scholarly journals Homoplasy as an Auxiliary Criterion for Species Delimitation

2021 ◽  
Vol 9 (2) ◽  
pp. 273
Author(s):  
Angela Conti ◽  
Debora Casagrande Pierantoni ◽  
Vincent Robert ◽  
Gianluigi Cardinali ◽  
Laura Corte
Keyword(s):  
New Species ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Species Delimitation ◽  
Convergent Evolution ◽  
Simulated Data ◽  
Single Element ◽  
Phylogenetic Reconstructions ◽  
Taxonomic Markers ◽  
Auxiliary Test

Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers ITS and LSU in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases—as expected—with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.

scholarly journals A comprehensive phylogenetic analysis of the serpin superfamily

2020 ◽  
Author(s):  
Matthew A. Spence ◽  
Matthew D. Mortimer ◽  
Ashley M. Buckle ◽  
Bui Quang Minh ◽  
Colin J. Jackson
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Convergent Evolution ◽  
Alternative Hypothesis ◽  
Structural Alignment ◽  
High Homology ◽  
Physiological Processes ◽  
New Directions ◽  
Hub Proteins

Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer (HGT) due to their unexpectedly high homology. Here we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central “hub” of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of HGT. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.

scholarly journals A Comprehensive Phylogenetic Analysis of the Serpin Superfamily

2021 ◽  
Author(s):  
Matthew A Spence ◽  
Matthew D Mortimer ◽  
Ashley M Buckle ◽  
Bui Quang Minh ◽  
Colin J Jackson
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Convergent Evolution ◽  
Alternative Hypothesis ◽  
Structural Alignment ◽  
High Homology ◽  
Physiological Processes ◽  
New Directions ◽  
Hub Proteins

Abstract Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer due to their unexpectedly high homology. Here, we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6,000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central “hub” of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of horizontal gene transfer. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.

Introduction

2021 ◽  
pp. 1-6
Author(s):  
Thomas E. Schindler
Keyword(s):  
Antibiotic Resistance ◽  
New Species ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Molecular Biology ◽  
Women Scientists ◽  
Systematic Bias ◽  
Bacterial Genetics ◽  
Replica Plating ◽  
One Step

This chapter relates how one day in 1950, Esther Zimmer Lederberg cleverly re-purposed her compact makeup pad and invented replica plating. This whimsical experiment led to an elegant technique for duplicating many bacterial clones in one step, a clever invention that epitomized her experimental creativity. The chapter shows how the Lederbergs established the field of bacterial genetics years before the birth of molecular biology and together discovered bacterial sex (or horizontal gene transfer, HGT) the peculiar processes that enable bacteria to rapidly spread their genes, leading to antibiotic resistance and the evolution of new species. The stellar reputation of her brilliant husband and collaborator, however, diminished Esther Lederberg’s legacy. The systematic bias against giving due credit for achievements of women scientists whose work is misattributed to their scientific colleagues is known as the Matilda Effect. Esther Lederberg’s story is sadly similar to those of many exemplary women scientists.

scholarly journals Hortense: Horizontal gene transfer detection directly from proteomic MS/MS data

2017 ◽  
Author(s):  
Kathrin Trappe ◽  
Ben Wulf ◽  
Joerg Doellinger ◽  
Sven Halbedel ◽  
Thilo Muth ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Large Scale ◽  
Genomic Sequence ◽  
Simulated Data ◽  
Negative Control ◽  
Detection Methods ◽  
Resistant Bacteria ◽  
Antimicrobial Resistance Genes

Horizontal gene transfer (HGT) is a powerful mechanism that allows bacteria to directly transfer long stretches of genomic sequence from one individual to another. The transfer of antimicrobial resistance genes is a prominent example of HGT events in the context of multi-resistant bacteria which pose a high risk to human health. While several approaches for HGT detection exist on the genomic level, to the best of our knowledge, HGT events have not been investigated in a detailed mass spectrometry (MS)-based proteomic study. However, the mere presence of a gene does not necessarily correlate with its expression at the protein level. Consequently, to draw conclusions with respect to the expression of HGT-mediated genes, MS-based proteomics can be employed. We developed a first computational approach - called Hortense - for automated HGT detection directly from shotgun proteomics experiments. We extend the standard database search by a critical cross-validation to unravel potential HGT proteins. A proteogenomic extension gives information about the genomic origin and enables an integration with existing genome-based methods. We successfully validated our approach on simulated data, and further evaluated it on real data from a transgenic organism and a negative control from an organism not harboring a transferred gene. Our results indicate that our method facilitates MS-based analysis for proteomic evidence of HGT events. Especially as an orthogonal approach to genome-based HGT detection methods, our proposed workflow is a first step toward a systematic and large scale analysis of HGT events in, e.g., antimicrobial resistance context. Hortense is publicly available at https://gitlab.com/rki_bioinformatics/.

scholarly journals Hortense: Horizontal gene transfer detection directly from proteomic MS/MS data

2017 ◽  
Author(s):  
Kathrin Trappe ◽  
Ben Wulf ◽  
Joerg Doellinger ◽  
Sven Halbedel ◽  
Thilo Muth ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Large Scale ◽  
Genomic Sequence ◽  
Simulated Data ◽  
Negative Control ◽  
Detection Methods ◽  
Resistant Bacteria ◽  
Antimicrobial Resistance Genes

Horizontal gene transfer (HGT) is a powerful mechanism that allows bacteria to directly transfer long stretches of genomic sequence from one individual to another. The transfer of antimicrobial resistance genes is a prominent example of HGT events in the context of multi-resistant bacteria which pose a high risk to human health. While several approaches for HGT detection exist on the genomic level, to the best of our knowledge, HGT events have not been investigated in a detailed mass spectrometry (MS)-based proteomic study. However, the mere presence of a gene does not necessarily correlate with its expression at the protein level. Consequently, to draw conclusions with respect to the expression of HGT-mediated genes, MS-based proteomics can be employed. We developed a first computational approach - called Hortense - for automated HGT detection directly from shotgun proteomics experiments. We extend the standard database search by a critical cross-validation to unravel potential HGT proteins. A proteogenomic extension gives information about the genomic origin and enables an integration with existing genome-based methods. We successfully validated our approach on simulated data, and further evaluated it on real data from a transgenic organism and a negative control from an organism not harboring a transferred gene. Our results indicate that our method facilitates MS-based analysis for proteomic evidence of HGT events. Especially as an orthogonal approach to genome-based HGT detection methods, our proposed workflow is a first step toward a systematic and large scale analysis of HGT events in, e.g., antimicrobial resistance context. Hortense is publicly available at https://gitlab.com/rki_bioinformatics/.

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