scholarly journals Genomic signature of kin selection in an ant with obligately sterile workers

2016 ◽  
Author(s):  
Michael R. Warner ◽  
Alexander S. Mikheyev ◽  
Timothy A. Linksvayer
Keyword(s):  
Kin Selection ◽  
Social Evolution ◽  
Genomic Signature ◽  
Evolution Of Cooperation ◽  
Comparative Genomic ◽  
Genome Wide ◽  
Theoretical Predictions ◽  
Approaches To Study ◽  
Worker Caste ◽  
Upregulated Genes

AbstractKin selection is thought to drive the evolution of cooperation and conflict, but the specific genes and genome-wide patterns shaped by kin selection are unknown. We identified thousands of genes associated with the sterile ant worker caste, the archetype of an altruistic phenotype shaped by kin selection, and then used population and comparative genomic approaches to study patterns of molecular evolution at these genes. Consistent with population genetic theoretical predictions, worker-upregulated genes showed relaxed adaptive evolution compared to genes upregulated in reproductive castes. Worker-upregulated genes included more taxonomically-restricted genes, indicating that the worker caste has recruited more novel genes, yet these genes also showed relaxed selection. Our study identifies a putative genomic signature of kin selection and helps to integrate emerging sociogenomic data with longstanding social evolution theory.

scholarly journals The evolution of cooperation in simple molecular replicators

2017 ◽  
Vol 284 (1864) ◽  
pp. 20171967 ◽  
Author(s):  
Samuel R. Levin ◽  
Stuart A. West
Keyword(s):  
Life History ◽  
Kin Selection ◽  
Overlapping Generations ◽  
Social Evolution ◽  
Tree Of Life ◽  
Evolution Of Cooperation ◽  
Replication Rate ◽  
Limited Diffusion

In order for the first genomes to evolve, independent replicators had to act cooperatively, with some reducing their own replication rate to help copy others. It has been argued that limited diffusion explains this early cooperation. However, social evolution models have shown that limited diffusion on its own often does not favour cooperation. Here we model early replicators using social evolution tools. We show that: (i) replicators can be considered to be cooperating as a result of kin selection; (ii) limited diffusion on its own does not favour cooperation; and (iii) the addition of overlapping generations, probably a general trait of molecular replicators, promotes cooperation. These results suggest key life-history features in the evolution of the genome and that the same factors can favour cooperation across the entire tree of life.

scholarly journals Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan Filée ◽  
Sarah Farhat ◽  
Dominique Higuet ◽  
Laure Teysset ◽  
Dominique Marie ◽  
...  
Keyword(s):  
Transposable Elements ◽  
High Throughput Sequencing ◽  
Comparative Genomic ◽  
Ltr Retrotransposon ◽  
Genomic Evolution ◽  
Genome Wide ◽  
Genomic Analyses ◽  
Different Types ◽  
Evolutionary Success ◽  
Low Coverage

Abstract Background With the expansion of high throughput sequencing, we now have access to a larger number of genome-wide studies analyzing the Transposable elements (TEs) composition in a wide variety of organisms. However, genomic analyses often remain too limited in number and diversity of species investigated to study in depth the dynamics and evolutionary success of the different types of TEs among metazoans. Therefore, we chose to investigate the use of transcriptomes to describe the diversity of TEs in phylogenetically related species by conducting the first comparative analysis of TEs in two groups of polychaetes and evaluate the diversity of TEs that might impact genomic evolution as a result of their mobility. Results We present a detailed analysis of TEs distribution in transcriptomes extracted from 15 polychaetes depending on the number of reads used during assembly, and also compare these results with additional TE scans on associated low-coverage genomes. We then characterized the clades defined by 1021 LTR-retrotransposon families identified in 26 species. Clade richness was highly dependent on the considered superfamily. Copia elements appear rare and are equally distributed in only three clades, GalEa, Hydra and CoMol. Among the eight BEL/Pao clades identified in annelids, two small clades within the Sailor lineage are new for science. We characterized 17 Gypsy clades of which only 4 are new; the C-clade largely dominates with a quarter of the families. Finally, all species also expressed for the majority two distinct transcripts encoding PIWI proteins, known to be involved in control of TEs mobilities. Conclusions This study shows that the use of transcriptomes assembled from 40 million reads was sufficient to access to the diversity and proportion of the transposable elements compared to those obtained by low coverage sequencing. Among LTR-retrotransposons Gypsy elements were unequivocally dominant but results suggest that the number of Gypsy clades, although high, may be more limited than previously thought in metazoans. For BEL/Pao elements, the organization of clades within the Sailor lineage appears more difficult to establish clearly. The Copia elements remain rare and result from the evolutionary consistent success of the same three clades.

scholarly journals Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

2021 ◽  
Author(s):  
Xinxin Yi ◽  
Jing Liu ◽  
Shengcai Chen ◽  
Hao Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Wide ◽  
A Genome ◽  
Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

scholarly journals Agent based models to investigate cooperation between cancer cells

2015 ◽  
Author(s):  
Joao Xavier ◽  
William Chang
Keyword(s):  
Growth Factor ◽  
Cancer Cells ◽  
Solid Tumor ◽  
Kin Selection ◽  
Evolution Of Cooperation ◽  
Emergent Properties ◽  
Agent Based Model ◽  
Agent Based ◽  
Chemical Gradients ◽  
Close Proximity

We present a type of agent-based model that uses off-lattice spheres to represent individual cells in a solid tumor. The model calculates chemical gradients and determines the dynamics of the tumor as emergent properties of the interactions between the cells. As an example, we present an investigation of cooperation among cancer cells where cooperators secrete a growth factor that is costly to synthesize. Simulations reveal that cooperation is favored when cancer cells from the same lineage stay in close proximity. The result supports the hypothesis that kin selection, a theory that explains the evolution of cooperation in animals, also applies to cancers.

Genomic characterisation of multiple myeloma: study of a Portuguese cohort

2021 ◽  
pp. jclinpath-2020-207204
Author(s):  
Alexandra Couto Oliveira ◽  
Ilda Patrícia Ribeiro ◽  
Luís Miguel Pires ◽  
Ana Cristina Gonçalves ◽  
Artur Paiva ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Clinical Practice ◽  
Prognostic Value ◽  
Clinical Presentation ◽  
Comparative Genomic Hybridisation ◽  
Comparative Genomic ◽  
Genomic Alterations ◽  
Genomic Complexity ◽  
Genome Wide ◽  
Trisomy 9

Multiple myeloma (MM) genomic complexity reflects in the variable patients’ clinical presentation. Genome-wide studies seem to be a reasonable alternative to identify critical genomic lesions. In the current study, we have performed the genomic characterisation of a Portuguese cohort of patients with MM by array comparative genomic hybridisation. Overall, the most frequently detected alterations were 13q deletions, gains of 1q, 19p, 15q, 5p and 7p and trisomy 9. Even though some identified genomic alterations were previously associated with a prognostic value, other abnormalities remain with unknown, but putative significance for patients’ clinical practice. These genomic alterations should be further assessed as possible biomarkers.

scholarly journals Evolution of strong reproductive isolation in plants: broad-scale patterns and lessons from a perennial model group

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190544 ◽  
Author(s):  
Huiying Shang ◽  
Jaqueline Hess ◽  
Melinda Pickup ◽  
David L. Field ◽  
Pär K. Ingvarsson ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Association Studies ◽  
Great Promise ◽  
Genome Wide Association Studies ◽  
Model Group ◽  
Recombination Rates ◽  
Genome Wide ◽  
Theoretical Predictions ◽  
Tree Topologies ◽  
Exemplary Model

Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

scholarly journals Comparative Analysis of Whole-Genome and Methylome Profiles of a Smooth and a Rough Mycobacterium abscessus Clinical Strain

2019 ◽  
Vol 10 (1) ◽  
pp. 13-22 ◽  
Author(s):  
Chiranjibi Chhotaray ◽  
Shuai Wang ◽  
Yaoju Tan ◽  
Amjad Ali ◽  
Muhammad Shehroz ◽  
...  
Keyword(s):  
Single Molecule ◽  
Gene Clusters ◽  
Mycobacterium Abscessus ◽  
Clinical Strain ◽  
Comparative Genomic ◽  
Illumina Hiseq ◽  
Clinical Strains ◽  
Synonymous Mutations ◽  
Pan Genome ◽  
Genome Wide

Mycobacterium abscessus is a fast growing Mycobacterium species mainly causing skin and respiratory infections in human. M. abscessus is resistant to numerous drugs, which is a major challenge for the treatment. In this study, we have sequenced the genomes of two clinical M. abscessus strains having rough and smooth morphology, using the single molecule real-time and Illumina HiSeq sequencing technology. In addition, we reported the first comparative methylome profiles of a rough and a smooth M. abscessus clinical strains. The number of N4-methylcytosine (4mC) and N6-methyladenine (6mA) modified bases obtained from smooth phenotype were two-fold and 1.6 fold respectively higher than that of rough phenotype. We have also identified 4 distinct novel motifs in two clinical strains and genes encoding antibiotic-modifying/targeting enzymes and genes associated with intracellular survivability having different methylation patterns. To our knowledge, this is the first report about genome-wide methylation profiles of M. abscessus strains and identification of a natural linear plasmid (15 kb) in this critical pathogen harboring methylated bases. The pan-genome analysis of 25 M. abscessus strains including two clinical strains revealed an open pan genome comprises of 7596 gene clusters. Likewise, structural variation analysis revealed that the genome of rough phenotype strain contains more insertions and deletions than the smooth phenotype and that of the reference strain. A total of 391 single nucleotide variations responsible for the non-synonymous mutations were detected in clinical strains compared to the reference genome. The comparative genomic analysis elucidates the genome plasticity in this emerging pathogen. Furthermore, the detection of genome-wide methylation profiles of M. abscessus clinical strains may provide insight into the significant role of DNA methylation in pathogenicity and drug resistance in this opportunistic pathogen.

Sign in / Sign up

Export Citation Format

Share Document