Neogene diversification in the temperate lichen-forming fungal genus Parmelia (Parmeliaceae,Ascomycota)

The lichen-forming genus Parmelia Acharius occurs worldwide but its centre of distribution is in the northern hemisphere and it is widespread in boreal-temperate Eurasia and North America. Recent molecular work on Parmelia has identified phylogenetic relationships within two major groups of the genus: P. saxatilis s. lat. and P. sulcata s. lat. However, little is known about the diversification and historical biogeography of these groups. Here we have used a dataset of two genetic markers and 64 samples to estimate phylogenetic relationships within Parmelia. The dated phylogeny provides evidence for major diversification during the Neogene and Pleistocene. These diversification events are probably correlated with climatic changes during these periods. Evidence of gene flow within species between populations from North America and Europe has been found in three species: P. sulcata Taylor, P. saxatilis (L.) Acharius and P. barrenoae Divakar, M.C. Molina & A. Crespo. Cryptic species recently segregated on the basis of molecular differences (P. encryptata A. Crespo, Divakar & M.C. Molina vs. P. sulcata and P. saxatilis vs. P. mayi Divakar, A. Crespo & M.C. Molina) do not share a common ancestor. Moreover, the P. saxatilis complex is remarkably diverse. Two morphotypes of P. saxatilis s. lat. were shown to represent independent monophyletic lineages. Consequently, two species (P. sulymae Goward, Divakar, & M.C. Molina & A. Crespo and P. imbricaria Goward, Divakar, M.C. Molina & A. Crespo) are newly described here.     

Migration between continents: geographical structure and long-distance gene flow in Porpidia flavicunda (lichen-forming Ascomycota)

Historical and contemporary geographical distribution ranges with their associated gene flow patterns interact to produce the genetic diversity observed today. Often it is not possible to separate out the impacts of historical events, e.g. past fragmentation, and contemporary gene flow, e.g. long-distance dispersal. Porpidia flavicunda is a lichen-forming ascomycete occurring circumpolar in the boreal to arctic zones for which vegetation history suggests that its distribution pattern has stayed broadly the same over the past millennia. DNA-sequence diversity in P. flavicunda can, thus, be expected to predominantly represent geographical population differentiation and its contemporary migration rates. The population sample consists of 110 specimens collected in Northern Québec, Baffin Island, Western Greenland and Northern Scandinavia. DNA-sequence data sets of three nuclear gene fragments (LSU, RPB2 and beta-tubulin) were analysed for genetic diversity within, and differentiation between, geographical regions. Tests of population subdivision employing analyses of molecular variance and exact tests of haplotype frequency distributions showed significant structure between the geographical regions. However, the lack of fixed nucleotide polymorphisms and the wide sharing of identical haplotypes between geographical regions suggest recurrent long-distance gene flow of propagules. Still, the means by which propagules are dispersed remain to be discovered. Inference of migration rates shows that in many cases a sufficiently high amount of migrants is exchanged between geographical regions to prevent drastic population differentiation through genetic drift. The observed haplotype distributions and migration rates point to a gene flow model of isolation by distance.     

Testing "species pair" hypotheses: evolutionary processes in the lichen-forming species complex Porpidia flavocoerulescens and Porpidia melinodes

Pairs of taxa are commonly found in lichen-forming ascomycetes that differ primarily in their reproductive modes: one taxon reproduces sexually, the other vegetatively. The evolutionary processes underlying such "species pairs" are unknown. The species pair formed by Porpidia flavocoerulescens (sexual) and Porpidia melinodes (vegetative) was chosen to investigate four previously proposed hypotheses. These hypotheses posit that species pairs are either two monophyletic, independently evolving species with contrasting reproductive mode; a single outcrossing species polymorphic with regard to its reproductive modes; a sexual mother lineage frequently giving rise to asexual spin-offs; or a complex of cryptic species. The phylogenetic patterns observed within the species pair in the present study were analyzed using stringent hypothesis testing and visualizations of relationships and conflict based on tree and network reconstructions. DNA sequences at the three analyzed loci revealed the same four to five deeply divergent lineages. A detailed analysis of DNA-sequence variability revealed closely linked gene loci, but high levels of conflict within each of the gene fragments, as well as between observed genetic lineages. The observed patterns of phylogenetic relationships, linkage, and conflict are not congruent with any of the previously proposed species pair hypotheses. Rather, it is proposed that the observed results can be explained by conflicting reproductive and nutritional requirements imposed by an obligate symbiotic lifestyle. These interacting constraints produce recurring selective sweeps within predominantly vegetatively reproducing lineages and are the main forces that shape the evolution within the investigated species pair.     

Molecular phylogeny of Heteroplacidium, Placidium, and related catapyrenioid genera (Verrucariaceae, lichen-forming Ascomycota)

? Premise of the study: Verrucariaceae is a fascinating lineage of lichenized fungi for which generic and species delimitation is problematic due to the scarcity of discriminating morphological characters. Members of this family inhabit rocks, but they further colonize soils, barks, mosses, and other lichens. Our aim is to contribute to the DNA-based inference of the Verrucariaceae tree of life and to investigate characters that could be useful for proposing a more natural classification. We focused on catapyrenioid genera, which are often part of biological soil crusts, a cryptogam-dominated ecosystem contributing to soil formation and stabilization in arid environments. Understanding their evolution and taxonomy is essential to assess their roles in these fragile and important ecosystems. ? Methods: A multigene phylogeny of Verrucariaceae including catapyrenioid genera is presented. We further examined the phylogenetic relationships among members of Heteroplacidium and Placidium. The evolution of selected characters was inferred using the latter phylogeny. ? Key results: Anthracocarpon and Involucropyrenium were closely related to Endocarpon. Placidium comprised two monophyletic clades sister to Heteroplacidium. Inferred ancestral states of diagnostic characters revealed that the type of medulla and the pycnidia location were homoplasious within the Placidium clade. In contrast, the presence of rhizines was a synapomorphy for Clavascidium. ? Conclusions: Our results provide new information on the usefulness of characters for delineating groups in Verrucariaceae. Taxonomic changes are proposed to reflect more natural groupings: Heteroplacidium podolepis is transferred to Placidium, and Clavascidium is recognized as a different genus. Eight new combinations are proposed for Clavascidium.     

Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions

ABSTRACT: BACKGROUND: Factors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent estimates suggest that major radiations within some genera in the largest clade of macrolichens (Parmeliaceae, Ascomycota) vastly predate the Pleistocene. To better understand the temporal placement and sequence of diversification events in lichens, we estimated divergence times in a common lichen-forming fungal genus, Melanohalea, in the Northern Hemisphere. Divergence times were estimated using both concatenated gene tree and coalescence-based multilocus species tree approaches to assess the temporal context of major radiation events within Melanohalea. In order to complement our understanding of processes impacting genetic differentiation, we also evaluated the effects of Pleistocene glacial cycles on population demographics of distinct Melanohalea lineages, differing in reproductive strategies. RESULTS: We found that divergence estimates, from both concatenated gene tree and coalescence-based multilocus species tree approaches, suggest that diversification within Melanohalea occurred predominantly during the Miocene and Pliocene, although estimated of divergence times differed by up to 8.3 million years between the two methods. These results indicate that, in some cases, taxonomically diagnostic characters may be maintained among divergent lineages for millions of years. In other cases, similar phenotypic characters among non-sister taxa, including reproductive strategies, suggest the potential for convergent evolution due to similar selective pressures among distinct lineages. Our analyses provide evidence of population expansions predating the last glacial maximum in the sampled lineages. These results suggest that Pleistocene glaciations were not inherently unfavorable or restrictive for some Melanohalea species, albeit with apparently different demographic histories between sexually and vegetatively reproducing lineages. CONCLUSIONS: Our results contribute to the understanding of how major changes during the Miocene and Pliocene have been important in promoting diversification within common lichen-forming fungi in the northern Hemisphere. Additionally, we provide evidence that glacial oscillations have influenced current population structure of broadly distributed lichenized fungal species throughout the Holarctic.     

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.     

地衣型真菌石果衣(疣孢菌科，子囊菌门)次级代谢产物的多样性

地衣能够产生大量的新型次级代谢产物,但以往对石果衣Endocarpon pusillum的研究中未能检测出任何次级代谢产物。然而,对其共生菌进行基因组测序发现其中含有14个沉默的PKS基因和2个沉默的NRPS基因。在此研究中,为激活其途径,使用了优化马铃薯培养基和大米培养基对石果衣共生真菌进行了培养。从优化马铃薯培养物中分离得到9个次级代谢产物,包括2个新的异吲哚-1-酮类化合物(1, 2)。而从大米培养物中分离到3个已知化合物和1个新的萘醌类化合物(9)。通过核磁共振和质谱数据确定了新化合物的结构。研究结果表明,大量地衣中未能检测出任何次级代谢产物,或仅能检测出少量次级代谢产物,可能与其基因组中的沉默基因有关。因此,通过对沉默基因的激活方法为地衣次级代谢产物资源的研究与开发开辟了有效途径。     

中国绿杯菌属研究(英文)

对采自中国12个省的绿杯菌属Chlorociboria标本进行了分类研究,鉴定出3个种,分别为小孢绿杯菌C.aeruginascens、绿杯菌C.aeruginosa和波托绿杯菌C.poutoensis。其中波托绿杯菌为中国新记录种,对该种的形态学特征进行了描述和图示,并对其分类地位提供了DNA序列分析的佐证。     

Phylogenetic relationships of Oriental torrent frogs in the genus Amolops and its allies (Amphibia, Anura, Ranidae)

We investigated the phylogenetic relationships among 20 species of Oriental torrent frogs in the genus Amolops and its allies from China and Southeast Asia based on 1346-bp sequences of the mitochondrial 12S and 16S rRNA genes. Oriental species of the tribe Ranini form a monophyletic group containing 11 clades (Rana temporaria + Pseudoamolops, R. chalconota, four clades of Amolops, Meristogenys, three clades of Huia species, and Staurois) for which the phylogenetic relationships are unresolved. The genus Amolops consists of southern Chinese, southwestern Chinese, Thai, and Vietnamese-Malaysian lineages, but their relationships are also unresolved. The separation of southern and southwestern lineages within China conforms to previous morphological and karyological results. Species of Huia do not form a monophyletic group, whereas those of Meristogenys are monophyletic. Because P. sauteri is a sister species of R. temporaria, distinct generic status of Pseudoamolops is unwarranted.     

Taxonomic and evolutionary relationships in the genus Vella L. (Cruciferae)

Thirty-two differential characters are numerically analysed for the six existing taxa of the genus Vella L. The closely related monotypic genus Boleum Desv. is also included for comparison. Most of the characters used are morphological, but cariological, ecological and biogeographical aspects have also been studied. The results indicate that four distinct species, one ( V. pseudocytisus L.) with three sub-species, should be distinguished. The new combination V. anremerica (Lit. et Maire) Gómez-Campo (basionym: V. pseudocytisus L. subsp. anremerica Lit. et Maire) and the new name V. pseudocytisus L. subsp. paui Gómez-Campo for V. pseudocytisus L. var. glabrescens Willk., nornen nudum are presented. A key is given to aid identification of these taxa. Their conservation status is also discussed.     

Relationship between the algal partners and the growth of lichen-forming fungus Porpidia crustulata

In recent years, examinations based on morphological characters and phylogenetic analyses have begun to reveal the diversity of photobionts in lichen symbioses. However, still little is known regarding genetic diversity and ecological adaptation of algal partners in lichen symbioses. In this study, we investigated the photobiont Chlorella “sp. GC” (Trebouxiophyceae), a partner of Porpidia crustulata from the Guancen Mountains, China. We examined the relationship between photobiont layer thickness and Porpidia crustulata growth over a 6-year period (2007–2012). Although Porpidia crustulata exhibited moderate growth rates (0.4–0.62 mm year^?1), photobiont layer became increasingly thinner over the six-year period. We speculate that prolonged exposure to sunlight and desiccation may deleteriously alter photobiont morphology and physiology. Porpidia crustulata may be forced into a state of physiological dormancy.     

High photobiont diversity associated with the euryoecious lichen-forming ascomycete Lecanora rupicola (Lecanoraceae, Ascomycota)

The diversity and phylogenetic position of photobionts in the widespread saxicolous, crustose lichen-forming ascomycete Lecanora rupicola s.l. is presented. The algal partners of this lichen species complex belong to diverse and unrelated lineages in the genus Trebouxia . Specimens were sampled from different habitats and geographical origins. Either whole thallus DNA extractions or minute fragments of the algal layer of the lichen thallus were subjected to polymerase chain reaction, using primers that specifically amplify internal transcribed spacer rDNA of the photobionts. No correlations between different chemical races of L. rupicola with particular lineages of Trebouxia spp. were found. Irrespective of the different algal partners, all lichen thalli abundantly developed ascomata. L. rupicola apparently maintains full fecundity with a low degree of selectivity for photobionts, which promotes the occurrence of this lichen-forming species in ample ecological situations.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 283–293.     

木霉属研究概况

木霉属Trichoderma真菌种类众多、分布广泛,是一类重要的可再生自然资源,具有较高经济价值和应用前景。简要概述其经济重要性、分类学研究和系统发育等方面的研究现状及进展,遵循现行命名法规采用该类群的正确名称,并对后续研究提出了建议。     

Molecular evolutionary relationships in the avian genus Anthus (Pipits: Motacillidae)

Nucleotide sequences for 1035 bp of the mitochondrial cytochrome b gene were used to determine the molecular evolutionary relationships of species in the cosmopolitan avian genus Anthus. Phylogenetic analysis of these mtDNA sequences supported four major clades within the genus: (1) the small-bodied African pipits, (2) a largely Palearctic clade, (3) a largely South American clade, and (4) an African-Eurasian-Australian clade. Anthus hellmayri, A. correndera, and A. rubescens are shown to be paraphyletic. The possibility of paraphyly within A. similis is instead inferred to be the discovery of a new species and supported by reference to the museum voucher specimen. Sequence divergence suggests a Pliocene/Miocene origin for the genus. Although Anthus cytochrome b is found not to be behaving in a clocklike fashion across all taxa, speciation during the Pleistocene epoch can be reasonably inferred for the 66% of sister pairs that are diverging in a clocklike manner. Base compositions at each codon position are similar to those found across a growing number of avian lineages. The resulting phylogenetic hypothesis is compared to previous hypotheses of Anthus relationships, all of which deal with relationships of a particular species or a particular species complex; roughly half of these previous hypotheses are supported.     

Molecular phylogeny of the entomopathogenic fungi of the genus Cordyceps (Ascomycota:Clavicipitaceae) and its evolutionary implications

Cordyceps is an endoparasite ascomycetous genus containing approximately 450 species with a diversity of insect hosts,traditionally included in the family Clavicipitaceae of Ascomycota.Establishing the relationships among species with a varied range of morphologies and hosts is of importance to our understanding of the phylogeny and co-evolution of parasites and hosts in entomopathogenic ascomycetes.To this end,we used a combination of molecular index and morphological characters from 40 representative species to carry out comprehensive molecular phylogenetic analyses.Based on the phylogenetic tree,we used the program DISCRETE for inferring the rates of evolution and finding ancestral states of morphological character.The phylogenetic analyses revealed two important points.(i) Types of perithecia attached to stroma reflected an evolutionary trend in Cordyceps.The vertically immersed perithecia form was the ancestral state,superficial and obliquely immersed perithecia were derived characters,obliquely immersed was irreversible.Species with obliquely immersed perithecia were in a closely related group and were the derived group.(ii) A strong correlation between fungal relatedness and the microhabitat supported the hypothesis that the host jumps through commingling in soil microhabitats.Based on the results of these analyses,host switching explains the diversity of entomopathogenic fungi of the genus Cordyceps.     

A phylogenetic study of the genus Haligena (Halosphaeriales, Ascomycota)

The genus Haligena (Halosphaeriales, Ascomycota), with two accepted species, is encountered frequently in marine habitats, especially on wood in temperate regions. Phylogenetic analyses of Haligena elaterophora (type species) and H. salina were undertaken, with partial large subunit ribosomal DNA sequences, to determine their relationships with other closely related genera in the order. The genus was shown to be polyphyletic within the Halosphaeriales with the type species forming a basal clade to the order. Haligena salina constituted a sister clade with weak support of Neptunella longirostris in all analyses. Haligena elaterophora and H. salina differ significantly in the nature of their ascospore appendages: wider, more sticky and strap-like in H. elaterophora and spoon-shaped at the point of attachment; in H. salina they are longer and narrower, finely drawn out filaments. A new genus, Morakotiella, is introduced to accommodate H. salina.     

Molecular phylogeny of the entomopathogenic fungi of the genus Cordyceps (Ascomycota: Clavicipitaceae) and its evolutionary implications

Abstract Cordyceps is an endoparasite ascomycetous genus containing approximately 450 species with a diversity of insect hosts, traditionally included in the family Clavicipitaceae of Ascomycota. Establishing the relationships among species with a varied range of morphologies and hosts is of importance to our understanding of the phylogeny and co‐evolution of parasites and hosts in entomopathogenic ascomycetes. To this end, we used a combination of molecular index and morphological characters from 40 representative species to carry out comprehensive molecular phylogenetic analyses. Based on the phylogenetic tree, we used the program DISCRETE for inferring the rates of evolution and finding ancestral states of morphological character. The phylogenetic analyses revealed two important points. (i) Types of perithecia attached to stroma reflected an evolutionary trend in Cordyceps. The vertically immersed perithecia form was the ancestral state, superficial and obliquely immersed perithecia were derived characters, obliquely immersed was irreversible. Species with obliquely immersed perithecia were in a closely related group and were the derived group. (ii) A strong correlation between fungal relatedness and the microhabitat supported the hypothesis that the host jumps through commingling in soil microhabitats. Based on the results of these analyses, host switching explains the diversity of entomopathogenic fungi of the genus Cordyceps.