Divergent Selection Research Articles

Inbreeding depression for litter size in two mice lines under divergent selection for environmental birth weight variability using genomic data.

Inbreeding depression (ID) is usually observed as reduced survival and fertility and may have a variable impact in different populations. The aim of this study was to estimate ID from genomic and pedigree data in the litter size (LS) of the high variability line (H-Line) and the low variability line (L-Line). Of these, the L-Line performed better on traits related to robustness. A total of 1587 females from 26 selection generations were genotyped with a high-density SNP array. LS data of 732 L-Line and 648 of H-Line animals were used. The following were calculated: pedigree inbreeding coefficient (FPED), genomic inbreeding derived from different genomic matrices (FNEJ, FL&H, FVR1, FVR2 and FYAN), from runs of homozygosity (FROH) and from homozygosity by descent probabilities (FHBD). FROH were calculated in the 19 autosomes (CHR). FROH and FHBD were divided into 9 lengths and age classes, respectively. All the inbreeding coefficients were standardized by the mean inbreeding coefficient of the 1st generation. Regression coefficients (b) obtained from genomic data were between -3.71 with FVR2 and -5.09 with FHBD in the H-Line, and that estimated from FPED was -5.67. In the L-Line the b obtained from genomic data were between -3.52 with FVR2 and -4.55 with FHBD, and that obtained with FPED was -4.08. Significant ID effects were detected in CHR13 in the H-Line and CHR1 and CHR9 in the L-Line. The b negative trended to be lower as the ROH length increased. The age of the homozygosity by descent segment performed differently in each line, for example FHBD raised 128 generations ago produced a significant positive effect only in the L-Line. The effect of global inbreeding coefficients on the LS was negative in both lines with a higher impact in the H-Line than in the L-Line, suggesting the L-Line having higher robustness. CHR 1, 9 and 13 were candidates for future gene search. In general, more recent FROH and FHBD presented negative effects on LS while older FROH and FHBD presented positive effects on LS in both selected lines.

Moisture-responsive root-branching pathways identified in diverse maize breeding germplasm.

Plants grow complex root systems to extract unevenly distributed resources from soils. Spatial differences in soil moisture are perceived by root tips, leading to the patterning of new root branches toward available water in a process called hydropatterning. Little is known about hydropatterning behavior and its genetic basis in crop plants. Here, we developed an assay to measure hydropatterning in maize and revealed substantial differences between tropical/subtropical and temperate maize breeding germplasm that likely resulted from divergent selection. Genetic analysis of hydropatterning confirmed the regulatory role of auxin and revealed that the gaseous hormone ethylene locally inhibits root branching from air-exposed tissues. Our results demonstrate how distinct signaling pathways translate spatial patterns of water availability to developmental programs that determine root architecture.

Selective Diversity in RNA Viruses: Do They Know How to Evolve? A Hypothesis.

Genetic diversity of viral populations is almost unanimously attributed to the build-up of random mutations along with accidental recombination events. This passive role of viruses in the selection of viable genotypes is widely acknowledged. According to the hypothesis presented here, populations of steady-state error copies of a master viral sequence would have a dominant mutant rather than a random pool of heterogeneous viral genomes with changes scattered uniformly without any preferential distribution. It would let viruses face the selection stage of host surveillance having a preceding set of potential survivors or "guard" genomes among an ordinary cloud of random quasispecies.

Distinct immune cell infiltration patterns in pancreatic ductal adenocarcinoma (PDAC) exhibit divergent immune cell selection and immunosuppressive mechanisms

Pancreatic ductal adenocarcinoma has a dismal prognosis. A comprehensive analysis of single-cell multi-omic data from matched tumour-infiltrated CD45+ cells and peripheral blood in 12 patients, and two published datasets, reveals a complex immune infiltrate. Patients have either a myeloid-enriched or adaptive-enriched tumour microenvironment. Adaptive immune cell-enriched is intrinsically linked with highly distinct B and T cell clonal selection, diversification, and differentiation. Using TCR data, we see the largest clonal expansions in CD8 effector memory, senescent cells, and highly activated regulatory T cells which are induced within the tumour from naïve cells. We identify pathways that potentially lead to a suppressive microenvironment, including investigational targets TIGIT/PVR and SIRPA/CD47. Analysis of patients from the APACT clinical trial shows that myeloid enrichment had a shorter overall survival compared to those with adaptive cell enrichment. Strategies for rationale therapeutic development in this disease include boosting of B cell responses, targeting immunosuppressive macrophages, and specific Treg cell depletion approaches.

Influence of MHC on genetic diversity and testicular expression of linked olfactory receptor genes

BackgroundOlfactory receptor (OR) genes are highly polymorphic and form extensive families that recognize a wide range of vertebrate odorants. To explore the genetic diversity of MHC-linked OR genes and their connection to MHC genes, we conducted a combined haplotype analysis of MHC-linked OR and MHC class I genes to determine the influence of MHC on OR diversity, which could be associated with MHC-based mate selection.ResultsWe selected nine MHC-linked OR genes based on their expression levels in pig testes and developed a sequence-based typing method for these genes. We then performed high-resolution typing of these OR genes, along with three major classical MHC class I genes (SLA-1, -2, and − 3), in 48 pigs across six breeds. We observed significantly higher allelic diversity (P < 0.01) in ORs with strong linkage disequilibrium (LD) to SLA compared to those with weak or no LD, and we identified 48 SLA class I-OR haplotypes using the expectation-maximization algorithm. The genetic diversity of SLA-linked ORs was positively correlated with their expression levels in the testis. Specifically, SLA-linked ORs with higher testicular expression (FPKM ≥ 0.1) exhibited an increase in the number of codons under mutually diversifying selection with SLA compared to those with lower expression (FPKM < 0.1).ConclusionsThe presence of evolutionary interactions between MHC and linked OR genes supports the potential involvement of MHC-linked ORs in MHC-based mate selection. The use of combined haplotype information for MHC and linked ORs could provide new insights into the reproductive biology of animals.

Using Practice Employment Tests to Improve Diversity in Recruitment and Selection Through Equalizing Preparation Opportunities

Using Practice Employment Tests to Improve Diversity in Recruitment and Selection Through Equalizing Preparation Opportunities

Assessment of Field Pea (Pisum sativum var. arvense) Genotypes for Morphological Traits, Quality Traits and Molecular Characterization using SSR Marker

Background: Field pea is an important cool season grain legume crop. This study was conducted on field pea to explore phenotypic and molecular diversity among field pea genotypes, catering to current and future crop improvement. Methods: In this investigation forty-six genotypes of field pea were evaluated in randomized block design to assess phenotypic diversity for morphological and quality traits, alongside molecular characterization using simple sequence repeat (SSR) markers. Result: Variability analysis displayed substantial variability for all traits among test genotypes. Cluster analysis grouped the all genotypes into three distinct multi-genotypic clusters with clusters II and III having highest inter-cluster distance. Molecular characterization revealed the detection of 43 repeatable alleles by 14 polymorphic SSR markers, spanning a size range of 150 bp (AA122) to 970 bp (AA504), with a maximum of 4 fragments intensified by AD147, D21, AA504, AA122 and A9. Utilizing Jaccard dissimilarity coefficients and UNJ methods, all forty-six genotypes were grouped into three clusters. This study on field pea facilitates the identification of diverse parent selections capable of producing desirable segregants in future breeding programs.

Co-evolution of the humoral immune and serotonergic systems in chickens selected for high or low blood antibody titer response to sheep red blood cells.

Serotonin is a potent immunomodulatory neurohormone. Activities of the serotonergic and immune systems are often reported together in poultry studies with unidirectional analyses focused on serotonergic signaling mediating immune response. Considering serotonin's relevance across a range of immune-related poultry topics, elucidation of whether the immune system affects the serotonergic system can provide valuable insights into the bi-directionality of poultry neuroendocrine-immune interactions. The present study sought to determine whether selection for divergence in blood antibody titers to a non-pathogenic antigen coincides with parallel changes in the chicken's serotonergic system over the life of the bird. We utilized generations 49 and 50 male and female White Leghorn chickens (n = 10-12/chickens/line/sex/age) that have been selected long-term for high (HAS) or low (LAS) blood antibody response to intravenous sheep red blood cell injection. Because serotonin is predominantly produced in the gut and acts as an interkingdom signaling molecule, the first experiment sampled cecal tissue and luminal content samples from male and female HAS and LAS chickens at 293 days of age. In the second experiment, cecal tissue and luminal content, as well as plasma, were collected from HAS and LAS chickens at 28 and 56 days of age. Serotonin and its main metabolite, 5-hydroxyindoleacetic acid (5-HIAA), concentrations were determined in cecal tissue, luminal content, and plasma samples. Immunoglobulins IgA and IgY concentrations were analyzed in cecal luminal content or plasma, respectively. The HAS chickens had lower (p < 0.05) cecal IgA concentrations but higher (p < 0.05) plasma IgY concentrations than LAS chickens, suggesting a compensatory response within the intestinal tract following selection for high or low blood antibody titers. Serotonin and 5-HIAA concentrations in the ceca and plasma diverged (p < 0.05) in a pattern that mirrored ceca IgA and plasma IgY differences according to genetic line. The results from this study demonstrate that evolutionary selection pressure for humoral immune response in chickens causes responses in the serotonergic system at both enteric and systemic levels.

Zymocin-like killer toxin gene clusters in the nuclear genomes of filamentous fungi.

Zymocin-like killer toxins are anticodon nucleases secreted by some budding yeast species, which kill competitor yeasts by cleaving tRNA molecules. They are encoded by virus-like elements (VLEs), cytosolic linear DNA molecules that are also called killer plasmids. To date, toxins of this type have been found only in budding yeast species (Saccharomycotina). Here, we show that the nuclear genomes of many filamentous fungi (Pezizomycotina) contain small clusters of genes coding for a zymocin-like ribonuclease (γ-toxin), a chitinase (toxin α/β-subunit), and in some cases an immunity protein. The γ-toxins from Fusarium oxysporum and Colletotrichum siamense abolished growth when expressed intracellularly in S. cerevisiae. Phylogenetic analysis of glycoside hydrolase 18 (GH18) domains shows that the chitinase genes in the gene clusters are members of the previously described C-II subgroup of Pezizomycotina chitinases. We propose that the Pezizomycotina gene clusters originated by integration of a yeast-like VLE into the nuclear genome, but this event must have been ancient because (1) phylogenetically, the Pezizomycotina C-II chitinases and the Saccharomycotina VLE-encoded toxin α/β subunit chitinases are sister clades with neither of them nested inside the other, and (2) many of the Pezizomycotina toxin cluster genes contain introns, whereas VLEs do not. One of the toxin gene clusters in Fusarium graminearum is a locus that has previously been shown to be under diversifying selection in North American populations of this plant pathogen. We also show that two genera of agaric mushrooms (Basidiomycota) have acquired toxin gene clusters by horizontal transfers from different Pezizomycotina donors.

Assessing genomic diversity and signatures of selection in Qingyuan Wapiti.

Red deer is a species of family Cervidae that is widely distributed in the world and is often raised to provide antlers, as a trophy or traditional medicine materials, and meat. Currently, the whole genomic data for red deer are very limited. Qingyuan Wapiti (QYW), China's first breed of red deer by artificial breeding, is well known for its high yield of antlers and large body size. The phylogenetic tree showed that QYW had a closer genetic relationship with Tarim red deer than European red deer. To explore the genetic diversity and selection signatures, the whole genome of 28 QYW individuals was sequenced, and 19 401 749 biallelic SNPs and 1 849 784 indels were obtained. The value of observed heterozygosity, expected heterozygosity, and nucleotide diversity were 0.258598, 0.268844, and 0.002193, respectively. Based on Tajima's D and integrated haplotype score analyses, the candidate regions containing 187 genes were detected, including PLD1, ANTXR1, PLCL1, CPE, and CTNNA3, which have been reported to be correlated with osteogenesis and mineralization, growth, and body size by previous studies. The results obtained in this study will contribute to elucidating the genetic mechanisms underlying the formation of excellent traits in QYW and provide the whole genome data for future exploration of genomic diversity and adaptation evolution of red deer worldwide.

Multi-rank smart reserves: A general framework for selection and matching diversity goals

Multi-rank smart reserves: A general framework for selection and matching diversity goals

Microbial consortium enrichment with alkaline-treated eucalyptus kraft lignin promotes selective bacterial diversity

Microbial consortium enrichment with alkaline-treated eucalyptus kraft lignin promotes selective bacterial diversity

From feather pecking to immunity: Immune differences between lines selected for high and low feather pecking.

Feather pecking (FP) is a serious behavioral disorder in laying hens, leading to feather damage, skin lesions, and often resulting in cannibalism. The mechanisms underlying FP are not clear yet, but recently the role of the immune system as a cause has been discussed. In humans, the interrelation between personality traits and the immune system is well-documented, with impulsivity and hyperactivity linked to distinct alterations in blood immune cell numbers and to elevated levels of pro-inflammatory cytokines. Similarly, FP in hens is associated with impulsivity and hyperactivity, suggesting a possible connection between FP and immune cell alterations. In this study numbers of leukocyte subsets in blood, spleen and cecal tonsils, along with mitogen-induced lymphocyte proliferative response and antibody concentrations across hens selectively bred for high (HFP) and low (LFP) feather pecking behavior were analyzed. Results showed that divergent selection altered FP behavior, with HFP hens showing about 10 times more pecking behavior than hens of the LFP line. HFP hens had lower numbers of T helper cells, CD4+ CD25high as well as B cells compared to LFP hens. Furthermore, HFP hens demonstrated a stronger proliferation of T cells when stimulated with ConA, while showed a weaker response in T cell-dependent B cell proliferation when stimulated with PWM, compared to LFP hens. Antibody plasma concentrations were similar between both lines. These findings highlight substantial immunological differences between HFP and LFP hens, especially in T cell immunity, and support the hypothesis that FP may be an immune-related behavioral response.

Directional Selection and Evolution of Polygenic Traits in Eastern Eurasia: Insights from Ancient DNA.

This study explores directional selection on physical and psychosocial phenotypes in Eastern Eurasian populations, utilizing a dataset of 1245 ancient genomes. By analyzing polygenic scores (PGS) for traits including height, educational attainment (EA), IQ, autism, schizophrenia, and others, we observed significant temporal trends spanning the Holocene era. The results suggest positive selection for cognitive-related traits such as IQ, EA and autism spectrum disorder (ASD), alongside negative selection for anxiety and depression. The results for height were mixed and showed nonlinear relationships with Years Before Present (BP). These trends were partially mediated by genetic components linked to distinct ancestral populations. Regression models incorporating admixture, geography, and temporal variables were used to account for biases in population composition over time. Latitude showed a positive effect on ASD PGS, EA and height, while it had a negative effect on skin pigmentation scores. Additionally, latitude exhibited significant nonlinear effects on multiple phenotypes. The observed patterns highlight the influence of climate-mediated selection pressures on trait evolution. Spline regression revealed that several polygenic scores had nonlinear relationships with years BP. The findings provide evidence for complex evolutionary dynamics, with distinct selective pressures shaping phenotypic diversity across different timescales and environments.

Deep R-gene discovery in HLB resistant wild Australian limes uncovers evolutionary features and potentially important loci for hybrid breeding

Huanglongbing (HLB) is a devastating citrus disease that threatens the citrus industry worldwide. HLB is associated with the bacteria Candidatus Liberibacter asiaticus (CLas) and as of today, there are no tools for economically viable disease management. Several wild Australian limes have been identified to be HLB resistant and their resistance is hypothesized to be conferred by resistance genes (R-genes), which mediate pathogen-specific defense responses. The aim of this study was to gain insight into the genomic features of R-genes in Australian limes, in comparison to susceptible citrus cultivars. In this study, we used five citrus genomes, including three Australian limes (Citrus australasica, C. glauca and C. inodora) and two cultivated citrus species (C. clementina and C. sinensis). Our results indicate up to 70% of the R-genes were identified in the unannotated regions in the original genome annotation of each species, owing to the use of a R-gene specific pipeline. Surprisingly, the two cultivated species harbored 15.8 to 104% more R-genes than the Australian limes. In all species, over 75% of the R-genes occurred in clusters and nearly 80% were concentrated in three chromosomes (Chr3, 5 and 7). The syntenic R-gene based phylogenic classification grouped the five species according to their HLB-resistance levels, reflecting the association between these R-genes and their distinct Australian origins. Domain structure analysis revealed substantial similarities in the R-genes between wild Australian limes and cultivated citrus. Investigation of chromosomal sites underlying Australian specific R genes revealed diversifying selection signatures on several chromosomal regions. The findings in this study will aid in the development of tools for genome-assisted breeding for HLB-resistant varieties.

Predicting the Aquatic Toxicity of Pharmaceutical and Personal Care Products: A Multitasking Modeling Approach

Pharmaceutical and Personal Care Products (PPCPs) have become a significant environmental concern due to their widespread use, persistence, and potential toxicity, often referred to as forever chemicals. This study aims to develop and validate robust in silico models for predicting the aquatic toxicity of PPCPs. To do so, we resorted to the ECOTOX database and employed a Python-based tool to prepare and curate the dataset. Multitasking Quantitative Structure–Toxicity Relationship (mt-QSTR) models were then developed employing the Box–Jenkins moving average approach, incorporating both linear and non-linear frameworks based on diverse feature selection algorithms and machine learning techniques. To further improve the external predictivity, a consensus modeling approach was also implemented. The most accurate model achieved an overall predictive accuracy exceeding 85%, providing valuable insights into the structural features influencing PPCP toxicity. Key factors contributing to high aquatic toxicity included high lipophilicity, mass density, molecular mass, and reduced electronegativity. This work offers a foundation for designing safer PPCPs with reduced environmental impact, aligning with sustainable chemical development goals.

Operating Characteristics of the Simulated Healthy Participant Approach in Impaired Clearance Studies.

Minimizing harm is a cornerstone of ethical research practices. A drug that has undergone extensive clinical pharmacological testing in healthy participants (HPs) and a diverse selection of patients can be described with a sufficiently predictive population pharmacokinetic (PopPK) model. In impaired clearance trials, recruitment is minimized and underpowered for all but major exposure differences. Virtual HP arms have been reported to support similar conclusions to conventional impaired clearance studies, and further minimize potential harm of drug exposure without medical benefit by eliminating an arm of the study. However, the extent to which the conventional analysis of impairment studies compare to the simulation approach is unknown. Here we assess the operating characteristics of the virtual cohort approach along with the conventional approach through controlled simulations. These simulations included a simple, widely accessible PopPK model and several internal models that have been used in a previous meta-analysis of the virtual cohort approach. In the pairwise comparisons assessed, the virtual cohort simulation approach had greater power per sample size than the conventional approach and the same power under the null hypothesis. Given key methodological differences, it is recommended that the simulation and conventional approaches be treated as having approximately the same power under equivalent conditions. These results provide a strong justification for the use of the virtual cohort approach when an adequate PopPK model is available, minimizing unnecessary exposure to study drugs that will not benefit healthy study participants.

Small-scale genetic differentiation in mean flowering time, but not in plasticity, along a geothermal heating gradient.

Genetic differentiation in traits is assumed to frequently occur in response to divergent natural selection. For example, developmental traits might respond to differences in climate. However, little is known about when and at which spatial scales environmental differences lead to genetic differentiation, and to what extent there is genetic differentiation also in trait plasticity. Using a crossing design and a greenhouse heating experiment, we investigated genetic differentiation in thermal sensitivity of flowering time in a perennial herb along small-scale gradients in geothermal soil heating in Iceland. We found additive genetic variation in both flowering time and thermal plasticity of flowering time. Genetic differentiation in median flowering date of individuals showed a counter-gradient pattern; flowering being earlier at higher greenhouse temperatures, while at a given temperature individuals originating from warmer soils flowered later than individuals from colder soils. We found no corresponding pattern for plasticity, suggesting that genetic differentiation in phenology in response to soil heating has occurred through changes in trait means rather than in plasticity. Findings such as these, identifying genetic trait differentiation along an environmental gradient are key to understand how environmental variation can drive the process of local adaptation, and to predict responses to future environmental changes.

Inferring herbicide non-target-site cross-resistance from dose response and mixture treatments.

Herbicide cross-resistance is of increasing concern because it compromises the effectiveness of both existing and new chemical options. However, a common misconception is that if a weed population shows dose-response shifts to two herbicides, it is cross-resistant to both. The possibility that individual plants may possess different resistance mechanisms is often overlooked. To better characterise non-target-site cross-resistance, we propose that the accession be treated with mixtures of the two herbicides of interest. A population model could be used to simulate the expected dose responses to the mixtures, assuming different cross-resistance levels in the population, as well as synergistic or antagonistic effects between the two herbicides. The simulated responses can then be compared with the actual responses, and the cross-resistance level approximated. We demonstrated this approach from a mathematical standpoint and validated it with experimental data from glasshouse tests on four well-characterised biotypes of Lolium multiflorum and two commercial herbicides, clodinafop and iodosulfuron. Results also showed that understanding chemical interactions such as synergy and antagonism is crucial to a better estimate of cross-resistance levels. Because this method utilises standard dose-response tests, it is potentially easier and less time-consuming than those involving plant cloning or divergent recurrent selection. Quick characterisation of the degree of cross-resistance provides important insights as to whether chemical rotations or mixtures can still effectively control the weed population displaying resistances to multiple herbicides. This approach could be applied more broadly in cross-resistance studies with other xenobiotics. © 2025 Society of Chemical Industry.

Metabolic Performance of Mealworms and Black Soldier Fly Larvae Reared on Food and Agricultural Waste and By-Products.

Mealworms and black soldier fly (BSF) larvae are two of the most reared insects at an industrial scale. Both may feed on by-products from agricultural and food industries. Feed efficiency is one of the most important aspects of such processes and varies between species and feed substrates and depends on the metabolic performance of the larvae. Compared to each other, both species may hold advantageous capabilities affecting their feed efficiency, likely depending on the feed substrate. We reared mealworms and BSF larvae on a diverse selection of by-products from agricultural and food industries, quantified major metabolic rates across their life spans, and compared their performances. The type of feed substrates had stronger effects on the growth of mealworms than on black soldier fly larvae. Generally, BSF larvae were advantageous in terms of the highest maximal specific growth rate (0.50-0.77 day-1) and feed assimilation rate (0.81-1.16 day-1) and shortest development period (23-25 days) but disadvantageous in terms of metabolic maintenance cost (0.07-0.21 day-1). In mealworms, the maximal specific growth rates were 0.02-0.11 day-1, the highest feed assimilation rates were 0.16-0.37 day-1, and the development period was at least 65-93 days, while maintenance was only 0.02-0.05 day-1. In contrast to the BSF larvae, the specific maintenance rate was weight dependent in the mealworms and lowest in the largest individuals. The combined outcome of these metabolic rates resulted in an average carbon net growth efficiency, NGE*avg of 0.16-0.40 in mealworms and 0.33-0.56 in BSF larvae across their life span. It thus seems that BSF larvae are more versatile and somewhat more efficient at converting diverse feed substrates into growth than mealworms. Differences in NGE*avg affected the substrate conversion efficiencies (i.e., the ratio of the weight gain of the larvae to the reduced weight of feed substrates) and may thus impact the overall outcome of insect farming.