The effects of sample size on population genomic analyses--implications for the tests of neutrality

Adaptation in a keystone grazer under novel predation pressure

Understanding how species adapt to environmental change is necessary to protect biodiversity and ecosystem services. Growing evidence suggests species can adapt rapidly to novel selection pressures like predation from invasive species, but the repeatability and predictability of selection remain poorly understood in wild populations. We tested how a keystone aquatic herbivore, Daphnia pulicaria, evolved in response to predation pressure by the introduced zooplanktivore Bythotrephes longimanus. Using high-resolution 210Pb-dated sediment cores from 12 lakes in Ontario (Canada), which primarily differed in invasion status by Bythotrephes, we compared Daphnia population genetic structure over time using whole-genome sequencing of individual resting embryos. We found strong genetic differentiation between populations approximately 70 years before versus 30 years after reported Bythotrephes invasion, with no difference over this period in uninvaded lakes. Compared with uninvaded lakes, we identified, on average, 64 times more loci were putatively under selection in the invaded lakes. Differentiated loci were mainly associated with known reproductive and stress responses, and mean body size consistently increased by 14.1% over time in invaded lakes. These results suggest Daphnia populations were repeatedly acquiring heritable genetic adaptations to escape gape-limited predation. More generally, our results suggest some aspects of environmental change predictably shape genome evolution.

No evidence that ACE2 or TMPRSS2 drive population disparity in COVID risks

Early in the SARS-CoV2 pandemic, in this journal, Hou et al. (BMC Med 18:216, 2020) interpreted public genotype data, run through functional prediction tools, as suggesting that members of particular human populations carry potentially COVID-risk-increasing variants in genes ACE2 and TMPRSS2 far more often than do members of other populations. Beyond resting on predictions rather than clinical outcomes, and focusing on variants too rare to typify population members even jointly, their claim mistook a well known artifact (that large samples reveal more of a population's variants than do small samples) as if showing real and congruent population differences for the two genes, rather than lopsided population sampling in their shared source data. We explain that artifact, and contrast it with empirical findings, now ample, that other loci shape personal COVID risks far more significantly than do ACE2 and TMPRSS2-and that variation in ACE2 and TMPRSS2 per se unlikely exacerbates any net population disparity in the effects of such more risk-informative loci.

A phenome-wide association and Mendelian randomisation study of alcohol use variants in a diverse cohort comprising over 3 million individuals

BACKGROUND

Alcohol consumption is associated with numerous negative social and health outcomes. These associations may be direct consequences of drinking, or they may reflect common genetic factors that influence both alcohol consumption and other outcomes.

METHODS

We performed exploratory phenome-wide association studies (PheWAS) of three of the best studied protective single nucleotide polymorphisms (SNPs) in genes encoding ethanol metabolising enzymes (ADH1B: rs1229984-T, rs2066702-A; ADH1C: rs698-T) using up to 1109 health outcomes across 28 phenotypic categories (e.g., substance-use, mental health, sleep, immune, cardiovascular, metabolic) from a diverse 23andMe cohort, including European (N ≤ 2,619,939), Latin American (N ≤ 446,646) and African American (N ≤ 146,776) populations to uncover new and perhaps unexpected associations. These SNPs have been consistently implicated by both candidate gene studies and genome-wide association studies of alcohol-related behaviours but have not been investigated in detail for other relevant phenotypes in a hypothesis-free approach in such a large cohort of multiple ancestries. To provide insight into potential causal effects of alcohol consumption on the outcomes significant in the PheWAS, we performed univariable two-sample and one-sample Mendelian randomisation (MR) analyses.

FINDINGS

The minor allele rs1229984-T, which is protective against alcohol behaviours, showed the highest number of PheWAS associations across the three cohorts (N = 232, European; N = 29, Latin American; N = 7, African American). rs1229984-T influenced multiple domains of health. We replicated associations with alcohol-related behaviours, mental and sleep conditions, and cardio-metabolic health. We also found associations with understudied traits related to neurological (migraines, epilepsy), immune (allergies), musculoskeletal (fibromyalgia), and reproductive health (preeclampsia). MR analyses identified evidence of causal effects of alcohol consumption on liability for 35 of these outcomes in the European cohort.

INTERPRETATION

Our work demonstrates that polymorphisms in genes encoding alcohol metabolising enzymes affect multiple domains of health beyond alcohol-related behaviours. Understanding the underlying mechanisms of these effects could have implications for treatments and preventative medicine.

FUNDING

MVJ, NCK, SBB, SSR and AAP were supported by T32IR5226 and 28IR-0070. SSR was also supported by NIDA DP1DA054394. NCK and RBC were also supported by R25MH081482. ASH was supported by funds from NIAAA K01AA030083. JLMO was supported by VA 1IK2CX002095. JLMO and JJMM were also supported by NIDA R21DA050160. JJMM was also supported by the Kavli Postdoctoral Award for Academic Diversity. EGA was supported by K01MH121659 from the NIMH/NIH, the Caroline Wiess Law Fund for Research in Molecular Medicine and the ARCO Foundation Young Teacher-Investigator Fund at Baylor College of Medicine. MSA was supported by the Instituto de Salud Carlos III and co-funded by the European Union Found: Fondo Social Europeo Plus (FSE+) (P19/01224, PI22/00464 and CP22/00128).

Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)

The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the closure of all U.S. black abalone fisheries since 1993. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS remains unknown. To address these uncertainties, we sequenced and analysed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Outside the inversion, genetic differentiation between sites is minimal and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Demographic inference does indicate a severe population bottleneck beginning just 15 generations in the past, but this decline is short lived, with present-day size far exceeding the pre-bottleneck status quo. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of population genetic structure, uniform diversity and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.

A Large-Scale Meta-Analysis Reveals Positive Feedback between Macrophages and T Cells That Sensitizes Tumors to Immunotherapy

Although considerable efforts have been dedicated to identifying predictive signatures for immune checkpoint inhibitor (ICI) treatment response, current biomarkers suffer from poor generalizability and reproducibility across different studies and cancer types. The integration of large-scale multiomics studies holds great promise for discovering robust biomarkers and shedding light on the mechanisms of immune resistance. In this study, we conducted the most extensive meta-analysis involving 3,037 ICI-treated patients with genetic and/or transcriptomics profiles across 14 types of solid tumor. The comprehensive analysis uncovered both known and novel reliable signatures associated with ICI treatment outcomes. The signatures included tumor mutational burden (TMB), IFNG and PDCD1 expression, and notably, interactions between macrophages and T cells driving their activation and recruitment. Independent data from single-cell RNA sequencing and dynamic transcriptomic profiles during the ICI treatment provided further evidence that enhanced cross-talk between macrophages and T cells contributes to ICI response. A multivariable model based on eight nonredundant signatures significantly outperformed existing models in five independent validation datasets representing various cancer types. Collectively, this study discovered biomarkers predicting ICI response that highlight the contribution of immune cell networks to immunotherapy efficacy and could help guide patient treatment.

SIGNIFICANCE

Identification of robust immunogenomic connections, particularly macrophage T-cell interactions, in a large-scale pan-cancer meta-analysis and development of a predictive model for immunotherapy response that outperformed existing models could facilitate clinical decision-making.

Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)

The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the species' designation as critically endangered. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS is unknown. To address these uncertainties, we sequenced and analyzed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Genetic divergence between sites is minimal, and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Despite this, however, demographic inference confirms a severe population bottleneck beginning around the time of WS onset, highlighting the temporal offset that may occur between a population collapse and its potential impact on genetic diversity. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of genetic structure, uniform diversity, and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.

The pace of mitochondrial molecular evolution varies with seasonal migration distance

Animals that engage in long-distance seasonal migration experience strong selective pressures on their metabolic performance and life history, with potential consequences for molecular evolution. Species with slow life histories typically show lower rates of synonymous substitution (dS) than "fast" species. Previous research suggests long-distance seasonal migrants have a slower life history strategy than short-distance migrants, raising the possibility that rates of molecular evolution may covary with migration distance. Additionally, long-distance migrants may face strong selection on metabolically-important mitochondrial genes due to their long-distance flights. Using over 1,000 mitochondrial genomes, we assessed the relationship between migration distance and mitochondrial molecular evolution in 39 boreal-breeding migratory bird species. We show that migration distance correlates negatively with dS, suggesting that the slow life history associated with long-distance migration is reflected in rates of molecular evolution. Mitochondrial genes in every study species exhibited evidence of purifying selection, but the strength of selection was greater in short-distance migrants, contrary to our predictions. This result may indicate effects of selection for cold tolerance on mitochondrial evolution among species overwintering at high latitudes. Our study demonstrates that the pervasive correlation between life history and molecular evolutionary rates exists in the context of differential adaptations to seasonality.

Contrasting whole-genome and reduced representation sequencing for population demographic and adaptive inference: an alpine mammal case study

Genomes capture the adaptive and demographic history of a species, but the choice of sequencing strategy and sample size can impact such inferences. We compared whole genome and reduced representation sequencing approaches to study the population demographic and adaptive signals of the North American mountain goat (Oreamnos americanus). We applied the restriction site-associated DNA sequencing (RADseq) approach to 254 individuals and whole genome resequencing (WGS) approach to 35 individuals across the species range at mid-level coverage (9X) and to 5 individuals at high coverage (30X). We used ANGSD to estimate the genotype likelihoods and estimated the effective population size (Ne), population structure, and explicitly modelled the demographic history with δaδi and MSMC2. The data sets were overall concordant in supporting a glacial induced vicariance and extremely low Ne in mountain goats. We evaluated a set of climatic variables and geographic location as predictors of genetic diversity using redundancy analysis. A moderate proportion of total variance (36% for WGS and 21% for RADseq data sets) was explained by geography and climate variables; both data sets support a large impact of drift and some degree of local adaptation. The empirical similarities of WGS and RADseq presented herein reassuringly suggest that both approaches will recover large demographic and adaptive signals in a population; however, WGS offers several advantages over RADseq, such as inferring adaptive processes and calculating runs-of-homozygosity estimates. Considering the predicted climate-induced changes in alpine environments and the genetically depauperate mountain goat, the long-term adaptive capabilities of this enigmatic species are questionable.

Robustness of genetic diversity measures under spatial sampling and a new frequency-independent measure

The genetic diversity of a taxon has often been estimated by genetic diversity measures. However, they assume random sampling of individuals which is often inapplicable. Except when the distribution of the taxon is limited, researchers conventionally choose several sampling locations from the known distribution and then collect individuals from each location. Spatial sampling is a formalized version of the conventional sampling, which objectively provides geographically even sampling locations to cover genetic variation in a taxon assuming isolation by distance. To evaluate the validity of the spatial sampling in estimating genetic diversity, we conducted coalescent simulation experiments. The sampling locations were selected by spatial sampling and one sample was collected from each location for the sake of theoretical simplicity. We also devised a new measure of genetic diversity, ς, which assumes spatial sampling and is independent of allele frequency. This new measure places an emphasis on rare and phylogenetically distant alleles which have relatively small effect on nucleotide diversity. Therefore, it can complementarily serve for conservation studies although it cannot be used to estimate population mutation rate. We compared ς with the other diversity measures in the experiments. Nucleotide diversity, expected heterozygosity and ς showed within 3% relative biases on average while Watterson's theta was 31% overestimation on average. Thus, genetic diversities other than Watterson's theta held good robustness under the spatial sampling.

The mutational landscape of the adult healthy parous and nulliparous human breast

The accumulation of somatic mutations in healthy human tissues has been extensively characterized, but the mutational landscape of the healthy breast is still poorly understood. Our analysis of whole-genome sequencing shows that in line with other healthy organs, the healthy breast during the reproduction years accumulates mutations with age, with the rate of accumulation in the epithelium of 15.24 ± 5 mutations/year. Both epithelial and stromal compartments contain mutations in breast-specific driver genes, indicative of subsequent positive selection. Parity- and age-associated differences are evident in the mammary epithelium, partly explaining the observed difference in breast cancer risk amongst women of different childbearing age. Parity is associated with an age-dependent increase in the clone size of mutated epithelial cells, suggesting that older first-time mothers have a higher probability of accumulating oncogenic events in the epithelium compared to younger mothers or nulliparous women. In conclusion, we describe the reference genome of the healthy female human breast during reproductive years and provide evidence of how parity affects the genomic landscape of the mammary gland.

Diversity and Pathobiology of an Ilarvirus Unexpectedly Detected in Diverse Plants and Global Sequencing Data

High-throughput sequencing (HTS) and sequence mining tools revolutionized virus detection and discovery in recent years, and implementing them with classical plant virology techniques results in a powerful approach to characterize viruses. An example of a virus discovered through HTS is Solanum nigrum ilarvirus 1 (SnIV1) (Bromoviridae), which was recently reported in various solanaceous plants from France, Slovenia, Greece, and South Africa. It was likewise detected in grapevines (Vitaceae) and several Fabaceae and Rosaceae plant species. Such a diverse set of source organisms is atypical for ilarviruses, thus warranting further investigation. In this study, modern and classical virological tools were combined to accelerate the characterization of SnIV1. Through HTS-based virome surveys, mining of sequence read archive datasets, and a literature search, SnIV1 was further identified from diverse plant and non-plant sources globally. SnIV1 isolates showed relatively low variability compared with other phylogenetically related ilarviruses. Phylogenetic analyses showed a distinct basal clade of isolates from Europe, whereas the rest formed clades of mixed geographic origin. Furthermore, systemic infection of SnIV1 in Solanum villosum and its mechanical and graft transmissibility to solanaceous species were demonstrated. Near-identical SnIV1 genomes from the inoculum (S. villosum) and inoculated Nicotiana benthamiana were sequenced, thus partially fulfilling Koch's postulates. SnIV1 was shown to be seed-transmitted and potentially pollen-borne, has spherical virions, and possibly induces histopathological changes in infected N. benthamiana leaf tissues. Overall, this study provides information to better understand the diversity, global presence, and pathobiology of SnIV1; however, its possible emergence as a destructive pathogen remains uncertain. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Venom phenotype conservation suggests integrated specialization in a lizard-eating snake

Biological specialization reduces the size of niche space while increasing efficiency in the use of available resources. Specialization often leads to phenotypic changes via natural selection aligning with niche space constraints. Commonly observed changes are in size, shape, behavior, and traits associated with feeding. One often selected trait for dietary specialization is venom, which, in snakes, often shows variation dependent on diet across and within species. The Neotropical Blunt-headed Treesnake (Imantodes cenchoa) is a highly specialized, rear-fanged, arboreal, lizard hunter that displays a long thin body, enlarged eyes, and a large Duvernoy's gland. However, toxin characterization of I. cenchoa has never been completed. Here, we use RNA-seq and mass spectrometry to assemble, annotate, and analyze the venom gland transcriptomes of four I. cenchoa from across their range. We find a lack of significant venom variation at the sequence and expression levels, suggesting venom conservation across the species. We propose this conservation provides evidence of a specialized venom repertoire, adapted to maximize efficiency of capturing and processing lizards. Importantly, this study provides the most complete venom gland transcriptomes of I. cenchoa and evidence of venom specialization in a rear-fanged snake, giving insight into selective pressures of venom across all snake species.

Both selection and drift drive the spatial pattern of adaptive genetic variation in a wild mammal

The major histocompatibility complex (MHC) has been intensively studied for the relative effects of different evolutionary forces in recent decades. Pathogen-mediated balancing selection is generally thought to explain the high polymorphism observed in MHC genes, but it is still unclear to what extent MHC diversity is shaped by selection relative to neutral drift. In this study, we genotyped MHC class II DRB genes and 15 neutral microsatellite loci across 26 geographic populations of European badgers (Meles meles) covering most of their geographic range. By comparing variation of microsatellite and diversity of MHC at different levels, we demonstrate that both balancing selection and drift have shaped the evolution of MHC genes. When only MHC allelic identity was investigated, the spatial pattern of MHC variation was similar to that of microsatellites. By contrast, when functional aspects of the MHC diversity (e.g., immunological supertypes) were considered, balancing selection appears to decrease genetic structuring across populations. Our comprehensive sampling and analytical approach enable us to conclude that the likely mechanisms of selection are heterozygote advantage and/or rare-allele advantage. This study is a clear demonstration of how both balancing selection and genetic drift simultaneously affect the evolution of MHC genes in a widely distributed wild mammal.

Dual Domestication, Diversity, and Differential Introgression in Old World Cotton Diploids

Domestication in the cotton genus is remarkable in that it has occurred independently four different times at two different ploidy levels. Relatively little is known about genome evolution and domestication in the cultivated diploid species Gossypium herbaceum and Gossypium arboreum, due to the absence of wild representatives for the latter species, their ancient domestication, and their joint history of human-mediated dispersal and interspecific gene flow. Using in-depth resequencing of a broad sampling from both species, we provide support for their independent domestication, as opposed to a progenitor-derivative relationship, showing that diversity (mean π = 6 × 10-3) within species is similar, and that divergence between species is modest (FST = 0.413). Individual accessions were homozygous for ancestral single-nucleotide polymorphisms at over half of variable sites, while fixed, derived sites were at modest frequencies. Notably, two chromosomes with a paucity of fixed, derived sites (i.e., chromosomes 7 and 10) were also strongly implicated as having experienced high levels of introgression. Collectively, these data demonstrate variable permeability to introgression among chromosomes, which we propose is due to divergent selection under domestication and/or the phenomenon of F2 breakdown in interspecific crosses. Our analyses provide insight into the evolutionary forces that shape diversity and divergence in the diploid cultivated species and establish a foundation for understanding the contribution of introgression and/or strong parallel selection to the extensive morphological similarities shared between species.

Transfer learning for genotype-phenotype prediction using deep learning models

BACKGROUND

For some understudied populations, genotype data is minimal for genotype-phenotype prediction. However, we can use the data of some other large populations to learn about the disease-causing SNPs and use that knowledge for the genotype-phenotype prediction of small populations. This manuscript illustrated that transfer learning is applicable for genotype data and genotype-phenotype prediction.

RESULTS

Using HAPGEN2 and PhenotypeSimulator, we generated eight phenotypes for 500 cases/500 controls (CEU, large population) and 100 cases/100 controls (YRI, small populations). We considered 5 (4 phenotypes) and 10 (4 phenotypes) different risk SNPs for each phenotype to evaluate the proposed method. The improved accuracy with transfer learning for eight different phenotypes was between 2 and 14.2 percent. The two-tailed p-value between the classification accuracies for all phenotypes without transfer learning and with transfer learning was 0.0306 for five risk SNPs phenotypes and 0.0478 for ten risk SNPs phenotypes.

CONCLUSION

The proposed pipeline is used to transfer knowledge for the case/control classification of the small population. In addition, we argue that this method can also be used in the realm of endangered species and personalized medicine. If the large population data is extensive compared to small population data, expect transfer learning results to improve significantly. We show that Transfer learning is capable to create powerful models for genotype-phenotype predictions in large, well-studied populations and fine-tune these models to populations were data is sparse.

The Relative Power of Structural Genomic Variation versus SNPs in Explaining the Quantitative Trait Growth in the Marine Teleost Chrysophrys auratus

Background: Genetic diversity provides the basic substrate for evolution. Genetic variation consists of changes ranging from single base pairs (single-nucleotide polymorphisms, or SNPs) to larger-scale structural variants, such as inversions, deletions, and duplications. SNPs have long been used as the general currency for investigations into how genetic diversity fuels evolution. However, structural variants can affect more base pairs in the genome than SNPs and can be responsible for adaptive phenotypes due to their impact on linkage and recombination. In this study, we investigate the first steps needed to explore the genetic basis of an economically important growth trait in the marine teleost finfish Chrysophrys auratus using both SNP and structural variant data. Specifically, we use feature selection methods in machine learning to explore the relative predictive power of both types of genetic variants in explaining growth and discuss the feature selection results of the evaluated methods. Methods: SNP and structural variant callers were used to generate catalogues of variant data from 32 individual fish at ages 1 and 3 years. Three feature selection algorithms (ReliefF, Chi-square, and a mutual-information-based method) were used to reduce the dataset by selecting the most informative features. Following this selection process, the subset of variants was used as features to classify fish into small, medium, or large size categories using KNN, naïve Bayes, random forest, and logistic regression. The top-scoring features in each feature selection method were subsequently mapped to annotated genomic regions in the zebrafish genome, and a permutation test was conducted to see if the number of mapped regions was greater than when random sampling was applied. Results: Without feature selection, the prediction accuracies ranged from 0 to 0.5 for both structural variants and SNPs. Following feature selection, the prediction accuracy increased only slightly to between 0 and 0.65 for structural variants and between 0 and 0.75 for SNPs. The highest prediction accuracy for the logistic regression was achieved for age 3 fish using SNPs, although generally predictions for age 1 and 3 fish were very similar (ranging from 0–0.65 for both SNPs and structural variants). The Chi-square feature selection of SNP data was the only method that had a significantly higher number of matches to annotated genomic regions of zebrafish than would be explained by chance alone. Conclusions: Predicting a complex polygenic trait such as growth using data collected from a low number of individuals remains challenging. While we demonstrate that both SNPs and structural variants provide important information to help understand the genetic basis of phenotypic traits such as fish growth, the full complexities that exist within a genome cannot be easily captured by classical machine learning techniques. When using high-dimensional data, feature selection shows some increase in the prediction accuracy of classification models and provides the potential to identify unknown genomic correlates with growth. Our results show that both SNPs and structural variants significantly impact growth, and we therefore recommend that researchers interested in the genotype–phenotype map should strive to go beyond SNPs and incorporate structural variants in their studies as well. We discuss how our machine learning models can be further expanded to serve as a test bed to inform evolutionary studies and the applied management of species.

Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis

Australian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.

Genomic insights into the historical and contemporary demographics of the grey reef shark

Analyses of genetic diversity can shed light on both the origins of biodiversity hotspots, as well as the conservation status of species that are impacted by human activities. With these objectives, we assembled a genomic dataset of 14,935 single nucleotide polymorphisms from 513 grey reef sharks (Carcharhinus amblyrhynchos) sampled across 17 locations in the tropical Indo-Pacific. We analysed geographic variation in genetic diversity, estimated ancient and contemporary effective population size (N_e) across sampling locations (using coalescent and linkage disequilibrium methods) and modelled the history of gene flow between the Coral Triangle and the Coral Sea. Genetic diversity decreased with distance away from the Coral Triangle and north-western Australia, implying that C. amblyrhynchos may have originated in this region. Increases in N_e were detected across almost all sampling locations 40,000-90,000 generations ago (approximately 0.6-1.5 mya, given an estimated generation time of 16.4 years), suggesting a range expansion around this time. More recent, secondary increases in N_e were inferred for the Misool and North Great Barrier Reef sampling locations, but joint modelling did not clarify whether these were due to population growth, migration, or both. Despite the greater genetic diversity and ancient N_e observed at sites around Australia and the Coral Triangle, remote reefs around north-western New Caledonia had the highest contemporary N_e, demonstrating the importance of using multiple population size assessment methods. This study provides insight into both the past and present demographics of C. amblyrhynchos and contributes to our understanding of evolution in marine biodiversity hotspots.

Glial changes in schizophrenia: Genetic and epigenetic approach

BACKGROUND

Schizophrenia (SCZ) is a severe mental illness that affects one percent of the population, affecting how people think, feel, and behave. Evidence suggests glial cell alteration and some researchers have found genetic risk loci and epigenetic marks that may regulate glia-related genes implicated in SCZ.

AIM

The aim of this study is to identify genetic and epigenetic changes that have been reported in glial cells or glial-associated genes in SCZ.

MATERIALS AND METHODS

We searched the articles from PubMed, PubMed Central, Medline, Medscape, and Embase databases up to December 2020 to identify relevant peer-reviewed articles in English. The titles and abstracts were screened to eliminate irrelevant citations.

RESULTS

Twenty-four original articles were included in the review. Studies were categorized into the following four thematic via: (1) oligodendrocytes, (2) microglia, (3) astrocytes, and (4) perspectives.

CONCLUSION

This study is the first of its kind to review research on genetic variants and epigenetic modifications associated with glia-related genes implicated in SCZ. Epigenetic evidence is considerably less than genetic evidence in this field. Understanding the pathways of some risk genes and their genetic and epigenetic regulation allows us to understand and find potential targets for future interventions in this mental illness.

Genetic diversity in the IZUMO1-JUNO protein-receptor pair involved in human reproduction

Fertilization in mammals begins with the union of egg and sperm, an event that starts a cascade of cellular processes. The molecular-level understanding of these processes can guide the development of new strategies for controlling and/or promoting fertilization, and inform researchers and medical professional on the best choice of interventions. The proteins encoded by the IZUMO1 and JUNO genes form a ligand-receptor protein pair involved in the recognition of sperm and egg. Due to their role in the fertilization process, these proteins are potential targets for the development of novel anti-contraceptive, as well as infertility treatments. Here we present a comprehensive analysis of these gene sequences, with the objective of identifying evolutionary patterns that may support their relevance as targets for preventing or improving fertility among humans. JUNO and IZUMO1 gene sequences were identified within the genomes of over 2,000 humans sequenced in the 1000 Genomes Project. The human sequences were subjected to analyses of nucleotide diversity, deviation from neutrality of genetic variation, population-based differentiation (F_ST), haplotype inference, and whole chromosome scanning for signals of positive or of balancing selection. Derived alleles were determined by comparison to archaic hominin and other primate genomes. The potential effect of common non-synonymous variants on protein-protein interaction was also assessed. IZUMO1 displays higher variability among human individuals than JUNO. Genetic differentiation between continental population pairs was within whole-genome estimates for all but the JUNO gene in the African population group with respect to the other 4 population groups (American, East Asian, South Asian, and European). Tajima’s D values demonstrated deviation from neutrality for both genes in comparison to a group of genes identified in the literature as under balancing or positive selection. Tajima’s D for IZUMO1 aligns with values calculated for genes presumed to be under balancing selection, whereas JUNO’s value aligned with genes presumed to be under positive selection. These inferences on selection are both supported by SNP density, nucleotide diversity and haplotype analysis. A JUNO haplotype carrying 3 derived alleles out of 5, one of which is a missense mutation implicated in polyspermy, was found to be significant in a population of African ancestry. Polyspermy has a disadvantageous impact on fertility and its presence in approximately 30% of the population of African ancestry may be associated to a potentially beneficial role of this haplotype. This role has not been established and may be related to a non-reproductive role of JUNO. The high degree of conservation of the JUNO sequence combined with a dominant haplotype across multiple population groups supports JUNO as a potential target for the development of contraceptive treatments. In addition to providing a detailed account of human genetic diversity across these 2 important and related genes, this study also provides a framework for large population-based studies investigating protein-protein interactions at the genome level.

The first insight into the genetic structure of the population of modern Serbia

The complete understanding of the genomic contribution to complex traits, diseases, and response to treatments, as well as genomic medicine application to the well-being of all humans will be achieved through the global variome that encompasses fine-scale genetic diversity. Despite significant efforts in recent years, uneven representation still characterizes genomic resources and among the underrepresented European populations are the Western Balkans including the Serbian population. Our research addresses this gap and presents the first ever targeted sequencing dataset of variants in clinically relevant genes. By measuring population differentiation and applying the Principal Component and Admixture analysis we demonstrated that the Serbian population differs little from other European populations, yet we identified several novel and more frequent variants that appear as its unique genetic determinants. We explored thoroughly the functional impact of frequent variants and its correlation with the health burden of the population of Serbia based on a sample of 144 individuals. Our variants catalogue improves the understanding of genetics of modern Serbia, contributes to research on ancestry, and aids in improvements of well-being and health equity. In addition, this resource may also be applicable in neighboring regions and valuable in worldwide functional analyses of genetic variants in individuals of European descent.

WP, Sterkhova VV, Kusamba C, Rödel M, Penner J, Peterson AT, Brown RM. Rivers, not refugia, drove diversification in arboreal, sub-Saharan African snakes

The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo-species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river-refuge hypotheses on diversification in the arboreal sub-Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo-distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid-Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river-refuge hypotheses in favor of the river-barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east-central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.

Sex-linked genetic diversity and differentiation in a globally distributed avian species complex

Sex chromosomes often bear distinct patterns of genetic variation due to unique patterns of inheritance and demography. The processes of mutation, recombination, genetic drift and selection also influence rates of evolution on sex chromosomes differently than autosomes. Measuring such differences provides information about how these processes shape genomic variation and their roles in the origin of species. To test hypotheses and predictions about patterns of autosomal and sex-linked genomic diversity and differentiation, we measured population genetic statistics within and between populations and subspecies of the barn swallow (Hirundo rustica) and performed explicit comparisons between autosomal and Z-linked genomic regions. We first tested for evidence of low Z-linked genetic diversity and high Z-linked population differentiation relative to autosomes, then for evidence that the Z chromosome bears greater ancestry information due to faster lineage sorting. Finally, we investigated geographical clines across hybrid zones for evidence that the Z chromosome is resistant to introgression due to selection against hybrids. We found evidence that the barn swallow mating system, demographic history and linked selection each contribute to low Z-linked diversity and high Z-linked differentiation. While incomplete lineage sorting is rampant across the genome, our results indicate faster sorting of ancestral polymorphism on the Z. Finally, hybrid zone analyses indicate barriers to introgression on the Z chromosome, suggesting that sex-linked traits are important in reproductive isolation, especially in migratory divide regions. Our study highlights how selection, gene flow and demography shape sex-linked genetic diversity and underlines the relevance of the Z chromosome in speciation.

Genomic divergence landscape in recurrently hybridizing Chironomus sister taxa suggests stable steady state between mutual gene flow and isolation

Divergence is mostly viewed as a progressive process often initiated by selection targeting individual loci, ultimately resulting in ever increasing genomic isolation due to linkage. However, recent studies show that this process may stall at intermediate stable equilibrium states without achieving complete genomic isolation. We tested the extent of genomic isolation between two recurrently hybridizing nonbiting midge sister taxa, Chironomus riparius and Chironomus piger, by analyzing the divergence landscape. Using a principal component-based method, we estimated that only about 28.44% of the genomes were mutually isolated, whereas the rest was still exchanged. The divergence landscape was fragmented into isolated regions of on average 30 kb, distributed throughout the genome. Selection and divergence time strongly influenced lengths of isolated regions, whereas local recombination rate only had minor impact. Comparison of divergence time distributions obtained from several coalescence-simulated divergence scenarios with the observed divergence time estimates in an approximate Bayesian computation framework favored a short and concluded divergence event in the past. Most divergence happened during a short time span about 4.5 million generations ago, followed by a stable equilibrium between mutual gene flow through ongoing hybridization for the larger part of the genome and isolation in some regions due to rapid purifying selection of introgression, supported by high effective population sizes and recombination rates.

Expanding the Geographic Characterisation of Epstein-Barr Virus Variation through Gene-Based Approaches

The Epstein-Barr Virus (EBV) infects the vast majority of human individuals worldwide (~90%) and is associated with several diseases, including different types of cancer and multiple sclerosis, which show wide variation in incidence among global geographical regions. Genetic variants in EBV genomic sequences have been used to determine the geographical structure of EBV isolates, but our understanding of EBV diversity remains highly incomplete. We generated sequences for 13 pivotal EBV genes derived from 103 healthy individuals, expanding current EBV diversity datasets with respect to both geographic coverage and number of isolates per region. These newly generated sequences were integrated with the more than 250 published EBV genomes, generating the most geographically comprehensive data set of EBV strains to date. We report remarkable variation in single-gene phylogenies that, when analysed together, show robust signals of population structure. Our results not only confirm known major global patterns of geographic variation, such as the clear separation of Asian isolates from the rest, and the intermixed relationships among African, European and Australian isolates, but yield novel phylogenetic relationships with previously unreported populations. We provide a better understanding of EBV's population structure in South America, Africa and, by the inclusion of Turkey and Georgia, we also gain insight into EBV diversity in Western Asia, a crossroads connecting Europe, Africa and Asia. In summary, our results provide a detailed world-wide characterisation of EBV genetic clusters, their enrichment in specific geographic regions, novel inter-population relationships, and a catalogue of geographically informative EBV genetic variants.

Comparative genetic diversity of Cryptosporidium species causing human infections

Parasites sometimes expand their host range and cause new disease aetiologies. Genetic changes can then occur due to host-specific adaptive alterations, particularly when parasites cross between evolutionarily distant hosts. Characterizing genetic variation in Cryptosporidium from humans and other animals may have important implications for understanding disease dynamics and transmission. We analyse sequences from four loci (gp60, HSP-70, COWP and actin) representing multiple Cryptosporidium species reported in humans. We predicted low genetic diversity in species that present unusual human infections due to founder events and bottlenecks. High genetic diversity was observed in isolates from humans of Cryptosporidium meleagridis, Cryptosporidium cuniculus, Cryptosporidium hominis and Cryptosporidium parvum. A deviation of expected values of neutrality using Tajima's D was observed in C. cuniculus and C. meleagridis. The high genetic diversity in C. meleagridis and C. cuniculus did not match our expectations but deviations from neutrality indicate a recent decrease in genetic variability through a population bottleneck after an expansion event. Cryptosporidium hominis was also found with a significant Tajima's D positive value likely caused by recent population expansion of unusual genotypes in humans. These insights indicate that changes in genetic diversity can help us to understand host-parasite adaptation and evolution.

Population structure and genetic diversity of Trichomonas vaginalis clinical isolates in Australia and Ghana

Population genetic studies of Trichomonas vaginalis have detected high genetic diversity associated with phenotypic differences in clinical presentations. In this study, microscopy and next generation-multi-locus sequence typing (NG-MLST) were used to identify and genetically characterise T. vaginalis isolates from patients in Australia and Ghana. Seventy-one polymorphic nucleotide sites, 36 different alleles, 48 sequence types, 24 of which were novel, were identified among 178 isolates, revealing a geneticallly diverse T. vaginalis population. Polymorphism was found at most loci, clustering genotypes into eight groups among both Australian and Ghanaian isolates, although there was some variation between countries. The number of alleles for each locus ranged from two to nine. Study results confirmed geographic expansion and diversity of the T. vaginalis population. Two-type populations in almost equal frequencies and a third unassigned group were identified in this study. Linkage disequilibrium was observed, suggesting T. vaginalis population is highly clonal. Multillocus disequilibrium was observed even when analysing clades separately, as well as widespread clonal genotypes, suggesting that there is no evidence of recent recombination. A more comprehensive study to assess the extent of genetic diversity and population structure of T. vaginalis and their potential impact on varied pathology observed among infected individuals is recommended.

Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated

Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated subpopulations. The reconstruction of core genome-wide strains from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel life span and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.

The genomic pool of standing structural variation outnumbers single nucleotide polymorphism by threefold in the marine teleost Chrysophrys auratus

Recent studies have highlighted an important role of structural variation (SV) in ecological and evolutionary processes, but few have studied nonmodel species in the wild. As part of our long-term research programme on the nonmodel teleost fish Australasian snapper (Chrysophrys auratus), we aim to build one of the first catalogues of genomic variants (SNPs and indels, and deletions, duplications and inversions) in fishes and evaluate overlap of genomic variants with regions under putative selection (Tajima's D and π), and coding sequences (genes). For this, we analysed six males and six females from three locations in New Zealand and generated a high-resolution genomic variation catalogue. We characterized 20,385 SVs and found they intersected with almost a third of all annotated genes. Together with small indels, SVs account for three times more variation in the genome in terms of bases affected compared to SNPs. We found that a sizeable portion of detected SVs was in the upper and lower genomic regions of Tajima's D and π, indicating that some of these have an effect on the phenotype. Together, these results shed light on the often neglected genomic variation that is produced by SVs and highlights the need to go beyond the mere measure of SNPs when investigating evolutionary processes, such as species diversification and adaptation.

Analysis of biogeographic ancestry reveals complex genetic histories for indigenous communities of St. Vincent and Trinidad

OBJECTIVES

From a genetic perspective, relatively little is known about how mass emigrations of African, European, and Asian peoples beginning in the 16th century affected Indigenous Caribbean populations. Therefore, we explored the impact of serial colonization on the genetic variation of the first Caribbean islanders.

MATERIALS AND METHODS

Sixty-four members of St. Vincent's Garifuna Community and 36 members of Trinidad's Santa Rosa First People's Community (FPC) of Arima were characterized for mitochondrial DNA and Y-chromosome diversity via direct sequencing and targeted SNP and STR genotyping. A subset of 32 Garifuna and 18 FPC participants were genotyped using the GenoChip 2.0 microarray. The resulting data were used to examine genetic diversity, admixture, and sex biased gene flow in the study communities.

RESULTS

The Garifuna were most genetically comparable to African descendant populations, whereas the FPC were more similar to admixed American groups. Both communities also exhibited moderate frequencies of Indigenous American matrilines and patrilines. Autosomal SNP analysis indicated modest Indigenous American ancestry in these populations, while both showed varying degrees of African, European, South Asian, and East Asian ancestry, with patterns of sex-biased gene flow differing between the island communities.

DISCUSSION

These patterns of genetic variation are consistent with historical records of migration, forced, or voluntary, and suggest that different migration events shaped the genetic make-up of each island community. This genomic study is the highest resolution analysis yet conducted with these communities, and provides a fuller understanding of the complex bio-histories of Indigenous Caribbean peoples in the Lesser Antilles.

Assessing the Effectiveness of Direct Data Merging Strategy in Long-Term and Large-Scale Pharmacometabonomics

Because of the extended period of clinic data collection and huge size of analyzed samples, the long-term and large-scale pharmacometabonomics profiling is frequently encountered in the discovery of drug/target and the guidance of personalized medicine. So far, integration of the results (ReIn) from multiple experiments in a large-scale metabolomic profiling has become a widely used strategy for enhancing the reliability and robustness of analytical results, and the strategy of direct data merging (DiMe) among experiments is also proposed to increase statistical power, reduce experimental bias, enhance reproducibility and improve overall biological understanding. However, compared with the ReIn, the DiMe has not yet been widely adopted in current metabolomics studies, due to the difficulty in removing unwanted variations and the inexistence of prior knowledges on the performance of the available merging methods. It is therefore urgently needed to clarify whether DiMe can enhance the performance of metabolic profiling or not. Herein, the performance of DiMe on 4 pairs of benchmark datasets was comprehensively assessed by multiple criteria (classification capacity, robustness and false discovery rate). As a result, integration/merging-based strategies (ReIn and DiMe) were found to perform better under all criteria than those strategies based on single experiment. Moreover, DiMe was discovered to outperform ReIn in classification capacity and robustness, while the ReIn showed superior capacity in controlling false discovery rate. In conclusion, these findings provided valuable guidance to the selection of suitable analytical strategy for current metabolomics.

Unexpected population fragmentation in an endangered seabird: the case of the Peruvian diving-petrel

In less than one century, the once-abundant Peruvian diving petrel has become the first endangered seabird of the Humboldt Current System (HCS). This small endemic petrel of the South American Pacific coast is now an important indicator of ongoing habitat loss and of the success of local conservation policies in the HCS - an ecoregion designated as a priority for the conservation of global biodiversity. Yet so far, poorly understood life history traits such as philopatry or dispersal ability may strongly influence the species' response to ecosystem changes, but also our capacity to assess and interpret this response. To address this question, we explore the range-wide population structure of the Peruvian diving petrel, and show that this small seabird exhibits extreme philopatric behavior at the island level. Mitochondrial DNA sequences and genome-wide SNP data reveal significant isolation and low migration at very short distances, and provide strong evidence for questioning the alleged recovery in the Peruvian and Chilean populations of this species. Importantly, the full demographic independence between colonies makes local population rescue through migration unlikely. As a consequence, the Peruvian diving petrel appears to be particularly vulnerable to ongoing anthropogenic pressure. By excluding immigration as a major factor of demographic recovery, our results highlight the unambiguously positive impact of local conservation measures on breeding populations; yet at the same time they also cast doubt on alleged range-wide positive population trends. Overall, the protection of independent breeding colonies, and not only of the species as a whole, remains a major element in the conservation strategy for endemic seabirds. Finally, we underline the importance of considering the philopatric behavior and demographic independence of breeding populations, even at very fine spatial scales, in spatial planning for marine coastal areas.

Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining foothill yellow-legged frog

Genomic data have the potential to inform high resolution landscape genetic and biological conservation studies that go far beyond recent mitochondrial and microsatellite analyses. We characterize the relationships of populations of the foothill yellow-legged frog, Rana boylii, a declining, "sentinel" species for stream ecosystems throughout its range in California and Oregon. We generated RADseq data and applied phylogenetic methods, hierarchical Bayesian clustering, PCA and population differentiation with admixture analyses to characterize spatial genetic structure across the species range. To facilitate direct comparison with previous analyses, we included many localities and individuals from our earlier work based on mitochondrial DNA. The results are striking, and emphasize the power of our landscape genomic approach. We recovered five extremely differentiated primary clades that indicate that R. boylii may be the most genetically differentiated anuran yet studied. Our results provide better resolution and more spatially consistent patterns than our earlier work, confirming the increased resolving power of genomic data compared to single-locus studies. Genomic structure is not equal across the species distribution. Approximately half the range of R. boylii consists of a single, relatively uniform population, while Sierra Nevada and coastal California clades are deeply, hierarchically substructured with biogeographic breaks observed in other codistributed taxa. Our results indicate that clades should serve as management units for R. boylii rather than previously suggested watershed boundaries, and that the near-extinct population from southwestern California is particularly diverged, exhibits the lowest genetic diversity, and is a critical conservation target for species recovery.

Genetic divergence and fine scale population structure of the common bottlenose dolphin (Tursiops truncatus, Montagu) found in the Gulf of Guayaquil, Ecuador

The common bottlenose dolphin, Tursiops truncatus, is widely distributed along the western coast of South America. In Ecuador, a resident population of bottlenose dolphins inhabits the inner estuarine area of the Gulf of Guayaquil located in the southwestern part of the country and is under threat from different human activities in the area. Only one genetic study on South American common bottlenose dolphins has been carried out to date, and understanding genetic variation of wildlife populations, especially species that are identified as threatened, is crucial for defining conservation units and developing appropriate conservation strategies. In order to evaluate the evolutionary link of this population, we assessed the phylogenetic relationships, phylogeographic patterns, and population structure using mitochondrial DNA (mtDNA). The sampling comprised: (i) 31 skin samples collected from free-ranging dolphins at three locations in the Gulf of Guayaquil inner estuary, (ii) 38 samples from stranded dolphins available at the collection of the “Museo de Ballenas de Salinas,” (iii) 549 mtDNA control region (mtDNA CR) sequences from GenBank, and (iv) 66 concatenated sequences from 7-mtDNA regions (12S rRNA, 16S rRNA, NADH dehydrogenase subunit I–II, cytochrome oxidase I and II, cytochrome b, and CR) obtained from mitogenomes available in GenBank. Our analyses indicated population structure between both inner and outer estuary dolphin populations as well as with distinct populations of T. truncatus using mtDNA CR. Moreover, the inner estuary bottlenose dolphin (estuarine bottlenose dolphin) population exhibited lower levels of genetic diversity than the outer estuary dolphin population according to the mtDNA CR. Finally, the estuarine bottlenose dolphin population was genetically distinct from other T. truncatus populations based on mtDNA CR and 7-mtDNA regions. From these results, we suggest that the estuarine bottlenose dolphin population should be considered a distinct lineage. This dolphin population faces a variety of anthropogenic threats in this area; thus, we highlight its fragility and urge authorities to issue prompt management and conservation measures.

Effect of HIV/HCV Co-Infection on the Protease Evolution of HIV-1B: A Pilot Study in a Pediatric Population

This pilot study evaluates in pediatric patients the impact of HIV/HCV coinfection in the molecular evolution of the HIV-1 subtype B protease (HIV-1BPR). For this study, HIV-1B/HCV coinfected (15) and HIV-1B monoinfected (56) patients with available HIV-1B pol sequences were enrolled. Both groups of patients had comparable gender frequencies and average age, time of infection, antiretroviral treatment (ART) exposure and time under ART. Prevalence of drug resistance mutations (DRM), genetic diversity, number of synonymous (d_S) and non-synonymous (d_N) mutations per site and selection pressures (d_N - d_S) in the HIV-1BPR were estimated and compared between mono- and coinfected patients. Both HIV-1B populations presented similar genetic diversity (0.050 ± 0.02 vs. 0.045 ± 0.01) and d_S (0.074 ± 0.03 vs. 0.078 ± 0.04). In turn, in coinfected patients the HIV-1BPR had higher d_N (0.045 ± 0.01 vs. 0.024 ± 0.01) and d_N-d_S (-0.026 ± 0.02 vs. -0.048 ± 0.04) values, and less amino acid sites under purifying selection (4.2% vs. 42.1%) than in monoinfected patients. Accordingly, in co-infection with HCV, the HIV-1BPR sites 50, 53, 82, 84 and 88 - associated with resistance to PIs - were under neutral evolution, whereas these sites were under purifying selection in monoinfected patients. This pilot study suggests that HIV-1B may evolve differently in the presence than in the absence of HCV.

Genetic diversity of Taenia saginata (Cestoda: Cyclophyllidea) from Lao People's Democratic Republic and northeastern Thailand based on mitochondrial DNA

BACKGROUND

Taenia saginata is a tapeworm found in cattle worldwide. Analysis of genetic diversity in different geographical populations of T. saginata not only helps to understand the origin, transmission and spread of this organism, but also to evaluate the selection pressures acting on T. saginata and how it is responding to them. However, there are few reports of the genetic variability of T. saginata populations in different regions of the world, including Lao PDR and Thailand. We report the genetic diversity of T. saginata populations in Lao PDR and northeastern Thailand together with sequences of T. saginata from other countries deposited in GenBank.

RESULTS

Mitochondrial cox1 sequence analysis revealed that 15 and 8 haplotypes were identified in 30 and 21 T. saginata isolates from Lao PDR and northeastern Thailand, respectively. Fifty-three haplotypes were identified from 98 sequences. Phylogenetic tree and haplotype network analyses revealed that global isolates of T. saginata were genetically divided into five groups (A, B, C1, C2 and D). Taenia saginata isolates from Lao PDR and northeastern Thailand belonged to either Group A or B. Taenia saginata from western Thailand clustered in groups C1, C2 and D, and populations from the northeast and western Thailand were found to be genetically distinct. Taenia saginata isolates in Lao PDR and Thailand were also found to be genetically diverse but the degree of genetic differentiation was low.

CONCLUSIONS

Taenia saginata populations from Lao PDR and northeastern Thailand are genetically distinct from the population in western Thailand and it is proposed that T. saginata has been dispersed by different transmission routes in Southeast Asia.

A wild origin of the loss-of-function lycopene beta cyclase (CYC-b) allele in cultivated, red-fleshed papaya (Carica papaya)

PREMISE OF THE STUDY

The red flesh of some papaya cultivars is caused by a recessive loss-of-function mutation in the coding region of the chromoplast-specific lycopene beta cyclase gene (CYC-b). We performed an evolutionary genetic analysis of the CYC-b locus in wild and cultivated papaya to uncover the origin of this loss-of-function allele in cultivated papaya.

METHODS

We analyzed the levels and patterns of genetic diversity at the CYC-b locus and six loci in a 100-kb region flanking CYC-b and compared these to genetic diversity levels at neutral autosomal loci. The evolutionary relationships of CYC-b haplotypes were assessed using haplotype network analysis of the CYC-b locus and the 100-kb CYC-b region.

KEY RESULTS

Genetic diversity at the recessive CYC-b allele (y) was much lower relative to the dominant Y allele found in yellow-fleshed wild and cultivated papaya due to a strong selective sweep. Haplotype network analyses suggest the y allele most likely arose in the wild and was introduced into domesticated varieties after the first papaya domestication event. The shared haplotype structure between some wild, feral, and cultivated haplotypes around the y allele supports subsequent escape of this allele from red cultivars back into wild populations through feral intermediates.

CONCLUSIONS

Our study supports a protracted domestication process of papaya through the introgression of wild-derived traits and gene flow from cultivars to wild populations. Evidence of gene flow from cultivars to wild populations through feral intermediates has implications for the introduction of transgenic papaya into Central American countries.

SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)

Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen‐induced selection event. Using ddRADseq, we genotyped over 18,000 SNPs across the genome in native pre‐epizootic western US birds, introduced birds from Hawaii and the eastern United States, post‐epizootic eastern birds, and western birds sampled across a similar time span. We found 14% and 7% reductions in nucleotide diversity, respectively, in Hawaiian and pre‐epizootic eastern birds relative to pre‐epizootic western birds, as well as elevated levels of linkage disequilibrium and other signatures of founder events. Despite finding numerous significant frequency shifts (outlier loci) between pre‐epizootic native and introduced populations, we found no signal of reduced genetic diversity, elevated linkage disequilibrium, or outlier loci as a result of the epizootic. Simulations demonstrate that the proportion of outliers associated with founder events could be explained by genetic drift. This rare view of genetic evolution across time in an invasive species provides direct evidence that demographic shifts like founder events have genetic consequences more widespread across the genome than natural selection.