scholarly journals Faster rates of molecular sequence evolution in reproduction-related genes and in species with hypodermic sperm morphologies

2021 ◽  
Author(s):  
R Axel W Wiberg ◽  
Jeremias N Brand ◽  
Lukas Schaerer
Keyword(s):  
Sexual Selection ◽  
Sequence Evolution ◽  
Model Species ◽  
Free Living ◽  
Molecular Sequence ◽  
Functional Annotations ◽  
Genome Wide ◽  
Large Genus ◽  
Signatures Of Selection ◽  
Efficiency Of Selection

Sexual selection is expected to drive the evolution of many striking behaviours and morphologies, leaving signatures of selection at loci underlying these phenotypes. However, relatively few studies have contrasted molecular sequence evolution at such loci across lineages that differ in their sexual selection context. Our comparative genomics study of Macrostomum, a large genus of free-living simultaneously hermaphroditic flatworms, takes advantage of functional annotations from the model species, M. lignano, and transcriptome assemblies of 97 congeners. We compare molecular sequence evolution in species with contrasting sperm morphologies, which are strongly associated with multiple convergent shifts in the mating strategy and thus reflect the sexual selection context in Macrostomum. The sperm of most reciprocally mating species carry lateral bristles, likely functioning as anchoring mechanisms against post-copulatory sperm removal. Hypodermically mating species lack these bristles, potentially as adaptations to a different environment experienced by hypodermic sperm. We document faster molecular sequence evolution in reproduction-related, compared to ubiquitously-expressed, genes across all sperm morphologies, consistent with more intense selection acting on the former. Furthermore, we observed faster molecular sequence evolution in species with hypodermic sperm morphologies, in both reproduction-related and ubiquitously-expressed genes. These genome-wide patterns suggest that shifts to hypodermic mating reduce the efficiency of selection, possibly due to higher selfing rates in hypodermically mating species. Moreover, we find little evidence for convergent amino acid changes across species. We provide the first comprehensive comparative analysis of molecular sequence evolution in a group of simultaneously hermaphroditic animals, across well-replicated contrasts of lineages with divergent sperm morphologies.

scholarly journals An investigation of MHC-dependent sexual selection in a free-living population of sheep

2020 ◽  
Author(s):  
Wei Huang ◽  
Jill G. Pilkington ◽  
Josephine M. Pemberton
Keyword(s):  
Sexual Selection ◽  
Mixed Models ◽  
Gene Clusters ◽  
Inbreeding Avoidance ◽  
Free Living ◽  
Mating Patterns ◽  
Disassortative Mating ◽  
Mhc Genes ◽  
Genome Wide ◽  
Polymorphic Gene

AbstractMHC genes are one of the most polymorphic gene clusters in vertebrates and play an essential role in adaptive immunity. There is evidence that sexual selection also plays a role in maintaining MHC diversity, but the specific mechanisms are controversial. In this study, we investigate evidence for non-random MHC-dependent mating patterns in a free-living population of Soay sheep. Using a large number of sheep diplotyped at the MHC class IIa region and genome-wide SNPs, together with field observations of consorts, we found sexual selection against one of eight haplotypes, C, in males at the pre-copulatory stage and sexual selection on female MHC heterozygosity acting in opposition directions at the pre- and post-copulatory stages. We also found disassortative mating at the post-copulatory stage, along with strong evidence of inbreeding avoidance at both stages. However, results from generalized linear mixed models suggest that the pattern of MHC-dependent disassortative mating could be a by-product of inbreeding avoidance. These results suggest that there is selection on the MHC at the pre- and post-copulatory stages, but that apparent disassortative mating with respect to the MHC may be driven by inbreeding avoidance.

scholarly journals Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

2020 ◽  
Vol 6 (45) ◽  
pp. eabd0079
Author(s):  
Xing-Xing Shen ◽  
Jacob L. Steenwyk ◽  
Abigail L. LaBella ◽  
Dana A. Opulente ◽  
Xiaofan Zhou ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Filamentous Fungi ◽  
Common Ancestor ◽  
Evolutionary Change ◽  
Sequence Evolution ◽  
Last Common Ancestor ◽  
Molecular Sequence ◽  
Genome Wide ◽  
Similarities And Differences ◽  
Genome Scale

Ascomycota, the largest and most well-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts). Despite its importance, we lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period. Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina differ greatly in their genome properties and enabled inference of the direction of evolutionary change. The Saccharomycotina typically have smaller genomes, lower guanine-cytosine contents, lower numbers of genes, and higher rates of molecular sequence evolution compared with Pezizomycotina. These results provide a robust evolutionary framework for understanding the diversity and ecological lifestyles of the largest fungal phylum.

scholarly journals Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

2020 ◽  
Author(s):  
Xing-Xing Shen ◽  
Jacob L. Steenwyk ◽  
Abigail L. LaBella ◽  
Dana A. Opulente ◽  
Xiaofan Zhou ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Filamentous Fungi ◽  
Cell Biology ◽  
Gc Content ◽  
Sequence Evolution ◽  
Last Common Ancestor ◽  
Ancestral State ◽  
Molecular Sequence ◽  
Genome Wide ◽  
Genome Scale

AbstractAscomycota, the largest and best-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts); organisms from all three subphyla have been invaluable as models in diverse fields (e.g., biotechnology, cell biology, genetics, and medicine). Despite its importance, we still lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. To address these gaps, we examined 1,107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species to infer the Ascomycota phylogeny, estimate its timetree, and examine the evolution of key genomic properties. We inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran (~563 ± 68 million years ago). Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina, the two taxon-rich subphyla, differed greatly in their genome properties. Saccharomycotina typically have smaller genomes, lower GC contents, lower numbers of genes, and higher rates of molecular sequence evolution compared to Pezizomycotina. Ancestral state reconstruction showed that the genome properties of the Saccharomycotina and Pezizomycotina last common ancestors were very similar, enabling inference of the direction of evolutionary change. For example, we found that a lineage-specific acceleration led to a 1.6-fold higher evolutionary rate in Saccharomycotina, whereas the 10% difference in GC content between Saccharomycotina and Pezizomycotina genomes stems from a trend toward AT bases within budding yeasts and toward GC bases within filamentous fungi. These results provide a robust evolutionary framework for understanding the diversification of the largest fungal phylum.

scholarly journals A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Wim Gorssen ◽  
Roel Meyermans ◽  
Steven Janssens ◽  
Nadine Buys
Keyword(s):  
Association Studies ◽  
Genome Wide Association Studies ◽  
Single Nucleotide ◽  
Future Studies ◽  
Snp Data ◽  
Animal Populations ◽  
Genome Wide ◽  
Starting Point ◽  
Different Populations ◽  
Signatures Of Selection

Abstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. Results The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). Conclusions We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.

scholarly journals Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses

PLoS ONE ◽  
2017 ◽  
Vol 12 (1) ◽  
pp. e0171088 ◽  
Author(s):  
George Msalya ◽  
Eui-Soo Kim ◽  
Emmanuel L. K. Laisser ◽  
Maulilio J. Kipanyula ◽  
Esron D. Karimuribo ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genome Wide ◽  
Signatures Of Selection ◽  
Friesian Cattle

scholarly journals An infanticide attempt by a free-roaming feral stallion ( Equus caballus )

2008 ◽  
Vol 5 (1) ◽  
pp. 23-25 ◽  
Author(s):  
Meeghan E Gray
Keyword(s):  
Sexual Selection ◽  
Genetic Analysis ◽  
Equus Caballus ◽  
Adult Males ◽  
Free Living ◽  
Feral Horses ◽  
Selection Hypothesis ◽  
Sexual Selection Hypothesis ◽  
In Captivity

Infanticide by adult males occurs in a variety of species. While infanticidal attacks have been documented in several equid species in captivity, it has never been witnessed in free-roaming feral horses. I report an infanticide attempt by a free-living feral stallion on a recently born female foal. The stallion picked up the foal by the shoulders, tossed it around twice and bit in on the neck several times. The dam of the foal charged the stallion and successfully protected her foal from additional attacks. The foal survived the attack and later weaned successfully. The stallion recently took over the band and was excluded as the sire through genetic analysis. While this type of attack is rare, this case lends support to the sexual selection hypothesis and further demonstrates that equids have evolved with the risk of infanticide. Furthermore, it shows that maternal protectiveness can be successful against attacks by infanticidal males.

scholarly journals Generalizing rate heterogeneity across sites in statistical phylogenetics

2020 ◽  
Vol 20 (4) ◽  
pp. 410-436
Author(s):  
Sarah E Heaps ◽  
Tom MW Nye ◽  
Richard J Boys ◽  
Tom A Williams ◽  
Svetlana Cherlin ◽  
...  
Keyword(s):  
Linear Models ◽  
Sequence Data ◽  
Sequence Evolution ◽  
Rate Matrix ◽  
Molecular Sequence Data ◽  
Instantaneous Rate ◽  
Sequence Composition ◽  
Molecular Sequence ◽  
Selective Constraints ◽  
Posterior Inference

Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterized by an instantaneous rate matrix. Early models assumed the same rate matrix governed substitutions at all sites of the alignment, ignoring variation in evolutionary pressures. Substantial improvements in phylogenetic inference and model fit were achieved by augmenting these models with multiplicative random effects that describe the result of variation in selective constraints and allow sites to evolve at different rates which linearly scale a baseline rate matrix. Motivated by this pioneering work, we consider an extension using a quadratic, rather than linear, transformation. The resulting models allow for variation in the selective coefficients of different types of point mutation at a site in addition to variation in selective constraints. We derive properties of the extended models. For certain non-stationary processes, the extension gives a model that allows variation in sequence composition, both across sites and taxa. We adopt a Bayesian approach, describe an MCMC algorithm for posterior inference and provide software. Our quadratic models are applied to alignments spanning the tree of life and compared with site-homogeneous and linear models.

scholarly journals The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Naihui Zhou ◽  
Yuxiang Jiang ◽  
Timothy R. Bergquist ◽  
Alexandra J. Lee ◽  
Balint Z. Kacsoh ◽  
...  
Keyword(s):  
Protein Function ◽  
Functional Annotation ◽  
Protein Function Prediction ◽  
Mutation Screening ◽  
Function Prediction ◽  
Long Term Memory ◽  
Functional Annotations ◽  
Genome Wide ◽  
New Development ◽  
Working Together

Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.

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