Phylogeny of Recent Canidae (Mammalia, Carnivora): relative reliability and utility of morphological and molecular datasets

Zrzavý, J. & ?i?ánková, V. (2004). Phylogeny of Recent Canidae (Mammalia, Carnivora): relative reliability and utility of morphological and molecular datasets. — Zoologica Scripta, 33, 311–333. Phylogenetic relationships within the Canidae are examined, based on three genes (cytb, COI, COII) and 188 morphological, developmental, behavioural and cytogenetic characters. Both separate and combined phylogenetic analyses were performed. To inspect the phylogenetic ‘behaviour’ of individual taxa, basic phylogenetic analysis was followed by experimental cladistic analyses based on different data‐partition combinations and taxon‐removal analyses. The following phylogeny of the Recent Canidae is preferred: (1) Urocyon is the most basal canid; (2) Vulpes is a monophyletic genus (including Fennecus and Alopex); (3) the doglike canids (DC) form a clade (=Dusicyon + Pseudalopex + Lycalopex + Cerdocyon + Atelocynus + Chrysocyon + Speothos + Lycaon + Cuon + Canis), split into two subclades, South American and Afro‐Holarctic, with uncertain position of the Chrysocyon + Speothos subclade; (4) Canis is paraphyletic due to the position of Lycaon and Cuon. Otocyon and Nyctereutes are the most problematic canid genera, causing an unresolved branching pattern of Otocyon, Vulpes, Nyctereutes and DC clades. Reclassification of the two basal species of ‘Canis’ into separate genera is proposed (Schaeffia for ‘C.’ adustus, Lupulella for ‘C.’ mesomelas). Although the morphological dataset ranked poorly in both separate and simultaneous analyses (measured by number of minimum‐length topologies, relative number of resolved nodes in the strict consensus of all minimum‐length topologies, consistency and retention indices, nodal dataset influence, and number of extra steps required by the data partition to reach the topology of the combined tree), the morphological synapomorphies represent nearly one quarter of all synapomorphies in the combined tree. Among the hidden morphological support of the combined tree the developmental and behavioural characters are conspicuously abundant.     

Global interrelationships of Plesiosauria (Reptilia,Sauropterygia) and the pivotal role of taxon sampling in determining the outcome of phylogenetic analyses

Previous attempts to resolve plesiosaurian phylogeny are reviewed and a new phylogenetic data set of 66 taxa (67% of ingroup taxa examined directly) and 178 characters (eight new) is presented. We recover two key novel results: a monophyletic Plesiosauridae comprising Plesiosaurus dolichodeirus, Hydrorion brachypterygius, Microcleidus homalospondylus, Occitanosaurus tournemirensis and Seeleyosaurus guilelmiimperatoris; and five plesiosaurian taxa recovered outside the split between Plesiosauroidea and Pliosauroidea. These taxa are Attenborosaurus conybeari, ‘Plesiosaurus’macrocephalus and a clade comprising Archaeonectrus rostratus, Macroplata tenuiceps and BMNH 49202. Based on this result, a new name, Neoplesiosauria, is erected for the clade comprising Plesiosauroidea and Pliosauroidea. Taxon subsamples of the new dataset are used to simulate previous investigations of global plesiosaurian relationships. Based on these simulations, most major differences between previous global phylogenetic hypotheses can be attributed to differences in taxon sampling. These include the position of Leptocleididae and Polycotylidae and the monophyly or paraphyly of Rhomaleosauridae. On this basis we favour the results recovered by our, larger analysis. Leptocleididae and Polycotylidae are sister taxa, forming a monophyletic clade within Plesiosauroidea, indicating that the large‐headed, short‐necked ‘pliosauromorph’ body plan evolved twice within Plesiosauria. Rhomaleosauridae forms the monophyletic sister taxon of Pliosauridae within Pliosauroidea. Problems are identified with previous phylogenetic definitions of plesiosaurian clades and new, stem‐based definitions are presented that should maintain their integrity over a range of phylogenetic hypotheses. New, rank‐free clade names Cryptoclidia and Leptocleidia are erected to replace the superfamilies Cryptoclidoidea and Leptocleidoidea. These were problematic as they were nested within the superfamily Plesiosauroidea. The incongruence length difference test indicates no significant difference in levels of homoplasy between cranial and postcranial characters.     

Towards a phylogeny and evolution of Acochlidia (Mollusca: Gastropoda: Opisthobranchia)

The Acochlidia are unique among opisthobranch gastropods in combining extremely high morphological and ecological diversity with modest species diversity. The phylogeny of acochlidians has never been addressed by cladistic means, as their evolution has remained unknown. This study gives a first overview on more than 150 biological and morphological characters that are potentially useful for phylogenetic analysis. Based on 107 characters, a parsimony analysis (PAUP) was performed for all 27 valid acochlidian species together with 11 (plus two) outgroup taxa. The resulting strict consensus tree shows a moderate overall resolution, with at least some bootstrap support for most resolved nodes. The Acochlidia are clearly monophyletic, and originate from an unresolved basal opisthobranch level. The Acochlidia split into the Hedylopsacea (Tantulum (Hedylopsis (Pseudunela (Strubellia (‘Acochlidium’, ‘Palliohedyle’))))) and Microhedylacea (Asperspina (Pontohedyle, ‘Parhedyle’, ‘Microhedyle’, (Ganitus, Paraganitus))). The formerly enigmatic Ganitidae, resembling sacoglossan opisthobranchs by having dagger‐like rachidian radular teeth, are likely to be highly derived microhedylids. The paraphyly of some of the traditionally recognized family level taxa induced a preliminary reclassification. From the phylogenetic hypothesis obtained, we conclude that the acochlidian ancestor was marine mesopsammic. The colonization of limnic systems occurred twice, independently: first in the Caribbean (with the development of the small interstitial Tantulum elegans), and second in the Indo‐Pacific, with a radiation of large‐sized benthic acochlidian species. The evolution of extraordinary reproductive features, such as hypodermic impregnation by a complex copulative aparatus in hedylopsaceans, cutaneous insemination via spermatophores in microhedylaceans, and gonochorism in Microhedylidae s.l. (including Ganitidae), is discussed. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 124–154.     

An assessment of the status of Polycirridae genera (Annelida: Terebelliformia) and evolutionary transformation series of characters within the family

A phylogenetic analysis was performed to determine the monophyly of non‐monotypic genera of the terebelliform family Polycirridae, i.e. Polycirrus, Amaeana, Lysilla, and Hauchiella, and the evolution of characters among members of this clade. The monotypic genera, Enoplobranchus and Biremis, were also included, together with members of both known species in Hauchiella. Representative species were included for remaining genera: 14 species of Polycirrus, six species of Amaeana, and six species of Lysilla. Out‐groups consisted of representatives of Spionidae, Cirratulidae, and Sabellariidae, as well as several species of Telothelepodidae. A total of 40 in‐ and out‐group species were coded for 50 subjects (‘characters’) and 117 subject–predicate relationships (‘states’). Although results are consistent with recent phylogenetic studies within Terebelliformia that suggest Polycirridae monophyly, only Hauchiella was found to be monophyletic, albeit part of the more inclusive clade comprising remaining polycirrid genera. Evolutionary transformation series are discussed for selected characters in relation to the non‐monophyly of Polycirrus, Lysilla, and Amaeana. Implications for the use of supraspecific taxa as ‘taxonomic surrogates’ are highlighted. The definition of Polycirridae is emended. © 2015 The Linnean Society of London     

Exploring myrmecophily based on the phylogenetic interrelationships of Falagonia Sharp, 1883 (Coleoptera: Staphylinidae: Aleocharinae) and allied genera

The taxonomy of Lomechusini Fleming has a complex history. Recent studies have shown that this group is polyphyletic; however, little is known about the evolutionary interrelationships among its constituent genera. The goals of the present study are to infer the phylogenetic relationships of Falagonia Sharp and closely related genera; to define the boundaries of those genera based on synapomorphic characters; and to explore the evolution of myrmecophily within the lineage. The phylogenetic analyses are based exclusively on morphological characters of adults. A total of 36 operational taxonomic units were used for the analysis. The best trees were selected based on maximum parsimony and Bayesian inference. During the parsimony reconstruction, different weighting strategies were used to recover the most robust phylogenetic hypothesis. Although minor differences were observed in the results of the different analyses, the topologies were consistent throughout. Several groups of genera proposed by Seevers (1965), such as the ‘Tetradonia’ and ‘Ecitopora’ groups, were not recovered. Thus, these may represent nonmonophyletic groups that were based on nonsynapomorphic diagnostic characters. Our analyses consistently recovered the genera Asheidium Santiago‐Jiménez, Delgadoidium Santiago‐Jiménez, Falagonia, Newtonidium Santiago‐Jiménez, Pseudofalagonia Santiago‐Jiménez, Sharpidium Santiago‐Jiménez, Tetradonia Wasmann and Thayeridium Santiago‐Jiménez, forming a monophyletic group that we have called the ‘Asheidium complex’. Falagonia mexicana Sharp shows seven autapomorphies, none of which were used to establish the genus. Based on the phylogenetic results, myrmecophily has evolved independently at least three times within the lineage. This study, based on morphological characters, is one of the first approaches towards gaining an understanding of the phylogenetic relationships within the polyphyletic tribe Lomechusini.     

Miniatures,morphology and molecules: Paedocypris and its phylogenetic position (Teleostei,Cypriniformes)

We review the morphological and molecular evidence that Mayden & Chen recently used to infer that the developmentally truncated fish genus Paedocypris is not a member of the teleost order Cypriniformes or carp‐like fishes, but is ‘the basal sister group to all Cypriniformes’. This hypothesis contradicts several previous studies that used molecular sequence data or morphological characters. A review of the morphological characters that Mayden & Chen discussed and mapped onto their ‘simplified tree’ shows that these, analysed alone, rather support a close relationship of the cyprinids Sundadanio, Danionella, and Paedocypris. We also present four additional analyses of morphological data, which all contradict Mayden & Chen's result. Despite its highly reductive skeleton, posing a serious problem when analysing its phylogenetic position with skeletal characters, the presence in Paedocypris of the basioccipital masticatory plate is compelling evidence that it is a member of the Cyprinoidei (Cyprinidae plus Psilorhynchidae). Our reanalysis and exploration of their molecular sequence data shows that only a single gene, EGR3, of the six nuclear genes analysed by Mayden & Chen, is responsible for the position of Paedocypris as ‘the basal sister group to all Cypriniformes’. Three independent methods to visualize and analyse phylogenetic signal and conflict of data sets (phylogenetic networks, splits analysis methods or SAMS, and site‐wise likelihood analyses) reveal a high level of character conflict and noise in Mayden & Chen's data set. The ‘basal’ position of Paedocypris seems to be the outcome of the interplay of two long‐branch effects. We apply the same analytical methods to the data set from Rüber et al.'s molecular analysis of the phylogenetic position of Paedocypris and discuss our findings. We conclude that none of the molecular data sets compiled to date can establish the phylogenetic position of Paedocypris with confidence. Morphological data suggest that Paedocypris and Danionella are sister genera, and that their closest relative is Sundadanio, although the position of these three miniatures among cyprinoids is still unclear. © 2014 The Linnean Society of London     

Phylogeny of New Zealand hepialid moths (Lepidoptera: Hepialidae) inferred from a cladistic analysis of morphological data

The phylogeny of the New Zealand hepialid moths was estimated from a cladistic analysis of sixty‐three morphological characters, from all life cycle stages. One hundred and sixteen maximum parsimony trees were produced. The phylogenetic reconstruction indicated that the currently recognized generic concepts, and the four informal lineages hypothesized in a previous morphological taxonomic revision, were monophyletic. The relationships of species within genus Wiseana were not fully resolved. Analysis of a data set of thirty‐nine adult male characters from the New Zealand taxa and the Australian genera Jeana, Oxycanus and Trictena supported the monophyly of the New Zealand ‘Oxycanus’ s.s lineage.     

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.     

Taxonomic classification of the reef coral family Lobophylliidae (Cnidaria: Anthozoa: Scleractinia)

Lobophylliidae is a family‐level clade of corals within the ‘robust’ lineage of Scleractinia. It comprises species traditionally classified as Indo‐Pacific ‘mussids’, ‘faviids’, and ‘pectiniids’. Following detailed revisions of the closely related families Merulinidae, Mussidae, Montastraeidae, and Diploastraeidae, this monograph focuses on the taxonomy of Lobophylliidae. Specifically, we studied 44 of a total of 54 living lobophylliid species from all 11 genera based on an integrative analysis of colony, corallite, and subcorallite morphology with molecular sequence data. By examining coral skeletal features at three distinct levels – macromorphology, micromorphology, and microstructure – we built a morphological matrix comprising 46 characters. Data were analysed via maximum parsimony and transformed onto a robust molecular phylogeny inferred using two nuclear (histone H3 and internal transcribed spacers) and one mitochondrial (cytochrome c oxidase subunit I) DNA loci. The results suggest that micromorphological characters exhibit the lowest level of homoplasy within Lobophylliidae. Molecular and morphological trees show that Symphyllia, Parascolymia, and Australomussa should be considered junior synonyms of Lobophyllia, whereas Lobophyllia pachysepta needs to be transferred to Acanthastrea. Our analyses also lend strong support to recent revisions of Acanthastrea, which has been reorganized into five separate genera (Lobophyllia, Acanthastrea, Homophyllia, Sclerophyllia, and Micromussa), and to the establishment of Australophyllia. Cynarina and the monotypic Moseleya remain unchanged, and there are insufficient data to redefine Oxypora, Echinophyllia, and Echinomorpha. Finally, all lobophylliid genera are diagnosed under the phylogenetic classification system proposed here, which will facilitate the placement of extinct taxa on the scleractinian tree of life.     

Phylogeny and classification of Ochlerotatus and allied taxa (Diptera: Culicidae: Aedini) based on morphological data from all life stages

The phylogenetic relationships and generic assignments of ‘Ochlerotatus’ and related taxa of uncertain taxonomic position in the classification of Aedini previously proposed by the authors in 2004 and 2006 are explored using 297 characters from eggs, fourth‐instar larvae, pupae, adults and immature habitat coded for 158 exemplar species. The ingroup comprises 54 species and the outgroup includes four non‐aedine species and 100 aedine species, 21 of which were previously classified as incertae sedis. Data are analysed in a total‐evidence approach using implied weighting. The analysis produced 158 most parsimonious cladograms. The strict consensus tree (SCT) corroborates the monophyly of the 30 generic‐level taxa recognized previously that are included in the analysis. Overall, the results show remarkable congruence with those obtained previously despite differences in the taxa and morphological characters analysed in this and the two previous studies. All species of Ochlerotatus s.s., subgenus ‘Ochlerotatus’sensu auctorum, Geoskusea, Levua, Pseudoskusea and Rhinoskusea included in the analysis fall within a single clade that is treated as genus Ochlerotatus; thus, the last four taxa are restored to their previous subgeneric rank within this genus. Nine additional subgenera, of which four are new, are proposed for monophyletic clades of Ochlerotatus species based on the strength of character support and application of the principle of equivalent rank. Acartomyia stat. nov. , Culicelsa stat. nov. , Gilesia stat. nov. , Protoculex stat. nov. and Chrysoconops stat. nov. are resurrected from synonymy with Ochlerotatus; and Empihals subgen. nov. (type species: Culex vigilax Skuse), Pholeomyia subgen. nov. (type species: Aedes calcariae Marks), Buvirilia subgen. nov. (type species: Aedes edgari Stone & Rosen) and Sallumia subgen. nov. (type species: Aedes hortator Dyar & Knab) are described as new. The sister group of Ochlerotatus includes a number of species that were previously regarded as incertae sedis in ‘Oc. (Finlaya)’ and ‘Oc. (Protomacleaya)’. Based on previous observations, refined relationships and new character support, three additional genera are recognized for species previously included in ‘Finlaya’, i.e. Danielsia stat. nov . (type species: Danielsia albotaeniata Leicester), Luius gen. nov. (type species: Aedes fengi Edwards) and Hopkinsius gen. nov. (type species: Aedes ingrami Edwards). Additionally, Alloeomyia subgen. nov. (type species: Culex pseudotaeniatus Giles) and Yamada subgen. nov. (type species: Aedes seoulensis Yamada) are introduced as subgenera of Collessius and Hopkinsius, respectively. As is usual with generic‐level groups of Aedini, the newly recognized genera and subgenera are polythetic taxa that are diagnosed by unique combinations of characters. The analysis corroborates the previous observation that ‘Oc. (Protomacleaya)’ is a polyphyletic assemblage of species. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 29–114.     

Phylogeny and evolution of the South African genus Metalasia (Asteraceae–Gnaphalieae) inferred from molecular and morphological data

Metalasia is a genus in tribe Gnaphalieae (Asteraceae), endemic to South Africa and with its main distribution in the Cape Floristic Region. The genus comprises 57 species and, with a number of closely related genera, it constitutes the ‘Metalasia clade’. A species‐level phylogenetic analysis is presented, based on DNA sequences from two nuclear (internal and external transcribed spacer: ITS, ETS) and two plastid (psbA‐trnH, trnL‐trnF) regions together with morphological data. Analyses combining molecular and morphological data attempt not only to resolve species interrelationships, but also to detect patterns in character evolution. Phylogenetic analyses corroborate our earlier study and demonstrate that Metalasia is formed of two equally sized, well‐supported sister groups, one of which is characterized by papillose cypselas. The results differ greatly from earlier hypotheses based on morphology alone, as few morphological characters support the phylogenetic patterns obtained. The two clades of Metalasia do, however, appear to differ in distribution, corresponding to the different rainfall regimes of South Africa. Analyses show a few taxa to be problematic; one example is the widely distributed M. densa which appears to be an intricate species complex. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 173–198.     

Comparative vegetative anatomy and classification of Diseae (Orchidaceae)

The leaf, stem, root, tuber and dropper anatomy of the orchid tribe Diseae (including the subtribes Satyriinae, Disinae, Brownlecinac, Huttonaeinae and Coryciinae) is reviewed. The study is largely based on investigations of 123 species, and data from several previous publications have also been incorporated. Two characters were identified as being taxonomically valuable: (1) the presence of sclerenchyma caps associated with leaf vascular bundles, and (2) the degree of dissection of the siphonostele of the tuber (‘polystelic’ or ‘monostelic’). The phylogenetic analysis shows that anatomical characters do not change the basic structure of a cladogram that is based on morphological characters. The taxa of Diseae are discussed on the basis of anatomical data. Subtribes Satyriinae (excluding the anatomically unusual genus Pachites), Brownleeinae, Huttonaeinae, and Coryciinae are uniform in. critical anatomical characters. However, subtribe Disinae is rather diverse in vegetative anatomy. Disa sect. Micranthae differs from the rest of the genus in its leaf anatomy. The occurrence of foliar sclerenchyma bundle caps and ‘polystelic’ tubers supports the incorporation of Herschelianthe in Disa sect. Stenocarpa.     

Palaeomorphology: fossils and the inference of cladistic relationships

Edgecombe, G.D. 2010. Palaeomorphology: fossils and the inference of cladistic relationships. —Acta Zoologica (Stockholm) 91 : 72–80 Twenty years have passed since it was empirically demonstrated that inclusion of extinct taxa could overturn a phylogenetic hypothesis formulated upon extant taxa alone, challenging Colin Patterson’s bold conjecture that this phenomenon ‘may be non‐existent’. Suppositions and misconceptions about missing data, often couched in terms of ‘wildcard taxa’ and ‘the missing data problem’, continue to cloud the literature on the topic of fossils and phylogenetics. Comparisons of real data sets show that no a priori (or indeed a posteriori) decisions can be made about amounts of missing data and most properties of cladograms, and both simulated and real data sets demonstrate that even highly incomplete taxa can impact on relationships. The exclusion of fossils from phylogenetic analyses is neither theoretically nor empirically defensible.     

Taxonomic revision and phytogeographic studies in Euphorbia (Euphorbiaceae) in the Khorassan provinces of Iran

This study is focused on the genus Euphorbia L. in a part of northeast Iran, viz. the three Khorassan provinces. Since there are many taxa of Euphorbia in Iran which are used in different industries and have significant effects on human and non‐human life it is important to revise their taxonomy. With about 90 species, following Turkey with 91 species, Iran is the second richest country for Euphorbia in Asia. Of these, 30 species are distributed in the Khorassan provinces. This is the first comprehensive work on the genus in this region. According to ‘Flora Iranica’, there are 17 species of Euphorbia in northeast Iran, while according to our results, there are 30 species of Euphorbia in the Khorassan provinces alone. In addition to various new taxonomic and biogeographic results, a new species, viz. E. chamanbidensis, is described. Euphorbia chamanbidensis is closely related to E. aucheri, but seed micro‐morphological characters differentiate them. Two identification keys to the Euphorbia species of the studied area are provided, one based on macro‐morphological characters and another based on seed micro‐morphological characters. Phytogeographic analysis and distribution maps for all species are also presented.     

Legs of deception: disagreement between molecular markers and morphology of long‐legged flies (Diptera,Dolichopodidae)

Conflicting hypotheses in phylogenetics and systematics, generated by different data sets (e.g. morphological versus molecular), are common in biology. The clarification of such instances may allow understanding general mechanisms involved in the speciation process in an evolutionary light. Here, we present and discuss the case of the Dolichopus plumipes species group in the long‐legged flies, Dolichopodidae. A phylogenetic survey was performed based on both morphological and molecular data. The full data set comprises 31 morphological characters and 2252 molecular characters (mitochondrial – COI: 810; 12S: 343; 16S: 514; nuclear – ITS2: 585) of 49 different species, represented by 82 specimens. The molecular phylogenetic analysis revealed a clade (composed by the species D. plumipes, Dolichopus wahlbergi, Dolichopus polleti, Dolichopus simplex, and Dolichopus nigricornis) that disagrees with the traditional morphological view based on external characters. In particular, specimens of the species D. plumipes and D. simplex were indistinguishable with the molecular markers used here. Yet, we still consider D. plumipes and D. simplex as two distinct taxa and provide explanatory hypotheses on the evolutionary background. The conspicuous male secondary sexual characters (present in plumipes but not in simplex) are key factors in sexual selection and their presumably rapid reduction in D. simplex is thought to be of main importance for the explanation of the speciation process. The plumipes–simplex case may therefore be viewed as a paradigmatic illustration showing that a better integration of the molecular and morphological approaches is needed to understand and clarify the, in some cases, complex systematics and phylogeny of organisms.