scholarly journals Evolutionary analyses of the gasdermin family suggest conserved roles in infection response despite loss of pore-forming functionality

BMC Biology ◽  
2022 ◽  
Vol 20 (1) ◽  
Author(s):  
Diego Angosto-Bazarra ◽  
Cristina Alarcón-Vila ◽  
Laura Hurtado-Navarro ◽  
María C. Baños ◽  
Jack Rivers-Auty ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Family Members ◽  
Cartilaginous Fish ◽  
Limited Information ◽  
Functional Roles ◽  
Ancestral Lineage ◽  
Wide Range ◽  
History Of ◽  
Infection Response ◽  
Pore Forming Proteins

Abstract Background Gasdermins are ancient (>500million-years-ago) proteins, constituting a family of pore-forming proteins that allow the release of intracellular content including proinflammatory cytokines. Despite their importance in the immune response, and although gasdermin and gasdermin-like genes have been identified across a wide range of animal and non-animal species, there is limited information about the evolutionary history of the gasdermin family, and their functional roles after infection. In this study, we assess the lytic functions of different gasdermins across Metazoa species, and use a mouse model of sepsis to evaluate the expression of the different gasdermins during infection. Results We show that the majority of gasdermin family members from distantly related animal clades are pore-forming, in line with the function of the ancestral proto-gasdermin and gasdermin-like proteins of Bacteria. We demonstrate the first expansion of this family occurred through a duplication of the ancestral gasdermin gene which formed gasdermin E and pejvakin prior to the divergence of cartilaginous fish and bony fish ~475 mya. We show that pejvakin from cartilaginous fish and mammals lost the pore-forming functionality and thus its role in cell lysis. We describe that the pore-forming gasdermin A formed ~320 mya as a duplication of gasdermin E prior to the divergence of the Sauropsida clade (the ancestral lineage of reptiles, turtles, and birds) and the Synapsid clade (the ancestral lineage of mammals). We then demonstrate that the gasdermin A gene duplicated to form the rest of the gasdermin family including gasdermins B, C, and D: pore-forming proteins that present a high variation of the exons in the linker sequence, which in turn allows for diverse activation pathways. Finally, we describe expression of murine gasdermin family members in different tissues in a mouse sepsis model, indicating function during infection response. Conclusions In this study we explored the evolutionary history of the gasdermin proteins in animals and demonstrated that the pore-formation functionality has been conserved from the ancient proto-gasdermin protein. We also showed that one gasdermin family member, pejvakin, lost its pore-forming functionality, but that all gasdermin family members, including pejvakin, likely retained a role in inflammation and the physiological response to infection.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Phylogenetic Network ◽  
Parametric Bootstrap ◽  
Lineage Sorting ◽  
Test Statistic ◽  
Sequence Alignments ◽  
Wide Range ◽  
History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

Comparative mitochondrial phylogeography of two legless lizards (Pygopodidae) from Queensland’s fragmented woodlands

2020 ◽  
Vol 66 (3-4) ◽  
pp. 142-150
Author(s):  
Jessica Worthington Wilmer ◽  
Andrew P. Amey ◽  
Carmel McDougall ◽  
Melanie Venz ◽  
Stephen Peck ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
The West ◽  
European Settlement ◽  
Low Genetic Diversity ◽  
Eastern Australia ◽  
Wide Range ◽  
History Of ◽  
Open Forests ◽  
Fossorial Species

Sclerophyll woodlands and open forests once covered vast areas of eastern Australia, but have been greatly fragmented and reduced in extent since European settlement. The biogeographic and evolutionary history of the biota of eastern Australia’s woodlands also remains poorly known, especially when compared to rainforests to the east, or the arid biome to the west. Here we present an analysis of patterns of mitochondrial genetic diversity in two species of Pygopodid geckos with distributions centred on the Brigalow Belt Bioregion of eastern Queensland. One moderately large and semi-arboreal species, Paradelma orientalis, shows low genetic diversity and no clear geographic structuring across its wide range. In contrast a small and semi-fossorial species, Delma torquata, consists of two moderately divergent clades, one from the ranges and upland of coastal areas of south-east Queensland, and other centred in upland areas further inland. These data point to varying histories of geneflow and refugial persistance in eastern Australia’s vast but now fragmented open woodlands. The Carnarvon Ranges of central Queensland are also highlighted as a zone of persistence for cool and/or wet-adapted taxa, however the evolutionary history and divergence of most outlying populations in these mountains remains unstudied.

scholarly journals Evolutionary History of LTR Retrotransposon Chromodomains in Plants

2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Anton Novikov ◽  
Georgiy Smyshlyaev ◽  
Olga Novikova
Keyword(s):  
Evolutionary History ◽  
Higher Plants ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Moss Species ◽  
Plant Genomes ◽  
Group I ◽  
Wide Range ◽  
History Of ◽  
Computer Based

Chromodomain-containing LTR retrotransposons are one of the most successful groups of mobile elements in plant genomes. Previously, we demonstrated that two types of chromodomains (CHDs) are carried by plant LTR retrotransposons. Chromodomains from group I (CHD_I) were detected only in Tcn1-like LTR retrotransposons from nonseed plants such as mosses (including the model moss species Physcomitrella) and lycophytes (the Selaginella species). LTR retrotransposon chromodomains from group II (CHD_II) have been described from a wide range of higher plants. In the present study, we performed computer-based mining of plant LTR retrotransposon CHDs from diverse plants with an emphasis on spike-moss Selaginella. Our extended comparative and phylogenetic analysis demonstrated that two types of CHDs are present only in the Selaginella genome, which puts this species in a unique position among plants. It appears that a transition from CHD_I to CHD_II and further diversification occurred in the evolutionary history of plant LTR retrotransposons at approximately 400 MYA and most probably was associated with the evolution of chromatin organization.

scholarly journals GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects

2019 ◽  
Vol 36 (11) ◽  
pp. 2604-2619 ◽  
Author(s):  
Elodie Laine ◽  
Yasaman Karami ◽  
Alessandra Carbone
Keyword(s):  
Evolutionary History ◽  
Recent Progress ◽  
State Of The Art ◽  
Fast Method ◽  
Biological Sequences ◽  
Epistatic Model ◽  
Input Alignment ◽  
Wide Range ◽  
History Of ◽  
Better Than

Abstract The systematic and accurate description of protein mutational landscapes is a question of utmost importance in biology, bioengineering, and medicine. Recent progress has been achieved by leveraging on the increasing wealth of genomic data and by modeling intersite dependencies within biological sequences. However, state-of-the-art methods remain time consuming. Here, we present Global Epistatic Model for predicting Mutational Effects (GEMME) (www.lcqb.upmc.fr/GEMME), an original and fast method that predicts mutational outcomes by explicitly modeling the evolutionary history of natural sequences. This allows accounting for all positions in a sequence when estimating the effect of a given mutation. GEMME uses only a few biologically meaningful and interpretable parameters. Assessed against 50 high- and low-throughput mutational experiments, it overall performs similarly or better than existing methods. It accurately predicts the mutational landscapes of a wide range of protein families, including viral ones and, more generally, of much conserved families. Given an input alignment, it generates the full mutational landscape of a protein in a matter of minutes. It is freely available as a package and a webserver at www.lcqb.upmc.fr/GEMME/.

scholarly journals MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations

GigaScience ◽  
2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Mengni Liu ◽  
Jianyu Chen ◽  
Xin Wang ◽  
Chengwei Wang ◽  
Xiaolong Zhang ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Cancer Evolution ◽  
Evolutionary Patterns ◽  
Evolutionary Trajectory ◽  
Wide Range ◽  
Heterogeneous Features ◽  
History Of ◽  
Somatic Alterations ◽  
Tumor Biopsies

Abstract Background Multi-region sequencing (MRS) has been widely used to analyze intra-tumor heterogeneity (ITH) and cancer evolution. However, comprehensive analysis of mutational data from MRS is still challenging, necessitating complicated integration of a plethora of computational and statistical approaches. Findings Here, we present MesKit, an R/Bioconductor package that can assist in characterizing genetic ITH and tracing the evolutionary history of tumors based on somatic alterations detected by MRS. MesKit provides a wide range of analysis and visualization modules, including ITH evaluation, metastatic route inference, and mutational signature identification. In addition, MesKit implements an auto-layout algorithm to generate phylogenetic trees based on somatic mutations. The application of MesKit for 2 reported MRS datasets of hepatocellular carcinoma and colorectal cancer identified known heterogeneous features and evolutionary patterns, together with potential driver events during cancer evolution. Conclusions In summary, MesKit is useful for interpreting ITH and tracing evolutionary trajectory based on MRS data. MesKit is implemented in R and available at https://bioconductor.org/packages/MesKit under the GPL v3 license.

scholarly journals Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae

2013 ◽  
Vol 94 (4) ◽  
pp. 738-748 ◽  
Author(s):  
Ying Tao ◽  
Mang Shi ◽  
Christina Conrardy ◽  
Ivan V. Kuzmin ◽  
Sergio Recuenco ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Evolutionary Rate ◽  
Mammalian Species ◽  
Evolutionary Analysis ◽  
Viral Pathogens ◽  
Genomic Features ◽  
Wide Range ◽  
History Of ◽  
Multiple Species

Polyomaviruses (PyVs) have been identified in a wide range of avian and mammalian species. However, little is known about their occurrence, genetic diversity and evolutionary history in bats, even though bats are important reservoirs for many emerging viral pathogens. This study screened 380 specimens from 35 bat species from Kenya and Guatemala for the presence of PyVs by semi-nested pan-PyV PCR assays. PyV DNA was detected in 24 of the 380 bat specimens. Phylogenetic analysis revealed that the bat PyV sequences formed 12 distinct lineages. Full-genome sequences were obtained for seven representative lineages and possessed similar genomic features to known PyVs. Strikingly, this evolutionary analysis revealed that the bat PyVs were paraphyletic, suggestive of multiple species jumps between bats and other mammalian species, such that the theory of virus–host co-divergence for mammalian PyVs as a whole could be rejected. In addition, evidence was found for strong heterogeneity in evolutionary rate and potential recombination in a number of PyV complete genomes, which complicates both phylogenetic analysis and virus classification. In summary, this study revealed that bats are important reservoirs of PyVs and that these viruses have a complex evolutionary history.

scholarly journals Triplet-based similarity score for fully multilabeled trees with poly-occurring labels

2020 ◽  
Author(s):  
Simone Ciccolella ◽  
Giulia Bernardini ◽  
Luca Denti ◽  
Paola Bonizzoni ◽  
Marco Previtali ◽  
...  
Keyword(s):  
Open Source ◽  
Evolutionary History ◽  
Similarity Measures ◽  
Real Data ◽  
Similarity Score ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Wide Range ◽  
Golden Standard ◽  
History Of

Abstract Motivation The latest advances in cancer sequencing, and the availability of a wide range of methods to infer the evolutionary history of tumors, have made it important to evaluate, reconcile and cluster different tumor phylogenies. Recently, several notions of distance or similarities have been proposed in the literature, but none of them has emerged as the golden standard. Moreover, none of the known similarity measures is able to manage mutations occurring multiple times in the tree, a circumstance often occurring in real cases. Results To overcome these limitations, in this article, we propose MP3, the first similarity measure for tumor phylogenies able to effectively manage cases where multiple mutations can occur at the same time and mutations can occur multiple times. Moreover, a comparison of MP3 with other measures shows that it is able to classify correctly similar and dissimilar trees, both on simulated and on real data. Availability and implementation An open source implementation of MP3 is publicly available at https://github.com/AlgoLab/mp3treesim. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Evolutionary History of the Toll-Like Receptor Gene Family across Vertebrates

2019 ◽  
Vol 12 (1) ◽  
pp. 3615-3634 ◽  
Author(s):  
Guangshuai Liu ◽  
Huanxin Zhang ◽  
Chao Zhao ◽  
Honghai Zhang
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Receptor Gene ◽  
Purifying Selection ◽  
Protein Architecture ◽  
Wide Range ◽  
History Of ◽  
Membrane Bound

Abstract Adaptation to a wide range of pathogenic environments is a major aspect of the ecological adaptations of vertebrates during evolution. Toll-like receptors (TLRs) are ancient membrane-bound sensors in animals and are best known for their roles in detecting and defense against invading pathogenic microorganisms. To understand the evolutionary history of the vertebrate TLR gene family, we first traced the origin of single-cysteine cluster TLRs that share the same protein architecture with vertebrate TLRs in early-branching animals and then analyzed all members of the TLR family in over 200 species covering all major vertebrate clades. Our results indicate that although the emergence of single-cysteine cluster TLRs predates the separation of bilaterians and cnidarians, most vertebrate TLR members originated shortly after vertebrate emergence. Phylogenetic analyses divided 1,726 vertebrate TLRs into 8 subfamilies, and TLR3 may represent the most ancient subfamily that emerged before the branching of deuterostomes. Our analysis reveals that purifying selection predominated in the evolution of all vertebrate TLRs, with mean dN/dS (ω) values ranging from 0.082 for TLR21 in birds to 0.434 for TLR11 in mammals. However, we did observe patterns of positive selection acting on specific codons (527 of 60,294 codons across all vertebrate TLRs, 8.7‰), which are significantly concentrated in ligand-binding extracellular domains and suggest host–pathogen coevolutionary interactions. Additionally, we found stronger positive selection acting on nonviral compared with viral TLRs, indicating the more essential nonredundant function of viral TLRs in host immunity. Taken together, our findings provide comprehensive insight into the complex evolutionary processes of the vertebrate TLR gene family, involving gene duplication, pseudogenization, purification, and positive selection.

scholarly journals Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta

2021 ◽  
Vol 288 (1943) ◽  
pp. 20202934
Author(s):  
Jiaming Hu ◽  
Michael V. Westbury ◽  
Junxia Yuan ◽  
Zhen Zhang ◽  
Shungang Chen ◽  
...  
Keyword(s):  
Late Pleistocene ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Mitochondrial Genomes ◽  
Effective Population ◽  
Wide Range ◽  
Two Samples ◽  
Spotted Hyenas ◽  
History Of ◽  
Close Relatives

Cave hyenas (genus Crocuta ) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta . Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta . Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62–2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.

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