Sum Of Branch Lengths Research Articles

Genetic differentiation among Himalayan and local Mahseer populations

This study of Genetic Differentiation among Himalayan & local Mahseer concerns with a conservation plan is a fundamental part of the hydro projects still in the pipeline. In-situ conservation and gene banking also serve as the best medium for the same. Despite conservation programs, re-examination and revision of these conservation areas to update the number and lists of endangered status are mandatory. Fish samples collected from 8 different waterbodies {Chambal River, Rana Pratap Sagar Dam, Bassi Dam, Kali Sindh River, Parwan River, Badi Lake, Daya Dam, and Madar Tank} representing two major drainage systems (the Bay of Bengal and the Arabian Sea) of India. For the cytochrome oxidase subunit I, a total of 32 sequences was generated, whereas, for the ATPase 6 gene, a total of 66 sequences were generated. Two mitochondrial regions COI and ATPase6 were amplified using the set (Forward & Reverse primer set) of published primers (COI-Fish F-1/Fish R-1. BOLD-IDS was used to test the efficiency of DNA barcoding as a species identification tool using a blind sampling test, the sample selected & sequenced were known only to the submitting individual. Mismatch distributions to evaluate the hypothesis of recent population growth with 99,999 permutations as implemented in ARLEQUIN 3.0.1 was used. This distribution is unimodal in populations that have passed through a recent demographic expansion and are multimodal in stable populations. A DNA sequence of Himalayan Mahseer (Tor tor) was downloaded from NCBI Gene Bank and the sequences generated in the present study were compared (Using MEGA7 Software) with the downloaded sequence. It’s derived that the stocks of Rajasthan Mahseer are quite distinct from the Himalayan stocks. The minimum genetic (116.06) distance was noticed for both Daya dam and Madar Tank and the highest (125.35) was for Bassi Dam. The evolutionary history was inferred using the Minimum Evolution method. The optimal tree with the sum of branch length 123.79668059. The significantly higher genetic distance between Rajasthan and Himalayan stocks could be due to geographic location and mainly isolated aquatic resources. Similar findings have also been reported by earlier workers.

Molecular Characterization of Trichoderma spp. Isolates by Internal Transcribed Spacer (ITS) Region Sequencing Technique and its Use as a Biocontrol Agent

Objective: In the present investigation, Trichoderma spp., isolated from rhizospheric soil, has been identified by Internal Transcribed Spacer (ITS) region sequencing technique and its antagonistic activity was evaluated against A. niger. Methods: The sequencing analysis was done with its ITS1 region of the rRNA gene. Using the ITS1 amplified products for all isolated fungi, a bi-directional DNA sequencing was done with high quality bases (>98% - 100%). Antagonistic activity was done using dual culture technique. Results: All of the ITS1 nucleotide sequences obtained in this study matched 97% - 100% with the published sequence of Trichoderma spp. The results confirmed the strains as T. asperellum and T. viride with gene bank accession no. (ZTa); MK937669 and (ZTv); MK503705, respectively. When phylogenetic analysis was done for the isolates, the optimal tree with the sum of branch length = 0.69585023 and 0.10077756 for T. asperellum and T. viride, respectively, was observed. There were a total of 678 and 767 for T. asperellum and T. viride positions in the final dataset, respectively. Antagonistic activity was done for the isolated strains of Trichoderma spp. against A. niger, and it was found that T. asperellum showed maximum antagonistic activity (79.33±7.09%). Conclusion: The findings prolong the genome availability for relative investigations pointing out phenotypic variances to compare with Trichoderma genetic diversity. The present investigation delivered the Bases of future studies for better knowledge in understanding the complicated connections of Trichoderma spp. to be used as an effective biocontrol agent.

Molecular Phylogenetic Analysis of Turbo brunneus (R.1798), Cypraea annulus (L.1758) and Babylonia spirata (L.1758)

Over the past few decades, biologists from many disciplines have turned to phylogenetic analyses to interpret variation in biological systems. Phylogenetic relationships with a high potential in the absence of sufficient morphological characters can be resolved by molecular phylogenetic techniques according to coded characters. A number of mtDNA genes have been targeted in marine gastropods for phylogenetic purpose; these include the ribosomal RNA genes 28S, 18S, 16S and 12S, Cytochrome oxidase I (COI) and cytochrome b (Cyt-b). In the present study, SSU rRNA in Turbo brunneus, 18S rRNA in Cypraea annulus and COI gene in Babylonia spirata were successfully amplified and sequenced. Phylogenetic tree of the three species were constructed by using neighbor-joining tree. The optimal tree with the sum of branch length = 1.47445020 was observed. Turbo brunneus was phylogenetically closer to the clade of Cypraea annulus than that of Babylonia spirata. The mitochondrial genomes are informative for mollusc phylogeny, which give a proper phylogenetic approach.

3D multifractal characterization of computed tomography images of soils under different tillage management: Linking multifractal parameters to physical properties

Multifractal analysis of pore images obtained from X-ray computed tomography (CT) was used to characterize the scaling properties of macropores in soils with different managements and their correspondence with macroscopic physical properties related with the soil functions.We used CT images of twenty undisturbed soil columns to examine the multifractal properties of the pores identified by X-ray computed tomography (CT-Porosity). Multifractal spectra successfully describe the scaling of the pore network in all soil columns. The dimensions and scaling parameters of these spectra correlate with macroscopic magnitudes, namely, CT-Porosity, surface area of the pore walls, tortuosity, and bulk density. We also found strong correlations between the singularity spectra and the topological descriptors of the pore network skeleton: total slab voxels, number of branches per path, number of endpoints and sum of branch length, among others. These correlations show that the complexity of the CT-Porosity can be related quantitatively with physical properties, the organization of the pore skeleton and solute transport.

The systematics and biogeography of African tailorbirds (Cisticolidae: Artisornis) with comment on the choice of Bayesian branch-length prior when analyzing heterogeneous data

The Long-billed Tailorbird (Artisornis moreaui), one of Africa’s rarest birds, has a strikingly disjunct distribution, the origin of which has long puzzled biogeographers. One small population (subspecies moreaui) occurs in sub-montane forest in the East Usambara Mountains, a sky island near the coast of northern Tanzania, and another (subspecies sousae) on Serra Jeci in northwestern Mozambique, 950km away. The African Tailorbird, the putative sister-species of Long-billed Tailorbird, also occurs in the East Usambara Mountains and on Serra Jeci, but in addition occupies all the Eastern Arc Mountain forests between these disjunct sites. Stuart (1981) hypothesized that the two tailorbird distributions could be explained by strong ecological competition, with African Tailorbird populations having eliminated Long-billed Tailorbird populations via competitive exclusion in montane forests between the East Usambara and Serra Jeci. If such competitive exclusion explains these geographic distributions, the co-occurrence of the two species in the East Usambara and at Serra Jeci may be ephemeral, with the status of Long-billed Tailorbird especially in doubt. We sought to (1) determine whether the two species of African tailorbirds are indeed sister-species, and (2) test predictions from Stuart’s (1981) competitive exclusion hypothesis using genetic data. Phylogenetic analyses of our seven gene dataset (3 mtDNA, 4 introns; 4784bp) indeed place these two species together in the genus Artisornis. Instead of finding shallow divergence among African Tailorbird populations and deep divergence between Long-billed Tailorbird populations as expected from Stuart’s hypothesis, we recover deep genetic divergence and geographic structure among populations of both tailorbird species. This result is consistent with long-term co-existence of the two species at East Usambara and Serra Jeci. Observational data from both the East Usambara and Serra Jeci suggest that the two species have diverged in use of forest canopy strata. From a conservation standpoint, our results suggest that extinction of the Long-billed Tailorbird as a function of competition with African Tailorbird is highly unlikely, and should not be viewed as imminent. Threats to its survival are instead anthropogenic, and conservation measures should take this into account. Finally, our empirical results suggest that mis-specification of the branch-length prior in Bayesian analyses of mitochondrial DNA data can have a profound effect on the overall tree-length (sum of branch-lengths), whereas the topology and support values tend to remain more stable. In contrast, mis-specification of the branch-length prior had a lesser impact on all aspects of the nuclear-only DNA analyses. This problem may be exacerbated when mitochondrial and nuclear DNA analyses are combined in a total evidence approach.

Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re‐examination of 16 grassland biodiversity studies

Summary Hundreds of experiments have now manipulated species richness (SR) of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether phylogenetic diversity (PD) among species, often quantified as the sum of branch lengths on a molecular phylogeny leading to all species in a community, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function than SR because evolutionary relatedness represents the degree of ecological and functional differentiation among species. But studies to date have provided mixed support for this hypothesis. Here, we reanalyse data from 16 experiments that have manipulated plant SR in grassland ecosystems and examined the impact on above‐ground biomass production over multiple time points. Using a new molecular phylogeny of the plant species used in these experiments, we quantified how the PD of plants impacts average community biomass production as well as the stability of community biomass production through time. Using four complementary analyses, we show that, after statistically controlling for variation in SR, PD (the sum of branches in a molecular phylogenetic tree connecting all species in a community) is neither related to mean community biomass nor to the temporal stability of biomass. These results run counter to past claims. However, after controlling for SR, PD was positively related to variation in community biomass over time due to an increase in the variances of individual species, but this relationship was not strong enough to influence community stability. In contrast to the non‐significant relationships between PD, biomass and stability, our analyses show that SR per se tends to increase the mean biomass production of plant communities, after controlling for PD. The relationship between SR and temporal variation in community biomass was either positive, non‐significant or negative depending on which analysis was used. However, the increases in community biomass with SR, independently of PD, always led to increased stability. These results suggest that PD is no better as a predictor of ecosystem functioning than SR. Synthesis. Our study on grasslands offers a cautionary tale when trying to relate PD to ecosystem functioning suggesting that there may be ecologically important trait and functional variation among species that is not explained by phylogenetic relatedness. Our results fail to support the hypothesis that the conservation of evolutionarily distinct species would be more effective than the conservation of SR as a way to maintain productive and stable communities under changing environmental conditions.

Usutu Virus in Migratory Song Thrushes, Spain

Usutu Virus in Migratory Song Thrushes, Spain

Mudas de Jasminum mesnyi Hance produzidas com substratos à base de lodo de esgoto compostado

Entre as alternativas de disposição de resíduos urbanos está o reaproveitamento do lodo de esgoto no cultivo de plantas ornamentais e florestais. Objetivou-se, com este trabalho, avaliar o crescimento de Jasminum mesnyi (jasmim amarelo) em substratos à base de lodo de esgoto aeróbio compostado com resíduos de podas de árvores trituradas, com diferentes níveis de fertilizante e comparar o desempenho em relação às mudas produzidas em substrato comercial à base de casca de Pinus compostada e vermiculita. Três níveis de fertilizante foram testados (0; 2,7 e 4 g dm-3) em três tipos de substrato: comercial e compostos à base de podas e lodo nas proporções 3:1 (v/v) e 2:1 (v/v). Foram mensuradas as seguintes variáveis: somatória do comprimento dos ramos, altura e biomassa aérea seca (folhas e ramos). O crescimento obtido com o uso dos compostos à base de lodo de esgoto foi superior ao obtido com o substrato comercial para todos os níveis de fertilização. Os maiores crescimentos das mudas de jasmim amarelo foram observados com os compostos nas proporções de 3:1 e 2:1 (v/v) associados à adição de 4 g dm-3 de fertilizante e com o composto na proporção de 2:1 com a adição de 2,7 g dm-3 de fertilizante.

Robustness of Compound Dirichlet Priors for Bayesian Inference of Branch Lengths

We modified the phylogenetic program MrBayes 3.1.2 to incorporate the compound Dirichlet priors for branch lengths proposed recently by Rannala, Zhu, and Yang (2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.) as a solution to the problem of branch-length overestimation in Bayesian phylogenetic inference. The compound Dirichlet prior specifies a fairly diffuse prior on the tree length (the sum of branch lengths) and uses a Dirichlet distribution to partition the tree length into branch lengths. Six problematic data sets originally analyzed by Brown, Hedtke, Lemmon, and Lemmon (2010. When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates. Syst. Biol. 59:145-161) are reanalyzed using the modified version of MrBayes to investigate properties of Bayesian branch-length estimation using the new priors. While the default exponential priors for branch lengths produced extremely long trees, the compound Dirichlet priors produced posterior estimates that are much closer to the maximum likelihood estimates. Furthermore, the posterior tree lengths were quite robust to changes in the parameter values in the compound Dirichlet priors, for example, when the prior mean of tree length changed over several orders of magnitude. Our results suggest that the compound Dirichlet priors may be useful for correcting branch-length overestimation in phylogenetic analyses of empirical data sets.

Tail Paradox, Partial Identifiability, and Influential Priors in Bayesian Branch Length Inference

Recent studies have observed that Bayesian analyses of sequence data sets using the program MrBayes sometimes generate extremely large branch lengths, with posterior credibility intervals for the tree length (sum of branch lengths) excluding the maximum likelihood estimates. Suggested explanations for this phenomenon include the existence of multiple local peaks in the posterior, lack of convergence of the chain in the tail of the posterior, mixing problems, and misspecified priors on branch lengths. Here, we analyze the behavior of Bayesian Markov chain Monte Carlo algorithms when the chain is in the tail of the posterior distribution and note that all these phenomena can occur. In Bayesian phylogenetics, the likelihood function approaches a constant instead of zero when the branch lengths increase to infinity. The flat tail of the likelihood can cause poor mixing and undue influence of the prior. We suggest that the main cause of the extreme branch length estimates produced in many Bayesian analyses is the poor choice of a default prior on branch lengths in current Bayesian phylogenetic programs. The default prior in MrBayes assigns independent and identical distributions to branch lengths, imposing strong (and unreasonable) assumptions about the tree length. The problem is exacerbated by the strong correlation between the branch lengths and parameters in models of variable rates among sites or among site partitions. To resolve the problem, we suggest two multivariate priors for the branch lengths (called compound Dirichlet priors) that are fairly diffuse and demonstrate their utility in the special case of branch length estimation on a star phylogeny. Our analysis highlights the need for careful thought in the specification of high-dimensional priors in Bayesian analyses.

Genetic divergence of Octopus vulgaris species in the eastern Mediterranean

Abstract Nucleotide divergence in cytochrome c oxidase subunit I ( COI ) gene of mitochondrial DNA was analyzed to determine interpopulational variation of common octopus ( Octopus vulgaris ) species sampled along eastern Mediterranean. Nucleotide composition and nucleotide pair frequency analyses of 440 individuals representing 11 populations were investigated. Estimation of evolutionary divergence between sequences was conducted using Tamura-Nei model. Considering 440 individuals, 35 (5%) variable sites and an average variation of 1.9% were found between specimens. Highest divergence was found between Med11 and Med04-Med07 populations; with a genetic distance value of 0.039 (3.9%). Estimation of transition/transversion bias ( R ) was made under the Tamura-Nei model and resulted as 2.32. Phylogenetic tree was constructed using four methods: neighbor joining (NJ), minimum evolution (ME), maximum likelihood (ML) and unweighted pair-group method of arithmetic average (UPGMA). Results from clustering patterns of the consensus tree, with the sum of branch length = 0.05189, pointed out a correlation between genetic and geographic distance.

Random local neighbor joining: A new method for reconstructing phylogenetic trees

We have developed a new method for reconstructing phylogenetic trees called random local neighbor-joining (RLNJ). Our method is different from the neighbor-joining method (NJ) of Saitou and Nei and affords a more thorough sampling of solution space by randomly searching for local pair of neighbors in each step. Results using the RLNJ method to analyze yeast data show an increasing possibility to get a smaller S value (sum of branch lengths) compared with the NJ method as cases with more taxa are analyzed and many individual runs using the RLNJ method usually generate more than one topology with small S values. Computer simulation shows the fact that the RLNJ method can improve the possibility of recovering correct topology significantly by affording more than one topology. In addition, when using the RLNJ method, computer simulation also shows that the proportion of correct topologies ( P C) will increase as the number of different topologies decreases and as the proportion of “most frequent topology” increases. Thus, the number of different topologies and the proportion of “most frequent topology” can be used as auxiliary criteria to evaluate reliability of a phylogenetic tree.

Unique Solvability of Certain Hybrid Networks from Their Distances

Phylogenetic relationships among taxa have usually been represented by rooted trees in which the leaves correspond to extant taxa and interior vertices correspond to extinct ancestral taxa. Recently, more general graphs than trees have been investigated in order to be able to represent hybridization, lateral gene transfer, and recombination events. A model is presented in which the genome at a vertex is represented by a binary string. In the presence of hybridization and the absence of convergent evolution and homoplasies, the evolution is modeled by an acyclic digraph. It is shown how distances are most naturally related to the vertices rather than to the edges. Indeed, distances are computed in terms of the “originating weights” at vertices. It is shown that some distances may not in fact correspond to the sum of branch lengths on any path in the graph. In typical applications, direct measurements can be made only on the leaves, including the root. A study is made of how to infer the originating weights at interior vertices from such information.

Vasopressin-induced neurotrophism in cultured hippocampal neurons via V1 receptor activation.

Structural enhancement of nerve cell morphology has been postulated to be an integral step in the cellular process leading to information storage in the nervous system. To investigate this postulate, we determined whether vasopressin (AVP), a neural peptide that can enhance memory function, would enhance the cytoarchitectural features of hippocampal neurons in culture. Results of these studies demonstrated that in the presence of serum, vasopressin (1 microM), induced a significant increase in the number of neurites, in neuritic length, and in neurite diameter following 48 h of exposure. Morphological complexity was also enhanced following vasopressin exposure as indicated by a significant increase in the number of filopodia/branches, in the sum of branch lengths, and in the number of branch bifurcation points. The number of microspikes decorating neuritic branches was also significantly increased following vasopressin exposure. To determine whether the neurotrophic effect of vasopressin was dependent upon factors present in serum, hippocampal nerve cells were cultured in serum-free media and exposed to 100-1000 nM AVP. Results of these studies demonstrated that in the absence of serum, AVP induced significant enhancement of hippocampal nerve cell growth and that the minimally effective concentration was reduced from 1 microM, as required in the presence serum, to 100 nM. In addition, the time required for a significant increase in nerve cell growth to become apparent decreased from 48 to 24 h. These results demonstrate that AVP-induced neurotrophism is not dependent upon unidentified factors in serum. AVP-induced neurotrophism was found to be mediated by V1 receptor activation. Significant enhancement of nerve cell growth occurred following exposure to V1 receptor agonist (100-1000 nM), whereas exposure to V2 receptor agonist (100-1000 nM) did not increase any of the morphological parameters measured. Considered together, these data indicate that vasopressin can exert a significant neurotrophic effect upon hippocampal nerve cells in culture. Moreover, AVP-induced neurotrophism is a direct effect and not dependent upon unidentified factors present in serum. Enhancement of hippocampal nerve cell growth occurred in the presence of a specific V1 receptor agonist and not following exposure to a V2 agonist, suggesting that activation of the phosphatidyl inositol pathway via V1 receptor activation mediates AVP-induced neurotrophism. Results of these studies are discussed with respect to their implications for understanding vasopressin involvement during neural development and induction of cytoarchitectural modifications associated with memory formation.

Implications of Minimal Length Trees

Fitch, W. M. and T. F. Smith (Department of Physiological Chemistry, University of Wisconsin, Madison, Wisconsin 53706 and Department of Physics, Northern Michigan University, Marquette, Michigan 49855) 1982. Implications of minimal length trees. Syst. Zool., 31:68-75.-Trees with branch length assignments may be constrained so that the sum of branches connecting any two labelled tips of the tree is at least as large as a previously observed distance value. When the sum of all branch lengths is minimized under this constraint, one has a minimal length tree. Two conditions regarding minimal length trees, one proved necessary and the other conjectured to be sufficient, are presented. They provide. simple tests of minimality and raise problems in the interpretation of the individual branch values. [Minimal trees; Hamiltonian circuits; evolutionary rates; maximum parsimony.] One of the commonly employed criteria in systematics has been the minimization of the length of trees constructed from distance or dissimilarity data. This criterion is but one of a more general class in which hierarchical clusterings are evaluated by some objective function on the dissimilarity data. These objective functions have included statistical measures such as Chi-squared or the sum of deviations between the tree implied distances and the measured distances as well as various correlation coefficients between the tree-implied relations and the measured values. The popularity of minimizing the sum of branch lengths as an objective function arises from two considerations. The first is its conceptual simplicity, the fact that one is minimizing over an understood model parameter, such as the number of genetic fixation events. The second is that there have been reasonable, if not compelling, epistemological arguments put forward (Farris, 1978; Fitch, 1971) including the recognition that the amount of historical change cannot be less than the amount required to account for observed differences. Unfortunately, there are no proven, mathematically efficient methods for generating both the tree topology and the minimal sum of its branch lengths given no other data than the dissimilarity measures. Note the existence of two independent but interrelated problems. One is to determine the minimal tree length given a specific tree topology. Two is to determine which tree topology gives the lowest minimum. The best that can currently be done rigorously is to assign the minimum branch lengths for a tree of given branching topology using Linear Programming (Waterman et al., 1977). Yet even here there is the problem of practical computer time limitations which generally restrict the Linear Programming to trees of less than 30 terminal taxa. There are, of course, various heuristic algorithms for trying to find the tree of minimal length directly from a set of inter-taxa distances, the most commonly employed being the Wagner distance algorithm (Farris, 1972). In this study, we examine the properties of a tree that is of minimal length given the branching topology (problem one above). Two conditions for minimal length (one of which is also conjectured to be sufficient) are proven necessary and discussed. These properties thus may be used to test a claim of the minimality of any tree. Because of the widespread use and debate surrounding the minimal length criterion, we have carefully stated both our definitions and theorems. This has been done with the minimum of mathematical jargon but with every attempt at maxi-