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The Tibetan Plateau's distinctive high-altitude environment, marked by extreme cold and reduced oxygen levels, presents considerable survival challenges for both humans and mammals. Natural selection has led to the accumulation of adaptive mutations in Tibetan pigs, enabling them to develop distinctive adaptive phenotypes. Here, we aim to uncover the genetic mechanisms underlying the adaptation of Tibetan pigs to high-altitude hypoxia. Therefore, we conducted a systematic analysis of 140 whole-genome sequencing (WGS) data points from different representing pig populations. Our analysis identified a total of 27,614,561 mutations, including 22,386,319 single-nucleotide variants (SNVs) and 5,228,242 insertions/deletions (INDELs, size < 50 bp). A total of 11% (2,678,569) of the SNVs were newly identified in our project, significantly expanding the dataset of genetic variants in Tibetan pigs. Compared to other pig breeds, Tibetan pigs are uniquely adapted to high-altitude environments, exhibiting the highest genetic diversity and the lowest inbreeding coefficient. Employing the composite of multiple signals (CMS) method, we scanned the genome-wide Darwinian positive selection signals and identified 32,499 Tibetan pig positively selected SNVs (TBPSSs) and 129 selected genes (TBPSGs), including 213 newly discovered genes. Notably, we identified eight genes (PHACTR1, SFI1, EPM2A, SLC30A7, NKAIN2, TNNI3K, and PLIN2) with strong nature selection signals. They are likely to improve cardiorespiratory function and fat metabolism to help Tibetan pigs become adapted to the high-altitude environment. These findings provide new insights into the genetic mechanisms of high-altitude adaptation and the adaptive phenotypes of Tibetan pigs. [ABSTRACT FROM AUTHOR]

Natural or artificial selection causes animals to adapt to their environment. The adaptive changes generated by the rumen population and metabolism form the basis of ruminant evolution. In particular, the adaptive drive for environmental adaptation reflects the high-quality traits of sheep that have migrated from other places or have been distant from their origins for a long time. The Hu sheep is the most representative sheep breed in the humid and low-altitude environments (Tai Lake region) in East Asia and has been widely introduced into the arid and high-altitude environments (Tibetan Plateau and Hotan region), resulting in environmental adaptive changes in the Hu sheep. In this study, a joint analysis of the rumen microbial metagenome and metabolome was conducted on Hu sheep from different regions (area of origin and area of introduction) with the objective of investigating the quality traits of Hu sheep and identifying microorganisms that influence the adaptive drive of ruminants. The results demonstrated that the growth performance of Hu sheep was altered due to changes in rumen tissue and metabolism following their introduction to the arid area at relatively high altitude. Metagenomic and metabolomic analyses (five ramsper area) revealed that 3580 different microorganisms and 732 different metabolites were identified in the rumen fluid of arid sheep. Among these, the representative upregulated metabolites were 4,6-isocanedione, methanesulfonic acid and N2-succinyl-L-arginine, while the dominant microorganism was Prevotella ruminicola. The downregulated metabolites were identified as campesterol, teprenone and dihydroclavaminic acid, while the disadvantaged microorganisms were Dialister_succinatiphilus, Prevotella_sp._AGR2160, Prevotella_multisaccharivorax and Selenomonas_bovis. The results of the Pearson analysis indicated that the rumen microbiota and metabolite content of sheep were significantly altered and highly correlated following their relocation from a humid lowland to an arid upland. In particular, the observed changes in rumen microorganisms led to an acceleration of body metabolism, rendering sheep highly adaptable to environmental stress. Prevotella_ruminicola was identified as playing an important role in this process. These findings provide insights into the environmental adaptation mechanisms of sheep. [ABSTRACT FROM AUTHOR]

Natural transformation is the only mechanism of genetic exchange controlled by the recipient bacteria. We quantified its rates in 786 clinical strains of the human pathogens Legionella pneumophila (Lp) and 496 clinical and environmental strains of Acinetobacter baumannii (Ab). The analysis of transformation rates in the light of phylogeny revealed they evolve by a mixture of frequent small changes and a few large quick jumps across 6 orders of magnitude. In standard conditions close to half of the strains of Lp and a more than a third in Ab are below the detection limit and thus presumably non-transformable. Ab environmental strains tend to have higher transformation rates than the clinical ones. Transitions to non-transformability were frequent and usually recent, suggesting that they are deleterious and subsequently purged by natural selection. Accordingly, we find that transformation decreases genetic linkage in both species, which might accelerate adaptation. Intragenomic conflicts with chromosomal mobile genetic elements (MGEs) and plasmids could explain these transitions and a GWAS confirmed systematic negative associations between transformation and MGEs: plasmids and other conjugative elements in Lp, prophages in Ab, and transposable elements in both. In accordance with the hypothesis of modulation of transformation rates by genetic conflicts, transformable strains have fewer MGEs in both species and some MGEs inactivate genes implicated in the transformation with heterologous DNA (in Ab). Innate defense systems against MGEs are associated with lower transformation rates, especially restriction-modification systems. In contrast, CRISPR-Cas systems are associated with higher transformation rates suggesting that adaptive defense systems may facilitate cell protection from MGEs while preserving genetic exchanges by natural transformation. Ab and Lp have different lifestyles, gene repertoires, and population structure. Nevertheless, they exhibit similar trends in terms of variation of transformation rates and its determinants, suggesting that genetic conflicts could drive the evolution of natural transformation in many bacteria. Bacterial species exhibit large variations in their transformation rates. This study of Legionella pneumophila and Acinetobacter baumannii shows that their transformation rates evolve by sudden quick changes, likely caused by intragenomic conflicts between mobile genetic elements and the host bacterium. [ABSTRACT FROM AUTHOR]

Background: Lithospermeae is the largest tribe within Boraginaceae. The tribe has been the focus of multiple phylogenetic studies over the last 15 years, with most focused on one genus or a few genera. In the present study, we newly sequenced 69 species of Lithospermeae and relatives to analyze the phylogenomic relationships among its members as well as the evolution of the plastid genome. Results: The phylogeny of Lithospermeae resolved from the plastid genome and nrDNA cistron is generally congruent with prior studies, but is better resolved and supported. Increasing character sampling across the plastid genome results in gradually more similar trees to that from the entire plastid genome. Overall, plastid genome structure was quite consistent across Lithospermeae. Codon Usage Bias (CUB) analyses demonstrate that across Lithospermeae plastid genomes were rich in AT and poor in GC. Mutation may play a greater role than selection across the plastid genome of Lithospermeae. The present study is the first to highlight the CUB characteristics of Lithospermeae species, which can help elucidate the mechanisms underlying patterns of molecular evolution and improve the expression levels of exogenous genes by codon optimization. Conclusions: This study provides a comprehensive phylogenomic analysis of Lithospermeae, significantly enhancing our understanding of the phylogenetic relationships and plastid genome evolution within this largest tribe of Boraginaceae. By utilizing an expanded genomic sampling approach, we have achieved increased resolution and support among the evolutionary relationships of the tribe, in line with but improving upon previous studies. The analyses of plastid genome structure revealed consistency across Lithospermeae, with a notable CUB. This study marks the first investigation into the CUB of Lithospermeae species and sets the stage for further research on the molecular evolution of plastid genomes across Boraginaceae. [ABSTRACT FROM AUTHOR]

Unpredictably fluctuating environments create complex selective landscapes that shape the distribution of key life history traits. Identifying the mechanisms behind dynamic patterns of selection is difficult, yet essential for predicting responses to climate change. We combine long-term measures with field manipulation of natural selection on breeding date in a wild bird to investigate whether highly variable spring cold snaps drive fluctuating selection. We show that variation in cold snap intensity leads to fluctuating selection on breeding date—in weak cold snap years, selection was consistently negative; however, in strong cold snap years, its direction reversed. These patterns were mirrored in a field experiment; nests that were food supplemented during cold snaps avoided cold snap mortality leading earlier breeders to have higher fitness. In contrast, in the non-supplemented group earlier breeders had higher cold snap nest mortality and selection was positive. Using nearly a century of climate data, we show that cold snaps are becoming less frequent and paradoxically occurring later which should allow earlier breeders to avoid them, potentially releasing conflicting selection pressures and facilitating a rapid phenological shift. Thus, rather than constraining a species' ability to adapt, climate change can enable a rapid shift to a new phenotypic optimum. [ABSTRACT FROM AUTHOR]

The Spherical Tokamak for Energy Production (STEP) programme hypothesizes that a compact machine offers a route to reduced capital cost that directly tackles the barrier to entry of this potentially transformative technology. History has shown that with an unsolved, complex and highly interdependent design challenge, there is a need to balance exploration of the problem with progress. Almost all complex systems arise from the evolutionary improvement of simpler systems which is an approach the programme has adopted by working through a virtual natural selection of design families towards a single concept consistent with the initiating hypothesis. Issues are uncovered and solved more rapidly this way because the effort is focused on an end. In this current phase, STEP has had to be an agile fast-moving programme to work with what emerges as well as what was planned, to sit with uncertainty and to embrace self-organizing principles. The complex decision-making and compromises in emerging trades have led to a concept respectful of the tight aspect ratio hypothesis which carefully balances cost, performance and deliverability. It remains a high-risk and high-reward programme, but the character of the challenge is better understood building confidence and enhancing capability to advance the evolving design further. This article is part of the theme issue 'Delivering Fusion Energy – The Spherical Tokamak for Energy Production (STEP)'. [ABSTRACT FROM AUTHOR]

The Halimedineae are marine green macroalgae that play crucial roles as primary producers in various habitats, including coral reefs, rocky shores, embayments, lagoons, and seagrass beds. Several tropical species have calcified thalli, which contribute significantly to the formation of coral reefs. In this study, we investigated the codon usage patterns and the main factors influencing codon usage bias in 16 chloroplast genomes of the suborder Halimedineae. Nucleotide composition analysis revealed that the codons of these species were enriched in A/U bases and preferred to end in A/U bases, and the distribution of GC content followed a trend of GC1 > GC2 > GC3. 30 optimal codons encoding 17 amino acids were identified, and most of the optimal codons and all of the over-expressed codons preferentially ended with A/U. The neutrality plot, effective number of codons (ENc) plot, and parity rule 2 (PR2) plot analysis indicated that natural selection played a major role in shaping codon usage bias of the most Halimedineae species. The genetic relationships based on their RSCU values and chloroplast protein-coding genes showed the closely related species have similar codon usage patterns. This study describes, for the first time, the codon usage patterns and characterization of Halimedineae chloroplast genomes, and provides new insights into the evolution of this suborder. [ABSTRACT FROM AUTHOR]

Oxford ragwort (Senecio squalidus) is one of only two homoploid hybrid species known to have originated very recently, so it is a unique model for determining genomic changes and stabilization following homoploid hybrid speciation. Here, we provide a chromosome-level genome assembly of S. squalidus with 95% of the assembly contained in the 10 longest scaffolds, corresponding to its haploid chromosome number. We annotated 30,249 protein-coding genes and estimated that ∼62% of the genome consists of repetitive elements. We then characterized genome-wide patterns of linkage disequilibrium, polymorphism, and divergence in S. squalidus and its two parental species, finding that (1) linkage disequilibrium is highly heterogeneous, with a region on chromosome 4 showing increased values across all three species but especially in S. squalidus ; (2) regions harboring genetic incompatibilities between the two parental species tend to be large, show reduced recombination, and have lower polymorphism in S. squalidus ; (3) the two parental species have an unequal contribution (70:30) to the genome of S. squalidus , with long blocks of parent-specific ancestry supporting a very rapid stabilization of the hybrid lineage after hybrid formation; and (4) genomic regions with major parent ancestry exhibit an overrepresentation of loci with evidence for divergent selection occurring between the two parental species on Mount Etna. Our results show that both genetic incompatibilities and natural selection play a role in determining genome-wide reorganization following hybrid speciation and that patterns associated with homoploid hybrid speciation—typically seen in much older systems—can evolve very quickly following hybridization. • The genome of S. squalidus , a recent homoploid hybrid species, is presented • Sorting of parental alleles is associated with presence of genetic incompatibilities • Fixed alleles from the major parent are associated with divergent natural selection • Typical patterns of hybrid speciation appear <300 generations after speciation Nevado et al. report genomic reorganization following hybrid speciation. They find that the typical genomic signatures of homoploid hybrid species are well established ∼300 generations after hybridization and that both pre-existing genetic incompatibilities and divergent natural selection play an important role following hybrid speciation. [ABSTRACT FROM AUTHOR]

Polygonati Rhizoma and Polygonati odorati Rhizoma, known as "Huangjing" and "Yuzhu" in China, are medicinal Polygonatum species resources with top-grade medical and edible properties. The chloroplast (cp) genome has been used to study species diversity, evolution, and breeding of species for applications in genetic engineering. Codon usage bias (CUB), a common and complex natural phenomenon, is essential for studies of codon optimization of exogenous genes, genetic engineering, and molecular evolution. However, the CUB of medicinal Polygonatum species chloroplast genomes has not been systematically studied. In our study, a detailed analysis of CUB was performed in the medicinal Polygonatum species chloroplast genomes. We investigated the codon bias of 204 plastid protein-coding genes (PCGs) in 4 medicinal Polygonatum species using CodonW and CUSP online software. Through the analysis of the codon bias index, we found that the medicinal Polygonatum species chloroplast genomes had weak codon usage bias. In addition, our results also showed a high preference for AT bases in medicinal Polygonatum species chloroplast genomes, and the preference to use AT-ending codons was observed in these species chloroplast genomes. The neutrality plot, ENC plot, PR2-Bias plot, and correspondence analysis showed that compared with mutation pressure, natural selection was the most important factor of CUB. Based on the comparative analysis of high-frequency codons and high expression codons, we also determined the 10-11 optimal codons of investigative medicinal Polygonatum species. Furthermore, the result of RSCU-based cluster analysis showed that the genetic relationship between different medicinal Polygonatum species could be well reflected. This study provided an essential understanding of CUB and evolution in the medicinal Polygonatum species chloroplast genomes. [ABSTRACT FROM AUTHOR]

The relative magnitude of additive genetic vs. residual variation for fitness traits is important in models for predicting the rate of evolution and population persistence in response to changes in the environment. In many annual plants, lifetime reproductive fitness is correlated with end-of-season plant biomass, which can vary significantly from plant to plant in the same population. We measured end-of-season plant biomasses and obtained single nucleotide polymorphism (SNP) genotypes of plants in a dense, natural population of the annual plant species Impatiens capensis with hierarchical size structure. These data were used to estimate the amount of heritable variation for position in the size hierarchy and for plant biomass. Additive genetic variance for a position in the size hierarchy and plant biomass were both significantly different from zero. These results are discussed in relationship to the theory for the heritability of fitness in natural populations and ecological factors that potentially influence heritable variation for fitness in this species. [ABSTRACT FROM AUTHOR]

Social interactions are ubiquitous in nature and can shape the fitness of individuals through social selection. This type of selection arises when phenotypes of neighbors influence the fitness of a focal individual. Quantifying social selection is crucial to better characterize the overall selective landscape. For example, if intraspecific competition is strong, traits that are beneficial for an individual could be detrimental to competitors. In this study, we quantified social selection acting on three key ecological traits (body mass, wing length, and laying date) in wild Tree swallow (Tachycineta bicolor) females. We used reproductive success measured at three stages throughout the breeding season as fitness proxies to assess selection acting at those decisive moments. We also quantified the effects of environment on selection using measures of conspecifics' density, type of agricultural landscape, and presence of interspecific competitors. Overall, we found no strong evidence of social selection on these traits in our study system, although there were marginally nonsignificant selection gradients suggesting the positive effect of larger neighbors. Environmental variables affected reproductive success but did not strongly affect social selection gradients. Our study calls for more social selection estimates to be reported across environments to better understand its importance in wild populations. [ABSTRACT FROM AUTHOR]

Island biotas provide unparalleled opportunities to examine evolutionary processes. Founder effects and bottlenecks, e.g. typically decrease genetic diversity in island populations, while selection for reduced dispersal can increase population structure. Given that support for these generalities mostly comes from single-species analyses, assemblage-level comparisons are needed to clarify how (i) colonization affects the gene pools of interacting insular organisms, and (ii) patterns of genetic differentiation vary within assemblages of organisms. Here, we use genome-wide sequence data from ultraconserved elements (UCEs) to compare the genetic diversity and population structure of mainland and island populations of nine ant species in coastal southern California. As expected, island populations (from Santa Cruz Island) had lower expected heterozygosity and Watterson's theta compared to mainland populations (from the Lompoc Valley). Island populations, however, exhibited smaller genetic distances among samples, indicating less population subdivision. Within the focal assemblage, pairwise F st values revealed pronounced interspecific variation in mainland-island differentiation, which increases with gyne body size. Our results reveal population differences across an assemblage of interacting species and illuminate general patterns of insularization in ants. Compared to single-species studies, our analysis of nine conspecific population pairs from the same island-mainland system offers a powerful approach to studying fundamental evolutionary processes. [ABSTRACT FROM AUTHOR]

Convergence is considered powerful evidence for adaptation to similar natural selection pressures. However, for many ecologically and morphologically convergent species, it remains unclear whether convergence extends to reproductive strategies, which are particularly important because of their tight connection to fitness. Here, by measuring key life-history traits (e.g. reproductive status, egg size, oviposition frequency, reproductive effort) across a full annual cycle comprising both reproductive and non-reproductive seasons, we discover divergence in reproductive strategies in two Anolis lizards that are otherwise strikingly convergent in ecology, morphology, and behaviour. The Cuban brown anole (Anolis sagrei) rapidly produces many small eggs during a concentrated summer reproductive season, whereas the Puerto Rican crested anole (Anolis cristatellus) produces comparatively fewer, larger eggs over a longer period. Thus, despite evolving highly convergent ecomorphological phenotypes and both being constrained to a single-egg clutch, these species exhibit marked divergence in life-history trade-off strategies along the fast–slow continuum. Our results indicate that ecomorphological convergence evolved uncoupled from life-history pathways in these species. [ABSTRACT FROM AUTHOR]

Evolutionary biology is poised for a third major synthesis. The first presented Darwin's evidence from natural history. The second incorporated genetic mechanisms. The third will be based on energy and biophysical processes. It should include the equal fitness paradigm (EFP), which quantifies how organisms convert biomass into surviving offspring. Natural selection tends to maximise energetic fitness, E=PcohGFQ$$ E={P}_{\mathrm{coh}}\mathrm{GFQ} $$, wherePcoh$$ {P}_{\mathrm{coh}} $$ is mass‐specific rate of cohort biomass production, G$$ G $$ is generation time, F$$ F $$ is fraction of cohort production that is passed to surviving offspring, and Q$$ Q $$ is energy density of biomas. At steady state, parents replace themselves with offspring of equal mass‐specific energy content, E$$ E $$ ≈ 22.4 kJ/g, and biomass, M$$ M $$ ≈ 1 g/g. The EFP highlights: (i) the energetic basis of survival and reproduction; (ii) how natural selection acts directly on the parameters of M$$ M $$; (iii) why there is no inherent intrinsic fitness advantage for higher metabolic power, ontogenetic or population growth rate, fecundity, longevity, or resource use efficiency; and (iv) the role of energy in animals with a variety of life histories. Underlying the spectacular diversity of living things is pervasive similarity in how energy is acquired from the environment and used to leave descendants offspring in future generations. [ABSTRACT FROM AUTHOR]

Spatially divergent natural selection can drive adaptation to contrasting environments and thus the evolution of ecotypes. In perennial plants, selection shapes life history traits by acting on subsequent life stages, each contributing to fitness. While evidence of adaptation in perennial plants is common, the expression of life history traits is rarely characterized, limiting our understanding of their role in adaptive evolution. We conducted a multi‐year reciprocal transplant experiment with seedlings from low and high elevation populations of the alpine carnation Dianthus carthusianorum to test for adaptation linked to contrasting climates and inferred specific contributions of early life stages to fitness. We assessed genotype by environment interactions in single fitness components, applied matrix population models to achieve an integrated estimate of fitness through population growth rates, and performed trade‐off analyses to investigate the advantage of alternate life history traits across environments. We found evidence of genotype by environment interactions consistent with elevational adaptation at multiple stages of the early life cycle. Estimates of population growth rates corroborated a strong advantage of the local genotype. Early reproduction and survival are alternate major contributors to adaptation at low and high elevation, respectively, and are linked by trade‐offs that underlie the evolution of divergent life history traits across environments. While these traits have a strong genetic basis, foreign populations express co‐gradient plasticity, reflecting the adaptive strategy of the local populations. Our study reveals that selection associated to climate has driven the evolution of divergent life histories and the formation of elevational ecotypes. While the high energy environment and strong competition favor investment in early reproduction at low elevation, limiting resources favor a more conservative strategy relying on self‐maintenance at high elevation. The co‐gradient plasticity expressed by high‐elevation populations may facilitate their persistence under warming climatic conditions. [ABSTRACT FROM AUTHOR]

Natural selection is known to favor specific gene combinations, thereby shaping the evolution of recombination rates, often through epistatic interactions. However, the dynamics of these interacting factors within natural populations remain poorly understood. In this study, we investigate the long‐term maintenance of a complex polymorphism involving linked, nonoverlapping chromosomal inversions in a natural population of Drosophila mediopunctata. Remarkably, even after 30 years—equivalent to roughly 340 generations—two major features have remained unexpectedly stable: the linkage disequilibrium (LD) between inversions, which deviates significantly from the theoretical prediction of decay, and a consistent seasonal cycle pattern of heterozygous excess and homozygous deficiencies. We explored the roles of recombination suppression, epistatic selection, and overdominance in maintaining this stability, examining their alignment with previously described patterns. Our findings reveal that moderate selection coefficients, such as s = 0.0407, are sufficient to maintain the observed LD for the most common haplotypes, albeit leading to an unstable equilibrium. Simulations further reveal that the introduction of overdominance stabilizes the system, enabling the long‐term persistence of this complex inversion polymorphism across various frequency scenarios. The stability of this system appears to hinge on a delicate balance between LD, recombination rates, and selective pressures, with overdominance playing a critical role. Our findings highlight the significance of epistatic interactions and selective pressures in shaping evolutionary pathways in natural populations and offer a compelling example of natural selection acting on a complex inversion polymorphism, providing valuable insights into the evolutionary dynamics governing inversion systems. [ABSTRACT FROM AUTHOR]

Natural selection favors individuals with the highest inclusive fitness (i.e., total number of descendants). In cases where one sex is more productive, one or both parents may maximize their inclusive fitness by investing in the offspring of the more prolific sex. Such preferential production can lead to skewed sex ratios at various life history stages, including at birth, resulting in secondary sex ratio bias. Several competing hypotheses have been proposed to explain observed variation in secondary sex ratios including Fisher's frequency dependence and two hypotheses related to maternal condition: Trivers–Willard and the local resource hypotheses. Although it has been shown that maternal condition can influence the number of offspring produced in white‐tailed deer, there is no consensus as to which of the hypotheses drives sex ratio bias in wild populations. Using a spatiotemporally extensive dataset of pregnant white‐tailed deer from Mississippi, USA, we examined fetal sex ratio in relation to the Fisherian frequency‐dependence hypothesis and hypotheses related to maternal condition. While there was a male‐sex ratio bias in pregnant females that reduced in intensity with the number of offspring, there was no support for condition‐related hypotheses. Instead, secondary sex ratios for white‐tailed deer in Mississippi were nearly consistent with Fisherian frequency dependence. Our findings add to the body of literature on secondary sex biases in white‐tailed deer and help inform sex bias ratios for a southern population of a cervid of management importance in the US. [ABSTRACT FROM AUTHOR]

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 FST‐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 FST 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. [ABSTRACT FROM AUTHOR]

The distribution of alleles highly specific to Europeans in the Koryak gene pool, which formed as a result of intensive interethnic admixture in the Northern Priokhotie, characterized by the prevailing genetic contribution from males of Eastern European origin, was analyzed. The loci rs16891982 (SLC45A2 gene), rs1426654 (SLC24A5 gene), rs1408799 (TYRP1 gene), rs1076563 (DRD2 gene), rs3827760 (EDAR gene), and rs1448485 (OCA2 gene), which are mainly associated with the pigmentation system, were selected for analysis. High heterogeneity was found in the frequency of European-specific alleles, ranging from 1.4% for the variant rs1076563-C of the DRD2 gene to 14.7% for the variant rs1426654-A of the SLC24A5 gene. The reasons for the uneven influx of European-specific alleles into the Koryak gene pool are discussed. It is possible that the formation of genetic structure of modern Koryaks under intensive interethnic admixture was accompanied by the influence of natural selection on some parts of the genome. [ABSTRACT FROM AUTHOR]

At issue is the degree to which Charles Darwin's theory of evolution by means of natural selection is to blame for violence caused by communism, Nazism, and other societal dysfunctions. Conservative Christian opponents claim Darwinism undermines Biblical authority and supports ideologies causing violence. Secular and Christian supporters of Darwinism argue that Darwinism has not promoted violence but has been used to provide a scientific rationale for violence that would have been caused anyway. Moreover, Christian supporters of Darwinism maintain that Darwinism is by no means incompatible with the Bible. This paper examines claims by both sides as well as the attempts by Darwinism's Christian opponents to supplant Darwinism with theories which they hope will restore Biblical authority, including Creationism, Creation Science, and Intelligent Design theory. The paper concludes that despite the legal setbacks encountered by adherents to these alternative theories, the conflict continues. [ABSTRACT FROM AUTHOR]

Simple Summary: There are thousands of species of non-biting midges. They face various living pressures which may influence their codon usage in mitochondrial genomes. Codon usage analysis has been conducted on only a few species, and the codon usage across Chironomidae is still unclear. In this study, we sequenced a new mitochondrial genome and compared codon usage across as many genera as possible. Limited variation was observed in most genera, except one which presented a weaker codon usage bias. We speculated that most of its mitochondrial genes experienced natural selection. Additionally, three genes, ND1, ND2 and ND3, were found to have experienced natural selection across most genera. To some extent, this work adds to our understanding of the evolution and phylogeny of non-biting midges. The codon usage patterns of mitochondrial genomes offer insights into the evolutionary and phylogenetic studies of species. Codon usage analysis has been conducted in a few Chironomidae species, and the codon usage patterns in other species remain ambiguous. We aim to reveal the codon usage differences in the mitochondrial genomes across this family. We sequenced the first mitochondrial genome of the genus Conchapelopia and the third mitochondrial genome of the subfamily Tanypodinae. Then, we analyzed its relative synonymous codon usage and effective number of codons with registered mitochondrial genomes from 28 other genera. The results indicated that there was limited variation in codon usage across five subfamilies, Chironominae, Orthocladiinae, Diamesinae, Prodiamesinae and Tanypodinae. While Parochlus steinenii from Podonominae presented a weaker codon bias, P. steinenii possessed the most genes experiencing natural selection. Additionally, ND1, ND2 and ND3 were found to be the most frequently selected genes across all species. Our findings contribute to further understanding the evolutionary and phylogenetic relationships of Chironomidae. [ABSTRACT FROM AUTHOR]

Premise: Clines—or the geographic sorting of phenotypes across continual space—provide an opportunity to understand the interaction of dispersal, selection, and history in structuring polymorphisms. Methods: In this study, we combine field‐sampling, genetics, climatic analyses, and machine learning to understand a flower color polymorphism in the wide‐ranging desert annual Encelia farinosa. Results: We find evidence for replicated transitions in disk floret color from brown to yellow across spatial scales, with the most prominent cline stretching ~100 km from southwestern United States into México. Because population structure across the cline is minimal, selection is more likely than drift to have an important role in determining cline width. Conclusions: Given that the cline aligns with a climatic transition but there is no evidence for pollinator preference for flower color, we hypothesize that floret color likely varies as a function of climatic conditions. [ABSTRACT FROM AUTHOR]

Common ash, Fraxinus excelsior, is threatened by the invasive pathogen Hymenoscyphus fraxineus, which causes ash dieback. The pathogen is rapidly spreading throughout Europe with severe ecological and economic consequences. Multiple studies have presented evidence for the existence of a small fraction of genotypes with low susceptibility. Such genotypes can be targets for natural and artificial selection to conserve F. excelsior and associated ecosystems. To resolve the genetic architecture of variation in susceptibility it is necessary to analyze segregating populations. Here we employed about 1000 individuals of each of four single-tree progenies from potentially tolerant mother trees to identify full-sibling (full-sib) families. To this end, we first genotyped all 4000 individuals and the four mothers with eight SSR markers. We then used the program COLONY to predict full-sibs without knowledge of the paternal genotypes. For each single-tree progeny, COLONY predicted dozens of full-sib families, ranging from 3–166 individuals. In the next step, 910 individuals assigned to full-sib families with more than 28 individuals were subjected to high-resolution genotyping using over one million genome-wide SNPs which were identified with Illumina low-coverage resequencing. Using these SNP genotyping data in principal component analyses we were able to assign individuals to full-sib families with high confidence. Together the analyses revealed five large families with 73–212 individuals. These can be used to generate genetic linkage maps and to perform quantitative trait locus analyses for ash dieback susceptibility. The elucidation of the genetic basis of natural variation in ash may support breeding and conservation efforts and may contribute to more robust forest ecosystems. [ABSTRACT FROM AUTHOR]

Blue whales (Balaenoptera musculus) are the largest living animal and, like other baleen whales, became endangered due to whaling. Here, we used population genomics to infer the number, distribution and other characteristics of subspecies and populations. We used the largest DNA dataset in blue whales, both in terms of genomic markers (16,661 SNPs and mtDNA) and geographic coverage (n = 276 for SNPs; n = 531 for mtDNA). We found greatest divergence among the eastern Pacific, Indo‐western Pacific and Antarctic blue whales. There were indications that natural selection in different environments promoted divergence among these groupings. Within these regions, there was divergence between the eastern North and eastern South Pacific, and among the eastern Indian Ocean, the western South Pacific and the northern Indian Ocean. There was no divergence within the Antarctic. These findings are consistent with the current classification of Antarctic and Indo‐western Pacific blue whales in the Southern Hemisphere as different subspecies but call into question the subspecies taxonomy of eastern Pacific blue whales. The study shows that opposite breeding seasons on either side of the equator do not necessarily inhibit connectivity across the equator, and reinforces that population structure needs to be well understood to conserve the diversity within species. [ABSTRACT FROM AUTHOR]

Context: Brassica juncea germplasm exhibits significant variations in flowering timing and vernalisation requirements. However, knowledge gaps exist with respect to variations in expression and the divergent evolution of flowering genes in B. juncea subgenomes. Aims: This study aims to examine the role of flowering genes in defining trait variation and to identify indications of directional selection on these genes. Methods: Employing a combination of genome-wide association studies, functional genomics and population genetic assays, we explored the genetic architecture underlying flowering time variation within expansive germplasm collections of this allopolyploid and its progenitor species. Key results: Genome-wide association studies aided in predicting 17 and 34 candidate genes in B. rapa and B. juncea , respectively. Seven of these (FT , FLC , BAG4 , ELF4-L2 , EFM , SEP4 , and LSH6) were predicted in both B. juncea and B. rapa. Some genes, GA20OX3 , NF-YA1 , PI , MMP , RPS10B , CRY2 , AGL72 , LFY , TOC1 , ELF5 , EFM , FLC and TFL1 exhibited directional selection as inferred from negative Tajima's D and Fu's Fs statistics. Conclusions: Common predicted genes are known influencers of flowering time and phenological changes between species as well as across zones of adaptation. An analysis of gene expression patterns indicates that the gene expression bias in resynthesised B. juncea could be influenced by the cytoplasmic background. Most expression variants are found in B genome copies. Some genes lacked expression variation in their diploid progenitors, whereas these genes exhibit expression variation in polyploid species. Implications: This study highlights that integrating genome-wide association studies with molecular signals of natural selection can effectively contribute to our understanding of the ecological genetics of adaptive evolution. Brassica juncea is farmed around the world, and varies widely in flowering time and the need for cold temperatues to trigger flowering. We used a range of molecular techniques to understand the genetics and evolution underpinning that variation, in contemporary breeds and ancestor species. This article belongs to the Collection Plant breeding- and genetics-based tools for food security under changing climate. [ABSTRACT FROM AUTHOR]

Simple Summary: Sturnidae sensu lato (Muscicapoidea) consists of Sturnidae, Mimidae, and Buphagidae. However, the deep-node evolutionary relationships within this group remain undetermined, and few efforts have been made to elucidate their mitogenomic evolution. Here, we focus on Sturnidae sensu lato and present five newly sequenced mitogenomes. Together with analysis of publicly available data, comprehensive analyses of mitogenome features, codon usage and aversion, RNA and CR structures, and phylogeny are performed. In conclusion, we determine the basic organizations of Sturnidae sensu lato mitogenomes, demonstrate the pervasiveness of natural selection in forming the CUB patterns, depict the RNA secondary structures, and construct both the backbone and deep-node relationships within Sturnidae sensu lato. The main finding of our research is obtained through codon aversion motifs (CAM) analyses. The surprisingly unique CAMs from 11 mt PCGs for each species offer new opportunities for the identification of the molecular species identification of these taxa. This work can shed new light on the mitogenomic evolution of Sturnidae sensu lato. The Sturnidae family comprises 123 recognized species in 35 genera. The taxa Mimidae and Buphagidae were formerly treated as subfamilies within Sturnidae. The phylogenetic relationships among the Sturnidae and related taxa (Sturnidae sensu lato) remain unresolved due to high rates of morphological change and concomitant morphological homoplasy. This study presents five new mitogenomes of Sturnidae sensu lato and comprehensive mitogenomic analyses. The investigated mitogenomes exhibit an identical gene composition of 37 genes—including 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes—and one control region (CR). The most important finding of this study is drawn from CAM analyses. The surprisingly unique motifs for each species provide a new direction for the molecular species identification of avian. Furthermore, the pervasiveness of the natural selection of PCGs is found in all examined species when analyzing their nucleotide composition and codon usage. We also determine the structures of mt-tRNA, mt-rRNA, and CR structures of Sturnidae sensu lato. Lastly, our phylogenetic analyses not only well support the monophyly of Sturnidae, Mimidae, and Buphagidae, but also define nine stable subclades. Taken together, our findings will enable the further elucidation of the evolutionary relationships within Sturnidae sensu lato. [ABSTRACT FROM AUTHOR]

The Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular rhythms through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes at the copy number and sequence levels, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3 , which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa. [ABSTRACT FROM AUTHOR]

Codon usage bias refers to the preferential use of synonymous codons, a widespread phenomenon found in bacteria, plants, and animals. Codon bias varies among species, families, and groups within kingdoms and between genes within an organism. Codon usage bias (CUB) analysis sheds light on the evolutionary dynamics of various species and optimizes targeted gene expression in heterologous host plants. As a significant order of gymnosperms, species within Gnetales possess extremely high ecological and pharmaceutical values. However, comprehensive analyses of CUB within the chloroplast genomes of Gnetales species remain unexplored. A systematic analysis was conducted to elucidate the codon usage patterns in 13 diverse Gnetales species based on the chloroplast genomes. Our results revealed that chloroplast coding sequences (cp CDSs) in 13 Gnetales species display a marked preference for AT bases and A/T-ending codons. A total of 20 predominantly high-frequency codons and between 2 and 7 optimal codons were identified across these species. The findings from the ENC-plot, PR2-plot, and neutrality analyses suggested that both mutation pressure and natural selection exert influence on the codon bias in these 13 Gnetales species, with natural selection emerging as the predominant influence. Correspondence analysis (COA) demonstrated variation in the codon usage patterns among the Gnetales species and indicated mutation pressure is another factor that could impact CUB. Additionally, our research identified a positive correlation between the measure of idiosyncratic codon usage level of conservatism (MILC) and synonymous codon usage order (SCUO) values, indicative of CUB's potential influence on gene expression. The comparative analysis concerning codon usage frequencies among the 13 Gnetales species and 4 model organisms revealed that Saccharomyces cerevisiae and Nicotiana tabacum were the optimal exogenous expression hosts. Furthermore, the cluster and phylogenetic analyses illustrated distinct patterns of differentiation, implying that codons, even with weak or neutral preferences, could affect the evolutionary trajectories of these species. Our results reveal the characteristics of codon usage patterns and contribute to an enhanced comprehension of evolutionary mechanisms in Gnetales species. [ABSTRACT FROM AUTHOR]

Identifying genomic regions under selection is essential for understanding the genetic mechanisms driving species evolution and adaptation. Traditional methods often fall short in detecting complex, spatially varying selection signals. Recent advances in deep learning, however, present promising new approaches for uncovering subtle selection signals that traditional methods might miss. In this study, we utilized the deep learning framework DeepGenomeScan to detect spatially varying selection signatures across 15 bovine populations worldwide. Our analysis uncovered novel insights into selective sweep hotspots within the bovine genome, revealing key genes associated with physiological and adaptive traits that were previously undetected. We identified significant quantitative trait loci linked to milk protein and fat percentages. By comparing the selection signatures identified in this study with those reported in the Bovine Genome Variation Database, we discovered 38 novel genes under selection that were not identified through traditional methods. These genes are primarily associated with milk and meat yield and quality. Our findings enhance our understanding of spatially varying selection's impact on bovine genomic diversity, laying a foundation for future research in genetic improvement and conservation. This is the first deep learning-based study of selection signatures in cattle, offering new insights for evolutionary and livestock genomics research. [ABSTRACT FROM AUTHOR]

Background: The hepatitis B e antigen (HBeAg)‐negative infection Phase 3 is characterized by no or minimal signs of hepatic inflammation and the absence of hepatic fibrosis. However, underlying molecular mechanisms leading to this benign phenotype are poorly understood. Methods: Genotype A, B and D HBeAg‐negative patient isolates with precore mutation G1896A from Phase 3 were analysed in comparison with respective HBeAg‐positive rescue mutant and HBeAg‐positive wild‐type reference genomes regarding differences in viral replication, morphogenesis, infectivity and impact on NF‐E2‐related factor 2 (Nrf2)/antioxidant response element (ARE)‐dependent gene expression and cellular kinome. Results: In comparison with reference genomes, the patient isolates are characterized by a lower intra‐ and extracellular hepatitis B surface antigen (HBsAg)‐amount, and HBsAg‐retention in the endoplasmic reticulum. Rescue of HBeAg expression increased HBsAg‐amount but not its release. Expression of the isolated genomes is associated with a higher Nrf2/ARE‐dependent gene expression as compared to reference genomes independent of HBeAg expression. Kinome analyses revealed a decreased activity of receptors involved in regulation of proliferative pathways for all patient isolates compared to the reference genomes. No specific conserved mutations could be found between all genomes from Phase 3. Conclusions: HBeAg‐negative genomes from Phase 3 exhibit distinct molecular characteristics leading to lower HBsAg synthesis and release, enhanced oxidative stress protection and decreased activity of key kinases, triggering an antiproliferative stage, which might contribute to the lower probability of hepatocellular carcinoma. The observed differences cannot be associated with loss of HBeAg or specific mutations common to all analysed isolates, indicating the phenotype of Phase 3 derived genomes to be the result of a multifactorial process likely reflecting a conserved natural selection process. [ABSTRACT FROM AUTHOR]

Reproductive traits co‐evolve and form successful life‐history strategies adapted to the biology and environment of a particular taxon, maximizing offspring and species survival chances, therefore studies investigating differences in adaptive traits across different environments can enhance our understanding of the natural selection process and evolution. Herein, we address whether the reproductive strategies of phylogenetically closely related fishes are influenced by habitat predictability, using three species of the Lebiasinidae family as models. The predominance of larger and mature individuals during the flood season, with high waters characterized by smaller immature individuals, suggests a seasonal reproductive strategy for Nannostomus trifasciatus. Copella callolepis, which inhabits both habitats, also showed a single reproductive peak. However, compared to N. trifasciatus, this species displayed late spawning, restricted to the flood season, as indicated by the higher abundance of larger and mature individuals during this period and the presence of smaller (juveniles) and spawned individuals in the following season. The reproductive tactics observed in N. marginatus differed significantly from the single reproductive peak of the other species, as two reproductive peaks were observed: one during the flood season and another during the low water season. In conclusion, our study demonstrates that the environment strongly influences reproductive strategies for lebiasinids. N. marginatus, restricted to small water bodies, exhibited an opportunistic reproductive strategy, whereas the species inhabiting main rivers, N. trifasciatus and C. callolepis, exhibited a more seasonal strategy. [ABSTRACT FROM AUTHOR]

An infant's face‐ and speech‐processing system develops during the first year from broad and non‐specific to becoming a system that is tuned to the faces and languages to which they are most exposed. This phenomenon is called perceptual narrowing. Before 9 months of age, infants are capable of discriminating and recognizing individuals from any type of race/species faces. However, with increased exposure to own‐race and own‐species faces and lack of exposure to other types of faces, by 9 months of age, they have improved their ability to discriminate own‐race faces, while they show increased difficulty in the discrimination of faces from other races and species. According to the literature, we can conclude that, by 12 months of age, most human perceptual systems have become perceptually tuned and adult‐like; however, this is not true. In the following sections, we will argue that perceptual narrowing for faces occurs during the same developmental period as it does for language, and that it can be prevented or modulated with sufficient exposure to unfamiliar sounds or face types. We conclude that narrowing has been designed by natural selection to tailor an individual's cognition to their local social context. It might occur for every domain pertaining to social communication—from speech processing to emotion or gesture perception—in a process that gradually adapts the infant to their native social group. [ABSTRACT FROM AUTHOR]

Giraffes exhibit a large sexual dimorphism in body size. Whether sexual dimorphisms also exist in body proportions of the axial and appendicular skeleton has been debated, particularly regarding the giraffe's iconic long neck. We examined the anatomical proportions of the neck, forelegs, hindlegs, and body trunk of the Masai giraffe (G. tippelskirchi) in captive and wild populations. We found that female Masai giraffes have proportionally longer necks relative to their forelegs than males in contradiction to the original necks-for-sex hypothesis that proposed that the evolution of the giraffe's long neck was driven by male-male competition. However, male neck width and apparent mass are proportionally larger than females', supporting a modification of the necks-for-sex hypothesis. Moreover, male foreleg length is proportionally longer whereas female trunk length is proportionally longer. These sexual dimorphisms were found in both captive and wild Masai giraffes. We speculate that the initial evolution of the giraffe's long neck and legs was driven by interspecific competition and the maternal nutritional demands of gestation and lactation through natural selection to gain a competitive advantage in browsing, and then later the neck mass was further increased as a consequence of male-male competition and sexual selection. Differences in the proportions of major body components define sex phenotypes, but several giraffes display opposite-sex phenotypes with a significantly higher level of discordancy seen in captive males. We speculate that body proportion sexual dimorphisms are maintained in the wild by natural and/or sexual selection, but in captivity selection is relaxed resulting in a higher occurrence of discordances in sexual phenotypes. [ABSTRACT FROM AUTHOR]

Whether natural selection leads to attachment in monogamous pair bonds has seldom been addressed. Operationally defining attachment as a behavioral modifier that decreases divorce probability with pair duration, we develop a model for the evolution of attachment. If divorce (the ending of a pair bond when both individuals survive to the next breeding season) is more likely to occur out of poor-quality reproductive opportunities (i.e., poor territory or low-quality mate), individuals in experienced pairs are more likely to be found in high-quality opportunities. Consequently, when divorce decisions occur using imperfect information from reproductive success, pair duration provides individuals with information about the quality of their reproductive opportunity and attachment can evolve. We show that high survival rates, divorce propensities, and probabilities of nest failure favor the evolution of attachment. Attachment is also more likely to evolve when individuals can directly assess the quality of their reproductive opportunity (as opposed to relying on imperfect information from reproductive success), when the quality of the reproductive opportunity has adult survival ramifications, and when divorce coevolves with attachment. We show that our core conclusions are robust to a variety of assumptions using individual-based simulations. Our results clarify how attachment can be adaptive and suggest that studying pair bonds as dynamic entities is a promising avenue for future work. [ABSTRACT FROM AUTHOR]

Evolution requires selection. Molecular/chemical/preDarwinian evolution is no exception. One molecule must be selected over another for molecular evolution to occur and advance. Evolution, however, has no goal. The laws of physics have no utilitarian desire, intent or proficiency. Laws and constraints are blind to "usefulness." How then were potential multi-step processes anticipated, valued and pursued by inanimate nature? Can orchestration of formal systems be physico-chemically spontaneous? The purely physico-dynamic self-ordering of Chaos Theory and irreversible non-equilibrium thermodynamic "engines of disequilibria conversion" achieve neither orchestration nor formal organization. Natural selection is a passive and after-the-fact-of-life selection. Darwinian selection reduces to the differential survival and reproduction of the fittest already-living organisms. In the case of abiogenesis, selection had to be 1) Active, 2) Pre-Function, and 3) Efficacious. Selection had to take place at the molecular level prior to the existence of non-trivial functional processes. It could not have been passive or secondary. What naturalistic mechanisms might have been at play? [ABSTRACT FROM AUTHOR]

During the past few decades, fitness-centered and trait-centered definitions of natural selection have coexisted in the philosophical literature. The former render natural selection definitionally dependent on the presence of fitness differences, where “fitness” is understood as a distinct property from actual reproductive success. On the other hand, trait-centered definitions see selection as definitionally dependent on the presence of a causal relation between a trait (not necessarily fitness) and reproductive success. Interestingly, endorsers of these definitions have rarely–and usually only cursorily–critically engaged the views of the other camp. Therefore, a critical comparison of the two kinds of definitions is lacking in the literature. This paper starts filling this void by opening a discussion about which of the two kinds of definition is more appropriate. I first argue that fitness-centered definitions have difficulties in accommodating cases of opposing selection on correlated traits, whereas trait-centered views have no such problems. To do so, I revisit an old argument put forth by Elliott Sober and I show that recent attempts from the fitness-centered camp to reply to Sober’s charge are unsuccessful. I then show that fitness-centered views also have problems with a different type of case, namely opposing selection on a single trait; trait-centered views, on the other hand, may accommodate such cases if, as I propose here, we specify that the causal relation that figures prominently in them is understood as a relation of contributing causation. These arguments suggest that trait-centered definitions of selection are preferable to fitness-centered ones. [ABSTRACT FROM AUTHOR]

Proponents of the extended evolutionary synthesis have argued that there are explanatory gaps in evolutionary biology that cannot be bridged by standard evolutionary theory. In this paper, we consider what sort of explanatory gaps they are referring to. We outline three possibilities: data-based gaps, implementation-based gaps, and framework-based gaps. We then examine the purported evolutionary gaps and attempt to classify them using this taxonomy. From there we reconsider the significance of the gaps and what they imply for the proposed need for an extended evolutionary synthesis. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Agricultural Science & Technology (1008-0864) is the property of Journal of Agricultural Science & Technology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Ranaviruses, members of the genus Ranavirus within the family Iridoviridae, have become a significant concern for amphibian populations globally, along with other cold‐blooded vertebrates, due to their emergence as a significant threat. We employed bioinformatics tools to examine the codon usage patterns in 61 DNA pol genes from Ranavirus, Lymphocystivirus, Megalocytivirus, and two unclassified ranaviruses, as no prior studies had been conducted on this topic. The results showed a slight or low level of codon usage bias (CUB) in the DNA pol genes of Ranavirus. Relative synonymous codon usage (RSCU) analysis indicated that the predominant codons favored in Ranavirus DNA pol genes terminate with C or G. Correlation analysis examining nucleotide content, third codon position, effective number of codons (ENC), correspondence analysis (COA), Aroma values, and GRAVY values indicated that the CUB across DNA pol genes could be influenced by both mutation pressure and natural selection. The neutrality plot indicated that natural selection is the primary factor driving codon usage. Furthermore, the analysis of the codon adaptation index (CAI) illustrated the robust adaptability of Ranavirus DNA pol genes to their hosts. Analysis of the relative codon deoptimization index (RCDI) suggested that Ranavirus DNA pol genes underwent greater selection pressure from their hosts. These findings will aid in comprehending the factors influencing the evolution and adaptation of Ranavirus to its hosts. [ABSTRACT FROM AUTHOR]

Codon usage bias (CUB) is the phenomenon of non-uniform usage of synonymous codons in which some codons are more used than others and it helps in understanding the molecular organization of genome. Bioinformatic approach was used to analyze the protein-coding sequences of genes associated with Parkinson's disease (PD) to explore compositional features and codon usage pattern as no details work was reported yet. The average improved effective number of codons (Nc) and Nc prime were 42.74 and 44.26 respectively, indicated that CUB was low in these genes. In most of the genes, the overall GC content was almost 50% and GC content at the 1st codon position was the highest while GC content at the 2nd codon position was lowest. Relative synonymous codon usage (RSCU) analysis elucidated over-represented (p > 1.6) and under-represented codons (p < 0.6). The GTG (Val) is the only codon over-represented in all genes. Over-represented codons except (GTG) were A or T ending while under-represented codons (except ACT) were G or C ending. The codons namely TTA (Leu), CTA (Leu), ATC (Ile), ATA (Ile), AGT (Ser), AAC (Asn), TGT (Cys), TGC (Cys), CGC (Arg), AGA (Arg), and AGG (Arg) were absent in SNCA1 to SNCA8 genes. The codon TCG (Ser) was absent in all genes except UCHL1 and PINK1. Correspondence analysis (COA) revealed that the pattern of codon usage differs among genes associated with PD. Neutrality plot analysis indicated some of the points are diagonal distribution suggested that mutation pressure influenced the CUB in genes associated with PD. [ABSTRACT FROM AUTHOR]

Climate change is having an impact on locally adapted species, including the cork oak (Quercus suber L.), a key tree species in the Mediterranean region especially due to its role in carbon sequestration. Notably, the Maâmora forest in Morocco stands as the largest forest in the Mediterranean basin with the highest diversity compared to similar forests across Morocco. In this study, we genotyped 240 samples from natural populations of cork oak in the Maâmora forest using seven microsatellite markers, to investigate signatures of local adaptation. Using a genomic scan approach, we identified outliers loci experiencing divergent natural selection pressures, which were later correlated with climatic, edaphic, and geographic conditions of the Maâmora forest. Statistical analysis of the data shows a high allelic variation. The detection of outliers, carried out using BayeScan v2.1 software, revealed the presence of two significant outliers loci ZAG20-171 (qvalue = 0.0004) and MSQ4-211 (qvalue = 0.04). The result of the environmental association analysis revealed a significant correlation between locus ZAG20-171 with mean diurnal range, isothermality, annual precipitation, precipitation of the driest month, precipitation of the wettest quarter and altitude. This work aims to help understanding the genetic basis of adaptation in Q. suber L., and thus the selection of suitable provenances for further breeding efforts. [ABSTRACT FROM AUTHOR]

The naturally selected fungal crop (Leucoagaricus gongylophorus) farmed by leafcutter ants shows striking parallels with artificially selected plant crops domesticated by humans (e.g. polyploidy, engorged nutritional rewards, and dependence on cultivation). To date, poorly resolved L. gongylophorus genome assemblies based on short-read sequencing have constrained hypotheses about how millions of years under cultivation by ants shaped the fungal crop genome and potentially drove domestication. We use PacBio HiFi sequencing of L. gongylophorus from the leafcutter ant Atta colombica to identify 18 putatively novel biosynthetic gene clusters that likely cemented life as a cultivar (e.g. plant fragment degradation, ant–farmer communication, and antimicrobial defense). Comparative analyses with cultivated and free-living fungi showed genomic signatures of stepwise domestication transitions: (i) free-living to ant-cultivated: loss of genes conferring stress response and detoxification; (ii) hyphal food to engorged nutritional rewards: expansions of genes governing cellular homeostasis, carbohydrate metabolism, and siderophore biosynthesis; and (iii) detrital provisioning to freshly cut plant fragments: gene expansions promoting cell wall biosynthesis, fatty acid metabolism, and DNA repair. Comparisons across L. gongylophorus fungi farmed by 3 leafcutter ant species highlight genomic signatures of exclusively vertical clonal propagation and widespread transposable element activity. These results show how natural selection can shape domesticated cultivar genomes toward long-term ecological resilience of farming systems that have thrived across millennia. [ABSTRACT FROM AUTHOR]

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Hidden colors are a widespread phenomenon in the animal kingdom, particularly in anurans. In some cases, hidden colors are suddenly exposed during defensive displays to startle predators, others seemingly remain hidden—particularly from researchers. Amazonian species of Neotropical harlequin toads (genus Atelopus) show striking and consistent ventral sexual dichromatism where females show and males generally lack melanization. Inspired by these observations we undertook a deeper inquiry across this species-rich genus. We collected data on ventral sexual dichromatism in Atelopus species and scored expression of sex-specific ventral melanization (i.e. black, brown and/or grey coloration). Ventral sexual dichromatism was present throughout the entire range of the genus and in almost all phylogenetic groups. However, there was a clear geographic signal with this trait being most common and widespread in Amazonian Atelopus species. Ventral melanization was correlated with temperature and elevation. Focusing on the Amazonian species, we present hypotheses on potential functions of sexually dimorphic ventral patterns and sex-specific ventral melanization as a baseline to further investigate the dynamics of sexual and natural selection as potential drivers of these traits. Selective pressures on less exposed body parts, such as ventral sides, likely differ considerably from those on dorsal appearance. Given the amount of research on amphibian coloration, it is remarkable how little we know about the evolution, function and underlying mechanisms of ventral appearance. We hope our work will spark more interest in the flip side of amphibians, thereby broadening our understanding of animal coloration. [ABSTRACT FROM AUTHOR]

We collected 56 specimens of Laelaps chini from the endemic Hengduan Mountain rat species (Eothenomys miletus) and obtained the first complete mitochondrial genome of L. chini by next-generation sequencing (NGS). The L. chini mitogenome is 16,507 bp in size and contains 37 genes and a control region of 2380 bp in length. The L. chini mitogenome has a high AT content and a compact arrangement with four overlapping regions ranging from 1 to 2 bp and 16 spacer regions ranging from 1 to 48 bp. We analyzed 13 protein-coding genes of L. chini mitogenome and found that protein-coding genes in the L. chini mitogenome preferred codons ending in A/U and codon usage pattern was mainly influenced by natural selection. Cox1 has the slowest evolution rate and cox3 has the fastest evolution rate. We combined the mitochondrial genome of eight species of gamasid mites in the superfamily Dermanyssoidea from Genbank and the L. chini mitochondrial genome to analyze its rearrangement patterns and breakpoint numbers. We found that the L. chini mitogenome showed a novel arrangement pattern and nine species of gamasid mites in the superfamily Dermanyssoidea, which have been sequenced complete mitochondrial genomes to date, all showed different degrees of rearrangement. Laelaps chini, Echinolaelaps echidninus and Echinolaelaps fukinenensis were closely related species based on genetic distance and phylogenetic analyses. Notably they are clustered with Varroa destructor of the family Varroidae, suggesting that the family Varroidae is more closely related to the family Laelapidae, but more data are needed to test whether Varroa can be classified under the family Laelapidae. The L. chini mitogenome is the first complete mitochondrial genome for the genus Laelaps, and contributes to further exploration of the mitochondrial gene rearrangements and phylogeny for the superfamily Dermanyssoidea. [ABSTRACT FROM AUTHOR]

Research on firm survival has primarily focused on input and outcomes. We shift the conversation by performing a systematic analysis of moderating role of firm size in the relationship between firm survival and strategic adaptation. After establishing a theoretical framework, we empirically assess the impact of strategic adaptation through digital transformation and public financial aid on the likelihood of firm survival. We find that smart working helped small firms, while home delivery and e-commerce had no effect on their survival. In contrast, liquidity support from the government and deferral of credit benefited micro firms. Our study emphasizes the importance of analyzing survival probabilities by differentiating firms by size, with the ultimate goal of exploring how selection or strategic adaptation processes may variably impact them. [ABSTRACT FROM AUTHOR]

Urbanization is one of the most significant contributors to the Anthropocene, and urban evolutionary ecology has become an important field of research. While it is commonly assumed that cities impose new and stronger selection, the contradictory assertion that selection may be relaxed in cities is also frequently mentioned, and overall, our understanding of the effects of urbanization on natural selection is incomplete. In this review, we first conduct a literature search to find evidence for patterns of natural selection on phenotypic traits including morphology, physiology, behaviour and life history, in urban and non‐urban populations of animals and plants. This search reveals that coefficients of natural selection in the context of urbanization are scarce (n = 8 studies providing selection gradients/differentials that include a total of n = 200 coefficients) and a lack of standardized methods hinders quantitative comparisons across studies (e.g. with meta‐analysis). These studies, however, provide interesting insight on the agents shaping natural selection in cities and improve our mechanistic understanding of selection processes at different spatial scales. We then perform a second literature search to review genomic studies assessing selection intensity in cities, on the genome of non‐human natural populations. While this search returns 383 articles, only 34 of these truly investigate footprints of selection associated with urbanization, and only one study provides urban genetic selection coefficients. Here again, we find highly heterogeneous approaches, yet some studies provide strong evidence of genomic footprints of urban adaptation. In neither the phenotypic nor genomic literature review were we able to quantitatively assess natural selection across urban versus non‐urban habitats. Thus, we propose a roadmap of how future studies should provide standardized metrics to facilitate mega‐ or meta‐analyses and explore generalized effects of urbanization on selection. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Each generation, spontaneous mutations introduce heritable changes that tend to reduce fitness in populations of highly adapted living organisms. This erosion of fitness is countered by natural selection, which keeps deleterious mutations at low frequencies and ultimately removes most of them from the population. The classical way of studying the impact of spontaneous mutations is via mutation accumulation (MA) experiments, where lines of small effective population size are bred for many generations in conditions where natural selection is largely removed. Such experiments in microbes, invertebrates, and plants have generally demonstrated that fitness decays as a result of MA. However, the phenotypic consequences of MA in vertebrates are largely unknown, because no replicated MA experiment has previously been carried out. This gap in our knowledge is relevant for human populations, where societal changes have reduced the strength of natural selection, potentially allowing deleterious mutations to accumulate. Here, we study the impact of spontaneous MA on the mean and genetic variation for quantitative and fitness-related traits in the house mouse using the MA experimental design, with a cryopreserved control to account for environmental influences. We show that variation for morphological and life history traits accumulates at a sufficiently high rate to maintain genetic variation and selection response. Weight and tail length measures decrease significantly between 0.04% and 0.3% per generation with narrow confidence intervals. Fitness proxy measures (litter size and surviving offspring) decrease on average by about 0.2% per generation, but with confidence intervals overlapping zero. When extrapolated to humans, our results imply that the rate of fitness loss should not be of concern in the foreseeable future. Spontaneous mutations tend to reduce fitness in populations of living organisms, but this erosion of fitness is countered by natural selection. This study uses the first mutation accumulation experiment in a mammal to show that even in the absence of natural selection, the rate of fitness loss should not be of concern, which is reassuring for humans. [ABSTRACT FROM AUTHOR]

Summary Climate change is disrupting floral traits that mediate mutualistic and antagonistic species interactions. Plastic responses of these traits to multiple shifting conditions may be adaptive, depending on natural selection in new environments. We manipulated snowmelt date over three seasons (3–11 d earlier) in factorial combination with growing‐season precipitation (normal, halved, or doubled) to measure plastic responses of volatile emissions and other floral traits in Ipomopsis aggregata. We quantified how precipitation and early snowmelt affected selection on traits by seed predators and pollinators. Within years, floral emissions did not respond to precipitation treatments but shifted with snowmelt treatment depending on the year. Across 3 yr, emissions correlated with both precipitation and snowmelt date. These effects were driven by changes in soil moisture. Selection on several traits changed with earlier snowmelt or reduced precipitation, in some cases driven by predispersal seed predation. Floral trait plasticity was not generally adaptive. Floral volatile emissions shifted in the face of two effects of climate change, and the new environments modulated selection imposed by interacting species. The complexity of the responses underscores the need for more studies of how climate change will affect floral volatiles and other floral traits. [ABSTRACT FROM AUTHOR]

Introduction: Multifarious selective pressures can interact to affect species' life history evolution, with predation and thermal exposure as selective pressures for nesting birds. Gray Vireos (Vireo vicinior) seemingly nest on the periphery of their nesting substrate because of lower predation rates, thereby increasing exposure to weather. We explored how nest placement and vegetation structure can be used to account for the increased weather exposure that Gray Vireos experience when nesting on the periphery of the nesting substrate to avoid predation. Methods: For each Gray Vireo nest, we placed temperature and light data loggers at three locations: at the nest site, at the opposite orientation of the nest within the nesting tree, and at the same orientation of the nest but in an adjacent tree. To measure nest orientation, we recorded the inverse compass azimuth (+/-1°) from the nest toward the trunk of the nesting tree, while accounting for declination. Nest temperatures and light exposure were compared across various dimensions of nest placement. Results: The orientation of nests was cooler than the opposite orientation in the mornings and in the late afternoons. When nests were placed in hotter orientations (e.g., south- or west-facing), nests surrounded by more foliage or placed closer to the interior of trees could compensate for the increased exposure. Discussion: Our findings suggest Gray Vireos accounted for the increased thermal exposure that comes from predator avoidance by using secondary dimensions of nest placement. Specifically, nests could be placed in orientations with cooler temperatures or in hotter orientations with greater shade potential. These results highlight how the interactive selection pressures of predation risk and microclimate can be tiered and shape life-history characteristics of birds. [ABSTRACT FROM AUTHOR]