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 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 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.

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 Coloring inside the lines: genomic architecture and evolution of a widespread color pattern in frogs

2021 ◽  
Author(s):  
Sandra Goutte ◽  
Imtiyaz Hariyani ◽  
Kole Deroy Utzinger ◽  
Yann Bourgeois ◽  
Stephane Boissinot
Keyword(s):  
Evolutionary History ◽  
Genetic Basis ◽  
Molecular Level ◽  
Parallel Evolution ◽  
Color Pattern ◽  
Evolutionary Dynamic ◽  
Ideal System ◽  
Terrestrial Habitats ◽  
History Of ◽  
Repeated Evolution

Traits shared among distantly related lineages are indicators of common evolutionary constraints, at the ecological, physiological or molecular level. The vertebral stripe is a color pattern that is widespread across the anuran phylogeny. Despite its prevalence in the order, surprisingly little is known about the genetic basis and evolutionary dynamic of this color pattern. Here we combine histology, genome- and transcriptome-wide analyses with order-scale phylogenetic comparative analyses to investigate this common phenotype. We show that the vertebral stripe has evolved hundreds of times in the evolutionary history of anurans and is selected for in terrestrial habitats. Using the Ethiopian Ptychadena radiation as a model system, we demonstrate that variation at the ASIP gene is responsible for the different vertebral stripe phenotypes. Alleles associated to these phenotypes are younger than the split between closely related Ptychadena species, thus indicating that the vertebral stripe results from parallel evolution within the group. Our findings demonstrate that this widespread color pattern evolves rapidly and recurrently in terrestrial anurans, and therefore constitute an ideal system to study repeated evolution.

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 Buchnera has changed flatmate but the repeated replacement of co-obligate symbionts is not associated with the ecological expansions of their aphid hosts

2016 ◽  
Author(s):  
A.S. Meseguer ◽  
A. Manzano-Marín ◽  
A. Coeur d’Acier ◽  
A-L. Clamens ◽  
M. Godefroid ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Aphid Species ◽  
Buchnera Aphidicola ◽  
Evolutionary Transitions ◽  
Symbiotic Associations ◽  
Metabolic Functions ◽  
History Of ◽  
Serratia Symbiotica ◽  
Bacterial Genes

AbstractSymbiotic associations with bacteria have facilitated important evolutionary transitions in insects and resulted in long-term obligate interactions. Recent evidence suggests that these associations are not always evolutionarily stable and that symbiont replacement and/or supplementation of an obligate symbiosis by an additional bacterium has occurred during the history of many insect groups. Yet, the factors favoring one symbiont over another in this evolutionary dynamic are not well understood; progress has been hindered by our incomplete understanding of the distribution of symbionts across phylogenetic and ecological contexts. While many aphids are engaged into an obligate symbiosis with a single Gammaproteobacterium, Buchnera aphidicola, in species of the Lachninae subfamily, this relationship has evolved into a “ménage à trois”, in which Buchnera is complemented by a cosymbiont, usually Serratia symbiotica. Using deep sequencing of 16S rRNA bacterial genes from 128 species of Cinara (the most diverse Lachninae genus), we reveal a highly dynamic dual symbiotic system in this aphid lineage. Most species host both Serratia and Buchnera but, in several clades, endosymbionts related to Sodalis, Erwinia or an unnamed member of the Enterobacteriaceae have replaced Serratia. Endosymbiont genome sequences from four aphid species+confirm that these coresident symbionts fulfill essential metabolic functions not ensured by Buchnera. We further demonstrate through comparative phylogenetic analyses that co-symbiont replacement is not associated with the adaptation of aphids to new ecological conditions. We propose that symbiont succession was driven by factors intrinsic to the phenomenon of endosymbiosis, such as rapid genome deterioration or competitive interactions between bacteria with similar metabolic capabilities.

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.

scholarly journals New Clues about the Evolutionary History of Metabolic Losses in Bacterial Endosymbionts, Provided by the Genome of Buchnera aphidicola from the Aphid Cinara tujafilina

2011 ◽  
Vol 77 (13) ◽  
pp. 4446-4454 ◽  
Author(s):  
Araceli Lamelas ◽  
María José Gosalbes ◽  
Andrés Moya ◽  
Amparo Latorre
Keyword(s):  
Evolutionary History ◽  
Acyrthosiphon Pisum ◽  
Bacterial Genome ◽  
Last Common Ancestor ◽  
Symbiotic Association ◽  
Gene Repertoire ◽  
Buchnera Aphidicola ◽  
Content Type ◽  
History Of ◽  
Serratia Symbiotica

ABSTRACTThe symbiotic association between aphids (Homoptera) andBuchnera aphidicola(Gammaproteobacteria) started about 100 to 200 million years ago. As a consequence of this relationship, the bacterial genome has undergone a prominent size reduction. The downsize genome process starts when the bacterium enters the host and will probably end with its extinction and replacement by another healthier bacterium or with the establishment of metabolic complementation between two or more bacteria. Nowadays, several complete genomes ofBuchnera aphidicolafrom four different aphid species (Acyrthosiphon pisum,Schizaphis graminum,Baizongia pistacea, andCinara cedri) have been fully sequenced.C. cedribelongs to the subfamily Lachninae and harbors two coprimary bacteria that fulfill the metabolic needs of the whole consortium:B. aphidicolawith the smallest genome reported so far and “CandidatusSerratia symbiotica.” In addition,Cinara tujafilina, another member of the subfamily Lachninae, closely related toC. cedri, also harbors “Ca.Serratia symbiotica” but with a different phylogenetic status than the one fromC. cedri. In this study, we present the complete genome sequence ofB. aphidicolafromC. tujafilinaand the phylogenetic analysis and comparative genomics with the otherBuchneragenomes. Furthermore, the gene repertoire of the last common ancestor has been inferred, and the evolutionary history of the metabolic losses that occurred in the different lineages has been analyzed. Although stochastic gene loss plays a role in the genome reduction process, it is also clear that metabolism, as a functional constraint, is also a powerful evolutionary force in insect endosymbionts.

scholarly journals Fine-scale cospeciation between Brachycaudus and Buchnera aphidicola : bacterial genome helps define species and evolutionary relationships in aphids

2008 ◽  
Vol 276 (1654) ◽  
pp. 187-196 ◽  
Author(s):  
Emmanuelle Jousselin ◽  
Yves Desdevises ◽  
Armelle Coeur d'acier
Keyword(s):  
Species Delimitation ◽  
Evolutionary History ◽  
Bacterial Genome ◽  
Specific Interaction ◽  
Essential Amino Acids ◽  
Buchnera Aphidicola ◽  
Species Definition ◽  
Taxonomic Level ◽  
History Of ◽  
Definition Of

Aphids harbour an obligatory symbiont, Buchnera aphidicola , providing essential amino acids not supplied by their diet. These bacteria are transmitted vertically and phylogenic analyses suggest that they have ‘cospeciated’ with their hosts. We investigated this cospeciation phenomenon at a fine taxonomic level, within the aphid genus Brachycaudus . We used DNA-based methods of species delimitation in both organisms, to avoid biases in the definition of aphid and Buchnera species and to infer association patterns without the presumption of a specific interaction. Our results call into question certain ‘taxonomic’ species of Brachycaudus and suggest that B. aphidicola has diversified into independently evolving entities, each specific to a ‘phylogenetic’ Brachycaudus species. We also found that Buchnera and their hosts simultaneously diversified, in parallel. These results validate the use of Buchnera DNA data for inferring the evolutionary history of their host. The Buchnera genome evolves rapidly, making it the perfect tool for resolving ambiguities in aphid taxonomy. This study also highlights the usefulness of species delimitation methods in cospeciation studies involving species difficult to conceptualize—as is the case for bacteria—and in cases in which the taxonomy of the interacting organisms has not been determined independently and species definition depends on host association.

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