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At least 19 recordsLinked to original sources

PubMed2026

PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks.

Phylogenetic diversity (PD) plays an important role in biodiversity, conservation, and evolutionary studies by measuring the diversity of a set of taxa based on their phylogenetic relationships. In phylogenetic trees, a subset of k taxa with maximum PD can be found by a simple and efficient greedy algorithm. However, this algorithmic tractability is lost when considering phylogenetic networks, which incorporate reticulate evolutionary events such as hybridization and horizontal gene transfer. To address this challenge, we introduce PaNDA (Phylogenetic Network Diversity Algorithms), the first software package and interactive graphical user-interface for exploring, visualizing, and maximizing diversity in phylogenetic networks. PaNDA includes a novel algorithm to find a subset of k taxa with maximum diversity, running in polynomial time for networks of bounded scanwidth, a measure of tree-likeness of a network that grows slower than the well-known level measure. This algorithm considers the variant of PD on networks in which the branch lengths of all paths from the root to the selected taxa contribute towards their diversity. We demonstrate the scalability of this algorithm on simulated networks, successfully analyzing level-15 networks with up to 200 taxa in seconds. We also provide a proof-of-concept analysis using a phylogenetic network on Xiphophorus species, illustrating how the tool can support diversity studies based on real genomic data. The software is easily installable and freely available at https://github.com/nholtgrefe/panda. Additionally, we extend the definition of PD to semi-directed phylogenetic networks, which are mixed graphs increasingly used in phylogenetic analysis to model uncertainty of the root location. We prove that finding a subset of k taxa with maximum diversity remains NP-hard on semi-directed networks, but do present a polynomial-time algorithm for networks with bounded level.

network↗

PubMed2006

Phylogenetic diversity within seconds.

We consider a (phylogenetic) tree with n labeled leaves, the taxa, and a length for each branch in the tree. For any subset of k taxa, the phylogenetic diversity is defined as the sum of the branch-lengths of the minimal subtree connecting the taxa in the subset. We introduce two time-efficient algorithms (greedy and pruning) to compute a subset of size k with maximal phylogenetic diversity in O(n log k) and O[n + (n-k) log (n-k)] time, respectively. The greedy algorithm is an efficient implementation of the so-called greedy strategy (Steel, 2005; Pardi and Goldman, 2005), whereas the pruning algorithm provides an alternative description of the same problem. Both algorithms compute within seconds a subtree with maximal phylogenetic diversity for trees with 100,000 taxa or more.

Algorithms↗

PubMed2005

Phylogenetic diversity and the greedy algorithm.

Given a phylogenetic tree with leaves labeled by a collection of species, and with weighted edges, the "phylogenetic diversity" of any subset of the species is the sum of the edge weights of the minimal subtree connecting the species. This measure is relevant in biodiversity conservation where one may wish to compare different subsets of species according to how much evolutionary variation they encompass. In this note we show that phylogenetic diversity has an attractive mathematical property that ensures that we can solve the following problem easily by the greedy algorithm: find a subset of the species of any given size k of maximal phylogenetic diversity. We also describe an extension of this result that also allows weights to be assigned to species.

Algorithms↗

PubMedDate not supplied

Phylogenetic diversity of parabasalian symbionts from termites, including the phylogenetic position of Pseudotrypanosoma and Trichonympha.

The phylogenetic diversity of parabasalian flagellates from termite hindguts has been examined by small subunit ribosomal RNA (rRNA) amplification and sequencing. Two species of particular interest, the giant trichomonad Pseudotrypanosoma giganteum and the hypermastigote Trichonympha magna, were isolated from the gut of Porotermes adamsoni by micropipetting, and the rRNA genes from these small populations amplified and sequenced. rRNA genes representing Hypermastigida and the Trichomonadida families Devescovinidae and Trichomonadidae, were also recovered by amplification from whole hindguts of three termites, P. adamsoni, Cryptotermes brevis, and Cryptotermes dudleyi. The parabasalian rRNA genes from C. brevis were found to comprise a unique and extremely heterogeneous lineage with no clear affinities to any known parabasalian rRNAs. In addition, one of the sequences isolated from P. adamsoni was found to be similar to another uncharacterised rRNA gene from Reticulitermes flavipes. The phylogeny of all known parabasalian small subunit rRNAs was examined with these new sequences. We find many taxonomic groups to be supported by rRNA, but not all. We have found the root of parabasalia to be very difficult to discern accurately, but have nevertheless identified several possible positions.

Animals↗

PubMed2002

Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene g20.

In order to characterize the genetic diversity and phylogenetic affiliations of marine cyanophage isolates and natural cyanophage assemblages, oligonucleotide primers CPS1 and CPS8 were designed to specifically amplify ca. 592-bp fragments of the gene for viral capsid assembly protein g20. Phylogenetic analysis of isolated cyanophages revealed that the marine cyanophages were highly diverse yet more closely related to each other than to enteric coliphage T4. Genetically related marine cyanophage isolates were widely distributed without significant geographic segregation (i.e., no correlation between genetic variation and geographic distance). Cloning and sequencing analysis of six natural virus concentrates from estuarine and oligotrophic offshore environments revealed nine phylogenetic groups in a total of 114 different g20 homologs, with up to six clusters and 29 genotypes encountered in a single sample. The composition and structure of natural cyanophage communities in the estuary and open-ocean samples were different from each other, with unique phylogenetic clusters found for each environment. Changes in clonal diversity were also observed from the surface waters to the deep chlorophyll maximum layer in the open ocean. Only three clusters contained known cyanophage isolates, while the identities of the other six clusters remain unknown. Whether or not these unidentified groups are composed of bacteriophages that infect different Synechococcus groups or other closely related cyanobacteria remains to be determined. The high genetic diversity of marine cyanophage assemblages revealed by the g20 sequences suggests that marine viruses can potentially play important roles in regulating microbial genetic diversity.

Bacteriophages↗

PubMed1999

Phylogenetic diversity of termite gut spirochaetes.

A molecular phylogenetic analysis was done of not-yet-cultured spirochaetes inhabiting the gut of the termite, Reticulitermes flavipes (Kollar). Ninety-eight clones of near-full-length spirochaetal 16S rDNA genes were classified by ARDRA pattern and by partial sequencing. All clones grouped within the genus Treponema, and at least 21 new species of Treponema were recognized within R. flavipes alone. Analysis of 190 additional clones from guts of Coptotermes formosanus Shiraki and Zootermopsis angusticollis (Hagen), as well as published data on clones from Cryptotermes domesticus (Haviland), Mastotermes darwiniensis Froggatt, Nasutitermes lujae (Wasmann) and Reticulitermes speratus(Kolbe), revealed a similar level of novel treponemal phylogenetic diversity in these representatives of five of the seven termite families. None of the clones was closely related (i.e. all bore < or = 91% sequence similarity) to any previously recognized treponeme. The data also revealed the existence of two major phylogenetic groups of treponemes: one containing all of the currently known isolates of Treponema and a large number of phylotypes from the human gingival crevice, but only a minority of the termite gut spirochaete clones; another containing the majority of termite spirochaete clones and two Spirochaeta (S. caldaria and S. stenostrepta), which, although free living, group within the genus Treponema on the basis of 16S rRNA sequence. Signature nucleotides that almost perfectly distinguished the latter group, herein referred to as the 'termite cluster', occurred at the following (E. coli numbering) positions: 289-G x C-311; A at 812; and an inserted nucleotide at 1273. The emerging picture is that the long-recognized and striking morphological diversity of termite gut spirochaetes is paralleled by their phylogenetic diversity and may reflect substantial physiological diversity as well.

Animals↗

PubMed1993

Immunoglobulin heavy chain constant and heavy chain variable region genes in phylogenetically diverse species of bony fish.

Genomic DNA from 18 phylogenetically diverse species of bony fish was hybridized with probes specific for the channel catfish immunoglobulin heavy chain constant (CH) gene, as well as with immunoglobulin heavy chain variable (VH) probes specific for five channel catfish VH gene families. The results showed that CH probes strongly hybridized only to genomic fragments from other catfish species. In contrast, restricted DNA from most other species hybridized with at least two channel catfish VH probes. In those species whose DNA hybridized with multiple VH probes, the restriction pattern of hybridizing fragments was probe-dependent. These studies suggest that (1) the CH gene defined in channel catfish appears to share similarity only with CH genes in other catfish species, (2) families of VH genes appear to have diverged in early phylogenetic lineages of teleosts, and (3) VH genes similar to those defined in catfish appear to be widely represented in phylogenetically diverse species of teleosts.

Animals↗

PubMed2005

Activity and phylogenetic diversity of bacterial cells with high and low nucleic acid content and electron transport system activity in an upwelling ecosystem.

We evaluated whether bacteria with higher cell-specific nucleic acid content (HNA) or an active electron transport system, i.e., positive for reduction of 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), were responsible for the bulk of bacterioplankton metabolic activity. We also examined whether the phylogenetic diversity of HNA and CTC-positive cells differed from the diversity of Bacteria with low nucleic acid content (LNA). Bacterial assemblages were sampled both in eutrophic shelf waters and in mesotrophic offshore waters in the Oregon coastal upwelling region. Cytometrically sorted HNA, LNA, and CTC-positive cells were assayed for their cell-specific [3H]leucine incorporation rates. Phylogenetic diversity in sorted non-radioactively labeled samples was assayed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes. Cell-specific rates of leucine incorporation of HNA and CTC-positive cells were on average only slightly greater than the cell-specific rates of LNA cells. HNA cells accounted for most bacterioplankton substrate incorporation due to high abundances, while the low abundances of CTC-positive cells resulted in only a small contribution by these cells to total bacterial activity. The proportion of the total bacterial leucine incorporation attributable to LNA cells was higher in offshore regions than in shelf waters. Sequence data obtained from DGGE bands showed broadly similar phylogenetic diversity across HNA, LNA, and CTC-positive cells, with between-sample and between-region variability in the distribution of phylotypes. Our results suggest that LNA bacteria are not substantially different from HNA bacteria in either cell-specific rates of substrate incorporation or phylogenetic composition and that they can be significant contributors to bacterial metabolism in the sea.

Bacteria↗

PubMed2004

Variation in sulfide tolerance of photosystem II in phylogenetically diverse cyanobacteria from sulfidic habitats.

Physiological and molecular phylogenetic approaches were used to investigate variation among 12 cyanobacterial strains in their tolerance of sulfide, an inhibitor of oxygenic photosynthesis. Cyanobacteria from sulfidic habitats were found to be phylogenetically diverse and exhibited an approximately 50-fold variation in photosystem II performance in the presence of sulfide. Whereas the degree of tolerance was positively correlated with sulfide levels in the environment, a strain's phenotype could not be predicted from the tolerance of its closest relatives. These observations suggest that sulfide tolerance is a dynamic trait primarily shaped by environmental variation. Despite differences in absolute tolerance, similarities among strains in the effects of sulfide on chlorophyll fluorescence induction indicated a common mode of toxicity. Based on similarities with treatments known to disrupt the oxygen-evolving complex, it was concluded that sulfide toxicity resulted from inhibition of the donor side of photosystem II.

Cyanobacteria↗

PubMed2000

Phylogenetic diversity of rhizobial strains nodulating Robinia pseudoacacia L.

Lack of knowledge exists regarding the diversity of rhizobial strains nodulating black locust (Robinia pseudoacacia L.), which is a neophytic tree species widely distributed in Europe. Seventeen rhizobial strains isolated from nodules of black locust at a German location were examined by phenotypic characterization and 16S rDNA analysis. The isolates were classified in nine 16S rDNA genotypes using a set of seven endonucleases. Based on RFLP analysis and sequencing, the strains were shown to belong to the genera Mesorhizobium (76%) and Rhizobium (24%). Five genotypes were identical to the species Mesorhizobium amorphae, Mesorhizobium loti, Mesorhizobium huakuii, Rhizobium leguminosarum and Rhizobium tropici. A strong similarity between the 16S rDNA sequence of another two genotypes and M. amorphae (99.9%) as well as the Mesorhizobium strain R88b (99.8%) was found. The two remaining genotypes were classified in the genus Rhizobium, without a significant relationship at the species level. Comparing isolates nodulating Rob. pseudoacacia and Amorpha fruticosa, a parallel picture of phylogenetic diversity was detected with a range of phylogenetically different rhizobia and M. amorphae dominating. For this study, 18 rhizobial strains which had originally been isolated from a forest in Maryland where black locust is native were additionally analysed. Results revealed seven genotypes all belonging to the genus Mesorhizobium, with four genotypes identical to the isolates from the German sampling location. Whereas the genotype identical to M. amorphae dominated within the strains obtained from the German location, the dominance of a genotype identical to M. huakuii was found among the strains from the native location. Summarizing data from both locations, Rob. pseudoacacia was nodulated with various genomic species, most of which belonged to the genus Mesorhizobium. Concerning phenotypic features such as growth rate, pH tolerance or use of certain carbohydrates, most isolates corresponded to described species and genera. However, there were differences in salt tolerance between these isolates and the corresponding reference strains. Overall, the results demonstrated a high phenotypic and phylogenetic diversity of rhizobial strains nodulating Rob. pseudoacacia. This may be a characteristic of neophytic and other widely spread legumes and may contribute to the success of black locust as a pioneer tree species for the temperate zone.

DNA, Bacterial↗

PubMed1999

Phylogenetic Diversity and Population Densities of Culturable Cellulolytic Soil Bacteria across an Agricultural Encatchment.

> Abstract A typical, small encatchment (catena Bölkendorf) in the moraine, northeast German agricultural landscape Schorfheide-Chorin was studied with respect to summit, midslope, and foot-slope positions at northern and southern slope exposure, respectively, including a central noncultivated kettle hole position (pot hole). Across the sequence of seven distinct sampling positions, soil organic carbon and total nitrogen contents, soil gravimetric water content, and soil microbial biomass displayed maxima at the kettle hole position. Soil pH revealed a decreasing trend at the northern exposed slope and a minimum at the kettle hole position. Against this background, the population density of total culturable bacteria clearly displayed a minimum at the kettle hole position, whereas the population density of carboxymethylcellulose decomposing bacteria was not clearly differentiated in relation to sampling positions. To study the phylogenetic diversity of culturable cellulolytic bacteria, 311 isolates were obtained from the sampling positions across the entire encatchment and examined by restriction analysis of PCR-amplified 16S rDNA. Using the restriction enzyme ScrFI, isolates were classified into 31 pattern groups. Although the ratio of actinomycetes within total isolates ranged from 0.73 to 0.94, only 16 pattern groups originated from actinomycetes, but 15 from other bacteria. At all sampling positions, a dominant pattern group was identified, containing 38 to 65% of total isolates. Two site-specific pattern groups could be identified, representing significant parts of the total population, which were highly specific for the kettle hole (19% of total isolates) and for foot- and midslope positions (15-18% of total isolates), respectively. In general, the composition of cellulolytic isolates across the encatchment displayed differences with respect to slope positions, but was not significantly affected by soil properties. Based on 16S rDNA sequence analysis, isolates of the dominant as well as the specific pattern groups could be assigned to the genus Streptomyces. Furthermore, sequencing of 16S rDNA of isolates of another three pattern groups revealed a high phylogenetic diversity among these isolates, including cellulomonads and bacilli.http://link.springer-ny.com/link/service/journals/00248/bibs/37n4p238.html

Journal Article↗

PubMed1996

Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes speratus.

The phylogenetic diversity of the intestinal microflora of a lower termite, Reticulitermes speratus, was examined by a strategy which does not rely on cultivation of the resident microorganisms. Small-subunit rRNA genes (16S rDNAs) were directly amplified from the mixed-population DNA of the termite gut by the PCR and were clonally isolated. Analysis of partial 16S rDNA sequences showed the existence of well-characterized genera as well as the presence of bacterial species for which no 16S rDNA sequence data are available. Of 55 clones sequenced, 45 were phylogenetically affiliated with four of the major groups of the domain Bacteria: the Proteobacteria, the spirochete group, the Bacteroides group, and the low-G+C-content gram-positive bacteria. Within the Proteobacteria, the 16S rDNA clones showed a close relationship to those of cultivated species of enteric bacteria and sulfate-reducing bacteria, while the 16S rDNA clones in the remaining three groups showed only distant relationships to those of known organisms in these groups. Of the remaining 10 clones, among which 8 clones formed a cluster, there was only very low sequence similarity to known 16S rRNA sequences. None of these clones were affiliated with any of the major groups within the domain Bacteria. The 16S rDNA gene sequence data show that the majority of the intestinal microflora of R. speratus consists of new, uncultured species previously unknown to microbiologists.

Animals↗

PubMed1987

Blood type compatibility of lower vertebrates: phylogenetic diversity in blood transfusion between fish species.

Bidirectional transfusion was investigated using phylogenetically different fish species, including twelve from ten genera. Three different modalities were used: long-lasting persistence when rainbow trout received allogenic erythrocytes, slow rejection when rainbow trout received heterogenic erythrocytes (salmon) and acute rejection after receiving xenogenic erythrocytes (goldfish, carp and Tilapia). Changes were measured in serum using transfused erythrocytes and hemolytic assays. The responses were species specific for large taxonomic fish groups characteristic of their phylogenetic interrelations. Findings concerning the evolution of compatibility of fish blood types, in view of the taxonomy and phylogeny of vertebrates, are interesting since phylogenetic diversity in transfusion demonstrates that erythrocyte types and serum types exist even in lower vertebrates.

Animals↗

PubMed2001

Phylogenetic diversity of a SRB-rich marine biofilm.

This study was conducted to characterize the phylogenetic diversity of a corrosive marine biofilm based on 16S rDNA. Results of phylogenetic analysis indicated that, out of the 112 clones developed, 52 clones (46.4%) were affiliated with two families of sulfate-reducing bacteria: Desulfovibrionaceae and Desulfobacteriaceae. Another 44 clones (39.3%) were affiliated with the Clostridiaceae family of low G+C, gram-positive bacteria. Three clones (2.7%) were closely related to Chlorobium vibrioforme, a green sulfur bacterium.

Base Sequence↗

PubMed2003

Distribution and phylogenetic diversity of the subsurface microbial community in a Japanese epithermal gold mine.

Distribution and phylogenetic diversity of microbial communities in hot, deep underground environments in the Hishikari epithermal gold mine, southern part of Kyushu, Japan, were evaluated using molecular phylogenetic analyses. Samples included drilled cores such as andesitic volcanic rock (0.95-1.78 Ma) and the oceanic sedimentary basement rock of Shimanto-Supergroup (100 Ma), as well as geothermal hot aquifer waters directly collected from two different sites: AW-site (71.5 degrees C, pH 6.19) and XW-site (85.0 degrees C, pH 6.80) at a depth of 350 mbls (meters below land surface). Based on PCR-amplified 16S rRNA gene clone analysis, the microbial communities in the drilled cores and the hot aquifer water from the XW-site consisted largely of the 16S rRNA gene sequences, closely related to the sequences often found in marine environments, while the aquifer water from the AW-site contained 16S rRNA gene sequences representing members of Aquificales, thermophilic methanotrophs within the gamma-subdivision of the Proteobacteria and uncultivated strains within the beta-subdivision of Proteobacteria. The cultivable microbial community detected by enrichment cultivation analysis largely matched that detected by the culture-independent molecular analysis.

Bacteria↗

PubMed1993

Phylogenetic diversity of phytopathogenic mycoplasmalike organisms.

By using specific primers, the 16S rRNA genes of Japanese mycoplasmalike organisms (MLOs) were amplified by polymerase chain reactions from MLO-enriched fractions of plants infected with each of six different MLOs. Each of the polymerase chain reaction fragments (length, 1,370 nucleotides) was directly sequenced in both strands by using 17 oligonucleotide primers. A phylogenetic tree constructed by using the sequence data showed that these Japanese MLOs are phylogenetically diverse microorganisms that fall into three groups, group I (onion yellows, tomato yellows, mulberry dwarf, and paulownia witches' broom MLOs), group II (tsuwabuki witches' broom MLO), and group III (rice yellow dwarf MLO). A high level of sequence homology (99%) between the Oenothera hookeri MLO and the severe strain of the western aster yellows MLO on the one hand and group I MLOs on the other indicates that the O. hookeri MLO and the severe strain of the western aster yellows MLO belong to group I and suggests that these MLOs, isolated from two geographically separated locations, descended from a very similar ancestor. Although group I contains phylogenetically identical MLOs, the organisms are transmitted by diverse insect vectors. The three MLO groups are more closely related to Acholeplasma laidlawii than to Mycoplasma gallisepticum. Thus, although MLOs are phylogenetically diverse, they are evolutionarily distant from other mollicutes. These data, together with other information (including phylogenetic relationships, vector specificity, plant-pathogenic properties, and habitat in plant phloem sieve tubes), suggest that MLOs could be classified into at least three phylogenetic groups (groups I through III).

Acholeplasma↗

PubMed2001

Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes.

The phylogenetic diversity of green nonsulfur bacteria in nine stratified freshwater lakes was investigated. A set of oligonucleotide primers was developed that permitted the selective amplification of 16S rRNA gene sequences of this group. Subsequently, amplification products were separated by denaturing gradient gel electrophoresis (DGGE) and sequenced, which yielded a total of 19 novel sequence types. Ten of the sequences were related to those of different cultivated members of the C hloroflexus assemblage, whereas nine fell into the T78 group of environmental clones. For the latter subgroup of the green nonsulfur bacteria, no molecular isolate from freshwater plankton has been reported so far. Several of the sequence types occurred in more than one lake, indicating that not only relatives of the C hloroflexus assemblage, but also bacteria of the clone T78 group represent indigenous bacteria of nonthermal stratified freshwater ecosystems. Our results indicate that the natural diversity in the phylum of the green nonsulfur bacteria has been significantly underestimated in the past.

Bacteria↗

PubMed2005

Molecular phylogenetic diversity of the bacterial community in the gut of the termite Coptotermes formosanus.

The phylogenetic diversity of the bacterial community in the gut of the termite Coptotermes formosanus was investigated using a 16S rRNA gene clone library constructed by PCR. After screening by restriction fragment length polymorphism (RFLP) analysis, 49 out of 261 clones with unique RFLP patterns were sequenced and phylogenetically analyzed. Many of the clones (94%) were derived from Bacteroidales, Spirochaetes, and low G + C content gram-positive bacteria consisting of Clostridiales, Mycoplasmatales, Bacillales, and Lactobacillales. In addition, a few clones derived from Actinobacteria, Proteobacteria, Planctomycetes, Verrucomicrobia, and the candidate phylum "Synergistes" were also found. The most frequently identified RFLP type, BCf1-03, was assigned to the order Bacteroideales, and it constituted about 70% of the analyzed clones. The phylogenetic analysis revealed that the representative clones found in this study tended to form some clusters with the sequences cloned from the termite gut in several other studies, suggesting the existence of termite-specific bacterial lineages.

Animals↗