Phylogenetic relationships of Gomphillaceae and Asterothyriaceae: evidence from a combined Bayesian analysis of nuclear and mitochondrial sequences

Size: px
Start display at page:

Download "Phylogenetic relationships of Gomphillaceae and Asterothyriaceae: evidence from a combined Bayesian analysis of nuclear and mitochondrial sequences"

Transcription

1 Mycologia, 96(2), 2004, pp by The Mycological Society of America, Lawrence, KS Phylogenetic relationships of Gomphillaceae and Asterothyriaceae: evidence from a combined Bayesian analysis of nuclear and mitochondrial sequences Robert Lücking 1 Department of Botany, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, Illinois Bryan L. Stuart Department of Zoology, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, Illinois H. Thorsten Lumbsch Department of Botany, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, Illinois Abstract: The phylogeny and systematic position of Gomphillaceae was reconstructed using a combined Bayesian analysis of nuclear LSU rdna and mitochondrial SSU rdna sequences. Twenty-four partial sequences of 12 taxa (11 Gomphillaceae and one Asterothyriaceae) plus two new sequences of Stictis radiata (Ostropales outgroup) were generated and aligned with the corresponding sequences retrieved from GenBank, resulting in an alignment of 82 taxa that was analyzed using a Bayesian approach with Markov chain Monte Carlo (B/MCMC) methods. Our results confirm Gomphillaceae sensu Vezda and Poelt plus Asterothyriaceae to be a monophyletic group, with an unresolved relationship between the two families. Placement of Gomphillaceae and Asterothyriaceae within Ostropales sensu Kauff and Lutzoni, as sister of Thelotremataceae, also is strongly supported. Alternative hypotheses placing Gomphillaceae in Lecanorales (Cladoniaceae), Agyriales (Baeomycetaceae) or within bitunicate Ascomycota (Arthoniomycetes, Chaetothyriomycetes, Dothideomycetes) were rejected with our dataset. After recent synonymization of Dimerella with Coenogonium (Ostropales: Coenogoniaceae), we propose the new combination Coenogonium pineti (one of our Ostropales outgroup taxa in this analysis). Key words: foliicolous lichens, Lecanoromycetes, mitochondrial small-subunit rdna, nuclear large subunit rdna, systematics Accepted for publication August 26, Corresponding author. INTRODUCTION The ascomycete families Gomphillaceae and Asterothyriaceae form a medium-size group of mainly tropical, crustose microlichens (Lücking 1999, Vezda 1979, Vezda and Poelt 1987). Numerous species grow on leaves and form an important part of the tropical diversity in the phyllosphere (Lücking 2001). The Gomphillaceae morphologically are remarkable for the presence of peculiarly shaped conidiomata that are called hyphophores, while many Asterothyriaceae are characterized by a unique thallus cortex (Henssen and Lücking 2002, Vezda 1979). Despite their importance for tropical lichen diversity and their morphological peculiarities, the phylogeny and taxonomy of Gomphillaceae and Asterothyriaceae largely has been unsettled. The Gomphillaceae consist of almost 300 species currently classified into 14 genera (Lücking 1997, Vezda and Poelt 1987). While most species grow on living leaves, taxa occurring on bark of vascular plants, over bryophytes, on soil and rock surfaces and even lichenicolous species also are known in this group (Lücking 1997, Lücking and Kalb 2002, Lücking and Sérusiaux 1998, Vezda and Poelt 1987). Members of this family are characterized by apothecioid ascomata with hemiangiocarpous development, a hamathecium consisting of thin, strongly gelatinized and richly branched and anastomosing paraphyses, and nonamyloid asci corresponding to the annelasceous type (Lücking 1997, Vezda and Poelt 1987). Apothecial morphology is variable, ranging from sessile and biatorine (e.g., Gyalideopsis, Echinoplaca) to vertically elongate (Gomphillus) or immersed-erumpent and zeorine apothecia (Calenia, Gyalectidium) (FIG. 1). The conidiomata, the socalled hyphophores, are usually stipitate and produce conidia ( diahyphae ) at their tips, but many variations of this basic scheme occur and derived types even resemble disk-shape diaspores or campylidioid conidiomata (FIG. 2). Both apothecial morphology and hyphophore type are employed for the delimitation of genera in the family. Gomphillaceae originally was based on a single, monospecific taxon, Gomphillus calycioides, an enigmatic lichen usually growing over bryophytes and characterized by elongate apothecia with very long asci and filiform ascospores (Nylander 1860, Hafell- 283

2 284 MYCOLOGIA FIG. 1. Morphological variation of apothecia in selected genera of Asterothyriaceae (A) and Gomphillaceae (B H) A. Asterothyrium longisporum (immersed-erumpent with recurved lobules). B. Gomphillus ophiosporus (vertically elongate). C. Gyalideopsis vulgaris (sessile). D. Tricharia albostrigosa (sessile). E. Tricharia longispora (shortly stipitate). F. Echinoplaca atrofusca (adnate and spot-like). G. Calenia aspidota (immersed-erumpent). H. Aulaxina submuralis (carbonized).

3 LÜCKING ET AL: PHYLOGENY OF GOMPHILLACEAE 285 FIG. 2. Morphological variation of hyphophores in selected genera of Gomphillaceae. A. Calenia monospora (stipitate with apical bunch of diahyphae visible). B. Tricharia cuneata (spatulate). C. Calenia aspidota (setiform). D. Tricharia dilatata (hand-shaped). E. Echinoplaca gemmifera (resembling disk-shaped isidia). F. Gyalideopsis hyalina (resembling campylidia of Pilocarpaceae). G. Gyalectidium filicinum (squamiform wirh horns). H. Hippocrepidea nigra (lunular).

4 286 MYCOLOGIA TABLE I. Species and specimens of lichenized and nonlichenzied Ascomycota used in the current study. Taxa for which sequences have been newly obtained are in boldface. F denotes voucher specimens deposited at the Field Museum of Natural History Species Specimen GenBank acc. no. nulsu mtssu Absconditella sphagnorum AY AY Adelolecia pilati AY AY Agonimia tristicula AY AY Ainoa mooreana AY AY Arthonia dispersa AY AY Aspergillus flavus AF AFU29214 Aspergillus nidulans AF V00653 Asterothyrium longisporum Costa Rica (Cartago: Orosi), Lücking s.n. (F, AY AY sample No. 4) Aulaxina quadrangula Costa Rica (Puntarenas: Las Cruces, Lücking AY AY s.n. (F, sample No. 66) Baeomyces placophyllus AF AY Beauveria bassiana AF AB Berlesiella nigerrima AY AY Bryophagus gloeocapsa AF AY Cainia graminis AF AF Calenia monospora Costa Rica (Cartago: Orosi), Lücking s.n. (F, AY AY sample No. 1a) Calenia phyllogena Costa Rica (Heredia: La Selva), Lücking s.n. AY AY (F, sample No. 32) Calicium viride AF AY Caloplaca flavorubescens AY AY Capnodium citri AY AF Capronia mansonii AY AF Cephalotheca sulfurea AF AF Ceramothyrium carniolicum AY AF Cladonia rangiferina AY AY Coenogonium pineti AY AY Combea mollusca AY AY Dendrographa minor AY AY Diploschistes cinereocaesius AY AY Diploschistes muscorum AY AY Diploschistes rampoddensis AF AF Diploschistes thunbergianus AF AF Dothidea ribesia AY AY Echinoplaca diffluens Mexico (Veracruz: Lost Tuxtlas), Herrera et AY AY al s.n. (F, sample No. M12) Echinoplaca epiphylla Mexico (Veracruz: Lost Tuxtlas), Herrera et AY AY al s.n. (F, sample No. M13) Echinoplaca leucotrichoides Costa Rica (Heredia: La Selva), Lücking s.n. AY AY (F, sample No. 18) Echinoplaca lucernifera Costa Rica (Puntarenas: Monteverde), Lücking AY AY s.n. (F, sample No. 59a) Eurotium rubrum AY AF Glyphium elatum AF AF Gomphillus ophiosporus Costa Rica (Puntarenas: Las Alturas), Will- AY AY Wolf 10006a (F, sample No. 101) Gyalecta jenensis AF AF Gyalectidium imperfectum Costa Rica (Cartago: Orosi) Lücking s.n. (F, sample No. 2) AY AY341372

5 LÜCKING ET AL: PHYLOGENY OF GOMPHILLACEAE 287 TABLE I. Continued Species Specimen GenBank acc. no. nulsu mtssu Gyalideopsis sp. nov. Costa Rica (Puntarenas: Altamira), Nelsen AY AY a (F, sample No. 103) Lecania cyrtella AY AY Lecanora intumescens AY AY Lecidella meiococca AY AY Lepraria usnica AY AY Lobaria pulmonaria AF AF Myriangium duriaei AY AY Nephroma bellum AY AY Neurospora crassa M38154 Z34001 Ochrolechia balcanica AF AF Ochrolechia parella AF AF Ochrolechia tartarea AY AY Orceolina antarctica AF AY Orceolina kerguelensis AF AF Penicillium chrysogenum AF Z23072 Pertusaria albescens AF AF Pertusaria corallina AY AY Pertusaria scaberula AF AF Pertusaria subventosa AY AY Physcia aipolia AY AY Placopsis bicolor AY AY Placopsis gelida AY AY Pyrrhospora quernea AY AY Raciborskiomyces longisetosum AY AY Ramonia sp. AY AY Schismatomma pericleum AF AY Scoliciosporum umbrinum AY AY Speerschneidera euploca AY AY Steinera glaucella AY AY Stictis radiata AY AY Stictis radiata Costa Rica (Cartago: Irazú), Will-Wolf s.n. (F, AY AY sample No. 100) Stylodothis puccinioides AY AF Thelotrema lepadinum AY AY Thelotrema suecicum AY AY Trapelia coarctata AF AY Trapelia placodioides AF AF Trapeliopsis flexuosa AF AY Trapeliopsis granulosa AF AF Tricharia longispora Costa Rica (Heredia: La Selva), Lücking s.n. AY AY (F, sample No. 37) Xanthoria parietina AF AY Xylaria hypoxylon AF AF Xylographa vitiligo AY AY ner 1984, Vezda 1979, Vezda and Poelt 1987). Because its apothecia superficially resemble podetia, Gomphillus was placed close to genera such as Cladonia and Baeomyces (Räsänen 1943, Sato 1954), although Nylander (1860), Santesson (1952) and Jahns (1970) had observed that the apothecia are vertically elongate and what was erroneously interpreted as stipe represented a part of the hymenium. Based on similarities in hamathecium structure and ascus type, Vezda (1979) suggested that Gomphillus calycioides is related to four genera previously included in Asterothyriaceae (Santesson 1952), viz. Calenia, Gyalectidium, Echinoplaca and Tricharia. This view was supported by the discovery of hyphophores in a second species of the genus, Gomphillus americanus (Vezda and Poelt 1987). The genera pro-

6 288 MYCOLOGIA ducing hyphophores and having a hamathecium composed of anastomosing paraphyses subsequently were transferred from Asterothyriaceae to the resurrected Gomphillaceae, while taxa lacking hyphophores and having unbranched paraphyses were retained in Asterothyriaceae s.str. (Eriksson and Hawksworth 1987, Vezda and Poelt 1987). The systematic positions and the homogeneity of the two families have been questioned by various authors. Hafellner (1984, 1988) interpreted the asci of Gomphillus as being fissitunicate and separated the genus into an independent order Gomphillales. Based on the ascus type, he suggested a close relationship to bitunicate ascomycetes that currently are placed in Arthoniomycetes, Dothideomycetes and Chaetothyriomycetes (Eriksson 2001). As regards the Asterothyriaceae, some genera were transferred from that family to a separate family Solorinellaceae (Vezda and Poelt 1990), while Psorotheciopsis was included in Megalosporaceae (Vezda 1973) and Asterothyrium itself was suggested as belonging in Thelotremataceae (Aptroot in Aptroot et al 1994). Anatomical, ontogenetic and phenotype-based phylogenetic evidence, however, suggest that Gomphillaceae and Asterothyriaceae sensu Vezda and Poelt (1987) are monophyletic and best placed in Ostropales (Henssen and Lücking 2002, Lücking 1997, 1999). Recent molecular analyses indicate that the circumscription of this order needs clarification. In the most recent Outline of the Ascomycetes (Eriksson et al 2003), Gyalectales (including Gyalectaceae and Coenogoniaceae) and Ostropales (including Asterothyriaceae, Graphidaceae, Odontotremataceae, Phaneromycetaceae, Solorinellaceae, Stictidaceae and Thelotremataceae) are listed separately and Gomphillaceae are included among Ascomycota: Families of uncertain positions. However, Kauff and Lutzoni (2002) showed that Gyalectales are nested within and form part of Ostropales, which was confirmed in a subsequent analysis by Lumbsch et al (2004). To clarify the uncertain phylogenetic relationships of Gomphillaceae and to test the alternative relationships suggested by various authors, we gathered molecular data of representatives of this family and the Asterothyriaceae. For this purpose, we targeted the nuclear LSU (nulsu) and the mitochondrial SSU (mtssu) region of the ribosomal DNA because combined analyses of these two genes have been used successfully in previous approaches to the phylogeny of Lecanoromycetes (Lumbsch and Schmitt 2002, Lumbsch et al 2004). We chose a Bayesian approach that allows efficient analysis of datasets while employing complex nucleotide substitution models in a parametric statistical framework (Huelsenbeck et al 2001, Larget and Simon 1999). Bayesian phylogenetics also allows simultaneous estimation of uncertainty in the phylogenetic topography, as well as hypothesis testing of alternative topographies, because posterior probabilities of alternative trees can be calculated (Huelsenbeck et al 2000). Our Ostropales outgroup taxa includes the widespread lichen Dimerella pineti (Coenogoniaceae). Because the genus Dimerella recently has been synonymized with Coenogonium, which was confirmed by a molecular phylogenetic analysis (Kauff and Lutzoni 2002, Lücking and Kalb 2000), we propose the new combination Coenogonium pineti in this paper. MATERIALS AND METHODS Taxon sampling. Sequence data of the nulsu rdna and mtssu rdna were collected from a total of 82 euascomycetes. Twenty-four new sequences were obtained from 12 species, as listed in TABLE I. Taxa were sampled to ensure that representatives of the major clades within Lecanoromycetes and taxa of the major classes of euascomycetes were included in the study. Molecular methods. Small samples prepared from freshly collected and frozen herbarium specimens were deep frozen at 80 C for 30 min and ground with sterile plastic pestles. Total genomic DNA was extracted using PureGene Animal Tissue DNA Isolation Protocol (Gentra Systems Inc.). Nuclear LSU rrna was amplified by the polymerase chain reaction (PCR; 95 C 3 min, then 35 cycles of 95 C 45 s, 54 C 45 s, 72 C 1 min) using the forward primers LIC15R, LR0R, LIC24R (Miadlikowska et al 2002, Miadlikowska and Lutzoni 2000, Rehner and Samuels 1994) or ALR1 (Döring et al 2000), and the reverse primer LR3 (Vilgalys and Hester 1990). Mitochondrial SSU rrna was amplified by PCR (95 C 3 min, 55 C 1 min, 72 C 1 min, then 35 cycles of 94 C 1 min, 55 C 1 min, 72 C 1 min) using the primers mrssu1 (Zoller et al 1999) and MSU7 (Zhou and Stanosz 2001). Adding 5 L of purified, 10 mg/ml bovine serum albumin (BSA, New England BioLabs Inc.) to 25 L total PCR reactions greatly improved amplification success. PCR products were electrophoresed in a 1% low-melt agarose TALE gel stained with ethidium bromide and visualized under ultraviolet light. The bands containing DNA were excised and agarose was digested from bands using GELase (Epicentre Technologies). PCR products were sequenced with the amplifying primers in both directions by direct double-strand cycle sequencing using Big Dye version 1 chemistry (Perkin Elmer). Cycle sequencing products were precipitated with ethanol and 3 M sodium acetate and sequenced with a Prism 3100 Genetic Analyzer (ABI). Sequences were edited with Sequencher version 4.1 (Genecodes). About 300 bp of the 5 part of the nulsu could be generated for representatives of Gomphillaceae and Asterothyriaceae. This limitation probably was due to a splicosomal intron specific to these two families, starting at about position 350 of the 5 part of the nulsu, and this phenomenon is currently under further investigation by us.

7 LÜCKING ET AL: PHYLOGENY OF GOMPHILLACEAE 289 TABLE II. Probabilities of five phylogenetic null hypotheses being correct. Each test is based on a B/MCMC tree sample of 1000 trees. Probabilities significant at 0.1% are denoted *** Null hypothesis Gomphillaceae placed in Arthoniomycetes Gomphillaceae placed in Chaetothyriomycetes Gomphillaceae placed in Dothideomycetes Gomphillaceae placed in Agyriales Gomphillaceae placed in Lecanorales Probability 0.00*** 0.00*** 0.00*** 0.00*** 0.00*** Sequence alignments. The mtssu dataset contains sequence portions that are highly variable. Because standard multiple alignment programs, such as Clustal (Thompson et al 1994), become less reliable when sequences are highly divergent, we instead have used an alignment procedure employing a linear Hidden Markov Model (HMM) for the alignment, as implemented in the software SAM (Hughey and Krogh 1996; compbio/sam.html). Sequences of 82 species (TABLE II) were aligned separately for the two genes. Regions that could not be aligned with statistical confidence were excluded from the phylogenetic analysis. Phylogenetic analysis. The alignment was analyzed using the programs PAUP* 4.0b10 (Swofford 2003) and MrBayes 3.0 (Huelsenbeck and Ronquist 2001). The polarity of characters was assessed selecting four representatives of Dothideomycetes as outgroup because this group repeatedly was found as basal within inoperculate euascomycetes in recent phylogenetic estimates of euascomycetes (e.g., Liu et al 1999, Lumbsch et al 2002). The data were analyzed using a Bayesian approach (Huelsenbeck et al 2000, Larget and Simon 1999). Posterior probabilities were approximated by sampling trees using a Markov chain Monte Carlo (MCMC) method. The posterior probabilities of each branch were calculated by counting the frequency of trees that were visited during the course of MCMC analysis. The program MrBayes was used to sample trees. The analysis was performed assuming the general time-reversible model (Rodriguez et al 1990), including estimation of invariant sites and assuming a discrete gamma distribution with six rate categories (GTR I G) for the single-gene and the combined analyses. The nucleotide substitution model was selected with a likelihood ratio test (Huelsenbeck and Crandall 1997) with the program Modeltest (Posada and Crandall 1998). No molecular clock was assumed. Initial runs were conducted, starting with random, NJ or ME trees to check the number of simultaneous MCMC chains necessary to avoid being trapped on local optima. For this, the separate initial analyses were run with generations with an increasing number of chains (starting with four). When the separate analyses converged at a similar likelihood value, it was assumed that the number of chains was sufficient. This was the case with eight chains. To allow an additional range of security, we have chosen to run the analyses employing 12 simultaneous chains that started with a random tree. The analyses started with a random tree and was run with generations. Eleven of these chains were heated. During its search in the universe of trees, a cold chain might become stuck in isolated peaks. To circumvent this, heated chains that can jump to other areas in the universe of trees run simultaneously. These heated chains act as scouts to enable the cold chain to escape local optima. Every 100th tree sampled was saved into a file. We plotted the log-likelihood scores of sample points against generation time using Microsoft Excel and determined that stationarity was achieved when the log-likelihood values of the sample points reached a stable equilibrium value (Huelsenbeck and Ronquist 2001). The initial 2000 trees that showed a linear increase in likelihood values were discarded as burn-in before stationarity was reached. Using PAUP*, majority-rule consensus trees were calculated from trees sampled after reaching likelihood convergence to calculate the posterior probabilities of the tree nodes. Unlike nonparametric bootstrap values (Felsenstein 1985), these are estimated probabilities of the clades under the assumed model (Rannala and Yang 1996) and hence posterior probabilities equal to and above 95% are considered significant supports. Phylogenetic trees were drawn using TreeView (Page 1996). We used a Bayesian approach to examine the heterogeneity in phylogenetic signal between the two data partitions (Buckley et al 2002). For the two genes and the concatenated analyses, the set of topologies reaching 0.95 posterior probability was estimated. The combined analysis topology then was compared for conflict with the 0.95 posterior intervals of the single gene analyses. If no conflict was evident, it was assumed that the two datasets were congruent and could be combined. If conflict was evident, the two datasets were interpreted as incongruent and thus the concatenated analysis might be potentially misleading (Bull et al 1993). Five hypothesized phylogenetic relationships of Gomphillaceae expressed in recent publications were tested as null hypotheses using a MCMC tree sampling procedure as described above. For hypothesis testing, a run as described above was performed with the same settings as in the estimation of the phylogeny. One thousand trees at the equilibrium state per null hypothesis were used from this analysis. The probability of the null hypothesis being correct is calculated by counting the presence of this topology in the MCMC sample (Lewis 2001, Lumbsch et al 2004). The frequency of trees in the MCMC sample agreeing with the null hypothesis was calculated using the filter command in PAUP* with constraints used to describe the null hypothesis. The constraints were constructed so that only the single node of interest was resolved. To examine the possibility that the inferred phylogenetic relationships were due to long-branch attraction (Felsenstein 1978), we employed a 2 -test for deviant nucleotide composition using TREE-PUZZLE (Strimmer and von Haeseler 1996) and a relative-rate test using RRTREE (Robinson-Rechavi and Huchon 2000). RESULTS We generated a total of 12 new mitochondrial SSU rdna and 12 new nuclear LSU rdna sequences for

8 290 MYCOLOGIA this study (TABLE I). The sequences were aligned with 70 mtssu and 70 nulsu rdna sequences obtained from Genbank (TABLE I) to produce a matrix of 270 unambiguously aligned nucleotide position characters in the nu LSU and 766 in the mt SSU dataset. One hundred thirty-three characters in the nu LSU and 656 in the mt SSU dataset were variable. The Bayesian approach for testing datasets for incongruence indicated that the topology of the majorityrule consensus tree from the combined analysis lies within the 0.95 posterior intervals for the two separate datasets (data not shown). This is consistent with the hypothesis that the two partitions have evolved along the same underlying topology and hence a combined analysis was performed. The combined alignment is available in TreeBASE (http:// herbaria.harvard.edu/treebase/). The likelihood parameters in the sample of the combined analysis (values of the separate analyses not shown) had these average values ( one standard deviation): base frequenices (A) ( 0.008), (C) ( 0.005), (G) ( 0.006), (T) ( 0.008), rate matrix r(ac) ( 0.104), r(ag) ( 0.219), r(at) ( 0.201), r(cg) ( 0.103), r(ct) ( 0.389), r(gt) 1.0 ( 0.0), gamma shape parameter alpha ( 0.032), and the proportion of invariable site p(invar) ( 0.092). In the majority-rule consensus tree of sampled trees (FIG. 3), the currently accepted classes, such as Lecanoromycetes or Sordariomycetes (Eriksson et al 2003), are monophyletic with strong support (posterior probability [pp] 1.0 for all classes). Chaetothyriomycetes and Eurotiomycetes appear as a sister group of Lecanoromycetes, but this relationship lacks support. The Lecanoromycetes includes two major clades, one comprising Ostropales sensu lato and the other Lecanorales, Pertusariales and Agyriales. The latter group, however, again lacks support. Ostropales sensu lato is strongly supported (pp 1.0). Within this order, Stictidaceae (Stictis, Absconditella) appear basal, while monophyletic Thelotremataceae (Diploschistes, Thelotrema) are strongly supported (pp 1.0). Gyalectaceae (Bryophagus, Xerothrema, Gyalecta) appear paraphyletic when including Bryophagus, whereas Coenogoniaceae is represented by a single species only (Coenogonium pineti [Schrad. ex Ach.] Lücking & Lumbsch comb. nov.; Lecidea pineti Schrad. ex Ach., Lich. Univ.: ; Acharius, Syn. Lich.: ; Dimerella pineti [Schrad. ex Ach.] Vezda, Lich. Sel. Exs. (Pruhonice) 52, No ). Gomphillaceae plus Asterothyriaceae form a monophyletic lineage within Ostropales sensu lato (pp 1.0), and this lineage is sister of Thelotremataceae, supported by pp of The only representative of Asterothyriaceae, Asterothyrium longisporum, is nested within Gomphillaceae. The chiefly nonlichenized Stictidaceae show a sister-group relationship with other taxa of Ostropales sensu lato. To evaluate the potential presence of long-branch attraction, we performed a 2 -test and a relative-rate test. All sequences included in the study passed the 2 -test (P for Asterothyriaceae/Gomphillaceae, P for other euascomycetes), indicating that none of the sequences had a significantly deviating nucleotide composition. The results of the relative-rate tests showed that the Asterothyriaceae/Gomphillaceae and Thelotremataceae clades do not differ significantly in their substitution rate from other Lecanoromycetes. The results were not significant in all three cases examined (P for Asterothyriaceae/Gomphillaceae versus Thelotremataceae, P for Thelotremataceae versus other Lecanoromycetes excluding Asterothyriaceae/Gomphillaceae, P for Asterothyriaceae/Gomphillaceae versus other Lecanoromycetes excluding Thelotremataceae). DISCUSSION Our analysis confirms that Gomphillaceae and Asterothyriaceae (here represented by the single species Asterothyrium longisporum) are closely related and form a monophyletic lineage that is part of the Ostropalean clade in Lecanoromycetes. These results correspond well to previous studies on the anatomy and ontogeny of Gomphillaceae and Asterothyriaceae, including phenotype-based phylogenetic approaches (Aptroot and Lücking 2003, Dennetière and Péroni 1998, Henssen and Lücking 2002, Lücking 1997, 1999, Vezda 1979, Vezda and Poelt 1987). They also support the utility of phenotype-based analyses for hypothesis-building, even in lichen-forming fungi that are notorious for their variable and often homoplasious morphological characters. It also is clear from the analysis that Gomphillus is related closely to other members of Gomphillaceae sensu Vezda and Poelt (1987) and does not form an isolated member of this family, although its very elongate asci and ascospores are different from the clavate to ovoid asci and ellipsoid to cylindrical ascospores found in all other genera. We were unable to confirm a sister group relationship between the Asterothyriaceae and Gomphillaceae, as assumed in previous contributions (Henssen and Lücking 2002, Lücking 1997, 1999). However, because only one representative of the first family could be included in this analysis, this might be an artifact of insufficient taxon sampling. Generic delim-

9 LÜCKING ET AL: PHYLOGENY OF GOMPHILLACEAE 291 FIG. 3. Majority-rule consensus tree based on trees from a B/MCMC tree sampling procedure. Posterior probabilities equal or above 0.95 indicated at branches. Ordinal and/or class placement of taxa indicated at margin.

10 292 MYCOLOGIA itation within Gomphillaceae is also in flux (Lücking 1997) and is being studied by us using a larger set of mtssu and nulsu data. Taxa included here that are currently assigned to the genera Calenia and Echinoplaca accordingly do not form monophyletic groups in our analysis. However, our data suggest that taxa with sessile or adnate, biatorine apothecia (Gyalideopsis, Gomphillus, Tricharia, Echinoplaca) are derived from those with immersed-erumpent, zeorine or carbonized apothecia (Calenia, Gyalectidium, Aulaxina). This contradicts previous hypotheses about the evolution of the group (Lücking 1997) but is in accordance with our present results that Gomphillaceae plus Asterothyriaceae are sister of Thelotremataceae (here represented by Thelotrema and Diploschistes), which are characterized by immersed-erumpent, zeorine apothecia. Indeed, the sister-group relationship of Asterothyriaceae plus Gomphillaceae with Thelotremataceae is supported significantly. However, the branch leading to the Gomphillaceae is unusually long, suggesting that this relationship might be due to long-branch attraction (Felsenstein 1978). If two unrelated lineages have had an accelerated substitution rate compared to other included groups in a study, they will have accumulated characters that will distance them from other taxa in an analysis, resulting in a false clustering based on convergences (Swofford et al 1996). However, the results of the 2 -test and the relative-rate tests reject such an assumption. The Asterothyriaceae/Gomphillaceae clade and the Thelotremataceae do not differ significantly in their nucleotide composition and substitution rate from the other Lecanoromycetes. Our studies thus confirm placement of Gomphillaceae/Asterothyriaceae as a further clade within Ostropales sensu lato (Kauff and Lutzoni 2002), as previously suggested by Lücking (1997) and Henssen and Lücking (2002). This order originally was restricted to the chiefly nonlichenized Stictidaceae and allies, while lichenized Thelotremataceae and Graphidaceae were kept in a separate order Graphidales (Sherwood 1977). Recent molecular studies have not demonstrated only that Graphidales but also Gyalectales, with the two families Gyalectaceae and Coenogoniaceae, form part of Ostropales (Kalb et al pers comm 2003, Kauff and Lutzoni 2002, Lumbsch et al 2004, Winka et al 1998). Thus, Ostropales, in its present circumscription, consists of four lineages: (i) Stictidaceae and allies (Ostropales s.str.), (ii) Gyalectaceae/Coenogoniaceae (former Gyalectales), (iii) Thelotremataceae/Graphidaceae (former Graphidales), and (iv) Gomphillaceae/Asterothyriaceae (former Gomphillales). In all available analyses, Stictidaceae and allies, which include a few lichenized forms (Absconditella, Conotrema) but are otherwise nonlichenized, appear to be basal within the order and either monophyletic (Lumbsch et al 2004) or paraphyletic. Gyalectaceae/ Coenogoniaceae are related most closely to Thelotremataceae/Gomphillaceae and appear either paraphyletic (Lumbsch et al 2004) or monophyletic (Kauff and Lutzoni 2002), depending on whether Bryophagus is included here or in the Stictidaceae lineage. The Thelotremataceae/Graphidaceae clade always appears monophyletic in different studies (Kalb et al pers comm 2003, Kauff and Lutzoni 2002, Lumbsch et al 2004) and so does the previously unexplored Gomphillaceae/Asterothyriaceae clade in our study. Experience with Lecanoromycetes has shown that initially paraphyletic lineages eventually turn out to be monophyletic in more detailed studies with higher taxa and character resolution (Lumbsch et al 2004), and this cannot be excluded for Ostropales sensu lato, in which case the previously distinguished orders Gyalectales, Graphidales and Gomphillales could be reinstated or more appropriately be used at the subordinal level. This would correspond to the situation in Lecanorales sensu lato, where Peltigerineae and Teloschistineae currently are listed as suborders (Eriksson et al 2003) but could also be treated as orders parallel to Lecanorales sensu stricto. ACKNOWLEDGMENTS We wish to thank Jutta Buschbom (Chicago) for advice with sequencing of lichens. The sampling of specimens from which new sequences were generated was supported by the National Science Foundation (Grant DEB to Robert Lücking), the Mexican CONACYT (Grant V to María Herrera-Campos and Robert Lücking) and the Deutsche Forschungsgemeinschaft (grants LU 597/1-1-LU 597/ 4-1 to Robert Lücking). DNA extraction and sequencing at the Field Museum s Pritzker Laboratory for Molecular Systematics and Evolution were supported by start-up funds of the Field Museum to Robert Lücking. LITERATURE CITED Aptroot A, Kärnefeldt I, Tibell L Discussion 6: Caliciales, Graphidales, and Teloschistales. In: Hawksworth DL, ed. Ascomycete systematics. Problems and perspectives in the nineties (NATO ASI Series, Series A: Life Sciences, Vol. 29). Plenum Press, New York and London. p , Lücking R Phenotype-based phylogenetic analysis does not support generic separation of Gyalidea and Solorinella (Ostropales: Asterothyriaceae). Biblioth Lichenol 86: Buckley TR, Arensburger P, Simon C, Chambers GK

11 LÜCKING ET AL: PHYLOGENY OF GOMPHILLACEAE 293 Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera. Syst Biol 51:4 18. Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL, Waddell PJ Partitioning and combining data in phylogenetic analysis. Syst Biol 42: Dennetière B, Péroni J Approche phylogénétique des Gomphillaceae. Cryptogamie Bryol Lichénol 19: Döring H, Clerc P, Grube M, Wedin M Mycobiontspecific PCR primers for the amplification of nuclear ITS and LSU rdna from lichenized ascomycetes. Lichenologist 32: Eriksson OE, ed Outline of Ascomycota. Myconet 7: 1 88., Baral HO, Currah RS, Hansen K, Kurtzman CP, Rambold G, Laessøe T Outline of Ascomycota Myconet 9:1 89., Hawksworth DL Outline of the ascomycetes Systema Ascomycetum 6: Felsenstein J Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: Hafellner J Studien in Richtung einer natürlicheren Gliederung der Sammelfamilien Lecanoraceae und Lecideaceae. Beih Nova Hedwigia 79: Principles of classification and main taxonomic groups. In: Galun M, ed. CRC handbook of lichenology. Vol. III. Boca Raton, Florida: CRC Press. p Henssen A, Lücking R Morphology, anatomy, and ontogeny in the Asterothyriaceae (Ascomycetes: Ostropales), a greatly misunderstood group of lichenized fungi. Ann Bot Fenn 39: Huelsenbeck JP, Crandall KA Phylogeny estimation and hypothesis testing using maximum likelihood. Ann Rev Ecol Syst 28: , Ronquist F MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: , Rannala B, Masly JP Accommodating phylogenetic uncertainty in evolutionary studies. Science 288: , Ronquist F, Nielsen R, Bollback JP Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: Hughey R, Krogh A SAM: sequence alignment and modeling software system. Technical Report UCSC- CRL-96-22, University of California, Santa Cruz, California. Jahns HM Untersuchungen zur Entwicklungsgeschichte der Cladoniaceen mit besonderer Berücksischtigung des Podetien-Problems. Nova Hedwigia 20: Kauff F, Lutzoni F Phylogeny of Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits. Mol Phyl Evol 25: Larget B, Simon DL Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16: Lewis PO Phylogenetic systematics turns over a new leaf. TREE 16: Liu YJ, Whelen S, Hall BD Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Mol Biol Evol 16: Lücking R Additions and corrections to the knowledge of the foliicolous lichen flora of Costa Rica. The family Gomphillaceae. Biblioth Lichenol 65: Addiciones y correcciones al conocimiento de la líquenoflora foliícola de Costa Rica. La familia Asterothyriaceae y el género Chroodiscus (Thelotremataceae), con un análisis filogenético. Cryptogamie Mycol 20: Lichens on leaves in tropical rain forests: life in a permanently ephemerous environment. Diss. Bot. 346:41 77., Kalb K Foliikole Flechten aus Brasilien (vornehmlich Amazonien), inklusive einer Checkliste und Bemerkungen zu Coenogonium und Dimerella (Gyalectaceae). Bot. Jahrb. Syst. 122:1 61., New species and further additions to the foliicolous lichen flora of Kenya (East Africa), including the first lichenicolous Aulaxina (Ostropales: Gomphillaceae). Bot J Linn Soc 139: , Sérusiaux E Gyalideopsis cochlearifera, a new pantropical, commensalistic species on foliicolous Gomphillaceae. Lichenologist 30: Lumbsch HT, Schmitt I Molecular data shake the Pertusariaceae tree into order. Lichenology 1:37 43., Wirtz N, Lindemuth R, Schmitt I Higher level phylogenetic relationships of euascomycetes (Pezizomycotina) inferred from a combined analysis of nuclear and mitochondrial sequence data. Mycol Progress 1:57 70., Schmitt I, Palice Z, Wiklund E, Ekman S, Wedin M Supraordinal phylogenetic relationships of lichen-forming discomycetes (Lecanoromycetes) based on a combined Bayesian analysis of nuclear and mitochondrial sequences. Mol Phyl Evol (In press). Miadlikowska J, Lutzoni F Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical and large subunit nuclear ribosomal RNA data. Int J Plant Sci 161: , McCune B, Lutzoni F Pseudocyphellaria perpetua, a new lichen from western North America. Bryologist 105:1 10. Nylander W De lichenibus nonnullis europaeis. Flora 43: Page RDM Treeview: an application to display phylogenetic trees on personal computers. Comp Appl Biosci 12: Posada D, Crandall KA Modeltest: testing the model of DNA substitution. Bioinformatics 14: Rannala B, Yang Z Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J Mol Evol 43: Räsänen V Das System der Flechten. Acta Bot Fenn 9(IV):1 82. Rehner SA, Samuels GJ Taxonomy and phylogeny of

12 294 MYCOLOGIA Gliocladium analysed from nuclear large subunit ribosomal DNA sequences. Mycol. Res. 98: Robinson-Rechavi M, Huchon D RRTree: relativerate tests between groups of sequences on a phylogenetic tree. Bioinformatics 16: Rodriguez F, Oliver JF, Martín A, Medina JR The general stochastic model of nucleotide substitution. J Theor Biol 142: Santesson R Foliicolous lichens I. A revision of the taxonomy of the obligately foliicolous, lichenized fungi. Symb Bot Ups 12(1): Sato MM Enumeration of lichens collected in Tohoku-district, Japan. 1. Anziaceae and Baeomycetaceae. Bull Yamagata Univ Nat Sci 3: Sherwood MA The Ostropalean fungi. Mycotaxon 5: Strimmer K, von Haeseler A Quartet-puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13: Swofford DL PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates., Olsen GJ, Waddell PJ, Hillis DM Phylogenetic inference. In: Hillis DM, Moritz C, Marble BK, eds. Molecular systematics. 2nd ed. Sunderland, MA: Sinauer Associates. p Thompson JD, Higgins DG, Gibson TJ Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: Vezda A Foliicole Flechten aus der Republik Guinea (W.-Afrika). I. Acta Mus Sil Ser A 22: Flechtensystematische Studien. XI. Beiträge zur Kenntnis der Familie Asterothyriaceae (Discolichenes). Folia Geobot Phytotax Praha 14: Flechtensystematische Studien. XII. Die Familie Gomphillaceae und ihre Gliederung. Folia Geobot Phytotax Praha 22: Solorinellaceae, eine neue Familie der lichenisierten Ascomyceten. Phyton Horn Austria 30: Vilgalys R, Hester M Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172: Winka K, Ahlberg C, Eriksson OE Are there lichenized Ostropales? Lichenologist 30: Zhou S, Stanosz GR Primers for amplification of mt SSU rdna, and a phylogenetic study of Botryosphaeria and associated anamorphic fungi. Mycol Res 105: Zoller S, Scheidegger C, Sperisen C PCR primers for the amplification of mitochondrial small subunit ribosomal DNA of lichen-forming ascomycetes. Lichenologist 31:

Data Partitions and Complex Models in Bayesian Analysis: The Phylogeny of Gymnophthalmid Lizards

Data Partitions and Complex Models in Bayesian Analysis: The Phylogeny of Gymnophthalmid Lizards Syst. Biol. 53(3):448 469, 2004 Copyright c Society of Systematic Biologists ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/10635150490445797 Data Partitions and Complex Models in Bayesian Analysis:

More information

Bayesian Phylogeny and Measures of Branch Support

Bayesian Phylogeny and Measures of Branch Support Bayesian Phylogeny and Measures of Branch Support Bayesian Statistics Imagine we have a bag containing 100 dice of which we know that 90 are fair and 10 are biased. The

More information

A data management framework for the Fungal Tree of Life

A data management framework for the Fungal Tree of Life Web Accessible Sequence Analysis for Biological Inference A data management framework for the Fungal Tree of Life Kauff F, Cox CJ, Lutzoni F. 2007. WASABI: An automated sequence processing system for multi-gene

More information

Missing data and the accuracy of Bayesian phylogenetics

Missing data and the accuracy of Bayesian phylogenetics Journal of Systematics and Evolution 46 (3): 307 314 (2008) (formerly Acta Phytotaxonomica Sinica) doi: 10.3724/SP.J.1002.2008.08040 http://www.plantsystematics.com Missing data and the accuracy of Bayesian

More information

Molecular phylogenetic study at the generic boundary between the lichen-forming fungi Caloplaca and Xanthoria (Ascomycota, Teloschistaceae)

Molecular phylogenetic study at the generic boundary between the lichen-forming fungi Caloplaca and Xanthoria (Ascomycota, Teloschistaceae) Mycol. Res. 107 (11): 1266 1276 (November 2003). f The British Mycological Society 1266 DOI: 10.1017/S0953756203008529 Printed in the United Kingdom. Molecular phylogenetic study at the generic boundary

More information

PHYML Online: A Web Server for Fast Maximum Likelihood-Based Phylogenetic Inference

PHYML Online: A Web Server for Fast Maximum Likelihood-Based Phylogenetic Inference PHYML Online: A Web Server for Fast Maximum Likelihood-Based Phylogenetic Inference Stephane Guindon, F. Le Thiec, Patrice Duroux, Olivier Gascuel To cite this version: Stephane Guindon, F. Le Thiec, Patrice

More information

A short guide to phylogeny reconstruction

A short guide to phylogeny reconstruction A short guide to phylogeny reconstruction E. Michu Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic ABSTRACT This review is a short introduction to phylogenetic

More information

A comparison of methods for estimating the transition:transversion ratio from DNA sequences

A comparison of methods for estimating the transition:transversion ratio from DNA sequences Molecular Phylogenetics and Evolution 32 (2004) 495 503 MOLECULAR PHYLOGENETICS AND EVOLUTION www.elsevier.com/locate/ympev A comparison of methods for estimating the transition:transversion ratio from

More information

Evaluating the Performance of a Successive-Approximations Approach to Parameter Optimization in Maximum-Likelihood Phylogeny Estimation

Evaluating the Performance of a Successive-Approximations Approach to Parameter Optimization in Maximum-Likelihood Phylogeny Estimation Evaluating the Performance of a Successive-Approximations Approach to Parameter Optimization in Maximum-Likelihood Phylogeny Estimation Jack Sullivan,* Zaid Abdo, à Paul Joyce, à and David L. Swofford

More information

Multiple Losses of Flight and Recent Speciation in Steamer Ducks Tara L. Fulton, Brandon Letts, and Beth Shapiro

Multiple Losses of Flight and Recent Speciation in Steamer Ducks Tara L. Fulton, Brandon Letts, and Beth Shapiro Supplementary Material for: Multiple Losses of Flight and Recent Speciation in Steamer Ducks Tara L. Fulton, Brandon Letts, and Beth Shapiro 1. Supplementary Tables Supplementary Table S1. Sample information.

More information

Phylogenetic systematics turns over a new leaf

Phylogenetic systematics turns over a new leaf 30 Review Phylogenetic systematics turns over a new leaf Paul O. Lewis Long restricted to the domain of molecular systematics and studies of molecular evolution, likelihood methods are now being used in

More information

Molecular Clocks and Tree Dating with r8s and BEAST

Molecular Clocks and Tree Dating with r8s and BEAST Integrative Biology 200B University of California, Berkeley Principals of Phylogenetics: Ecology and Evolution Spring 2011 Updated by Nick Matzke Molecular Clocks and Tree Dating with r8s and BEAST Today

More information

Rules and Format for Taxonomic Nucleotide Sequence Annotation for Fungi: a proposal

Rules and Format for Taxonomic Nucleotide Sequence Annotation for Fungi: a proposal Rules and Format for Taxonomic Nucleotide Sequence Annotation for Fungi: a proposal The need for third-party sequence annotation Taxonomic names attached to nucleotide sequences occasionally need to be

More information

(Anisoptera: Libellulidae)

(Anisoptera: Libellulidae) Odonatohgica34(2): 173178 June I, 2005 The morphological forms of Palpopleuralucia (Drury) are separatespecies as evidenced by DNA sequencing (Anisoptera: Libellulidae) A. Mitchell¹ and M.J. Samways ²

More information

Protocols. Internal transcribed spacer region (ITS) region. Niklaus J. Grünwald, Frank N. Martin, and Meg M. Larsen (2013)

Protocols. Internal transcribed spacer region (ITS) region. Niklaus J. Grünwald, Frank N. Martin, and Meg M. Larsen (2013) Protocols Internal transcribed spacer region (ITS) region Niklaus J. Grünwald, Frank N. Martin, and Meg M. Larsen (2013) The nuclear ribosomal RNA (rrna) genes (small subunit, large subunit and 5.8S) are

More information

Comparing Bootstrap and Posterior Probability Values in the Four-Taxon Case

Comparing Bootstrap and Posterior Probability Values in the Four-Taxon Case Syst. Biol. 52(4):477 487, 2003 Copyright c Society of Systematic Biologists ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/10635150390218213 Comparing Bootstrap and Posterior Probability Values

More information

Supporting Online Material for

Supporting Online Material for www.sciencemag.org/cgi/content/full/312/5781/1762/dc1 Supporting Online Material for Silk Genes Support the Single Origin of Orb Webs Jessica E. Garb,* Teresa DiMauro, Victoria Vo, Cheryl Y. Hayashi *To

More information

The enigmatic monotypic crab plover Dromas ardeola is closely related to pratincoles and coursers (Aves, Charadriiformes, Glareolidae)

The enigmatic monotypic crab plover Dromas ardeola is closely related to pratincoles and coursers (Aves, Charadriiformes, Glareolidae) Short Communication Genetics and Molecular Biology, 33, 3, 583-586 (2010) Copyright 2010, Sociedade Brasileira de Genética. Printed in Brazil www.sbg.org.br The enigmatic monotypic crab plover Dromas ardeola

More information

A Step-by-Step Tutorial: Divergence Time Estimation with Approximate Likelihood Calculation Using MCMCTREE in PAML

A Step-by-Step Tutorial: Divergence Time Estimation with Approximate Likelihood Calculation Using MCMCTREE in PAML 9 June 2011 A Step-by-Step Tutorial: Divergence Time Estimation with Approximate Likelihood Calculation Using MCMCTREE in PAML by Jun Inoue, Mario dos Reis, and Ziheng Yang In this tutorial we will analyze

More information

Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae

Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae Mycologia, 98(6), 2006, pp. 1053 1064. # 2006 by The Mycological Society of America, Lawrence, KS 66044-8897 Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae David M. Geiser 1 Department of Plant

More information

Name Class Date. binomial nomenclature. MAIN IDEA: Linnaeus developed the scientific naming system still used today.

Name Class Date. binomial nomenclature. MAIN IDEA: Linnaeus developed the scientific naming system still used today. Section 1: The Linnaean System of Classification 17.1 Reading Guide KEY CONCEPT Organisms can be classified based on physical similarities. VOCABULARY taxonomy taxon binomial nomenclature genus MAIN IDEA:

More information

Name: Class: Date: Multiple Choice Identify the choice that best completes the statement or answers the question.

Name: Class: Date: Multiple Choice Identify the choice that best completes the statement or answers the question. Name: Class: Date: Chapter 17 Practice Multiple Choice Identify the choice that best completes the statement or answers the question. 1. The correct order for the levels of Linnaeus's classification system,

More information

Lab 2/Phylogenetics/September 16, 2002 1 PHYLOGENETICS

Lab 2/Phylogenetics/September 16, 2002 1 PHYLOGENETICS Lab 2/Phylogenetics/September 16, 2002 1 Read: Tudge Chapter 2 PHYLOGENETICS Objective of the Lab: To understand how DNA and protein sequence information can be used to make comparisons and assess evolutionary

More information

The Central Dogma of Molecular Biology

The Central Dogma of Molecular Biology Vierstraete Andy (version 1.01) 1/02/2000 -Page 1 - The Central Dogma of Molecular Biology Figure 1 : The Central Dogma of molecular biology. DNA contains the complete genetic information that defines

More information

DnaSP, DNA polymorphism analyses by the coalescent and other methods.

DnaSP, DNA polymorphism analyses by the coalescent and other methods. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Author affiliation: Julio Rozas 1, *, Juan C. Sánchez-DelBarrio 2,3, Xavier Messeguer 2 and Ricardo Rozas 1 1 Departament de Genètica,

More information

ARTICLE IN PRESS. Molecular Phylogenetics and Evolution xxx (2005) xxx xxx

ARTICLE IN PRESS. Molecular Phylogenetics and Evolution xxx (2005) xxx xxx Molecular Phylogenetics and Evolution xxx (2005) xxx xxx MOLECULAR PHYLOGENETICS AND EVOLUTION www.elsevier.com/locate/ympev Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene

More information

A branch-and-bound algorithm for the inference of ancestral. amino-acid sequences when the replacement rate varies among

A branch-and-bound algorithm for the inference of ancestral. amino-acid sequences when the replacement rate varies among A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites Tal Pupko 1,*, Itsik Pe er 2, Masami Hasegawa 1, Dan Graur 3, and Nir Friedman

More information

Microbiology Laboratory: MOLECULAR IDENTIFICATION OF UNKNOWN BACTERIA

Microbiology Laboratory: MOLECULAR IDENTIFICATION OF UNKNOWN BACTERIA Microbiology Laboratory: MOLECULAR IDENTIFICATION OF UNKNOWN BACTERIA Classical Microbiology courses are typically structured to introduce the identification of bacterial species using a series of biochemical

More information

Phylogenetic Trees Made Easy

Phylogenetic Trees Made Easy Phylogenetic Trees Made Easy A How-To Manual Fourth Edition Barry G. Hall University of Rochester, Emeritus and Bellingham Research Institute Sinauer Associates, Inc. Publishers Sunderland, Massachusetts

More information

A combinatorial test for significant codivergence between cool-season grasses and their symbiotic fungal endophytes

A combinatorial test for significant codivergence between cool-season grasses and their symbiotic fungal endophytes A combinatorial test for significant codivergence between cool-season grasses and their symbiotic fungal endophytes Ruriko Yoshida Dept. of Statistics University of Kentucky Joint work with C.L. Schardl,

More information

BASIC STATISTICAL METHODS FOR GENOMIC DATA ANALYSIS

BASIC STATISTICAL METHODS FOR GENOMIC DATA ANALYSIS BASIC STATISTICAL METHODS FOR GENOMIC DATA ANALYSIS SEEMA JAGGI Indian Agricultural Statistics Research Institute Library Avenue, New Delhi-110 012 seema@iasri.res.in Genomics A genome is an organism s

More information

Bio-Informatics Lectures. A Short Introduction

Bio-Informatics Lectures. A Short Introduction Bio-Informatics Lectures A Short Introduction The History of Bioinformatics Sanger Sequencing PCR in presence of fluorescent, chain-terminating dideoxynucleotides Massively Parallel Sequencing Massively

More information

Statistics Graduate Courses

Statistics Graduate Courses Statistics Graduate Courses STAT 7002--Topics in Statistics-Biological/Physical/Mathematics (cr.arr.).organized study of selected topics. Subjects and earnable credit may vary from semester to semester.

More information

PROC. CAIRO INTERNATIONAL BIOMEDICAL ENGINEERING CONFERENCE 2006 1. E-mail: msm_eng@k-space.org

PROC. CAIRO INTERNATIONAL BIOMEDICAL ENGINEERING CONFERENCE 2006 1. E-mail: msm_eng@k-space.org BIOINFTool: Bioinformatics and sequence data analysis in molecular biology using Matlab Mai S. Mabrouk 1, Marwa Hamdy 2, Marwa Mamdouh 2, Marwa Aboelfotoh 2,Yasser M. Kadah 2 1 Biomedical Engineering Department,

More information

Current Motif Discovery Tools and their Limitations

Current Motif Discovery Tools and their Limitations Current Motif Discovery Tools and their Limitations Philipp Bucher SIB / CIG Workshop 3 October 2006 Trendy Concepts and Hypotheses Transcription regulatory elements act in a context-dependent manner.

More information

Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective

Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective Alexandros Stamatakis Institute of Computer Science, Foundation for Research and Technology-Hellas P.O. Box 1385, Heraklion,

More information

4 Techniques for Analyzing Large Data Sets

4 Techniques for Analyzing Large Data Sets 4 Techniques for Analyzing Large Data Sets Pablo A. Goloboff Contents 1 Introduction 70 2 Traditional Techniques 71 3 Composite Optima: Why Do Traditional Techniques Fail? 72 4 Techniques for Analyzing

More information

Lecture/Recitation Topic SMA 5303 L1 Sampling and statistical distributions

Lecture/Recitation Topic SMA 5303 L1 Sampling and statistical distributions SMA 50: Statistical Learning and Data Mining in Bioinformatics (also listed as 5.077: Statistical Learning and Data Mining ()) Spring Term (Feb May 200) Faculty: Professor Roy Welsch Wed 0 Feb 7:00-8:0

More information

Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals

Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals Xiaohui Xie 1, Jun Lu 1, E. J. Kulbokas 1, Todd R. Golub 1, Vamsi Mootha 1, Kerstin Lindblad-Toh

More information

HCRI Project Final Report Format

HCRI Project Final Report Format HCRI Project Final Report Format I. Report Title: Characterizing green algal biodiversity of Hawaiian reef and estuarine communities: expansion of the sequence diversity assessment framework to distinguish

More information

Protein Sequence Analysis - Overview -

Protein Sequence Analysis - Overview - Protein Sequence Analysis - Overview - UDEL Workshop Raja Mazumder Research Associate Professor, Department of Biochemistry and Molecular Biology Georgetown University Medical Center Topics Why do protein

More information

Nucleic Acid Techniques in Bacterial Systematics

Nucleic Acid Techniques in Bacterial Systematics Nucleic Acid Techniques in Bacterial Systematics Edited by Erko Stackebrandt Department of Microbiology University of Queensland St Lucia, Australia and Michael Goodfellow Department of Microbiology University

More information

Point of View. Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data JOHN J. WIENS AND MATTHEW C.

Point of View. Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data JOHN J. WIENS AND MATTHEW C. Systematic Biology Advance Access published March 28, 2011 Point of View c The Author(s) 2011. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.

More information

ABSTRACT. Promega Corporation, Updated September 2008. http://www.promega.com/pubhub. 1 Campbell-Staton, S.

ABSTRACT. Promega Corporation, Updated September 2008. http://www.promega.com/pubhub. 1 Campbell-Staton, S. A Modified Wizard SV Genomic DNA Purification System Protocol to Purify Genomic DNA... A Modified Wizard SV Genomic DNA Purification System Protocol to Purify Genomic DNA from Shed Reptile Skin ABSTRACT

More information

An experimental study comparing linguistic phylogenetic reconstruction methods *

An experimental study comparing linguistic phylogenetic reconstruction methods * An experimental study comparing linguistic phylogenetic reconstruction methods * François Barbançon, a Steven N. Evans, b Luay Nakhleh c, Don Ringe, d and Tandy Warnow, e, a Palantir Technologies, 100

More information

RETRIEVING SEQUENCE INFORMATION. Nucleotide sequence databases. Database search. Sequence alignment and comparison

RETRIEVING SEQUENCE INFORMATION. Nucleotide sequence databases. Database search. Sequence alignment and comparison RETRIEVING SEQUENCE INFORMATION Nucleotide sequence databases Database search Sequence alignment and comparison Biological sequence databases Originally just a storage place for sequences. Currently the

More information

Algorithms in Computational Biology (236522) spring 2007 Lecture #1

Algorithms in Computational Biology (236522) spring 2007 Lecture #1 Algorithms in Computational Biology (236522) spring 2007 Lecture #1 Lecturer: Shlomo Moran, Taub 639, tel 4363 Office hours: Tuesday 11:00-12:00/by appointment TA: Ilan Gronau, Taub 700, tel 4894 Office

More information

Maximum-Likelihood Estimation of Phylogeny from DNA Sequences When Substitution Rates Differ over Sites1

Maximum-Likelihood Estimation of Phylogeny from DNA Sequences When Substitution Rates Differ over Sites1 Maximum-Likelihood Estimation of Phylogeny from DNA Sequences When Substitution Rates Differ over Sites1 Ziheng Yang Department of Animal Science, Beijing Agricultural University Felsenstein s maximum-likelihood

More information

Real-Time PCR Vs. Traditional PCR

Real-Time PCR Vs. Traditional PCR Real-Time PCR Vs. Traditional PCR Description This tutorial will discuss the evolution of traditional PCR methods towards the use of Real-Time chemistry and instrumentation for accurate quantitation. Objectives

More information

Supplementary Methods

Supplementary Methods Supplementary Methods DNA Sequencing Methods Most of the tissues used in this study are directly linked to morphological voucher specimens in publicly accessible natural history collections. However, 17

More information

The Techniques of Molecular Biology: Forensic DNA Fingerprinting

The Techniques of Molecular Biology: Forensic DNA Fingerprinting Revised Fall 2011 The Techniques of Molecular Biology: Forensic DNA Fingerprinting The techniques of molecular biology are used to manipulate the structure and function of molecules such as DNA and proteins

More information

Visualization of Phylogenetic Trees and Metadata

Visualization of Phylogenetic Trees and Metadata Visualization of Phylogenetic Trees and Metadata November 27, 2015 Sample to Insight CLC bio, a QIAGEN Company Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.clcbio.com support-clcbio@qiagen.com

More information

Potential study items for students at the Botanic Garden Meise

Potential study items for students at the Botanic Garden Meise Potential study items for students at the Botanic Garden Meise 1. Visualizing plant biodiversity. Vast amounts of plant biodiversity data are available in global repositories such as the Global Biodiversity

More information

Speciation in fig pollinators and parasites

Speciation in fig pollinators and parasites Molecular Ecology (2002) 11, 1573 1578 Blackwell Science, Ltd SHORT COMMUNICATION Speciation in fig pollinators and parasites GEORGE D. WEIBLEN* and GUY L. BUSH *Department of Plant Biology, University

More information

2.3 Identify rrna sequences in DNA

2.3 Identify rrna sequences in DNA 2.3 Identify rrna sequences in DNA For identifying rrna sequences in DNA we will use rnammer, a program that implements an algorithm designed to find rrna sequences in DNA [5]. The program was made by

More information

Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources

Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources 1 of 8 11/7/2004 11:00 AM National Center for Biotechnology Information About NCBI NCBI at a Glance A Science Primer Human Genome Resources Model Organisms Guide Outreach and Education Databases and Tools

More information

Tutorial 5: Hypothesis Testing

Tutorial 5: Hypothesis Testing Tutorial 5: Hypothesis Testing Rob Nicholls nicholls@mrc-lmb.cam.ac.uk MRC LMB Statistics Course 2014 Contents 1 Introduction................................ 1 2 Testing distributional assumptions....................

More information

DNA Barcoding in Plants: Biodiversity Identification and Discovery

DNA Barcoding in Plants: Biodiversity Identification and Discovery DNA Barcoding in Plants: Biodiversity Identification and Discovery University of Sao Paulo December 2009 W. John Kress Department of Botany National Museum of Natural History Smithsonian Institution New

More information

Rapid Acquisition of Unknown DNA Sequence Adjacent to a Known Segment by Multiplex Restriction Site PCR

Rapid Acquisition of Unknown DNA Sequence Adjacent to a Known Segment by Multiplex Restriction Site PCR Rapid Acquisition of Unknown DNA Sequence Adjacent to a Known Segment by Multiplex Restriction Site PCR BioTechniques 25:415-419 (September 1998) ABSTRACT The determination of unknown DNA sequences around

More information

Genome Explorer For Comparative Genome Analysis

Genome Explorer For Comparative Genome Analysis Genome Explorer For Comparative Genome Analysis Jenn Conn 1, Jo L. Dicks 1 and Ian N. Roberts 2 Abstract Genome Explorer brings together the tools required to build and compare phylogenies from both sequence

More information

Supplementary Information - PCR amplification PCR amplification reactions for the partial mitochondrial cytochrome oxidase subunit I (COI), the

Supplementary Information - PCR amplification PCR amplification reactions for the partial mitochondrial cytochrome oxidase subunit I (COI), the Supplementary Information - PCR amplification PCR amplification reactions for the partial mitochondrial cytochrome oxidase subunit I (COI), the ribosomal 16S rdna gene and a fragment of the nuclear single

More information

DNA and Forensic Science

DNA and Forensic Science DNA and Forensic Science Micah A. Luftig * Stephen Richey ** I. INTRODUCTION This paper represents a discussion of the fundamental principles of DNA technology as it applies to forensic testing. A brief

More information

Next Generation Sequencing Technologies in Microbial Ecology. Frank Oliver Glöckner

Next Generation Sequencing Technologies in Microbial Ecology. Frank Oliver Glöckner Next Generation Sequencing Technologies in Microbial Ecology Frank Oliver Glöckner 1 Max Planck Institute for Marine Microbiology Investigation of the role, diversity and features of microorganisms Interactions

More information

Data for phylogenetic analysis

Data for phylogenetic analysis Data for phylogenetic analysis The data that are used to estimate the phylogeny of a set of tips are the characteristics of those tips. Therefore the success of phylogenetic inference depends in large

More information

Sequence Analysis 15: lecture 5. Substitution matrices Multiple sequence alignment

Sequence Analysis 15: lecture 5. Substitution matrices Multiple sequence alignment Sequence Analysis 15: lecture 5 Substitution matrices Multiple sequence alignment A teacher's dilemma To understand... Multiple sequence alignment Substitution matrices Phylogenetic trees You first need

More information

Mitochondrial DNA Analysis

Mitochondrial DNA Analysis Mitochondrial DNA Analysis Lineage Markers Lineage markers are passed down from generation to generation without changing Except for rare mutation events They can help determine the lineage (family tree)

More information

PHYLOGENETIC RELATIONSHIPS WITHIN IGUANIDAE INFERRED USING MOLECULAR AND MORPHOLOGICAL DATA AND A PHYLOGENETIC TAXONOMY OF IGUANIAN LIZARDS

PHYLOGENETIC RELATIONSHIPS WITHIN IGUANIDAE INFERRED USING MOLECULAR AND MORPHOLOGICAL DATA AND A PHYLOGENETIC TAXONOMY OF IGUANIAN LIZARDS Herpetologica, 59(3), 2003, 399 419 Ó 2003 by The Herpetologists League, Inc. PHYLOGENETIC RELATIONSHIPS WITHIN IGUANIDAE INFERRED USING MOLECULAR AND MORPHOLOGICAL DATA AND A PHYLOGENETIC TAXONOMY OF

More information

Data Integration. Lectures 16 & 17. ECS289A, WQ03, Filkov

Data Integration. Lectures 16 & 17. ECS289A, WQ03, Filkov Data Integration Lectures 16 & 17 Lectures Outline Goals for Data Integration Homogeneous data integration time series data (Filkov et al. 2002) Heterogeneous data integration microarray + sequence microarray

More information

Evidence from Mitochondrial DNA That Head Lice and Body Lice of Humans (Phthiraptera: Pediculidae) are Conspecific

Evidence from Mitochondrial DNA That Head Lice and Body Lice of Humans (Phthiraptera: Pediculidae) are Conspecific SHORT COMMUNICATION Evidence from Mitochondrial DNA That Head Lice and Body Lice of Humans (Phthiraptera: Pediculidae) are Conspecific N. P. LEO, 1,2 N.J.H. CAMPBELL, 2 X. YANG, 3 K. MUMCUOGLU, 4 AND S.

More information

Hierarchical Bayesian Modeling of the HIV Response to Therapy

Hierarchical Bayesian Modeling of the HIV Response to Therapy Hierarchical Bayesian Modeling of the HIV Response to Therapy Shane T. Jensen Department of Statistics, The Wharton School, University of Pennsylvania March 23, 2010 Joint Work with Alex Braunstein and

More information

Service courses for graduate students in degree programs other than the MS or PhD programs in Biostatistics.

Service courses for graduate students in degree programs other than the MS or PhD programs in Biostatistics. Course Catalog In order to be assured that all prerequisites are met, students must acquire a permission number from the education coordinator prior to enrolling in any Biostatistics course. Courses are

More information

A Tutorial in Genetic Sequence Classification Tools and Techniques

A Tutorial in Genetic Sequence Classification Tools and Techniques A Tutorial in Genetic Sequence Classification Tools and Techniques Jake Drew Data Mining CSE 8331 Southern Methodist University jakemdrew@gmail.com www.jakemdrew.com Sequence Characters IUPAC nucleotide

More information

Bayesian coalescent inference of population size history

Bayesian coalescent inference of population size history Bayesian coalescent inference of population size history Alexei Drummond University of Auckland Workshop on Population and Speciation Genomics, 2016 1st February 2016 1 / 39 BEAST tutorials Population

More information

The Phylogenetic Relationships of the Shags and Cormorants: Can Sequence Data Resolve a Disagreement between Behavior and Morphology?

The Phylogenetic Relationships of the Shags and Cormorants: Can Sequence Data Resolve a Disagreement between Behavior and Morphology? Molecular Phylogenetics and Evolution Vol. 17, No. 3, December, pp. 345 359, 2000 doi:10.1006/mpev.2000.0840, available online at http://www.idealibrary.com on The Phylogenetic Relationships of the Shags

More information

GenBank, Entrez, & FASTA

GenBank, Entrez, & FASTA GenBank, Entrez, & FASTA Nucleotide Sequence Databases First generation GenBank is a representative example started as sort of a museum to preserve knowledge of a sequence from first discovery great repositories,

More information

A COMPARISON OF PHYLOGENETIC RECONSTRUCTION METHODS ON AN INDO-EUROPEAN DATASET

A COMPARISON OF PHYLOGENETIC RECONSTRUCTION METHODS ON AN INDO-EUROPEAN DATASET Transactions of the Philological Society Volume 103:2 (2005) 171 192 A COMPARISON OF PHYLOGENETIC RECONSTRUCTION METHODS ON AN INDO-EUROPEAN DATASET By LUAY NAKHLEH a,tandy WARNOW b,don RINGE c AND STEVEN

More information

Genetic Analysis. Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis

Genetic Analysis. Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis Genetic Analysis Phenotype analysis: biological-biochemical analysis Behaviour under specific environmental conditions Behaviour of specific genetic configurations Behaviour of progeny in crosses - Genotype

More information

Notes on the genus punctelia in Denmark Christensen, Steen; Søchting, Ulrik

Notes on the genus <em>punctelia</em> in Denmark Christensen, Steen; Søchting, Ulrik university of copenhagen Notes on the genus punctelia in Denmark Christensen, Steen; Søchting, Ulrik Published in: Graphis Scripta Publication date: 2007 Document Version Publisher final version

More information

Learning outcomes. Knowledge and understanding. Competence and skills

Learning outcomes. Knowledge and understanding. Competence and skills Syllabus Master s Programme in Statistics and Data Mining 120 ECTS Credits Aim The rapid growth of databases provides scientists and business people with vast new resources. This programme meets the challenges

More information

Gene Expression Assays

Gene Expression Assays APPLICATION NOTE TaqMan Gene Expression Assays A mpl i fic ationef ficienc yof TaqMan Gene Expression Assays Assays tested extensively for qpcr efficiency Key factors that affect efficiency Efficiency

More information

Borges, J. L. 1998. On exactitude in science. P. 325, In, Jorge Luis Borges, Collected Fictions (Trans. Hurley, H.) Penguin Books.

Borges, J. L. 1998. On exactitude in science. P. 325, In, Jorge Luis Borges, Collected Fictions (Trans. Hurley, H.) Penguin Books. ... In that Empire, the Art of Cartography attained such Perfection that the map of a single Province occupied the entirety of a City, and the map of the Empire, the entirety of a Province. In time, those

More information

Forensic DNA Testing Terminology

Forensic DNA Testing Terminology Forensic DNA Testing Terminology ABI 310 Genetic Analyzer a capillary electrophoresis instrument used by forensic DNA laboratories to separate short tandem repeat (STR) loci on the basis of their size.

More information

An Introduction to Phylogenetics

An Introduction to Phylogenetics An Introduction to Phylogenetics Bret Larget larget@stat.wisc.edu Departments of Botany and of Statistics University of Wisconsin Madison February 4, 2008 1 / 70 Phylogenetics and Darwin A phylogeny is

More information

Molecular methods for identifying food and airborne fungi

Molecular methods for identifying food and airborne fungi Molecular methods for identifying food and airborne fungi An overview Jos Houbraken CBS-KNAW Fungal Biodiversity Centre Utrecht, the Netherlands Overview presentation Introduction Material & Methods: from

More information

Extensive Cryptic Diversity in Indo-Australian Rainbowfishes Revealed by DNA Barcoding

Extensive Cryptic Diversity in Indo-Australian Rainbowfishes Revealed by DNA Barcoding Extensive Cryptic Diversity in Indo-Australian Rainbowfishes Revealed by DNA Barcoding Kadarusman, Hubert N, Hadiaty R.K #, Sudarto, Paradis E., Pouyaud L. Akademi Perikanan Sorong, Papua Barat, Indonesia

More information

Troubleshooting Sequencing Data

Troubleshooting Sequencing Data Troubleshooting Sequencing Data Troubleshooting Sequencing Data No recognizable sequence (see page 7-10) Insufficient Quantitate the DNA. Increase the amount of DNA in the sequencing reactions. See page

More information

Introduction to Phylogenetic Analysis

Introduction to Phylogenetic Analysis Subjects of this lecture Introduction to Phylogenetic nalysis Irit Orr 1 Introducing some of the terminology of phylogenetics. 2 Introducing some of the most commonly used methods for phylogenetic analysis.

More information

COMMUNITY UNIT SCHOOL DISTRICT 200. Course Description

COMMUNITY UNIT SCHOOL DISTRICT 200. Course Description Forensic Science High School Elective Course Description Forensic Science is a one semester high school level course that satisfies a CUSD200 graduation requirement in the area of science. Successful completion

More information

A Primer of Genome Science THIRD

A Primer of Genome Science THIRD A Primer of Genome Science THIRD EDITION GREG GIBSON-SPENCER V. MUSE North Carolina State University Sinauer Associates, Inc. Publishers Sunderland, Massachusetts USA Contents Preface xi 1 Genome Projects:

More information

Phylogeny and phylogenetic classification of the tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannides)

Phylogeny and phylogenetic classification of the tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannides) Cladistics Cladistics 5 (009) 49 467 10.1111/j.1096-0031.009.0054.x Phylogeny and phylogenetic classification of the tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannides) Jose G.

More information

Core Bioinformatics. Degree Type Year Semester. 4313473 Bioinformàtica/Bioinformatics OB 0 1

Core Bioinformatics. Degree Type Year Semester. 4313473 Bioinformàtica/Bioinformatics OB 0 1 Core Bioinformatics 2014/2015 Code: 42397 ECTS Credits: 12 Degree Type Year Semester 4313473 Bioinformàtica/Bioinformatics OB 0 1 Contact Name: Sònia Casillas Viladerrams Email: Sonia.Casillas@uab.cat

More information

Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers

Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers Shu-Miaw Chaw*, Christopher L. Parkinson, Yuchang Cheng*, Thomas M. Vincent,

More information

MYCOTAXON. Volume 112, pp. 371 375 April June 2010. Five new records for the lichen biota of Turkey. Kadir Kınalıoğlu

MYCOTAXON. Volume 112, pp. 371 375 April June 2010. Five new records for the lichen biota of Turkey. Kadir Kınalıoğlu MYCOTAXON Volume 112, pp. 371 375 April June 2010 Five new records for the lichen biota of Turkey Kadir Kınalıoğlu kkinalioglu@hotmail.com Giresun University, Faculty of Science and Arts, Department of

More information

Tutorial for proteome data analysis using the Perseus software platform

Tutorial for proteome data analysis using the Perseus software platform Tutorial for proteome data analysis using the Perseus software platform Laboratory of Mass Spectrometry, LNBio, CNPEM Tutorial version 1.0, January 2014. Note: This tutorial was written based on the information

More information

PHYLOGENY AND EVOLUTION OF NEWCASTLE DISEASE VIRUS GENOTYPES

PHYLOGENY AND EVOLUTION OF NEWCASTLE DISEASE VIRUS GENOTYPES Eötvös Lóránd University Biology Doctorate School Classical and molecular genetics program Project leader: Dr. László Orosz, corresponding member of HAS PHYLOGENY AND EVOLUTION OF NEWCASTLE DISEASE VIRUS

More information

Essentials of Real Time PCR. About Sequence Detection Chemistries

Essentials of Real Time PCR. About Sequence Detection Chemistries Essentials of Real Time PCR About Real-Time PCR Assays Real-time Polymerase Chain Reaction (PCR) is the ability to monitor the progress of the PCR as it occurs (i.e., in real time). Data is therefore collected

More information

Speculative Moves: Multithreading Markov Chain Monte Carlo Programs

Speculative Moves: Multithreading Markov Chain Monte Carlo Programs Speculative Moves: Multithreading Markov Chain Monte Carlo Programs Jonathan M. R. Byrd, Stephen A. Jarvis and Abhir H. Bhalerao Department of Computer Science, University of Warwick, Coventry, CV4 7AL,

More information

Phylogenetic studies of cyanobacterial lichens

Phylogenetic studies of cyanobacterial lichens Phylogenetic studies of cyanobacterial lichens Filip Högnabba Botanical Museum Finnish Museum of Natural History University of Helsinki Finland Plant Biology Department of Biological and Environmental

More information

Molecular and Cell Biology Laboratory (BIOL-UA 223) Instructor: Ignatius Tan Phone: 212-998-8295 Office: 764 Brown Email: ignatius.tan@nyu.

Molecular and Cell Biology Laboratory (BIOL-UA 223) Instructor: Ignatius Tan Phone: 212-998-8295 Office: 764 Brown Email: ignatius.tan@nyu. Molecular and Cell Biology Laboratory (BIOL-UA 223) Instructor: Ignatius Tan Phone: 212-998-8295 Office: 764 Brown Email: ignatius.tan@nyu.edu Course Hours: Section 1: Mon: 12:30-3:15 Section 2: Wed: 12:30-3:15

More information

Activity IT S ALL RELATIVES The Role of DNA Evidence in Forensic Investigations

Activity IT S ALL RELATIVES The Role of DNA Evidence in Forensic Investigations Activity IT S ALL RELATIVES The Role of DNA Evidence in Forensic Investigations SCENARIO You have responded, as a result of a call from the police to the Coroner s Office, to the scene of the death of

More information