Supraordinal phylogenetic relationships of Lecanoromycetes based on a Bayesian analysis of combined nuclear and mitochondrial sequences

Phylogenetic relationships of lichen-forming discomycetes and their relatives in the class Lecanoromycetes were examined by using nuclear large subunit and mitochondrial small subunit ribosomal DNA sequences. Ninety-eight partial sequences of 53 ascomycetes were generated and aligned with the corresponding sequences retrieved from GenBank resulting in an alignment of 100 taxa that was analyzed using a Bayesian approach with Markov chain Monte Carlo (B/MCMC) methods. The analysis revealed the monophyly of the Lecanoromycetes with two major clades: one clade including the monophyletic orders Graphidales and Ostropales and the paraphyletic Gyalectales, the other clade including the monophyletic Lecanorales (incl. Caliciales, Peltigerales, and Teloschistales) and a clade containing the polyphyletic Agyriales, a yet undescribed order Umbilicariales (including Elixiaceae and Umbilicariaceae), and Pertusariales. The monophyly of the Pertusariales was not resolved. Testing of alternative hypotheses revealed that a placement of Chaetothyriomycetes and Eurotiomycetes within Lecanoromycetes and the monophyly of Agyriales s. lat. (incl. Elixiaceae and Schaereriaceae) and Ostropales s. lat. (incl. Graphidales) can be rejected, while monophyly of Gyalectales and the Pertusariales and placement of Umbilicariales on the Lecanorales branch cannot be rejected with the current data set.     

Testing for endemism, genotypic diversity and species concepts in Antarctic terrestrial microalgae of the Tribonemataceae (Stramenopiles, Xanthophyceae)

The genetic diversity of all available culture strains of the Tribonemataceae ( Stramenopiles , Xanthophyceae ) from Antarctica was assessed using the chloroplast-encoded psbA /rbcL spacer region sequences, a highly variable molecular marker, to test for endemism when compared with their closest temperate relatives. There was no species endemic for Antarctica, and no phylogenetic clade corresponded to a limited geographical region. However, species of the Tribonemataceae may have Antarctic populations that are distinct from those of other regions because the Antarctic strain spacer sequences were not identical to sequences from temperate regions. Spacer sequences from five new Antarctic isolates were identical to one or more previously available Antarctic strains, indicating that the Tribonemataceae diversity in Antarctic may be rather limited. Direct comparisons of the spacer sequences and phylogenetic analyses of the more conserved rbcL gene revealed that current morphospecies were inadequate to describe the actual biodiversity of the group. For example, the genus Xanthonema , as currently circumscribed, was paraphyletic. Fortunately, the presence of distinctive sequence regions within the psbA/rbcL spacer, together with differences in the rbcL phylogeny, provided significant autoapomorphic criteria to re-define the Tribonemataceae species.     

新疆石人沟山区岩面生地衣群落分布格局的环境解释

地衣作为真菌和绿藻/蓝绿藻的成功共生体,广泛分布在陆地生态中的各种栖息地。岩面生地衣作为陆地生态系统的主要组成部分,在干旱和半干旱地区陆地食物链中具有重要地位,同时对岩石的生物腐蚀和土壤的形成有重要作用。岩面生地衣的多样性和分布格局强烈地受到海拔、湿度、温度、降水量、太阳辐射强度和基物的特征(岩石类型、岩石大小、岩石的化学成分和营养成分)等多种因素的影响。为了研究乌鲁木齐县石人沟山区岩面生地衣群落与基物间的关系,该研究在乌鲁木齐县石人沟山区设立16个样地,计测样地中岩面生地衣的盖度,包括坡度、坡向、光照强度等7个环境因子,采用典范对应分析法(CCA)对各群落的物种分布格局与环境因子的关系进行了探讨。结果表明:石人沟山区的岩面生地衣共有27种,隶属于7目9科15属。其中,黄枝衣目、茶渍目和鸡皮衣目的种类较多,占该地区岩面生地衣总数的74.07%。CCA排序结果显示坡度、坡向、光照强度、湿度、岩石pH值是5个影响岩面生地衣种类分布格局的主要环境因子,并显示了岩面生地衣与样地间的对应性。     

南极鱼类后生动物寄生虫研究进展: 线虫、绦虫与桡足类

极端的环境造就了南极独特的生物群体, 其中鱼类是南大洋生态系统中最具多样性的脊椎动物, 也是许多寄生虫的中间或终末宿主。南极鱼类寄生虫种类丰富, 是南大洋海洋生物多样性的重要组成部分。探究南极鱼类及其寄生虫的营养关系可为阐释南极海洋生态系统功能及其变动提供重要的生态数据。虽然关于南极鱼类寄生虫的研究已有一百多年的历史, 但这些研究主要集中在寄生虫的种类鉴定、区系调查和组织病理等方面。由于南极鱼类寄生虫研究跨度时间长、地域范围广, 相关研究较为零散。文章综述了南极鱼类寄生线虫、绦虫以及桡足类的种类组成、宿主范围和地理分布等方面的研究, 并对今后开展南极鱼类寄生虫研究工作提出了展望。     

Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota)

The genus Lecidea Ach. sensu lato (sensu Zahlbruckner) includes almost 1200 species, out of which only 100 species represent Lecidea sensu stricto (sensu Hertel). The systematic position of the remaining species is mostly unsettled but anticipated to represent several unrelated lineages within Lecanoromycetes. This study attempts to elucidate the phylogenetic placement of members of this heterogeneous group of lichen-forming fungi and to improve the classification and phylogeny of Lecanoromycetes. Twenty-five taxa of Lecidea sensu lato and 22 putatively allied species were studied in a broad selection of 268 taxa, representing 48 families of Lecanoromycetes. Six loci, including four ribosomal and two protein-coding genes for 315- and 209-OTU datasets were subjected to maximum likelihood and Bayesian analyses. The resulting well supported phylogenetic relationships within Lecanoromycetes are in agreement with published phylogenies, but the addition of new taxa revealed putative rearrangements of several families (e.g. Catillariaceae, Lecanoraceae, Lecideaceae, Megalariaceae, Pilocarpaceae and Ramalinaceae). As expected, species of Lecidea sensu lato and putatively related taxa are scattered within Lecanoromycetidae and beyond, with several species nested in Lecanoraceae and Pilocarpaceae and others placed outside currently recognized families in Lecanorales and orders in Lecanoromycetidae. The phylogenetic affiliations of Schaereria and Strangospora are outside Lecanoromycetidae, probably with Ostropomycetidae. All species referred to as Lecidea sensu stricto based on morphology (including the type species, Lecidea fuscoatra [L.] Ach.) form, with Porpidia species, a monophyletic group with high posterior probability outside Lecanorales, Peltigerales and Teloschistales, in Lecanoromycetidae, supporting the recognition of order Lecideales Vain. in this subclass. The genus name Lecidea must be redefined to apply only to Lecidea sensu stricto and to include at least some members of the genus Porpidia. Based on morphological and chemical similarities, as well as the phylogenetic relationship of Lecidea pullata sister to Frutidella caesioatra, the new combination Frutidella pullata is proposed here.     

The distribution of ascus types and photobiontal selection in Lecanoromycetes (Ascomycota) against the background of a revised SSU nrDNA phylogeny

Within the last decade, molecular methods have revealed the relationships in many groups of lichenized Ascomycetes. However, the published phylogenies were often contradictory with respect to higher taxonomic levels. To achieve a more convincing overall picture of phylogenetic relationships of and within the Lecanoromycetes, we set up an alignment of all publicly available SSU nrDNA sequences of the Pezizomycotina, discarded those of insufficient quality, and added 21 newly obtained sequences representing groups that were not or under-represented so far. The alignment of 635 taxa and a subset of 166 Lecanoromycetes were analysed with different phylogenetic algorithms. The best phylogenetic trees, with respect to length, resolution, and support, were obtained with the Parsimony Ratchet method and DNAPARS (Phylip). According to these results, the Lecanoromycetes were subdivided into eight monophyletic clades representing the following orders: Acarosporales ad. int., Agyriales, Baeomycetales, Gyalectales, Icmadophilales ad. int., Lecanorales, Ostropales, and Pertusariales. These clades are distributed in two monophyletic groups corresponding to the two different types of ascomatal ontogeny. The taxa of the Lecanorales-clade differ from the other orders by the absence of a primary cyanobiont and of phycobionts of the genera Coccomyxa and Trentepohlia, in combination with the presence of an amyloid reaction of the ascus tips (lacking amyloid flanks). The Lecanorales-clade is subdivided into nine groups which are treated here at the level of suborders: Lecideineae, Teloschistineae, Physciineae, Bacidiineae ad int., Sphaerophorineae ad int., Rhizocarpineae ad int., Psorineae ad int., Cladoniineae, and Lecanorineae. The amyloid reaction pattern of the ascus apex correlates with this grouping at suborder rank. Peltigerales were excluded from the Lecanorales but included in the Lecanoromycetes based on morpho-anatomical features. The Lichinales were excluded from the Lecanoromycetes, while the position of the Umbilicariaceae remains unclear.     

Cell wall-less, free-living spirochetes in Antarctica

The phylogeny of an Antarctic, cell wall-less, bacterial strain was determined by sequencing PCR amplified 16S rDNA, and comparison of the sequence with other bacterial 16S rRNA sequences available in databanks. Although the strain was phenotypically very similar to members of the genus Anaeroplasma, phylogenetic analyses showed it was a member of the order Spirochaetales. Until now, the order was one of the few bacterial orders in which phylogeny was reflected in a uniform morphology of its members. The viability of wall-less cells in cultures of spirochetes and spirochetal infective material warrants reinvestigation.     

The polar lichens Caloplaca darbishirei and C. soropelta highlight the direction of bipolar migration

A proper phytogeographic affiliation of Antarctic lichen species has become feasible using molecular phylogeographic methods. Caloplaca citrina is a heterogeneous taxon including several species which occurs in polar regions and is common in Antarctica. Collections of C. citrina from the Antarctic were revised using morphological, anatomical and molecular characters (ITS). They were found to belong to two species: Caloplaca darbishirei (C.W. Dodge & G.E. Baker) Cretz. and C. soropelta (E.S. Hansen, Poelt & S?chting) S?chting. The molecular phylogeny showed them to be sister species, but well separated. Morphological and chemical characters, ecology and distribution of the species are discussed. C. darbishirei is the most common species in the Antarctic, and it is so far known only from Antarctica and Southern South America. C. soropelta, reported here as new to South America, is a bipolar species with all close relatives in the Southern Hemisphere; it is therefore most likely that the species colonized the Arctic from the south. C. citrina s. str. is not confirmed to occur in Antarctica. The study emphasizes the suitability of genotyping for understanding the taxonomy and phylogeography of bipolar lichens.     

New Asellota from the Antarctic deep sea (Crustacea, Isopoda, Asellota), with descriptions of two new genera

Two new genera, Reductosoma gen.n. (Desmosomatidae) and Desmostylis gen.n. (Desmosomatidae), and five new species are described from the Maud Rise and the Gunnerus Ridgc, Antarctica. Two new species of the Desmosomatidae (Eugerdellatinae and Desmosomatinae) are described: Reduetosoma gunnera gen. et sp.n. and Desmosoma hesslera sp.n.; one species of the Munnopsidae (Eurycopinae), Disconectes colernuni sp.n.; and two species of the Macrostylidae from the Antarctic deep sea, Desmostylis obscurus gen. et sp.n. and Macrostylis sarsi sp.n. Comments on the phylogeny and zoogeography are given.     

Molecular analysis of fungal diversity associated with three bryophyte species in the Fildes Region, King George Island, maritime Antarctica

The fungal communities associated with three bryophytes species (the liverwort Barbilophozia hatcheri, the mosses Chorisodontium aciphyllum and Sanionia uncinata) in the Fildes Region, King George Island, maritime Antarctica, were studied using clone library analysis. Fungal communities showed low diversity; the 680 clones belonged to 93 OTUs. Of these, 78 belonged to the phylum Ascomycota, 13 to the phylum Basidiomycota, 1 to the phylum Zygomycota, and 1 to an unknown phylum. Among the OTUs, the most common orders in the Ascomycota were Helotiales (42 OTUs) and Chaetothyriales (14 OTUs) and the most common orders in the Basidiomycota were Sebacinales (3 OTUs) and Platygloeales (3 OTUs). Most OTUs clustered within clades that contained phylotypes identified from samples in Antarctic or Arctic ecosystems or from bryophytes in other ecosystems. In addition, we found that host-related factor may shape the fungal communities associated with bryophytes in this region. This is the first systematic study of the fungal community in Antarctic bryophytes to be performed using culture-independent method and the results may improve understanding of the endophytic fungal evolution and ecology in the Antarctic ecosystem.     

The evolution of polar fish hemoglobin: a phylogenetic analysis of the ancestral amino acid residues linked to the root effect

Originating from a benthic ancestor, the suborder Notothenioidei (the dominant fish fauna component of the Antarctic sea) underwent a remarkable radiation, which led notothenioids to fill several niches. The ecological importance of notothenioids in Antarctica and their biochemical adaptations have prompted great efforts to study their physiology and phylogeny, with special attention to the evolutionary adaptation of the oxygen-transport system. We herewith report the evolutionary history of alpha- and beta-globins under the assumption of the molecular clock hypothesis as a basis for reconstructing the phylogenetic relationships among species. These studies have been extended to fish species of other latitudes, including the Arctic region. The northern and southern polar oceans have very different characteristics; indeed, in many respects the Antarctic and Arctic ichthyofaunas are more dissimilar than similar. Our results show that the inferred phylogeny of Arctic and Antarctic globins is different. Taking advantage of the wealth of information collected on structure and function of hemoglobins, we have attempted to investigate the evolutionary history of an important physiological feature in fish, the Root effect. The results suggest that the amino acid residues reported to play a key role in the Root effect may be regarded as ancestor characters, but the lack of this effect in extant species can hardly be associated with the presence of synapomorphies.     

Evidence of hidden biodiversity, ongoing speciation and diverse patterns of genetic structure in giant Antarctic amphipods

Recent molecular research on Antarctic benthic organisms has challenged traditional taxonomic classifications, suggesting that our current perceptions of Antarctic biodiversity and species distributions must be thoroughly revised. Furthermore, genetic differentiation at the intraspecific level remains poorly understood, particularly in eastern Antarctica. We addressed these issues using DNA sequence data for two sibling amphipod species that could be collected on a circum-Antarctic scale: Eusirus perdentatus and Eusirus giganteus. Haplotype networks and Bayesian phylogenies based on mitochondrial (COI, CytB) and nuclear (ITS2) DNA provided strong evidence of multiple cryptic species of Eusirus, with several occurring in sympatry and at least one likely to have a true circum-Antarctic distribution. Within species, gene flow was often highly restricted, consistent with a brooding life history and in some cases suggestive of current or future allopatric speciation. Patterns of genetic structure were not always predictable: one cryptic species showed preliminary evidence of high genetic differentiation across ～150 km in eastern Antarctica (F(ST) > 0.47, P < 0.01), yet another was remarkably homogenous across ～5000 km (F(ST) = 0.00, P = 1.00). Genetic diversity also varied among cryptic species, independent of sample size (π = 0.00-0.99). These results indicate several hidden levels of genetic complexity in these Antarctic amphipods that are neither apparent from previous taxonomic or ecological studies nor predictable from their life history. Such genetic diversity and structure may reflect different modes of survival for Antarctic benthic organisms during historic glacial cycles, and/or subsequent re-establishment of populations on the shelf, and highlight our misunderstanding of Antarctic marine species diversity.     

Surviving out in the cold: Antarctic endemic invertebrates and their refugia

Aim To identify Antarctic palaeoendemic taxa and their probable glacial refugia from regional groups of endemic species records. Location Antarctica. Methods We compiled a list of Antarctic non‐marine invertebrates from published literature, and then deleted all records relating to non‐endemic, zoochoric (phoretic and parasitic), marine and partially identified species to leave only the elements endemic to Antarctica. We then used cluster analysis and principal components analysis to identify regional groupings within this endemic fauna. Results Some 170+ of the reported 520+ Antarctic invertebrates are free‐living and endemic, but only nine of these are pan‐Antarctic, with the majority having either ‘continental’/eastern or ‘maritime’/western distributions. Main conclusions All invertebrates endemic to continental Antarctica are confined to, or found adjacent to, ice‐free palaeorefugial mountains, nunataks and coastal exposures. By contrast, only one maritime Antarctic palaeorefugium has been identified, and most endemic taxa are currently associated with coastal lowland neorefugia. We suggest which regions of Antarctica (1) are likely to be refugial, and (2) simply require more data in order that the nature and origin of their fauna can be elucidated.     

Bacterial diversity of a soil sample from Schirmacher Oasis, Antarctica.

The bacterial diversity of a soil sample collected in the vicinity of Lake Zub, Schirmacher Oasis, Antarctica, was determined both by establishing pure colonies of culturable bacteria and by cloning the total 16S rDNA of the soil and establishing the phylogeny of the clones. Analysis of the 16S rRNA gene clones indicated that the bacteria belonged to the classes alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria, Gemmatimonas, Bacteriodetes, Actinobacteria, Chloroflexi and Chlamydiae. In addition, seven clones were categorized as unidentified and unculturable in the classes of beta-Proteobacteria, Actinobacteria, Chloroflexi and Chlamydiae. Further, the culturable bacteria from the same site were identified as belonging to the genera Pseudomonas, Sphingobacterium, Arthrobacter, Micrococcus, Brevondimonas, Rhodococcus and Microbacterium. These results identify for the first time the presence of bacteria belonging to the genera Brevundimonas, Microbacterium, Rhodococcus, Serratia, Enterobacter, Rhodopseudomonas, Sphingomonas, Acidovorax, Burkholderia, Nevskia, Gemmatimonas, Xanthomonas and Flexibacter in Antarctica. Further, comparison of the Antarctic soil bacterial diversity with other cold habitats of Antarctica like from sediments, ice and cyanobacterial mat samples indicated that the bacterial diversity in soil was similar to the diversity observed in the continental shelf sediment sample. The Antarctic soil clones also resembled the bacterial diversity of soils from other geographical regions, but were unique in that none of the clones from the soil belonged to the uncultured Y, O, G, A and B groups common to all soil samples.     

Nematodes from saline and freshwater lakes of the Vestfold Hills,East Antarctica,including the description of <Emphasis Type="Italic">Hypodontolaimus antarcticus</Emphasis> sp. n.

The invertebrate fauna of many Antarctic ice-free areas, even those close to permanent research stations, can be poorly known. Here we describe some nematodes from freshwater and saline, marine-derived lakes of the Vestfold Hills, East Antarctica. The freshwater lakes contained the widespread East Antarctic endemic species, Plectus frigophilus Kirjanova, 1958. The saline lakes were inhabited by two recently described species, Halomonhystera halophila Andrássy, 2006 and Halomonhystera continentalis Andrássy, 2006, and by a new species described in this report, Hypodontolaimus antarcticus sp. n. Originally marine but now brackish Highway Lake contained a nematode fauna with both freshwater and marine-derived components. The nematode fauna of Antarctica now consists of 54 named species, 22 of which are found in East Antarctica.     

Multiple colonization and dispersal events hide the early origin and induce a lack of genetic structure of the moss Bryum argenteum in Antarctica

The dispersal routes of taxa with transoceanic disjunctions remain poorly understood, with the potential roles of Antarctica not yet demonstrated. Mosses are suitable organisms to test direct intra‐Antarctic dispersal, as major component of the extant Antarctic flora, with the cosmopolitan moss Bryum argenteum as ideal target species. We analyzed the genetic structure of B. argenteum to provide an evolutionary time frame for its radiation and shed light into its historical biogeography in the Antarctic region. We tested two alternative scenarios: (a) intra‐Antarctic panmixia and (b) intra‐Antarctic genetic differentiation. Furthermore, we tested for evidence of the existence of specific intra‐Antarctic dispersal routes. Sixty‐seven new samples (40 collected in Antarctica) were sequenced for ITS nrDNA and rps4 cpDNA regions, and phylogenetic trees of B. argenteum were constructed, with a focus on its Southern Hemisphere. Combining our new nrDNA dataset with previously published datasets, we estimated time‐calibrated phylogenies based on two different substitution rates (derived from angiosperms and bryophytes) along with ancestral area estimations. Minimum spanning network and pairwise genetic distances were also calculated. B. argenteum was potentially distributed across Africa and Antarctica soon after its origin. Its earliest intra‐Antarctic dispersal and diversification occurred during a warming period in the Pliocene. On the same timescale, a radiation took place involving a dispersal event from Antarctica to the sub‐Antarctic islands. A more recent event of dispersal and diversification within Antarctica occurred during a warm period in the Pleistocene, creating favorable conditions also for its colonization outside the Antarctic continent worldwide. We provide evidence supporting the hypothesis that contemporary populations of B. argenteum in Antarctica integrate a history of both multiple long‐range dispersal events and local persistence combined with in situ diversification. Our data support the hypothesis that B. argenteum has been characterized by strong connectivity within Antarctica, suggesting the existence of intra‐Antarctic dispersal routes.     

The sister group relation of parmeliaceae (Lecanorales, Ascomycota)

The family Parmeliaceae (Lecanorales, Ascomycota) is possibly the largest, best known and most thoroughly studied lichen family within its order. Despite this fact the relationship between Parmeliaceae and other groups in Lecanorales is still poorly known. The aim of the present study is to contribute to finding the sister group of Parmeliaceae as an aid in future studies on the phylogeny and character evolution of the group. We do this by sampling all potential relatives to the Parmeliaceae that we have identified, i.e. Gypsoplaca, Japewia, Mycoblastus, Protoparmelia, and Tephromela, a good representation of the major groups within the Parmeliaceae s. lat. and a good representation of other taxa in the core Lecanorales. We use molecular data from two genes, the large subunit of the nuclear ribosomal RNA gene (nrLSU) and the small subunit of the mitochondrial ribosomal RNA gene (mrSSU), and a Bayesian analysis of the combined data. The results show that the closest relatives to Parmeliaceae are the two genera Protoparmelia and Gypsoplaca, which are crustose lichens. Parmeliaceae in our sense is a well supported group, including also the family segregates Alectoriaceae, Hypogymniaceae, Usneaceae and Anziaceae.     

中国鸡皮衣目地衣的研究

鸡皮衣目主要特征是子囊果为半被果型,子囊壁厚且淀粉质,侧丝通常分枝,孢子大型,光合共生物为绿藻。收录了中国鸡皮衣目69种9变种4变型,共82个分类单位,隶属于3科4属。