Selective Sweeps

Repeated global adaptation across plant species

Global adaptation occurs when all populations of a species undergo selection toward a common optimum. This can occur by a hard selective sweep with the emergence of a new globally advantageous allele that spreads throughout a species' natural range until reaching fixation. This evolutionary process leaves a temporary trace in the region affected, which is detectable using population genomic methods. While selective sweeps have been identified in many species, there have been few comparative and systematic studies of the genes involved in global adaptation. Building upon recent findings showing repeated genetic basis of local adaptation across independent populations and species, we asked whether certain genes play a more significant role in driving global adaptation across plant species. To address this question, we scanned the genomes of 17 plant species to identify signals of repeated global selective sweeps. Despite the substantial evolutionary distance between the species analyzed, we identified several gene families with strong evidence of repeated positive selection. These gene families tend to be enriched for reduced pleiotropy, consistent with predictions from Fisher's evolutionary model and the cost of complexity hypothesis. We also found that genes with repeated sweeps exhibit elevated levels of gene duplication. Our findings contrast with recent observations of increased pleiotropy in genes driving local adaptation, consistent with predictions based on the theory of migration-selection balance.

Evolution of parasites in the Anthropocene: new pressures, new adaptive directions

The Anthropocene is seeing the human footprint rapidly spreading to all of Earth's ecosystems. The fast-changing biotic and abiotic conditions experienced by all organisms are exerting new and strong selective pressures, and there is a growing list of examples of human-induced evolution in response to anthropogenic impacts. No organism is exempt from these novel selective pressures. Here, we synthesise current knowledge on human-induced evolution in eukaryotic parasites of animals, and present a multidisciplinary framework for its study and monitoring. Parasites generally have short generation times and huge fecundity, features that predispose them for rapid evolution. We begin by reviewing evidence that parasites often have substantial standing genetic variation, and examples of their rapid evolution both under conditions of livestock production and in serial passage experiments. We then present a two-step conceptual overview of the causal chain linking anthropogenic impacts to parasite evolution. First, we review the major anthropogenic factors impacting parasites, and identify the selective pressures they exert on parasites through increased mortality of either infective stages or adult parasites, or through changes in host density, quality or immunity. Second, we discuss what new phenotypic traits are likely to be favoured by the new selective pressures resulting from altered parasite mortality or host changes; we focus mostly on parasite virulence and basic life-history traits, as these most directly influence the transmission success of parasites and the pathology they induce. To illustrate the kinds of evolutionary changes in parasites anticipated in the Anthropocene, we present a few scenarios, either already documented or hypothetical but plausible, involving parasite taxa in livestock, aquaculture and natural systems. Finally, we offer several approaches for investigations and real-time monitoring of rapid, human-induced evolution in parasites, ranging from controlled experiments to the use of state-of-the-art genomic tools. The implications of fast-evolving parasites in the Anthropocene for disease emergence and the dynamics of infections in domestic animals and wildlife are concerning. Broader recognition that it is not only the conditions for parasite transmission that are changing, but the parasites themselves, is needed to meet better the challenges ahead.

Size-selective harvesting drives genomic shifts in a harvested population

Overfishing not only drastically reduces the number of fish in an exploited population but is also often selective for body size by removing the largest individuals from a population. Here, we study experimentally the evolutionary effects of size-selective harvesting using whole-genome sequencing on a model organism, the zebrafish (Danio rerio). We demonstrate genomic shifts in the populations exposed to size-selective harvesting for five generations and show reduced genetic diversity in all harvested lines, including the control line (non-size-selected). We also determine differences in groups of genes related to certain gene ontology annotations between size-selectively harvested lines, with enrichment in nervous system related genes in the large-selected lines. Our results illuminate the biological processes underlying fisheries-induced genetic changes and hence contribute toward the understanding of the changes potentially associated with the vulnerability of an exploited population to future stressors.

iHDSel software: The price equation and the population stability index to detect genomic patterns compatible with selective sweeps. An example with SARS-CoV-2

A large number of methods have been developed and continue to evolve for detecting the signatures of selective sweeps in genomes. Significant advances have been made, including the combination of different statistical strategies and the incorporation of artificial intelligence (machine learning) methods. Despite these advances, several common problems persist, such as the unknown null distribution of the statistics used, necessitating simulations and resampling to assign significance to the statistics. Additionally, it is not always clear how deviations from the specific assumptions of each method might affect the results. In this work, allelic classes of haplotypes are used along with the informational interpretation of the Price equation to design a statistic with a known distribution that can detect genomic patterns caused by selective sweeps. The statistic consists of Jeffreys divergence, also known as the population stability index, applied to the distribution of allelic classes of haplotypes in two samples. Results with simulated data show optimal performance of the statistic in detecting divergent selection. Analysis of real severe acute respiratory syndrome coronavirus 2 genome data also shows that some of the sites playing key roles in the virus's fitness and immune escape capability are detected by the method. The new statistic, called JHAC , is incorporated into the iHDSel (informed HacDivSel) software available at https://acraaj.webs.uvigo.es/iHDSel.html.

Quantification of rearrangements and evolution of mitochondrial gene order of Acari (Chelicerata: Arachnida)

Invertebrate mitogenomes are generally fixed with formal 37 genes: 13 PCGs encoded subunits of OXPHOS, 2 ribosomal RNA (rRNA) functional in the translation of these PCGs and 22 transfer RNA (tRNA) genes. The order of these genes varies greatly among organisms and named rearrangement. Rearrangement patterns of mitochondrial genomes may shed light on mutation processes and evolutionary relationships of organisms. Mitochondrial gene organization is highly variable among Acari, so rearrangement is a very common mitogenomic pattern in this group. In this study, 258 unique Acari (Acariformes + Parasitiformes) mitogenomes were downloaded from NCBI and studied about rearrangement patterns. Sixty-seven mitotypes were determined among Acari and the most rearranged genes were trnL1 and nad2. Following that, trnI, trnS1, trnN, trnE, trnT, and trnP genes are remarkably mobile (RF > 95%). Conversely, atp6, cox3, trnG, and cytb genes also appears to be quite stable (RF < 20%). Within Acari, mean distance calculations are varied from 1.210 in atp8 to 0.155 in rrnS. Contrary to expectations, among Acari mobile tRNA genes appear to be conserved in sequences, whereas PCGs have higher distance values and seem to be mutated. Consistently, tRNA genes seem saturated, but some PCGs (atp6, cox genes, cytb, nad1, and nad6) are not saturated. These values do not correlate with each other (p > 0.005). This discrepancy may indicate that the genes were rearranged after mutation load; consistent with this, DAMBE saturation values are also not correlated with RF values. Parasitiformes mitogenomes are more mobile than Acariformes mitogenomes and may be under the effect of selective sweeping.

A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model

The aye-aye (Daubentonia madagascariensis) is one of the 25 most endangered primate species in the world, maintaining amongst the lowest genetic diversity of any primate measured to date. Characterizing patterns of genetic variation within aye-aye populations, and the relative influences of neutral and selective processes in shaping that variation, is thus important for future conservation efforts. In this study, we performed the first whole-genome scans for recent positive and balancing selection in the species, utilizing high-coverage population genomic data from newly sequenced individuals. We generated null thresholds for our genomic scans by creating an evolutionarily appropriate baseline model that incorporates the demographic history of this aye-aye population, and identified a small number of candidate genes. Most notably, a suite of genes involved in olfaction - a key trait in these nocturnal primates - were identified as experiencing long-term balancing selection. We also conducted analyses to quantify the expected statistical power to detect positive and balancing selection in this population using site frequency spectrum-based inference methods, once accounting for the potentially confounding contributions of population history, recombination and mutation rate variation, and purifying and background selection. This work, presenting the first high-quality, genome-wide polymorphism data across the functional regions of the aye-aye genome, thus provides important insights into the landscape of episodic selective forces in this highly endangered species.

Signatures of selection analyses reveal genomic differences among three heavy pig breeds that constitute the genetic backbone of a dry-cured ham production system

The Italian pig farming industry is unique in its focus on raising heavy pigs primarily for the production of high-quality dry-cured hams. These products require pigs to be slaughtered at a live weight of around 170 kg at 9 months of age. The primary breeds used in this system are Italian Duroc, Italian Landrace, and Italian Large White which are crossed to produce lines that meet standard requirements. Over the past four decades, selection and breeding programmes for these breeds have been subjected to distinct selective pressures to highlight the characteristics of each breed. In this study, we investigated the genome of these breeds by analysing high-density single nucleotide polymorphism data from over 9 000 pigs to scan for signatures of selection using four different methods, two within breeds and two across breeds. This allowed to identify the genomic regions that differentiate these breeds as well as any relevant genes and biological terms. On a global scale, we found that the Italian Duroc breed exhibited a higher genetic differentiation from the Italian Landrace and Italian Large White breeds, with a pairwise FST value of 0.20 compared with the 0.13 between Italian Landrace and Italian Large White. This may reflect either their different origins or the different breeding goals, which are more similar for the Italian Landrace and Italian Large White breeds. Despite these genetic differences at a global level, few signatures of selection regions reached complete fixation, possibly due to challenges in detecting selection linked to quantitative polygenic traits. The differences among the three breeds are confirmed by the low level of overlap in the regions detected. Genetic enrichment analyses of the three breeds revealed pathways and genes related to various productive traits associated with growth and fat deposition. This may indicate a common selection direction aimed at enhancing specific production traits, though different biological mechanisms are likely targeted by the same directional selection in these three breeds. Therefore, these genes may play a critical role in determining the distinctive characteristics of Italian Duroc, Italian Landrace, and Italian Large White, and potentially influence the traits in crossbred pigs derived from them. Overall, the insights gained from this study will contribute to understanding how directional selection has shaped the genome of these heavy pig breeds and to better address selection strategies aimed at enhancing the meat processing industry linked with dry-cured ham production chains.

Tree Sequences as a General-Purpose Tool for Population Genetic Inference

As population genetic data increase in size, new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient but are not interchangeable with existing data structures used for many population genetic inference methodologies such as the use of convolutional neural networks applied to population genetic alignments. To better utilize these new data structures, we propose and implement a graph convolutional network to directly learn from tree sequence topology and node data, allowing for the use of neural network applications without an intermediate step of converting tree sequences to population genetic alignment format. We then compare our approach to standard convolutional neural network approaches on a set of previously defined benchmarking tasks including recombination rate estimation, positive selection detection, introgression detection, and demographic model parameter inference. We show that tree sequences can be directly learned from using a graph convolutional network approach and can be used to perform well on these common population genetic inference tasks with accuracies roughly matching or even exceeding that of a convolutional neural network-based method. As tree sequences become more widely used in population genetic research, we foresee developments and optimizations of this work to provide a foundation for population genetic inference moving forward.

Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India

The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population FST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and FST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir- and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.

Analysis of genetic evolutionary differences among four Tibetan pig populations in China

Tibetan pigs are a locally bred domestic pig breed originating from the Tibetan Plateau in China. They can be categorized into four distinct groups based on their geographical locations: Sichuan Tibetan pigs, Tibetan pigs from Tibet, Yunnan Tibetan pigs, and Gansu Tibetan pigs. This study aimed to explore population diversity, genetic structure and selection signals among Tibetan pigs in four Chinese national nature reserves. The results show that there is different observed heterozygosity among Tibetan pig populations (0.1957-0.1978). Ratio of runs of homozygosity (Froh) calculation of four Tibetan pig populations by runs of homozygosity (ROH) revealed the presence of inbreeding within the population (0.0336-0.0378). Analysis of the genetic structure demonstrated distinct population stratification among the four Tibetan pig populations, with each showing relatively independent evolutionary directions. Furthermore, Five methods (FST, Piratio, ROD, Tajima's D, XP-CLR) were used to artificially select evolutionary trajectories. The results mainly involved processes such as DNA repair, immune regulation, muscle fat deposition and adaptation to hypoxia. In conclusion, this study enhances our understanding of the genetic characteristics of Tibetan pig populations and provides a theoretical reference for the conservation of resources across different populations of Tibetan pigs.

A Dominance Hypothesis Argument for Historical Genetic Gains and the Fixation of Heterosis in Octoploid Strawberry

Heterosis was the catalyst for the domestication of cultivated strawberry (Fragaria × ananassa), an interspecific hybrid species that originated in the 1700s. The hybrid origin was discovered because the phenotypes of spontaneous hybrids transgressed those of their parent species. The transgressions included fruit yield increases and other genetic gains in the twentieth century that sparked the global expansion of strawberry production. The importance of heterosis to the agricultural success of the hybrid species, however, has remained a mystery. Here we show that heterosis has disappeared (become fixed) among improved hybrids within a population (the California population) that has been under long-term selection for increased fruit yield, weight, and firmness. We found that the highest yielding hybrids are among the most highly inbred (59-79%), which seems counterintuitive for a highly heterozygous, outbreeder carrying heavy genetic loads. Although faint remnants of heterosis were discovered, the between-parent allele frequency differences and dispersed favorable dominant alleles necessary for heterosis have decreased nearly genome-wide within the California population. Conversely, heterosis was prevalent and significant among wide hybrids, especially for fruit count, a significant driver of genetic gains for fruit yield. We attributed the disappearance (fixation) of heterosis within the California population to increased homozygosity of favorable dominant alleles and inbreeding associated with selection, random genetic drift, and selective sweeps. Despite historical inbreeding, the highest yielding hybrids reported to-date are estimated to be heterozygous for 20,370-44,280 of 97,000-108,000 genes in the octoploid genome, the equivalent of an entire diploid genome or more.

Spatial sorting caused by downstream dispersal: implication for morphological evolution in isolated populations of fat minnow inhabiting small streams flowing through terraced rice paddies

The evolutionary forces arising from differential dispersal are known as "spatial sorting," distinguishing them from natural selection arising from differential survival or differential reproductive success. Spatial sorting is often considered to be transient because it is offset by the return of dispersers in many cases. However, in riverine systems, spatial sorting by downstream dispersal can be cumulative in habitats upstream of migration barriers such as weirs or falls, which can block the return of the dispersers. Terraced rice paddies are often found on steep mountain slopes in Japan and often incorporate small streams with numerous migration barriers. This study investigated the morphological features of fat minnow, Rhynchocypris oxycephalus jouyi (Cyprinidae), inhabiting above-barrier habitats of the small streams flowing through flood-prone terraced rice paddies and examined their function via a mark-recapture experiment. Although this study did not reveal a consistent pattern across all local populations, some above-barrier populations were characterized by individuals with a thinner caudal peduncle, thinner body, and longer ventral caudal fin lobes than those in neighbouring mainstream populations. A mark-recapture experiment during minor flooding showed that a thinner caudal peduncle and deeper body helped fat minnow avoid downstream dispersal and ascend a small step, and suggested that a longer ventral caudal fin lobe was important for ascending. These results suggest that the caudal morphologies of some above-barrier populations avoid or reduce the risk of downstream dispersal, supporting the idea that spatial sorting shapes functional traits, enhancing the spatial persistence of individuals in upstream habitats.

Tree sequences as a general-purpose tool for population genetic inference

As population genetics data increases in size new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient, but are not interchangeable with existing data structures used for many population genetic inference methodologies such as the use of convolutional neural networks (CNNs) applied to population genetic alignments. To better utilize these new data structures we propose and implement a graph convolutional network (GCN) to directly learn from tree sequence topology and node data, allowing for the use of neural network applications without an intermediate step of converting tree sequences to population genetic alignment format. We then compare our approach to standard CNN approaches on a set of previously defined benchmarking tasks including recombination rate estimation, positive selection detection, introgression detection, and demographic model parameter inference. We show that tree sequences can be directly learned from using a GCN approach and can be used to perform well on these common population genetics inference tasks with accuracies roughly matching or even exceeding that of a CNN-based method. As tree sequences become more widely used in population genetics research we foresee developments and optimizations of this work to provide a foundation for population genetics inference moving forward.

Characterising the Genomic Landscape of Differentiation Between Annual and Perennial Rye

Annuality and perenniality represent two different life-history strategies in plants, and an analysis of genomic differentiation between closely related species of different life histories bears the potential to identify the underlying targets of selection. Additionally, understanding the interactions between patterns of recombination and signatures of natural selection is a central aim in evolutionary biology, because patterns of recombination shape the evolution of genomes by affecting the efficacy of selection. Here, our aim was to characterise the landscape of genomic differentiation between weedy annual rye (Secale cereale L.) and wild perennial rye (Secale strictum C. Presl), and explore the extent to which signatures of selection are influenced by recombination rate variation. We used population-level sequence data of annual and perennial rye to analyse population structure and their demographic history. Based on our analyses, annual and perennial rye diverged approximately 26,500 years ago (ya) from an ancestral population size of ~85,000 individuals. We analysed patterns of genetic diversity and genetic differentiation, and found highly differentiated regions located in low-recombination regions, indicative of linked selection. Although all highly differentiated regions, as revealed by F ST-outlier scans, were located in low-recombining regions, not all chromosomes showed this tendency. We therefore performed a gene ontology enrichment analysis, which showed that highly differentiated regions comprise genes involved in photosynthesis. This enrichment was confirmed when F ST outlier scans were performed separately in low- and intermediate-recombining regions, but not in high-recombining regions, suggesting that local recombination rate variation in rye affects outlier scans. Cultivated rye is an annual crop, but the introduction of perenniality may be advantageous in regions with poor soil quality or under low-input farming. Although the resolution of our analysis is limited to a broad-scale, knowledge about the evolutionary divergence between annual and perennial rye might support breeding efforts towards perennial rye cultivation.

X centromeric drive may explain the prevalence of polycystic ovary syndrome and other conditions: Genomic structure of the human X chromosome pericentromeric region is consistent with meiotic drive associated with PCOS and other conditions

X chromosome centromeric drive may explain the prevalence of polycystic ovary syndrome and contribute to oocyte aneuploidy, menopause, and other conditions. The mammalian X chromosome may be vulnerable to meiotic drive because of X inactivation in the female germline. The human X pericentromeric region contains genes potentially involved in meiotic mechanisms, including multiple SPIN1 and ZXDC paralogs. This is consistent with a multigenic drive system comprising differential modification of the active and inactive X chromosome centromeres in female primordial germ cells and preferential segregation of the previously inactivated X chromosome centromere to the polar body at meiosis I. The drive mechanism may explain differences in X chromosome regulation in the female germlines of the human and mouse and, based on the functions encoded by the genes in the region, the transmission of X pericentromeric genetic or epigenetic variants to progeny could contribute to preeclampsia, autism, and differences in sexual differentiation.

Polygenic dynamics underlying the response of quantitative traits to directional selection

We study the response of a quantitative trait to exponential directional selection in a finite haploid population, both at the genetic and the phenotypic level. We assume an infinite sites model, in which the number of new mutations per generation in the population follows a Poisson distribution (with mean Θ) and each mutation occurs at a new, previously monomorphic site. Mutation effects are beneficial and drawn from a distribution. Sites are unlinked and contribute additively to the trait. Assuming that selection is stronger than random genetic drift, we model the initial phase of the dynamics by a supercritical Galton-Watson process. This enables us to obtain time-dependent results. We show that the copy-number distribution of the mutant in generation n, conditioned on non-extinction until n, is described accurately by the deterministic increase from an initial distribution with mean 1. This distribution is related to the absolutely continuous part W+ of the random variable, typically denoted W, that characterizes the stochasticity accumulating during the mutant's sweep. A suitable transformation yields the approximate dynamics of the mutant frequency distribution in a Wright-Fisher population of size N. Our expression provides a very accurate approximation except when mutant frequencies are close to 1. On this basis, we derive explicitly the (approximate) time dependence of the expected mean and variance of the trait and of the expected number of segregating sites. Unexpectedly, we obtain highly accurate approximations for all times, even for the quasi-stationary phase when the expected per-generation response and the trait variance have equilibrated. The latter refine classical results. In addition, we find that Θ is the main determinant of the pattern of adaptation at the genetic level, i.e., whether the initial allele-frequency dynamics are best described by sweep-like patterns at few loci or small allele-frequency shifts at many. The number of segregating sites is an appropriate indicator for these patterns. The selection strength determines primarily the rate of adaptation. The accuracy of our results is tested by comprehensive simulations in a Wright-Fisher framework. We argue that our results apply to more complex forms of directional selection.

Genome structural variants shape adaptive success of an invasive urban malaria vector Anopheles stephensi

Global changes are associated with the emergence of several invasive species. However, the genomic determinants of the adaptive success of an invasive species in a new environment remain poorly understood. Genomic structural variants (SVs), consisting of copy number variants, play an important role in adaptation. SVs often cause large adaptive shifts in ecologically important traits, which makes SVs compelling candidates for driving rapid adaptations to environmental changes, which is critical to invasive success. To address this problem, we investigated the role SVs play in the adaptive success of Anopheles stephensi , a primary vector of urban malaria in South Asia and an invasive malaria vector in several South Asian islands and Africa. We collected whole genome sequencing data from 115 mosquitoes from invasive island populations and four locations from mainland India, an ancestral range for the species. We identified 2,988 duplication copy number variants and 16,038 deletions in these strains, with ∼50% overlapping genes. SVs are enriched in genomic regions with signatures of selective sweeps in the mainland and invasive island populations, implying a putative adaptive role of SVs. Nearly all high-frequency SVs, including the candidate adaptive variants, in the invasive island populations are present on the mainland, suggesting a major contribution of existing variation to the success of the island populations. Among the candidate adaptive SVs, three duplications involving toxin-resistance genes evolved, likely due to the widespread application of insecticides in India since the 1950s. We also identify two SVs associated with the adaptation of An. stephensi larvae to brackish water in the island and two coastal mainland populations, where the mutations likely originated. Our results suggest that existing SVs play a vital role in the evolutionary success of An. stephensi in new environmental conditions.

Two decades of molecular surveillance in Senegal reveal rapid changes in known drug resistance mutations over time

BACKGROUND

Drug resistance in Plasmodium falciparum is a major threat to malaria control efforts. Pathogen genomic surveillance could be invaluable for monitoring current and emerging parasite drug resistance.

METHODS

Data from two decades (2000-2020) of continuous molecular surveillance of P. falciparum parasites from Senegal were retrospectively examined to assess historical changes in malaria drug resistance mutations. Several known drug resistance markers and their surrounding haplotypes were profiled using a combination of single nucleotide polymorphism (SNP) molecular surveillance and whole genome sequence based population genomics.

RESULTS

This dataset was used to track temporal changes in drug resistance markers whose timing correspond to historically significant events such as the withdrawal of chloroquine (CQ) and the introduction of sulfadoxine-pyrimethamine (SP) in 2003. Changes in the mutation frequency at Pfcrt K76T and Pfdhps A437G coinciding with the 2014 introduction of seasonal malaria chemoprevention (SMC) in Senegal were observed. In 2014, the frequency of Pfcrt K76T increased while the frequency of Pfdhps A437G declined. Haplotype-based analyses of Pfcrt K76T showed that this rapid increase was due to a recent selective sweep that started after 2014.

DISCUSSION (CONCLUSION)

The rapid increase in Pfcrt K76T is troubling and could be a sign of emerging amodiaquine (AQ) resistance in Senegal. Emerging AQ resistance may threaten the future clinical efficacy of artesunate-amodiaquine (ASAQ) and AQ-dependent SMC chemoprevention. These results highlight the potential of molecular surveillance for detecting rapid changes in parasite populations and stress the need to monitor the effectiveness of AQ as a partner drug for artemisinin-based combination therapy (ACT) and for chemoprevention.

A comparative analysis reveals the genomic diversity among 8 Muscovy duck populations

The Muscovy duck (Cairina moschata) is a waterfowl indigenous to the neotropical regions of Central and South America. It has low demand for concentrated feed and strong adaptability to different rearing conditions. After introduced to China through Eurasian commercial trade, Muscovy ducks have a domestication history of around 300 years in the Fujian Province of China. In the 1990s, the commodity Muscovy duck breed "Crimo," cultivated in Europe, entered the Chinese market for consumption and breeding purposes. Due to the different selective breeding processes, Muscovy ducks have various populational traits and lack transparency of their genetic background. To remove this burden in the Muscovy duck breeding process, we analyzed genomic data from 8 populations totaling 83 individuals. We identify 11.24 million single nucleotide polymorphisms (SNPs) and categorized these individuals into the Fujian-bred and the Crimo populations according to phylogenetic analyses. We then delved deeper into their evolutionary relationships through assessing population structure, calculating fixation index (FST) values, and measuring genetic distances. Our exploration of runs of homozygosity (ROHs) and homozygous-by-descent (HBD) uncovered genomic regions enriched for genes implicated in fatty acid metabolism, development, and immunity pathways. Selective sweep analyses further indicated strong selective pressures exerted on genes including TECR, STAT2, and TRAF5. These findings provide insights into genetic variations of Muscovy ducks, thus offering valuable information regarding genetic diversity, population conservation, and genome associated with the breeding of Muscovy ducks.

Insights into spinach domestication from genome sequences of two wild spinach progenitors, Spinacia turkestanica and Spinacia tetrandra

Cultivated spinach (Spinacia oleracea) is a dioecious species. We report high-quality genome sequences for its two closest wild relatives, Spinacia turkestanica and Spinacia tetrandra, which are also dioecious, and are used to study the genetics of spinach domestication. Using a combination of genomic approaches, we assembled genomes of both these species and analyzed them in comparison with the previously assembled S. oleracea genome. These species diverged c. 6.3 million years ago (Ma), while cultivated spinach split from S. turkestanica 0.8 Ma. In all three species, all six chromosomes include very large gene-poor, repeat-rich regions, which, in S. oleracea, are pericentromeric regions with very low recombination rates in both male and female genetic maps. We describe population genomic evidence that the similar regions in the wild species also recombine rarely. We characterized 282 structural variants (SVs) that have been selected during domestication. These regions include genes associated with leaf margin type and flowering time. We also describe evidence that the downy mildew resistance loci of cultivated spinach are derived from introgression from both wild spinach species. Collectively, this study reveals the genome architecture of spinach assemblies and highlights the importance of SVs during the domestication of cultivated spinach.

Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution

Theory predicts that compensatory genetic changes reduce negative indirect effects of selected variants during adaptive evolution, but evidence is scarce. Here, we test this in a wild population of Hawaiian crickets using temporal genomics and a high-quality chromosome-level cricket genome. In this population, a mutation, flatwing, silences males and rapidly spread due to an acoustically-orienting parasitoid. Our sampling spanned a social transition during which flatwing fixed and the population went silent. We find long-range linkage disequilibrium around the putative flatwing locus was maintained over time, and hitchhiking genes had functions related to negative flatwing-associated effects. We develop a combinatorial enrichment approach using transcriptome data to test for compensatory, intragenomic coevolution. Temporal changes in genomic selection were distributed genome-wide and functionally associated with the population's transition to silence, particularly behavioural responses to silent environments. Our results demonstrate how 'adaptation begets adaptation'; changes to the sociogenetic environment accompanying rapid trait evolution can generate selection provoking further, compensatory adaptation.

Genetic assessment and candidate genes identification for breed-specific characteristics of Qingyuan partridge chicken based on runs of homozygosity

BACKGROUND

Several core breeding and supporting lines of the Qingyuan partridge chicken, a representative local chicken breed in China, have been developed over 20 years. Consequently, its economic traits related to growth and reproduction have been significantly improved by breeding selection and commercial utilization, but some characteristic traits, such as partridge feathers, high meat quality and sufficient flavor, have always been retained. However, effective methods for genetic assessment and functional gene exploration of similar trait groups are lacking. The presence of identical haplotype fragments transmitted from parent to offspring results in runs of homozygosity (ROH), which offer an efficient solution. In this study, genomes of 134 Qingyuan partridge chickens representing two breeding populations and one preserved population were re-sequenced to evaluate the genetic diversity and explore functional genes by analyzing the diversity, distribution, and frequency of ROH.

RESULTS

The results showed a low level of genomic linkage and degree of inbreeding within both the bred and preserved populations, suggesting abundant genetic diversity and an adequate genetic potential of the Qingyuan partridge chicken. Throughout the long-term selection process, 21 genes, including GLI3, ANO5, BLVRA, EFNB2, SLC5A12, and SVIP, associated with breed-specific characteristics were accumulated within three ROH islands, whereas another 21 genes associated with growth traits including IRX1, IRX2, EGFR, TPK1, NOVA1, BDNF and so on were accumulated within five ROH islands.

CONCLUSIONS

These findings provide new insights into the genetic assessment and identification of genes with breed-specific and selective characteristics, offering a solid genetic basis for breeding and protection of Qingyuan partridge chickens.

Temporal challenges in detecting balancing selection from population genomic data

The role of balancing selection in maintaining genetic variation remains an open question in population genetics. Recent years have seen numerous studies identifying candidate loci potentially experiencing balancing selection, most predominantly in human populations. There are however numerous alternative evolutionary processes that may leave similar patterns of variation, thereby potentially confounding inference, and the expected signatures of balancing selection additionally change in a temporal fashion. Here we use forward-in-time simulations to quantify expected statistical power to detect balancing selection using both site frequency spectrum- and linkage disequilibrium-based methods under a variety of evolutionarily realistic null models. We find that whilst site frequency spectrum-based methods have little power immediately after a balanced mutation begins segregating, power increases with time since the introduction of the balanced allele. Conversely, linkage disequilibrium-based methods have considerable power whilst the allele is young, and power dissipates rapidly as the time since introduction increases. Taken together, this suggests that site frequency spectrum-based methods are most effective at detecting long-term balancing selection (>25N generations since the introduction of the balanced allele) whilst linkage disequilibrium-based methods are effective over much shorter timescales (<1N generations), thereby leaving a large time frame over which current methods have little power to detect the action of balancing selection. Finally, we investigate the extent to which alternative evolutionary processes may mimic these patterns, and demonstrate the need for caution in attempting to distinguish the signatures of balancing selection from those of both neutral processes (e.g. population structure and admixture) as well as of alternative selective processes (e.g. partial selective sweeps).

Genome-wide analysis reveals genomic diversity and signatures of selection in Qinchuan beef cattle

BACKGROUND

Indigenous Chinese cattle have abundant genetic diversity and a long history of artificial selection, giving local breeds advantages in adaptability, forage tolerance and resistance. The detection of selective sweeps and comparative genome analysis of selected breeds and ancestral populations provide a basis for understanding differences among breeds and for the identification and utilization of candidate genes. We investigated genetic diversity, population structure, and signatures of selection using genome-wide sequencing data for a new breed of Qinchuan cattle (QNC, n = 21), ancestral Qinchuan cattle (QCC, n = 20), and Zaosheng cattle (ZSC, n = 19).

RESULTS

A population structure analysis showed that the ancestry components of QNC and ZSC were similar. In addition, the QNC and ZSC groups showed higher proportions of European taurine ancestry than that of QCC, and this may explain the larger body size of QNC, approaching that of European cattle under long-term domestication and selection. A neighbor-joining tree revealed that QCC individuals were closely related, whereas QNC formed a distinct group. To search for signatures of selection in the QNC genome, we evaluated nucleotide diversity (θπ), the fixation index (FST) and Tajima's D. Overlapping selective sweeps were enriched for one KEGG pathway, the apelin signaling pathway, and included five candidate genes (MEF2A, SMAD2, CAMK4, RPS6, and PIK3CG). We performed a comprehensive review of genomic variants in QNC, QCC, and ZSC using whole-genome sequencing data. QCC was rich in novel genetic diversity, while diversity in QNC and ZSC cattle was reduced due to strong artificial selection, with divergence from the original cattle.

CONCLUSIONS

We identified candidate genes associated with production traits. These results support the success of selective breeding and can guide further breeding and resource conservation of Qinchuan cattle.

Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex

The economically significant genus Prunus includes fruit and nut crops that have been domesticated for shared and specific agronomic traits; however, the genomic signals of convergent and divergent selection have not been elucidated. In this study, we aimed to detect genomic signatures of convergent and divergent selection by conducting comparative population genomic analyses of the apricot-peach-plum-mei (APPM) complex, utilizing a haplotype-resolved telomere-to-telomere (T2T) genome assembly and population resequencing data. The haplotype-resolved T2T reference genome for the plum cultivar was assembled through HiFi and Hi-C reads, resulting in two haplotypes 251.25 and 251.29 Mb in size, respectively. Comparative genomics reveals a chromosomal translocation of ~1.17 Mb in the apricot genomes compared with peach, plum, and mei. Notably, the translocation involves the D locus, significantly impacting titratable acidity (TA), pH, and sugar content. Population genetic analysis detected substantial gene flow between plum and apricot, with introgression regions enriched in post-embryonic development and pollen germination processes. Comparative population genetic analyses revealed convergent selection for stress tolerance, flower development, and fruit ripening, along with divergent selection shaping specific crop, such as somatic embryogenesis in plum, pollen germination in mei, and hormone regulation in peach. Notably, selective sweeps on chromosome 7 coincide with a chromosomal collinearity from the comparative genomics, impacting key fruit-softening genes such as PG, regulated by ERF and RMA1H1. Overall, this study provides insights into the genetic diversity, evolutionary history, and domestication of the APPM complex, offering valuable implications for genetic studies and breeding programs of Prunus crops.

Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits

BACKGROUND

Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS).

RESULTS

In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits.

CONCLUSIONS

The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.

Determinants of rapid adaptation in species with large variance in offspring production

The speed of population adaptation to changing biotic and abiotic environments is determined by the interaction between genetic drift, positive selection and linkage effects. Many marine species (fish, crustaceans), invertebrates and pathogens of humans and crops, exhibit sweepstakes reproduction characterized by the production of a very large amount of offspring (fecundity phase) from which only a small fraction may survive to the next generation (viability phase). Using stochastic simulations, we investigate whether the occurrence of sweepstakes reproduction affects the efficiency of a positively selected unlinked locus, and thus, the speed of adaptation since fecundity and/or viability have distinguishable consequences on mutation rate, probability and fixation time of advantageous alleles. We observe that the mean number of mutations at the next generation is always the function of the population size, but the variance increases with stronger sweepstakes reproduction when mutations occur in the parents. On the one hand, stronger sweepstakes reproduction magnifies the effect of genetic drift thus increasing the probability of fixation of neutral allele and decreasing that of selected alleles. On the other hand, the time to fixation of advantageous (as well as neutral) alleles is shortened by stronger sweepstakes reproduction. Importantly, fecundity and viability selection exhibit different probabilities and times to fixation of advantageous alleles under intermediate and weak sweepstakes reproduction. Finally, alleles under both strong fecundity and viability selection display a synergistic efficiency of selection. We conclude that measuring and modelling accurately fecundity and/or viability selection are crucial to predict the adaptive potential of species with sweepstakes reproduction.

Demographic fluctuations and selection during host-parasite co-evolution interactively increase genetic diversity

Host-parasite interactions can cause strong demographic fluctuations accompanied by selective sweeps of resistance/infectivity alleles. Both demographic bottlenecks and frequent sweeps are expected to reduce the amount of segregating genetic variation and therefore might constrain adaptation during co-evolution. Recent studies, however, suggest that the interaction of demographic and selective processes is a key component of co-evolutionary dynamics and may rather positively affect levels of genetic diversity available for adaptation. Here, we provide direct experimental testing of this hypothesis by disentangling the effects of demography, selection and their interaction in an experimental host-parasite system. We grew 12 populations of a unicellular, asexually reproducing algae (Chlorella variabilis) that experienced either growth followed by constant population sizes (three populations), demographic fluctuations (three populations), selection induced by exposure to a virus (three populations), or demographic fluctuations together with virus-induced selection (three populations). After 50 days (~50 generations), we conducted whole-genome sequencing of each algal host population. We observed more genetic diversity in populations that jointly experienced selection and demographic fluctuations than in populations where these processes were experimentally separated. In addition, in those three populations that jointly experienced selection and demographic fluctuations, experimentally measured diversity exceeds expected values of diversity that account for the cultures' population sizes. Our results suggest that eco-evolutionary feedbacks can positively affect genetic diversity and provide the necessary empirical measures to guide further improvements of theoretical models of adaptation during host-parasite co-evolution.

Sweepstakes reproduction facilitates rapid adaptation in highly fecund populations

Adaptation enables natural populations to survive in a changing environment. Understanding the mechanics of adaptation is therefore crucial for learning about the evolution and ecology of natural populations. We focus on the impact of random sweepstakes on selection in highly fecund haploid and diploid populations partitioned into two genetic types, with one type conferring selective advantage. For the diploid populations, we incorporate various dominance mechanisms. We assume that the populations may experience recurrent bottlenecks. In random sweepstakes, the distribution of individual recruitment success is highly skewed, resulting in a huge variance in the number of offspring contributed by the individuals present in any given generation. Using computer simulations, we investigate the joint effects of random sweepstakes, recurrent bottlenecks and dominance mechanisms on selection. In our framework, bottlenecks allow random sweepstakes to have an effect on the time to fixation, and in diploid populations, the effect of random sweepstakes depends on the dominance mechanism. We describe selective sweepstakes that are approximated by recurrent sweeps of strongly beneficial allelic types arising by mutation. We demonstrate that both types of sweepstakes reproduction may facilitate rapid adaptation (as defined based on the average time to fixation of a type conferring selective advantage conditioned on fixation of the type). However, whether random sweepstakes cause rapid adaptation depends also on their interactions with bottlenecks and dominance mechanisms. Finally, we review a case study in which a model of recurrent sweeps is shown to essentially explain population genomic data from Atlantic cod.

Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data

Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized by numerous small insular populations with large phenotypic diversity. Using the newly available genome for this species, we characterized more than 300,000 SNPs, merging genotyping-by-sequencing (GBS) data with previously published restriction site-associated DNA sequencing (RAD-Seq) data, providing a dataset of 16 island populations (191 individuals) across the range of species distribution (Menorca, Mallorca, and Cabrera). Results indicate that each islet hosts a well-differentiated population (F ST = 0.247 ± 0.09), with no recent immigration/translocation events. Contrary to expectations, most populations harbor a considerable genetic diversity (mean nucleotide diversity, P i = 0.144 ± 0.021), characterized by overall low inbreeding values (F IS < 0.1). While the genetic diversity significantly decreased with decreasing islet surface, maintenance of substantial genetic diversity even in tiny islets suggests variable selection or other mechanisms that buffer genetic drift. Maximum-likelihood tree based on concatenated SNP data confirmed the existence of the two major independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of evidence, including admixture and root testing, robustly placed the origin of the species in the Mallorca Island, rather than in Menorca. Outlier analysis mainly retrieved a strong signature of genome differentiation between the two major archipelagos, especially in the sexual chromosome Z. A set of proteins were target of multiple outliers and primarily associated with binding and catalytic activity, providing interesting candidates for future selection studies. This study provides the framework to explore crucial aspects of the genetic basis of phenotypic divergence and insular adaptation.

Genome-wide mining of diversity and evolutionary signatures revealed selective hotspots in Indian Sahiwal cattle

The Sahiwal cattle breed is the best indigenous dairy cattle breed, and it plays a pivotal role in the Indian dairy industry. This is due to its exceptional milk-producing potential, adaptability to local tropical conditions, and its resilience to ticks and diseases. The study aimed to identify selective sweeps and estimate intrapopulation genetic diversity parameters in Sahiwal cattle using ddRAD sequencing-based genotyping data from 82 individuals. After applying filtering criteria, 78,193 high-quality SNPs remained for further analysis. The population exhibited an average minor allele frequency of 0.221 ± 0.119. Genetic diversity metrics, including observed (0.597 ± 0.196) and expected heterozygosity (0.433 ± 0.096), nucleotide diversity (0.327 ± 0.114), the proportion of polymorphic SNPs (0.726), and allelic richness (1.323 ± 0.134), indicated ample genomic diversity within the breed. Furthermore, an effective population size of 74 was observed in the most recent generation. The overall mean linkage disequilibrium (r2) for pairwise SNPs was 0.269 ± 0.057. Moreover, a greater proportion of short Runs of Homozygosity (ROH) segments were observed suggesting that there may be low levels of recent inbreeding in this population. The genomic inbreeding coefficients, computed using different inbreeding estimates (FHOM, FUNI, FROH, and FGROM), ranged from -0.0289 to 0.0725. Subsequently, we found 146 regions undergoing selective sweeps using five distinct statistical tests: Tajima's D, CLR, |iHS|, |iHH12|, and ROH. These regions, located in non-overlapping 500 kb windows, were mapped and revealed various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK), as well as production traits (NRXN1, PLCE1, GHR). Notably, we identified interleukin 2 (IL2) on Chr17: 35217075-35223276 as a gene linked to tick resistance and uncovered a cluster of genes (HSPA8, UBASH3B, ADAMTS18, CRTAM) associated with heat stress. These findings indicate the evolutionary impact of natural and artificial selection on the environmental adaptation of the Sahiwal cattle population.

Dissecting the genomic regions of selection on the X chromosome in different cattle breeds

Mammalian X and Y chromosomes independently evolved from various autosomes approximately 300 million years ago (MYA). To fully understand the relationship between genomic composition and phenotypic diversity arising due to the course of evolution, we have scanned regions of selection signatures on the X chromosome in different cattle breeds. In this study, we have prepared the datasets of 184 individuals of different cattle breeds and explored the complete X chromosome by utilizing four within-population and two between-population methods. There were 23, 25, 30, 17, 17, and 12 outlier regions identified in Tajima's D, CLR, iHS, ROH, FST, and XP-EHH. Bioinformatics analysis showed that these regions harbor important candidate genes like AKAP4 for reproduction in Brown Swiss, MBTS2 for production traits in Brown Swiss and Guernsey, CXCR3 and CITED1 for health traits in Jersey and Nelore, and BMX and CD40LG for regulation of X chromosome inactivation in Nelore and Gir. We identified genes shared among multiple methods, such as TRNAC-GCA and IL1RAPL1, which appeared in Tajima's D, ROH, and iHS analyses. The gene TRNAW-CCA was found in ROH, CLR and iHS analyses. The X chromosome exhibits a distinctive interaction between demographic factors and genetic variations, and these findings may provide new insight into the X-linked selection in different cattle breeds.

Does size-selective harvesting erode adaptive potential to thermal stress?

Overharvesting is a serious threat to many fish populations. High mortality and directional selection on body size can cause evolutionary change in exploited populations via selection for a specific phenotype and a potential reduction in phenotypic diversity. Whether the loss of phenotypic diversity that accompanies directional selection impairs response to environmental stress is not known. To address this question, we exposed three zebrafish selection lines to thermal stress. Two lines had experienced directional selection for (1) large and (2) small body size, and one was (3) subject to random removal of individuals with respect to body size (i.e. line with no directional selection). Selection lines were exposed to three temperatures (elevated, 34°C; ambient, 28°C; low, 22°C) to determine the response to an environmental stressor (thermal stress). We assessed differences among selection lines in their life history (growth and reproduction), physiological traits (metabolic rate and critical thermal max) and behaviour (activity and feeding behaviour) when reared at different temperatures. Lines experiencing directional selection (i.e. size selected) showed reduced growth rate and a shift in average phenotype in response to lower or elevated thermal stress compared with fish from the random-selected line. Our data indicate that populations exposed to directional selection can have a more limited capacity to respond to thermal stress compared with fish that experience a comparable reduction in population size (but without directional selection). Future studies should aim to understand the impacts of environmental stressors on natural fish stocks.

The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome†

Recombination is a central evolutionary process that reshuffles combinations of alleles along chromosomes, and consequently is expected to influence the efficacy of direct selection via Hill-Robertson interference. Additionally, the indirect effects of selection on neutral genetic diversity are expected to show a negative relationship with recombination rate, as background selection and genetic hitchhiking are stronger when recombination rate is low. However, owing to the limited availability of recombination rate estimates across divergent species, the impact of evolutionary changes in recombination rate on genomic signatures of selection remains largely unexplored. To address this question, we estimate recombination rate in two Ficedula flycatcher species, the taiga flycatcher (Ficedula albicilla) and collared flycatcher (Ficedula albicollis). We show that recombination rate is strongly correlated with signatures of indirect selection, and that evolutionary changes in recombination rate between species have observable impacts on this relationship. Conversely, signatures of direct selection on coding sequences show little to no relationship with recombination rate, even when restricted to genes where recombination rate is conserved between species. Thus, using measures of indirect and direct selection that bridge micro- and macro-evolutionary timescales, we demonstrate that the role of recombination rate and its dynamics varies for different signatures of selection.

Species-specific effects of production practices on genetic diversity in plant reintroduction programs

Plant production practices can influence the genetic diversity of cultivated plant materials and, ultimately, their potential to adapt to a reintroduction site. A common step in the plant production process is the application of seed pretreatment to alleviate physiological seed dormancy and successfully germinate seeds. In production settings, the seeds that germinate more rapidly may be favored in order to fill plant quotas. In this study, we investigated how the application of cold-moist stratification treatments with different durations can lead to differences in the genetic diversity of the propagated plant materials. Specifically, we exposed seeds of three Viola species to two different cold stratification durations, and then we analyzed the genetic diversity of the resulting subpopulations through double-digestion restriction site-associated sequencing (ddRADseq). Our results show that, in two out of three species, utilizing a short stratification period will decrease the genetic diversity of neutral and expressed loci, likely due to the imposition of a genetic bottleneck and artificial selection. We conclude that, in some species, the use of minimal stratification practices in production may jeopardize the adaptive potential and long-term persistence of reintroduced populations and suggest that practitioners carefully consider the evolutionary implications of their production protocols. We highlight the need to consider the germination ecology of target species when selecting the length of dormancy-breaking pretreatments.

A theory of oligogenic adaptation of a quantitative trait

Rapid phenotypic adaptation is widespread in nature, but the underlying genetic dynamics remain controversial. Whereas population genetics envisages sequential beneficial substitutions, quantitative genetics assumes a collective response through subtle shifts in allele frequencies. This dichotomy of a monogenic and a highly polygenic view of adaptation raises the question of a middle ground, as well as the factors controlling the transition. Here, we consider an additive quantitative trait with equal locus effects under Gaussian stabilizing selection that adapts to a new trait optimum after an environmental change. We present an analytical framework based on Yule branching processes to describe how phenotypic adaptation is achieved by collective changes in allele frequencies at the underlying loci. In particular, we derive an approximation for the joint allele-frequency distribution conditioned on the trait mean as a comprehensive descriptor of the adaptive architecture. Depending on the model parameters, this architecture reproduces the well-known patterns of sequential, monogenic sweeps, or of subtle, polygenic frequency shifts. Between these endpoints, we observe oligogenic architecture types that exhibit characteristic patterns of partial sweeps. We find that a single compound parameter, the population-scaled background mutation rate Θbg, is the most important predictor of the type of adaptation, while selection strength, the number of loci in the genetic basis, and linkage only play a minor role.

Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models

The detection of selective sweeps from population genomic data often relies on the premise that the beneficial mutations in question have fixed very near the sampling time. As it has been previously shown that the power to detect a selective sweep is strongly dependent on the time since fixation as well as the strength of selection, it is naturally the case that strong, recent sweeps leave the strongest signatures. However, the biological reality is that beneficial mutations enter populations at a rate, one that partially determines the mean wait time between sweep events and hence their age distribution. An important question thus remains about the power to detect recurrent selective sweeps when they are modeled by a realistic mutation rate and as part of a realistic distribution of fitness effects, as opposed to a single, recent, isolated event on a purely neutral background as is more commonly modeled. Here we use forward-in-time simulations to study the performance of commonly used sweep statistics, within the context of more realistic evolutionary baseline models incorporating purifying and background selection, population size change, and mutation and recombination rate heterogeneity. Results demonstrate the important interplay of these processes, necessitating caution when interpreting selection scans; specifically, false-positive rates are in excess of true-positive across much of the evaluated parameter space, and selective sweeps are often undetectable unless the strength of selection is exceptionally strong.

Revisiting the Role of Genetic Variation in Adaptation

AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.

Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome

Detecting natural selection is one of the major goals of evolutionary genomics. Here, we sequenced the whole genome of 25 Picea abies individuals and quantified the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we showed that both negative selection and the rate of positively selected substitutions are very limited in coding regions. We found a positive correlation between the rate of adaptive substitutions and recombination rate and a negative correlation between the rate of adaptive substitutions and gene density, suggesting a widespread influence from Hill-Robertson interference on the efficiency of protein adaptation in P. abies. Finally, the distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicated the impact of natural selection on the genomic architecture of Norway spruce. Further gene ontology enrichment analysis for genes located in regions identified as undergoing either positive or long-term balancing selection also highlighted the specific molecular functions and biological processes that appear to be targets of selection in Norway spruce.

Weak seed banks influence the signature and detectability of selective sweeps

Seed banking (or dormancy) is a widespread bet-hedging strategy, generating a form of population overlap, which decreases the magnitude of genetic drift. The methodological complexity of integrating this trait implies it is ignored when developing tools to detect selective sweeps. But, as dormancy lengthens the ancestral recombination graph (ARG), increasing times to fixation, it can change the genomic signatures of selection. To detect genes under positive selection in seed banking species it is important to (1) determine whether the efficacy of selection is affected, and (2) predict the patterns of nucleotide diversity at and around positively selected alleles. We present the first tree sequence-based simulation program integrating a weak seed bank to examine the dynamics and genomic footprints of beneficial alleles in a finite population. We find that seed banking does not affect the probability of fixation and confirm expectations of increased times to fixation. We also confirm earlier findings that, for strong selection, the times to fixation are not scaled by the inbreeding effective population size in the presence of seed banks, but are shorter than would be expected. As seed banking increases the effective recombination rate, footprints of sweeps appear narrower around the selected sites and due to the scaling of the ARG are detectable for longer periods of time. The developed simulation tool can be used to predict the footprints of selection and draw statistical inference of past evolutionary events in plants, invertebrates, or fungi with seed banks.

Analysis of the Selection Signal of the Tibetan Black Chicken Genome Based on Whole-Genome Sequencing

BACKGROUND

The Tibetan chicken has adapted well to high altitudes genetically after its long-term habitation in the plateau. In this study, we analyzed the selection signal of Tibetan black chickens (TBCs) and discovered genes associated with the characteristics of germplasm.

METHODS

Whole-genome sequencing (WGS) was used to identify the single-nucleotide polymorphism (SNP) markers and genetic structures in the genome of Tibetan black chickens. Further, we performed a comparative population genomics analysis between the genomic data obtained in this present study and the genomic data for five wild red jungle fowls (RJFs) accessed from the NCBI database (GenBank accession number PRJNA241474). Thereafter, the Fst and Pi selections were used to identify genes under positive selection in the Tibetan black chicken genome.

RESULTS

A total of 9,490,690 SNPs were identified in the Tibetan black chickens. In addition, the results from the gene ontology (GO) analysis showed that 732 genes of TBCs were enriched in a total of 210 GO terms with specific molecular functions such as regulation of cellular catabolic process, the MAPK signaling pathway, regulation of ion transport, growth, morphogenesis and lung alveolus development which may provide a better mechanism to facilitate oxygen transport and utilization in TBCs. Moreover, the results from the KEGG analysis showed that 732 genes of the TBCs were significantly enriched in the calcium signaling pathway, circadian entrainment (ADCY1, GNG7 and PER3), oxytocin signaling pathway and pathways of multiple neurodegeneration diseases. In addition, the CD86 antigen (CD86) was identified as a gene associated with the immune response in chickens. It was also revealed that genes such as TRIT1, HPCAL4, NT5C1A and HEYL were discovered under selection in Tibetan black chickens on chromosome 23. These genes may be related to the local adaptive characteristics of Tibetan black chickens, for instance, NT5C1A and HEYL may be involved in the high-altitude adaption of oxygen delivery in Tibetan black chickens.

CONCLUSIONS

In summary, we found that selection mainly affects the disease resistance and cold acclimatization of Tibetan black chickens. Hence, these results may provide important genetic information for the evolution and breeding of Tibetan black chickens.

Genome-wide study of globally distributed respiratory syncytial virus (RSV) strains implicates diversification utilizing phylodynamics and mutational analysis

Respiratory syncytial virus (RSV) is a common respiratory pathogen that causes mild cold-like symptoms and severe lower respiratory tract infections, causing hospitalizations in children, the elderly and immunocompromised individuals. Due to genetic variability, this virus causes life-threatening pneumonia and bronchiolitis in young infants. Thus, we examined 3600 whole genome sequences submitted to GISAID by 31 December 2022 to examine the genetic variability of RSV. While RSVA and RSVB coexist throughout RSV seasons, RSVA is more prevalent, fatal, and epidemic-prone in several countries, including the United States, the United Kingdom, Australia, and China. Additionally, the virus's attachment glycoprotein and fusion protein were highly mutated, with RSVA having higher Shannon entropy than RSVB. The genetic makeup of these viruses contributes significantly to their prevalence and epidemic potential. Several strain-specific SNPs co-occurred with specific haplotypes of RSVA and RSVB, followed by different haplotypes of the viruses. RSVA and RSVB have the highest linkage probability at loci T12844A/T3483C and G13959T/C2198T, respectively. The results indicate that specific haplotypes and SNPs may significantly affect their spread. Overall, this analysis presents a promising strategy for tracking the evolving epidemic situation and genetic variants of RSV, which could aid in developing effective control, prophylactic, and treatment strategies.

Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters

The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We amalgamated a pipeline of tools to predict BGCs based on shared promoter motifs and located 3800 ICS BGCs in 3300 genomes, making ICS BGCs the fifth largest class of specialized metabolites compared to canonical classes found by antiSMASH. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1/2 gene cluster family (GCF), which was prior only studied in yeast, is present in ∼30% of all Ascomycetes. The dit variety ICS exhibits greater similarity to bacterial ICS than other fungal ICS, suggesting a potential convergence of the ICS backbone domain. The evolutionary origins of the dit GCF in Ascomycota are ancient and these genes are diversifying in some lineages. Our results create a roadmap for future research into ICS BGCs. We developed a website (https://isocyanides.fungi.wisc.edu/) that facilitates the exploration and downloading of all identified fungal ICS BGCs and GCFs.

Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models

The detection of selective sweeps from population genomic data often relies on the premise that the beneficial mutations in question have fixed very near the sampling time. As it has been previously shown that the power to detect a selective sweep is strongly dependent on the time since fixation as well as the strength of selection, it is naturally the case that strong, recent sweeps leave the strongest signatures. However, the biological reality is that beneficial mutations enter populations at a rate, one that partially determines the mean wait time between sweep events and hence their age distribution. An important question thus remains about the power to detect recurrent selective sweeps when they are modelled by a realistic mutation rate and as part of a realistic distribution of fitness effects (DFE), as opposed to a single, recent, isolated event on a purely neutral background as is more commonly modelled. Here we use forward-in-time simulations to study the performance of commonly used sweep statistics, within the context of more realistic evolutionary baseline models incorporating purifying and background selection, population size change, and mutation and recombination rate heterogeneity. Results demonstrate the important interplay of these processes, necessitating caution when interpreting selection scans; specifically, false positive rates are in excess of true positive across much of the evaluated parameter space, and selective sweeps are often undetectable unless the strength of selection is exceptionally strong.

Teaser Text

Outlier-based genomic scans have proven a popular approach for identifying loci that have potentially experienced recent positive selection. However, it has previously been shown that an evolutionarily appropriate baseline model that incorporates non-equilibrium population histories, purifying and background selection, and variation in mutation and recombination rates is necessary to reduce often extreme false positive rates when performing genomic scans. Here we evaluate the power to detect recurrent selective sweeps using common SFS-based and haplotype-based methods under these increasingly realistic models. We find that while these appropriate evolutionary baselines are essential to reduce false positive rates, the power to accurately detect recurrent selective sweeps is generally low across much of the biologically relevant parameter space.

Two decades of molecular surveillance in Senegal reveal changes in known drug resistance mutations associated with historical drug use and seasonal malaria chemoprevention

Drug resistance in Plasmodium falciparum is a major threat to malaria control efforts. We analyzed data from two decades (2000-2020) of continuous molecular surveillance of P. falciparum parasite strains in Senegal to determine how historical changes in drug administration policy may have affected parasite evolution. We profiled several known drug resistance markers and their surrounding haplotypes using a combination of single nucleotide polymorphism (SNP) molecular surveillance and whole-genome sequence (WGS) based population genomics. We observed rapid changes in drug resistance markers associated with the withdrawal of chloroquine and introduction of sulfadoxine-pyrimethamine in 2003. We also observed a rapid increase in Pfcrt K76T and decline in Pfdhps A437G starting in 2014, which we hypothesize may reflect changes in resistance or fitness caused by seasonal malaria chemoprevention (SMC). Parasite populations evolve rapidly in response to drug use, and SMC preventive efficacy should be closely monitored.

Mining for a New Class of Fungal Natural Products: The Evolution, Diversity, and Distribution of Isocyanide Synthase Biosynthetic Gene Clusters

The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) have notable bioactivities that mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We developed the first genome-mining pipeline to identify ICS BGCs, locating 3,800 ICS BGCs in 3,300 genomes. Genes in these clusters share promoter motifs and are maintained in contiguous groupings by natural selection. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1 / 2 gene cluster family (GCF), which was thought to only exist in yeast, is present in ∼30% of all Ascomycetes, including many filamentous fungi. The evolutionary history of the dit GCF is marked by deep divergences and phylogenetic incompatibilities that raise questions about convergent evolution and suggest selection or horizontal gene transfers have shaped the evolution of this cluster in some yeast and dimorphic fungi. Our results create a roadmap for future research into ICS BGCs. We developed a website ( www.isocyanides.fungi.wisc.edu ) that facilitates the exploration, filtering, and downloading of all identified fungal ICS BGCs and GCFs.

Effect of beneficial sweeps and background selection on genetic diversity in changing environments

Neutral theory predicts that the genetic diversity within a population is proportional to the effective population size. In contrast, the observed genetic diversity for various species vary in a narrow range for several orders of magnitude change in the population sizes (Lewontin's paradox). The selective sweeps and background selection, reduce the genetic variation at the linked neutral sites and have been studied considering the environment to be selectively constant. However, in a natural population, the selective environment varies with time. Here, we investigate the impact of selective sweeps and background selection on neutral genetic diversity when the selection coefficient changes periodically over time. The reduction in genetic variation due to selective sweeps is known to depend on the conditional fixation time. Here, we find that the effect of changing environment on conditional mean fixation time is most substantial for the randomly mating population than the inbreeding population with arbitrary inbreeding coefficient. We also study the effect of background selection on neutral sites when the selection coefficient of linked deleterious mutation change periodically in time. In the slowly changing environment, we find that neutral heterozygosity is significantly different, and the site frequency spectrum has a different shape than that in the static environment.

Population genomics of helminth parasites

Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.

Fluctuating selection and the determinants of genetic variation

Recent studies of cosmopolitan Drosophila populations have found hundreds to thousands of genetic loci with seasonally fluctuating allele frequencies, bringing temporally fluctuating selection to the forefront of the historical debate surrounding the maintenance of genetic variation in natural populations. Numerous mechanisms have been explored in this longstanding area of research, but these exciting empirical findings have prompted several recent theoretical and experimental studies that seek to better understand the drivers, dynamics, and genome-wide influence of fluctuating selection. In this review, we evaluate the latest evidence for multilocus fluctuating selection in Drosophila and other taxa, highlighting the role of potential genetic and ecological mechanisms in maintaining these loci and their impacts on neutral genetic variation.