Sylvain G. Razafimandimbison

Bio: Sylvain G. Razafimandimbison is an academic researcher from Swedish Museum of Natural History. The author has contributed to research in topics: Monophyly & Genus. The author has an hindex of 25, co-authored 86 publications receiving 1699 citations. Previous affiliations of Sylvain G. Razafimandimbison include Uppsala University & Royal Swedish Academy of Sciences.

Recent origin and phylogenetic utility of divergent ITS putative pseudogenes: A case study from Naucleeae (Rubiaceae)

Abstract: The internal transcribed spacer (ITS) of nuclear ribosomal DNA has been widely used by systematists for reconstructing phylogenies of closely related taxa. Although the occurrence of ITS putative pseudogenes is well documented for many groups of animals and plants, the potential utility of these pseudogenes in phylogenetic analyses has often been underestimated or even ignored in part because of deletions that make unambiguous alignment difficult. In addition, long branches often can lead to spurious relationships, particularly in parsimony analyses. We have discovered unusually high levels of ITS polymorphism (up to 30%, 40%, and 14%, respectively) in three tropical tree species of the coffee family (Rubiaceae), Adinauclea fagifolia, Haldina cordifolia, and Mitragyna rubrostipulata. Both secondary structure stability and patterns of nucleotide substitutions in a highly conserved region (5.8S gene) were used for distinguishing presumed functional sequences from putative pseudogenes. The combination of both criteria was the most powerful approach. The sequences from A. fagifolia appear to be a mix of functional genes and highly distinct putative pseudogenes, whereas those from H. cordifolia and M. rubrostipulata were identified as putative pseudogenes. We explored the potential utility of the identified putative pseudogenes in the phylogenetic analyses of Naucleeae sensu lato. Both Bayesian and parsimony trees identified the same monophyletic groups and indicated that the polymorphisms do not transcend species boundaries, implying that they do not predate the divergence of these three species. The resulting trees are similar to those produced by previous analyses of chloroplast genes. In contrast to results of previous studies therefore, divergent putative pseudogenes can be useful for phylogenetic analyses, especially when no sequences of their functional counterparts are available. Our studies clearly show that ITS polymorphism may not necessarily mislead phylogenetic inference. Despite using many different PCR conditions (different primers, higher denaturing temperatures, and absence or presence of DMSO and BSA-TMACl), we recovered only a few functional ITS copies from A. fagifolia and none from H. cordifolia and M. rubrostipulata, which suggests that PCR selection is occurring and/or the presumed functional alleles are located at minor loci (with few ribosomal DNA copies).

Spatial structure and the effects of host and soil environments on communities of ectomycorrhizal fungi in wooded savannas and rain forests of Continental Africa and Madagascar

Abstract: Mycorrhizal fungi play a key role in mineral nutrition of terrestrial plants, but the factors affecting natural distribution, diversity and community composition of particularly tropical fungi remain poorly understood. This study addresses shifts in community structure and species frequency of ectomycorrhizal (EcM) fungi in relation to host taxa, soil depth and spatial structure in four contrasting African ecosystems. We used the rDNA and plastid trnL intron sequence analysis for identification of fungi and host plants, respectively. By partitioning out spatial autocorrelation in plant and fungal distribution, we suggest that African EcM fungal communities are little structured by soil horizon and host at the plant species and family levels. These findings contrast with patterns of vegetation in these forests and EcM fungal communities in other tropical and temperate ecosystems. The low level of host preference indirectly supports an earlier hypothesis that pioneer Phyllanthaceae may facilitate the establishment of late successional Fabaceae and potentially other EcM host trees by providing compatible fungal inoculum in deforested and naturally disturbed ecosystems of tropical Africa.

Phylogeny and classification of Naucleeae s.l. (Rubiaceae) inferred from molecular (ITS, rBCL, and tRNT-F) and morphological data

Abstract: Parsimony analyses of the tribe Naucleeae sensu lato (s.l.) using the noncoding internal transcribed spacer (ITS) regions of nuclear rDNA, the protein-coding rbcL and noncoding trnT-F regions of chloroplast DNA, and morphological data were performed to construct new intratribal classification, test the monophyly of previous subtribal circumscriptions, and evaluate the generic status of Naucleeae s.l. Fifty-two ITS, 45 rbcL, and 55 trnT-F new sequences are published here. Our study supports the monophyly of the subtribes Anthocephalidae, Mitragynae, Uncariae all sensu Haviland and Naucleinae sensu Ridsdale. There was no support for Cephalanthidae sensu Haviland and Adininae sensu Ridsdale. Naucleeae can be subdivided into six highly supported and morphologically distinct subtribes, Breoniinae, Cephalanthinae, Corynantheinae, Naucleinae, and Mitragyninae, Uncarinae, plus one, Adininae, which is poorly supported. The relationships among these subtribes were largely unresolved. We maintain the following 22 genera: Adina, Adinauclea, Breonadia, Breonia, Burttdavya, Cephalanthus, Gyrostipula, Haldina, Janotia, Ludekia, Metadina, Mitragyna, Myrmeconauclea, Nauclea, Neolamarckia, Neonauclea, Ochreinauclea, Pausinystalia, Pertusadina, Sarcocephalus, Sinoadina, and Uncaria. Pseudocinchona is reestablished. Corynanthe is restricted to C. paniculata and Hallea is reincluded in Mitragyna. Our results were inconclusive for assessing the relationships among Adina, Adinauclea, Metadina, and Pertusadina due to lack of resolution.

Phylogeny and circumscription of Sapindaceae revisited: molecular sequence data, morphology and biogeography support recognition of a new family, Xanthoceraceae.

Abstract: Background and aims Recent studies have adopted a broad definition of Sapindaceae that includes taxa traditionally placed in Aceraceae and Hippocastanaceae, achieving monophyly but yielding a family difficult to characterize and for which no obvious morphological synapomorphy exists. This expanded circumscription was necessitated by the finding that the monotypic, temperate Asian genus Xanthoceras, historically placed in Sapindaceae tribe Harpullieae, is basal within the group. Here we seek to clarify the relationships of Xanthoceras based on phylogenetic analyses using a dataset encompassing nearly 3/4 of sapindaceous genera, comparing the results with information from morphology and biogeography, in particular with respect to the other taxa placed in Harpullieae. We then re-examine the appropriateness of maintaining the current broad, morphologically heterogeneous definition of Sapindaceae and explore the advantages of an alternative family circumscription. Methods Using 243 samples representing 104 of the 142 currently recognized genera of Sapindaceae s. lat. (including all in Harpullieae), sequence data were analyzed for nuclear (ITS) and plastid (matK, rpoB, trnD-trnT, trnK-matK, trnL-trnF and trnS-trnG) markers, adopting the methodology of a recent family-wide study, performing single-gene and total evidence analyses based on maximum likelihood (ML) and maximum parsimony (MP) criteria, and applying heuristic searches developed for large datasets, viz, a new strategy implemented in RAxML (for ML) and the parsimony ratchet (for MP). Bootstrap analyses were performed for each method to test for congruence between markers. Key results Our findings support earlier suggestions that Harpullieae are polyphyletic: Xanthoceras is confirmed as sister to all other sampled taxa of Sapindaceae s. lat.; the remaining members belong to three other clades within Sapindaceae s. lat., two of which correspond respectively to the groups traditionally treated as Aceraceae and Hippocastanaceae, together forming a clade sister to the largely tropical Sapindaceae s. str., which is monophyletic and morphologically coherent provided Xanthoceras is excluded. Conclusion To overcome the difficulties of a broadly circumscribed Sapindaceae, we resurrect the historically recognized temperate families Aceraceae and Hippocastanaceae, and describe a new family, Xanthoceraceae, thus adopting a monophyletic and easily characterized circumscription of Sapindaceae nearly identical to that used for over a century.

Polyphyly of Mussaenda inferred from ITS and trnT-F data and its implication for generic limits in Mussaendeae (Rubiaceae).

Abstract: Although recognition of Mussaenda as a separate genus has been widely accepted, its generic circumscriptions have always been controversial. In this first molecular phylogenetic study focused specifically on Mussaenda sensu lato (s.l.) and its allied genera, parsimony analyses were based on both ITS and trnT-F sequence data to (1) test the monophyly of Mussaenda s.l. as presently circumscribed, (2) assess the phylogenetic relationships within the tribe Mussaendeae as currently delimited, (3) evaluate the phylogenetic value of the morphological characters traditionally and/or currently used to circumscribe Mussaendeae, (4) and make inferences on the biogeographical origin of Mussaenda. Of the 63 trnT-F and 38 ITS sequences included in our studies, 52 and 36 sequences, respectively, are newly published here. Our results highly support the polyphyly of Mussaenda s.l. as currently delimited but further support the monophyly of Mussaendeae sensu Bremer and Thulin. The Malagasy Mussaenda are more closely related to Landiopsis than they are to the African and Asian Mussaenda. Pseudomussaenda and the Afro-Asian Mussaenda clade are resolved as sister groups. Aphaenandra is nested within the Afro-Asian Mussaenda clade. As a result, we merge Aphaenandra in Mussaenda, which is now restricted to include only the African and Asian Mussaenda representatives. We describe a new genus Bremeria to accommodate all Indian Ocean (Madagascar and the Mascarenes) Mussaenda species and make 19 new combinations. The newly delimited Mussaenda is diagnosed by reduplicate-valvate aestivation and glabrous styles, whereas Bremeria can be distinguished from the remaining Mussaendeae genera by having both reduplicate- and induplicate-valvate aestivation and densely pubescent styles. Our studies strongly suggest an African origin of the newly delimited Mussaenda. Finally, descriptions of the newly circumscribed Mussaendaand Bremeria are provided.

Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages

Abstract: The ectomycorrhizal (EcM) symbiosis involves a large number of plant and fungal taxa worldwide During studies on EcM diversity, numerous misidentifications, and contradictory reports on EcM status have been published This review aims to: (1) critically assess the current knowledge of the fungi involved in the EcM by integrating data from axenic synthesis trials, anatomical, molecular, and isotope studies; (2) group these taxa into monophyletic lineages based on molecular sequence data and published phylogenies; (3) investigate the trophic status of sister taxa to EcM lineages; (4) highlight other potentially EcM taxa that lack both information on EcM status and DNA sequence data; (5) recover the main distribution patterns of the EcM fungal lineages in the world Based on critically examining original reports, EcM lifestyle is proven in 162 fungal genera that are supplemented by two genera based on isotopic evidence and 52 genera based on phylogenetic data Additionally, 33 genera are highlighted as potentially EcM based on habitat, although their EcM records and DNA sequence data are lacking Molecular phylogenetic and identification studies suggest that EcM symbiosis has arisen independently and persisted at least 66 times in fungi, in the Basidiomycota, Ascomycota, and Zygomycota The orders Pezizales, Agaricales, Helotiales, Boletales, and Cantharellales include the largest number of EcM fungal lineages Regular updates of the EcM lineages and genera therein can be found at the UNITE homepage http://uniteutee/EcM_lineages The vast majority of EcM fungi evolved from humus and wood saprotrophic ancestors without any obvious reversals Herbarium records from 11 major biogeographic regions revealed three main patterns in distribution of EcM lineages: (1) Austral; (2) Panglobal; (3) Holarctic (with or without some reports from the Austral or tropical realms) The holarctic regions host the largest number of EcM lineages; none are restricted to a tropical distribution with Dipterocarpaceae and Caesalpiniaceae hosts We caution that EcM-dominated habitats and hosts in South America, Southeast Asia, Africa, and Australia remain undersampled relative to the north temperate regions In conclusion, EcM fungi are phylogenetically highly diverse, and molecular surveys particularly in tropical and south temperate habitats are likely to supplement to the present figures Due to great risk of contamination, future reports on EcM status of previously unstudied taxa should integrate molecular identification tools with axenic synthesis experiments, detailed morphological descriptions, and/or stable isotope investigations We believe that the introduced lineage concept facilitates design of biogeographical studies and improves our understanding about phylogenetic structure of EcM fungal communities

Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

Abstract: The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).