Annie Tillier

Communities and populations of sebacinoid basidiomycetes associated with the achlorophyllous orchid Neottia nidus‐avis (L.) L.C.M. Rich. and neighbouring tree ectomycorrhizae

Several achlorophyllous orchids associate with ectomycorrhizal hymenomycetes deriving carbon from surrounding trees for the plant. However, this has not been shown for achlorophyllous orchids associating with species of Rhizoctonia, a complex of basal lineages of hymenomycetes that are the most common orchid partners. We analysed Neottia nidus‐avis, an achlorophyllous orchid symbiotic with a Rhizoctonia, to identify its symbionts by internal transcribed spacer (ITS) sequencing. Analysis of 61 root systems from 23 French populations showed that N. nidus‐avis associates highly specifically with a group of species of Sebacinaceae. Their diversity emphasizes the need for further investigations in the Sebacinaceae systematics. Sebacinoid ITS sequences were often identical within orchid populations and a trend to regional variation in symbionts was observed. Using ITS and intergenic spacer (IGS) polymorphism, we showed that each root system harboured a single species, but that several genets colonized it. However, no polymorphism of these markers was found among portions of each root: this is consistent with the putative mode of entry of the fungus, i.e. from the rhizome into roots but not repeatedly from the soil. In addition, ectomycorrhizae were always found within the N. nidus‐avis root systems: 120 of the 144 ectomycorrhizae typed by ITS sequencing were colonized by a sebacinoid fungus identical in ITS sequence to the respective orchid symbiont (even for the IGS polymorphism in some cases). Because sebacinoids were demonstrated recently to be ectomycorrhizal, the orchid is likely to derive its resources from surrounding trees, a mycorrhizal cheating strategy similar to other myco‐heterotrophic plants studied to date.

Patterns of septal biomineralization in Scleractinia compared with their 28S rRNA phylogeny: a dual approach for a new taxonomic framework

A molecular phylogeny of the Scleractinia is reconstructed from approximately 700 nucleotides of the 5′end of the 28S rDNA obtained from 40 species. A comparison of molecular phylogenic trees with biomineralization patterns of coral septa suggests that at least five clades are corroborated by both types of data. Agaricidae and Dendrophylliidae are found to be monophyletic, that is supported by microstructural data. Conversely, Faviidae and Caryophylliidae are found to be paraphyletic: Cladocora should be excluded from the faviids, whereas Eusmilia should be excluded from the caryophylliids. The conclusion is also supported by the positions, sizes and shapes of centres of calcification. The traditional Guyniidae are diphyletic, corroborating Stolarskis hypothesis ‘A’. Some results from our most parsimonious trees are not strongly statistically supported but corroborated by other molecular studies and microstructural observations. For example, in the scleractinian phylogenetic tree, there are several lines of evidence (including those from our data) to distinguish a Faviidae–Mussidae lineage and a Dendrophylliidae–Agaricidae–Poritidae–Siderastreidae lineage. From a methodological standpoint, our results suggest that co‐ordinated studies creating links between biomineralization patterns and molecular phylogeny may provide an efficient working approach for a re‐examination of scleractinian classification. This goal is important because in the evolutionary scheme proposed by Wells that presently remains the basic framework in coral studies, patterns of septal microstructures are involved. Validating from molecular phylogenies a given microstructural character state as a potential synapomorphy for a clade is the only way to include fossils in the coral classification, an approach that should allow the unity of coral classification to be maintained up to the origin of the phylum in the Triassic times.

The phylogenetic position of Siboglinidae (Annelida) inferred from 18S rRNA, 28S rRNA and morphological data

We assess the phylogenetic position of Siboglinidae (previously known as the phyla Pogonophora and Vestimentifera, but now referred to Annelida) in parsimony analyses of 1100 bp from 18S rRNA, 320 bp from the D1 region of 28S rRNA, and 107 morphological characters, totaling 667 parsimony informative characters. The 34 terminal taxa, apart from six siboglinids, include polychaete members of Sabellida, Terbelliformia, Cirratuliformia and Spionida, plus two Aciculata polychaetes as outgroups. Our results contradict most recent hypotheses in showing a sistergroup relationship between Siboglinidae and Oweniidae, and in that the latter taxon is not a member of Sabellida. Furthermore, our results indicate that Sabellariidae is not closely related to Sabellida, that Serpulidae may be nested within Sabellidae, and that Alvinellidae is nested within Ampharetidae.

Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus

The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimuras two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA “universal” barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed.

Assessment of otocephalan and protacanthopterygian concepts in the light of multiple molecular phylogenies

The rise of cladistics in ichthyology has dramatically improved our knowledge of teleostean basal interrelationships. However, some questions have remained open, among them the reliability of the Otocephala, a clade grouping clupeomorphs and ostariophysans, and the relationships of the Esocoidei. These two questions have been investigated in the light of new DNA sequences (from 28S and rhodopsin genes) and sequences from data banks (cytochrome b, 12-16S, 18S, MLL and RAG1). The ability of each of these markers to resolve basal teleostean interrelationships is assessed, and the cytochrome b was not found appropriate. Practical (i.e. different taxonomic samplings) and epistemological grounds led us to perform multiple separated phylogenetic analyses, in order to estimate the reliability of the above clades from their repeatability among trees from independent sequence data. The Otocephala are found monophyletic from most of the datasets; otherwise, they are not significantly contradicted from the others, which exhibit unresolved relationships. We conclude that the evidence provided here favours the sister-group relationship of clupeomorphs and ostariophysans. Morphological evidence including fossils is discussed, concluding that morphological works have not yet provided sufficient data to support this group. Salmonids and esocoids are found sister-groups from every molecular dataset in which these groups were sampled. Based on these convincing results, the Protacanthopterygii of Johnson and Patterson [1] are redefined, including the Esocoidei.

Systématique moléculaire des phlebotominae : étude pilote. paraphylie du genre phlebotomus

Phylogenetic relationships among Phlebotominae were inferred through a pilot study using parsimony analysis of the D2 domain of ribosomal DNA sequences: 455 pairs of bases were sequenced in nine species of Phlebotomine sandflies which belong to the genera Lutzomyia, Phlebotomus and Sergentomyia. Two taxa are used as outgroups: Psychoda sp. and Nemapalpus flavus which is the sister group of the Phlebotominae. The South American genus Lutzomyia appears to be monophyletic. The Mediterranean species Sergentomyia dentata is its sister group and is not clustered with the Old World genus Phlebotomus. The latter is a paraphyletic genus with an early individualization of the branch including the closely related subgenera Phlebotomus and Paraphlebotomus, and a late individualization of the subgenus Larroussius. These results have some consequences on the biogeography of the leishmaniasis in the Old World.

Phylogenetic Relationships of the Tribe Paini (Amphibia, Anura, Ranidae) Based on Partial Sequences of Mitochondrial 12s and 16s rRNA Genes

Abstract Partial sequences of mitochondrial 12S and 16S rRNA genes from 19 Asian frog species of the tribe Paini (Ranidae, Dicroglossinae) allowed a first molecular study of the phylogenetic relationships of this tribe. This analysis confirmed that this tribe is a monophyletic group, but suggested relationships did not agree with previous generic classification of this clade based on morphology. Two major clades were recognized within the Paini. For one of them, the generic name Quasipaa is available. Phylogenetic relationships within the other group are not yet fully clarified and need further study.

Phylogeny of Hesionidae (Aciculata, Polychaeta), assessed from morphology, 18S rDNA, 28S rDNA, 16S rDNA and COI

We assess phylogenetic relationships within the polychaete family Hesionidae from morphological data combined with nucleotide data from 18S rDNA, 28S rDNA, 16S rDNA and COI. Parsimony and Bayesian analyses were performed on two data sets; the first was based on a more restricted set of terminals with both morphological and molecular data (17 ingroup terminals), while the second included additional taxa with morphological data only (25 ingroup terminals). The different sets of terminals yielded fully congruent results, as did the parsimony and the Bayesian analyses. Our results indicate high levels of homoplasy in traditionally used morphological characters in the group, and that Hesioninae, Gyptini and Gyptis are nonmonophyletic. Hesionini (mainly Hesione and Leocrates), Psamathini (mainly Hesiospina, Micropodarke, Nereimyra, Psamathe and Syllidia), Ophiodrominae (Gyptini and Ophiodromini) and Ophiodromini (mainly Heteropodarke, Ophiodromus and Podarkeopsis) are monophyletic and agree with previous classifications, and Hesionini is probably the sister to all other hesionids. The placements of the small hesionids capricornia and Lizardia, the hydrothermal vent taxa Hesiodeira and Hesiolyra, and the newly described Hesiobranchia, remain uncertain.

Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae)

Open-habitat chats (genera Myrmecocichla, Cercomela, Oenanthe and relative) are a morphologically and ecologically cohesive group of genera with unclear phylogenetic relationships. They are distributed mostly in open, arid and/or rocky habitats of Africa and Eurasia. Here, we present the most comprehensive molecular phylogenetic analysis of this group to date, with a complete taxon sampling at the species level. The analysis, based on a multilocus dataset including three mitochondrial and three nuclear loci, allows us to elucidate the phylogenetic relationships and test the traditional generic limits. All genera are non-monophyletic, suggesting extensive convergence on similar plumage patterns in unrelated species. While the colour pattern appear to be a poor predictor of the phylogenetic relationships, some of the ecological and behavioural traits agree relatively well with the major clades. Following our results, we also propose a revised generic classification for the whole group.

Evolution within the nuthatches (Sittidae: Aves, Passeriformes): molecular phylogeny, biogeography, and ecological perspectives

AbstractA comprehensive phylogeny of the nuthatches, genus Sitta, is proposed based on 21 of the 24–28 species recognized in the genus and three genes, two mitochondrial (cytochrome b and cytochrome oxidase subunit I) and one nuclear (RAG1). This phylogeny is well resolved and reveals several major clades within nuthatches. Przevalski’s Nuthatch Sitta przewalskii is sister to all other nuthatches, without any close relatives in our sampling. The larger species S. carolinensis and S. magna, despite their disjunct distributions, are sister taxa at the base of the tree. The next clade comprises the europaea group, which is sister to the two rock nuthatches (S. tephronota and S. neumayer), and to the Beautiful Nuthatch Sitta formosa of southeast Asia, although with less support. All these species use plastering to reduce the entrance of their hole or to build their nest with mud on rocks, but their ecologies are not as specialized as those of the rock nuthatches. The Asian small species (represented by S. azurea, S. frontalis and S. oenochlamys) form a well-supported clade. We confirm a single origin for the canadensis group that also includes the Yunnan nuthatch Sitta yunnanensis. Both are sister group to the two sibling species of North America (S. pygmaea and S. pusilla); all these species dig their own nest in trunks and are closely associated with coniferous forest. A biogeographical analysis supports the hypothesis of Asia being the center of diversification for nuthatches, with several independent dispersal events to North America.ZusammenfassungEvolution innerhalb der Kleiber (Sittidae: Aves, Passeriformes): molekulare Phylogenie, Biogeographie und ökologische Gegebenheiten Auf der Grundlage von 21 der 24–28 derzeit anerkannten Kleiberaten schlagen wir eine umfassende Phylogenie der Gattung Sitta vor. Zwei Mitochondriengene (Cytochrom-b, COI) und ein Kerngen (RAG1) wurden herangezogen; die Phylogenie ist gut aufgelöst und weist mehrere größere Äste innerhalb der Kleiberverwandtschaft aus. Der chinesische Przhewalski-Kleiber (S. przhewalskii) ist Schwesterart zu allen anderen Kleibern und weist innerhalb der einbezogenen Taxa keine nahen Verwandten aus. Die größeren Arten S. carolinensis und S. magna sind trotz ihrer weit disjunkten Verbreitung in Nordamerika und Südostasien Geschwisterarten und stehen als nächster Ast nahe der Basis des genetischen Baumes. Der weitere Baum ist in zwei Hauptäste gegliedert. Einer umfasst die europaea-Artengruppe, in die auch der Himalayakleiber (S. himalayana) einbezogen ist, zusätzlich Felsenkleiber (S. tephronota), Klippenkleiber (S. neumayer) und der südostasiatische Prachtkleiber (S. formosa). Alle diese Arten verkleben die Höhleneingänge oder bauen die Nester gänzlich aus Lehm an Felsen; das Nestbauverhalten von Felsen- und Klippenkleiber ist am höchsten spezialisiert. Die asiatischen kleinen Arten, die hier von S. azurea, S. frontalis und S. oenochlamys repräsentiert sind, stellen einen Teil das anderen gut unterstützten phylogenetischen Hauptastes dar. Ihm gegenüber steht ein vielfältig strukturierter Ast mit acht Arten, die in oftmals winzigen Reliktarealen in der Westpaläarktis leben (S. whiteheadi, S. ledenti, S. krueperi), teils in China (S. yunnanensis, S. villosa) oder in Nordamerika (S. pusilla, S. pygmaea, S. canadensis). Wir bestätigen einen gemeinsamen Ursprung der canadensis-Gruppe, die auch den Yunnankleiber (S. yunnanensis) umfasst. Der gesamte Ast ist Schwestergruppe zu den kleinen nordamerikanischen Geschwisterarten S. pygmaea und S.pusilla. Alle diese Arten hacken ihre Nesthöhle eigenständig in Baumstämme und sind eng an Nadelbäume gebunden. Eine biogeografische Analyse unterstützt die Hypothese, dass Asien das Diversifikationszentrum der Kleiber darstellt. Von dort brachten mehrere voneinander unabhängige Ausbreitungsereignisse Gattungsvertreter nach Nordamerika.