scholarly journals Modeling Mito-nuclear Compatibility and Its Role in Species Identification

2020 ◽  
Vol 70 (1) ◽  
pp. 133-144 ◽  
Author(s):  
Débora Princepe ◽  
Marcus A M De Aguiar
Keyword(s):  
Spatial Distribution ◽  
Phylogenetic Tree ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Genetic Material ◽  
Dna Barcode ◽  
Model Parameters ◽  
Uniparental Inheritance ◽  
Speciation Process ◽  
Nuclear Interactions

Abstract Mitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speciation—as suggested by recent observations of coevolution with the nuclear DNA, along with the fact that respiration depends on coordination of genes from both sources. Here, we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the speciation process itself. We simulate the evolution of a population of individuals who carry a recombining nuclear genome and a mitochondrial genome inherited maternally. We compare a null model fitness landscape that lacks any mito-nuclear interaction against a scenario in which interactions influence fitness. Fitness is assigned to individuals according to their mito-nuclear compatibility, which drives the coevolution of the nuclear and mitochondrial genomes. Depending on the model parameters, the population breaks into distinct species and the model output then allows us to analyze the accuracy of mtDNA barcode for species identification. Remarkably, we find that species identification by mtDNA is equally accurate in the presence or absence of mito-nuclear coupling and that the success of the DNA barcode derives mainly from population geographical isolation during speciation. Nevertheless, selection imposed by mito-nuclear compatibility influences the diversification process and leaves signatures in the genetic content and spatial distribution of the populations, in three ways. First, speciation is delayed and the resulting phylogenetic trees are more balanced. Second, clades in the resulting phylogenetic tree correlate more strongly with the spatial distribution of species and clusters of more similar mtDNA’s. Third, there is a substantial increase in the intraspecies mtDNA similarity, decreasing the number of alleles substitutions per locus and promoting the conservation of genetic information. We compare the evolutionary patterns observed in our model to empirical data from copepods (Tigriopus californicus). We find good qualitative agreement in the geographic patterns and the topology of the phylogenetic tree, provided the model includes selection based on mito-nuclear interactions. These results highlight the role of mito-nuclear compatibility in the speciation process and its reconstruction from genetic data.[Mito-nuclear coevolution; mtDNA barcode; parapatry; phylogeny.]

scholarly journals DEVELOPMENT OF SPECIFIC PRIMERS FOR INTER SPECIES PHYLOGENY RELATIONSHIP ON Crocodilian sp

2015 ◽  
Vol 2 (1) ◽  
pp. 301
Author(s):  
Herdhanu Jayanto ◽  
Budi Setiadi Daryono
Keyword(s):  
Phylogenetic Tree ◽  
Species Identification ◽  
Cytochrome B ◽  
Phylogenetic Trees ◽  
Species Level ◽  
False Identification ◽  
Specific Primer ◽  
Specific Primers ◽  
Species Phylogeny ◽  
Bioinformatics Tools

<p>Poaching, trafficking, and illegal product trading are classic activities which frequently faced by Crocodilian group. To overcome, laws need supporting methods for a decision of these all activities which threaten crocodile species. This will require species identification that associated to taxonomy classification. Crocodilian species are very similar in morphology. This may result to a false identification especially when working on incomplete specimen. Currently, twenty-four existing Crocodilian species are continuously revised to improve the precise placement and/or acceptance of certain species on Crocodilian classification. Herein we address this issue using Cytochrome-b. The idea was to obtain genus specific primer from Cytochrome-b and then tested the precision of the designed primers using bioinformatics tools’ Primer-BLAST and CLC sequence Viewer 6. The designed primers showed a highly specificity on species level. The phylogenetic tree constructed by is relatively precise compared to reported phylogenetic trees. These specific primers together with the genus specific primers may give valuable and important support for the effective and efficient identification of Crocodilian group.</p><p><br /><strong>Keywords</strong>: Crocodilian, illegal trading, Cytochrome-b , specific primer, bioinformatic</p>

scholarly journals The screening and identification of DNA barcode sequences for Rehmannia

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hongying Duan ◽  
Wanshen Wang ◽  
Yunpeng Zeng ◽  
Mengmeng Guo ◽  
Yanqing Zhou
Keyword(s):  
Genetic Variation ◽  
Phylogenetic Tree ◽  
Species Identification ◽  
Intraspecific Variation ◽  
Systematic Study ◽  
Dna Barcode ◽  
Barcoding Gap ◽  
Screening And Identification ◽  
Interspecific And Intraspecific Variation ◽  
Interspecific Diversity

AbstractIn this study, ITS, ITS2, matK, rbcL and psbA-trnH in Rehmannia were successfully amplified and sequenced, but some ITS sequences need to be proofread according to ITS2 sequences. Compared with rbcL, matK and psbA-trnH, ITS and ITS2 had higher mutation rate and more information sites, and ITS2 had higher interspecific diversity and lower intraspecific variation in Rehmannia, but the interspecific genetic variation of rbcL and matK was lower. Furthermore, the obvious barcoding gap was found in psbA-trnH or ITS2 + psbA-trnH, and the overlap between interspecific and intraspecific variation of ITS, ITS2 or matK was less. In addition, the phylogenetic tree based on ITS or ITS2 indicated that R. glutinosa, R. chingii or R. henryi with obvious monophyly could be successfully identified, but R. piasezkii and R. elata were clustered into one branch, R. solanifolia could not be distinguished from R. glutinosa, and R. chingii was closer to R. henryi. In phylogenetic tree based on psbA-trnH or ITS2 + psbA-trnH, cultivars and wild varieties of R. glutinosa could be distinguished, were clearly separated from other Rehmannia species, and cultivars or wild varieties of R. glutinosa could be also distinguished by matK. Taken together, ITS2 has great potential in systematic study and species identification of Rehmannia, the combination of ITS2 and psbA-trnH might be the most suitable DNA barcode for Rehmannia species.

First molecular phylogeny of Agrilus (Coleoptera: Buprestidae), the largest genus on Earth, with DNA barcode database for forestry pest diagnostics

2018 ◽  
Vol 109 (2) ◽  
pp. 200-211 ◽  
Author(s):  
I. Kelnarova ◽  
E. Jendek ◽  
V.V. Grebennikov ◽  
L. Bocak
Keyword(s):  
Species Identification ◽  
Northern Hemisphere ◽  
Phylogenetic Trees ◽  
Dna Barcode ◽  
Intraspecific Variability ◽  
Molecular Data ◽  
Rapid Identification ◽  
Species Group ◽  
Molecular Phylogenetic ◽  
Multiple Species

AbstractAll more than 3000 species of Agrilus beetles are phytophagous and some cause economically significant damage to trees and shrubs. Facilitated by international trade, Agrilus species regularly invade new countries and continents. This necessitates a rapid identification of Agrilus species, as the first step for subsequent protective measures. This study provides the first DNA reference library for ~100 Agrilus species from the Northern Hemisphere based on three mitochondrial markers: cox1–5′ (DNA barcode fragment), cox1–3′, and rrnL. All 329 Agrilus records available in the Barcode of Life Database format, including specimen images and geo data, are released through a public dataset ‘Agrilus1 329’ available at: dx.doi.org/10.5883/DS-AGRILUS1. All Agrilus species were identified using adult morphology and by using molecular phylogenetic trees, as well as distance- and tree-based algorithms. Most DNA-based species limits agree well with the morphology-based identification. Our results include cases of high intraspecific variability and multiple species para- and polyphyly. DNA barcoding is a powerful species identification tool in Agrilus, although it frequently fails to recover morphologically-delimited Agrilus species-group. Even though the current three-gene database covers only ~3% of the known Agrilus diversity, it contains representatives of all principal lineages from the Northern Hemisphere and represents the most extensive dataset built for DNA-delimited species identification within this genus so far. Molecular data analyses can rapidly and cost-effectively identify an unknown sample, including immature stages and/or non-native taxa, or species not yet formally named.

Simulation of mechanically stirred two-phase liquid-gas flow

1986 ◽  
Vol 51 (5) ◽  
pp. 1001-1015 ◽  
Author(s):  
Ivan Fořt ◽  
Vladimír Rogalewicz ◽  
Miroslav Richter
Keyword(s):  
Spatial Distribution ◽  
Velocity Field ◽  
Gas Flow ◽  
Liquid Velocity ◽  
Model Parameters ◽  
Two Phase ◽  
Mean Velocity ◽  
Rushton Turbine ◽  
Low Viscosity ◽  
Volumetric Gas Flow Rate

The study describes simulation of the motion of bubbles in gas, dispersed by a mechanical impeller in a turbulent low-viscosity liquid flow. The model employs the Monte Carlo method and it is based both on the knowledge of the mean velocity field of mixed liquid (mean motion) and of the spatial distribution of turbulence intensity ( fluctuating motion) in the investigated system - a cylindrical tank with radial baffles at the wall and with a standard (Rushton) turbine impeller in the vessel axis. Motion of the liquid is then superimposed with that of the bubbles in a still environment (ascending motion). The computation of the simulation includes determination of the spatial distribution of the gas holds-up (volumetric concentrations) in the agitated charge as well as of the total gas hold-up system depending on the impeller size and its frequency of revolutions, on the volumetric gas flow rate and the physical properties of gas and liquid. As model parameters, both liquid velocity field and normal gas bubbles distribution characteristics are considered, assuming that the bubbles in the system do not coalesce.

scholarly journals Computing nearest neighbour interchange distances between ranked phylogenetic trees

2021 ◽  
Vol 82 (1-2) ◽  
Author(s):  
Lena Collienne ◽  
Alex Gavryushkin
Keyword(s):  
Cancer Research ◽  
Computational Complexity ◽  
Phylogenetic Tree ◽  
Shortest Path ◽  
Phylogenetic Trees ◽  
Shortest Paths ◽  
Nearest Neighbour ◽  
Tree Inference ◽  
Subtree Prune And Regraft ◽  
Comparison Algorithms

AbstractMany popular algorithms for searching the space of leaf-labelled (phylogenetic) trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are given by pairs of trees connected by one rearrangement operation (sometimes called a move). Most popular are the classical nearest neighbour interchange, subtree prune and regraft, and tree bisection and reconnection moves. The problem of computing distances, however, is $${\mathbf {N}}{\mathbf {P}}$$ N P -hard in each of these graphs, making tree inference and comparison algorithms challenging to design in practice. Although anked phylogenetic trees are one of the central objects of interest in applications such as cancer research, immunology, and epidemiology, the computational complexity of the shortest path problem for these trees remained unsolved for decades. In this paper, we settle this problem for the ranked nearest neighbour interchange operation by establishing that the complexity depends on the weight difference between the two types of tree rearrangements (rank moves and edge moves), and varies from quadratic, which is the lowest possible complexity for this problem, to $${\mathbf {N}}{\mathbf {P}}$$ N P -hard, which is the highest. In particular, our result provides the first example of a phylogenetic tree rearrangement operation for which shortest paths, and hence the distance, can be computed efficiently. Specifically, our algorithm scales to trees with tens of thousands of leaves (and likely hundreds of thousands if implemented efficiently).

scholarly journals Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process

2000 ◽  
Vol 64 (1) ◽  
pp. 202-236 ◽  
Author(s):  
Carl R. Woese ◽  
Gary J. Olsen ◽  
Michael Ibba ◽  
Dieter Söll
Keyword(s):  
Genetic Code ◽  
Phylogenetic Trees ◽  
Genetic Material ◽  
Evolutionary Process ◽  
Group Iv ◽  
Evolutionary Relationships ◽  
Evolutionary Stage ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases ◽  
The Individual

SUMMARY The aminoacyl-tRNA synthetases (AARSs) and their relationship to the genetic code are examined from the evolutionary perspective. Despite a loose correlation between codon assignments and AARS evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. Nevertheless, the AARSs are very informative about the evolutionary process. Examination of the phylogenetic trees for each of the AARSs reveals the following. (i) Their evolutionary relationships mostly conform to established organismal phylogeny: a strong distinction exists between bacterial- and archaeal-type AARSs. (ii) Although the evolutionary profiles of the individual AARSs might be expected to be similar in general respects, they are not. It is argued that these differences in profiles reflect the stages in the evolutionary process when the taxonomic distributions of the individual AARSs became fixed, not the nature of the individual enzymes. (iii) Horizontal transfer of AARS genes between Bacteria and Archaea is asymmetric: transfer of archaeal AARSs to the Bacteria is more prevalent than the reverse, which is seen only for the “gemini group.” (iv) The most far-ranging transfers of AARS genes have tended to occur in the distant evolutionary past, before or during formation of the primary organismal domains. These findings are also used to refine the theory that at the evolutionary stage represented by the root of the universal phylogenetic tree, cells were far more primitive than their modern counterparts and thus exchanged genetic material in far less restricted ways, in effect evolving in a communal sense.

scholarly journals The seven sisters DANCe

2018 ◽  
Vol 612 ◽  
pp. A70 ◽  
Author(s):  
J. Olivares ◽  
E. Moraux ◽  
L. M. Sarro ◽  
H. Bouy ◽  
A. Berihuete ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Model Comparison ◽  
Precise Determination ◽  
Model Parameters ◽  
Data Sets ◽  
Adequate Model ◽  
Comparison Results ◽  
Bayesian Evidence ◽  
Mass Segregation

Context. Membership analyses of the DANCe and Tycho + DANCe data sets provide the largest and least contaminated sample of Pleiades candidate members to date. Aims. We aim at reassessing the different proposals for the number surface density of the Pleiades in the light of the new and most complete list of candidate members, and inferring the parameters of the most adequate model. Methods. We compute the Bayesian evidence and Bayes Factors for variations of the classical radial models. These include elliptical symmetry, and luminosity segregation. As a by-product of the model comparison, we obtain posterior distributions for each set of model parameters. Results. We find that the model comparison results depend on the spatial extent of the region used for the analysis. For a circle of 11.5 parsecs around the cluster centre (the most homogeneous and complete region), we find no compelling reason to abandon King’s model, although the Generalised King model introduced here has slightly better fitting properties. Furthermore, we find strong evidence against radially symmetric models when compared to the elliptic extensions. Finally, we find that including mass segregation in the form of luminosity segregation in the J band is strongly supported in all our models. Conclusions. We have put the question of the projected spatial distribution of the Pleiades cluster on a solid probabilistic framework, and inferred its properties using the most exhaustive and least contaminated list of Pleiades candidate members available to date. Our results suggest however that this sample may still lack about 20% of the expected number of cluster members. Therefore, this study should be revised when the completeness and homogeneity of the data can be extended beyond the 11.5 parsecs limit. Such a study will allow for more precise determination of the Pleiades spatial distribution, its tidal radius, ellipticity, number of objects and total mass.

scholarly journals Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D Penny ◽  
M D Hendy ◽  
L R Foulds
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Protein Sequences ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Minimal Tree ◽  
Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

scholarly journals ESTIMATE OF STAND DENSITY INDEX FOR EUCALYPTUS UROPHYLLA USING DIFFERENT FIT METHODS

2016 ◽  
Vol 40 (5) ◽  
pp. 921-929 ◽  
Author(s):  
Ernani Lopes Possato ◽  
Natalino Calegario ◽  
Gilciano Saraiva Nogueira ◽  
Elliezer de Almeida Melo ◽  
Joyce de Almeida Alves
Keyword(s):  
Stochastic Frontier Analysis ◽  
Stochastic Frontier ◽  
Genetic Material ◽  
Stand Density ◽  
Model Parameters ◽  
Eucalyptus Urophylla ◽  
Frontier Analysis ◽  
Density Index ◽  
Number Of Stems ◽  
Stand Density Index

ABSTRACT The Reineke stand density index (SDI) was created on 1933 and remains as target of researches due to its importance on helping decision making regarding the management of population density. Part of such works is focused on the manner by which plots were selected and methods for the fit of Reineke model parameters in order to improve the definition of SDI value for the genetic material evaluated. The present study aimed to estimate the SDI value for Eucalyptus urophylla using the Reineke model fitted by the method of linear regression (LR) and stochastic frontier analysis (SFA). The database containing pairs of data number of stems per hectare (N) and mean quadratic diameter (Dq) was selected in three intensities, containing the 8, 30 and 43 plots of greatest density, and models were fitted by LR and SFA on each selected intensities. The intensity of data selection altered slightly the estimates of parameters and SDI when comparing the fits of each method. On the other hand, the adjust method influenced the mean estimated values of slope and SDI, which corresponded to -1.863 and 740 for LR and -1.582 and 810 for SFA.

scholarly journals Bird Species Identification Using Spectrogram Based on Multi-Channel Fusion of DCNNs

Entropy ◽  
2021 ◽  
Vol 23 (11) ◽  
pp. 1507
Author(s):  
Feiyu Zhang ◽  
Luyang Zhang ◽  
Hongxiang Chen ◽  
Jiangjian Xie
Keyword(s):  
Species Identification ◽  
Feature Fusion ◽  
Bird Species ◽  
The Other ◽  
Identification Accuracy ◽  
Mean Average Precision ◽  
Training Dataset ◽  
Model Parameters ◽  
Average Precision ◽  
Fusion Mode

Deep convolutional neural networks (DCNNs) have achieved breakthrough performance on bird species identification using a spectrogram of bird vocalization. Aiming at the imbalance of the bird vocalization dataset, a single feature identification model (SFIM) with residual blocks and modified, weighted, cross-entropy function was proposed. To further improve the identification accuracy, two multi-channel fusion methods were built with three SFIMs. One of these fused the outputs of the feature extraction parts of three SFIMs (feature fusion mode), the other fused the outputs of the classifiers of three SFIMs (result fusion mode). The SFIMs were trained with three different kinds of spectrograms, which were calculated through short-time Fourier transform, mel-frequency cepstrum transform and chirplet transform, respectively. To overcome the shortage of the huge number of trainable model parameters, transfer learning was used in the multi-channel models. Using our own vocalization dataset as a sample set, it is found that the result fusion mode model outperforms the other proposed models, the best mean average precision (MAP) reaches 0.914. Choosing three durations of spectrograms, 100 ms, 300 ms and 500 ms for comparison, the results reveal that the 300 ms duration is the best for our own dataset. The duration is suggested to be determined based on the duration distribution of bird syllables. As for the performance with the training dataset of BirdCLEF2019, the highest classification mean average precision (cmAP) reached 0.135, which means the proposed model has certain generalization ability.

Sign in / Sign up

Export Citation Format

Share Document