Phylogeny for the faint of heart: a tutorial

Baldauf, Sandra L.

doi:10.1016/s0168-9525(03)00112-4

Cited by 189 publications

(139 citation statements)

References 17 publications

(14 reference statements)

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“…There are usually two parts to the model: the branching diagram and the process. The overwhelming majority of branching diagrams in the literature are tree diagrams, and in all likelihood for most purposes these are the correct kinds of diagram to use [91]. However, if evolutionary history of the evolving objects under study has contained introgressive events, then a simple diverging tree cannot be used.…”

Section: Analysis Of Path Lengths On Four Different Hypothesesmentioning

confidence: 99%

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data

McInerney

Pisani

O’Connell

2015

Phil. Trans. R. Soc. B

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One contribution of 17 to a theme issue 'Eukaryotic origins: progress and challenges'. The literature is replete with manuscripts describing the origin of eukaryotic cells. Most of the models for eukaryogenesis are either autogenous (sometimes called slow-drip), or symbiogenic (sometimes called big-bang). In this article, we use large and diverse suites of 'Omics' and other data to make the inference that autogeneous hypotheses are a very poor fit to the data and the origin of eukaryotic cells occurred in a single symbiosis.

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Section: Analysis Of Path Lengths On Four Different Hypothesesmentioning

confidence: 99%

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data

McInerney

Pisani

O’Connell

2015

Phil. Trans. R. Soc. B

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“…Usually bootstrap values ≥0.7 is needed to have confidence that genes are inserted in the proper location within the tree. The bootstrap value for Gayal IFNT is 0.3 (Baldauf 2003). Also, this sequence was derived from genomic DNA, and its trophoblast-dependent expression remains uncertain (Rajaravindra et al 2006).…”

Section: The Origins Of Ifntmentioning

confidence: 99%

“…Reproduction (2017) 154 F1-F10 www.reproduction-online.org were examined rather than AA sequence divergence in order to obtain a more complete picture of IFNT gene variant evolution and to strengthen their correct placement within the tree (Baldauf 2003). Since an exact identity of these variants is not required for this discussion, variants were given arbitrary numbers to identify them (Supplementary Table 2 for the GenBank accession number key, see section on supplementary data given at the end of this article).…”

Section: F6mentioning

confidence: 99%

The evolution of interferon-tau

Ealy¹,

Wooldridge²

2017

Reproduction

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Thirty years ago, a novel type I interferon (IFN) was identified by molecular cloning of cDNA libraries constructed from RNA extracted from ovine and bovine pre-implantation embryos. This protein was eventually designated as IFN-tau (IFNT) to highlight its trophoblast-dependent expression. IFNT function is not immune related. Instead, it interacts with the maternal system to initiate the establishment and maintenance of pregnancy. This activity is indispensable for the continuation of pregnancy. Our review will describe how IFNT evolved from other type I IFNs to function in this new capacity. IFNT genes have only been identified in pecoran ruminants within the Artiodactyla order (e.g. cattle, sheep, goats, deer, antelope, giraffe). The ancestral IFNT gene emerged approximately 36 million years ago most likely from rearrangement and/or insertion events that combined an ancestral IFN-omega (IFNW) gene with a trophoblast-specifying promoter/enhancer. Since then, IFNT genes have duplicated, likely through conversion events, and mutations have allowed them to adapt to their new function in concert with the emergence of different species. Multiple IFNT polymorphisms have been identified in cattle, sheep and goats. These genes and gene alleles encode proteins that do not display identical antiviral, antiproliferative and antiluteolytic activities. The need for multiple IFNT genes, numerous alleles and distinct activities remains debatable, but the consensus is that this complexity in IFNT expression and biological activity must be needed to provide the best opportunity for pregnancy to be recognized by the maternal system so that gestation may continue. Reproduction (2017) 154 F1-F10

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“…The taxonomic relationship between plant, bacteria and fungi Further to root the tree, it is necessary to add an outgroup, which is a (unrelated) group of species or single species that is not included in the group of species under the study [26]. The outgroup Halobacterium sp.…”

Section: Analysis Of Phylogenetic Consequencesmentioning

confidence: 99%

Computational Phylogenetic Study and Data Mining Approach to Laccase Enzyme Sequences

Satpathy¹,

Behera²,

Padhi³

et al. 2013

J Phylogen Evolution Biol

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Currently data mining is an essential tool to discover the hidden data and important patterns from a large data set. The present work is a pilot study that compares the result of sequence based phylogenetic study and some of the physicochemical and structural feature based clustering of Laccase enzyme sequences. Total of 50 homologous sequences were obtained specific to each of the organism like plant, fungi and bacteria. Multiple sequences alignment of sequences was performed followed by phylogenetic tree construction and consistency study also to observe the major clusters. Again the major domain and motif analysis was done to support the study in the divergence pattern of Laccase enzyme sequences. There after 13 numbers of physicochemical and structural features were computed for each enzyme sequences. Then data normalisation and k-means clustering technique revealed that the fungi, bacteria and plant were obtained in three distinct clusters. The analysis indicates that the result of sequence based classification is in a good agreement with physicochemical basis of classification of proteins. The methods can be further optimised for different clustering algorithm to obtain specific physicochemical features that would help to classification of proteins.

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Phylogeny for the faint of heart: a tutorial

Cited by 189 publications

References 17 publications

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data

The evolution of interferon-tau

Computational Phylogenetic Study and Data Mining Approach to Laccase Enzyme Sequences

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