Molecular Phylogenetics And Evolution - Smithsonian Institution

1m ago
1 Views
0 Downloads
1,011.59 KB
12 Pages
Last View : 1m ago
Last Download : n/a
Upload by : Sasha Niles
Transcription

Molecular Phylogenetics and Evolution 53 (2009) 122-133Contents lists available at ScienceDirectMolecular Phylogenetics and Evolutionjournal homepage: www.elsevier.com/locate/ympevELSEVIERDNA taxonomy in morphologically plastic taxa: Algorithmic species delimitationin the Boodlea complex (Chlorophyta: Cladophorales)Frederik Leliaerta*, Heroen Verbruggen3, Brian Wysorb, Olivier De Clerck3"Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Biology Department, Ghent University, Krijgslaan 281 58, 9000 Ghent, BelgiumbDepartment of Biology, Marine Biology and Environmental Science, Roger Williams University, 1 Old Ferry Road, Bristol, RI 02809, USAARTICLEINFOArticle history:Received 26 December 2008Revised 28 May 2009Accepted 5 June 2009Available online 11 June 2009Keywords:Cryptic speciesDNA barcodingnrDNA internal transcribed spacerGreen algaeMolecular phylogeneticsMorphological plasticitySiphonocladalesSpecies boundariesUlvophyceaeABSTRACTDNA-based taxonomy provides a convenient and reliable tool for species delimitation, especially inorganisms in which morphological discrimination is difficult or impossible, such as many algal taxa. Agroup with a long history of confusing species circumscriptions is the morphologically plastic Boodleacomplex, comprising the marine green algal genera Boodlea, Cladophoropsis, Phyllodictyon and Struveopsis.In this study, we elucidate species boundaries in the Boodlea complex by analysing nrDNA internal transcribed spacer sequences from 175 specimens collected from a wide geographical range. Algorithmicmethods of sequence-based species delineation were applied, including statistical parsimony networkanalysis, and a maximum likelihood approach that uses a mixed Yule-coalescent model and detects species boundaries based on differences in branching rates at the level of species and populations. Sequenceanalyses resulted in the recognition of 13 phylogenetic species, although we failed to detect sharp speciesboundaries, possibly as a result of incomplete reproductive isolation. We found considerable conflictbetween traditional and phylogenetic species definitions. Identical morphological forms were distributedin different clades (cryptic diversity), and at the same time most of the phylogenetic species contained amixture of different morphologies (indicating intraspecific morphological variation). Sampling outsidethe morphological range of the Boodlea complex revealed that the enigmatic, sponge-associated Cladophoropsis (Spongocladia) vaucheriiformis, also falls within the Boodlea complex. Given the observed evolutionary complexity and nomenclatural problems associated with establishing a Linnaean taxonomy forthis group, we propose to discard provisionally the misleading morphospecies and genus names, andrefer to clade numbers within a single genus, Boodlea. 2009 Elsevier Inc. All rights reserved.1. IntroductionDespite the wide acceptance of the idea that species represent afundamental unit of biological organization (Mayr, 1982), there hasbeen a great deal of disagreement with regard to the criteria usedto delimit species. This disagreement has led to a proliferation ofdifferent species concepts, followed by endless discussions on theirrespective value and applicability (Mayden, 1997). More recently,however, important conceptual progress has been made in thinking about species concepts (de Queiroz, 1998, 2007). A vast majority of evolutionary biologists now accepts that species are lineages.Coincidentally, and albeit being controversial at first, DNA sequences are being increasingly used to identify species (DNA bar-* Corresponding author. Address: Ghent University, Biology Department (WEI 1),Phycology Research Group. Krijgslaan 281, Building S8 (3rd floor), B-9000 Ghent,Belgium. Fax: 32 9 264 8599.E-mail addresses: frederik.leliaert@ugent.be (F. Leliaert), heroen.verbruggen ugent.be (H. Verbruggen), bwysor@rwu.edu (B. Wysor). olivier.declerck@ugent.be(0.0. Clerck).1055-7903/ - see front matter 2009 Elsevier Inc. All rights reserved.doi:10.1016/j.ympev.2009.06.004coding, Hebert et al., 2003). With recent advances in methods forsequence-based species delimitation, formal analyses of speciesboundaries have become possible (Templeton, 2001; Sites andMarshall, 2003; Wiens, 2007; Zhang et al., 2008). Several methodsfor detecting species limits from DNA sequence data are based ondiagnostic character variation. These methods, which are rooted inthe phylogenetic species concept, aggregate a priori populationsthat lack discrete differences into a single species, which are distinguished from other species by unique nucleotide differences (Cracraft, 1983; Davis and Nixon, 1992; Wiens and Penkrot, 2002;Monaghan et al., 2005). Other procedures aim to detect discontinuities in sequence variation associated with species boundaries,assuming that clusters of closely related sequences that are preceded by long branches are suggestive for genetic isolated entities(Hudson and Coyne, 2002). One of these methods, statistical parsimony (Templeton et al., 1992), separates groups of sequences intodifferent networks if genotypes are connected by long branchesthat are affected by homoplasy. Recently proposed, maximum likelihood approaches aim to determine species boundaries statistically from sequence data by analysing the dynamics of lineage

F. Leliaert et al./Molecular Phylogenetics and Evolution 53 (2009) 122-133123Fig. 1. Morphological diversity in the Boodlea complex. (A) Phyllodictyon anastomosans: stipitate reticulate blade composed of oppositely branching filaments, interconnectedby tenacular cells, in a single plane (FLU 09). (B) Phyllodictyon sp. from Kenya: detail of oppositely branching filaments characterized by very thick cells (HEC8669). (C)Boodlea siamensis: detail of a cushion-like thallus composed of irregularly branching filaments in three dimensions (TZ202). (D) Boodlea montagnei: reticulate blade composedof oppositely branching filaments, which are interconnected by tenacular cells (FLU 28). (E) Struveopsis siamensis: blade with oppositely branching filaments, which are notinterconnected (FL662b). (F) Cladophoropsis membranacea: unilateral branches without cross-walls (CsmemS). (G) Cladophoropsis vaucheriiformis: large, irregularly branchingclump, composed of filaments associated with sponge tissue (HEC11394).branching in phylogenetic trees, trying to determine the point oftransition from species-level (speciation) to population-level (coalescent) evolutionary processes (Pons et al., 2006; Fontaneto et al.,2007).Sequence-based species delimitation is particularly valuable inorganisms in which morphological discrimination is difficult orimpossible, such as in many algal groups (e.g., Saunders, 2005;Verbruggen et al., 2005, 2007; Harvey and Goff, 2006; Lilly et al.,2007; Vanormelingen et al., 2007). A group with a notorious longhistory of confusing species circumscriptions is the Boodlea complex, comprising the marine siphonocladalean green algal generaBoodlea, Cladophoropsis, Phyllodictyon and Struveopsis (Harvey,Table 1Survey of diagnostic features in the 13 recognized morphotypes.Morphological groupThallus architectureBranchesCross-wall atbranchesTenacularcellsAverage diameter and length/width (1/w) ratio of apicalcells1. Boodlea compositaCushions composed of tightlyinterwoven filamentsPresentRare80 urn 1/w: 32. Boodlea montagnei(Fig. ID)3. Boodlea siamensis(Fig. 1C)Reticulate blades without stipesPresentAbundant97 urn 1/w: 3PresentAbundant92 urn 1/w: 44. Boodlea sp.(Indonesia)Cushions borne on thick (c.600 pm), erect, branched filamentsPresentAbundant110 pm 1/w: 35. Cladophoropsismacromeres6. Cladophoropsismembranacea(Fig. IF)7. Cladophoropsisphilippinensis8. Cladophoropsissundanensis9. Cladophoropsisvaucheriiformis(Fig. 1G)10. Phyllodictyonanastomosans(Fig. 1A)11. Phyllodictyon sp.(Kenya) (Fig. IB)12. Siphonous sp.(Florida)13. Struveopsissiamensis (Fig. IE)Mats composed of looselyentangled filamentsCushions or mats composed oftightly interwoven filamentsOpposite, older cells producingadditional branches in threedimensionsOpposite or single, regular, in a singleplaneOpposite or single, older cellsproducing additional branches in threedimensionsOpposite or single, older cellsproducing additional branches in threedimensionsSingle, unilaterally organizedAbsentAbsent320 pm 1/w: 60Single, unilaterally or irregularlyorganizedAbsentGenerallyabsent185 pm 1/w: 45Cushions composed of looselyentangled filamentsCushions composed of tightlyinterwoven filamentsClumps of variable morphology,associated with sponge tissueSingle or opposite, irregularlyorganizedSingle or opposite, irregularlyorganizedGenerally single, irregularly organizedor filaments siphonousOnly present inolder nt510 pm 1/w: 40Absent90 pm 1/w: 35Occasionallypresent105 pm 1/w: 25Stipitate reticulate bladesGenerally opposite, regular, in a singleplanePresentAbundant100 pm 1/w: 3Clustered stipitate bladesGenerally opposite, regular toirregular, more or less in a single planeSiphonousPresentRare310 pm 1/w: 5AbsentAbsent87 pm 1/w: -PresentAbsent160 pm 1/w: 3Cushions composed of tightlyinterwoven filamentsIrregular cushionStipitate blades. Stipes and basalcells clavate with annularconstrictionsOpposite, regular, more or less in asingle plane

F. Leliaert et al. /Molecular Phylogenetics and Evolution 53 (2009) 122-133124Boodlea coacta*. B. composita,B. siamensis, Phyllodictyon anastomosans,Cladophoropsis membranacea*,Struveopsis siamensisCladophoropsis sundanensisStruvea(S. plumosa*, S. gardineri, S. thoracica,S. okamurae)Struvea elegansPhyllodictyon(P. pulcherrimum*, P. orientate, P. robustum)Apjohnia laetevirens*Chamaedoris(C. peniculum*. C. auriculata, C. delphinii)Fig. 2. Phylogenetic hypothesis of Boodlea and related genera based on Leliaertet al. (2007a,b, 2008). Taxa indicated by an asterisk represent generitypes.1859; Egerod, 1975). These seaweeds are widely distributed alongrocky coastlines and in coral reefs throughout the tropics and subtropics (Pakker et al., 1994). Previous taxonomic studies have attempted to delimit species based on the morphological speciesconcept, seeking to recognize species by discontinuities in morphological characters such as thallus architecture, branching pattern, type of tenacular cells and cell dimensions (Fig. 1 and Table1). More than 60 nominal species and infraspecific taxa have beenformally described (14 in Boodlea, 36 in Cladophoropsis, 7 in Phyllodictyon and 5 in Struveopsis) (Index Nominum Algarum, 2008), butthe relationships among these taxa were poorly understood. Thenumber of morphospecies in the Boodlea complex was recently reduced to 13 by Leliaert and Coppejans (2006, 2007b). Analysis ofmorphological variation in this group was found to be problematicbecause many of the morphological features exhibit intraspecificvariability to such an extent that generic boundaries are crossed.Molecular phylogenetic studies have shown that most representatives of Boodlea, Cladophoropsis, Phyllodictyon and Struveopsisare closely related to the morphologically well defined genera Chamaedoris, Struvea and Apjohnia (Kooistra et al., 1993; Leliaert et al.,2003, 2007c). Within this clade, Phyllodictyon was shown to benon-monophyletic with P. anastomosans being more closely relatedto Boodlea than to the other Phyllodictyon species (including thetype, P. pulcherrimum) (Leliaert et al., 2007a,b, 2008) (Fig. 2). Someother taxa are more distantly related; Boodlea vanbosseae Reinboldwas found to be allied with Cladophora catenata (Linnaeus) Kutzing, Anadyomene and Microdictyon (Leliaert et al., 2007b), whileCladophoropsis herpestica (Montagne) M.A. Howe falls within aclade of the Cladophora section Longi-articulatae (Leliaert et al.,2009).Species boundaries in the Boodlea complex have remaineduncertain because of low taxon sampling (Kooistra et al., 1993)or conservativeness of molecular markers (nuclear small and largesubunit rDNA, Leliaert et al., 2007c). In a phylogeographic study,van der Strate et al. (2002) demonstrated that Cladophoropsis membranacea consists of at least three cryptic species with overlappinggeographical distributions in the Atlantic Ocean, based on nrDNAinternal transcribed spacer (ITS) sequence divergence, differentialmicrosatellite amplification and thermal ecotypes. Biogeographicand systematic conclusions, however, were somewhat biased because only a single morphospecies was considered, and hence partof the genetic diversity within the species complex wasoverlooked.In this study, we aim to elucidate species boundaries within theBoodlea complex based on nrlTS sequences from 175 individualssampled worldwide. Given the inherent difficulties of identifyingspecies in this morphologically variable group of algae, we alsosampled outside the known morphological bounds of the Boodleacomplex, for example, including the sponge-associated Cladophoropsis (Spongocladia) vaucheriiformis. ITS sequences have beenshown to provide good resolution at and below the species-levelin a wide range of eukaryotic organisms, including siphonocladalean green algae (Bakker et al., 1992, 1995; van der Strate et al.,2002). Different methods of sequence-based species delineationwere applied, including statistical parsimony network analysis,and a maximum likelihood approach, using the recently developed"general mixed Yule-coalescent" (GMYC) model, which detectsspecies boundaries based on differences in branching rates at thelevel of species and populations.2. Materials and methods2.1. Taxon samplingWe sampled an extensive number of specimens (175) of thenominal species Boodlea composita, B. montagnei, B. siamensis,Cladophoropsis macromeres, C. membranacea, C. philippinensis, C.sundanensis, C. vaucheriiformis, P. anastomosans and Struveopsissiamensis from a broad geographical range (Table SI, online Supplementary material). Morphological species identification wasbased on differences in thallus architecture, presence of stipe cells,branching systems, timing of cross-wall formation, cell shape anddimensions, mode of thallus attachment and reinforcement, presence and morphology of tenacular cells, shape of crystalline cellinclusions, and cell wall thickness (Leliaert and Coppejans, 2006;2007a,b). A number of plants could not be assigned to a describedtaxon: a siphonous C/adopriorops/s-like specimen from Florida (designated as "siphonous sp."), three specimens from Indonesia withCladophoropsis philippinensis-like basal filaments and terminalBood/ea-like branches ("Boodlea sp."), and a P/ry/Zodictyon-like plantfrom Kenya with very large cells {"Phyllodictyon sp."). Collection ofspecimens and their preservation were carried out as described inLeliaert et al. (2007a). Published sequences from 42 isolates ofCladophoropsis membranacea (Kooistra et al., 1992; van der Strateet al., 2002) were also included. Voucher specimens from the latterstudy were kindly sent by Han van der Strate for morphologicalexamination.2.2. Gene sampling and phylogenetic analysesTotal genomic DNA was extracted from silica gel-dried specimens, herbarium material or from living plants in culture, andthe target region, comprising nrDNA internal transcribed spacer regions (ITS1, ITS2) and the 5.8S rDNA, was amplified and sequencedas described in Wysor (2002) and Leliaert et al. (2007a,b). The Primer sequences are given in Table S2 (online Supplementary material). The 175 ITS sequences were aligned using MUSCLE (Edgar,2004) via http://www.ebi.ac.uk/Tools/muscle/. The alignment(provided in a Supplementary online FASTA file) was straightforward and included a limited number of gaps. The amount of phylogenetic signal versus noise was assessed by calculating the /ssstatistic (a measure of substitution saturation in molecular phylogenetic datasets) with DAMBE v4.5.56 (Xia and Xie, 2001). Becausenearly no variation was found within rDNA 5.8S sequences, and because data of this region were unavailable for several isolates (vander Strate et al., 2002), this region was excluded for furtheranalysis.The dataset (ITS1-1TS2) was analysed with Bayesian inference(Bl) and maximum likelihood (ML), using MrBayes v3.1.2 (Ronquistand Huelsenbeck, 2003) and PhyML v2.4.4 (Guindon and Gascuel,

F. Leliaert et al./Molecular Phylogenetics and Evolution 53 (2009) 122-1332003), respectively. The alignment was analysed under a generaltime-reversible model with and gamma distribution split into fourcategories (GTR G4), as determined by the Akaike InformationCriterion in PAUP/Modeltest 3.6 (Swofford, 2002; Posada andCrandall, 1998). Bl consisted of two parallel runs each of four incrementally heated chains, and 3 million generations sampled every1000 generations. The output was diagnosed for convergence usingTracer v. 1.3 (Rambaut and Drummond, 2007a) and summary statistics and trees were generated using the last 2 million generations, well beyond the point at which convergence of parameterestimates had taken place. For the ML trees, the reliability of eachinternal branch was evaluated based on 1000 bootstrap replicates.One of the species delimitation algorithms described below requires a chronometric phylogram (chronogram) in which branchlengths are roughly proportional to time. In order to obtain a chronogram, we applied molecular clock analyses to our data. First, thevalidity of a strict (uniform) molecular clock was tested using alikelihood ratio test by comparing the ML scores obtained withor without constraining a strict molecular clock in PAUP (Posada,2003). A strict molecular clock was significantly rejected [InL without enforcing substitution rate constancy -18379.89, comparedto InL with enforcing substitution rate constancy -18515.78;-2AlnL 271.78, x2 statistic, d.f. (no. taxa - 2) 174, p 0.0000].Due to the violation of the strict molecular clock in our data, a relaxed molecular clock was used to estimate divergence times. Morespecifically, we applied the uncorrelated lognormal (UCLN) model(Drummond et al., 2006) implemented in BEAST vl.4.6 (Drummond and Rambaut, 2007). Two independent Markov chain MonteCarlo (MCMC) analyses were run for 7 million generations, sampling every 1000. The output was diagnosed for convergence usingTracer v.1.3, and summary statistics and trees were generatedusing the last 5 million generations with TreeAnnotator (Rambautand Drummond, 2007b). A logarithmic lineage-through-time plotof the ultrametric tree was generated using GENIE v3.0 (Pybusand Rambaut, 2002).2.3. Sequence-based species delimitationWe applied two empirical methods for testing species boundaries. First, we aimed to detect discontinuities in sequence variation by using a statistical parsimony analysis, which partitionsthe data into independent networks of haplotypes connected bychanges that are non-homoplastic with a 95% probability (Templeton et al., 1992). Statistical parsimony networks were constructedwith TCS 1.21 (Clement et al., 2000), with calculated maximumconnection steps at 95% and with alignment gaps treated as missing data. In the second procedure changes in branching rates weretested at the species boundary in our chronogram following Ponset al. (2006). The method exploits the differences in the rate of lineage branching at the level of species and populations, recognizableas a sudden increase of apparent diversification rate when ultrametric node height is plotted against the number of nodes in a lineage-through-time plot. The procedure uses waiting times betweensuccessive branching events on an ultrametric tree as raw data. Acombined model that separately describes population (a neutralcoalescent model) and speciation (a stochastic birth-only or Yulemodel) processes, i.e., a general mixed Yule-coalescent (GMYC)model, is fitted on the ultrametric tree. The method optimizes athreshold position of switching from interspecific to intraspecificevents such that nodes older than the threshold are consideredto be diversification events (i.e., reflect cladogenesis generatingthe isolated species) and nodes younger than the threshold reflectcoalescence occurring within each species. The number of shiftsand their location on the phylogenetic tree provides the numberof species and their relative age. A standard log-likelihood ratiotest (comparing the likelihood for the mixed model to that ob-125tained assuming a single branching process for the entire tree) isthen used to assess if there is significant evidence for the predictedshift in branching rates. A confidence interval for the number ofshifts is defined by 2 log likelihood units which is expected tobe x2 distributed with 3 of freedom. Model fitting and phylogenetic tests were performed using a script provided by T.G. Barraclough (Imperial College London), implemented in R using functionsof the APE library (Paradis et al., 2004).3. Results3.7. Morphological groupsOur dataset included 175 individuals distributed worldwide.We recognised 13 morphological entities based on differences inthallus architecture, branching system, cross-wall formation, celldimensions, and presence or absence of tenacular cells (Table 1).These morphological groups correspond to 10 currently recognizedspecies and three entities that could not be assigned to any previously described taxon. Most individuals could readily be assignedto one of the morphological entities. However, for a number ofspecimens unequivocal allocation to a single morphotype wasproblematic because of intermediate morphological features.These are indicated in Table SI (online Supplementary material).3.2. Sequence analysis and phytogenyVisual inspection of the electropherograms of the nrlTS sequences showed sequences with predominantly unambiguouspeaks, indicating low intra-individual variation. The small numberof ambiguities (or underlying peaks) constituted mainly singlenucleotide polymorphisms that were not phylogenetically informative. Our observations are in agreement with cloning resultsin Cladophoropsis membranacea by van der Strate et al. (2002),who also found very low intra-individual polymorphism, includingonly autapomorphic point mutations. The ITS alignment of 175 sequences was 924 sites in total (ITS1: 439 sites, 5.8S: 157 sites andITS2: 328 sites) and included 393 phylogenetic informative characters (ITS1: 226, 5.8S: 4 and ITS2: 163). For ITS1-1TS2 (excluding5.8S), ML optimization carried out during the model selection procedure estimated nucleotide frequencies as A 0.24, C 0.26,G 0.27 and T 0.23. The best fit to the data was obtained withsix substitution types and rates: AC 0.72, AC 2.48, AT 1.28,CG 0.67, CT 2.48, and GT 1.00, with among-site rate variation(gamma distribution shape parameter 0.94) and no separate rateclass for invariable sites. In total, 92 ribotypes were present. Substitution saturation test (Xia and Xie, 2001) showed that the ITSdataset did not suffer from saturation (fss 0.146 /ss.c 0.694,p 0.001).ML and BI yielded virtually identical tree topologies with comparable node support. The phylogenetic tree obtained from the MLanalysis (InL -4895.76), with indication of ML bootstrap valuesand BI posterior probabilities, is shown in Fig. 3. Four main clades(A-D), separated by long internal branches with high support wererecovered. The relaxed molecular clock analysis under a UCLNmodel yielded a virtual identical tree topology as the ML and BIanalyses (Fig. 4).3.3. Sequence-based species delimitationTwo algorithmic methods of sequence-based species delimitation were applied. In the first method, patterns of sequence variation were investigated for the presence of species-level groups byidentifying independent networks using statistical parsimony(Templeton et al., 1992). This network analysis separated the total

F. Leliaert et al. /Molecular Phylogenetics and Evolution 53 (2009) 122-133126ice a CmCITFG Canaryice a CmBonBO Carice a CmCVIBoaVPA Cape.Verdelacea CmCIFVT2 Canaryicea CmCVISanVBdG Cape.Verdeicea CmCIGCMP CmCIGCLP2 Canaryiacea CmCVISaISM Cape .Verdei ace a CmBonL Cari ace a CmCIGCLPI CanaryBcompl Cape.VerdeC membranacea CmCIFVPdR3 CmCIFVLPI CanaryC membranacea CmCIFVTI CanaryC membranacea CmCVISanTP1,.TP2,.VSA Cape.VerdeC membranacea CmCITFPdH, CmCITFC CanaryBcomp4 Cape .VerdeC vaucheriiformis ODC 1674 KenyaBW1079Pac.PanamaBW230 BW43 Pac. PanamaTts siamensis BcompG BonaireP anastomosans CANCAP725 MadeiraB siamensis BWsn Pac.MexicoP anastomosans BW1481 Pac.Panama00/100 - B siamensis BoOki JapanI C membranacea CmJapOJ JapanStruveopsis sp SF7694114 TaiwanC membranacea CmHawO HawaiiHV866 Philippines.nn,im „,-. C sundanensis ClosuSey616E Seychelles w*C vaucheriiformis HEC6166 MaldivesHEC6163 MaldivesC sundanensis FLsn ZanzibarC membranacea (2) CanaryC membranacea CmCIFVPdRI CmCIFVPdR2 CanaryC membranacea Soc318 SocotraC membranacea CmRS2 Red.Sea- C membranacea CmRS1 Red. Sea- C membranacea CmMedSL Meditsiphonous sp West4296 FloridaC membranacea DM L59461 BelizeDML68113 BahamasDML58207 BahamasDML58215 BahamasC membranacea CmCurW CmCurJT CarC membranacea CmBonLa CarC membranacea HV387 JamaicaC membranacea BW4 Car.PanamaC membranacea CmCVISalPdL2 Cape.Verde- C membranacea CmCVISalPdU Cape.VerdeC membranacea CmVIStXBB CmVIStXCB Carj- C membranacea CmMau Mauritianiajp— C membranacea CmCVISanTCV1,.2 Cape .VerdeGenera (thallus morphology)HI Cladophoropsis(cushions or mats, unilateral branching, tenacula rare Boodlea(3-dimensional reticulums, opposite branching, tenacula present)g Phyllodictyon(stipitate reticulate blades, opposite branching, tenacula present)g Struveopsis(stipitate blades, opposite branching, tenacula absent)g cushion composed of siphonous branches,irregular branching, tenacula absentPP498/100r- C vaucheriiformis FL954A,B Zanzibar9S/100]I— P anastomosans FL1010 ZanzibarP anastomosans FL959,966,985 Zanzibar99/100'— P anastomosans FLsn ZanzibarB composita FL923 Zanzibar99/100122 1 vaucheriiformis FL989 Zanzibar100* C vaucheriiformis HEC11135 MafiaC vaucheriiformis HEC11394 Pemba100/100 B siamensis FL714 ZanzibarP anastomosans FL994 FL980 ZanzibarB montagnei FL961 ZanzibarB composita ODC665 Tanzania00/IOoJ 100/100. B siamensis FL999 ZanzibarB composita FL950 ZanzibarB siamensis ODC1668 KenyaP kenyense HEC8669a Kenya- B composita FL986 ZanzibarB composita FL702 Zanzibar- S siamensis FL916 TanzaniaB composita FL1007 ZanzibarB composita PL694 ZanzibarB composita FL694B ZanzibarP anastomosans SaBra BrazilP anastomosans DJ6608 GhanaP anastomosans BWsn Pac.AustraliaP anastomosans DJ9274 GambiaP anastomosans BWsn FloridaP anastomosans SaMB StCroixP anastomosans DML68772 Belize! siamensis DML64212 Car.PanamaP anastomosans USJA73440 Costa.RicaP anastomosans (1) Car.PanamaBW920 Pac. PanamaDML40109FijiDML40014 FijiB montagnei PH648 PhilippinesB montagnei HV868 Philippinest00/1001 B montagnei FL1184 PhilippinesB montagnei PH646 Philippines— B montagnei PH467 Philippines7f/97j- C sp L0654203 IndonesiaC sp L0654201 L0654202 Indonesia00/1 ooi P anastomosans BW304, 1078 Car.PanamaDML68460 BonaireNP154BWsn2 Hawaii1001 C philippinensis PH172 Philippinesp.C philippinensis HV710 PhilippinesPH171 PhilippinesHV869 PhilippinesHV870 PhilippinesDML40381 FijiHV865 HV867 PhilippinesSOC201 SocotraP anastomosans SaGua Guam- P anastomosans CP13441 PapuaSOC254 SOC204 SOC226 SocotraB montagnei CP13133 Papua L1090 FL1110 HV864 PhilippinesFL1122 PhilippinesB montagnei FL1089 PhilippinesP anastomosans FL1185 PhilippinesP anastomosans FL1109 PhilippinesB montagnei FL1111 Philippinesclade D0.05 substitutions / site100/100 i C sundanensis HEC12976 TanzaniaC sundanensis FL901 TanzaniaC sundanensis KZN2148 5E.AfricaC membranacea Tittley301 ThailandC sundanensis FL1186 PhilippinesC sundanensis Dra ism a 509051 IndonesiaC sundanensis HEC11641,11671,11813b Sri.Lanka91 100j C membranacea PvR509099 IndonesiaC sundanensis Clear/509532 Indonesiasundanensis HEC11813a Sri.Lankasundanensis FL1119 PhilippinesC sundanensis OlsenS GuamC sundanensis PL 949 ZanzibarC sundanensis FL1182 PhilippinesC sundanensis Olsen3 Olsenl Olsen6 Olsen4 GuamC sundanensis BW1080 Car.Panama C sundanensis CsGua Guam71C sundanensis CsBon Bonairei- C sundanensis OlsenS Guam i C sundanensis Olsen9 GuamT- C sundanensis Olsen2 Guam,,P Fig. 3. Maximum likelihood phylogram of the Boodlea complex inferred from rDNA internal transcribed spacer sequences. ML bootstrap values and BI posterior probabilitiesare indicated at the branches. Terminal labels indicate morphospecies and sample region. The first column to the right of the tree indicates membership in statisticalparsimony networks. The second column indicates species boundaries identified by the likelihood analysis. The third (dark grey) column shows monophyletic consensusgroups of the former two analyses, representing putative phylogenetic species further discussed in this study. The fourth column indicates geographical distribution of thespecies. (1) includes the P. anastomosans samples BW95, BW747, BW847, BW1116, BW1426, BW1386 and BWsn; (2) includes the C membranacea samples: CmCILZPdC3,CmCILZPdC4, CmCILZPdC2, CmCILZPM, CmCILZPdC5 and CmCILZPdCl.

F. Leliaert et al./Molecular Phylogenetics and Evolution 53 (2009) 122-133127relative timescaleFig. 4. Ultrametric tree of the Boodlea complex based on a Bayesian analysis of nrlTS sequence data with divergence times estimated under a relaxed molecular clock using anuncorrelated lognormal (ULLN) model in BEAST. The graph below represents the corresponding lineage-through-time plot. The dotted vertical line indicates the maximumlikelihood transition point of the switch in branching rates, as estimated by a general mixed Yule-coalescent (GMYC) model.variation of ITS sequences into 16 groups based on a maximumconnection limit of 12 steps (branches of 13 steps or more fell outside of the 95% confidence interval for non-homoplastic connections) (Fig. 3). Two groups were found to be nested withi

Marshall, 2003; Wiens, 2007; Zhang et al., 2008). Several methods for detecting species limits from DNA sequence data are based on diagnostic character variation. These methods, which are rooted in the phylogenetic species concept, aggregate a priori populations that lack discrete differences into a single species, which are distin-

Related Documents:

Smithsonian STEAM Readers Aligned to Next Generation Science Standards Grades 3–5 Teacher Created Materials www.tcmpub.com (800) 858-7339 B3418 2019 Smithsonian Institution. The name “Smithsonian” and the Smithsonian logo are registered trademarks owned by the Smithsonian Institution.

Lecture 18 . Molecular Evolution and Phylogenetics . 6.047/6.878 - Computational Biology: Genomes, Networks,

Combinatorial Phylogenetics of Reconstruction Algorithms by Aaron Douglas Kleinman Doctor of Philosophy in Mathematics Designated Emphasis in Computational and Genomic Biology University of California, Berkeley Professor Lior Pachter, Chair Phylogenetics is the study of the evolutionary history

ing. The literature of molecular phylogenetics is large and complex23,24; the aim of this Review is to provide a starting point for exploring the methods further. Phylogenetic tree reconstruction: basic concepts A phylogeny is a tree containing nodes that ar

The journal Molecular Biology covers a wide range of problems related to molecular, cell, and computational biology, including genomics, proteomics, bioinformatics, molecular virology and immunology, molecular development biology, and molecular evolution. Molecular Biology publishes reviews, mini-reviews, and experimental and theoretical works .

Predicting adaptive evolution Robin M. Bush OPINION Phylogenetic trees reconstruct past evolution and can provide evidence of past evolutionary pressure on genes and on individual codons. In addition to tracing past evolutionary events, molecular phylogenetics might also be used to predict future evolution. Our ability to verify adaptive

Jan 31, 2011 · the molecular geometries for each chemical species using VSEPR. Below the picture of each molecule write the name of the geometry (e. g. linear, trigonal planar, etc.). Although you do not need to name the molecular shape for molecules and ions with more than one "central atom", you should be able to indicate the molecular geometryFile Size: 890KBPage Count: 7Explore furtherLab # 13: Molecular Models Quiz- Answer Key - Mr Palermowww.mrpalermo.comAnswer key - CHEMISTRYsiprogram.weebly.comVirtual Molecular Model Kit - Vmols - CheMagicchemagic.orgMolecular Modeling 1 Chem Labchemlab.truman.eduHow to Use a Molecular Model for Learning . - Chemistry Hallchemistryhall.comRecommended to you b

concerted evolution; molecular evolution; maximum likelihood; parsimony; evolution of novelty Abstract With the advent of high-throughput DNA sequencing and whole-genome analysis, it has become clear that the coding portions of the genome are organized hierarchically in gene families and superfamilies. Because the hierarchy

Apr 18, 2013 · systematics, integrating phylogenetic signal from the population up based on DNA and through time based on direct observation rather than inference. Molecular systematics in the 21st century For several years, molecular systematics has been the dominant phylogenetic paradigm [1]. By t

molecular systematics. While molecular phylogeny, in a really broad way, may be a domain of the biology, the molecular systematics might be viewed as more of a statistical science in which powerful computation based simulation experiments are used to infer phylogenetic trees from these biological data obtaine

The Chicago Manual of Style, latest edition Aircraft Names and Designations The Smithsonian National Air and Space Museum Directory of Airplanes, Their Designers and Manufacturers, edited by Dana Bell. (NASM Library: TL509 .S577 2002X) The Smithsonian and the Museum The Smithsonian

Molecular phylogeny of Panaspis and Afroablepharus skinks (Squamata: Scincidae) in the savannas of sub-Saharan Africa Maria F. Medina a , Aaron M. Bauer b , William

Evolution 2250e and Evolution 3250e are equipped with a 2500 VApower supply. The Evolution 402e and Evolution 600e are equipped with a 4400 VA power supply, and the Evolution 403e and Evolution 900e house 6000 VA power supplies. Internal high-current line conditioning circuitry filters RF noise on the AC mains, as well as

Chapter 4-Evolution Biodiversity Part I Origins of life Evolution Chemical evolution biological evolution Evidence for evolution Fossils DNA Evolution by Natural Selection genetic variability and mutation natural selection heritability differential reproduct

development, partly on the basis of own molecular phylogenetic analyses. Molecular methods have transformed taxonomy and phylogenetics. First molecu-lar analyses of Herrmann et al. (1999) and Lenk et al. (2001) found Pseudocerastes and Eristicophis, Vipera s. str., Dabo

Stanley, FIQQ 1ZZ, Falkland Islands Aldo O. Asensi: 15 rue Lamblardie, F-75012 Paris, France Olivier DeClerck: Phycology Research Group and Centre for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281, Building S8, 9000 Ghent, Belgium Dieter G. Müller: Department of Biology, University of Konstanz, D-78457 Konstanz, Germany

angiosperm flower evolution. Keywords: Angiosperm; Carpel; Origin; Comparative anatomy; Flower; Magnolia Background Before the debut of molecular phylogenetics, angiosperm systematics were dominated by a so-called classical bo-tanical doctrine, according to which Magnolia was o

Veer Bala Rastogi, Fundamentals of Molecular Biology 6. G. K. Pal and Ghaskadabi, Fundamentals of Molecular Biology 7. Text book of Molecular Biology, Verma and Agarwal 8. Robertis and DeRobertis, Cell and Molecular Biology 9. Buchanan B. B., Biochemistry and Molecular Biology of Plants 10. .

SEMESTER I Paper I Molecular Symmetry and Molecular Vibrations 1. Molecular Symmetry: a) Symmetry elements and symmetry operations with special reference to water, ammonia and ethane. b) Classification of molecules/ ions based on their symmetry properties. c) Derivation of matrices for rotation, reflection, rotation-reflection and .

The packet includes problems from different areas of the 2nd grade curriculum. It is expected that the students are entering into 3rd grade having mastered these areas. Particular areas of strength and growth are noted in your child’s report card. If your child completes the packet in June and doesn’t solve any math problems for the