Minimum Evolution Research Articles

Phylogenetic Relationships of Flounders from the Family Pleuronectidae (Ostichties: Pleuronectiformes) Based on 16S rRNA Gene

The systematics and phylogeny of flatfish is investigated on the basis of an incomplete nucleotide sequence of 16S rRNA and the complete Co-1 and Cyt-b sequences. In total 62 specimens of 14 species of our own collections were submitted to the GenBank/BOLD repositories and studied. Four types of gene trees were reconstructed: Bayesian (BA), maximum likelihood (ML), minimum evolution (ME), and neighbor joining (NJ). These trees showed basically similar topology. Two separate branches on the trees support the previously identified subfamilies Hippoglossoidinae and Pleuronectinae with the monophyletic status of these taxa. The subfamily Pleuronectinae can be considered monophyletic if the tribe Microstomini is excluded from it and genus Lepidopsetta is moved into the tribe Pleuronectini. Three sets of nucleotide sequences were formed and independently studied. One set included all the obtained 16S rRNA gene sequences (291 bp), the second set included a sample of longer 16S rRNA sequences (617 bp), and the third set consisted of three gene sequences: 16S rRNA, Co-1, and Cyt-b (2926 bp). All three data sets gave a similar phylogenetic signal, which is consistent with the traditional concept of the taxonomy of the Pleuronectiformes order; however, the second and third sets provided better resolution of topology.

Phylotranscriptomic analysis of Dillenia indica L. (Dilleniales, Dilleniaceae) and its systematics implication.

The recent massive development in the next-generation sequencing platforms and bioinformatics tools including cloud based computing have proven extremely useful in understanding the deeper-level phylogenetic relationships of angiosperms. The present phylotranscriptomic analyses address the poorly known evolutionary relationships of the order Dilleniales to order of the other angiosperms using the minimum evolution method. The analyses revealed the nesting of the representative taxon of Dilleniales in the MPT but distinct from the representative of the order Santalales, Caryophyllales, Asterales, Cornales, Ericales, Lamiales, Saxifragales, Fabales, Malvales, Vitales and Berberidopsidales.

Molecular characterization of Indian species of the genus Cornudiscoides Kulkarni, 1969 (Monogenoidea: Dactylogyridae)

Molecular characterization and phylogenetic study based on partial sequences of 28S and 18S ribosomal DNA (rDNA) of sixteen Indian species of the genus Cornudiscoides (Monogenoidea: Dactylogyridae) were conducted to decode the genetic relationship between them and with other members of the family Dactylogyridae. Blastn searches disclosed the significant similarity among the species of the Cornudiscoides for large ribosomal subunits as well as for small ribosomal subunit showing genetic relatedness. The phylogenetic tree using neighbour-joining (NJ) and minimum evolution (ME) methods for 28S ribosomal subunit depicted that all Cornudiscoides species clustering in a single clade and forming sister clade with other members of the family Dactylogyridae and similar results were obtained from 18S ribosomal subunit. Thus, the present study demonstrated that both 28S and 18S ribosomal subunits are very helpful in discriminating Cornudiscoides species (intra or interspecific variation) and in the establishment of the evolutionary relationship among them.

Politopos en filogenética

We introduce mathematical notions used in phylogenetics and three sorts of phylogenetics polytopes. The Tight span and the Lipschitz polytope are both associated to finite metric spaces and can be connected to distance-preserving embeddings, while the balanced minimum evolution (BME) polytope is associated to natural numbers.

On the approximability of the fixed-tree balanced minimum evolution problem.

The Fixed-Tree BMEP (FT-BMEP) is a special case of the Balanced Minimum Evolution Problem (BMEP) that consists of finding the assignment of a set of n taxa to the n leaves of a given unrooted binary tree so as to minimize the BMEP objective function. Deciding the computational complexity of the FT-BMEP has been an open problem for almost a decade. Here, we show that a few modifications to Fiorini and Joret’s proof of the mathcal {NP}-hardness of the BMEP suffice to prove the general mathcal {NP}-hardness of the FT-BMEP as well as its strong inapproximability.

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.

Transferability of wheat SSR markers for determination of genetic diversity and relationships of barley varieties

Simple sequence repeat (SSR) markers are simple PCR-based co-dominant markers, which are highly polymorphic and informative due to the number and frequency of alleles, and thus they are most utilized among the molecular markers. However, the development of SSR markers is costly and time-consuming. Cross-species transferability of SSRs allows the SSRs isolated from one species to apply on a closely related species, which increases the utility of previously isolated SSRs. This study demonstrated the cross-species transferability of 196 SSR primer pairs of wheat in genetic diversity analysis of 40 varieties of barley (Hordeum vulgare L.). Of the 196 SSR primer pairs assayed, 59 (30.1%) showed transferability. Of the 59 primer pairs, 21 pairs were polymorphic with the polymorphism information content ranging from 0.19 to 0.70. The number of alleles detected at each locus ranged from one to seven with an average of 3.57. Cluster analysis using the Minimum Evolution algorithm and the coefficient of Number of Differences assigned the genotypes into five groups.

Genetic Diversity and Phylogenetic Relationship in Four Channid Species Based on Sequence Variations in the Mitochondrial Cytochrome B Gene

This study was undertaken to determine the genetic variability and phylogenetic relationship of four channid species (Channa punctatus, C. marulius, C. striatus and C. gachua) from the family Channidae, using mitochondrial cytochrome b gene. A 309 bp segment of the cytochrome b gene was sequenced and analysed for intra-specific and inter-specific sequence variations. Channa marulius has the highest genetic similarity (98.55%) while C. gachua with minimum overall similarity (94.78%) is displaying the highest genetic variability. The maximum inter-specific similarity was observed between C. marulius and C. striatus (84.15%), hence phylogenetically more akin to each other and grouped into the same clade. Channa gachua and C. striatus are found most distantly related to the lowest inter-specific similarity of 77.58%. Phylogeny reconstruction using UPGMA, Minimum Evolution and Neighbour Joining methods generated a similar tree. Intra-specifically, C. punctatus and C. marulius showing a considerably greater degree of similarity suggest a tendency of their genome homogenization which makes these species vulnerable to environmental stresses. The data suggests that urgent steps need to be taken to conserve C. punctatus and C. marulius by initiating specific conservation strategies and suitable breeding programs to enhance their genome heterogeneity which may make these species hardy to withstand environmental vagaries.

Dissecting molecular evolutionary relationship of Krameriaceae inferred from phylotranscriptomic analysis

The systematic relationships of Krameriaceae have changed considerably. The phylotranscriptomic data sets provide highly informative data for resolving deeper‐level phylogenetic relationships. The phylotranscriptomic analyses to infer evolutionary relationships of Krameriaceae in the order Zygophyllales using the Minimum Evolution, Maximum Parsimony and Maximum Likelihood methods recovered similar topology and taxon proximity. Under the Zygophyllales clade, Krameria lanceolata Torr. of the family Krameriaceae nested with Tribulus eichlerianus K.L. Wilson and Larrea tridentata (Sessé & Moc. ex DC.) Coville belonging to the family Zygophyllaceae with strong nodal support. The phylotranscriptomic analyses suggest that the family Krameriaceae is sister to Zygophyllaceae.
 Bangladesh J. Plant Taxon. 27(2): 427-433, 2020 (December)

Evaluation of Genetic Diversity by DNA Barcoding of Local Lotus Populations from Thua Thien Hue Province

Background: DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus Nelumbo. Methods: Three chloroplast DNA regions (rbcL, matK, trnH-psbA) were tested for their suitability as DNA barcoding regions of thirty three lotus samples which were collected in Thua Thien Hue province, Vietnam. Universal primers were used and sequenced products were analyzed using Minimum Evolution method in the MEGA 7.0 program.Result: We did not observe high variability in nucleotide sequences within the rbcL region (0.135%). White Nelumbo, while, the most encoding matK (8.013%) and variable trnH-psbA (with different number of repeating regions TAAAA) intergenic regions was the most useful for Nelumbo barcoding. Individual application of the studied regions did not provide the expected results. None of the regions used in the study allowed the division of white and pink lotus varieties of N. nucifera specie according to the adopted classification of the genus Nelumbo. The results confirm that the use of matK, rbcL and trnH-psbA or combine all three regions together is insufficient for DNA barcoding in white and pink lotus varieties of N. nucifera specie and better discrimination within the genus Nelumbo. Our results also indicate the necessity of using a different region. All of the new sequences have been deposited in GeneBank under the following accession numbers: rbcL (MN011708 to MN068956); matK (MN011719 to MN068978) and trnH-psbA (MN011730 to MN086252).

Role of interfacial adhesion on minimum wear particle size and roughness evolution.

Adhesion between two bodies is a key parameter in wear processes. At the macroscale, strong adhesive bonds are known to lead to high wear rates, as observed in clean metal-on-metal contact. Reducing the strength of the interfacial adhesion is then desirable, and techniques such as lubrication and surface passivation are employed to this end. Still, little is known about the influence of adhesion on the microscopic processes of wear. In particular, the effects of interfacial adhesion on the wear particle size and on the surface roughness evolution are not clear and are therefore addressed here by means of molecular dynamics simulations. We show that, at short timescales, the surface morphology and not the interfacial adhesion strength dictates the minimum size of wear particles. However, at longer timescales, adhesion alters the particle motion and thus the wear rate and the surface morphology.

An information theory perspective on the balanced minimum evolution problem

We show that the Balanced Minimum Evolution Problem (BMEP) is a cross-entropy minimization problem. This new perspective both extends the previous interpretations of the BMEP length function described in the literature and enables the identification of an efficiently computable family of lower bounds on the value of the optimal solution to the problem.

Efficient Realization of Unitary Transformation at the Quantum Speed Limit

We numerically investigate the minimum time required to implement a target unitary transformation in a qubit network in which each qubit can be locally controlled. The speed limits are explicitly analyzed for qubit graphs used to represent simple models of a Ising spin chain, or a central spin which describes electron-nuclear spin interactions in NV centers. We study the tightness of the obtained speed limits via comparing with the bound derived by Arenz et al. It is shown that the limits capture the coupling constant present in the graph dependence of the minimum evolution time remarkably well.

Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data.

Characterizing intratumor heterogeneity (ITH) is crucial to understanding cancer development, but it is hampered by limits of available data sources. Bulk DNA sequencing is the most common technology to assess ITH, but involves the analysis of a mixture of many genetically distinct cells in each sample, which must then be computationally deconvolved. Single-cell sequencing is a promising alternative, but its limitations-for example, high noise, difficulty scaling to large populations, technical artifacts, and large data sets-have so far made it impractical for studying cohorts of sufficient size to identify statistically robust features of tumor evolution. We have developed strategies for deconvolution and tumor phylogenetics combining limited amounts of bulk and single-cell data to gain some advantages of single-cell resolution with much lower cost, with specific focus on deconvolving genomic copy number data. We developed a mixed membership model for clonal deconvolution via non-negative matrix factorization balancing deconvolution quality with similarity to single-cell samples via an associated efficient coordinate descent algorithm. We then improve on that algorithm by integrating deconvolution with clonal phylogeny inference, using a mixed integer linear programming model to incorporate a minimum evolution phylogenetic tree cost in the problem objective. We demonstrate the effectiveness of these methods on semisimulated data of known ground truth, showing improved deconvolution accuracy relative to bulk data alone.

DNA barcoding of black cherry aphid Myzus cerasi (Fabricus, 1775) (Hemiptera: Aphididae) populations collected from Prunus avium and Prunus cerasus

Sequences of the mitochondrial cytochrome oxidase I (COI) gene of one Greek and 25 Turkish Myzus cerasi (Fabricus) (Hemiptera: Aphididae) populations collected from Prunus avium and Prunus cerasus were analyzed. The partial coding region of COI studied is 605 bp for all the populations, from which 565 nucleotides were conserved, 40 were variable, 37 were singleton, and 3 were parsimony-informative. Four haplotypes were identified based on nucleotide substitutions and the mean of intraspecific divergence was calculated to be 0.3%. Phylogenetic trees were constructed using maximum likelihood, neighbor joining, and minimum evolution. Myzus persicae (Sulzer) and Myzus borealis Ossiannilson were included as outgroups. The population of M. cerasi from Isparta diverged from the rest of the groups and formed a clade (Haplotype B) with Myzus borealis. The rest of the haplotype diversity included Haplotype A and Haplotype C with individuals characterized as Myzus cerasi pruniavium and Haplotype D with Myzus cerasi cerasi. M. cerasi diverged into two subspecies and it must be reevaluated whether this pest is monophagous or oligophagous in terms of plant type dependence. Further studies will be required for a complete barcoding and host-specific status of black cherry aphid.

On the Balanced Minimum Evolution polytope

Recent advances on the polyhedral combinatorics of the Balanced Minimum Evolution Problem (BMEP) enabled the characterization of a number of facets of its convex hull (also referred to as the BMEP polytope) as well as the discovery of connections between this polytope and the permutoassociahedron. In this article, we extend these studies, by presenting new results concerning some fundamental characteristics of the BMEP polytope, new facet-defining inequalities in the case of six or more taxa, a number of valid inequalities, and a polynomial time oracle to recognize its vertices. Our aim is to broaden understanding of the polyhedral combinatorics of the BMEP with a view to developing new and more effective exact solution algorithms.

Level-1 phylogenetic networks and their balanced minimum evolution polytopes.

Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional over an appropriate polytope. Here we present polytopes that allow a similar linear programming approach to finding phylogenetic networks. We investigate a two-parameter family of polytopes that arise from phylogenetic networks, and which specialize to the Balanced Minimum Evolution polytopes as well as the Symmetric Travelling Salesman polytopes. We show that the vertices correspond to certain level-1 phylogenetic networks, and that there are facets or faces for every split. We also describe lower bound faces and a family of faces for every dimension.

The molecular phylogenetic of payangga (G. margaritacea), manggabai (G. giuris) and hulu’u from Limboto Lake based on cytochrome B sequences

Payangga (G. margaritacea), manggabai (G. giuris), and hulu’u are native fishes that live in Limboto Lake, Gorontalo. The aim of this research was to describe the molecular phylogenetic of payangga (G. margaritacea), manggabai (G. giuris), and hulu’u based on cytochrome b sequences. The phylogenetic three was reconstructed using MEGA 6.0 with Neighbour Joining (NJ) and Minimum Evolution (ME) methods. The result indicated that hulu’u was included in the same cluster with three comparable species, namely P. microps, P. minutus, and C. chanos, while G. giuris belongs to the same cluster as G. margaritacea.

Mitochondrial genes and nuclear gene variation among seven species of the genus Lisarda of subfamily Salyavatinae (Heteroptera: Reduviidae: Salyavatinae)

The sequence of three mitochondrial genes viz., 16S rRNA, 28S rRNA and COII of seven Lisarda Stål species were downloaded from the GenBank and were subjected to phylogenetic analyses to understand the intrageneric and intraspecific variations and the role of geographical isolation on speciation using CLUSTAL W in MEGA version 10.0. This analysis includes seven species of Lisarda such as Lisarda annularis (Walker), Lisarda conspersa (Walker), Lisarda crudelis (Stål), Lisarda inornata (Walker), Lisarda longispina Distant, Lisarda rhypara Stål and Lisarda schweinfurthi Reuter. The pair wise genetic distances were calculated and phylograms were constructed using maximum likelihood, neighbor-joining, minimum evolution, UPGMA and maximum parsimony methods. These preliminary analyses not only demarcated the seven species of Lisarda are revealed phylogenetic relationships and the role of geographical isolation on speciation.

Phylogeny of certain members of Hyrcanus group (Diptera: Culicidae) in China based on mitochondrial genome fragments

BackgroundSpecies of the Anopheles hyrcanus group are widely distributed in Palearctic and Oriental regions and some of them are important malaria vectors. The cryptic species of An. hyrcanus group was almost impossible to identify based only on their morphology. The phylogenetic relationship of An. hyrcanus group was also not clear.MethodsFive members of An. hyrcanus group were identified by rDNA ITS2 sequencing as An. yatsushiroensis, An. belenrae, An. kleini, An. lesteri and An. sineroides. The mitochondrial genome fragments were sequenced and annotated using the mitochondrial genome of An. sinensis as reference. Based on the four segments and Joint Data sequences of these species, and other four anopheline species downloaded from GenBank, intraspecific as well as interspecific genetic distances were calculated and the phylogenetic trees were reconstructed by the methods of neighbor joining, maximum parsimony, minimum evolution and maximum likelihood.FindingsFour parts of mitochondrial genomes, which were partial fragments COI + tRNA + COII (F5), ATP6 + COIII(F7 + F8), ND1(F19) and lrRNA (F21), were obtained. All fragments were connected as one sequence (referred as Joint Data), which had a total length of 3393 bp. All fragment sequences were highly conservative within species, with the maximum p distance (0.026) calculated by F19 of An. belenrae. The pairwise interspecific p distance calculated by each fragment showed minor or even no difference among An. sinensis, An. kleini and An. belenrae. However, interspecific p distances calculated by the Joint Data sequence ranged from 0.004 (An. belenrae vs An. kleini) to 0.089 (An. sineroides vs An. minimus), and the p distances of the six members of An. hyrcanus group were all less than 0.029. The phylogenetic tree showed two major clades: all subgenus Anopheles species (including six members of An. hyrcanus group, An. atroparvus and An. quadrimaculatus A) and subgenus Cellia (including An. dirus and An. minimus). The An. hyrcanus group was divided into two clusters as ((An. lesteri, An. sineroides) An. yatsushiroensis) and ((An. belenrae, An. sinensis) An. kleini)).ConclusionsThe An. hyrcanus group in this study could be divided into two clusters, in one of which An. belenrae, An. sinensis and An. kleini were most closely related. More molecular markers would make greater contribution to phylogenetic analysis.