was more closely related to the Asian elephant than to the African elephant. Our data also suggest that the sea cow–dugong divergence was likely as ancient as the dugong–manatee split, and it appears to have been much earlier (22 million years ago) than had been previously estimated (4–8 million years ago) by immunological comparison. Received: 8 August 1996 / Accepted: 30 September 1996     

Combined phylogenetic analysis of the subclass Marchantiidae (Marchantiophyta): towards a robustly diagnosed classification

The most extensive combined phylogenetic analyses of the subclass Marchantiidae yet undertaken was conducted on the basis of morphological and molecular data. The morphological data comprised 126 characters and 56 species. Taxonomic sampling included 35 ingroup species with all genera and orders of Marchantiidae sampled, and 21 outgroup species with two genera of Blasiidae (Marchantiopsida), 15 species of Jungermanniopsida (the three subclasses represented) and the three genera of Haplomitriopsida. Takakia ceratophylla (Bryophyta) was employed to root the trees. Character sampling involved 92 gametophytic and 34 sporophytic traits, supplemented with ten continuous characters. Molecular data included 11 molecular markers: one nuclear ribosomal (26S), three mitochondrial genes (nad1, nad5, rps3) and seven chloroplast regions (atpB, psbT‐psbH, rbcL, ITS, rpoC1, rps4, psbA). Searches were performed under extended implied weighting, weighting the character blocks against the average homoplasy. Clade stability was assessed across three additional weighting schemes (implied weighting corrected for missing entries, standard implied weighting and equal weighting) in three datasets (molecular, morphological and combined). The contribution from different biological phases regarding node recovery and diagnosis was evaluated. Our results agree with many of the previous studies but cast doubt on some relationships, mainly at the family and interfamily level. The combined analyses underlined the fact that, by combining data, taxonomic enhancements could be achieved regarding taxon delimitation and quality of diagnosis. Support values for many clades of previous molecular studies were improved by the addition of morphological data. The long‐held assumption that morphology may render spurious or low‐quality results in this taxonomic group is challenged. The morphological trends previously proposed are re‐evaluated in light of the new phylogenetic scheme.     

The evolutionary relationships of two families of cottoid fishes of Lake Baikal (East Siberia) as suggested by analysis of mitochondrial DNA

Fragments of mtDNA genes Cyt B, ATPase 6, and ATPase 8 of six cottoid fishes species of Lake Baikal (East Siberia) were amplified and sequenced. In addition mtDNAs of the same fish were subjected to restriction analysis. The data obtained were used to construct phylogenetic trees. The topology of the ATPase tree differs from those of the Res (restriction) and Cyt B trees. Clustering of species within the trees confirms the viewpoint of Taliev (1955, Baicalian Sculpins (Cottoidei)) according to which Baikalian cottoids originate from two ancestral forms. The times of branching obtained do not confirm the existing viewpoint according to which the two golomyankas (Comephorus baicalensis and Comephorus dybowskii) are pre-Baikal (Myocene) relicts: these two species may have originated 1.2–1.8 million years ago in Baikal, and they seem to represent an example of rapid morphological evolution which resulted in the formation of a new family. Correspondence to: S. Ja. Slobodyanuk     

Morphological Evidence for the Phylogeny of Cetacea

A cladistic analysis of 54 extant and extinct cetacean taxa scored for 304 morphological characters supports a monophyletic Odontoceti, Mysticeti, Autoceta, and Cetacea. Forcing a sister-group relationship between Mysticeti and Physeteridae, as suggested by some, but not all, molecular studies, requires an additional 72 steps. In agreement with recent molecular studies, morphological data divide extant mysticetes into two clades: Balaenopteroidea (Eschrichtiidae + Balaenopteridae) and Balaenoidea (Balaenidae + Neobalaenidae). Cetotheriopsinae is removed from Cetotheriidae, elevated to Family Cetotheriopsidae, and placed within the Superfamily Eomysticetoidea. All extant mysticetes and all cetotheriids are placed in a new Parvorder Balaenomorpha, which is diagnosed by many morphological characters, including fusion of the anterior and posterior processes of petrosal to ectotympanic bulla, pronounced median keel on palate, and absence of ventral margin of sigmoid process of bulla. Many of the clades within Odontoceti in the most parsimonious trees of this study are at odds with recent phylogenetic analyses. For example, Platanistidae is not closely related to the extinct odontocete families Squalodontidae and Squalodelphinidae. Instead, it is more closely related to extant river-dwelling odontocetes (i.e., Lipotes, Inia), suggesting a single dispersal of odontocetes into freshwater habitats. We found several characters to support Physeteroidea (Physeteridae + Ziphiidae), a taxon considered paraphyletic by several molecular and some morphological analyses. Lack of agreement on the phylogeny within Odontoceti indicates that additional analyses, which include molecular and anatomical data as well as extant and extinct taxa, are needed.     

Extinct large colobines from the Plio-Pleistocene of Africa

Three genera and six species of extinct African Plio-Pleistocene Colobinae are discussed. One new genus, Rhinocolobus and three new species, R. turkanaensis, Cercopithecoides kimeui and Paracolobus mutiwa are named. These colobines show a diversity in postcranial and dental morphology not seen among extant species. Rhinocolobus was most similar to extant Colobus in postcranial morphology and had similar high-cusped shearing teeth. Cercopithecoides shows a number of postcranial skeletal features typical of terrestrial cercopithecid species and has lower cusped teeth. Paracolobus, while generally more similar to Rhinocolobus than to Cercopithecoides, is intermediate in some features of its postcranial morphology. The distribution of the various taxa among East and South African sites with different palaeoenvironments is generally consistent with the morphological interpretation. With the exception of Cercopithecoides kimeui, which persisted a little longer, these large colobines disappear from the fossil record about 1.8 million years ago. Their disappearance coincides with an interval of increasing aridity documented at Olduvai Gorge, the Omo Valley, and East Turkana.     

Phylogeny and taxonomy of European funnel‐web spiders of the Tegenaria−Malthonica complex (Araneae: Agelenidae) based upon morphological and molecular data

The taxonomy and systematics of European house spiders, currently constituting the ill‐defined Tegenaria?Malthonica complex (including Aterigena) in the family Agelenidae, are revised. In Europe four monophyletic genera and 81 species are defined. One genus, Eratigena gen. nov. , and seven species are described as new; at species level 17 new synonyms and 20 new combinations are proposed, and the original combination of 14 species is reinstated. Five species could not be placed (incertae sedis) because of insufficient material and one taxon is regarded as ‘nomen dubium’. On the basis of a detailed morphological assessment, 88 characters were chosen for a cladistic analysis. Phylogenetically informative characters include mostly spination patterns as well as spinneret and genital structures. In addition to morphology, three gene sections [cytochrome c oxidase subunit 1 (CO1), nicotinamide adenine dinucleotide dehydrogenase subunit 1 (NADH1) 28S] were analysed. Morphological and molecular analyses were performed individually and in combination applying maximum parsimony and Bayesian tree search methods. In all resulting trees Malthonica and Tegenaria in their present composition are either polyphyletic or paraphyletic. Consequently, we redefined the two genera and erected a new genus, Eratigena gen. nov. Identification keys are provided for the European agelenid genera as well as for the European species of Tegenaria and Eratigena gen. nov. The genera and most of the constituent species are described and illustrated. The new classification has also been applied to some extra European members of the Tegenaria‐Malthonica complex resulting in additional three new synonyms, seven reversals to the original combination, and four new combinations. © 2013 The Linnean Society of London