Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene

Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 120 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae.     

木灵藓科分类与系统学研究：历史、问题和展望

木灵藓科(Orthotrichaceae)是藓类植物中的第3大科。该科不仅种类多, 生态类型特殊, 而且是世界公认的多样化程度高、分类难度大、系统关系复杂的类群。当代木灵藓科植物分类系统学研究主要集中在该科的地区志编写和专属分类修订。目前, 除了热带美洲、热带非洲的变齿藓属(Zygodon)和火藓属(Schlotheimia)部分类群外, 木灵藓科主要类群的分类修订工作已基本完成, 但是有关亚科和属的划分和地位以及各属之间的关系等方面仍存在众多争议。木灵藓科分支系统学研究也不够系统全面, 有的仅应用了单个基因片段, 或者只涉及少数类群。因此, 需要基于更多的分子和形态学性状, 进一步开展世界木灵藓科植物的系统发育研究, 建立一个更趋自然的木灵藓科分类系统。     

Molecular phylogeny and systematics of flowering plants of the family Crassulaceae DC

Crassulaceae (orpine or stonecrop family) is the most species-rich (ca. 1400 spp) family in the order Saxifragales. Most members of the family are succulent plants. Phenotypic diversity and large number of species complicates systematics of the family and obscures reconstruction of relationship within it. Phylogenetic analyzes based on morphological and molecular markers placed Crassulaceae as one of the crown clades of Saxifragales. In this contribution a review of phylogenetic studies on the family Crassulaceae, based on DNA nucleotide sequence comparisons is presented; major clades established in the family are characterised; their structure and polyphylesis of some genera are discussed. It is shown that the traditional taxonomic structure of Crassulaceae contradicts pattern of phylogenetic relationships between its members. We critically analyzed recent taxonomic systems of the family and stress that homoplasy of morphological characters does not allow to use them to reconstruct relationships between crassulacean taxa even at the low taxonomic levels.     

Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence

The genus Mus encompasses 38 species of mice divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . Each of these four taxa is characterized by discrete morphological as well as biochemical traits. We used two different molecular approaches to determine the relationships between these subgenera: DNA/DNA hybridization and 12S rRNA mitochondrial sequences. We compared the resulting phylogenies from each method and with phylogenies derived from morphological data. The degree of resolution of each molecular approach is discussed. The two molecular studies indicate that Mus , Pyromys , Nannomys and Coelomys are clearly distinct monophyletic groups, as previously indicated by morphological data and other biochemical and molecular approaches. There is one divergence between previous morphological and the molecular and morphological studies presented here: the position of the Indian species Mus famulus . This taxon, which was formerly included in the subgenus Coelomys , is demonstrated here to belong to the subgenus Mus. We also propose the following relationships within Mus sensu lato : Mus and Pyromys are the closest relatives, followed by Nannomys and Coelomys , whose relationships are still unclear. This arrangement is more robustly supported by DNA/DNA hybridization than by 12S rRNA data. A molecular time scale for the evolution within Mus sensu lato is proposed, using as a reference the Mus/Rattus divergence estimated by the fossil record at around 12 mya.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 137 , 385–401.     

More evidence for pervasive paraphyly in scleractinian corals: Systematic study of Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular and morphological data

Coral taxonomy and systematics continue to be plagued by a host of problems. Due to high phenotypic variability within species, morphological approaches have often failed to recognize natural taxa, and molecular techniques have yet to be applied to many groups. Here, we summarize the levels of paraphyly found for scleractinian corals and test, based on new data, whether paraphyly is also a significant problem in Faviidae, the second-most speciose hermatypic scleractinian family. Using both DNA sequence and morphological data we find that, regardless of analysis technique (maximum parsimony, maximum likelihood and Bayesian likelihood), many conventional taxonomic groups are not monophyletic. Based on two mitochondrial markers (COI and a noncoding region) that we amplified for 81 samples representing 41 faviid species and 13 genera, five genera that are represented by more than one species are paraphyletic, as is the family Faviidae. The morphological characters currently used to identify these corals similarly fail to recover many genera. Furthermore, trees based on both data types are incongruent, and total evidence analysis does little to salvage conventional taxonomic groupings. Morphological convergence, phenotypic variability in response to the environment, and recent speciation are likely causes for these conflicts, which suggest that the present classification of corals is in need of a major overhaul. We propose more detailed studies of problematic faviid taxa using standardized morphological, mitochondrial, and nuclear genetic markers to facilitate combining of data.     

The phylogenetic placement of Hollandichthys Eigenmann 1909 (Teleostei: Characidae) and related genera

The phylogenetic relationships among characids are complex with many genera remaining of uncertain systematic position inside the family. The genus Hollandichthys is one of these problematic genera. It has been considered as incertae sedis inside this family until two recently published phylogenies, one morphological and one molecular, arrived at alternative hypothesizes as to the relationships of Hollandichthys with Pseudochalceus or Rachoviscus, respectively. In this paper, we infer the phylogenetic relations of these taxa based on five genes (three mitochondrial - COI, ND2 and 16S; and two nuclear - Sia and Trop), totaling up to 2719 bp. The 41 analyzed species in the Characidae include four incertae sedis characid taxa once hypothesized as related to Hollandichthys, but never analyzed in a single phylogeny (Rachoviscus, Pseudochalceus, Nematocharax and Hyphessobrycon uruguayensis). Here we propose Rachoviscus as the sister-group of Hollandichthys, grouped in the large clade C previously defined, along with the remaining incertae sedis taxa studied here. In addition, we support the evidence that insemination evolved independently at least three times in the Characidae.     

Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family

The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichowensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis, that are consistent with or correspond to Barbini and Leuciscini. The Barbini includes taxa traditionally aligned with the subfamily Cyprininae sensu previous morphological revisionary studies by Howes (Barbinae, Labeoninae, Cyprininae and Schizothoracinae). The Leuciscini includes six other subfamilies that are mainly divided into three separate lineages. The relationships among genera and subfamilies are discussed as well as the possible origins of major lineages.     

A Molecular Phylogenetic Investigation of Bakuella,Anteholosticha, and Caudiholosticha (Protista,Ciliophora, Hypotrichia) Based on Three‐Gene Sequences

Traditionally classifications of the Urostyloida have been mainly based on morphology and morphogenesis. Recent molecular phylogenetic analyses have been largely based on single‐gene data for a limited number of taxa. Consequently, incongruence has arisen between the morphological/morphogenetic and the molecular data. In this study, the three phylogenetic markers (SSU rDNA, ITS1‐5.8S‐ITS2 region, and LSU‐rDNA) of three urostyloid genera represented by four species (Bakuella granulifera, Anteholosticha monilata, Caudiholosticha sylvatica, and C. tetracirra) were sequenced to investigate their phylogeny. The results show that: (1) all three genera should be regarded as the members of the order Urostyloida within the subclass Hypotrichia, as indicated by morphological characters; (2) phylogenetic analyses and sequence similarities both indicate that neither Anteholosticha nor Caudiholosticha are monophyletic and the systematic assignment of both genera awaits further evaluation; and (3) Bakuella has a closer relationship with Urostyla than with bakuellids (e.g. Apobakuella and Metaurostylopsis), suggesting Bakuella may belong to the family Urostylidae rather than the family Bakuellidae.     

Higher‐level phylogenetic affinities of the Neotropical genus Mastigodryas Amaral, 1934 (Serpentes: Colubridae), species‐group definition and description of a new genus for Mastigodryas bifossatus

Most Neotropical colubrid snakes belong to a single, well‐supported lineage. Relationships between the major constituents of this clade remain. Here, we explore the phylogenetic relationships of Mastigodryas and its affinities to other Neotropical colubrid genera by combining DNA and morphological data. Analyses demonstrate that the concatenation of multiple individuals into a single terminal can mask the detection of new taxa. Further, non‐random missing data and/or taxa in some empirical datasets can bias species tree analyses more than concatenation approaches. Our results place Mastigodryas in a strongly supported clade that includes Drymarchon, Rhinobothryum, Drymoluber, Simophis and Leptodrymus. Mastigodryas bifossatus is more closely related to species of Drymoluber and Simophis than to its congeners. Thus, we erect a new genus to accommodate it and recover a monophyletic Mastigodryas. We highlight the importance of the use of morphological characters to diagnose suprageneric clades by showing that some key external and hemipenial characteristics are phylogenetically informative.     

Molecular phylogeny of the diatom genera Amphora and Halamphora (Bacillariophyta) with a focus on morphological and ecological evolution

The taxonomic history of the diatom genus Amphora is one of a broad early morphological concept resulting in the inclusion of a diversity of taxa, followed by an extended period of revision and refinement. The introduction of molecular systematics has increased the pace of revision and has largely resolved the relationships between the major lineages, indicating homoplasy in the evolution of amphoroid symmetry. Within the two largest monophyletic lineages, the genus Halamphora and the now taxonomically refined genus Amphora, the intrageneric morphological and ecological relationships have yet to be explored within a phylogenetic framework. Critical among this is whether the range of morphological features exhibited within these diverse genera are reflective of evolutionary groupings or, as with many previously studied amphoroid features, are nonhomologous when examined phylogenetically. Presented here is a four‐marker molecular phylogeny that includes 31 taxa from the genus Amphora and 77 taxa from the genus Halamphora collected from fresh, brackish, and salt waters from coastal and inland habitats of the United States and Japan. These phylogenies illustrate complex patterns in the evolution of frustule morphology and ecology within the genera and the implications of this on the taxonomy, classification, and organization of the genera are discussed.     

Gametophytic simplicity in Laurasian and Gondwanan Polytrichopsida — the phylogeny and taxonomy of the Oligotrichum morphology

Abstract

Phylogenetic analyses have largely resolved generic and higher level relationships within the Polytrichopsida, enabling polarisation of characters and the identification of macro-evolutionary trends. Topologies show strong geographic patterning, with major groups having predominantly Northern or Southern Hemisphere distributions and some general morphologies having arisen independently on either side of the equator. While most cases of apparent convergence have been taxonomically visible due to sufficient higher-level characters being present to distinguish unrelated genera, convergent reduction may have resulted in conflation of similar gametophytic morphologies in classification. We present further evidence for the polyphyly of Oligotrichum DC. as currently circumscribed, showing how this morphology has probably arisen through reduction on multiple occasions to produce distinct lineages that have lacked taxonomic identity. We present a preliminary arrangement of the species currently recognised in Oligotrichum, accommodating selected Southern Hemisphere taxa in Itatiella G.L.Sm., and combining Atrichopsis compressa (Hook.f. & Wilson) G.L.Sm. and Oligotrichum tenuirostre (Hook.) A.Jaeger under Notoligotrichum G.L.Sm. For several species that clearly do not belong in Oligotrichum but remain of ambiguous affinity to other genera we avoid making new combinations, as ongoing combined molecular and morphological studies have considerable potential to elucidate their relationships in the near future.     

Grazing insects reduce algal biomass in a neotropical stream

The Darwinulidae are the only surviving post-Palaeozoic darwinulocopine family of an extensive radiation that reached its maximum in the Permian. Whereas at least some Palaeozoic darwinulids are known from sexual populations, the surviving lineages after the end-Permian mass extinction have abandoned sex since 200 million years ago. This makes the extant family Darwinulidae one of the few putative ancient asexual groups. Only about 30 species in 5 genera are presently known. The phylogeny of these taxa is here analysed using both morphological characters and molecular data. Twelve characters on valve morphology and 17 characters pertaining to appendages are used to construct the most parsimonious (unrooted) cladogram of 12 species in 5 genera. DNA sequences of one nuclear (ITS1) and a mitochondrial (COI) gene of 6 species in 5 genera are used to construct rooted maximum parsimony trees. Both molecular and morphological trees show a high degree of congruence, indicating that Alicenula and Vestalenula mostly cluster closely together, while Penthesilenula and Microdarwinula constitute a robust group. The position of the monospecific genus Darwinulais more variable, but is mostly closer to the two former genera. Congeneric species always cluster together in the morphological cladograms, and these results thus confirm that the five genera recognised by Rossetti & Martens (1998) are good phyletic units. An approximate molecular clock (calibrated with fossil data) indicates that the extant darwinulids share a common ancestor, which lived at least 100 million years ago.     

梧桐科分类学研究评述

梧桐科(Sterculiaceae)是锦葵目中的一个多型科,主要分布于热带和亚热带地区,只有少数种可分布到温带地区。由于该科植物的形态特征较为多样化,至今对于它的范围和所包含的属种数目在各国学者间仍没有达成共识。该文从梧桐科的分类地位和系统关系、属的分类地位和亲缘关系以及分类学新特征在梧桐科分类中的应用3个方面入手,分析了梧桐科分类学研究的历史、现状和存在的问题,特别是把来自分子资料的研究结果与传统分类进行了比较分析,试图为梧桐科的分类学研究提供更多的帮助。     

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 molecular phylogeny of Planorboidea (Gastropoda, Pulmonata): insights from enhanced taxon sampling

Planorbid gastropods are the most diverse group of limnic pulmonates, with both discoidal and highspired taxa. Phylogenetic relationships among these genera are confused and controversial. In particular, the monophyly of the limpet‐like taxa (traditionally Ancylidae) is disputed. Even recent molecular studies have concluded that substantially more work is necessary to solve the remaining issues concerning intergeneric phylogenetic relationships and higher taxa systematics. Planorbid snails are of great significance for humans as several members of this group are intermediate hosts of blood flukes (schistosomes) causing a chronic disease, schistosomiasis. We used the two independent molecular markers COI and 18S (concatenated dataset of 2837 nucleotide bp) to infer phylogenetic relationships of 26 genera (27 species) of Planorboidea, represented mostly by type species from mainly topotypical populations. With the majority of the taxa discussed not having been studied previously, this study attempted to test several hypotheses on planorbid phylogenetic relationships using Bayesian inference techniques. The monophyly of Planorboidea (= ‘Ancyloplanorbidae’) is strongly suggested on the basis of our extensive molecular analysis. Besides a distinct Burnupia clade, two major clades were recovered that correspond to family level taxa (traditional Bulinidae and Planorbidae). Considerable rearrangements of suprageneric taxa are evident from the phylogeny inferred. Therefore, the only clades recognized by current classifications and supported by our analysis are Planorbini and Segmentinini. The present study found that Ancylidae as traditionally understood, i.e. covering most freshwater limpet gastropods, is paraphyletic, as the genera of Burnupia and Protancylus have been shown to lie phylogenetically outside the Ancylini. Chromosome numbers and levels of polyploidy are discussed in the light of the new phylogeny. An earlier theory of shell shape evolution, i.e. that of patelliform taxa being most advanced, was not supported by this study; a limpet‐shaped taxon is most basal within Planorboidea. Although many taxa still remain to be studied, our results will hopefully contribute towards a better understanding of this very important group of freshwater organisms. Some taxonomic implications are discussed.     

Two apparently unrelated groups of symbiotic annelids,Nautiliniellidae and Calamyzidae (Phyllodocida,Annelida), are a clade of derived chrysopetalid polychaetes

Nautiliniellidae Miura and Laubier, 1989 is a small family of marine polychaetes with 20 currently described species in 11 genera, most of which are known to live symbiotically in the mantle cavity of bivalves, mainly from cold seeps and hydrothermal vents, while Calamyzidae (Hartmann‐Schröder, 1971) including only one described species, Calamyzas amphictenicola Arwidsson 1932 lives as an ectoparasite on ampharetid polychaetes in Swedish waters. Nautiliniellidae and Calamyzidae have both been considered to belong to Phyllodocida, but the few phylogenetic studies including these taxa have found their positions unstable. The internal relationships within Nautiliniellidae are also poorly understood. Using molecular information from both nuclear and mitochondrial genes and morphological data we assessed the systematic placement of Nautiliniellidae (seven species; collected from Pacific hydrothermal vents and cold seeps and one from Atlantic waters) and Calamyzas amphictenicola. Our results show that C. amphictenicola and Nautiliniellidae formed a well‐supported clade that is nested within Chrysopetalidae, a free‐living group of polychaetes. The chrysopetalid genus Vigtorniella Kiseleva 1992; a bacterial mat grazer found at methane seeps, anoxic basins and whalefalls, formed a paraphyletic grade with respect to the Nautiliniellidae–Calamyzas clade. The internal relationships within the Nautiliniellidae–Calamyzas clade as well as the relationships with their hosts are also examined. As a result we synonymize Calamyzidae and Nautiliniellidae with Chrysopetalidae, with the last as the oldest available family‐group name. Within Chrysopetalidae we refer to the subfamilies Chrysopetalinae Ehlers 1864; Dysponetinae Aguado, Nygren & Rouse, herein; and Calamyzinae Hartmann‐Schröder, 1971. Calamyzinae contains C. amphictenicola, all taxa formerly in Nautiliniellidae, and the chrysopetalid genus Vigtorniella.     

Molecular phylogeny of the hexagrammid fishes using a multi-locus approach

Ideally, organisms are grouped into monophyletic assemblages reflecting their evolutionary histories. Single (molecular) markers can reflect the evolutionary history of the marker, rather than the species in question, therefore, phylogenetic relationships should be inferred from adequate sampling of characters. Because the use of multiple loci greatly improves the resolving power of the molecular assay, we constructed a molecular phylogeny of the family Hexagrammidae based on six loci, including two mitochondrial and four nuclear loci. The resulting molecular phylogeny, from the combined data, was significantly different from the morphological topology suggested by Shinohara [Memoirs of the Faculty of Fisheries, Hokkaido University 41 (1994) 1]. Our data support a monophyletic assemblage for the genera Hexagrammos and Pleurogrammus. However, other taxa traditionally included in the family Hexagrammidae did not form a monophyletic assemblage. The monotypic genus Ophiodon was more closely associated with cottids than with other hexagrammids. Our data concur with the morphological topology in that the genera Zaniolepis and Oxylebius formed a monophyletic clade, which was distinct and basal to the remaining hexagrammids, seven cottids and one agonid.