Evolution Of Traits Research Articles

Phylogenetic placement of the leaf-footed bug tribes Agriopocorini, Amorbini, and Manocoreini (Heteroptera: Coreidae) using ultraconserved elements

Abstract The phytophagous insect superfamily Coreoidea (Heteroptera) is a diverse group of ~3100 species in five extant families, with many of agricultural importance and model organisms in behavioural studies. Most species (~2800 species) are classified in the family Coreidae (four subfamilies, 37 tribes). While previous phylogenetic studies have primarily focused on the larger and more diverse subfamilies and tribes of Coreidae, several smaller tribes remain poorly studied in a phylogenetic context. Here, we investigated the phylogenetic positions of three less diverse tribes using ultraconserved elements: Agriopocorini, Amorbini, and Manocoreini. Our study is the first to test phylogenetic hypotheses for the Agriopocorini and Amorbini in a cladistic analysis. All three tribes were recovered within the subfamily Coreinae with robust support. The monophyletic Agriopocorini were supported as the sister-group of Colpurini, the monophyletic Amorbini as sister to Mictini, and the monogeneric Manocoreini as sister to Dasynini + Homoeocerini. We briefly discuss the evolution of wing development in Coreidae, putative synapomorphies for clades of interest, and taxonomic considerations. Our study emphasizes the importance of including smaller, less diverse groups in phylogenetic analyses. By doing so, we gain valuable insights into evolutionary relationships, identify future investigations of trait evolution, and resolve systematic controversies.

Large effects and the infinitesimal model

The infinitesimal model of quantitative genetics relies on the Central Limit Theorem to stipulate that under additive models of quantitative traits determined by many loci having similar effect size, the difference between an offspring’s genetic trait component and the average of their two parents’ genetic trait components is Normally distributed and independent of the parents’ values. Here, we investigate how the assumption of similar effect sizes affects the model: if, alternatively, the tail of the effect size distribution is polynomial with exponent α<2, then a different Central Limit Theorem implies that sums of effects should be well-approximated by a “stable distribution”, for which single large effects are often still important. Empirically, we first find tail exponents between 1 and 2 in effect sizes estimated by genome-wide association studies of many human disease-related traits. We then show that the independence of offspring trait deviations from parental averages in many cases implies the Gaussian aspect of the infinitesimal model, suggesting that non-Gaussian models of trait evolution must explicitly track the underlying genetics, at least for loci of large effect. We also characterize possible limiting trait distributions of the infinitesimal model with infinitely divisible noise distributions, and compare our results to simulations.

An evolutionary innovation for mating facilitates ecological niche expansion and buffers species against climate change

One of the drivers of life's diversification has been the emergence of "evolutionary innovations": The evolution of traits that grant access to underused ecological niches. Since ecological interactions can occur separately from mating, mating-related traits have not traditionally been considered factors in niche evolution. However, in order to persist in their environment, animals need to successfully mate just as much as they need to survive. Innovations that facilitate mating activity may therefore be an overlooked determinant of species' ecological limits. Here, we show that species' historical niches and responses to contemporary climate change are shaped by an innovation involved in mating-a waxy, ultra-violet-reflective pruinescence produced by male dragonflies. Physiological experiments in two species demonstrate that pruinescence reduces heating and water loss. Phylogenetic analyses show that pruinescence is gained after taxa begin adopting a thermohydrically stressful mating behavior. Further comparative analyses reveal that pruinose species are more likely to breed in exposed, open-canopy microhabitats. Biogeographic analyses uncover that pruinose species occupy warmer and drier regions in North America. Citizen-science observations of Pachydiplax longipennis suggest that the extent of pruinescence can be optimized to match the local conditions. Finally, temporal analyses indicate that pruinose species have been buffered against contemporary climate change. Overall, these historical and contemporary patterns show that successful mating can shape species' niche limits in the same way as growth and survival.

Directional epistasis is common in morphological divergence.

Epistasis is often portrayed as unimportant in evolution. While random patterns of epistasis may have limited effects on the response to selection, systematic directional epistasis can have substantial effects on evolutionary dynamics. Directional epistasis occurs when allele substitutions that change a trait also modify the effects of allele substitution at other loci in a systematic direction. In this case, trait evolution may induce correlated changes in allelic effects and additive genetic variance (evolvability) that modify further evolution. Although theory thus suggests a potentially important role for directional epistasis in evolution, we still lack empirical evidence about its prevalence and magnitude. Using a new framework to estimate systematic patterns of epistasis from line-crosses experiments, we quantify its effects on 197 size-related traits from diverging natural populations in 24 animal and 17 plant species. We show that directional epistasis is common and tends to become stronger with increasing morphological divergence. In animals, most traits displayed negative directionality toward larger size, suggesting that epistatic constraints reducing evolvability toward larger size. Dominance was also common but did not systematically alter the effects of epistasis.

Effect of residence time on trait evolution in invasive plants: review and meta-analysis

The success of invasive species is often attributed to rapid post-introduction evolution, due to novel selection pressures at the introduced range. However, evolutionary shifts in invasion-promoting traits can also take place within the introduced range over time. Here, we first present a review of the proposed hypotheses regarding the selection pressures and trait divergence along gradients of invasion history and the studies that examined them. In addition, we present the results of a meta-analysis aimed to provide a more general overview of current knowledge on trait evolution with time since introduction. Invasion-promoting traits, including growth, competitive ability and dispersal ability, were proposed to decline in more established populations with a long invasion history due to the attenuation of selection pressures, such as enemy release or interspecific competition, while herbivore defence was suggested to increase. Our meta-analysis results reveal a general indication for the evolution of invasive plants with residence time for most of the studied traits. However, this divergence did not have a consistent direction in most traits, except for growth, which, in contrast with our prediction, increased with residence time. The lack of empirical support for the predicted change in most of the studied traits over time suggests trait evolution might be affected by other context-dependent factors such as climatic gradients along invasion routes. Similarly, the increased allocation to size in older and more established populations may be driven by increased conspecific competition pressure experienced in these populations. The general temporal effect found in our meta-analysis stresses the need to consider population age when comparing attributes of invasive plants between native and invasive ranges. Moreover, the increased size of invasive plants in older populations, suggests that the dominance of these plants might not attenuate with time since introduction, thus highlighting the need to further explore the long-term dynamics between invasive plants and their recipient native communities.

Impact of Homologous Recombination on Core Genome Evolution and Host Adaptation of Pectobacterium parmentieri.

Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability, and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri. Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified 7 lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. fastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging from 43 bp to 119 kb and 36 bp to 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in genes involved in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides (LPS), flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the potential role of homologous recombination in P. parmentieri's evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.

A phylogenetic framework to study desirable traits in the wild relatives of Theobroma cacao (Malvaceae)

AbstractCrop wild relatives (CWRs) of cultivated species may provide a source of genetic variation that can contribute to improving product quantity and quality. To adequately use these potential resources, it is useful to understand how CWRs are related to the cultivated species and to each other to determine how key crop traits have evolved and discover potentially usable genetic information. The chocolate industry is expanding and yet is under threat from a variety of causes, including pathogens and climate change. Theobroma cacao L. (Malvaceae), the source of chocolate, is a representative of the tribe Theobromateae that consists of four genera and c. 40 species that began to diversify over 25 million years ago. The great diversity within the tribe suggests that its representatives could exhibit advantageous agronomic traits. In this study, we present the most taxonomically comprehensive phylogeny of Theobromateae to date. DNA sequence data from WRKY genes were assembled into a matrix that included 56 morphological characters and analyzed using a Bayesian approach. The inclusion of a morphological data set increased resolution and support for some branches of the phylogenetic tree. The evolutionary trajectory of selected morphological characters was reconstructed onto the phylogeny. This phylogeny provides a framework for the study of morphological and physiological trait evolution, which can facilitate the search for agronomically relevant traits.

Psychological impact and development of autistic traits in children during the COVID 19 Pandemic: A study through Guardian

The COVID 19 pandemic has significantly affected people's lives worldwide. Although children may not experience severe physical symptoms of the disease, their psychological well-being can be greatly affected. The primary objective of this study was to examine the psychological impact of COVID-19 on children residing in the Kashmir valley in terms of evolution of autistic traits in them. Cross-sectional study was conducted amongst 300 family members of children aged between 4 to 16-years. Data was collected through an online questionnaire using Google Forms and purposive sampling technique was used to assess autism. The sample for the study consisted of children in the 4 year to 16-year age group. A self-designed validated questionnaire in Google Form was used to collect the information. Chidhood Autism Rating Scale-2 (CARS-2) was used in those with excessive mobile phone usage. The results of the study revealed that only 3% of the children were infected with COVID-19. 7% of the sample reported that a close family member of a child was infected. Furthermore, 76% of the sample reported that they discussed COVID-19 with their children. In terms of behavioral changes, 54% of the sample noticed a change in their child's behaviour during the COVID pandemic. Additionally, 51% reported a change in their children's learning patterns, and 48% reported that their child had become possessive about new things since the pandemic. Furthermore, 35% of the sample reported a change in their child's sleeping cycle, 22.7% reported a loss of appetite, and 56% reported that their child imagined and talked about COVID-19 with others. It was also found that 80.3% of the sample had adhered to COVID-19 precautions. Only 4.3% reported negative thoughts expressed by their children since the pandemic, while 88% reported that their children were ready to discuss in future COVID-19. In the 4 to 6 year age group, out of 12 children with excessive mobile phone use, it was found that two were having symptoms consistent with Autism Spectrum Disorder. Other common symptoms noticed in this age group were found to be clapping, single verbal sounds, inability to express needs, moderate abnormal listening response, echolalia and video dialoguing. Most families reported that their children were possessive about new things and most of them were not sitting at one place for a long time. A large percentage of families reported that they found changes in the sleep pattern and duration of sleep was more than 9 hours. It was also found that screen time during COVID-19 increased among school-going children.

Re-focusing sampling, design and experimental methods to assess rapid evolution by non-native plant species

AbstractEvolution can occur over contemporary timescales, which may be crucial for the invasive success of non-native plant species. Many studies have shown rapid evolution by comparing native and non-native populations in common gardens. However, our understanding of the mechanisms underpinning rapid evolution is still incomplete. Here, we identify the progress, applications, and limitations of studies on rapid evolution of non-native plants with respect to sampling, experimental design and experimental methods. To encompass broad variation within and between the ranges, we recommend sampling across large-scale environmental gradients. We also suggest careful consideration of pitfalls related to the choice of seed families and of the biotic interaction under focus. The latter should be chosen with a view on both the experimental treatment and the corresponding field data to estimate population history. Furthermore, we suggest exploiting multiple omics approaches to address the complexity of biotic interactions, and to account for non-adaptive evolution with molecular data on demographic history of populations. We also reviewed papers that studied rapid evolution in non-native plants and quantified how many of these met our criteria. We anticipate that disentangling adaptive and non-adaptive drivers of among-population variation can increase the accuracy of research on rapid evolution, and that integrating phenotypic, metabolomic and population genomic data can bring opportunities for studying complex biotic interactions. We also illustrate the importance of large collaborative networks and present our scientific network iCONNECT (integrative CONyza NEtwork for Contemporary Trait evolution), with the goal of motivating similar studies on the mechanistic understanding of rapid evolution.

Functional trait dataset of European groundwater Amphipoda: Niphargidae and Typhlogammaridae

Groundwater represents a vast, but mostly hidden and inaccessible ecosystem. Although often overlooked in freshwater research, groundwater organisms form a significant part of freshwater biodiversity, whereas their functions are crucial in different ecosystem processes. Knowledge on functional traits is generally lacking for most groundwater species worldwide, yet European groundwater amphipods, particularly the family Niphargidae, are an exception. They are well-researched and used as a model system in ecological and evolutionary studies. We focused on this group to assemble a first functional trait dataset dedicated to groundwater species. We gathered data for eight morphological functional traits quantified through 27 measurements for 1123 individuals which represent 180 species and 314 MOTUs. Besides functional trait data, every entry is accompanied with locality information, including habitat type, and DNA sequences if available. The structure of the dataset and data processing information provided along enable wide applicability and extension to other amphipod taxa. When coupled with phylogeny, the dataset may further enhance different aspects of groundwater research, including biodiversity patterns, community assembly processes, and trait evolution.

Dorsal and Ventral Plumage Coloration Evolve as Distinct Modules with Different Environmental Correlations.

AbstractMany animals exhibit contrast between their dorsal coloration and their ventral coloration. If selection acts differently on dorsal versus ventral coloration, ancestral covariance between these traits should break down, eventually leading to independent modules of trait evolution. Here, we compare the evolution of feather color across body regions for a clade of Australasian songbirds (Meliphagoidea). We find evidence for three modules of covarying color regions. Among these modules, ventral feathers evolve with high lability, evolving at three times the rate of dorsal plumage and 20 times the rate of flight feathers. While both dorsal plumage and ventral plumage are darker in areas with more precipitation and vegetation, we find that dorsal plumage is twice as similar to colors in satellite photos of background substrates. Overall, differential selection on ventral and dorsal colors likely maintains these as distinct modules over evolutionary timescales-a novel explanation for dorsoventral contrast in pigmentation.

Convergent genomic signatures associated with vertebrate viviparity

BackgroundViviparity—live birth—is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. Viviparous species exhibit remarkable levels of reproductive diversity, both in the amount of care provided by the parent during gestation, and the ways in which that care is delivered. The genetic basis of viviparity has garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale. Using whole genome data, we investigated the molecular basis of this innovation across the diversity of vertebrates to answer a long held question in evolutionary biology: is the evolution of convergent traits driven by convergent genomic changes?ResultsWe reveal convergent changes in protein family sizes, protein-coding regions, introns, and untranslated regions (UTRs) in a number of distantly related viviparous lineages. Specifically, we identify 15 protein families showing evidence of contraction or expansion associated with viviparity. We additionally identify elevated substitution rates in both coding and noncoding sequences in several viviparous lineages. However, we did not find any convergent changes—be it at the nucleotide or protein level—common to all viviparous lineages.ConclusionsOur results highlight the value of macroevolutionary comparative genomics in determining the genomic basis of complex evolutionary transitions. While we identify a number of convergent genomic changes that may be associated with the evolution of viviparity in vertebrates, there does not appear to be a convergent molecular signature shared by all viviparous vertebrates. Ultimately, our findings indicate that a complex trait such as viviparity likely evolves with changes occurring in multiple different pathways.

Taxonomic characterisation of the Regianum clade (genus Tuber) and the trait evolution of spore size among true truffles

The genus Tuber comprises ectomycorrhizal fungal species producing belowground ascomata, including the gastronomically most prominent hypogeous fungi. Since the discovery and description of new species are ongoing, the proportion of undescribed species can be considerable and the taxonomy of the genus goes often through changes. The taxonomy of the genus Tuber would therefore benefit from a periodic review. Tuber species described in Europe in recent decades include Tuber regianum, T. bernardinii and T. magentipunctatum. The common characteristics of these three species are the relatively small-sized spores with alveolate-reticulate ornamentation, a high number of spores per ascus (most frequently 6–8 spores) and small-sized ascomata with a verrucose-papillate or smooth surface. The present study aimed at examining the morphology and ecology of the three species, and providing a detailed taxonomic description of the Regianum clade using a multilocus phylogenetic analysis. In addition to this, we examined whether the apparently plesiomorphic morphological character states of this phylogenetically basal clade are the result of the conservation of ancestral character states. Our results show that in the case of certain morphological traits of the Regianum clade, the apparently plesiomorphic character states are indeed retained ancestral states, while in others, they are convergently reappeared ones. Furthermore, taking an overlook at all Tuber clades, we found that some morphological characters, such as spore length, number of spores per ascus and ascus length, changed together in the same evolutionary patterns, while others transformed in different ways within the genus.

Genome-Wide Identification, Sequence Alignment, and Transcription of Five Sex-Related Genes in Largemouth Bass (Micropterus Salmoides).

Largemouth bass (Micropterus Salmoides) is an economically important fish species in China. Most research has focused on its growth, disease resistance, and nutrition improvement. However, the sex-determining genes in largemouth bass are still unclear. The transforming growth factor-beta (TGF-β) gene family, including amh, amhr2 and gsdf, plays an important role in the sex determination and differentiation of various fishes. These genes are potentially involved in sex determination in largemouth bass. We performed a systematic analysis of 5 sex-related genes (amh, amhr2, gsdf, cyp19a1, foxl2) in largemouth bass using sequence alignment, collinearity analysis, transcriptome, and quantitative real-time polymerase chain reaction (qRT-PCR). This included a detailed assessment of their sequences, gene structures, evolutionary traits, and gene transcription patterns in various tissues including gonads, and at different developmental stages. Comparative genomics revealed that the 5 sex-related genes were highly conserved in various fish genomes. These genes did not replicate, mutate or lose in largemouth bass. However, some were duplicated (amh, amhr2 and gsdf), mutated (gsdf) or lost (amhr2) in other fishes. Some genes (e.g., gsdf) showed significant differences in genomic sequence between males and females, which may contribute to sex determination and sex differentiation in these fishes. qRT-PCR was applied to quantify transcription profiling of the 5 genes during gonadal development and in the adult largemouth bass. Interestingly, amh, amhr2 and gsdf were predominantly expressed in the testis, while cyp19a1 and foxl2 were mainly transcribed in the ovary. All 5 sex-related genes were differentially expressed in the testes and ovaries from the 56th day post-fertilization (dpf). We therefore speculate that male/female differentiation in the largemouth bass may begin at this critical time-point. Examination of the transcriptome data also allowed us to screen out several more sex-related candidate genes. Our results provide a valuable genetic resource for investigating the physiological functions of these 5 sex-related genes in sex determination and gonadal differentiation, as well as in the control of gonad stability in adult largemouth bass.

Effect of binocular visual cue availability on fruit and insect grasping performance in two cheirogaleids: Implications for primate origins hypotheses

Forward-facing eyes with parallel optic axes, which provide a wide field of binocular vision and precise depth perception, are among the diagnostic features of crown primates; however, the adaptive significance of this feature remains contentious. Two of the most prominent primate-origins hypotheses propose that either foraging for fruit or nocturnal predation on insects created selective pressures that led to the evolution of diagnostic primate traits, including a wide binocular field. To determine whether either of these hypotheses provides a viable explanation for the evolution of primates' derived eye orientation, the importance of binocular depth cues for the two tasks invoked by these hypotheses was evaluated experimentally in Microcebus murinus and Cheirogaleus medius, cheirogaleids' considered reasonable living analogs of the earliest euprimates. Performance in grasping insects and fruit was evaluated when the animals made use of their full binocular visual field and when their binocular visual field was restricted using a helmet-mounted blinder. Restriction of the binocular field had no effect on fruit grasping performance; however, restriction of the binocular field resulted in a significant deficit in insect predation performance. Differences in behavioral variables also suggest that insect predation is a more visually demanding task than fruit foraging. These results support the role of insect predation, but not fruit foraging, in contributing to the selective pressures that led to the evolution of parallel optic axes and a wide binocular field in crown primates.

Ancient trees are essential elements for high-mountain forest conservation: Linking the longevity of trees to their ecological function

Mature forests and their extremely old trees are rare and threatened ancient vestiges in remote European high-mountain regions. Here, we analyze the role that extremely long-living trees have in mature forests biodiversity in relation to their singular traits underlying longevity. Tree size and age determine relative growth rates, bud abortion, and the water status of long-living trees. The oldest trees suffer indefectible age-related constraints but possess singular evolutionary traits defined by fitness adaptation, modular autonomy, and a resilient metabolism that allow them to have irreplaceable roles in the ecosystem as biodiversity anchors of vulnerable lichen species like Letharia vulpina. We suggest that the role of ancient trees as unique biodiversity reservoirs is linked to their singular physiological traits associated with longevity. The set of evolutionarily plastic tools that can only be provided by centuries or millennia of longevity helps the oldest trees of mature forests drive singular ecological relationships that are irreplaceable and necessary for ecosystem dynamics.

Adaptation of the Coniferous Forests to Natural Fire Disturbances in the Altai Mountains, Xinjiang, China

The Altai Mountains, located in the northwesternmost part of China, have a harsh climate and little human activity, making it an excellent location to study forest ecology undisturbed by human interference. The forest is frequently struck by lightning and experiences long-term natural fire disturbances, leading to the evolution of unique fire adaptation traits in the major conifer species. To explore the role of natural fire disturbances in the Altai Mountain forest ecosystem, we conducted a study on the fire adaptation traits of Larix sibirica, Pinus sibirica, Picea obovata, and Abies sibirica, and reconstructed the fire history of the forest area over the past 100 years. We investigated three representative forest areas with varying fire disturbance conditions and habitats in the Altai Mountains. Data on fire disturbance conditions, relative air humidity, and species composition were collected in these areas. Basal diameter to diameter at breast height, relative bark thickness, and under-crown heights were measured and counted for each of the four species, and litter, bark, and wood layers were sampled and analyzed for physicochemical properties (ash, fat, and higher heating value) for each of the four species in the plots examined. We conducted a count of the four conifer species in the forest for each fire adaptation index and analyzed the differences in fire adaptation traits among the species. Larix sibirica showed fire-tolerant traits, Pinus sibirica displayed fire-embracer traits, and Picea obovata and Abies sibirica exhibited fire-avoider traits. Through the analysis of stand composition and exposure to fire disturbance in the different forest areas, we were able to correlate the fire-adaptive strategies of the four conifers with stand characteristics under varying fire disturbances and habitats. The interaction between forests and fires, and their adaptation to each other, ultimately create the current ecosystems in the Altai Mountains.

Mutualisms drive plant trait evolution beyond interaction-related traits.

Mutualisms have driven the evolution of extraordinary structures and behavioural traits, but their impact on traits beyond those directly involved in the interaction remains unclear. We addressed this gap using a highly evolutionarily replicated system - epiphytes in the Rubiaceae forming symbioses with ants. We employed models that allow us to test the influence of discrete mutualistic traits on continuous non-mutualistic traits. Our findings are consistent with mutualism shaping the pace of morphological evolution, strength of selection and long-term mean of non-mutualistic traits in function of mutualistic dependency. While specialised and obligate mutualisms are associated with slower trait change, less intimate, facultative and generalist mutualistic interactions - which are the most common - have a greater impact on non-mutualistic trait evolution. These results challenge the prevailing notion that mutualisms solely affect the evolution of interaction-related traits via stabilizing selection and instead demonstrate a broader role for mutualisms in shaping trait evolution.

Mosaic Evolution of Grasping and Genital Traits in Two Sympatric Scorpion Species with Reproductive Interference

Mosaic Evolution of Grasping and Genital Traits in Two Sympatric Scorpion Species with Reproductive Interference

Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae

Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. However, the potential of SCRaMbLE to study genomic rearrangements is currently hindered, because a strain containing all 16 synthetic chromosomes is not yet available. Here, we construct SparLox83R, a yeast strain containing 83 loxPsym sites distributed across all 16 chromosomes. SCRaMbLE of SparLox83R produces versatile genome-wide genomic rearrangements, including inter-chromosomal events. Moreover, when combined with synthetic chromosomes, SCRaMbLE of hetero-diploids with SparLox83R leads to increased diversity of genomic rearrangements and relatively faster evolution of traits compared to hetero-diploids only with wild-type chromosomes. Analysis of the SCRaMbLEd strain with increased tolerance to nocodazole demonstrates that genomic rearrangements can perturb the transcriptome and 3D genome structure and consequently impact phenotypes. In summary, a genome with sparsely distributed loxPsym sites can serve as a powerful tool for studying the consequence of genomic rearrangements and accelerating strain engineering in Saccharomyces cerevisiae.