Reconstructing the Phylogeny

Weyenberg, Grady; Yoshida, Ruriko

doi:10.1016/b978-0-12-801213-0.00012-5

Cited by 6 publications

(4 citation statements)

References 106 publications

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“…According to Weyenberg and Yoshida (2015) phylogenetic trees can be used to organise various types of biological data and to make inferences about possible occurrences in an organism's evolutionary past.…”

Section: Discussionmentioning

confidence: 99%

Identification of culturable bacteria associated with the rhizosphere of Lablab purpureus growing in Namibia

Kavishe,

Uzabakiriho,

Kennedy

et al. 2024

Preprint

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Dolichos lablab (Lablab purpureus (L.) Sweet)) is a multipurpose drought tolerant protein-rich legume crop native to Africa and grown in warm temperate to tropical climates for its edible seeds and manure. Lablab purpureus holds significant benefits to subsistence farmers and offers a great promise for sustainable crop productivity, especially in marginalised areas. Its uses range from human consumption as a vegetable to improving soil fertility, and as forage. Notwithstanding Lablab purpureus crucial potential functions in Namibia, there is currently limited information regarding the plant’s rhizosphere bacteria. The study aimed at identifying Lablab purpureus’ natural rhizosphere bacteria. Isolation of rhizosphere bacteria involved the use of general media (Luria Bertani agar and tryptic soy agar); selective media such as Rhizobium and Yeast Extract Mannitol (YEM) Congo red from soil sample extracts. Eighty-five strains of bacteria were isolated and were subsequently identified by 16S rRNA gene sequencing analysis. The results showed that they belonged to the following genera, Bacillus, Streptomyces, Exiguobacterium, Stutzerimonas, Rhizobium, Acidovorax, Agrobacterium, Psychrobacter, Priestia, Planococcus, Bhargavaea, Stenotrophomonas, Caulobacter, Peribacillus, Niallia, Athrobacter, Sphingobium, Enterobacter, Sphingobacterium, Sinorhizobium, Flavobacterium, Microbacterium, Metabacillus, Neobacillus, and Pseudomonas which are reported to have growth promoting substances. The study highlighted the potential use of these plant growth promoting rhizobacteria for inocula production or biofertilisers for enhancing growth and nutrient content of beans and other crops under field conditions. The study was the first report of Lablab purpureus’s rhizosphere associated bacteria in Namibia.

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Section: Discussionmentioning

confidence: 99%

Identification of culturable bacteria associated with the rhizosphere of Lablab purpureus growing in Namibia

Kavishe,

Uzabakiriho,

Kennedy

et al. 2024

Preprint

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“…Where each element on the main diagonal is equal to the negative of the sum of all other elements on the same matrix row (q kk = − ∑ i̸ =k q ki ). The transition rate matrix can be used to compute the transition probability matrix P(t) for a time interval t by taking the matrix exponential [48](Eq. 2).…”

Section: General Methodologymentioning

confidence: 99%

A simple correction to adjust for sampling biases in phylogeographic discrete trait analysis

Jorgensen,

Pons-Salort,

Grassly

2023

Preprint

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Discrete trait analysis (DTA) methods are widely used to infer patterns of movement between discrete geographic locations from genetic sequence data as they are simple and fast to implement. With the increasing interest in phylogeography for pathogen genomic epidemiology, accounting for and understanding the limitations of the methods used is becoming increasingly important. Applying DTA to location makes several strong simplifying assumptions, including the assumption of equal sampling probability across locations. This may lead to biased estimates of migration rates and ancestral locations where sampling rates vary. Here we investigate these biases using simulated migration and transmission data. We propose a simple correction to DTA for unequal sampling probability across locations when sampling rates are known or can be estimated. This correction to the migration rate matrix can be applied only to phylogenetic branches leading to sampled tips or to the whole phylogeny. We assess the performance of this correction using simulated data for a range of endemic transmission scenarios with varied sampling and migration rates. In a simple, two-location, case the correction performs significantly better than a standard DTA method in three of the four sampling rate distributions investigated. Applying the correction across only the tips of the phylogeny and over the full depth of the tree gives similar results, with the correction only at the tips performing marginally better in this simple two-location simulation. As migration is a key driver of infectious disease spread, improving estimates of migration with simple phylogenetic methods is a valuable development in infectious disease phylogeography.

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“…Dendrogram, düğümlerin hiyerarşinin bölgelerini temsil ettiği ve küme yapısını görselleştirmeye yardımcı olan ağaç benzeri bir yapıdır (Li, Ma et al 2018, Perret et al 2019. Bir dendrogramda, düğümler arasındaki benzerlik, onları birleştiren bağlantının mesafeleriyle ifade edilir ve her düğümün koordinatı, nesneler arasındaki farklılığı gösterir (Manning andSchütze 1999, Weyenberg andYoshida 2015). Her düğüm kendi kümesinde başlar ve en küçük mesafeye sahip düğümler kademeli olarak birleştirilir (Yang et al 2019).…”

Section: Bulgular Ve Tartışmaunclassified

“…Mesafe matrisi iki boyutlu, simetrik, negatif olmayan bir matristir ve bir kümedeki elemanlar arasında ikili mesafe tahminlerine karşılık gelir (University of Ljubljana ,Weyenberg and Yoshida 2015).…”

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Havzaların Benzerliklerini Tanımlamada Alternatif Bir Yaklaşım: Hiyerarşik Kümeleme Yöntemi Uygulaması

Aytaç

2021

Afyon Kocatepe University Journal of Sciences and Engineering

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Machine learning methods have widespread their use and strengthened their places in many areas. These procedures can be divided into three main branches as supervised, unsupervised, and reinforced learning and assist researchers to find connections in the data that cannot be seen or in situations that require long-term computation. Unsupervised methods are used to discover patterns or structures in data which does not have any labels. The hierarchical clustering process is one of the leading unsupervised methods. This study is an alternative approach to the process we used in defining the similarities of basins. The advantages of the proposed method are; reveals the relations between all basins, is less sensitive to noise in the data set, is more useful in applications with fewer basins, and is flexible in ensuring intra-cluster consistency. Some basins located in the north of Turkey based on their hydrological response units (HRU) images were hierarchically clustered and found out that and the two basins most similar to each other are the Ereğli and Çaykıyı catchments. A distance matrix was prepared to reveal the relations of the basins. Besides, to create independent clusters, four different statistical approaches were used to select the cut-off height of the dendrogram. To stay within the cluster numbers suggested by statistical methods and to ensure cluster homogeneity, 6 separate clusters were created. The distribution of the catchments depending on the clusters was illustrated. This study provides an alternative perspective for the clustering of basins based on HRU images.

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Reconstructing the Phylogeny

Cited by 6 publications

References 106 publications

Identification of culturable bacteria associated with the rhizosphere of Lablab purpureus growing in Namibia

Identification of culturable bacteria associated with the rhizosphere of Lablab purpureus growing in Namibia

A simple correction to adjust for sampling biases in phylogeographic discrete trait analysis

Havzaların Benzerliklerini Tanımlamada Alternatif Bir Yaklaşım: Hiyerarşik Kümeleme Yöntemi Uygulaması

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