Estimating diversifying selection and functional constraint in the presence of recombination

Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites

The vast amount of genome sequence data that is available, and that is predicted to drastically increase in the near future, can only be efficiently dealt with by building automated pipelines. Indeed, the Earth Biogenome Project will produce high-quality reference genome sequences for all 1.8 million named living eukaryote species, providing unprecedented insight into the evolution of genes and gene families, and thus on biological issues. Here, new modules for gene annotation, further BLAST search algorithms, further multiple sequence alignment methods, the adding of reference sequences, further tree rooting methods, the estimation of rates of synonymous and nonsynonymous substitutions, and the identification of positively selected amino acid sites, have been added to auto-phylo (version 2), a recently developed software to address biological problems using phylogenetic inferences. Additionally, we present auto-phylo-pipeliner, a graphical user interface application that further facilitates the creation and running of auto-phylo pipelines. Inferences on S-RNase specificity, are critical for both cross-based breeding and for the establishment of pollination requirements. Therefore, as a test case, we develop an auto-phylo pipeline to identify amino acid sites under positive selection, that are, in principle, those determining S-RNase specificity, starting from both non-annotated Prunus genomes and sequences available in public databases.

Genetic heterogeneity of chicken anemia virus isolated in selected Egyptian provinces as a preliminary investigation

Chicken anemia virus (CAV) is a widespread and economically significant pathogen in the poultry industry. In this study 110 samples were collected from various poultry farms in selected Egyptian provinces during 2021-2022 and were tested against CAV by Polymerase Chain Reaction (PCR), revealing 22 positive samples with 20% incidence rate. Full sequence analysis of five selected CAV strains revealed genetic variations in VP1, VP2, and VP3 genes. Phylogenetic analysis grouped the Egyptian strains with reference viruses, mainly in group II, while vaccines like Del-Rose were categorized in group III. Recombination events were detected between an Egyptian strain (genotype II) and the Del-Rose vaccine strain (genotype III), indicating potential recombination between live vaccine strains and field isolates. To evaluate pathogenicity, one Egyptian isolate (F883-2022 CAV) and Del-Rose vaccine were tested in Specific Pathogen Free (SPF) chicks. Chicks in the positive group displayed clinical symptoms, including weakness and stunted growth, with postmortem findings consistent with CAV infection. The vaccine group showed milder symptoms and less severe postmortem changes. This study provides important insights into the genetic diversity of CAV in selected Egyptian poultry farms showing recombination event between field strain and vaccine strains, highlighting the need for advanced vaccination programs, especially for broilers.

Exploring genetic diversity and variation of Ovar-DRB1 gene in Sudan Desert Sheep using targeted next-generation sequencing

INTRODUCTION

The Ovar-DRB1 gene, a crucial element of the Major Histocompatibility Complex (MHC) Class II region, initiates adaptive immunity by presenting antigens to T-cells. Genetic diversity in sheep, particularly in MHC Class II genes like Ovar-DRB1, directly influences the specturm of presented antigens impacting immune responses and disease susceptability. Understanding the allelic diversity of Ovar-DRB1 gene in Sudan Desert Sheep (SDS) is essential for uncovering the genetic basis of immune responses and disease resistance, given the the breeds significance in Sudan's unique environment.

METHODS

Utilizing Targeted Next-Generation Sequencing (NGS) we explore allelic diversity in Ovar-DRB1 gene within SDS. Successfully ampliying and and sequencing the second exon of this gene in 288 SDS samples representing six breeds provided a comprehensive allelic profile, enabling a detalied examination of the gene's genetic makeup.

RESULTS

We identifed forty-six alleles, including four previously unreported, enrichness the genetic diversity of SDS breeds. These alleles exhibiting non-uniform distribution, varying frequencies across breeds, indicating a breed-specific genetic landscape. Certain alleles, known and novel, show higher frequencies in specific populations, suggesting potential associations with adaptive immune responses. Identifying these alleles sets the stage for investigating their functional roles and implications for disease resistance. Genetic differentiation among SDS breeds, as indicated by FST values and clustering analyses, highlights a unique genetic makeup shaped by geographic and historical factors. These differentiation patterns among SDS breeds have broader implications for breed conservation and targeted breeding to enhance disease resistance in specific populations.

CONCLUSION

This study unveils Ovar-DRB1 gene allelic diversity in SDS breeds through targeted NGS and genetic analyses, revealing new alleles that underscore the breeds' unique genetic profile. Insights into the genetic factors governing immune responses and disease resistance emerge, promising for optimization of breeding strategies for enhanced livestock health in Sudan's unique environment.

Patterns of evolution in MHC class II DQA and DQB exon 2 genes of Alpine mountain hares, Lepus timidus varronis, and sympatric and parapatric brown hares, L. europaeus, from Switzerland

In natural populations, hybridization is known to occur between a wide range of species. However, its evolutionary significance is less clear. Genes involved in fighting pathogens are considered excellent candidates for studying adaptive introgression, although both introgression and balancing selection can generate similar patterns of diversity and differentiation. Here, we compared DQA and DQB MHC class II and microsatellite allelic diversity of sympatric and parapatric mountain (Lepus timidus) and brown hare (L. europaeus) populations from Switzerland. We detected higher genetic diversity in brown hares compared to mountain hares at both MHC and microsatellite loci. We consider the observed patterns of microsatellite diversity both for L. europaeus and L. timidus as result of stochastic demographic processes while the pattern of MHC polymorphism of the studied hare populations can be explained by pathogen-driven selection. Rare bidirectional gene flow between both hare species seems to occur specifically for MHC alleles. However, the high number of shared alleles showing similar high frequency in both species suggests that reciprocally exchanged MHC alleles are being maintained via balancing selection. Adaptation to similar pathogen communities can also lead to parallel selection of MHC alleles. Positive selection, recombination and mutations have played different roles in shaping the patterns of MHC allelic diversity in and differentiation between both species. Results for the latter evolutionary forces do not show a better matching between the sympatric populations compared to the parapatric ones, suggesting a minor role of introgression for the observed evolutionary patterns of the studied hare species.

Recent selection created distinctive variability patterns on MHC class II loci in three dolphin species from the Mediterranean Sea

The major histocompatibility complex (MHC) includes highly polymorphic genes involved in antigen presentation, which is crucial for adaptive immune response. They represent fitness related genetic markers particularly informative for populations exposed to environmental challenges. Here we analyse the diversity and evolutionary traits of MHC class II DQA and DQB genes in the dolphins Stenella coeruleoalba and Grampus griseus from the Mediterranean Sea. We found substantial nucleotide and functional diversity, as well as strong evidence of balancing selection indicated by allele and supertype frequencies, Tajima's D statistics and dN/dS tests. The Risso's dolphin, considered the least abundant in the region, showed the effect of divergent allele advantage at the nucleotide and functional-peptide levels. An outstanding polymorphism was found in the striped dolphin, particularly intriguing in the DQA gene where the Ewens-Watterson test detected a selection sweep that occurred in recent history. We hypothesize that morbillivirus, which has recurrently invaded Mediterranean populations over the last decades, exerted the detected selective pressure.

Diversity and phylogeography of begomoviruses and DNA satellites associated with the leaf curl and mosaic disease complex of eggplant

Eggplant is one of the important vegetable crops grown across the world, and its production is threatened by both biotic and abiotic stresses. Diseases caused by viruses are becoming major limiting factors for its successful cultivation. A survey for begomovirus-like symptoms in 72 eggplant fields located in six different Indian states revealed a prevalence of disease ranging from 5.2 to 40.2%, and the symptoms recorded were mosaic, mottling, petiole bending, yellowing, and upward curling, vein thickening, and enation of the leaves, and stunting of plants. The causal agent associated with these plants was transmitted from infected leaf samples to healthy eggplant seedlings via grafting and whiteflies (Bemisia tabaci). The presence of begomovirus was confirmed in 72 infected eggplant samples collected from the surveyed fields exhibiting leaf curl and mosaic disease by PCR using begomovirus specifc primers (DNA-A componet), which resulted in an expected amplicon of 1.2 kb. The partial genome sequence obtained from amplified 1.2 kb from all samples indicated that they are closely related begomovirus species, tomato leaf Karnataka virus (ToLCKV, two samples), tomato leaf curl Palampur virus (ToLCPalV, fifty eggplant samples), and chilli leaf curl virus (ChLCuV, twenty samples). Based on the partial genome sequence analysis, fourteen representative samples were selected for full viral genome amplification by the rolling circle DNA amplification (RCA) technique. Analyses of fourteen eggplant isolates genome sequences using the Sequence Demarcation Tool (SDT) indicated that one isolate had the maximum nucleotide (nt) identity with ToLCKV and eight isolates with ToLCPalV. Whereas, four isolates four isolates (BLC1-CH, BLC2-CH, BLC3-CH, BLC4-CH) are showing nucleotide identity of less than 91% with chilli infecting viruses begomoviruses with chilli infecting begomoviruses and as per the guidelines given by the ICTV study group for the classification of begomoviruses these isolates are considered as one novel begomovirus species, for which name, Eggplant leaf curl Chhattisgarh virus (EgLCuChV) is proposed. For DNA-B component, seven eggplant isolates had the highest nt identity with ToLCPalV infecting other crops. Further, DNA satellites sequence analysis indicated that four betasatellites identified shared maximum nucleotide identity with the tomato leaf curl betasatellite and five alphasatellites shared maximum nucleotide identity with the ageratum enation alphasatellite. Recombination and GC plot analyses indicated that the bulk of begomovirus genome and associated satellites presumably originated from of previously known mono and bipartite begomoviruses and DNA satellites. To the best of our knowledge, this is India's first report of ToLCKV and a noval virus, eggplant leaf curl Chhattisgarh virus associated with eggplant leaf curl disease.

Next-generation development and application of codon model in evolution

To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine.

Detection of positive selection acting on protein surfaces at the whole-genome scale in the human malaria parasite Plasmodium falciparum

The host-parasite evolutionary arms race is a fundamental process with medical implications. During this process, the host develops parasite resistance, and the parasite develops host immune evasion strategies. Thus, this process accelerates relevant protein evolution. This study test hypothesizes that proteins subject to sequence evolution structural constraints play a crucial role and that these constraints hinder the modification of such proteins in this process. These hypotheses were tested using Plasmodium falciparum model and evaluated protein structures predicted for the entire proteome by the AlphaFold method. Based on dN/dS test results and P. falciparum and P. reichenowi comparisons, the presented approach identified proteins subject to purifying selection acting on the whole sequence and buried residues (dN < dS) and positive selection on nonburied residues. Of the 26 proteins, some known antigens (ring-exported protein 3, RAP protein, erythrocyte binding antigen-140, and protein P47) targeted by the host immune system are promising vaccine candidates. The set also contained 11 enzymes, including FIKK kinase, which modifies host proteins. This set was compared with genes for which the dN/dS test suggested that positive selection acts on the whole gene (i.e., dN > dS). The present study found that such genes encode enzymes and antigenic vaccine candidates less frequently than genes for which evolution is not subject to selection constraints and positive selection acts on only exposed residues. The analysis was repeated comparing P. falciparum with P. alderi, which is more distantly related. The study discusses the potential implications of the presented methodology for rational vaccine design and the parasitology and evolutionary biology fields.

Structure and evolution of the squamate major histocompatibility complex as revealed by two Anolis lizard genomes

The major histocompatibility complex (MHC) is an important genomic region for adaptive immunity and has long been studied in ecological and evolutionary contexts, such as disease resistance and mate and kin selection. The MHC has been investigated extensively in mammals and birds but far less so in squamate reptiles, the third major radiation of amniotes. We localized the core MHC genomic region in two squamate species, the green anole (Anolis carolinensis) and brown anole (A. sagrei), and provide the first detailed characterization of the squamate MHC, including the presence and ordering of known MHC genes in these species and comparative assessments of genomic structure and composition in MHC regions. We find that the Anolis MHC, located on chromosome 2 in both species, contains homologs of many previously-identified mammalian MHC genes in a single core MHC region. The repetitive element composition in anole MHC regions was similar to those observed in mammals but had important distinctions, such as higher proportions of DNA transposons. Moreover, longer introns and intergenic regions result in a much larger squamate MHC region (11.7 Mb and 24.6 Mb in the green and brown anole, respectively). Evolutionary analyses of MHC homologs of anoles and other representative amniotes uncovered generally monophyletic relationships between species-specific homologs and a loss of the peptide-binding domain exon 2 in one of two mhc2β gene homologs of each anole species. Signals of diversifying selection in each anole species was evident across codons of mhc1, many of which appear functionally relevant given known structures of this protein from the green anole, chicken, and human. Altogether, our investigation fills a major gap in understanding of amniote MHC diversity and evolution and provides an important foundation for future squamate-specific or vertebrate-wide investigations of the MHC.

The Evolutionary Dynamics of the Mitochondrial tRNA in the Cichlid Fish Family

Simple Summary

Cichlids are a unique example of fish diversity and species richness which have been explained by sympatric speciation at different freshwater sources in Africa. The mitochondria contribute to cell vitality by providing energy. It contains a circular genome with an established translation system that is spatially independent of the cytosolic counterpart. The current study aimed to investigate the evolutionary dynamics of the mitochondrial tRNA and its role in cichlids’ diversity. The available cichlid mitogenomes in the public database were filtered, in addition to newly sequenced accessions from a specific cichlid group known as the haplotilapiine lineage that is widely distributed in the Egyptian sector of the Nile River. Based on the comparative analysis of mitogenomic data, we identified 22 tRNA genes, in which a single gene was D-armless, while the cloverleaf secondary structure subdivided into stem-loop formations was predicted and used to define the levels of genetic divergence for the remained tRNAs. Peculiarly, in cichlids, the formation known as “T-arm” showed the lowest polymorphism levels among other structures in contrast to other organisms (e.g., scorpions). Comparing the whole family to the specific haplotilapiine lineage showed that the tryptophan tRNA was the most conserved tRNA, with signatures of possible purifying selection.

Abstract

The mitochondrial transfer RNA genes (tRNAs) attract more attention due to their highly dynamic and rapidly evolving nature. The current study aimed to detect and evaluate the dynamics, characteristic patterns, and variations of mitochondrial tRNAs. The study was conducted in two main parts: first, the published mitogenomic sequences of cichlids mt tRNAs have been filtered. Second, the filtered mitochondrial tRNA and additional new mitogenomes representing the most prevalent Egyptian tilapiine were compared and analyzed. Our results revealed that all 22 tRNAs of cichlids folded into a classical cloverleaf secondary structure with four domains, except for trnS^GCU, missing the D domain in all cichlids. When consensus tRNAs were compared, most of the mutations were observed in the trnP at nucleotide levels (substitutions and indels), in contrast to trnL^UAA. From a structural perspective, the anticodon loop and T-loop formations were the most conserved structures among all parts of the tRNA in contrast to the A-stem and D-loop formations. The trnW was the lowest polymorphic unneutral tRNA among all cichlids (both the family and the haplotilapiine lineage), in contrast with the neutral trnD that was extremely polymorphic among and within the haplotilapiine lineage species compared to other cichlids species. From a phylogenetic perspective, the trnC was extremely hypervariable and neutral tRNA in both haplotilapiine lineage and cichlids but was unable to report correct phylogenetic signal for the cichlids. In contrast to trnI and trnY, less variable neutral tRNAs that were able to cluster the haplotilapiine lineage and cichlids species as previously reported. By observing the DNA polymorphism in the coding DNA sequences (CDS), the highest affected amino acid by non-synonymous mutations was isoleucine and was equally mutated to valine and vice versa; no correlation between mutations in CDS and tRNAs was statistically found. The current study provides an insight into the mitochondrial tRNA evolution and its effect on the cichlid diversity and speciation model at the maternal level.

Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed susceptibility to diverse animal species. We conducted this study to understand the spatial epidemiology, genetic diversity, and statistically significant genetic similarity along with per-gene recombination events of SARS-CoV-2 and related viruses (SC2r-CoVs) in animals globally. We collected a number of different animal species infected with SARS-CoV-2 and its related viruses. Then, we retrieved genome sequences of SARS-CoV-2 and SC2r-CoVs from GISAID and NCBI GenBank for genomic and mutational analysis. Although the evolutionary origin of SARS-CoV-2 remains elusive, the diverse SC2r-CoV have been detected in multiple Rhinolophus bat species and in Malayan pangolin. To date, human-to-animal spillover events have been reported in cat, dog, tiger, lion, gorilla, leopard, ferret, puma, cougar, otter, and mink in 25 countries. Phylogeny and genetic recombination events of SC2r-CoVs showed higher similarity to the bat coronavirus RaTG13 and BANAL-103 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the N protein from bats and pangolin showed close resemblance to SARS-CoV-2. The clustering of animal and human strains from the same geographical area has proved human-to-animal transmission of the virus. The Alpha, Delta and Mu-variant of SARS-CoV-2 was detected in dog, gorilla, lion, tiger, otter, and cat in the USA, India, Czech Republic, Belgium, and France with momentous genetic similarity with human SARS-CoV-2 sequences. The mink variant mutation (spike_Y453F) was detected in both humans and domestic cats. Moreover, the dog was affected mostly by clade O (66.7%), whereas cat and American mink were affected by clade GR (31.6 and 49.7%, respectively). The α-variant was detected as 2.6% in cat, 4.8% in dog, 14.3% in tiger, 66.7% in gorilla, and 77.3% in lion. The highest mutations observed in mink where the substitution of D614G in spike (95.2%) and P323L in NSP12 (95.2%) protein. In dog, cat, gorilla, lion, and tiger, Y505H and Y453F were the common mutations followed by Y145del, Y144del, and V70I in S protein. We recommend vaccine provision for pet and zoo animals to reduce the chance of transmission in animals. Besides, continuous epidemiological and genomic surveillance of coronaviruses in animal host is crucial to find out the immediate ancestor of SARS-CoV-2 and to prevent future CoVs threats to humans.

A brief history and popularity of methods and tools used to estimate micro-evolutionary forces

Population genetics is a field of research that predates the current generations of sequencing technology. Those approaches, that were established before massively parallel sequencing methods, have been adapted to these new marker systems (in some cases involving the development of new methods) that allow genome-wide estimates of the four major micro-evolutionary forces-mutation, gene flow, genetic drift, and selection. Nevertheless, classic population genetic markers are still commonly used and a plethora of analysis methods and programs is available for these and high-throughput sequencing (HTS) data. These methods employ various and diverse theoretical and statistical frameworks, to varying degrees of success, to estimate similar evolutionary parameters making it difficult to get a concise overview across the available approaches. Presently, reviews on this topic generally focus on a particular class of methods to estimate one or two evolutionary parameters. Here, we provide a brief history of methods and a comprehensive list of available programs for estimating micro-evolutionary forces. We furthermore analyzed their usage within the research community based on popularity (citation bias) and discuss the implications of this bias for the software community. We found that a few programs received the majority of citations, with program success being independent of both the parameters estimated and the computing platform. The only deviation from a model of exponential growth in the number of citations was found for the presence of a graphical user interface (GUI). Interestingly, no relationship was found for the impact factor of the journals, when the tools were published, suggesting accessibility might be more important than visibility.

BoLA-DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds

Autochthonous Sudanese cattle breeds, namely Baggara for beef and Butana and Kenana for dairy, are characterized by their adaptive characteristics and high performance in hot and dry agro-ecosystems. They are thus used largely by nomadic and semi-nomadic pastoralists. We analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus linked to the immune response, for the indigenous cattle of Sudan and in the context of the global cattle repository. Blood samples (n = 225) were taken from three indigenous breeds (Baggara; n = 113, Butana; n = 60 and Kenana; n = 52) distributed across six regions of Sudan. Nucleotide sequences were genotyped using the sequence-based typing method. We describe 53 alleles, including seven novel alleles. Principal component analysis (PCA) of the protein pockets implicated in the antigen-binding function of the MHC complex revealed that pockets 4 and 9 (respectively) differentiate Kenana-Baggara and Kenana-Butana breeds from other breeds. Venn analysis of Sudanese, Southeast Asian, European and American cattle breeds with 115 alleles showed 14 were unique to Sudanese breeds. Gene frequency distributions of Baggara cattle showed an even distribution suggesting balancing selection, while the selection index (ω) revealed the presence of diversifying selection in several amino acid sites along the BoLA-DRB3 exon 2 of these native breeds. The results of several PCA were in agreement with clustering patterns observed on the neighbor joining (NJ) trees. These results provide insight into their high survival rate for different tropical diseases and their reproductive capacity in Sudan's harsh environment.

Positive selection on the MHC class II DLA-DQA1 gene in golden jackals (Canis aureus) from their recent expansion range in Europe and its effect on their body mass index

Background

In Europe, golden jackals (Canis aureus) have been expanding their range out of the southern and southeastern Balkans towards central Europe continually since the 1960s. Here, we investigated the level of functional diversity at the MHC class II DLA-DQA1 exon 2 in golden jackal populations from Bulgaria, Serbia, and Hungary. Specifically, we tested for positive selection on and geographic variation at that locus due to adaptation to supposedly regionally varying pathogenic landscapes. To test for potential fitness effects of different protein variants on individual body condition, we used linear modeling of individual body mass indexes (bmi) and accounted for possible age, sex, geographical, and climatic effects. The latter approach was performed, however, only on Serbian individuals with appropriate data.

Results

Only three different DLA-DQA1 alleles were detected, all coding for different amino-acid sequences. The neutrality tests revealed no significant but positive values; there was no signal of spatial structuring and no deviation from the Hardy–Weinberg equilibrium across the studied range of expansion. However, we found a signal of trans-species polymorphism and significant test results for positive selection on three codons. Our information-theory based linear modeling results indicated an effect of ambient temperature on the occurrence of individual DLA-DQA1 genotypes in individuals from across the studied expansion range, independent from geographical position. Our linear modeling results of individual bmi values indicated that yearlings homozygous for DLA-DQA1*03001 reached values typical for adults contrary to yearlings carrying other genotypes (protein combinations). This suggested better growth rates and thus a possible fitness advantage of yearlings homozygous for DLA-DQA1*03001.

Conclusions

Our results indicate a demographic (stochastic) signal of reduced DLA-DQA1 exon 2 variation, in line with the documented historical demographic bottleneck. At the same time, however, allelic variation was also affected by positive selection and adaptation to varying ambient temperature, supposedly reflecting geographic variation in the pathogenic landscape. Moreover, an allele effect on body mass index values of yearlings suggested differential fitness associated with growth rates. Overall, a combination of a stochastic effect and positive selection has shaped and is still shaping the variation at the studied MHC locus.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01856-z.

On the Identification of Clinically Relevant Bacterial Amino Acid Changes at the Whole Genome Level Using Auto-PSS-Genome

The identification of clinically relevant bacterial amino acid changes can be performed using different methods aimed at the identification of genes showing positively selected amino acid sites (PSS). Nevertheless, such analyses are time consuming, and the frequency of genes showing evidence for PSS can be low. Therefore, the development of a pipeline that allows the quick and efficient identification of the set of genes that show PSS is of interest. Here, we present Auto-PSS-Genome, a Compi-based pipeline distributed as a Docker image, that automates the process of identifying genes that show PSS using three different methods, namely codeML, FUBAR, and omegaMap. Auto-PSS-Genome accepts as input a set of FASTA files, one per genome, containing all coding sequences, thus minimizing the work needed to conduct positively selected sites analyses. The Auto-PSS-Genome pipeline identifies orthologous gene sets and corrects for multiple possible problems in input FASTA files that may prevent the automated identification of genes showing PSS. A FASTA file containing all coding sequences can also be given as an external global reference, thus easing the comparison of results across species, when gene names are different. In this work, we use Auto-PSS-Genome to analyse Mycobacterium leprae (that causes leprosy), and the closely related species M. haemophilum, that mainly causes ulcerating skin infections and arthritis in persons who are severely immunocompromised, and in children causes cervical and perihilar lymphadenitis. The genes identified in these two species as showing PSS may be those that are partially responsible for virulence and resistance to drugs.

GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes

The dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters, such as dN/dS, but analyzing very large data sets poses a major statistical challenge. Here, I introduce genomegaMap for estimating within-species genome-wide variation in dN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: 1) It is fast no matter how large the sample size and 2) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well estimated even when genomegaMap’s simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions in Mycobacterium tuberculosis and describe a novel signature of selection in the cold-shock DEAD-box protein A gene deaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species.

Inference of population admixture network from local gene genealogies: a coalescent-based maximum likelihood approach

Motivation

Population admixture is an important subject in population genetics. Inferring population demographic history with admixture under the so-called admixture network model from population genetic data is an established problem in genetics. Existing admixture network inference approaches work with single genetic polymorphisms. While these methods are usually very fast, they do not fully utilize the information [e.g. linkage disequilibrium (LD)] contained in population genetic data.

Results

In this article, we develop a new admixture network inference method called GTmix. Different from existing methods, GTmix works with local gene genealogies that can be inferred from population haplotypes. Local gene genealogies represent the evolutionary history of sampled haplotypes and contain the LD information. GTmix performs coalescent-based maximum likelihood inference of admixture networks with inferred local genealogies based on the well-known multispecies coalescent (MSC) model. GTmix utilizes various techniques to speed up the likelihood computation on the MSC model and the optimal network search. Our simulations show that GTmix can infer more accurate admixture networks with much smaller data than existing methods, even when these existing methods are given much larger data. GTmix is reasonably efficient and can analyze population genetic datasets of current interests.

Availability and implementation

The program GTmix is available for download at: https://github.com/yufengwudcs/GTmix.

Supplementary information

Supplementary data are available at Bioinformatics online.

Analysis of selection in protein-coding sequences accounting for common biases

The evolution of protein-coding genes is usually driven by selective processes, which favor some evolutionary trajectories over others, optimizing the subsequent protein stability and activity. The analysis of selection in this type of genetic data is broadly performed with the metric nonsynonymous/synonymous substitution rate ratio (dN/dS). However, most of the well-established methodologies to estimate this metric make crucial assumptions, such as lack of recombination or invariable codon frequencies along genes, which can bias the estimation. Here, we review the most relevant biases in the dN/dS estimation and provide a detailed guide to estimate this metric using state-of-the-art procedures that account for such biases, along with illustrative practical examples and recommendations. We also discuss the traditional interpretation of the estimated dN/dS emphasizing the importance of considering complementary biological information such as the role of the observed substitutions on the stability and function of proteins. This review is oriented to help evolutionary biologists that aim to accurately estimate selection in protein-coding sequences.

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents

Hepatitis C virus (HCV; genus Hepacivirus) represents a major public health problem, infecting about three per cent of the human population. Because no animal reservoir carrying closely related hepaciviruses has been identified, the zoonotic origins of HCV still remain unresolved. Motivated by recent findings of divergent hepaciviruses in rodents and a plausible African origin of HCV genotypes, we have screened a large collection of small mammals samples from seven sub-Saharan African countries. Out of 4,303 samples screened, eighty were found positive for the presence of hepaciviruses in twenty-nine different host species. We, here, report fifty-six novel genomes that considerably increase the diversity of three divergent rodent hepacivirus lineages. Furthermore, we provide strong evidence for hepacivirus co-infections in rodents, which were exclusively found in four sampled species of brush-furred mice. We also detect evidence of recombination within specific host lineages. Our study expands the available hepacivirus genomic data and contributes insights into the relatively deep evolutionary history of these pathogens in rodents. Overall, our results emphasize the importance of rodents as a potential hepacivirus reservoir and as models for investigating HCV infection dynamics.

Site-Specific Amino Acid Distributions Follow a Universal Shape

In many applications of evolutionary inference, a model of protein evolution needs to be fitted to the amino acid variation at individual sites in a multiple sequence alignment. Most existing models fall into one of two extremes: Either they provide a coarse-grained description that lacks biophysical realism (e.g., dN/dS models), or they require a large number of parameters to be fitted (e.g., mutation-selection models). Here, we ask whether a middle ground is possible: Can we obtain a realistic description of site-specific amino acid frequencies while severely restricting the number of free parameters in the model? We show that a distribution with a single free parameter can accurately capture the variation in amino acid frequency at most sites in an alignment, as long as we are willing to restrict our analysis to predicting amino acid frequencies by rank rather than by amino acid identity. This result holds equally well both in alignments of empirical protein sequences and of sequences evolved under a biophysically realistic all-atom force field. Our analysis reveals a near universal shape of the frequency distributions of amino acids. This insight has the potential to lead to new models of evolution that have both increased realism and a limited number of free parameters.

Impact of homologous recombination on core genome phylogenies

BACKGROUND

Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate.

RESULTS

In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts.

CONCLUSIONS

Overall, these results have important implications for the application of core genome phylogenies in prokaryotes.

Predicting functional effects of missense variants in voltage-gated sodium and calcium channels

Malfunctions of voltage-gated sodium and calcium channels (encoded by SCNxA and CACNA1x family genes, respectively) have been associated with severe neurologic, psychiatric, cardiac, and other diseases. Altered channel activity is frequently grouped into gain or loss of ion channel function (GOF or LOF, respectively) that often corresponds not only to clinical disease manifestations but also to differences in drug response. Experimental studies of channel function are therefore important, but laborious and usually focus only on a few variants at a time. On the basis of known gene-disease mechanisms of 19 different diseases, we inferred LOF (n = 518) and GOF (n = 309) likely pathogenic variants from the disease phenotypes of variant carriers. By training a machine learning model on sequence- and structure-based features, we predicted LOF or GOF effects [area under the receiver operating characteristics curve (ROC) = 0.85] of likely pathogenic missense variants. Our LOF versus GOF prediction corresponded to molecular LOF versus GOF effects for 87 functionally tested variants in SCN1/2/8A and CACNA1I (ROC = 0.73) and was validated in exome-wide data from 21,703 cases and 128,957 controls. We showed respective regional clustering of inferred LOF and GOF nucleotide variants across the alignment of the entire gene family, suggesting shared pathomechanisms in the SCNxA/CACNA1x family genes.

Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen

Identifying genetic variation in bacteria that has been shaped by ecological differences remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show that derived alleles <300 bp apart in Neisseria gonorrhoeae exhibit more coupling linkage than repulsion linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles than synonymous alleles. This general pattern is driven by a small fraction of highly diverse genes, many of which exhibit evidence of interspecies horizontal gene transfer and an excess of intermediate frequency alleles. Extensive simulations show that two distinct forms of positive selection can create these patterns of genetic variation: directional selection on horizontally transferred alleles or balancing selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.

Molecular Targets for Coevolutionary Interactions Between Pacific Oyster Larvae and Their Sympatric Vibrios

Bacteria of the Vibrio genus are the most predominant infectious agents threatening marine wildlife and aquaculture. Due to the large genetic diversity of these pathogens, the molecular determinants of Vibrio virulence are only poorly understood. Furthermore, studies tend to ignore co-evolutionary interactions between different host populations and their locally encountered Vibrio communities. Here, we explore the molecular targets of such co-evolutionary interactions by analyzing the genomes of nine Vibrio strains from the Splendidus-clade showing opposite virulence patterns towards two populations of Pacific oysters introduced into European Wadden Sea. By contrasting Vibrio phylogeny to their host specific virulence patterns, we could identify two core genome genes (OG1907 and OG 3159) that determine the genotype by genotype (G × G) interactions between oyster larvae and their sympatric Vibrio communities. Both genes show positive selection between locations targeting only few amino acid positions. Deletion of each gene led to a loss of the host specific virulence patterns while complementation with OG3159 alleles from both locations could recreate the wild type phenotypes matching the origin of the allele. This indicates that both genes can act as a genetic switch for Vibrio-oyster coevolution demonstrating that local adaptation in distinct Vibrio lineages can rely on only few genes independent of larger pathogenicity islands or plasmids.

Mapping the drivers of within-host pathogen evolution using massive data sets

Differences among hosts, resulting from genetic variation in the immune system or heterogeneity in drug treatment, can impact within-host pathogen evolution. Genetic association studies can potentially identify such interactions. However, extensive and correlated genetic population structure in hosts and pathogens presents a substantial risk of confounding analyses. Moreover, the multiple testing burden of interaction scanning can potentially limit power. We present a Bayesian approach for detecting host influences on pathogen evolution that exploits vast existing data sets of pathogen diversity to improve power and control for stratification. The approach models key processes, including recombination and selection, and identifies regions of the pathogen genome affected by host factors. Our simulations and empirical analysis of drug-induced selection on the HIV-1 genome show that the method recovers known associations and has superior precision-recall characteristics compared to other approaches. We build a high-resolution map of HLA-induced selection in the HIV-1 genome, identifying novel epitope-allele combinations.

Genetic Diversity and Differentiation at Structurally Varying MHC Haplotypes and Microsatellites in Bottlenecked Populations of Endangered Crested Ibis

Investigating adaptive potential and understanding the relative roles of selection and genetic drift in populations of endangered species are essential in conservation. Major histocompatibility complex (MHC) genes characterized by spectacular polymorphism and fitness association have become valuable adaptive markers. Herein we investigate the variation of all MHC class I and II genes across seven populations of an endangered bird, the crested ibis, of which all current individuals are offspring of only two pairs. We inferred seven multilocus haplotypes from linked alleles in the Core Region and revealed structural variation of the class II region that probably evolved through unequal crossing over. Based on the low polymorphism, structural variation, strong linkage, and extensive shared alleles, we applied the MHC haplotypes in population analysis. The genetic variation and population structure at MHC haplotypes are generally concordant with those expected from microsatellites, underlining the predominant role of genetic drift in shaping MHC variation in the bottlenecked populations. Nonetheless, some populations showed elevated differentiation at MHC, probably due to limited gene flow. The seven populations were significantly differentiated into three groups and some groups exhibited genetic monomorphism, which can be attributed to founder effects. We therefore propose various strategies for future conservation and management.

Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore

Background

Different population trajectories are expected to impact the signature of neutral and adaptive processes at multiple levels, challenging the assessment of the relative roles of different microevolutionary forces. Here, we integrate adaptive and neutral variability patterns to disentangle how adaptive diversity is driven under different demographic scenarios within the Iberian wolf (Canis lupus) range. We studied the persistent, the expanding and a small, isolated group within the Iberian wolf population, using 3 MHC class II genes (DRB1, DQA1, and DQB1), which diversity was compared with 39 microsatellite loci.

Results

Both the persistent and the expanding groups show evidence of balancing selection, revealed by a significant departure from neutrality at MHC loci, significant higher observed and expected heterozygosity and lower differentiation at MHC than at neutral loci, and signs of positive selection. However, despite exhibiting a significantly higher genetic diversity than the isolated group, the persistent group did not show significant excess of MHC heterozygotes. The expanding group, while showing a similar level of genetic diversity than the persistent group, displays by contrast a significant excess of MHC heterozygotes, which is compatible with the heterozygote advantage mechanism. Results are not clear regarding the role of drift and selection in the isolated group due to the small size of this population. Although diversity indices of MHC loci correspond to neutral expectations in the isolated group, accelerated MHC divergence, revealed by a higher differentiation at MHC than neutral loci, may indicate diversifying selection.

Conclusion

Different selective pressures were observed in the three different demographic scenarios, which are possibly driven by different selection mechanisms to maintain adaptive diversity.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1420-5) contains supplementary material, which is available to authorized users.

LDJump: Estimating variable recombination rates from population genetic data

As recombination plays an important role in evolution, its estimation and the identification of hotspot positions is of considerable interest. We propose a novel approach for estimating population recombination rates based on genotyping or sequence data that involves a sequential multiscale change point estimator. Our method also permits demography to be taken into account. It uses several summary statistics within a regression model fitted on suitable scenarios. Our proposed method is accurate, computationally fast, and provides a parsimonious solution by ensuring a type I error control against too many changes in the recombination rate. An application to human genome data suggests a good congruence between our estimated and experimentally identified hotspots. Our method is implemented in the R‐package LDJump, which is freely available at https://github.com/PhHermann/LDJump.

Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates

BACKGROUND

An excess of nonsynonymous substitutions, over neutrality, is considered evidence of positive Darwinian selection. Inference for proteins often relies on estimation of the nonsynonymous to synonymous ratio (ω = dN/dS) within a codon model. However, to ease computational difficulties, ω is typically estimated assuming an idealized substitution process where (i) all nonsynonymous substitutions have the same rate (regardless of impact on organism fitness) and (ii) instantaneous double and triple (DT) nucleotide mutations have zero probability (despite evidence that they can occur). It follows that estimates of ω represent an imperfect summary of the intensity of selection, and that tests based on the ω > 1 threshold could be negatively impacted.

RESULTS

We developed a general-purpose parametric (GPP) modelling framework for codons. This novel approach allows specification of all possible instantaneous codon substitutions, including multiple nonsynonymous rates (MNRs) and instantaneous DT nucleotide changes. Existing codon models are specified as special cases of the GPP model. We use GPP models to implement likelihood ratio tests for ω > 1 that accommodate MNRs and DT mutations. Through both simulation and real data analysis, we find that failure to model MNRs and DT mutations reduces power in some cases and inflates false positives in others. False positives under traditional M2a and M8 models were very sensitive to DT changes. This was exacerbated by the choice of frequency parameterization (GY vs. MG), with rates sometimes > 90% under MG. By including MNRs and DT mutations, accuracy and power was greatly improved under the GPP framework. However, we also find that over-parameterized models can perform less well, and this can contribute to degraded performance of LRTs.

CONCLUSIONS

We suggest GPP models should be used alongside traditional codon models. Further, all codon models should be deployed within an experimental design that includes (i) assessing robustness to model assumptions, and (ii) investigation of non-standard behaviour of MLEs. As the goal of every analysis is to avoid false conclusions, more work is needed on model selection methods that consider both the increase in fit engendered by a model parameter and the degree to which that parameter is affected by un-modelled evolutionary processes.

The Diversity of Mammalian Hemoproteins and Microbial Heme Scavengers Is Shaped by an Arms Race for Iron Piracy

Iron is an essential micronutrient for most living species. In mammals, hemoglobin (Hb) stores more than two thirds of the body's iron content. In the bloodstream, haptoglobin (Hp) and hemopexin (Hpx) sequester free Hb or heme. Pathogenic microorganisms usually acquire iron from their hosts and have evolved complex systems of iron piracy to circumvent nutritional immunity. Herein, we performed an evolutionary analysis of genes coding for mammalian heme-binding proteins and heme-scavengers in pathogen species. The underlying hypothesis is that these molecules are engaged in a molecular arms race. We show that positive selection drove the evolution of mammalian Hb and Hpx. Positively selected sites in Hb are located at the interaction surface with Neisseria meningitidis heme scavenger HpuA and with Staphylococcus aureus iron-regulated surface determinant B (IsdB). In turn, positively selected sites in HpuA and IsdB are located in the flexible protein regions that contact Hb. A residue in Hb (S45H) was also selected on the Caprinae branch. This site stabilizes the interaction with Trypanosoma brucei hemoglobin-haptoglobin (HbHp) receptor (TbHpHbR), a molecule that also mediates trypanosome lytic factor (TLF) entry. In TbHpHbR, positive selection drove the evolution of a variant (L210S) which allows evasion from TLF but reduces affinity for HbHp. Finally, selected sites in Hpx are located at the interaction surface with the Haemophilus influenzae hemophore HxuA, which in turn displays fast evolving sites at the Hpx-binding interface. These results shed light into host-pathogens conflicts and establish the importance of nutritional immunity as an evolutionary force.

Microbial sequence typing in the genomic era

Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology.

Positive selection and climatic effects on MHC class II gene diversity in hares (Lepus capensis) from a steep ecological gradient

In natural populations, allelic diversity of the major histocompatibility complex (MHC) is commonly interpreted as resulting from positive selection in varying spatiotemporal pathogenic landscapes. Composite pathogenic landscape data are, however, rarely available. We studied the spatial distribution of allelic diversity at two MHC class II loci (DQA, DQB) in hares, Lepus capensis, along a steep ecological gradient in North Africa and tested the role of climatic parameters for the spatial distribution of DQA and DQB proteins. Climatic parameters were considered to reflect to some extent pathogenic landscape variation. We investigated historical and contemporary forces that have shaped the variability at both genes, and tested for differential selective pressure across the ecological gradient by comparing allelic variation at MHC and neutral loci. We found positive selection on both MHC loci and significantly decreasing diversity from North to South Tunisia. Our multinomial linear models revealed significant effects of geographical positions that were correlated with mean annual temperature and precipitation on the occurrence of protein variants, but no effects of co-occurring DQA or DQB proteins, respectively. Diversifying selection, recombination, adaptation to local pathogenic landscapes (supposedly reflected by climate parameters) and neutral demographic processes have shaped the observed MHC diversity and differentiation patterns.

Genes under positive selection in the core genome of pathogenic Bacillus cereus group members

In this comparative genomics study our aim was to unravel genes under positive selection in the core genome of the Bacillus cereus group. Indeed, the members of this group share close genetic relationships but display a rather large phenotypic and ecological diversity, providing a unique opportunity for studying how genomic changes reflect ecological adaptation during the divergence of a bacterial group. For this purpose, we screened ten completely sequenced genomes of four pathogenic Bacillus species, finding that 254 out of 3093 genes have codon sites with d_N/d_S (ω) values above one. These results remained unchanged after having disentangled the confounding effects of recombination and selection signature in a Bayesian framework. The presumably adaptive nucleotide polymorphisms are distributed over a wide range of biological functions, such as antibiotic resistance, DNA repair, nutrient uptake, metabolism, cell wall assembly and spore structure. Our results indicate that adaptation to animal hosts, whether as pathogens, saprophytes or symbionts, is the major driving force in the evolution of the Bacillus cereus group. Future work should seek to understand the evolutionary dynamics of both core and accessory genes in an integrative framework to ultimately unravel the key networks involved in host adaptation.

Genetic diversity of the toll-like receptor 2 (TLR2) in hare (Lepus capensis) populations from Tunisia

Toll-like receptors (TLRs) are a major group of proteins that recognize molecular components of infectious agents, known as pathogen associated molecular patterns (PAMPs). The structure of these genes is similar and characterized by the presence of an ectodomain, a signal transmembrane segment and a highly conserved cytoplasmic domain. The latter domain is homologous to the human interleukin-1 receptor (IL1R) and human IL-18 receptor (IL-18R) and designated TIR domain. The latter domain of the TLR genes was suggested to be very conservative and its evolution is driven by purifying selection. Variability and evolution of the TIR sequences of TLR2 gene were studied in three hare populations from Tunisia with different ecological characteristics (NT-North Tunisia with Mediterranean, CT-Central Tunisia with semi-arid, and ST-South Tunisia with arid climate). Sequencing of a 372bp fragment of TIR2 revealed 25 alleles among 110 hares. Twenty variable nucleotide positions were detected, of which 7 were non-synonymous. The highest variability was observed in CT, with 16 polymorphic positions. In ST, only 4 polymorphic nucleotide positions were detected with all diversity values lower than those recorded for the other two populations. By using several approaches, no positive selection was detected. However, evidence of purifying selection was found at two positions. The logistic models of the most common TIR2 protein variant that we run to examine whether its occurrence was affected by climatic variation independent of the geographic sample location suggested only a longitudinal effect. Finally, the mapping of the non-synonymous mutations to the inferred tertiary protein structure showed that they were all localized in the different loop regions. Among all non-synonymous substitutions, three were suggested to be deleterious as evidenced by PROVEAN analysis. The observed patterns of variability characterized by low genetic diversity in ST might suggest that the TIR region was more affected, than other markers, by genetic drift or/and that these patterns were shaped by different selective pressures under different ecological conditions. Notably, this low diversity was not detected by other (putatively neutral) microsatellite markers analysed in the course of other studies. But low diversity was also found for two MHC class II adaptive immune genes. As expected from functionally important regions, the evolution of the TIR2 domain is mainly driven by purifying selection. However, the occurrence of deleterious non-synonymous substitutions might highlight the flexible evolution of the TIR genes and/or their interactions with other proteins.

Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs

Toll-like receptors (TLRs) are an important component of innate immunity, the first line of pathogen defence. One of the major roles of TLRs includes recognition of pathogen-associated molecular patterns. Amphibians are currently facing population declines and even extinction due to chytridiomycosis caused by the Batrachochytrium dendrobatidis (Bd) fungus. Evidence from other vertebrates shows that TLR2 and TLR4 are involved in innate immunity against various fungi. Such genes therefore may play a functional role in amphibian-chytridiomycosis dynamics. Frogs from East Asia appear to be tolerant to Bd, so we examined the genetic diversity that underlies TLR2 and TLR4 from three Japanese Ranidae frog species, Rana japonica, R. ornativentris and R. tagoi tagoi (n = 5 per species). We isolated 27 TLR2 and 20 TLR4 alleles and found that these genes are evolutionarily conserved, with overall evidence supporting purifying selection. In contrast, site-by-site analysis of selection identified several specific codon sites under positive selection, some of which were located in the variable leucine rich repeat domains. In addition, preliminary expression levels of TLR2 and TLR4 from transcriptome data showed overall low expression. Although it remains unclear whether infectious pathogens are a selective force acting on TLRs of Japanese frogs, our results support that certain sites in TLRs of these species may have experienced pathogen-mediated selection.

Signatures of historical selection on MHC reveal different selection patterns in the moor frog (Rana arvalis)

MHC genes are key components in disease resistance and an excellent system for studying selection acting on genetic variation in natural populations. Current patterns of variation in MHC genes are likely to be influenced by past and ongoing selection as well as demographic fluctuations in population size such as those imposed by post-glacial recolonization processes. Here, we investigated signatures of historical selection and demography on an MHC class II gene in 12 moor frog populations along a 1700-km latitudinal gradient. Sequences were obtained from 207 individuals and consecutively assigned into two different clusters (northern and southern clusters, respectively) in concordance with a previously described dual post-glacial colonization route. Selection analyses comparing the relative rates of non-synonymous to synonymous substitutions (dN/dS) suggested evidence of different selection patterns in the northern and the southern clusters, with divergent selection prevailing in the south but uniform positive selection predominating in the north. Also, models of codon evolution revealed considerable differences in the strength of selection: The southern cluster appeared to be under strong selection while the northern cluster showed moderate signs of selection. Our results indicate that the MHC alleles in the north diverged from southern MHC alleles as a result of differential selection patterns.

Positive selection on human gamete-recognition genes

Coevolution of genes that encode interacting proteins expressed on the surfaces of sperm and eggs can lead to variation in reproductive compatibility between mates and reproductive isolation between members of different species. Previous studies in mice and other mammals have focused in particular on evidence for positive or diversifying selection that shapes the evolution of genes that encode sperm-binding proteins expressed in the egg coat or zona pellucida (ZP). By fitting phylogenetic models of codon evolution to data from the 1000 Genomes Project, we identified candidate sites evolving under diversifying selection in the human genes ZP3 and ZP2. We also identified one candidate site under positive selection in C4BPA, which encodes a repetitive protein similar to the mouse protein ZP3R that is expressed in the sperm head and binds to the ZP at fertilization. Results from several additional analyses that applied population genetic models to the same data were consistent with the hypothesis of selection on those candidate sites leading to coevolution of sperm- and egg-expressed genes. By contrast, we found no candidate sites under selection in a fourth gene (ZP1) that encodes an egg coat structural protein not directly involved in sperm binding. Finally, we found that two of the candidate sites (in C4BPA and ZP2) were correlated with variation in family size and birth rate among Hutterite couples, and those two candidate sites were also in linkage disequilibrium in the same Hutterite study population. All of these lines of evidence are consistent with predictions from a previously proposed hypothesis of balancing selection on epistatic interactions between C4BPA and ZP3 at fertilization that lead to the evolution of co-adapted allele pairs. Such patterns also suggest specific molecular traits that may be associated with both natural reproductive variation and clinical infertility.

Transcriptome analyses of immune tissues from three Japanese frogs (genus Rana ) reveals their utility in characterizing major histocompatibility complex class II

Background

In Japan and East Asia, endemic frogs appear to be tolerant or not susceptible to chytridiomycosis, a deadly amphibian disease caused by the chytrid fungus Batrachochytridium dendrobatidis (Bd). Japanese frogs may have evolved mechanisms of immune resistance to pathogens such as Bd. This study characterizes immune genes expressed in various tissues of healthy Japanese Rana frogs.

Results

We generated transcriptome data sets of skin, spleen and blood from three adult Japanese Ranidae frogs (Japanese brown frog Rana japonica, the montane brown frog Rana ornativentris, and Tago’s brown frog Rana tagoi tagoi) as well as whole body of R. japonica and R. ornativentris tadpoles. From this, we identified tissue- and stage-specific differentially expressed genes; in particular, the spleen was most enriched for immune-related genes. A specific immune gene, major histocompatibility complex class IIB (MHC-IIB), was further characterized due to its role in pathogen recognition. We identified a total of 33 MHC-IIB variants from the three focal species (n = 7 individuals each), which displayed evolutionary signatures related to increased MHC variation, including balancing selection. Our supertyping analyses of MHC-IIB variants from Japanese frogs and previously studied frog species identified potential physiochemical properties of MHC-II that may be important for recognizing and binding chytrid-related antigens.

Conclusions

This is one of the first studies to generate transcriptomic resources for Japanese frogs, and contributes to further understanding the immunogenetic factors associated with resistance to infectious diseases in amphibians such as chytridiomycosis. Notably, MHC-IIB supertyping analyses identified unique functional properties of specific MHC-IIB alleles that may partially contribute to Bd resistance, and such properties provide a springboard for future experimental validation.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4404-0) contains supplementary material, which is available to authorized users.

Severe infections emerge from commensal bacteria by adaptive evolution

Bacteria responsible for the greatest global mortality colonize the human microbiota far more frequently than they cause severe infections. Whether mutation and selection among commensal bacteria are associated with infection is unknown. We investigated de novo mutation in 1163 Staphylococcus aureus genomes from 105 infected patients with nose colonization. We report that 72% of infections emerged from the nose, with infecting and nose-colonizing bacteria showing parallel adaptive differences. We found 2.8-to-3.6-fold adaptive enrichments of protein-altering variants in genes responding to rsp, which regulates surface antigens and toxin production; agr, which regulates quorum-sensing, toxin production and abscess formation; and host-derived antimicrobial peptides. Adaptive mutations in pathogenesis-associated genes were 3.1-fold enriched in infecting but not nose-colonizing bacteria. None of these signatures were observed in healthy carriers nor at the species-level, suggesting infection-associated, short-term, within-host selection pressures. Our results show that signatures of spontaneous adaptive evolution are specifically associated with infection, raising new possibilities for diagnosis and treatment.

Mutation and recombination in pathogen evolution: Relevance, methods and controversies

Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.

Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian

BACKGROUND

Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites.

RESULTS

Using outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations.

CONCLUSION

Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.

Identification, genealogical structure and population genetics of S-alleles in Malus sieversii, the wild ancestor of domesticated apple

The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris. We further sequenced 8 nuclear genes to provide a neutral reference, and investigated the evolution of S-alleles via genealogical and population genetic analyses. Both shared ancestral polymorphism and an excess of non-synonymous substitution were detected in the S-RNases of the tribe Maleae in Rosaceae, indicating the action of long-term balancing selection. Approximate Bayesian Computations based on the reference neutral loci revealed a severe bottleneck in four of the six studied M. sieversii populations, suggesting that the low number of S-alleles found in this species is mainly the result of diversity loss due to a drastic population contraction. Such a bottleneck may lead to ambiguous footprints of ongoing balancing selection detected at the S-locus. This study not only elucidates the constituents and number of S-alleles in M. sieversii but also illustrates the potential utility of S-allele number shifts in demographic inference for self-incompatible plant species.

Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates

Studies of highly diverged species have revealed two mechanisms by which meiotic recombination is directed to the genome-through PRDM9 binding or by targeting promoter-like features-that lead to dramatically different evolutionary dynamics of hotspots. Here, we identify PRDM9 orthologs from genome and transcriptome data in 225 species. We find the complete PRDM9 ortholog across distantly related vertebrates but, despite this broad conservation, infer a minimum of six partial and three complete losses. Strikingly, taxa carrying the complete ortholog of PRDM9 are precisely those with rapid evolution of its predicted binding affinity, suggesting that all domains are necessary for directing recombination. Indeed, as we show, swordtail fish carrying only a partial but conserved ortholog share recombination properties with PRDM9 knock-outs.