Selection History Research Articles

Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history.

Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their demographic histories and distributions of fitness effects (DFE) of mutations. Here, we infer the demographic histories and DFEs for amino-acid changing mutations of 39 of the most prevalent and abundant commensal gut microbial species found in Westernized individuals over timescales exceeding human generations. Some species display contractions in population size and others expansions, with several of these events coinciding with several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with differences between accessory and core gene DFEs largely driven by genetic drift. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Together, these findings suggest that gut microbes have distinct demographic and selective histories.

Estimating financial and health burden by initial Medicare plan choice and history of cancer.

Understanding the downstream consequences of initial Medicare plan selection is necessary to ensure access to and affordability of health care services, especially for older adults with serious illness. We used 2008-2020 data from the Health and Retirement Study to estimate financial and health burden by initial Medicare plan selection (traditional Medicare without supplemental coverage, traditional Medicare plus supplemental coverage, or Medicare Advantage) and self-reported history of cancer. Initially choosing benefits with greater financial protections (either traditional Medicare plus supplemental coverage or Medicare Advantage) relative to traditional Medicare without supplemental coverage was associated with lower levels of out-of-pocket spending and a lower likelihood of reporting cost-related medication nonadherence and fair or poor health. Policymakers should consider improving the adequacy of traditional Medicare coverage to ensure the affordability of health care services and reduce the burden of serious illness among older adults, especially those with a history of cancer.

Registration of “Melka”: Stable and High Yielding Bread Wheat (Triticum aestivum L.) Variety for Highland Areas of Ethiopia

Food security is a major challenge in developing countries, including Ethiopia, due to factors like population growth, limited food production, malnutrition, and environmental degradation. Improving wheat yields in Ethiopia is crucial, but affected by diseases and environmental stresses. To address this, continuous research is vital to develop wheat varieties that are not only highly productive but also resistant to diseases and well-adapted to the specific conditions in Ethiopia. The “Melka” variety, a high-yielding, disease-resistant bread wheat variety, was developed under multiple evaluation stages before officially released, registered, and commercialized. “Melka” is a new variety, was introduced from CIMMTY, and has a pedigree name MANKU/3/MUU/FRNCLN//FRANCOLIN #1 and selection history CMSS13B00894S-099M-099Y-28M-0WGY. “Melka” is a bread wheat variety aimed at highland areas with good agronomic characteristics and late-maturing type. “Melka”, was a recently released variety, exhibits a significant yield advantage over standard check, with an overall mean of 30.54% Boru, and local check, with an overall mean of 58.10% Danda'a. It was recorded a better thousand-kernel weight (39.90 g) than standard check Boru (37.6 g), and local check Danda’a (32.70 g) and 71.7 hl /kg. Likewise, the “Melka” variety had bold seeds than checks. It possessed a 6.12% and 10.33 % HLW advantage over the Boru and Danda’a varieties respectively. Beyond its exceptional yield, this variety's distinctive feature lies in its enriched nutritional profile, particularly its high content of iron (Fe) 33.5 ppm and zinc (Zn) 38.1 ppm, which surpasses that of other available varieties. The recently released '“Melka”' wheat variety is stable and adaptable for Ethiopian highland agro ecologies. It exceeded standard checks in grain yield and is more resistant to stem, yellow and leaf rust diseases.

Mitochondrial genomes of the European sardine (Sardina pilchardus) reveal Pliocene diversification, extensive gene flow and pervasive purifying selection

The development of management strategies for the promotion of sustainable fisheries relies on a deep knowledge of ecological and evolutionary processes driving the diversification and genetic variation of marine organisms. Sustainability strategies are especially relevant for marine species such as the European sardine (Sardina pilchardus), a small pelagic fish with high ecological and socioeconomic importance, especially in Southern Europe, whose stock has declined since 2006, possibly due to environmental factors. Here, we generated sequences for 139 mitochondrial genomes from individuals from 19 different geographical locations across most of the species distribution range, which was used to assess genetic diversity, diversification history and genomic signatures of selection. Our data supported an extensive gene flow in European sardine. However, phylogenetic analyses of mitogenomes revealed diversification patterns related to climate shifts in the late Miocene and Pliocene that may indicate past divergence related to rapid demographic expansion. Tests of selection showed a significant signature of purifying selection, but positive selection was also detected in different sites and specific mitochondrial lineages. Our results showed that European sardine diversification has been strongly driven by climate shifts, and rapid changes in marine environmental conditions are likely to strongly affect the distribution and stock size of this species.

Genome-Wide Patterns of Homozygosity and Heterozygosity and Candidate Genes in Greek Insular and Mainland Native Goats.

Runs of homozygosity (ROHs) and heterozygosity (ROHets) serve for the identification of genomic regions as candidates of selection, local adaptation, and population history. The present study aimed to comprehensively explore the ROH and ROHet patterns and hotspots in Greek native dairy goats, Eghoria and Skopelos, genotyped with the Illumina Goat SNP50 BeadChip. SNP and functional enrichment analyses were conducted to further characterize hotspots and the candidate genes located within these genomic regions. Genetic relationships between and within breeds and inbreeding coefficients were also evaluated. Clear genetic differentiation and diversified management practices were depicted between the two native populations. The ROH and ROHet average genome coverage for Skopelos (65.35 and 35 Mb) and Eghoria (47.64 and 43 Mb) indicated differences in mainland and insular goats, with Skopelos showing more long ROH fragments, reflecting its geographic isolation and small population size. An ROH hotspot (CHR12: 43.59-44.61 Mb) detected in the Skopelos population has been also reported across European goats and co-localizes with a selection signal detected in the Egyptian Barki goats and sheep adapted to hot-arid conditions. A novel ROH hotspot (CHR18: 60.12-61.81 Mb), shared among the Greek breeds, harbors candidate genes enriched in biosynthesis, metabolism, and immune response. Two well-conserved ROHet islands were detected in Greek goats on chromosomes 1 and 18, with genes participating in development and embryogenesis. The Eghoria population showed the highest number of ROHet islands, potentially reflecting its adaptability to diverse environments. These findings offer new insights into the environmental adaptation and artificial selection in Greek goats and could be utilized in future breeding strategies for sustainable goat farming.

Optimising Exome Captures in Species With Large Genomes Using Species-Specific Repetitive DNA Blocker.

Large and highly repetitive genomes are common. However, research interests usually lie within the non-repetitive parts of the genome, as they are more likely functional, and can be used to answer questions related to adaptation, selection and evolutionary history. Exome capture is a cost-effective method for providing sequencing data from protein-coding parts of the genes. C0t-1 DNA blockers consist of repetitive DNA and are used in exome captures to prevent the hybridisation of repetitive DNA sequences to capture baits or bait-bound genomic DNA. Universal blockers target repetitive regions shared by many species, while species-specific c0t-1 DNA is prepared from the DNA of the studied species, thus perfectly matching the repetitive DNA contents of the species. So far, the use of species-specific c0t-1 DNA has been limited to a few model species. Here, we evaluated the performance of blocker treatments in exome captures of Pinus sylvestris, a widely distributed conifer species with a large (> 20 Gbp) and highly repetitive genome. We compared treatment with a commercial universal blocker to treatments with species-specific c0t-1 (30,000 and 60,000 ng). Species-specific c0t-1 captured more unique exons than the initial set of targets leading to increased SNP discovery and reduced sequencing of tandem repeats compared to the universal blocker. Based on our results, we recommend optimising exome captures using at least 60,000 ng of species-specific c0t-1 DNA. It is relatively easy and fast to prepare and can also be used with existing bait set designs.

Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data.

The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.

Transgressive segregation and the inheritance of paraquat resistance in Canada fleabane (Conyza canadensis)

Abstract Transgressive segregation refers to the phenomenon whereby the progeny of a diverse cross exhibit phenotypes that fall outside the range of the parents for a particular trait of interest. Segregants that exceed the parental values in life history traits contributing to survival and reproduction may represent beneficial new allelic combinations that are fitter than respective parental genotypes. In this research, we use geographically disparate paraquat resistant biotypes of horseweed (Canada fleabane) [Conyza canadensis (L.) Cronquist; syn. Erigeron canadensis L.] to explore transgressive segregation in biomass accumulation and the inheritance of the paraquat resistance trait in this highly self-fertilizing species. Results of this research indicated that the paraquat resistance traits in E. canadensis biotypes originating in California, USA and Ontario, Canada were not conferred by single major gene mechanisms. Segregating generations from crosses among resistant and susceptible biotypes all displayed transgressive segregation in biomass accumulation in the absence of the original selective agent, paraquat. However, when challenged with a discriminating dose of paraquat, progeny from the crosses of susceptible x resistant and resistant x resistant biotypes displayed contrasting responses with those arising from the cross of two resistant biotypes no longer displaying transgressive segregation. These results support the prediction that transgressive segregation is frequently expressed in self-fertilizing lineages and is positively correlated with the genetic diversity of the parental genotypes. When exposed to a new environment, transgressive segregation was observed regardless of parental identity or history. However, if hybrid progenies were returned to the parental environment with exposure to paraquat, the identity of fittest genotype (i.e., parent or segregant) depends on the history of directional selection in the parental lineages and the dose to which the hybrid progeny was exposed. It is only in the original selective environment that the impact of allelic fixation on transgressive segregation can be observed.

Successful Invasion Into New Environments Without Evidence of Rapid Adaptation by a Predatory Marine Gastropod.

Invasive species with native ranges spanning strong environmental gradients are well suited for examining the roles of selection and population history in rapid adaptation to new habitats, providing insight into potential evolutionary responses to climate change. The Atlantic oyster drill (Urosalpinx cinerea) is a marine snail whose native range spans the strongest coastal latitudinal temperature gradient in the world, with invasive populations established on the US Pacific coast. Here, we leverage this system using genome-wide SNPs and environmental data to examine invasion history and identify genotype-environment associations indicative of local adaptation across the native range, and then assess evidence for allelic frequency shifts that would signal rapid adaptation within invasive populations. We demonstrate strong genetic structuring among native regions which aligns with life history expectations, identifying southern New England as the source of invasive populations. Then, we identify putatively thermally adaptive loci across the native range but find no evidence of allele frequency shifts in invasive populations that suggest rapid adaptation to new environments. Our results indicate that while these loci may underpin local thermal adaptation in their native range, selection is relaxed in invasive populations, perhaps due to complex polygenic architecture underlying thermal traits and/or standing capacity for phenotypic plasticity. Given the prolific invasion of Urosalpinx, our study suggests population success in new environments is influenced by factors other than selection on standing genetic variation that underlies local adaptation in the native range and highlights the importance of considering population history and environmental selection pressures when evaluating adaptive capacity.

Repeated evolution on oceanic islands: comparative genomics reveals species-specific processes in birds

Understanding the interplay between genetic drift, natural selection, gene flow, and demographic history in driving phenotypic and genomic differentiation of insular populations can help us gain insight into the speciation process. Comparing patterns across different insular taxa subjected to similar selective pressures upon colonizing oceanic islands provides the opportunity to study repeated evolution and identify shared patterns in their genomic landscapes of differentiation. We selected four species of passerine birds (Common Chaffinch Fringilla coelebs/canariensis, Red-billed Chough Pyrrhocorax pyrrhocorax, House Finch Haemorhous mexicanus and Dark-eyed/island Junco Junco hyemalis/insularis) that have both mainland and insular populations. Changes in body size between island and mainland populations were consistent with the island rule. For each species, we sequenced whole genomes from mainland and insular individuals to infer their demographic history, characterize their genomic differentiation, and identify the factors shaping them. We estimated the relative (Fst) and absolute (dxy) differentiation, nucleotide diversity (π), Tajima’s D, gene density and recombination rate. We also searched for selective sweeps and chromosomal inversions along the genome. All species shared a marked reduction in effective population size (Ne) upon island colonization. We found diverse patterns of differentiated genomic regions relative to the genome average in all four species, suggesting the role of selection in island-mainland differentiation, yet the lack of congruence in the location of these regions indicates that each species evolved differently in insular environments. Our results suggest that the genomic mechanisms involved in the divergence upon island colonization—such as chromosomal inversions, and historical factors like recurrent selection—differ in each species, despite the highly conserved structure of avian genomes and the similar selective factors involved. These differences are likely influenced by factors such as genetic drift, the polygenic nature of fitness traits and the action of case-specific selective pressures.

Assessment of genetic diversity and heterotic alignment of CIMMYT and IITA maize inbred lines adapted to sub‐Saharan Africa

AbstractDespite the breeding efforts by many institutions, maize (Zea mays L.) productivity in sub‐Saharan Africa is still low. A limited number of productive maize hybrids have been developed partly due to a lack of knowledge on the diversity and heterotic relationship of the germplasm, especially in public breeding programs. Understanding the extent of diversity, structure, and heterotic grouping of available maize germplasm originating from different breeding programs is important to enhance long‐term genetic gain in hybrid maize breeding programs by optimizing heterotic pools using modern breeding tools. Information about the genetic structure of the available germplasm could help breeders design effective breeding strategies to improve yield. This study was conducted to determine the genetic diversity, population structure, and heterotic alignment among 187 elite maize inbred lines from the IITA (International Institute of Tropical Agriculture) and CIMMYT (International Maize and Wheat Improvement Center) maize breeding programs. The inbred lines were genotyped with 9857 Diversity Array Technology sequencing based single nucleotide polymorphism markers. Hierarchical clustering revealed three major groups, with some subgroups consistent with the selection history, and pedigree of the inbred lines. Three broad groups were detected: two consisting of CIMMYT lines and a mixed group consisting of both CIMMYT and IITA inbred lines. The STRUCTURE analysis revealed six subpopulations (fixation index value = 0.58), which depicts a moderate genetic diversity among the materials. Population 2 comprises the highest number of genotypes (102) from both programs. More than 89% of the elite lines had homozygosity exceeding 95%, with the remaining lines requiring further inbreeding through repeated self‐pollination. There was inconsistency in the predetermined heterotic groups' alignment between CIMMYT and IITA elite inbred lines. Analysis of molecular variance revealed that 96% of the total variation was accounted for by differences within groups, with the remaining 4% representing the variation between groups. This suggests that the two programs can benefit from germplasm exchange for the improvement of maize productivity.

Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history.

Wild populations are increasingly threatened by human-mediated climate change and land use changes. As populations decline, the probability of inbreeding increases, along with the potential for negative effects on individual fitness. Detecting and characterizing runs of homozygosity (ROHs) is a popular strategy for assessing the extent of individual inbreeding present in a population and can also shed light on the genetic mechanisms contributing to inbreeding depression. Here, we analyze simulated and empirical datasets to demonstrate the downstream effects of program selection and long-term demographic history on ROH inference, leading to context-dependent biases in the results. Through a sensitivity analysis we evaluate how various parameter values impact ROH-calling results, highlighting its utility as a tool for parameter exploration. Our results indicate that ROH inferences are sensitive to factors such as sequencing depth and ROH length distribution, with bias direction and magnitude varying with demographic history and the programs used. Estimation biases are particularly pronounced at lower sequencing depths, potentially leading to either underestimation or overestimation of inbreeding. These results are particularly important for the management of endangered species, as underestimating inbreeding signals in the genome can substantially undermine conservation initiatives. We also found that small true ROHs can be incorrectly lumped together and called as longer ROHs, leading to erroneous inference of recent inbreeding. To address these challenges, we suggest using a combination of ROH detection tools and ROH length-specific inferences, along with sensitivity analysis, to generate robust and context-appropriate population inferences regarding inbreeding history. We outline these recommendations for ROH estimation at multiple levels of sequencing effort, which are typical of conservation genomics studies.

Comparative population genomics analysis for chicken body sizes using genome-wide SNPs.

This study aims to investigate the selection history, genome regions, and candidate genes associated with different chicken body sizes, thereby providing insights into the genetic basis of complex economic traits such as chicken body size and growth. In this study, a total of 217 individuals from eight breeds were selected. According to body size, they were divided into two groups: large chickens and bantam chickens, with four breeds in each group. Firstly, we investigate population structure by principal component analysis (PCA), phylogenetic tree, and ancestry component analysis. Next, we recognize runs of homozygosity (ROH) islands through calculating ROH. Finally, we carry out selection signatures analysis utilizing population differentiation index and nucleic acid diversity. The population structure analysis show that large and bantam chickens are clearly separated. Large chickens are clustered together, the bantam chickens are relatively dispersed. The results of ROH island analysis show that 48 and 56 ROH islands were identified in large and bantam chickens respectively. Among the interesting ROH islands, a total of eight candidate genes were identified. In selection signatures analysis, a total of 322 selected genes were annotated in large chickens, such as POU1F1, BMP10, enrichment in 16 GO terms. In bantam chickens, a total of 447 selected genes were annotated, such as IGF1, GRB10, enrichment in 20 GO terms and 2 KEGG pathways. The haplotype analysis results show that GRB10 has differences in chickens of different body sizes. By population structure, ROH islands, and selection signatures analysis, we have identified multiple genes associated with chicken body size, growth, and development (such as BMP10, IGF1, GRB10, etc). This provides a theoretical reference for the subsequent development of molecular markers for chicken body size and the analysis of the genetic mechanism of chicken body size.

Impact of genotype × environment interaction and selection history on genomic prediction in maize (Zea mays L.)

AbstractBreeders made remarkable progress in improving productivity and stability of cultivars. Breeding progress relies on selecting favorable alleles for performance and stability to produce productive varieties across diverse environments. In this study, we analyzed the Genomes to Fields Initiative 2018–2019 genotype by environment interaction (G × E) dataset, focusing on three populations of double haploid (DH) lines derived from crossing inbrexpired Plant Variety Protection (ex‐PVP) inbred line PHW65 with inbred lines PHN11, Mo44, and MoG. PHW65 is an Iodent/Lancaster‐type inbred; PHN11 is an Iodent type ex‐PVP line; Mo44 is a tropical‐derived inbred; and MoG is an agronomically poor line derived from the variety Mastadon. Hybrids were produced by crossing the resulting DHs with Stiff Stalk testers PHT69 and LH195. The study's objective was to determine the donor inbreds' relative value and understand the impact of selection history on genomic prediction. We conducted a two‐stage analysis to compare hybrid performance and G × E variance of the populations. G × E variance for yield was significantly lower in the PHW65 × PHN11 population relative to the PHW65 × MoG population. The reduced G × E variance of the PHN11 population led to increased indirect prediction accuracy (when training and testing data are drawn from the same population but different environments). In cross‐validation, the PHN11 population had the greatest indirect prediction accuracy 45% of the time, followed by the Mo44 population (30%) and the MoG population (25%). Results demonstrate that prediction accuracy was greater in the population with the longest history of selection for favorable alleles (PHN11), contributing to greater yield stability.

Attentional Capture and Control.

The current review presents an integrated tripartite framework for understanding attentional control, emphasizing the interaction and competition among top-down, bottom-up, and selection-history influences. It focuses on attentional capture, which refers to conditions in which salient objects or events receive attentional priority even when they are inconsistent with the goals, tasks, and intentions of the observer. The review describes which components of the tripartite framework are in play when distraction by salient objects is prevented and the conditions in which there is no control over the occurrence of attentional capture. It then concludes that attentional capture can be controlled in a proactive way mainly by implicit statistical learning mechanisms associated with selection history. Current and lingering controversies regarding the control of attentional capture are also discussed.

The role of selection history in the learned predictiveness effect.

Previous research has shown that cues that are good predictors of relevant outcomes receive more attention than nonpredictive cues. This attentional bias is thought to stem from the different predictive value of cues. However, because successful performance requires more attention to predictive cues, the bias may be a lingering effect of previous attention to cues (i.e., a selection history effect) instead. Two experiments assessed the contribution of predictive value and selection history to the bias produced by learned predictiveness. In a first task, participants responded to pairs of cues, only one of which predicted the correct response. A second task was superficially very similar, but the correct response was determined randomly on each trial and participants responded based on some physical characteristic of a target stimulus in each compound. Hence, in this latter task, participants had to pay more attention to the target stimuli, but these stimuli were not consistently associated with a specific response. Results revealed no differences in the attentional bias toward the relevant stimuli in the two tasks, suggesting that the bias induced by learned predictiveness is a consequence of deploying more attention to predictive stimuli during training. Thus, predictiveness may not bias attention by itself, adding nothing over and above the effect expected by selection history. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

ASSESSING THE INFLUENCE OF CONTINUOUS PROFESSIONAL DEVELOPMENT PROGRAMMES ON THE TEACHING METHODOLOGIES OF HISTORY TEACHERS IN SENIOR SECONDARY SCHOOLS IN RIVERS STATE, NIGERIA

The study assessed the influence of continuous professional development programmes on the teaching methodologies of history teachers in senior secondary schools in Rivers State. Three research questions with corresponding three hypotheses guided the study. The study adopted descriptive survey designs. The population for the study consisted of 604 History teachers in public senior secondary schools in Rivers State. A retrieved sample was used for analysis, and there were 280 respondents. Stratified random sampling was used to stratify Rivers State into Rivers East, Rivers West and Rivers South East senatorial districts. Stage Quota sampling technique was applied to select History teachers from each senatorial district in Rivers State. The instrument constructed was a questionnaire titled “Influence of Continuous Professional Development Programmes on the Teaching Methodologies of History Teachers Questionnaire (ICPDPTMHTQ). The content and face validity instrument was validated by experts and History head teachers. Cronbach alpha was used to determine the reliability index of 0.80. Out of 302 copies of the instrument distributed to the respondents, 280 copies of the instruments were returned. Multiple Regression statistics method associated with ANOVA and t-test was used to answer research questions and test the hypotheses at 0.05 level of significance. The findings revealed that Continuous professional development significantly enhances teaching methods for history teachers in Rivers State. However, project-based learning, field trips, virtual tours, game-based learning, visual learning, and the Socratic method show no significant influence, indicated by high p-values and low coefficients. The study recommended that school administrators should be encouraged to offer CPD programmes that include training on innovative teaching strategies, like project-based learning and field trips, to enhance the overall effectiveness of history instruction.<p> </p><p><strong> Article visualizations:</strong></p><p><img src="/-counters-/soc/0702/a.php" alt="Hit counter" /></p>

Are selection history effects limited to implicit forms of memory? Evidence from intertrial repetition.

Selection history effects in visual attention are typically considered implicit memory effects. In three experiments, we investigated if a key selection history effect, intertrial priming, could be based on the incidental application of explicit memory. In the basic search task (Experiment 1), participants searched for real-world objects from different categories. We examined nonpredictive, intertrial repetition at two levels: (1) the repetition of target location from trial N-1 to trial N and (2) the repetition of target location and color within a category. Reliable repetition advantages were observed at both levels. In Experiments 2-4, we examined whether participants had explicit access to the target values driving the selection history effects here. In Experiments 2 and 3, participants could reliably report the properties of the immediately preceding search target. In Experiment 4, participants could reliably report the properties of the last target exemplar they had found in each of the 36 categories. These data indicate that guidance by selection history was based on the nonstrategic application of memory representations that could be explicitly retrieved and reported. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Improved inference of population histories by integrating genomic and epigenomic data.

With the availability of high-quality full genome polymorphism (SNPs) data, it becomes feasible to study the past demographic and selective history of populations in exquisite detail. However, such inferences still suffer from a lack of statistical resolution for recent, for example bottlenecks, events, and/or for populations with small nucleotide diversity. Additional heritable (epi)genetic markers, such as indels, transposable elements, microsatellites, or cytosine methylation, may provide further, yet untapped, information on the recent past population history. We extend the Sequential Markovian Coalescent (SMC) framework to jointly use SNPs and other hyper-mutable markers. We are able to (1) improve the accuracy of demographic inference in recent times, (2) uncover past demographic events hidden to SNP-based inference methods, and (3) infer the hyper-mutable marker mutation rates under a finite site model. As a proof of principle, we focus on demographic inference in Arabidopsis thaliana using DNA methylation diversity data from 10 European natural accessions. We demonstrate that segregating single methylated polymorphisms (SMPs) satisfy the modeling assumptions of the SMC framework, while differentially methylated regions (DMRs) are not suitable as their length exceeds that of the genomic distance between two recombination events. Combining SNPs and SMPs while accounting for site- and region-level epimutation processes, we provide new estimates of the glacial age bottleneck and post-glacial population expansion of the European A. thaliana population. Our SMC framework readily accounts for a wide range of heritable genomic markers, thus paving the way for next-generation inference of evolutionary history by combining information from several genetic and epigenetic markers.

Reward History and Statistical Learning Independently Impact Attention Search: An ERP Study.

Selection history is widely accepted as a vital source in attention control. Reward history indicates that a learned association captures attention even when the reward is no longer presented, while statistical learning indicates that a learned probability exerts its influence on attentional control (facilitation or inhibition). Existing research has shown that the effects of the reward history and statistical learning are additive, suggesting that these two components influence attention priority through different pathways. In the current study, leveraging the temporal resolution advantages of EEG, we explored whether these two components represent independent sources of attentional bias. The results revealed faster responses to the target at the high-probability location compared to low-probability locations. Both the target and distractor at high-probability locations elicited larger early Pd (50-150 ms) and Pd (150-250 ms) components. The reward distractor slowed the target search and elicited a larger N2pc (180-350 ms). Further, no interaction between statistical learning and the reward history was observed in RTs or N2pc. The different types of temporal progression in attention control indicate that statistical learning and the reward history independently modulate the attention priority map.