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 No evidence of positive assortative mating for genetic quality in fruit flies

2019 ◽  
Vol 286 (1912) ◽  
pp. 20191474
Author(s):  
Nathaniel P. Sharp ◽  
Michael C. Whitlock
Keyword(s):  
Sexual Selection ◽  
Assortative Mating ◽  
Genetic Variance ◽  
Genetic Load ◽  
Fruit Fly ◽  
Genetic Quality ◽  
Mating Patterns ◽  
Disassortative Mating ◽  
Deleterious Alleles ◽  
Positive Assortative Mating

In sexual populations, the effectiveness of selection will depend on how gametes combine with respect to genetic quality. If gametes with deleterious alleles are likely to combine with one another, deleterious genetic variation can be more easily purged by selection. Assortative mating, where there is a positive correlation between parents in a phenotype of interest such as body size, is often observed in nature, but does not necessarily reveal how gametes ultimately combine with respect to genetic quality itself. We manipulated genetic quality in fruit fly populations using an inbreeding scheme designed to provide an unbiased measure of mating patterns. While inbred flies had substantially reduced reproductive success, their gametes did not combine with those of other inbred flies more often than expected by chance, indicating a lack of positive assortative mating. Instead, we detected a negative correlation in genetic quality between parents, i.e. disassortative mating, which diminished with age. This pattern is expected to reduce the genetic variance for fitness, diminishing the effectiveness of selection. We discuss how mechanisms of sexual selection could produce a pattern of disassortative mating. Our study highlights that sexual selection has the potential to either increase or decrease genetic load.

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 Horizontal gene transfer of a unique nif island drives convergent evolution of free-living N2-fixing Bradyrhizobium

2021 ◽  
Author(s):  
Jinjin Tao ◽  
Sishuo Wang ◽  
Tianhua Liao ◽  
Haiwei Luo
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Agricultural Research ◽  
Current Knowledge ◽  
Gene Clusters ◽  
Soil Samples ◽  
Genomic Context ◽  
Free Living ◽  
Phylogenomic Analyses ◽  
Conserved Gene

SummaryThe alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the world’s soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that all nif-carrying free-living members comprise a cluster which branches off earlier than most symbiotic lineages. These results indicate that horizontal gene transfer (HGT) promotes nif expansion among the free-living Bradyrhizobium and that the free-living nif cluster represents a more ancestral version compared to that in symbiotic lineages. Further evidence for this rampant HGT is that the nif in free-living members consistently co-locate with several important genes involved in coping with oxygen tension which are missing from symbiotic members, and that while in free-living Bradyrhizobium nif and the co-locating genes show a highly conserved gene order, they each have distinct genomic context. Given the dominance of Bradyrhizobium in world’s soils, our findings have implications for global nitrogen cycles and agricultural research.

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 Identification of Immune Related LRR-Containing Genes in Maize (Zea maysL.) by Genome-Wide Sequence Analysis

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Wei Song ◽  
Baoqiang Wang ◽  
Xinghua Li ◽  
Jianfen Wei ◽  
Ling Chen ◽  
...  
Keyword(s):  
Zea Mays ◽  
Plant Disease Resistance ◽  
Interleukin 1 ◽  
Protein Structures ◽  
Gene Clusters ◽  
Amino Acid Sequences ◽  
Leucine Rich Repeat ◽  
Immune Receptors ◽  
Genome Wide ◽  
First Time

A large number of immune receptors consist of nucleotide binding site-leucine rich repeat (NBS-LRR) proteins and leucine rich repeat-receptor-like kinases (LRR-RLK) that play a crucial role in plant disease resistance. Although many NBS-LRR genes have been previously identified inZea mays, there are no reports on identifying NBS-LRR genes encoded in the N-terminal Toll/interleukin-1 receptor (TIR) motif and identifying genome-wide LRR-RLK genes. In the present study, 151 NBS-LRR genes and 226 LRR-RLK genes were identified after performing bioinformatics analysis of the entire maize genome. Of these identified genes, 64 NBS-LRR genes and four TIR-NBS-LRR genes were identified for the first time. The NBS-LRR genes are unevenly distributed on each chromosome with gene clusters located at the distal end of each chromosome, while LRR-RLK genes have a random chromosomal distribution with more paired genes. Additionally, six LRR-RLK/RLPs including FLS2, PSY1R, PSKR1, BIR1, SERK3, and Cf5 were characterized inZea maysfor the first time. Their predicted amino acid sequences have similar protein structures with their respective homologues in other plants, indicating that these maize LRR-RLK/RLPs have the same functions as their homologues act as immune receptors. The identified gene sequences would assist in the study of their functions in maize.

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.

scholarly journals A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 396 ◽  
Author(s):  
Trine B Rounge ◽  
Thomas Rohrlack ◽  
Alexander J Nederbragt ◽  
Tom Kristensen ◽  
Kjetill S Jakobsen
Keyword(s):  
Gene Clusters ◽  
Nonribosomal Peptide Synthetase ◽  
Nonribosomal Peptide ◽  
Genome Wide Analysis ◽  
Planktothrix Rubescens ◽  
Genome Wide ◽  
A Genome ◽  
Peptide Synthetase

scholarly journals Deep Sequencing of a Dimethylsulfoniopropionate-Degrading Gene (dmdA) by Using PCR Primer Pairs Designed on the Basis of Marine Metagenomic Data

2009 ◽  
Vol 76 (2) ◽  
pp. 609-617 ◽  
Author(s):  
Vanessa A. Varaljay ◽  
Erinn C. Howard ◽  
Shulei Sun ◽  
Mary Ann Moran
Keyword(s):  
Sequence Data ◽  
Gene Clusters ◽  
Amino Acid Identity ◽  
Metagenomic Data ◽  
Data Sets ◽  
Free Living ◽  
Metagenomic Sequence ◽  
Primer Sets ◽  
Design And Testing ◽  
Pcr Primer

ABSTRACT In silico design and testing of environmental primer pairs with metagenomic data are beneficial for capturing a greater proportion of the natural sequence heterogeneity in microbial functional genes, as well as for understanding limitations of existing primer sets that were designed from more restricted sequence data. PCR primer pairs targeting 10 environmental clades and subclades of the dimethylsulfoniopropionate (DMSP) demethylase protein, DmdA, were designed using an iterative bioinformatic approach that took advantage of thousands of dmdA sequences captured in marine metagenomic data sets. Using the bioinformatically optimized primers, dmdA genes were amplified from composite free-living coastal bacterioplankton DNA (from 38 samples over 5 years and two locations) and sequenced using 454 technology. An average of 6,400 amplicons per primer pair represented more than 700 clusters of environmental dmdA sequences across all primers, with clusters defined conservatively at >90% nucleotide sequence identity (∼95% amino acid identity). Degenerate and inosine-based primers did not perform better than specific primer pairs in determining dmdA richness and sometimes captured a lower degree of richness of sequences from the same DNA sample. A comparison of dmdA sequences in free-living versus particle-associated bacteria in southeastern U.S. coastal waters showed that sequence richness in some dmdA subgroups differed significantly between size fractions, though most gene clusters were shared (52 to 91%) and most sequences were affiliated with the shared clusters (∼90%). The availability of metagenomic sequence data has significantly enhanced the design of quantitative PCR primer pairs for this key functional gene, providing robust access to the capabilities and activities of DMSP demethylating bacteria in situ.

Sign in / Sign up

Export Citation Format

Share Document