Majority Rule Consensus Tree Research Articles

Genetic diversity and pathogenicity of Sphaceloma rosarum (teleomorph Elsinoë rosarum) causing spot anthracnose on roses

Roses produced or grown in the field, as well as pot‐grown and cut roses, are attacked by different fungal pathogens causing leaf spot diseases. The incorrect identification and scoring of these pathogens and the lack of information about their genetic and pathotype diversity hamper resistance breeding. This is especially true for the hemibiotrophic ascomycete Sphaceloma rosarum, which is often confused with other fungi. Here for the first time, the genetic variability between isolates at both the molecular and morphological level is analysed. Eighty leaf spot samples were collected from different rose genotypes at five different locations, and 15 single conidial isolates established. All of the samples showed high morphological similarities to the reference isolate CBS 213.33 that was obtained from a public repository. By sequencing a part of the large subunit (LSU) of the 28S ribosomal RNA and phylogenetic analysis, high sequence similarities were shown to other Sphaceloma species for 13 of the isolates and the CBS reference. One of the isolates clustered with Septoria species and another clustered with Seimatosporium species. UPGMA clustering with 145 polymorphic AFLP markers resulted in five distinct groups in the majority rule consensus tree for the 14 S. rosarum isolates, including the CBS reference. Jaccard similarities ranged from 0·31 to 0·91. A detached leaf assay using a differential set of five rose genotypes led to the classification of the five tested isolates as five distinct pathotypes. Therefore, grouping depending on the avirulence gene diversity was clearly different from clustering using selectively neutral AFLP markers that were evenly distributed throughout the genome.

Morphological and molecular characterisation of Hemicaloosia guangzhouensis n. sp. (Nematoda: Caloosiidae) from China

A new plant nematode species, Hemicaloosia guangzhouensis n. sp., collected from the soil associated with Schima superba in a forest park in Guangzhou, China is described. The new species is characterized by having a female with a slender body, 798–961 μm in length, stylet 59–69 μm long, tail 115–145 μm long, a membranous sheath closely adpressed to the entire body, lateral fields marked by one longitudinal line with breaks and anastomoses of transverse striae, total number of annuli 282–313, two lip annuli both projecting slightly anterior, excretory pore 51–58 annuli from anterior end, the number of annulus between vulva and anus 7–11, the number of annulus from vulva to tail terminus 58–69, spermatheca empty; and male unknown. The internal transcribed spacer of ribosomal RNA (ITS rRNA) gene, D2-D3 region of 28S ribosomal RNA (28S rRNA) gene, partial 18S ribosomal RNA (18S rRNA) gene of the new species were amplified and sequenced. The 50 % majority rule consensus trees inferred from ITS rRNA, 28S rRNA, partial 18S rRNA gene sequences of H. guangzhouensis n. sp. and some other species in the suborder Criconematina are also presented in this study. PCR-ITS-RFLP diagnostic profile generated by six restriction enzymes for H. guangzhouensis n. sp. is given.

Morphological phylogenetic analysis ofOphrys(Orchidaceae): insights from morpho-anatomical floral traits into the interspecific relationships in an unresolved clade

Reconstructing the phylogeny of the sexually deceptive orchid genus Ophrys is crucial to our understanding of the evolution of its complex floral morphology. Molecular phylogenetic analyses showed that section Pseudophrys forms a well supported clade with Ophrys bombyliflora, O. tenthredinifera and O. speculum, but were unable to elucidate the relationships between these four groups of taxa. Here we conduct a morphological phylogenetic analysis of this unresolved clade of Ophrys based on a data matrix of 45 macro- and micromorphological and anatomical floral characters, using maximum parsimony and Bayesian inference. Our cladistic analysis yielded a single most parsimonious tree and a Bayesian 50% majority-rule consensus tree which differed in their overall topology but agreed that O. tenthredinifera and O. bombyliflora are not sister groups. The phylogenetic placement of O. tenthredinifera was ambiguous since it shares six valid synapomorphies each with the cluster of O. speculum–O. bombyliflora and with section Pseudophrys. In contrast, O. bombyliflora is most likely the sister group to O. speculum, a finding that rejects an earlier morphological phylogenetic hypothesis and favours the existing molecular trees based on nuclear ITS rather than plastid data. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179, 454–476.

Td-DAMD-PCR assays for fingerprinting of commercial carnations

Dianthus L. is one of the highly valued plant species in the family Caryophyllaceae. More than 30,000 cultivars of commercial carnations have been recorded and there is a need for an effective and cheap method to reveal their genetic diversity and identify the cultivars. To the best of our knowledge this is the first report of implementation of the touchdown direct amplification of minisatellite-region DNA polymerase chain reaction (Td-DAMD-PCR) technique in the genus Dianthus. A total of 12 core minisatellite primers empirically selected from 22 primers were used in fingerprinting and phylogenetic studies of some commercial carnation cultivars. Analysis revealed that commercial carnations have a wide genetic base and they were probably obtained using inter-crosses between and among different species of the genus Dianthus. A total of 17 DNA markers were variety specific and most of the remaining markers obtained in the present study were useful in fingerprinting of the commercial varieties studied. Commercial varieties were differentiated in spray and standard carnation groups in a principal coordinate analysis and a Bayesian 50% majority-rule consensus tree. Td-DAMD-PCR markers reported in this study could be very useful in species identification, determination of genetic relationships, and phylogenetic studies of species of Dianthus.

New Early Eocene basal tapiromorph from southern China and its phylogenetic implications.

A new Early Eocene tapiromorph, Meridiolophus expansus gen. et sp. nov., from the Sanshui Basin, Guangdong Province, China, is described and discussed. It is the first reported Eocene mammal from the basin. The new taxon, represented by a left fragmentary mandible, is characterized by an expanded anterior symphyseal region, a long diastema between c1 and p1, a rather short diastema between p1 and p2, smaller premolars relative to molars, an incipient metaconid appressed to the protoconid on p3, a prominent entoconid on p4, molar metaconid not twinned, cristid obliqua extending mesially and slightly lingually from the hypoconid, inclined metalophid and hypolophid, and small hypoconulid on the lower preultimate molars. Meridiolophus is morphologically intermediate between basal Homogalax-like taxa and derived tapiromorphs (such as Heptodon). Phylogenetic analysis indicates Equidae is more closely related to Tapiromorpha than to Palaeotheriidae, although the latter is only represented by a single species Pachynolophus eulaliensis. ‘Isectolophidae’, with exception of Meridiolophus and Karagalax, has the closest affinity with Chalicotherioidea. Furthermore, the majority rule consensus tree shows that Meridiolophus is closer to Karagalax than to any other ‘isectolophid’, and both genera represent stem taxa to crown group Ceratomorpha.

Phylogeny of the tribe Archipini (Lepidoptera: Tortricidae: Tortricinae) and evolutionary correlates of novel secondary sexual structures.

We reconstructed a preliminary phylogeny for the economically important tribe Archipini (Lepidoptera: Tortricidae: Tortricinae) based on 135 exemplar species (including four outgroups) and a combined analyses of 28S rDNA and COI DNA using maximum parsimony, maximum likelihood, and Bayesian analyses. A summary tree was produced as the majority rule consensus tree by first assembling all clades that were present in more than 50% of analyses. Based on the results of the analyses, several taxonomic changes are suggested. After mapping secondary sexual characters (SSCs), host plant breadth, and geographic distribution onto the phylogeny, we examined correspondences among these traits using two-by-two χ2 tests and ancestral character state reconstructions. Absence of SSCs was associated with decreased host plant breadth and colonization of the New World, but was not significantly associated with the presence of other SSCs. There is a strong likelihood of an Australasian origin for Archipini. We propose the synonymy of Archepandemis Mutuura with Pandemis Hübner (new synonymy); the synonymy of Cudonigera Obraztsov & Powell with Choristoneura Lederer (new synonymy); and elevation of Anaphelia Razowski, Sacaphelia Razowski, and Zelotherses Lederer to genera from subgenera of Aphelia Hübner (revised status). Epiphyas Turner, may be subordinate within Clepsis Guenée, but further study is needed to confirm this.

Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods

The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses. Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to species trees. These methods play an important role in studying genome evolution as well as in inferring orthology relationships. A major issue with reconciliation methods is that the reliability of predicted evolutionary events may be questioned for various reasons: Firstly, there may be multiple equally optimal reconciliations for a given species tree–gene tree pair. Secondly, reconciliation methods can be misled by inaccurate gene or species trees. Thirdly, predicted events may fluctuate with method parameters such as the cost or rate of elementary events. For all of these reasons, confidence values for predicted evolutionary events are sorely needed. It was recently suggested that the frequency of each event in the set of all optimal reconciliations could be used as a support measure. We put this proposition to the test here and also consider a variant where the support measure is obtained by additionally accounting for suboptimal reconciliations. Experiments on simulated data show the relevance of event supports computed by both methods, while resorting to suboptimal sampling was shown to be more effective. Unfortunately, we also show that, unlike the majority-rule consensus tree for phylogenies, there is no guarantee that a single reconciliation can contain all events having above 50% support. In this paper, we detail how to rely on the reconciliation graph to efficiently identify the median reconciliation. Such median reconciliation can be found in polynomial time within the potentially exponential set of most parsimonious reconciliations.

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

Towards a natural classification of Sapotaceae subfamily Chrysophylloideae in Oceania and Southeast Asia based on nuclear sequence data

AbstractGeneric limits within subfamily Chrysophylloideae (Sapotaceae) from Oceania and Southeast Asia are reconciled based on a molecular phylogeny. We analysed sequences of nuclear ribosomal DNA (ETS, ITS) and the nuclear gene RPB2 with BEAST and parsimony jackknifing, using a sample of 168 terminals. Eight morphological characters were traced on a condensed majority–rule consensus tree to identify diagnostic character combinations for the genera. Accepted genera with character support are Magodendron, Pichonia, Planchonella, Pycnandra, Sersalisia, and Van–royena, while Beccariella and Niemeyera require amendment. Beccariella, a widely distributed group, is an illegitimate later homonym and we propose that the genus Pleioluma is resurrected in its place. The Australian genus Niemeyera is paraphyletic, but it is rendered monophyletic by reinstating Amorphospermum for N. antiloga. Beauvisagea, Blabeia, Fontbrunea, and Krausella are all segregates of Planchonella and rejected, while Wokoia is a later synonym of Pichonia. Planchonella baillonii, an endemic species of New Caledonia, is the sole member of an old lineage and firmly placed as the sister to a clade comprising the other congeners. Planchonella sandwicensis, a Hawaiian species, previously proposed to be a distinct genus, is a member of Planchonella. In the Pacific, P. tahitensis (including P. grayana) is a polymorphic species, widely distributed and adapted to a wide range of habitats. We provide a generic key (excluding Xantolis), diagnostic character combinations for all genera, and the necessary taxonomic combinations for Pichonia, Planchonella, Pleioluma, and Sersalisia to render each genus monophyletic.

First report of ‘Candidatus Liberibacter europaeus’ associated with psyllid infested Scotch broom

In the Canterbury region (mid-South Island), New Zealand, in November 2011, disease symptoms resembling those associated with 'Candidatus Liberibacter' species were observed in common or Scotch broom (Cytisus scoparius), an invasive leguminous exotic shrub. Symptoms included stunted growth of shoots, shortened internodes, and leaf dwarfing and leaf tip chlorosis (Fig. 1). A large population of broom psyllid, Arytainilla spartiophila, was noted on the plants. Total DNA was extracted from the stems of 19 Scotch broom plants as well as seven broom psyllid samples collected from infested plants using CTAB. Each DNA sample was tested for the presence of 'Ca. Liberibacter' by amplification of a partial 16S rDNA sequence using a liberibacter-specific semi-nested PCR based on primers Lib16s01F, Lib16s01R and OA2 (Beard et al., 2012). A 578 bp partial 16S rDNA fragment indicative of the presence of a 'Ca. Liberibacter' was amplified from 15 out of 19 plant samples and from five out of seven broom psyllid samples. Amplicons from seven of these samples were directly sequenced, trimmed to 510 bp and subsequently used in a phylogenetic comparison with partial 16S rDNA sequences of 'Ca. Liberibacter' from other hosts using Mr. Bayes v. 3.0b4. The resulting majority rule consensus tree clustered the partial 16S rDNA sequences from Scotch broom and broom psyllid with that of 'Ca. Liberibacter europaeus' (Fig. 2). 'Ca. L. europaeus' has been previously associated with the pear psyllid, Cacopsylla pyri, and shown to be transmitted to pear plants where it apparently behaves as an endophyte (Raddadi et al., 2011).

A nuclear single-nucleotide polymorphism (SNP) potentially useful for the separation of Rhodnius prolixus from members of the Rhodnius robustus cryptic species complex (Hemiptera: Reduviidae)

The design and application of rational strategies that rely on accurate species identification are pivotal for effective vector control. When morphological identification of the target vector species is impractical, the use of molecular markers is required. Here we describe a non-coding, single-copy nuclear DNA fragment that contains a single-nucleotide polymorphism (SNP) with the potential to distinguish the important domestic Chagas disease vector, Rhodnius prolixus, from members of the four sylvatic Rhodnius robustus cryptic species complex. A total of 96 primer pairs obtained from whole genome shotgun sequencing of the R. prolixus genome (12,626 random reads) were tested on 43 R. prolixus and R. robustus s.l. samples. One of the seven amplicons selected (AmpG) presented a SNP, potentially diagnostic for R. prolixus, on the 280th site. The diagnostic nature of this SNP was then confirmed based on the analysis of 154 R. prolixus and R. robustus s.l. samples representing the widest possible geographic coverage. The results of a 60% majority-rule Bayesian consensus tree and a median-joining network constructed based on the genetic variability observed reveal the paraphyletic nature of the R. robustus species complex, with respect to R. prolixus. The AmpG region is located in the fourth intron of the Transmembrane protein 165 gene, which seems to be in the R. prolixus X chromosome. Other possible chromosomal locations of the AmpG region in the R. prolixus genome are also presented and discussed.

New insights into the biogeography of south‐western Europe: spatial patterns from vascular plants using cluster analysis and parsimony

AbstractAimWe analysed the distributional pattern of the vascular flora of the Iberian Peninsula and Balearic archipelago using cluster and parsimony methods to delineate a biogeographical scheme for south‐western Europe and to compare the results with previous regionalizations. Additionally, we aim to identify areas of endemism.LocationSouth‐western Europe (Iberian Peninsula and the Balearic Islands).MethodsPattern analysis of a chorological dataset, consisting of the occurrences of 3041 vascular plant species in each of the 50 km × 50 km UTM cells of a grid covering Iberia and the Balearic Islands, was based on cluster analysis (unweighted pair‐group method using arithmetic averages; UPGMA) and parsimony analysis of endemicity (PAE). The Jaccard similarity index was used in the UPGMA, and the set of most parsimonious trees from the PAE were summarized in a 75% majority consensus tree.ResultsThe UPGMA dendrogram delineated two main branches in the study region: (1) an eastern area of six sectors including the Balearic Islands plus those regions of Iberia with basic substrates, and (2) a western area with three sectors comprising the regions with acidic soils. The majority rule consensus tree of 53 most parsimonious trees from PAE showed eight main clades similarly separating eastern Iberia plus the Balearic Islands with their basic substrates, from western Iberia with its acidic and basic substrates; in addition the PAE tree showed some previously undetected chorological patterns.Main conclusionsThe use of large and inclusive datasets allows for the recognition of different spatial patterns from those obtained using a limited number of endemic or indicator species. The analyses support some floristic regions previously recognized for Iberia, but not the classic Eurosiberian–Mediterranean division, and some transition territories. Our recognition of 19 areas of endemism consisting of two or more cells and 60 consisting of one cell in south‐western Europe is new.

An axiomatic study of Majority-rule (+ ) and associated consensus functions on hierarchies

Consensus trees have been used routinely in systematic biology for over 30 years with the majority-rule consensus tree among the most popular. In this paper we give axioms that characterize a new consensus function, called majority-rule (+), that is based on a generalization of majority-rule to the supertree case. In addition, two other related consensus functions are characterized.

Split-based computation of majority-rule supertrees

BackgroundSupertree methods combine overlapping input trees into a larger supertree. Here, I consider split-based supertree methods that first extract the split information of the input trees and subsequently combine this split information into a phylogeny. Well known split-based supertree methods are matrix representation with parsimony and matrix representation with compatibility. Combining input trees on the same taxon set, as in the consensus setting, is a well-studied task and it is thus desirable to generalize consensus methods to supertree methods.ResultsHere, three variants of majority-rule (MR) supertrees that generalize majority-rule consensus trees are investigated. I provide simple formulas for computing the respective score for bifurcating input- and supertrees. These score computations, together with a heuristic tree search minmizing the scores, were implemented in the python program PluMiST (Plus- and Minus SuperTrees) available from http://www.cibiv.at/software/plumist. The different MR methods were tested by simulation and on real data sets. The search heuristic was successful in combining compatible input trees. When combining incompatible input trees, especially one variant, MR(-) supertrees, performed well.ConclusionsThe presented framework allows for an efficient score computation of three majority-rule supertree variants and input trees. I combined the score computation with a heuristic search over the supertree space. The implementation was tested by simulation and on real data sets and showed promising results. Especially the MR(-) variant seems to be a reasonable score for supertree reconstruction. Generalizing these computations to multifurcating trees is an open problem, which may be tackled using this framework.

Phylogenetic reappraisal of Rhytidosteidae (Stereospondyli: Trematosauria), temnospondyl amphibians from the Permian and Triassic

All stereospondyl taxa previously placed within Rhytidosteidae are reviewed in a phylogenetic context. A parsimony analysis shows that Pneumatostega, Trucheosaurus, Rhytidosteus and Nanolania are placed outside Rhytidosteidae. If an implied weighting method is introduced in order to downweight homoplastic characters, then these taxa are placed within rhytidosteids (with the exception of Rhytidosteus), thus forming a resolved monophyletic group. This group is supported by four synapomorphies, including a twisted pterygoid quadrate ramus and sculpture consisting of a reticulate pattern with pustules or nodules at the junction between adjacent crests and ridges. Based on the topology of a majority rule consensus tree, we postulate a close relationship among all eastern Gondwanan rhytidosteids (Australian and Indian taxa) and among western Gondwanan taxa (South America, South Africa and Madagascar). Laurasian Boreopelta and Peltostega are successive paraphyletic taxa of both eastern and western groups. The Australian family ‘Derwentiidae’ is nested within Rhytidosteidae and is redefined as a subfamily (Derwentiinae nov.) which also includes Indobrachyops. Peltosteginae and Indobrachyopidae as currently defined in the literature are not supported. Rhytidosteinae is also not supported because Laidleria, Pneumatostega and Rhytidosteus do not emerge as a clade. The presence of the rhytidosteid Trucheosaurus major in the Late Permian of Australia suggests that rhytidosteids were already diversified at that time. Increasing efforts to collect Upper Permian and Lower Triassic rhytidosteids should help to improve stratigraphical, palaeogeographical and phylogenetic information regarding this widespread group of temnospondyls.

Taxonomic review and phylogenetic analysis of Enchodontoidei (Teleostei: Aulopiformes)

Enchodontoidei are extinct marine teleost fishes with a long temporal range and a wide geographic distribution. As there has been no comprehensive phylogenetic study of this taxon, we performed a parsimony analysis using a data matrix with 87 characters, 31 terminal taxa for ingroup, and three taxa for outgroup. The analysis produced 93 equally parsimonious trees (L = 437 steps; CI = 0. 24; RI = 0. 49). The topology of the majority rule consensus tree was: (Sardinioides + Hemisaurida + (Nardorex + (Atolvorator + (Protostomias + Yabrudichthys ) + (Apateopholis + (Serrilepis + (Halec + Phylactocephalus ) + (Cimolichthys + (Prionolepis + ( (Eurypholis + Saurorhamphus ) + (Enchodus + (Paleolycus + Parenchodus ))))))) + ( (Ichthyotringa + Apateodus ) + (Rharbichthys + (Trachinocephalus + ( (Apuliadercetis + Brazilodercetis ) + (Benthesikyme + (Cyranichthys + Robertichthys ) + (Dercetis + Ophidercetis )) + (Caudadercetis + (Pelargorhynchus + (Nardodercetis + (Rhynchodercetis + (Dercetoides + Hastichthys )))))). The group Enchodontoidei is not monophyletic. Dercetidae form a clade supported by the presence of very reduced neural spines and possess a new composition. Enchodontidae are monophyletic by the presence of middorsal scutes, and Rharbichthys was excluded. Halecidae possess a new composition, with the exclusion of Hemisaurida. This taxon and Nardorex are Aulopiformes incertae sedis.

Recent origin, active speciation and dispersal for the lichen genus Nephroma (Peltigerales) in Macaronesia

Aim We reconstructed the phylogeny of the lichen genus Nephroma (Peltigerales) to assess the relationships of species endemic to Macaronesia. We estimated dates of divergences to test the hypothesis that the species arose in Macaronesia (neo-endemism) versus the oceanic archipelagos serving as refugia for formerly widespread taxa (palaeo-endemism). Location Cosmopolitan with a special focus on the archipelagos of the Azores, Madeira and the Canary Islands. Methods DNA sequences were obtained from 18 species for three loci and analysed using maximum parsimony, maximum likelihood and Bayesian inferences. Divergence dates were estimated for the internal transcribed spacer (ITS)-based phylogeny using a relaxed molecular clock. Reconstruction of the ancestral geographical range was conducted using the Bayesian 50% majority rule consensus tree under a parsimony method. Results The backbone phylogenetic tree was fully supported, with Nephroma plumbeum as sister to all other species. Four strongly supported clades were detected: the Nephroma helveticum, the N. bellum, the N. laevigatum and the N. parile clades. The latter two share a common ancestor and each includes a widespread Holarctic species (N. laevigatum and N. parile, respectively) and all species endemic to Macaronesia. The data suggest a neo-endemic origin of Macaronesian taxa, a recent range expansion from Macaronesia of both widespread species, a range expansion limited to the Mediteranean Basin and south-western Europe for another taxon, and a long dispersal event that resulted in a speciation event in the western parts of North America. Main conclusions The Macaronesian endemic species belong to two sister clades and originated from a most recent common ancestor (MRCA) shared with one widely distributed taxon, either N. parile or N. laevigatum. Estimates of the mean divergence dates suggest that the endemics originated in the archipelagos after the rise of the volcanic islands, along with the ancestor to the now widespread species, which probably expanded their range beyond Macaronesia via long-distance dispersal. This study provides the first phylogenetic evidence of Macaronesian neo-endemism in lichenized fungi and provides support for the hypothesis that oceanic islands may serve as a source for the colonization of continents. However, further data are needed to properly assess the alternative hypothesis, namely colonization from western North America.

Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling

We describe a method for estimating species trees that relies on replicated subsampling of large data matrices. One application of this method is phylogeographic research, which has long depended on large datasets that sample intensively from the geographic range of the focal species; these datasets allow systematicists to identify cryptic diversity and understand how contemporary and historical landscape forces influence genetic diversity. However, analyzing any large dataset can be computationally difficult, particularly when newly developed methods for species tree estimation are used. Here we explore the use of replicated subsampling, a potential solution to the problem posed by large datasets, with both a simulation study and an empirical analysis. In the simulations, we sample different numbers of alleles and loci, estimate species trees using STEM, and compare the estimated to the actual species tree. Our results indicate that subsampling three alleles per species for eight loci nearly always results in an accurate species tree topology, even in cases where the species tree was characterized by extremely rapid divergence. Even more modest subsampling effort, for example one allele per species and two loci, was more likely than not (>50%) to identify the correct species tree topology, indicating that in nearly all cases, computing the majority-rule consensus tree from replicated subsampling provides a good estimate of topology. These results were supported by estimating the correct species tree topology and reasonable branch lengths for an empirical 10-locus great ape dataset.

Majority-rule (+) consensus trees

The construction of a consensus tree to summarize the information of a given set of phylogenetic trees is now routinely a part of many studies in systematic biology. One popular method is the majority-rule consensus tree. In this paper we introduce and characterize a new consensus method that refines the majority-rule tree by adding certain compatible clusters satisfying a simple criterion.

Parallelized phylogenetic post-analysis on multi-core architectures

Bioinformatics is experiencing a rapid and overwhelming accumulation of molecular sequence data, predominantly driven by novel wet-lab sequencing techniques. This trend poses scalability challenges for tool developers. In the field of phylogenetic inference (reconstruction of evolutionary trees from molecular sequence data), scalability is becoming an increasingly important issue for operations other than the tree reconstruction itself. In this paper we focus on post-analysis tasks in reconstructing very large trees, specifically the step of building (extended) majority rule consensus trees from a collection of equally plausible trees or a collection of bootstrap replicate trees. To this end we present non-parallel optimizations which establish our implementation as the fastest exact implementation in phylogenetics, and our novel parallelized routines are the first of their kind. Our non-parallel optimizations achieve a performance improvement of factor 50 compared to the previous version of our code and we achieve a maximum speedup of 5.5 on a 8-core Nehalem node for building consensus trees comprising up to 55,000 organisms. We also present a parallel approach for drawing bootstrap support values on a candidate tree, and experimentally assess our approach in order to better understand read-only versus read–write parallel hash table accesses on multi-core systems.