scholarly journals Genetic distance between complex repeats

2018 ◽  
Author(s):  
Luca Ferretti ◽  
Aurora Ruiz-Herrera ◽  
Alice Ledda
Keyword(s):  
Evolutionary History ◽  
Point Mutations ◽  
Pairwise Alignment ◽  
Genetic Distances ◽  
Repeat Sequence ◽  
Evolutionary Analysis ◽  
New Approach ◽  
Repeat Units ◽  
Repeat Domain ◽  
History Of

AbstractComplex nucleotide or aminoacid repeats with long units play an important role in proteins. The evolutionary analysis of these variants is challenging due to genetic diversity within repeat units as well as variability in the arrangement of different units along the repeat sequence. Here we present a new approach for the computation of genetic distances between complex repeats. This method takes into account evolutionary processes including point mutations, insertions and deletions of repeat units, as well as duplication of single units. We provide an algorithm for the computation of these distances along with the corresponding global pairwise alignment of repeats. As an example, we apply our approach to the evolution of repeat units in the highly polymorphic zinc-finger repeat domain of the PRDM9 protein across wild populations of house mice. This approach opens the way for new insights into the evolutionary history of polymorphic repeats.

scholarly journals Molecular evolutionary analysis of human primary microcephaly genes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Nashaiman Pervaiz ◽  
Hongen Kang ◽  
Yiming Bao ◽  
Amir Ali Abbasi
Keyword(s):  
Evolutionary History ◽  
Genetic Basis ◽  
Brain Size ◽  
Primate Species ◽  
Evolutionary Analysis ◽  
Australopithecus Afarensis ◽  
Primary Microcephaly ◽  
Modern Humans ◽  
History Of ◽  
The Brain

Abstract Background There has been a rapid increase in the brain size relative to body size during mammalian evolutionary history. In particular, the enlarged and globular brain is the most distinctive anatomical feature of modern humans that set us apart from other extinct and extant primate species. Genetic basis of large brain size in modern humans has largely remained enigmatic. Genes associated with the pathological reduction of brain size (primary microcephaly-MCPH) have the characteristics and functions to be considered ideal candidates to unravel the genetic basis of evolutionary enlargement of human brain size. For instance, the brain size of microcephaly patients is similar to the brain size of Pan troglodyte and the very early hominids like the Sahelanthropus tchadensis and Australopithecus afarensis. Results The present study investigates the molecular evolutionary history of subset of autosomal recessive primary microcephaly (MCPH) genes; CEP135, ZNF335, PHC1, SASS6, CDK6, MFSD2A, CIT, and KIF14 across 48 mammalian species. Codon based substitutions site analysis indicated that ZNF335, SASS6, CIT, and KIF14 have experienced positive selection in eutherian evolutionary history. Estimation of divergent selection pressure revealed that almost all of the MCPH genes analyzed in the present study have maintained their functions throughout the history of placental mammals. Contrary to our expectations, human-specific adoptive evolution was not detected for any of the MCPH genes analyzed in the present study. Conclusion Based on these data it can be inferred that protein-coding sequence of MCPH genes might not be the sole determinant of increase in relative brain size during primate evolutionary history.

Methodological Institutionalism: A New Approach to the Evolution of Economic Science

2008 ◽  
pp. 90-101 ◽  
Author(s):  
D. Frolov
Keyword(s):  
Economic Thought ◽  
History Of Economic Thought ◽  
Economic Science ◽  
Evolutionary Analysis ◽  
Scientific Communities ◽  
New Approach ◽  
Scientific Cognition ◽  
Norms And Values ◽  
History Of ◽  
Institutional Traps

In the article the perspective approach in philosophy of science - methodological institutionalism - is discussed which regards economic ideas as scientific and ideological institutions. This approach allows to apply tools of modern institutional theory to the history of economic thought. The evolutionary analysis of science should put an emphasis on studying status interests of scientists, local rationalities and informal hierarchies of scientific communities, informal norms and values, epistemological institutional "traps" and models of scientific cognition.

scholarly journals New Insights on the Evolutionary History of Aphids and Their Primary Endosymbiont Buchnera aphidicola

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Vicente Pérez-Brocal ◽  
Rosario Gil ◽  
Andrés Moya ◽  
Amparo Latorre
Keyword(s):  
Generation Time ◽  
Evolutionary History ◽  
Parallel Evolution ◽  
Aphid Species ◽  
Evolutionary Analysis ◽  
Buchnera Aphidicola ◽  
Genomic Features ◽  
Evolutionary Pattern ◽  
History Of ◽  
Molecular Evolutionary Analysis

Since the establishment of the symbiosis between the ancestor of modern aphids and their primary endosymbiont, Buchnera aphidicola, insects and bacteria have coevolved. Due to this parallel evolution, the analysis of bacterial genomic features constitutes a useful tool to understand their evolutionary history. Here we report, based on data from B. aphidicola, the molecular evolutionary analysis, the phylogenetic relationships among lineages and a comparison of sequence evolutionary rates of symbionts of four aphid species from three subfamilies. Our results support previous hypotheses of divergence of B. aphidicola and their host lineages during the early Cretaceous and indicate a closer relationship between subfamilies Eriosomatinae and Lachninae than with the Aphidinae. They also reveal a general evolutionary pattern among strains at the functional level. We also point out the effect of lifecycle and generation time as a possible explanation for the accelerated rate in B. aphidicola from the Lachninae.

scholarly journals Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yaodong Yang ◽  
Stéphanie Bocs ◽  
Haikuo Fan ◽  
Alix Armero ◽  
Luc Baudouin ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Evolutionary History ◽  
Elaeis Guineensis ◽  
Cocos Nucifera ◽  
Pollen Grains ◽  
Evolutionary Analysis ◽  
Salt Stress Response ◽  
Genomic Tools ◽  
History Of ◽  
Facultative Halophyte

AbstractCoconut (Cocos nucifera) is the emblematic palm of tropical coastal areas all around the globe. It provides vital resources to millions of farmers. In an effort to better understand its evolutionary history and to develop genomic tools for its improvement, a sequence draft was recently released. Here, we present a dense linkage map (8402 SNPs) aiming to assemble the large genome of coconut (2.42 Gbp, 2n = 32) into 16 pseudomolecules. As a result, 47% of the sequences (representing 77% of the genes) were assigned to 16 linkage groups and ordered. We observed segregation distortion in chromosome Cn15, which is a signature of strong selection among pollen grains, favouring the maternal allele. Comparing our results with the genome of the oil palm Elaeis guineensis allowed us to identify major events in the evolutionary history of palms. We find that coconut underwent a massive transposable element invasion in the last million years, which could be related to the fluctuations of sea level during the glaciations at Pleistocene that would have triggered a population bottleneck. Finally, to better understand the facultative halophyte trait of coconut, we conducted an RNA-seq experiment on leaves to identify key players of signaling pathways involved in salt stress response. Altogether, our findings represent a valuable resource for the coconut breeding community.

scholarly journals Evolutionary history of human colitis-associated colorectal cancer

Gut ◽  
2018 ◽  
Vol 68 (6) ◽  
pp. 985-995 ◽  
Author(s):  
Ann-Marie Baker ◽  
William Cross ◽  
Kit Curtius ◽  
Ibrahim Al Bakir ◽  
Chang-Ho Ryan Choi ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Copy Number ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Low Grade ◽  
Evolutionary Analysis ◽  
Single Nucleotide ◽  
Sequence Of Events ◽  
Mutation Burden ◽  
History Of

ObjectiveIBD confers an increased lifetime risk of developing colorectal cancer (CRC), and colitis-associated CRC (CA-CRC) is molecularly distinct from sporadic CRC (S-CRC). Here we have dissected the evolutionary history of CA-CRC using multiregion sequencing.DesignExome sequencing was performed on fresh-frozen multiple regions of carcinoma, adjacent non-cancerous mucosa and blood from 12 patients with CA-CRC (n=55 exomes), and key variants were validated with orthogonal methods. Genome-wide copy number profiling was performed using single nucleotide polymorphism arrays and low-pass whole genome sequencing on archival non-dysplastic mucosa (n=9), low-grade dysplasia (LGD; n=30), high-grade dysplasia (HGD; n=13), mixed LGD/HGD (n=7) and CA-CRC (n=19). Phylogenetic trees were reconstructed, and evolutionary analysis used to reveal the temporal sequence of events leading to CA-CRC.Results10/12 tumours were microsatellite stable with a median mutation burden of 3.0 single nucleotide alterations (SNA) per Mb, ~20% higher than S-CRC (2.5 SNAs/Mb), and consistent with elevated ageing-associated mutational processes. Non-dysplastic mucosa had considerable mutation burden (median 47 SNAs), including mutations shared with the neighbouring CA-CRC, indicating a precancer mutational field. CA-CRCs were often near triploid (40%) or near tetraploid (20%) and phylogenetic analysis revealed that copy number alterations (CNAs) began to accrue in non-dysplastic bowel, but the LGD/HGD transition often involved a punctuated ‘catastrophic’ CNA increase.ConclusionsEvolutionary genomic analysis revealed precancer clones bearing extensive SNAs and CNAs, with progression to cancer involving a dramatic accrual of CNAs at HGD. Detection of the cancerised field is an encouraging prospect for surveillance, but punctuated evolution may limit the window for early detection.

scholarly journals Does relaxing the infinite sites assumption give better tumor phylogenies? An ILP-based comparative approach

2017 ◽  
Author(s):  
Paola Bonizzoni ◽  
Simone Ciccolella ◽  
Gianluca Della Vedova ◽  
Mauricio Soto
Keyword(s):  
Evolutionary History ◽  
Cancer Genomics ◽  
Fundamental Problem ◽  
Comparative Approach ◽  
Cancer Evolution ◽  
Perfect Phylogeny ◽  
New Approach ◽  
Recurrent Mutations ◽  
History Of ◽  
The One

AbstractMost of the evolutionary history reconstruction approaches are based on the infinite site assumption, which is underlying the Perfect Phylogeny model and whose main consequence is that acquired mutation can never lost. This results in the clonal model used to explain cancer evolution. Some recent results gives a strong evidence that recurrent and back mutations are present in the evolutionary history of tumors [5,21], thus showing that more general models then the Perfect Phylogeny are required. We propose a new approach that incorporates the possibility of losing a previously acquired mutation, extending the Persistent Phylogeny model [1].We exploit our model to provide an ILP formulation of the problem of reconstructing trees on mixed populations, where the input data consists of the fraction of cells in a set of samples that have a certain mutation. This is a fundamental problem in cancer genomics, where the goal is to study the evolutionary history of a tumor. An experimental analysis shows the usefulness of allowing mutation losses, by studying some real and simulated datasets where our ILP approach provides a better interpretation than the one obtained under perfect phylogeny assumption. Finally, we show how to incorporate multiple back mutations and recurrent mutations in our model.

scholarly journals Genetic differentiation in the genus Characodon: implications for conservation and taxonomy

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11492
Author(s):  
Rosa G. Beltrán-López ◽  
Rodolfo Pérez-Rodríguez ◽  
Ofelia C. Montañez-García ◽  
Juan M. Artigas-Azas ◽  
Michael Köck ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Evolutionary History ◽  
Genetic Distances ◽  
Genetic Groups ◽  
Evolutionary Significant Units ◽  
Significant Genetic Structure ◽  
D Loop ◽  
History Of ◽  
The Subject ◽  
Phylogeographic Study

The subfamily Goodeinae is a group of fishes endemic to the Mexican highlands. Most of the species are restricted to small and isolated streams or springs. Within this subfamily, the genus Characodon is the earliest diverging lineage of which three species have been described: C. lateralis, C. audax, and C. garmani, with the latter, considered extinct. Characodon lateralis and C. audax are classed as endangered, and have been the subject of taxonomic controversy since their description: previous studies have recognized a genetic differentiation in two groups separated by the El Salto waterfall, but morphological analyses contradict these genetic results. We perform a phylogeographic study using the mitochondrial cytb gene and d-loop region to elucidate the evolutionary history of C. lateralis and C. audax. The results with both markers show the presence of two highly differentiated haplogroups; one distributed north and the other distributed south of the waterfall, with genetic distances of 1.7 and 13.1% with cytb and d-loop respectively, and divergence calculated to have occurred 1.41 Mya. Significant genetic structure was found within each haplogroup and suggests the existence of at least four Evolutionary Significant Units (ESUs) within the examined populations. The possible processes identified as contributing to the formation of differentiated genetic groups are isolation, low population size, recurrent bottlenecks, and the strong sexual selection exhibited by the genus.

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 Comparing the topology of phylogenetic network generators

2021 ◽  
Author(s):  
Remie Janssen ◽  
Pengyu Liu
Keyword(s):  
Bayesian Methods ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Random Trees ◽  
Phylogenetic Networks ◽  
Phylogeny Reconstruction ◽  
Evolutionary Analysis ◽  
Summary Statistics ◽  
History Of

Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive representation of evolutionary history compared to phylogenetic trees. Stochastic processes for generating random trees or networks are important tools in evolutionary analysis, especially in phylogeny reconstruction where they can be utilized for validation or serve as priors for Bayesian methods. However, as more network generators are developed, there is a lack of discussion or comparison for different generators. To bridge this gap, we compare a set of phylogenetic network generators by profiling topological summary statistics of the generated networks over the number of reticulations and comparing the topological profiles.

scholarly journals Sequence and evolutionary analysis of bacterial ribosomal S1 proteins

2020 ◽  
Author(s):  
Evgenia Deryusheva ◽  
Andrey Machulin ◽  
Maxim Matyunin ◽  
Oxana Galzitskaya
Keyword(s):  
Ribosomal Proteins ◽  
Evolutionary History ◽  
Tandem Repeats ◽  
Evolutionary Development ◽  
Evolutionary Analysis ◽  
Globular Domain ◽  
Bacterial Phyla ◽  
Percent Identity ◽  
The Family ◽  
History Of

The multi-domain bacterial S1 protein is the largest and most functionally important ribosomal protein of the 30S subunit, which interacts with both mRNA and proteins. The family of ribosomal S1 proteins differs in the classical sense from a protein with tandem repeats and has a “bead-on-string” organization, where each repeat is folded into a globular domain. Based on our recent data, the study of evolutionary relationships for the bacterial phyla will provide evidence for one of the proposed theories of the evolutionary development of proteins with structural repeats: from multiple repeats of assembles to single repeats, or vice versa. In this comparative analysis of 1333 S1 sequences that were identified in 24 different phyla; we demonstrate how such phyla can independently/dependently form during evolution. To our knowledge, this work is the first study of the evolutionary history of bacterial ribosomal S1 proteins. The collected and structured data can be useful to computer biologists as a resource for determining percent identity, amino acid composition and logo motifs, as well as dN/dS ratio in bacterial S1 protein. The obtained research data suggested that the evolutionary development of bacterial ribosomal proteins S1 evolved from multiple assemblies to single repeat. The presented data are integrated into the server, which can be accessed at http://oka.protres.ru:4200.

Sign in / Sign up

Export Citation Format

Share Document