Consensus Phylogenetic Tree Research Articles

First isolation of Rickettsia amblyommatis from Amblyomma mixtum in Colombia

BackgroundRickettsiae are obligate intracellular Gram-negative bacteria that are the causative agent of rickettsioses and are spread to vertebrate hosts by arthropods. There are no previous reports of isolation of Rickettsia amblyommatis for Colombia.MethodsA convenience sampling was executed in three departments in Colombia for direct collection of adult ticks on domestic animals or over vegetation. Ticks were screened for the presence of Rickettsia spp. by real-time polymerase chain reaction (qPCR) amplifying the citrate synthase gene (gltA), and the positive sample was processed for isolation and further molecular characterization by conventional PCR. The absolute and relative frequencies were calculated for several tick species variables. All products from conventional PCR were further purified and sequenced by the Sanger technique. Representative sequences of 18 Rickettsia species were downloaded from GenBank. Consensus phylogenetic trees were constructed for the gltA, ompB, ompA, and htrA genes with 1000 replicates, calculating bootstrap values through the maximum likelihood method and the generalized time reversible substitution model in the MEGA 7.0 software program.ResultsOne female Amblyomma mixtum collected on vegetation was amplified by qPCR (gltA), indicating a frequency of 1.6% (1/61) for Rickettsia spp. infection. Sequence analysis of a rickettsial isolate from this tick in BLASTn showed 100% identity with gltA (340 base pairs [bp]), 99.87% for ompB (782 bp), 98.99% for htrA (497 bp), and 100% for ompA (488 bp) to R. amblyommatis. Concatenated phylogenetic analysis confirmed these findings indicating that the isolate is grouped with other sequences of Amblyomma cajennense complex from Panama and Brazil within the R. amblyommatis clade.ConclusionsThis paper describes the isolation and early molecular identification of a R. amblyommatis strain from A. mixtum in Colombia.Graphical

Phylogenetic and functional signal in prezygapophyseal articular facet shape of the first post‐transitional vertebra in anthropoids

AbstractObjectivesPrevious studies of the prezygapophyseal articular facet (PAF) of the thoracolumbar vertebrae in primates have suggested that the morphology of this feature reflects relative mobility of the lower back, and therefore corresponds to locomotor behavior. Specifically, these studies suggest that the PAF morphology found in cercopithecoids reflects greater mobility of the lower back compared to a stiffer lower back adapted for forelimb‐dominated suspensory behaviors in hominoids. In this study, we sought to re‐examine this question in terms of both locomotor behavior and phylogenetic signal in a broad sample of anthropoid taxa.Materials and MethodsThe study sample consisted of 291 first post‐transitional vertebrae of wild‐caught individuals representing 27 extant anthropoid species (16 genera). Vertebrae were 3D scanned, and 19 landmarks were digitized. PAF shape was tested for the presence of a phylogenetic signal using the multivariate version of the K‐statistic (Kmult), and a chronometric consensus phylogenetic tree was mapped onto the major axes of shape space using species means to produce a phylomorphospace.ResultsResults showed that phylogenetic signal is statistically significant in PAF shape (Kmult = 0.3; p < 0.0001), and phylogenetic separation is apparent in the phylomorphospace, with some exceptions. However, certain aspects of PAF shape also appear to be associated with locomotor behavior within major taxonomic groups, such as hominoids and platyrrhines.DiscussionOur results suggest that both phylogenetic relatedness and function may contribute to PAF shape variation in anthropoids.

New Insights into Interspecific Hybridization in Lemna L. Sect. Lemna (Lemnaceae Martinov).

Duckweeds have been increasingly studied in recent years, both as model plants and in view of their potential applications as a new crop in a circular bioeconomy perspective. In order to select species and clones with the desired attributes, the correct identification of the species is fundamental. Molecular methods have recently provided a more solid base for taxonomy and yielded a consensus phylogenetic tree, although some points remain to be elucidated. The duckweed genus Lemna L. comprises twelve species, grouped in four sections, which include very similar sister species. The least taxonomically resolved is sect. Lemna, presenting difficulties in species delimitation using morphological and even barcoding molecular markers. Ambiguous species boundaries between Lemna minor L. and Lemna japonica Landolt have been clarified by Tubulin Based Polymorphism (TBP), with the discovery of interspecific hybrids. In the present work, we extended TBP profiling to a larger number of clones in sect. Lemna, previously classified using only morphological features, in order to test that classification, and to investigate the possible existence of other hybrids in this section. The analysis revealed several misidentifications of clones, in particular among the species L. minor, L. japonica and Lemna gibba L., and identified six putative ‘L. gibba’ clones as interspecific hybrids between L. minor and L. gibba.

An Evolutionary Perspective of the Lipocalin Protein Family.

The protein family of Lipocalins is ubiquitously present throughout the tree of life, with the exception of the phylum Archaea. Phylogenetic relationships of chordate Lipocalins have been proposed in the past based on protein sequence similarities, but their highly divergent primary structures and a shortage of experimental annotations in genome projects have precluded a well-supported hypothesis for their evolution. In this work we propose a novel topology for the phylogenetic tree of chordate Lipocalins, inferred from multiple amino acid sequence alignments. Sixteen jawed vertebrates with fair coverage by genomic sequencing were compared. The selected species span an evolutionary range of ∼400 million years, allowing for a balanced representation of all major vertebrate clades. A consensus phylogenetic tree is proposed following a comparison of sequence-based maximum-likelihood trees and protein structure dendrograms. This new phylogeny suggests an APOD-like common ancestor in early chordates, which gave rise, via whole-genome or tandem duplications, to the six Lipocalins currently present in fish (APOD, RBP4, PTGDS, AMBP, C8G, and APOM). Further gene duplications of APOM and PTGDS resulted in the altogether 15 Lipocalins found in contemporary mammals. Insights into the functional impact of relevant amino acid residues in early diverging Lipocalins are also discussed. These results should foster the experimental exploration of novel functions alongside the identification of new members of the Lipocalin family.

High-Throughput Single-Cell Technology Reveals the Contribution of Horizontal Gene Transfer to Typical Antibiotic Resistance Gene Dissemination in Wastewater Treatment Plants.

The spread of antibiotic resistance genes (ARGs) has gained much attention worldwide, while the contribution of vertical gene transfer (VGT) and horizontal gene transfer (HGT) is still elusive. Here, we improved an emerging high-throughput single-cell-based technology, emulsion, paired isolation, and concatenation polymerase chain reaction (epicPCR), by lengthening the sequence of ARG in the fused ARG-16S rRNA fragments to cover the variance of both ARG and its hosts. The improved epicPCR was applied to track the hosts of a widely detected ARG, sul1 gene, in five urban wastewater treatment plants (UWTPs) during two seasons. The sul1 host bacteria were highly diverse and mostly classified as Proteobacteria and Bacteroidetes. Clear seasonal divergence of α-diversity and interaction networks were present in the host community. The consensus phylogenetic trees of the sul1 gene and their host demonstrated incorrespondence on the whole and regularity on abundant groups, suggesting the important role of both HGT and VGT, respectively. The relative importance of these two ways was further measured; HGT (54%) generally played an equal or even more important role as VGT (46%) in UWTPs. The application of the improved epicPCR technology provides a feasible approach to quantify the relative contributions of VGT and HGT in environmental dissemination of ARGs.

Cyanobacteria and microalgae growing on monuments of UNESCO World Heritage site Champaner Pavagadh, India: biofilms and their exopolysaccharide composition.

The present study investigated the biofilm organisms growing on selected monuments of the Champaner Pavagadh complex (Gujarat, India), which is a UNESCO World Heritage Site. The cyanobacteria and microalgae were isolated from biofilms collected through non-destructive methods. The identification of these biological organisms was done using micro-morphological characters and confirmed by 16S rRNA gene sequencing. The exopolysaccharide of each of the isolated strains was extracted, hydrolysed and analysed by the HPTLC. Six isolated strains representing five cyanobacteria and one microalga belong to the genera Desmonostoc, Nostoc, Leptolyngbya, Chroococcidiopsis and Asterarcys. The relationships between substrates' specificity of these isolated biofilm organisms and those identified globally were evaluated using maximum parsimony analysis to generate a consensus phylogenetic tree. The five strains of cyanobacteria isolated were closely clustered with cyanobacteria belonging to a tropical region. At the generic level, no relationship between the species and substratum specificity was recorded. The exopolysaccharide analysis of the isolated strains revealed the presence of seven monosaccharides. While glucose was present in all the analysed species, the concentration of either fucose or arabinosewas high. The current study presents a novel HPTLC-based method for determination of monosaccharides composition from the extracellular polymeric substances.

Reconstructing ancestral chromosome numbers and inflorescence features in Eleusininae (Poaceae: Chloridoideae: Cynodonteae)

AbstractThe chromosome number in Poaceae has changed widely over 77 Myr of evolution and polyploidization. Chromosome number changes can suggest a high rate of diversification and evolutionary novelties, and such changes can contribute to speciation. Despite this, chromosome numbers alone do not allow the evolutionary history of a group to be traced. Combined phylogenetic and karyological analyses can clarify the evolutionary history of taxa and allow taxonomic relationships and hierarchical levels to be inferred. The subtribe Eleusininae is the largest of the subfamily Chloridoideae. This study aims to reconstruct their chromosome number evolution, for which ChromEvol 2.0 software was used. Haploid chromosome numbers of Eleusininae were retrieved from the literature, and a consensus phylogenetic tree of Eleusininae was reconstructed. It was possible to infer 41 events of chromosome rearrangements along the evolutionary history of Eleusininae, according to the probabilistic model used. Chromosome number evolution in Eleusininae was mainly influenced by polyploidy events. The ancestral basic chromosome number for Eleusininae was p = 6, but the most recent common ancestor showed p2 = 10. In addition, some derived basic chromosome numbers, such as x = 9, arose through dysploidy, whereas x = 20 was generated via polyploidy.

Proteomic similarity of the Littorinid snails in the evolutionary context.

BackgroundThe introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions.MethodsHere we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering—using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson–Foulds distance, the Fowlkes–Mallows index and cophenetic correlation.ResultsOverall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups (“saxatilis” and “obtusata” groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.

Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae)

Notholaenids are an unusual group of ferns that have adapted to, and diversified within, the deserts of Mexico and the southwestern United States. With approximately 40 species, this group is noted for being desiccation-tolerant and having “farina”—powdery exudates of lipophilic flavonoid aglycones—that occur on both the gametophytic and sporophytic phases of their life cycle. The most recent circumscription of notholaenids based on plastid markers surprisingly suggests that several morphological characters, including the expression of farina, are homoplasious. In a striking case of convergence, Notholaena standleyi appears to be distantly related to core Notholaena, with several taxa not before associated with Notholaena nested between them. Such conflicts can be due to morphological homoplasy resulting from adaptive convergence or, alternatively, the plastid phylogeny itself might be misleading, diverging from the true species tree due to incomplete lineage sorting, hybridization, or other factors. In this study, we present a species phylogeny for notholaenid ferns, using four low-copy nuclear loci and concatenated data from three plastid loci. A total of 61 individuals (49 notholaenids and 12 outgroup taxa) were sampled, including 31 out of 37 recognized notholaenid species. The homeologous/allelic nuclear sequences were retrieved using PacBio sequencing and the PURC bioinformatics pipeline. Each dataset was first analyzed individually using maximum likelihood and Bayesian inference, and the species phylogeny was inferred using *BEAST. Although we observed several incongruences between the nuclear and plastid phylogenies, our principal results are broadly congruent with previous inferences based on plastid data. By mapping the presence of farina and their biochemical constitutions on our consensus phylogenetic tree, we confirmed that the characters are indeed homoplastic and have complex evolutionary histories. Hybridization among recognized species of the notholaenid clade appears to be relatively rare compared to that observed in other well-studied fern genera.

PO-334 Distribution of copy number alterations defines clonal populations involved in the evolutionary transition from adenoma-to-carcinoma in colorectal cancer

Introduction Colorectal cancer progresses in a multi-step manner with adenoma being the most well-known precursor lesion. Malignant polyps, which are adenomas containing a focus of adenocarcinoma, are suitable models to study the evolution of colorectal cancer progression. Although the mutations that accrue during the adenoma-to-carcinoma transition have been previously described, the evolutionary dynamics of copy number alterations (CNAs) involved in this malignant transformation have not been fully understood. Material and methods Here, we performed low-pass whole genome sequencing and targeted deep sequencing of the benign and malignant portion of 23 cases. To validate subclonal copy number alterations we performed single-cell FISH analysis using six probes on chromosomes 5, 7, 8, 13, 18, and 20. We applied FISHtrees to reconstruct the phylogenetic tree of 200 single cells from the adenoma and 200 single cells from the adenocarcinoma portion. Results and discussions By inferring a consensus phylogenetic tree from the same lesion, we deciphered a pattern of branched evolution in all samples evaluated. Analysis of FISH data showed that the levels of genomic heterogeneity were highest in malignant polyps compared to non-progressed adenomas, with the adenoma component having a lower degree of chromosomal instability than the adenocarcinoma. Nevertheless, we observed different patterns of clonal evolution including neutral dynamics and punctuated evolution. We estimated which genomic SCNA showed the greatest allelic expansion comparing the carcinoma to the adenoma and defined this expansion as the fitness gain for the alteration. Genomic gains affecting chromosomes 7, 13, and 20 showed the highest fitness values. Interestingly, whole genome duplication, confirmed by image cytometry, appeared to be a decisive step in the transition from adenoma to carcinoma in 35% of the cases. Lastly, in half of the malignant polyps studied the main clone in the carcinoma component was already present in the adenoma, although at a low frequency and only detectable by single cell analysis. Conclusion In conclusion our data suggest that CNAs are early events in colorectal carcinogenesis that can determine the evolutionary transition from adenoma to adenocarcinoma.

Molecular diversity of Scutellonemabradys populations from Benin, based on ITS1 rDNA and COImtDNA

In Benin, yam production continues to face numerous productionconstraints, including yield and quality reduction by Scutellonema bradys. Implementation of efficient managementtechniques against this pest requires an improved understanding, including at themolecular level, of the pest. The current study aimed at identifying the Scutellonema spp. associated with yam in Benin andinvestigating the phylogenetic relationships between populations. Nematodes of thegenus Scutellonema were obtained from tubersexhibiting external dry rot symptoms. DNA was extracted from nematodes belonging to138 populations collected from 49 fields from 29 villages. For 51 of thesepopulations, both the ITS1 and COI regions could be amplified via PCR, sequenced, compared with available sequencesin the NCBI database and were identified as S.bradys. Maximum likelihood was used to construct 60% consensusphylogenetic trees based on 51 sequences. This phylogenetic analysis did not revealany genetic separation between populations by cultivar, village, cropping system norby agroecological zone. Neither could any subgroups within S. bradys be separated, indicating that no subspecies were present.An earlier published species-specific primer set was verified with the DNA of the 51sequences and was considered a reliable and rapid method for S. bradys identification.

Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure.

The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocannabaccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.

Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae.

Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is mitochondrial DNA analysis, which can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We determined the complete mitochondrial genome of a Central European red deer, Cervus elaphus hippelaphus, from Hungary by a next generation sequencing technology. The mitochondrial genome is 16 354 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region, all of which are arranged similar as in other vertebrates. We made phylogenetic analyses with the new sequence and 76 available mitochondrial sequences of Cervidae, using Bos taurus mitochondrial sequence as outgroup. We used 'neighbor joining' and 'maximum likelihood' methods on whole mitochondrial genome sequences; the consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Cervinae and Capreolinae, and five tribes, Cervini, Muntiacini, Alceini, Odocoileini, and Capreolini. The evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; which method could be used broadly in phylogenetic evolutionary analysis of animal taxa.

Delta-like 1 homolog in Capra hircus: molecular characteristics, expression pattern and phylogeny.

To research the molecular characteristics, expression pattern and phylogeny of the Delta-like 1 homolog gene (Dlk1) in goats. Dlk1 transcripts were identified in the Jianyang Da'er goats by reverse-transcription polymerase chain reaction (RT-PCR). Phylogenetic trees were constructed by Bayesian inference and neighbor-joining methods. Quantitative real-time PCR (qPCR), western blotting and in situ hybridization were performed to analyze the expression pattern of Dlk1. Five alternatively transcripts were identified in different tissues and designated as Dlk1-AS1, 2, 3, 4 and 5. Compared with the normal transcript Dlk1-AS1, Dlk1-AS4 and Dlk1-AS5 retained the identical open reading frame (ORF) and encoded proteins with truncated epidermal-growth-factor like repeats of 121 and 83 amino acids, respectively. Using the Bayesian inference method, the consensus phylogenetic tree indicated that caprine Dlk1 had a closer relationship with bovine Dlk1 than with Dlk1 from pigs, humans and mice. qPCR revealed high expression levels of Dlk1 in the kidney (P<0.01). However, mRNA and protein levels presented an inconsistent correlation, possibly because of post-transcriptional regulation. RNA in situ hybridization indicated that Dlk1 mRNA was localized in the interlobular bile duct and alongside the hepatocyte nuclei, in the epithelial cells of proximal and distal convoluted tubules and in the connective region between the mesothelium and myocardium in the heart. The Dlk1 gene in goats produces alternatively spliced transcripts, with specific expression and cellular localization patterns. These findings would lay the foundation for further study.

Transcriptional regulators of GntR family in Streptomyces coelicolor A3(2): analysis in silico and in vivo of YtrA subfamily.

Transcriptional factors of the GntR family regulate numerous physiological and morphological processes in response to the nutrient state of bacterial cells. The number of GntR transcriptional factors in genomes of soil-dwelling actinomycetes is one of the highest among bacteria, reflecting both the large size of their chromosomes and the complex ecological niche that they occupy. However, very little is known about the roles of GntRs in actinomycete biology. Here, we analyzed the genome of model actinomycete, Streptomyces coelicolor A3(2), in an attempt to gain new insights into the function of GntR family. All 56 GntR proteins of M145 strain were classified into FadR, HutC, MocR, YtrA, and DevA subfamilies according to their secondary structure. We then checked for the presence of GntR orthologs in six other sequenced Streptomyces and one Kitasatospora genomes, revealing that 12 GntRs were conserved in all analyzed strains. Genomic analysis of the less studied YtrA type regulators revealed 160 sequences present in 88 members of Coriobacteridae, Rubrobacteridae, and Actinobacteridae subclasses. These proteins form seven dense clusters on the consensus phylogenetic tree and their genes are usually co-located with the genes for transport proteins. Probable operator sites were identified for orthologous groups of Sco0823 and Sco3812 proteins. All S. coelicolor YtrA-like regulatory genes (SCO0823, SCO1728, SCO3812) were analyzed at transcriptional level, knocked out, and introduced on moderate copy number plasmid in M145 strain. Also, gene SCO0824, a part of putative SCO0823 operon, was studied. Results of these experiments are discussed here.

Towards a formal genealogical classification of the Lezgian languages (North Caucasus): testing various phylogenetic methods on lexical data.

A lexicostatistical classification is proposed for 20 languages and dialects of the Lezgian group of the North Caucasian family, based on meticulously compiled 110-item wordlists, published as part of the Global Lexicostatistical Database project. The lexical data have been subsequently analyzed with the aid of the principal phylogenetic methods, both distance-based and character-based: Starling neighbor joining (StarlingNJ), Neighbor joining (NJ), Unweighted pair group method with arithmetic mean (UPGMA), Bayesian Markov chain Monte Carlo (MCMC), Unweighted maximum parsimony (UMP). Cognation indexes within the input matrix were marked by two different algorithms: traditional etymological approach and phonetic similarity, i.e., the automatic method of consonant classes (Levenshtein distances). Due to certain reasons (first of all, high lexicographic quality of the wordlists and a consensus about the Lezgian phylogeny among Caucasologists), the Lezgian database is a perfect testing area for appraisal of phylogenetic methods. For the etymology-based input matrix, all the phylogenetic methods, with the possible exception of UMP, have yielded trees that are sufficiently compatible with each other to generate a consensus phylogenetic tree of the Lezgian lects. The obtained consensus tree agrees with the traditional expert classification as well as some of the previously proposed formal classifications of this linguistic group. Contrary to theoretical expectations, the UMP method has suggested the least plausible tree of all. In the case of the phonetic similarity-based input matrix, the distance-based methods (StarlingNJ, NJ, UPGMA) have produced the trees that are rather close to the consensus etymology-based tree and the traditional expert classification, whereas the character-based methods (Bayesian MCMC, UMP) have yielded less likely topologies.

Transmission clustering among newly diagnosed HIV patients in Chicago, 2008 to 2011: using phylogenetics to expand knowledge of regional HIV transmission patterns.

HIV transmission cluster analyses can inform HIV prevention efforts. We describe the first such assessment for transmission clustering among HIV patients in Chicago. We performed transmission cluster analyses using HIV pol sequences from newly diagnosed patients presenting to Chicago's largest HIV clinic between 2008 and 2011. We compared sequences through progressive pairwise alignment, using neighbor joining to construct an unrooted phylogenetic tree. We defined clusters as >2 sequences among which each sequence had at least 1 partner within a genetic distance of ≤1.5%. We used multivariable regression to examine factors associated with clustering and used geospatial analysis to assess geographic proximity of phylogenetically clustered patients. We compared sequences from 920 patients, median age of 35 years, 75% male, 67% black, 23% Hispanic, and 8% had a rapid plasma reagin titer ≥1:16 concurrent with their HIV diagnosis. We had HIV transmission risk data for 54%; 43% identified as men who have sex with men (MSM). Phylogenetic analysis demonstrated 123 patients (13%) grouped into 26 clusters, the largest having 20 members. In multivariable regression, age <25, black race, MSM status, male gender, higher HIV viral load, and rapid plasma reagin ≥1:16 associated with clustering. We did not observe geographic grouping of genetically clustered patients. Our results demonstrate high rates of HIV transmission clustering, without local geographic foci, among young black MSM in Chicago. Applied prospectively, phylogenetic analyses could guide prevention efforts and help break the cycle of transmission.

Functional and phylogenetic similarity of alien plants to co-occurring natives.

Over the years, several arguments have been proposed to explain the invasibility of a given community based on the properties of the recipient community. Here, I assessed whether the balance between native species' phylogenetic and functional variability determines vulnerability to invasion. I explored this hypothesis using a consensus phylogenetic tree and a database of leaf, height, and seed traits of alien and native species co-occurring over 83 sites worldwide. An analysis of contrasts between aliens and natives indicates that aliens are as phylogenetically close to the incumbent native community as natives are among themselves (aliens are nested within the native community phylogeny), but functionally distinct to the native community (aliens are more functionally distant to the community of native taxa than natives are among themselves). These contrasting trends are consistent for different comparison criteria (comparisons to all natives or to the nearest native) and comparisons both within and across communities, habitats, and continents. Furthermore, aliens are more functionally divergent than the native community and the closest native relative in both phylogenetically poor and rich communities. The phylogenetic similarity and functional distinctiveness of aliens with respect to the incumbent native community may explain why certain species succeed in some communities and not others. This is a step forward in resolving the long-standing debate on the role diversity--both phylogenetic and functional--plays in determining the success of introduced plants.

Nuclear DNA Content Variation in Life History Phases of the Bonnemasoniaceae (Rhodophyta)

Nuclear DNA content in gametophytes and sporophytes or the prostrate phases of the following species of Bonnemaisoniaceae (Asparagopsis armata, Asparagopsis taxiformis, Bonnemaisonia asparagoides, Bonnemaisonia clavata and Bonnemaisonia hamifera) were estimated by image analysis and static microspectrophotometry using the DNA-localizing fluorochrome DAPI (4′, 6-diamidino-2-phenylindole, dilactate) and the chicken erythrocytes standard. These estimates expand on the Kew database of DNA nuclear content. DNA content values for 1C nuclei in the gametophytes (spermatia and vegetative cells) range from 0.5 pg to 0.8 pg, and for 2C nuclei in the sporophytes or the prostrate phases range from 1.15–1.7 pg. Although only the 2C and 4C values were observed in the sporophyte or the prostrate phase, in the vegetative cells of the gametophyte the values oscillated from 1C to 4C, showing the possible start of endopolyploidy. The results confirm the alternation of nuclear phases in these Bonnemaisoniaceae species, in those that have tetrasporogenesis, as well as those that have somatic meiosis. The availability of a consensus phylogenetic tree for Bonnemaisoniaceae has opened the way to determine evolutionary trends in DNA contents. Both the estimated genome sizes and the published chromosome numbers for Bonnemaisoniaceae suggest a narrow range of values consistent with the conservation of an ancestral genome.

SUNPLIN: Simulation with Uncertainty for Phylogenetic Investigations

BackgroundPhylogenetic comparative analyses usually rely on a single consensus phylogenetic tree in order to study evolutionary processes. However, most phylogenetic trees are incomplete with regard to species sampling, which may critically compromise analyses. Some approaches have been proposed to integrate non-molecular phylogenetic information into incomplete molecular phylogenies. An expanded tree approach consists of adding missing species to random locations within their clade. The information contained in the topology of the resulting expanded trees can be captured by the pairwise phylogenetic distance between species and stored in a matrix for further statistical analysis. Thus, the random expansion and processing of multiple phylogenetic trees can be used to estimate the phylogenetic uncertainty through a simulation procedure. Because of the computational burden required, unless this procedure is efficiently implemented, the analyses are of limited applicability.ResultsIn this paper, we present efficient algorithms and implementations for randomly expanding and processing phylogenetic trees so that simulations involved in comparative phylogenetic analysis with uncertainty can be conducted in a reasonable time. We propose algorithms for both randomly expanding trees and calculating distance matrices. We made available the source code, which was written in the C++ language. The code may be used as a standalone program or as a shared object in the R system. The software can also be used as a web service through the link: http://purl.oclc.org/NET/sunplin/.ConclusionWe compare our implementations to similar solutions and show that significant performance gains can be obtained. Our results open up the possibility of accounting for phylogenetic uncertainty in evolutionary and ecological analyses of large datasets.