Phylogenetic methods

With the aim of inferring phylogenetic relationships among 86 species (including 45 species from Vietnam) mostly of the subfamily Convallarioideae (=Nolinoideae) (Asparagaceae sensu APG IV), we analyzed their chloroplast DNA sequences (rbcL and trnL-F) by both Bayesian inference (BI) and maximum likelihood (ML) methods. Our dataset included six of the seven tribes classified in this subfamily; Convallarieae, Dracaeneae, Liriopeae Nolineae, Polygonateae and Rusceae (Eriospermeae not examined).

17p dianmotminh02 03-05-2024 3 2   Download

Ebook "Introduction to computational biology: An evolutionary approach" Analysis of molecular sequence data is the main subject of this introduction to computational biology. There are two closely connected aspects to biological sequences: (i) their relative position in the space of all other sequences, and (ii) their movement through this sequence space in evolutionary time. Accordingly, the first part of the book deals with classical methods of sequence analysis: pairwise alignment, exact string matching, multiple alignment, and hidden Markov models.

329p tracanhphuonghoa1007 22-04-2024 10 2   Download

In Vietnam, SMEDI syndrome in sows caused by PPV is nationwide and has been of concern since the early 1990s. Previous studies have investigated the prevalence of PPVs using serological testing and PCR methods. The objective of this study is to analyze the genotypic prevalence of PPVs and molecular characterization of VP gene of PPV2 from slaughtered pigs in Central Vietnam.

10p viritesh 02-04-2024 1 1   Download

Ebook "Neanderthals revisited: New approaches and perspectives" presents cutting-edge research by leading scientists re-examining the major debates in Neanderthal research with the use of innovative state-of-the art methods and exciting new theoretical approaches. Topics addressed include the re-evaluation of Neanderthal anatomy, inferred adaptations and habitual activities, developmental patterns, phylogenetic relationships, and the Neanderthal extinction.

336p tachieuhoa 28-01-2024 3 2   Download

Ebook "Introduction to mathematical methods in bioinformatics" looks at the mathematical foundations of the models currently in use. All existing books on bioinformatics are software-orientated and they concentrate on computer implementations of mathematical models of biology. This book is unique in the sense that it looks at the mathematical foundations of the models, which are crucial for correct interpretation of the outputs of the models.

305p tachieuhoa 28-01-2024 6 2   Download

Part 2 book "Control of poultry mites" includes content: The testing of antibodies raised against poultry red mite antigens in an in vitro feeding assay; preliminary screen for vaccine candidates; endosymbiotic bacteria living inside the poultry red mite (Dermanyssus gallinae); molecular phylogenetic assessment of host range in five Dermanyssus species, monitoring of Dermanyssus gallinae in free-range poultry farms,...and other contents.

98p oursky10 04-12-2023 3 2   Download

The phylogenetic relationship of 83 taxa of Santalaceae s.l. was reconstructed based on the molecular data sets including the nuclear ribosomal (small and large subunit rDNA) and the chloroplast rbcL, matK, and trnL-F regions. The Maximum likelihood (ML) and Bayesian inference (BI) methods were used to build the phylogenetic trees.

8p viellenkullman 13-05-2022 6 1   Download

Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics.

14p vielonmusk 30-01-2022 7 1   Download

Single-cell sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under the infinite-sites assumption, violations of which, due to chromosomal deletions and loss of heterozygosity, necessitate the development of inference methods that utilize finite-sites models.

20p vialfrednobel 29-01-2022 5 0   Download

Single-cell sequencing promises a high-resolution view of genetic heterogeneity and clonal evolution in cancer. However, methods to infer tumor evolution from single-cell sequencing data lag behind methods developed for bulk-sequencing data. Here, we present OncoNEM, a probabilistic method for inferring intra-tumor evolutionary lineage trees from somatic single nucleotide variants of single cells.

14p viaristotle 29-01-2022 13 0   Download

Although scRNA-seq is now ubiquitously adopted in studies of intratumor heterogeneity, detection of somatic mutations and inference of clonal membership from scRNA-seq is currently unreliable. We propose DENDRO, an analysis method for scRNA-seq data that clusters single cells into genetically distinct subclones and reconstructs the phylogenetic tree relating the subclones.

15p viarchimedes 26-01-2022 6 0   Download

Ablepharus Lichtenstein, 1823, which includes ten species, is distributed in eastern Europe and Asia. Four species are recorded in Turkey: A. kitaibelii, A. chernovi, A. bivittatus, and A. budaki. After molecular and morphological studies in Anatolia, the phylogenetic relationship of the genus is still very complicated. Here, we investigate the taxonomic status of Ablepharus in Anatolia using morphological and molecular methods. The genetic structure of Ablepharus populations in Anatolia was analyzed using both the nuclear (CMOS) and mitochondrial (cyt b and COI) gene regions.

12p dolomite36 30-12-2021 16 1   Download

The codling moth (Cydia pomonella L., Lepidoptera: Tortricidae) is a well-known pest worldwide and was first reported in 1952 in Turkey. It is traditionally controlled with several pesticide applications during each apple production season. The genetic diversity of codling moths was investigated in this study, based on the partial mitochondrial cytochrome oxidase subunite I gene. Twenty-two haplotypes from 9 populations were studied. The results showed an average haplotype and nucleotide diversity of 0.835 and 0.571, respectively.

10p dolomite36 30-12-2021 4 0   Download

Eight extant species have been so far recognized for Calomyscus Thomas, 1905 which is distributed in the west of Asia. The only species which was reported from the Zagros Mountains in western and southern Iran was C. bailwardi. However, based on the integrative methods such as molecular, morphometric and karyological studies a new species is worth to be described other than C. bailwardi from the Zagros Mountains. In the present survey a new species which has been distributed in western regions of Iran was described as Calomyscus behzadi sp. nov.

16p dolomite36 30-12-2021 14 0   Download

Phylogenetic trees are useful tools to infer evolutionary relationships between genetic entities. Phylogenetics enables not only evolution-based gene clustering but also the assignment of gene duplication and deletion events to the nodes when coupled with statistical approaches such as bootstrapping. However, extensive gene duplication and deletion events bring along a challenge in interpreting phylogenetic trees and require manual inference.

7p langthannam 29-12-2021 14 0   Download

The cDNA encoding lipase enzyme was cloned from Olea europaea var. europaea cv. Gemlik leaves using the RACE method. The full nucleotide sequence was 1546 bp long and encoded a putative protein of 412 amino acid long protein. The amino acid sequence showed identity to Triacylglycerol Lipase 1 sequences from different plants. A phylogenetic tree was constructed showing relations with various plant lipases.

8p tudichquannguyet 29-11-2021 11 1   Download

Gene order changes, under rearrangements, insertions, deletions and duplications, have been used as a new type of data source for phylogenetic reconstruction. Because these changes are rare compared to sequence mutations, they allow the inference of phylogeny further back in evolutionary time. There exist many computational methods for the reconstruction of gene-order phylogenies, including widely used maximum parsimonious methods and maximum likelihood methods.

8p vilarryellison 29-10-2021 11 0   Download

The monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related to other carangimorphs based on substantial sequencing efforts and diversely analytical methods. In this study, we examined why this particular result is often obtained.

11p vibeauty 23-10-2021 7 1   Download

Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions.

15p vibeauty 23-10-2021 11 0   Download

Anthrax is a zoonotic disease caused by the gram-positive bacterium Bacillus anthracis. The most anthrax-endemic regions of Russia are Siberia and North Caucasus. Previously, genotyping of Russian B.anthracis isolates was carried out using canSNP and MLVA data; these methods yield lower resolution results compared to whole genome SNP analysis (wgSNP).

8p visilicon2711 20-08-2021 11 1   Download