Phylogeny of Glaucosomatidae inferred from molecular evidence

Most species of glaucosomatids (Teleostei: Glaucosomatidae) are endemic to Australia, except Glaucosoma buergeri that is widely distributed from Australia to Japan. This study elucidated phylogenetic relationships among glaucosomatids based on the morphological characters of the saccular‐otolith sagitta, in addition to molecular evidence of mitochondrial 16S rDNA, cytochrome oxidase I (COI) and cytochrome b (cyt b) sequences, and nuclear rhodopsin sequences. The topologies of individuals' phylogenetic trees, based on 16S rDNA, COI and cyt b sequences, were statistically indistinguishable from one another, and were only slightly different from a tree based on rhodopsin sequences. These molecular tree topologies, however, differed from species relationships in morphology‐based phylogenetic hypothesis proposed in previous studies. Specimens of G. buergeri from Australia and Taiwan showed differences in the sagitta and molecular differentiation at the four genes, suggesting a possible speciation event. Both molecular and morphological evidences indicate that Glaucosoma magnificum is the plesiomorphic sister species of other glaucosomatid species. Glaucosoma hebraicum is the sister species of a clade composed of G. buergeri and Glaucosoma scapulare. Molecular and morphological evidences also support the species status of G. hebraicum.     

New taxa refresh the phylogeny and classification of pleurostomatid ciliates (Ciliophora,Litostomatea)

A high diversity of pleurostomatid ciliates has been discovered in the last decade, and their systematics needs to be improved in the light of new findings concerning their morphology and molecular phylogeny. In this work, a new genus, Protolitonotus gen. n., and two new species, Protolitonotus magnus sp. n. and Protolitonotus longus sp. n., were studied. Furthermore, 19 novel nucleotide sequences of SSU rDNA, LSU rDNA and ITS1‐5.8S‐ITS2 were collected to determine the phylogenetic relationships and systematic positions of the pleurostomatid ciliates in this study. Based on both molecular and morphological data, the results demonstrated that: (i) as disclosed by the sequence analysis of SSU rDNA, LSU rDNA and ITS1‐5.8S‐ITS2, Protolitonotus gen. n. is sister to all other pleurostomatids and thus represents an independent lineage and a separate family, Protolitonotidae fam. n., which is defined by the presence of a semi‐suture formed by the right somatic kineties near the dorsal margin of the body; (ii) the families Litonotidae and Kentrophyllidae are both monophyletic based on both SSU rDNA and LSU rDNA sequences, whereas Amphileptidae are non‐monophyletic in trees inferred from SSU rDNA sequences; and (iii) the genera Loxophyllum and Kentrophyllum are both monophyletic, whereas Litonotus is non‐monophyletic based on SSU rDNA analyses. ITS1‐5.8S‐ITS2 sequence data were used for the phylogenetic analyses of pleurostomatids for the first time; however, species relationships were less well resolved than in the SSU rDNA and LSU rDNA trees. In addition, a major revision to the classification of the order Pleurostomatida is suggested and a key to its families and genera is provided.     

DNA‐based phylogeny of the marine genus Heterodrilus (Annelida,Clitellata, Naididae)

Heterodrilus is a group of marine Naididae, common worldwide in subtropical and tropical areas, and unique among the oligochaetes by their tridentate chaetae. The phylogenetic relationships within the group are assessed from the nuclear 18S rDNA gene, and the mitochondrial cytochrome c oxidase subunit I (COI) and 16S rDNA genes. Sequence data were obtained from 16 Heterodrilus species and 13 out‐group taxa; 48 sequences are new for this study. The data were analysed by Bayesian inference. Monophyly of the genus is corroborated by the resulting tree, with Heterodrilus ersei (a taxon representing a small group of species with aberrant male genitalia) proposed to be outside all other sampled species. Although earlier regarded as a member of the subfamily Rhyacodrilinae, both molecular and morphological data seem to support that Heterodrilus is closely related to Phallodrilinae. However, the results are not conclusive as to whether the genus is the sister group of, or a group nested inside, or separate from this latter subfamily. The studied sample of species suggests at least two major clades in Heterodrilus with different geographical distributions, in one of the clades, most species are from the Indo‐West Pacific Ocean, while in the other, the majority are from the Western Atlantic Ocean. Morphological characters traditionally used in Heterodrilus taxonomy are optimized on the phylogenetic tree, revealing a high degree of homoplasy.     

Phylogeny and reclassification of the Caucasigenini radiation from the Caucasus region (Gastropoda,Hygromiidae)

The Caucasigenini is an endemic radiation of hygromiid land snails from the Caucasus region. A phylogenetic analysis of morphological characters of the genitalia and the shell showed that the morphological characters are insufficient for resolving the relationships within the Caucasigenini. Convergences of the few parsimony informative characters in other groups of the Hygromiidae demonstrate that these characters are not reliable indicators of phylogenetic relationships. Phylogenetic analyses of sequences of cox1, 16S rDNA, 5.8S rDNA, ITS2 and 28S rDNA revealed several well‐supported groups. The relationships among these groups could not be resolved. It is likely that these groups originated in a rapid radiation during the uplift of the Caucasus. Based on the molecular phylogeny, we propose a new classification of the species of the Caucasigenini and establish a new genus, Lazicana gen. n.     

Laboulbeniales hyperparasites (Fungi,Ascomycota) of bat flies: Independent origins and host associations

The aim of this study was to explore the diversity of ectoparasitic fungi (Ascomycota, Laboulbeniales) that use bat flies (Diptera, Hippoboscoidea) as hosts. Bat flies themselves live as ectoparasites on the fur and wing membranes of bats (Mammalia, Chiroptera); hence this is a tripartite parasite system. Here, we collected bats, bat flies, and Laboulbeniales, and conducted phylogenetic analyses of Laboulbeniales to contrast morphology with ribosomal sequence data. Parasitism of bat flies by Laboulbeniales arose at least three times independently, once in the Eastern Hemisphere (Arthrorhynchus) and twice in the Western Hemisphere (Gloeandromyces, Nycteromyces). We hypothesize that the genera Arthrorhynchus and Nycteromyces evolved independently from lineages of ectoparasites of true bugs (Hemiptera). We assessed phylogenetic diversity of the genus Gloeandromyces by considering the LSU rDNA region. Phenotypic plasticity and position‐induced morphological adaptations go hand in hand. Different morphotypes belong to the same phylogenetic species. Two species, G. pageanus and G. streblae, show divergence by host utilization. In our assessment of coevolution, we only observe congruence between the Old World clades of bat flies and Laboulbeniales. The other associations are the result of the roosting ecology of the bat hosts. This study has considerably increased our knowledge about bats and their associated ectoparasites and shown the necessity of including molecular data in Laboulbeniales taxonomy.     

Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon‐rich Analyses of Five Genes

Photosynthetic euglenids acquired chloroplasts by secondary endosymbiosis, which resulted in changes to their mode of nutrition and affected the evolution of their morphological characters. Mapping morphological characters onto a reliable molecular tree could elucidate major trends of those changes. We analyzed nucleotide sequence data from regions of three nuclear‐encoded genes (nSSU, nLSU, hsp90), one chloroplast‐encoded gene (cpSSU) and one nuclear‐encoded chloroplast gene (psbO) to estimate phylogenetic relationships among 59 photosynthetic euglenid species. Our results were consistent with previous works; most genera were monophyletic, except for the polyphyletic genus Euglena, and the paraphyletic genus Phacus. We also analyzed character evolution in photosynthetic euglenids using our phylogenetic tree and eight morphological traits commonly used for generic and species diagnoses, including: characters corresponding to well‐defined clades, apomorphies like presence of lorica and mucilaginous stalks, and homoplastic characters like rigid cells and presence of large paramylon grains. This research indicated that pyrenoids were lost twice during the evolution of phototrophic euglenids, and that mucocysts, which only occur in the genus Euglena, evolved independently at least twice. In contrast, the evolution of cell shape and chloroplast morphology was difficult to elucidate, and could not be unambiguously reconstructed in our analyses.     

Morphology and evolution of respiratory structures in the pleopod exopodites of terrestrial Isopoda (Crustacea, Isopoda, Oniscidea)

The morphology of the respiratory structures located in the pleopod exopodites of terrestrial Isopoda is described for representative species of different genera. Special emphasis is set on the evolution of these lungs in the context of phylogenetic relationships as revealed by other morphological characters. In the most primitive species of the Oniscidea, and still of subordinate taxa of the Crinocheta, respiration takes place in the thin ventral integument of the exopodites. The evolution of dorsal respiratory fields with a weakly wrinkled surface occurred at least six times within the Crinocheta. In five of these cases, a further development can be observed. The evolution of a partly covered respiratory field with strongly wrinkled surface may have taken place six times. It is assumed that completely internalized lungs with spiracles surrounded by a water‐repellent surface microsculpture, evolved at least six times independently within the Oniscidea: in the Tylidae, Actaecia, Aphiloscia, the Eubelidae, the Armadillidae and in a taxon probably comprising Porcellionidae plus Armadillidiidae.     

Molecular phylogeny and taxonomy of the genus Chaetophora (Chlorophyceae,Chlorophyta), including descriptions of Chaetophoropsis aershanensis gen. et sp. nov.

The broadly defined genus Chaetophora consisted of species with minute, uniseriate branching filaments enveloped in soft or firm mucilage forming macroscopic growths that are spherical, hemispherical, and tubercular or arbuscular, growing epiphytically on freshwater aquatic plants and other submerged surfaces in standing or fast‐flowing water. Recent molecular analyses clearly showed that this genus was polyphyletic. In this study, eight strains of Chaetophora and three strains of Stigeoclonium were identified and successfully cultured. In combination with the morphological data, a concatenated data set of four markers (18S + 5.8S + ITS2+ partial 28S rDNA) was also used to determine their taxonomic relationships and phylogenetic positions. The molecular analysis resolved the broadly defined Chaetophora to at least two genera. Species with a globose thallus of genus Chaetophora formed a separate monophyletic clade, which clearly separated from, a type of lobe‐form Chaetophora species. Therefore, we propose to erect a new genus, Chaetophoropsis, which includes all globose species of the Chaetophora. Chaetophoropsis aershanensis was determined to be a new species, based on its special characteristic of profuse long rhizoids. Stigeoclonium polyrhizum, as the closest relative to Chaetophoropsis, revealed its distant relationships to other species of Stigeoclonium. A globose thallus with a thick, soft mucilage matrix, and special rhizoidal branches lent further support to the placement of S. polyrhizum in the genus Chaetophoropsis and had the closest relationship to C. aershanensis. Taxonomic diversity was proven by distinctive morphological differences and by phylogenetic divergence in the broadly defined Chaetophora identified herein.     

Phylogenetic analysis reveals a scattered distribution of autumn colours

Background and Aims

Leaf colour in autumn is rarely considered informative for taxonomy, but there is now growing interest in the evolution of autumn colours and different hypotheses are debated. Research efforts are hindered by the lack of basic information: the phylogenetic distribution of autumn colours. It is not known when and how autumn colours evolved.

Methods

Data are reported on the autumn colours of 2368 tree species belonging to 400 genera of the temperate regions of the world, and an analysis is made of their phylogenetic relationships in order to reconstruct the evolutionary origin of red and yellow in autumn leaves.

Key Results

Red autumn colours are present in at least 290 species (70 genera), and evolved independently at least 25 times. Yellow is present independently from red in at least 378 species (97 genera) and evolved at least 28 times.

Conclusions

The phylogenetic reconstruction suggests that autumn colours have been acquired and lost many times during evolution. This scattered distribution could be explained by hypotheses involving some kind of coevolutionary interaction or by hypotheses that rely on the need for photoprotection.Key words: Autumn colour, leaf colour, comparative analysis, coevolution, photoprotection, phylogenetic analysis     

Taxonomy, phylogeny, and distribution of Puccinia graminis, the black stem rust: new insights based on rDNA sequence data

Puccinia graminis (Uredinales) is an economically important and common host-alternating rust species on Berberidaceae/Poaceae (subfamilies Pooideae and Panicoideae) that has been spread globally by human activities from an unknown center of origin. To evaluate the taxonomic implications, phylogenetic relationships, and distribution/spread of this complex species, we sequenced and cladistically analyzed the ITS1, 5.8S, and ITS2 regions from herbarium specimens on various host plants from Iran (17), Europe (1), and North America (4). The ITS region plus the 5.8S gene ranged from 686 to 701 bp, including the flanking partial sequences of the 18S and 28S rDNA. Our phylogenetic analysis included 54 bp of the 18S sequence, the entire ITS1 + 5.8S + ITS2, and 58 bp of the 28S sequence. A second analysis used only the last 42 bp of ITS1, and all the 5.8S and ITS2, to incorporate data from additional sequences downloaded from GenBank. In addition to variation in sequence length, there was variation in sequence content. The analysis does not support classical morphology-based taxonomic concepts of the P. graminis complex. Also, host range, host taxonomy, and geographic origin provide minor information on taxonomic relationships. Puccinia graminis is most probably monophyletic. Coevolutionary aspects can hardly be discussed because of lack of sequence data from alternate host specimens. The occurrence of unrelated fungal taxa on the same host species suggests that, besides coevolution with the host, host jumps and hybridization may have played an important role in the evolution of P. graminis. From rDNA data we conclude that the pathogen was introduced to North America at least twice independently. For a new taxonomic concept, we think the complex has to be split into at least two species. New morphological features and further features other than sequence data, however, must be checked for taxonomic value first and, if necessary, be considered.     

THE EVOLUTION OF ELONGATE SHAPE IN DIATOMS1

Diatoms have been classified historically as either centric or pennate based on a number of features, cell outline foremost among them. The consensus among nearly every estimate of the diatom phylogeny is that the traditional pennate diatoms (Pennales) constitute a well‐supported clade, whereas centric diatoms do not. The problem with the centric–pennate classification was highlighted by some recent analyses concerning the phylogenetic position of Toxarium, whereby it was concluded that this “centric” diatom independently evolved several pennate‐like characters including an elongate, pennate‐like cell outline. We performed several phylogenetic analyses to test the hypothesis that Toxarium evolved its elongate shape independently from Pennales. First, we reanalyzed the original data set used to infer the phylogenetic position of Toxarium and found that a more thorough heuristic search was necessary to find the optimal tree. Second, we aligned 181 diatom and eight outgroup SSU rDNA sequences to maximize the juxtapositioning of similar primary and secondary structure of the 18S rRNA molecule over a much broader sampling of diatoms. We then performed a number of phylogenetic analyses purposely based on disparate sets of assumptions and found that none of these analyses supported the conclusion that Toxarium acquired its pennate‐like outline independently from Pennales. Our results suggest that elongate outline is congruent with SSU rDNA data and may be synapomorphic for a larger, more inclusive clade than the traditional Pennales.     

Phylogenetic relationships of Chalara and allied species inferred from ribosomal DNA sequences

The phylogenetic relationships of Chalara and allied taxa are studied based on ribosomal DAN sequences. Partial 28S rDNA and 18S rDNA regions from 26 strains were sequenced in this study. These and related sequences from GenBank were analyzed using parsimony and Bayesian analyses. Most of the Chalara species clustered in a strongly supported monophyletic lineage representing Helotiales. However, a few Chalara species appeared closely related to Xylariales. The phylogenetic significance of morphological characters observed in Chalara species are evaluated based on our sequence analyses. Conidial septation, conidial width and conidiophore pigmentation are thought to be indicative in understanding their evolutionary relationships. Sterile setae, which traditionally have been used to delimitate Chaetochalara from Chalara, are phylogenetically insignificant.     

共球藻纲丝状藻中国新记录属种——洪泛拟寇丽藻

从甘肃省张掖市黑河流域分离了一株不分枝的丝状绿藻,对其进行纯培养并保藏于中国科学院淡水藻种库,编号FACHB 2451。形态观察表明,该藻株具有相对较长的营养细胞 (细胞长为宽的3~8倍)、双叶形的片状叶绿体、末端细胞顶端钝圆或略尖细等特征。结合形态比较和基于18S rDNA 基因序列的系统发育分析,确定该藻株为中国淡水共球藻纲新记录属种——洪泛拟寇丽藻 (Koliellopsis inundata Lokhorst)。分子系统发育研究结果表明,所分离的藻株与分离自比利时与荷兰边境农地的洪泛拟寇丽藻模式藻株序列相似度极高,且拟寇丽藻属与寇丽藻属、针丝藻属和拟针丝藻属等不分枝丝状拟寇丽藻科成员亲缘关系密切,可以较好地聚成一个亚支。     

Phylogenetic relationships within the superfamily Desmodoroidea (Nematoda: Desmodorida), with descriptions of two new and one known species

Three nematode species of the superfamily Desmodoroidea Filipjev, 1922, were isolated from beach sediments in Wellington, New Zealand, for morphological and molecular analyses. Two of these species, D esmodorella verscheldei sp. nov. and D racograllus ngakei sp. nov. , were new to science and are described herein. Epsilonema rugatum Lorenzen, 1973, comb. nov. , which was originally described from New Zealand material as a subspecies of Epsilonema dentatum from Chile, is redescribed and elevated to the rank of species based on cuticular ornamentation. The phylogenetic relationships amongst the three Desmodoroidea families are investigated based on new and existing sequences of the D2 and D3 expansions segments of large subunit (LSU) 28S rRNA gene and small subunit (SSU) of 18S rDNA gene. Our analyses suggest that the Draconematidae is a sister taxon to the Desmodorinae and Spiriniinae, with the Draconematidae forming a monophyletic crown group and the Desmodorinae and Spiriniinae forming a paraphyletic stem group. Phylogenetic relationships between the Epsilonematidae and Stilbonematinae, however, could not be determined with certainty. The SSU and D2‐D3 of LSU consensus trees indicate that the morphological resemblance between the Draconematidae and Epsilonematidae, which are both characterized by swollen pharyngeal body regions and mid‐posterior body regions with specialized setae, reflects distinct and independently evolved adaptations to their unusual mode of locomotion, with differences in the structure and distribution of specialized setae between the two families also consistent with convergent evolution. We show that the family Desmodoridae and superfamily Desmodoroidea as currently defined are not monophyletic. It was not possible to determine whether the Prodesmodorinae are more closely related to the Desmodoroidea or Microlaimoidea, although it is clear that they do not belong to the Desmodoridae. The single Molgolaiminae sequence available formed a distinct clade together with the superfamily Microlaimoidea, and should therefore be placed with the latter. Clarifying the phylogenetic relationships within the Desmodoroidea will require greater focus on the Pseudonchinae, Molgolaiminae, and Epsilonematidae, for which no or very few sequences are available at present. © 2016 The Linnean Society of London     

A phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) based on direct optimization analysis of one nuclear and four mitochondrial genes

The phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) has been investigated using several different molecular datasets. These studies differed widely in taxonomic and locus sampling, and their results tended to lack resolution of internal nodes and were themselves largely incongruent. To address this, we assembled a data set of 5 loci (up to 3.5 kbp from 12S rDNA, 16S rDNA, tDNA‐valine, cytochrome b, and the nuclear gene c‐mos) for 43 species of megachiropterans and 6 microchiropteran outgroups. We analyzed these data with direct optimization under equal costs for substitutions and indels. We used POY in a parallel setting, and searches consisted of replicated swapping + refinements (ratcheting, tree fusing, and iterative pass optimization). Our results indicate that Megachiroptera and all recognized genera (including Pteropus) are monophyletic, and that Melonycteris is the sister group of the clade containing all the other genera. Clades previously proposed using molecular data, as well as many new and traditional groups, were well‐supported, and various sources suggest that the degree of conflict with morphological data may be considerably less marked than previously supposed. Analysis of individual loci suffer 70% loss in the number of compatible groups recovered across all analyses with respect to combined analyses. Our results indicate that, within Megachiroptera, nectarivory and cave‐dwelling originated several times, but echolocation (used for obstacle detection) evolved only once. Megachiropterans likely originated in SE Asia‐Melanesia, and colonized Africa at least four times.     

Phylogeny of the Saprininae reveals interesting ecological shifts in the history of the subfamily (Coleoptera: Histeridae)

A morphological data set for the histerid beetle subfamily Saprininae comprising 95 adult morphological characters scored (multistate coding) from 72 terminal taxa and four outgroups was developed in order to analyse and determine the relationships amongst the genera and subgenera of the Saprininae subfamily. Cladograms were rooted with exemplars of Dendrophilinae (genus Dendrophilus), Bacaniini (genus Bacanius), Abraeinae (genus Chaetabraeus), and Anapleini (genus Anapleus). Parsimony‐based phylogenetic analyses were performed based on the type species of each genus and subgenus of the Saprininae occurring around the world, with the exception of three taxa: Paramyrmetes foveipennis (type species of the genus Paramyrmetes), Satrapister nitens (type species of the genus Satrapister) and Xerosaprinus (Auchmosaprinus) laciniatus (type species of the subgenus Auchmosaprinus) that were not available. In addition, in order to test the monophyly of several questionable genera, multiple exemplars were added in a few cases. The analysis also included an exemplar of an apparently undescribed genus. The results of the analysis confirm the monophyly of the subfamily supported by two unique synapomorphies: (1) presence of sensory structures of the antenna; and (2) presence of the antennal cavity, as well as several other weaker synapomorphies. However, the phylogeny inferred here shows mostly low support for the deeper branches and consequently no major changes in the Saprininae classification are proposed. The presented cladogram is discussed together with its implications for the evolution of the subfamily. The most informative characters and their respective states are outlined. Multiple shifts in lifestyles have evolved during the evolutionary history of the group. Taxa found near the root of the cladogram are mostly nidicolous or myrmecophilous, and inquiliny is presumed to be the plesiomorphic lifestyle of the subfamily. The nidicolous lifestyle has undergone several transformations to other lifestyles and myrmecophily has evolved three times independently during the evolution of the subfamily. Termitoxeny has evolved two times independently in the group whereas ecological adaptation for life in caves has likewise evolved two times independently. The analyses yielded a large clade of predominantly psammophilous taxa; psammophily is thought to have evolved once and has been subsequently lost several times. © 2014 The Linnean Society of London