SSU rRNA reveals a sequential increase in shell complexity among the euglyphid testate amoebae (Rhizaria: Euglyphida)

The existing data on the molecular phylogeny of filose testate amoebae from order Euglyphida has revealed contradictions between traditional morphological classification and SSU rRNA phylogeny and, moreover, the position of several important genera remained unknown. We therefore carried out a study aiming to fill several important gaps and better understand the relationships among the main euglyphid testate amoebae and the evolutionary steps that led to the present diversity at a higher level. We obtained new SSU rRNA sequences from five genera and seven species. This new phylogeny obtained shows that (1) the clade formed by species of genera Assulina and Placocista branches unambiguously at the base of the subclade of Euglyphida comprising all members of the family Trinematidae and genus Euglypha, (2) family Trinematidae (Trachelocorythion, Trinema, and Corythion) branches as a sister group to genus Euglypha, (3) three newly sequenced Euglypha species (E. cf. ciliata, E. penardi, and E. compressa) form a new clade within the genus. Since our results show that Assulina and Placocista do not belong to the Euglyphidae (unless the Trinematidae are also included in this family), we propose the creation of a new family named Assulinidae. Consequently, we give a family status to the genera Euglypha and (tentatively) Scutiglypha, which become the new family Euglyphidae. The evolutionary pattern suggested by SSU rRNA phylogeny shows a clear tendency towards increasing morphological complexity of the shell characterised by changes in the symmetry (migration of the aperture to a ventral position and/or compression of the shell) and the appearance of specialised scales at the aperture (in families Trinematidae and Euglyphidae).     

Phylogenetic reconstruction and shell evolution of the Diplommatinidae (Gastropoda: Caenogastropoda)

The fascinating and often unlikely shell shapes in the terrestrial micromollusc family Diplommatinidae (Gastropoda: Caenogastropoda) provide a particularly attractive set of multiple morphological traits to investigate evolutionary patterns of shape variation. Here, a molecular phylogenetic reconstruction, based on five genes and 2700 bp, was undertaken for this family, integrated with ancestral state reconstruction and phylogenetic PCA of discrete and quantitative traits, respectively. We found strong support for the Diplommatininae as a monophyletic group, separating the Cochlostomatidae into a separate family. Five main clades appear within the Diplommatininae, corresponding with both coiling direction and biogeographic patterns. A Belau clade (A) with highly diverse (but always sinistral) morphology comprised Hungerfordia, Palaina, and some Diplommatina. Arinia (dextral) and Opisthostoma (sinistroid) are sister groups in clade B. Clade C and D solely contain sinistral Diplommatina that are robust and little ornamented (clade C) or slender and sculptured (clade D). Clade E is dextral but biogeographically diverse with species from all sampled regions save the Caroline Islands. Adelopoma, Diplommatina, Palaina, and Hungerfordia require revision to allow taxonomy to reflect phylogeny, whereas Opisthostoma is clearly monophyletic. Ancestral state reconstruction suggests a sinistral origin for the Diplommatinidae, with three reversals to dextrality.     

COI barcoding of Nebelid testate amoebae (Amoebozoa: Arcellinida): extensive cryptic diversity and redefinition of the Hyalospheniidae Schultze

We used Cytochrome Oxidase Subunit 1 (COI) to assess the phylogenetic relationships and taxonomy of Nebela sensu stricto and similar taxa (Nebela group, Arcellinida) in order to clarify the taxonomic validity of morphological characters. The COI data not only successfully separated all studied morphospecies but also revealed the existence of several potential cryptic species. The taxonomic implications of the results are: (1) Genus Nebela is paraphyletic and will need to be split into at least two monophyletic assemblages when taxon sampling is further expanded. (2) Genus Quadrulella, one of the few arcellinid genera building its shell from self-secreted siliceous elements, and the mixotrophic Hyalosphenia papilio branch within the Nebela group in agreement with the general morphology of their shell and the presence of an organic rim around the aperture (synapomorphy for Hyalospheniidae). We thus synonymise Hyalospheniidae and Nebelidae. Hyalospheniidae takes precedence and now includes Hyalosphenia, Quadrulella (previously in the Lesquereusiidae) and all Nebelidae with the exception of Argynnia and Physochila. Leptochlamys is Arcellinida incertae sedis. We describe a new genus Padaungiella Lara et Todorov and a new species Nebela meisterfeldi n. sp. Heger et Mitchell and revise the taxonomic position (and rank) of several taxa. These results show that the traditional morphology-based taxonomy underestimates the diversity within the Nebela group, and that phylogenetic relationships are best inferred from shell shape rather than from the material used to build the shell.     

Phylogenetic analyses of small subunit ribosomal RNA coding regions reveal a monophyletic lineage of euglyphid testate amoebae (Order Euglyphida)

The Testaceafilosia includes amoebae with filopodia and with a proteinaceous, agglutinated or siliceous test. To explore the deeper phylogeny of this group, we sequenced the small subunit ribosomal RNA coding region of 13 species, including the first sequence of an amoeba with an agglutinated test, Pseudodifflugia sp. Phylogenetic analyses using maximum parsimony and maximum likelihood methods as well as neighbor joining method yielded the following results: the order Euglyphida forms a monophyletic lineage with the sarcomonads as sister group. The next related taxa are the Chlorarachnea and the unidentified filose strain N-Por. In agreement with the previous studies the Phytomyxea branch off at the base of this lineage. The Monadofilosa (Testaceafilosia and Sarcomonadea) appear monophyletic. The Testaceafilosia are polyphyletic, because Pseudodifflugia sp. is positioned as the sister taxon to the sarcomonads. Within the order Euglyphida Paulinella branches off first, together with Cyphoderia followed by Tracheleuglypha. In maximum likelihood and neighbor joining analyses, the genus Euglypha is monophyletic. The branching pattern within the order Euglyphida reflects the evolution of shell morphology from simple to complex built test.     

Phylogenetic reconstruction of the evolution of stylar polymorphisms in Narcissus (Amaryllidaceae)

We investigated the origin of stylar polymorphisms in Narcissus, which possesses a remarkable range of stylar conditions and diverse types of floral morphology and pollination biology. Reconstruction of evolutionary change was complicated by incomplete resolution of trees inferred from two rapidly evolving chloroplast regions, but we bracketed reconstructions expected on the fully resolved plastid-based tree by considering all possible resolutions of polytomies on the shortest trees. Stigma-height dimorphism likely arose on several occasions in Narcissus and persisted across multiple speciation events. As proposed in published models, this rare type of stylar polymorphism is ancestral to distyly. While there is no evidence in Narcissus that dimorphism preceded tristyly, a rapid transition between them may explain the lack of a phylogenetic footprint for this evolutionary sequence. The single instances of distyly and tristyly in Narcissus albimarginatus and N. triandrus, respectively, are clearly not homologous, an evolutionary convergence unique to Amaryllidaceae. Floral morphology was likely an important trigger for the evolution of stylar polymorphisms: Concentrated-changes tests indicate that a long, narrow floral tube may have been associated with the emergence of stigma-height dimorphism and that this type of tube, in combination with a deep corona, likely promoted, or at least was associated with, the parallel origins of heterostyly.     

基于线粒体COI基因片段的麻蝇属(双翅目:麻蝇科)部分种类DNA分类研究

本研究在Pape(1996)提出的麻蝇属(双翅目:麻蝇科)分类系统基础上,选取麻蝇属54个物种(分属于30个亚属),基于线粒体COI基因片段,结合雄性成蝇尾器形态特征,对所选取的30个亚属进行了DNA分类研究,初步探明了各亚属的分类地位与系统发育关系.麻蝇属30个亚属内的平均遗传距离为6.0％(1.8％～11.0％),各亚属间的平均遗传距离为10.1％(5.2％ ～16.1％),亚属内与亚属间遗传距离差异较为明显,说明COI基因片段对麻蝇属各亚属级阶元能进行有效区分.     

Mitochondrial phylogenomics reveals insights into taxonomy and evolution of Penaeoidea (Crustacea: Decapoda)

The taxonomy and phylogeny of Penaeoidea have long been fraught with controversy. Here, we carried out the first mitochondrial phylogenomic analysis on all the penaeoid families and tribes, including nine newly sequenced and 14 published mitogenomes, towards elucidating the phylogeny and evolutionary history of Penaeoidea. All these nine mitogenomes exhibit the pancrustacean ground pattern, except that Benthonectes filipes contains two additional clusters of tRNA^Ala, tRNA^Arg and tRNA^Asn and an uncommon noncoding region. The resulted phylogenetic tree is generally well resolved with Benthesicymidae sister to Aristeidae, forming a clade with Solenoceridae. Contrary to traditional classification, this clade has a sister relationship with the tribe Penaeini of the family Penaeidae. The family Sicyoniidae is deeply nested within the penaeid tribe Trachypenaeini which forms a sister clade with the remaining penaeid tribe, Parapenaeini. As the family Penaeidae is recovered to be polyphyletic, the three tribes in Penaeidae are all elevated to familial status. On the other hand, the family Sicyoniidae is retained to accommodate Trachypenaeini because they are now synonyms and the former name is more senior. This work is the first molecular analysis concurring with the latest findings in fossil assessments showing that Parapeaneini is the most primitive in Penaeoidae. Our results also illustrate a shallow‐water origin and an onshore–offshore evolutionary shift in penaeoid shrimps.     

Ecology of testate amoebae communities from aquatic habitats in the Zackenberg area (Northeast Greenland)

A total of 67 taxa, belonging to 15 genera, were recorded from aquatic samples collected in Zackenberg (Northeast Greenland). Most taxa belong to the genera Difflugia, Centropyxis, Nebela and Euglypha. Trinema lineare showed the highest relative abundance. Seven taxa were recorded for the first time in the Arctic. A TWINSPAN classification reveals two groups, reflecting a local geographical distinction. In the ponds of the old Zackenberg delta area (group 1), two assemblages were found: the Paraquadrula globulosa-Cyphoderia perlucidus assemblage and the Difflugiella crenulata-Cryptodifflugia compressa assemblage. The lakes, the pools and ponds east of the Zackenberg river (group 2) also harbour two assemblages: the Trinema enchelys-Euglypha sp.1 assemblage and the Centropyxis aerophila-Difflugia globulosa assemblage. Although the lakes are chemically unique, having extremely low values for turbidity, colour, SiO²⁻ ₂, Cl⁻ and hardness, this is not reflected in the characteristic testacean communities. Accepted: 24 April 1999     

Phylogenetic relationships and taxonomy of subfamily Zygophylloideae (Zygophyllaceae) based on molecular and morphological data

Phylogenetic analysis of noncoding trnL plastid DNA sequences and morphological data for 43 species of Zygophylloideae, representing most of the morphological and geographical variation in the subfamily, indicates that the currently recognised genera Augea (monotypic, southern Africa), Tetraena (monotypic, China), and Fagonia (c. 30 species, widespread), are embedded in Zygophyllum (c. 150 species, widespread). A generic classification based on six monophyletic and morphologically distinctive entities is proposed: Roepera with c. 60 species in Australia and southern Africa, Zygophyllum with c. 50 species in Asia, Tetraena with c. 40 species in Africa and Asia, Augea with a single species in southern Africa, Melocarpum with two species in the Horn of Africa region, and Fagonia with c. 30 species in both the Old and the New World. Scanning electron microscopy studies of testa structure provided important characters for the delimitation of some genera. New combinations (61) are made in Roepera, a resurrected genus originally described from Australia, one new name is proposed in Zygophyllum, 35 new combinations are made in Tetraena, and two new combinations are made in Melocarpum (previously Zygophyllum sect. Melocarpum).     

Phylogenetic reconstruction of Polymastiidae (Demospongiae: Hadromerida) based on morphology

Phylogeny of the sponge family Polymastiidae was reconstructed based on 25 morphological characters. Twenty-one polymastiid species and three suberitid species, Suberites domuncula as outgroup, Aaptos aaptos and A. papillata as sister groups, were included in the analyses. The reconstructions were done in PAUP* running heuristic search with the parsimony criterion. We analysed three possible evolutionary scenarios based on three alternative interpretations of the body plan of Quasillina brevis and Ridleia oviformis: first—Ridleia possesses aquiferous papillae whereas Quasillina lacks them, second—both genera lack papillae and third—the body in both genera is a single hyper-developed papilla. All three scenarios excluded the secondary loss of the papillae in the polymastiid evolution. Scenario 2 also excluded the secondary loss of the regular choanosomal skeleton, while scenario 1 assumed its loss in Ridleia and scenario 3 admitted its loss in both Ridleia and Quasillina. We prioritised scenario 2 due to its maximal parsimony and rescaled consistency index and subsequently favoured the clustering of Ridleia and Quasillina separately from the monophyletic polymastiid clade. In all three scenarios Pseudotrachya hystrix clustered separately from other polymastiids in agreement with the molecular evidence, and thus the exclusion of Pseudotrachya from Polymastiidae was proposed. The relationships between A. papillata, Tentorium semisuberites, Polymastia uberrima, the clade Weberella bursa + Polymastia boletiformis and the main polymastiid clade were ambiguous. Meanwhile, all scenarios showed the non-monophyly of Polymastia and Aaptos. Our hypotheses should be tested by reconstructions based on larger taxon sampling of hadromerid species and larger sets of morphological and molecular characters before any ultimate taxonomic decisions are taken.     

Evaluating the use of dominant microbial consumers (testate amoebae) as indicators of blanket peatland restoration

Peatlands represent globally-important ecosystems and carbon stores. However, large areas of peatland have been drained for agriculture, or peat has been harvested for use as fuel or in horticulture. Increasingly, these landscapes are being restored through ditch blocking and rewetting primarily to improve biodiversity and promote peat accumulation. To date we have little knowledge of how these interventions influence the microbial communities in peatlands. We compared the responses of dominant microbial consumers (testate amoebae) to drainage ditch restoration relative to unblocked ditches in a UK upland blanket peatland (Migneint, North Wales). Two techniques were used for restoration: (i) dammed ditches with re-profiling; and (ii) dammed ditches with pools of open water behind each dam. Testate communities in the inter-ditch areas changed markedly over time and between treatments illustrating the potential of this group of organisms as indicators of blanket peatland restoration status. However, the responses of testate amoebae to peat rewetting associated with restoration were partially obscured by inter-annual variability in weather conditions through the course of the experiment. Although there was considerable variability in the response of testate amoebae communities to peatland drain blocking, there were clearly more pronounced changes in samples from the dammed and reprofiled treatments including an increase in diversity, and the appearance of unambiguous wet-indicator species in relatively high abundances (including Amphitrema stenostoma, Archerella flavum, Arcella discoides type, Difflugia bacillifera and Difflugia bacillarium). This reflects a shift towards overall wetter conditions across the site and the creation of new habitats. However, water-table was not a significant control on testate amoebae in this case, suggesting a poor relationship between water table and surface moisture in this sloping blanket peatland. Our findings highlight the potential of testate amoebae as bioindicators of peatland restoration success; however, there is a need for caution as mechanisms driving change in the microbial communities may be more complex than first assumed. Several factors need to be taken into account when implementing biomonitoring studies in peatlands including: (i) the natural variability of the peatland ecosystem under changing weather conditions; (ii) any disturbance connected with the restoration procedures; and (iii) the timescales over which the ecosystem responds to the management intervention. Our results also suggest an indicator species approach based on population dynamics may be more appropriate for biomonitoring peatland restoration than examining changes at the community level.     

Phylogenetic taxonomy of Hymenochaete and related genera (Hymenochaetales)

Species delimitation in Hymenochaete sensu lato was evaluated based on partial nucLSU rDNA sequences, isoenzyme analyses and morphological data. Analyses of LSU data revealed Hymenochaete sensu stricto and Pseudochaete as distinct monophyletic genera. Transfer of Hydnochaete olivacea into genus Pseudochaete and Dichochaete setosa into genus Hymenochaete (as H. resupinata) was supported by the results of molecular analyses. A new species Hymenochaete koeljalgii from Tanzania was described. The species of genus Hymenochaete sensu stricto were divided into four well-supported clades possessing no distinctive morphological characters.     

Ecology of terrestrial testate amoebae assemblages from coastal Lowlands on Devon Island (NWT,Canadian Arctic)

Summary Fifty-seven taxa belonging to 17 genera of testate rhizopods were recorded in samples of mosses, soils and lichens, collected from the Truelove and Sparbo Hardy Lowlands on the high arctic Devon Island (NWT, Canada). Different groups of habitats are characterized by particular assemblages of Testacea species, with the quantity and quality of the available water as important ecological parameters. The Assulina muscorum-Corythion dubium assemblage characterizes the most dry and acidic moss habitats, while the Paraquadrula irregularis assemblage is to be found in wet and rather neutral habitats. The sedge moss meadows with their more moderately coarse textured and poorly drained soils, bear a Plagiopyxis callida-Plagiopyxis declivis soil-dwelling testate amoebae assemblage. The Centropyxis minuta assemblage lives in the most coarsely textured soils. pH seems to play a subordinate role, not only in the mosses but also in the soils. Multivariate methods (cluster analysis and CANOCO) have been used to separate these different assemblages.     

Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COI sequences

Phylogenetic relationships within the subclass Pteriomorphia (Bivalvia) were examined using sequences of the mitochondrial cytochrome c oxidase subunit I gene. The resultant Minimum Evolution phylogenetic tree strongly supports the existing superfamily-level classification with all the members of each superfamily forming clades. At the same time, it is suggested that: (1) Ostreoidea shows a closer relationship to Pinnoidea and Pterioidea than to the other superfamilies; (2) Pectinoidea, Anomioidea, and Limoidea form a clade, (3) Arcoidea and Limopsoidea form a clade; (4) The subclass Anomalodesmata is closer to the subclass Heterodonta than to Mytiloidea; and (5) The subclass Pteriomorphia is monophyletic. Taking these results as well as published data for nuclear 18S ribosomal DNA (18S rDNA) and Myosin analyses into consideration, a new order-level classification system for Pteriomorphia is proposed.     

Phylogenetic relationships in the louse genus Penenirmus based on nuclear (EF-1α) and mitochondrial (COI) DNA sequences

Abstract. Ischnoceran lice in genus Penenirmus are parasites of birds in orders Piciformes and Passeriformes. No comprehensive revision of this genus has been published, but a few host-based revisions have been done. Here we present a phylogenetic analysis of Penenirmus based on nuclear (elongation factor-1 alpha) and mitochondrial (cytochrome oxidase I) gene sequences. Sequences from portions of both these genes provide a well resolved tree that is relatively stable across methods of analysis and to bootstrap resampling. Some aspects of the Penenirmus phylogeny reflect the phylogeny of their avian hosts. We identified monophyly of a group of Penenirmus species occurring on Passeriformes as well as monophyly of a group containing species sometimes placed in a genus Picophilopterus . Species of Penenirmus occurring on Old World barbets fall in several positions at the base of the tree, suggesting that other lineages of Penenirmus may be derived from those occurring on Old World barbets.     

祖先性状重建法揭示铁线蕨属植物孢子表面纹饰的形态多样性及其演化

蕨类植物孢子表面的纹饰形态复杂多样, 在分类学和古生物学研究中具有重要意义, 目前探索祖先性状演化常用形态学与系统发育学结合的方法。本文选取一回羽叶铁线蕨类植物为材料, 用扫描电子显微镜观察其孢子形态, 用5个叶绿体基因序列构建系统树, 用最大似然法和最大简约法来分析孢子性状的演化。结果表明: 一回羽叶铁线蕨类的孢子纹饰有5种类型, 即光滑、粗糙、颗粒、疣状及瘤状; 这一类群的祖先孢子纹饰有很大的可能是瘤状纹饰; 疣状纹饰可能是由瘤状纹饰演化而来; 孢子纹饰由简单向复杂演化, 越进化的物种其孢子纹饰越复杂。     

Phylogenetic relationships and evolution in Chrysosplenium (Saxifragaceae) based on matK sequence data

Chrysosplenium (Saxifragaceae) consists of 57 species widely distributed in temperate and arctic regions of the Northern Hemisphere, with two species restricted to the southern part of South America. Species relationships within the genus are highly problematic. The genus has traditionally been divided into two groups, sometimes recognized as sections (Oppositifolia and Alternifolia), based on leaf arrangement, or, alternatively, into 17 series. Based on morphological features, Hara suggested that the genus originated in South America and then subsequently migrated to the Northern Hemisphere. We conducted phylogenetic analyses of DNA sequences of the chloroplast gene matK for species of Chrysosplenium to elucidate relationships, test Hara's biogeographic hypothesis for the genus, and examine chromosomal and gynoecial diversification. These analyses revealed that both sections Oppositifolia and Alternifolia are monophyletic and form two large sister clades. Hence, leaf arrangement is a good indicator of relationships within this genus. Hara's series Pilosa and Macrostemon are each also monophyletic; however, series Oppositifolia, Alternifolia, and Nepalensia are clearly not monophyletic. MacClade reconstructions suggest that the genus arose in Eastern Asia, rather than in South America, with several independent migration events from Asia to the New World. In one well-defined subclade, species from eastern and western North America form a discrete clade, with Old World species as their sister group, suggesting that the eastern and western North American taxa diverged following migration to that continent. The South American species forms a clade with species from eastern Asia; this disjunction may be the result of ancient long-distance dispersal. Character mapping demonstrated that gynoecial diversification is dynamic, with reversals from inferior to half-inferior ovaries, as well as to ovaries that appear superior. Chromosomal evolution also appears to be labile with several independent origins of n = 12 (from an original number of n = 11) and multiple episodes of aneuploidy.     

Phylogenetic analysis and taxonomy of the poecilioid fishes (Teleostei: Cyprinodontiformes)

Evidence from morphology is used to infer the phylogeny of the superfamily Poecilioidea using other cyprinodontoid fishes as outgroups. The three equally most parsimonious trees resulting from the phylogenetic analysis support the monophyly of the families Anablepidae and Poeciliidae with respect to each other, but the previous taxonomy within the Poeciliinae is not consistent with the resultant phylogenetic trees. The Poeciliidae is recognized with three subfamilies: the Aplocheilichthyinae containing solely Aplocheilichthys spilauchen , the Procatopodinae containing Fluviphylax (Fluviphylacini) and the African lamp-eyed killifishes (Procatopodini), and the Poeciliinae. The inferred hierarchical relationships of included suprageneric taxa are: ((Oxyzygonectinae, Anablepinae) (Aplocheilichthyinae ((Fluviphylacini, Procatopodini) (Alfarini (Priapellini (Gambusini (Heterandrini (Cnesterodontini (Girardini, Poeciliini))))))))). The tribe Alfarini is resurrected and a new tribe, the Priapellini, is described. Tomeurus gracilis is not the most basal poeciliine, and facultative viviparity in Tomeurus is not a plesiomorphic intermediate condition of viviparity retained from the common ancestor of poeciliines. Facultative viviparity in Tomeurus is the result of an evolutionary loss of obligate viviparity. Tomeurus gracilis is recognized as a member of the tribe Cnesterodontini. Lamprichthys tanganicus and Micropanchax pelagicus are not sister taxa, and the pelagic lacustrine habits of these two species are inferred to have evolved independently. Based on the principles of vicariance biogeography, the origin of the Poecilioidea is inferred to have occurred before the separation of Africa and South America.