Learning from Protein Engineering by Deconvolution of Multi‐Mutational Variants

Angewandte Chemie International Edition, Год журнала: 2024, Номер 63(36)

Опубликована: Июнь 17, 2024

Abstract This review analyzes a development in biochemistry, enzymology and biotechnology that originally came as surprise. Following the establishment of directed evolution stereoselective enzymes organic chemistry, concept partial or complete deconvolution selective multi‐mutational variants was introduced. Early experiments led to finding mutations can interact cooperatively antagonistically with one another, not just additively. During past decade, this phenomenon shown be general. In some studies, molecular dynamics (MD) quantum mechanics/molecular mechanics (QM/MM) computations were performed order shed light on origin non‐additivity at all stages an evolutionary upward climb. Data used construct unique multi‐dimensional rugged fitness pathway landscapes, which provide mechanistic insights different from traditional landscapes. Along related line, biochemists have long tested result introducing two point enzyme for reasons, followed by comparison respective double mutant so‐called cycles, showed only additive effects, but more recently also uncovered cooperative antagonistic non‐additive effects. We conclude suggestions future work, call unified overall picture epistasis.

Язык: Английский

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Impacts of limits to adaptation on population and community persistence in a changing environment

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2025, Номер 380(1917)

Опубликована: Янв. 9, 2025

A key issue in predicting how ecosystems will respond to environmental change is understanding why populations and communities are able live reproduce some parts of ecological geographical space, but not others. The limits adaptation that cause niches vary position width across taxa contexts determine emerge from selection on phenotypes genomes. Ecological trade-offs mean can only be optimal environments unless these reshaped through evolution. However, the amount rate evolution limited by genetic architectures, developmental systems (including phenotypic plasticity) legacies recent evolutionary history. Here, we summarize adaptive their consequences time (evolutionary rescue) space (species’ range limits), relating theoretical predictions empirical tests. We then highlight avenues for future research this area, better connections between demography analysing genomic architecture adaptation, dynamics plasticity interactions biotic abiotic environment. Progress questions help us understand when where allow species persist face rapid change. This article part discussion meeting ‘Bending curve towards nature recovery: building Georgina Mace's legacy a biodiverse future’.

Язык: Английский

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Diverse pathways to speciation revealed by marine snails

Trends in Genetics, Год журнала: 2024, Номер 40(4), С. 337 - 351

Опубликована: Фев. 22, 2024

Speciation is a key evolutionary process that not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing on one-dimensional continuum, undifferentiated populations to species, obscured complexity speciation. Adding axes helped describe either routes or reproductive isolation in snails. Divergent selection repeatedly generated barriers between ecotypes, but appeared less important completing while genetic incompatibilities played role. Chromosomal inversions contributed barriers, with variable impact. A multidimensional (hypercube) approach supported framing questions identification knowledge gaps can be useful understand many other systems.

Язык: Английский

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Adaptation to seasonal reproduction and environment‐associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow

Evolutionary Applications, Год журнала: 2024, Номер 17(3)

Опубликована: Март 1, 2024

Understanding how marine organisms adapt to local environments is crucial for predicting populations will respond global climate change. The genomic basis, environmental factors and evolutionary processes involved in adaptation are however not well understood. Here we use Atlantic herring, an abundant, migratory widely distributed fish with substantial resources, as a model organism evaluate adaptation. We examined variation its correlation variables across broad gradient, 15 spawning aggregations Canada the United States. then compared our results available data of northeast populations. confirmed that population structure lies fraction genome including likely adaptive genetic variants functional importance. discovered 10 highly differentiated regions four chromosomes. Nine show strong association seasonal reproduction. One region, corresponding known inversion on chromosome 12, underlies latitudinal pattern discriminating north south biogeographic transition zone Scotian Shelf. Genome-environment associations indicate winter seawater temperature best correlates this inversion. at two so-called 'islands divergence' related reproduction appear be private northwest Atlantic. Populations share these divergent regions, simultaneously displaying significant diversity haplotype composition another which includes undescribed structural variant approximately 7.7 Mb long 8. Our suggest timing geographic location early development may under diverse selective pressures allelic fitness environments. study highlights role architecture, ancestral haplotypes selection maintaining divergence species large sizes presumably high gene flow.

Язык: Английский

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Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

Опубликована: Янв. 31, 2025

Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block can have effects on fitness. To study the role large in massive evolutionary radiation Lake Malawi cichlids, we used long-read technologies to identify four and two tandem span half each respective chromosome, which encompass over 10% genome. Each inversion is fixed one states within seven major ecogroups, suggesting they played separation lake lineages specific habitats. One exception benthic sub-radiation, where both inverted non-inverted continue segregate group. The histories three six suggest transferred from pelagic Diplotaxodon group ancestors at time sub-radiation was seeded. remaining found subset species living deep waters. We show some these as XY sex-determination systems but also likely limited total species. Our work suggests been under sexual natural selection cichlids will be understanding how this adaptive evolved.

Язык: Английский

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The interplay of local adaptation and gene flow may lead to the formation of supergenes

Molecular Ecology, Год журнала: 2024, Номер unknown

Опубликована: Фев. 28, 2024

Supergenes are genetic architectures resulting in the segregation of alternative combinations alleles underlying complex phenotypes. The co-segregation at linked loci is often facilitated by polymorphic chromosomal rearrangements suppressing recombination locally. involved many polymorphisms, including sexual, colour or behavioural polymorphisms numerous plants, fungi, mammals, fish, and insects. Despite a long history empirical theoretical research, formation supergenes remains poorly understood. Here, using two-island population model, we explore how gene flow evolution overdominant inversions may jointly lead to supergenes. We show that differentiated populations, both under disruptive selection, leads an increase frequency adapted, immigrant haplotypes. Indeed, rare allelic combinations, such as haplotypes, more frequently reshuffled than common therefore benefit from suppression generated inversions. When inversion capturing locally adapted haplotype spreads but associated with fitness cost hampering its fixation (e.g. recessive mutation load), maintenance non-inverted enhanced; certain conditions, persists alongside inverted local haplotype, while standard disappears. This establishes stable, polymorphism two non-recombining haplotypes encoding adaptive strategies, is, supergene. These results bring new light importance adaptation, overdominance, general.

Язык: Английский

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Genomic richness enables worldwide invasive success

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Фев. 28, 2024

Abstract Biological invasions are a major threat to biodiversity. Therefore, monitoring genomic features of invasive species is crucial understand their population structure and adaptive processes. However, resources scarce, compromising the study success. Here, we present reference genome Styela plicata , one most widespread marine species, combined with data 24 individuals from 6 populations distributed worldwide. We characterized large inversions in four chromosomes, accounting for ~ 15% size. These polymorphic through species’ distribution area, enriched genes enhancing fitness estuary harbor environments. Nonetheless, mask detection S. structure. When these structural variants removed, successfully identify main oceanographic barriers accurately characterize differentiation between within ocean basins. Several located chromosome 3 showcased as drivers biogeographic regions. Moreover, recover three mitogenomic clades, involving rearrangements leading cyto-nuclear coevolution likely involved mitochondrion during cell division. Our results suggest that contribute structuring adaptation processes, potentially success when colonizing new habitats.

Язык: Английский

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Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche

Molecular Ecology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 9, 2025

ABSTRACT How gene expression evolves to enable divergent ecological adaptation and how changes in relate genomic architecture are pressing questions for understanding the mechanisms enabling speciation. Furthermore, plasticity can both contribute be affected by process of is crucial evolution, colonisation novel niches response rapid environmental change. Here, we investigate role constitutive plastic differences between host races, or host‐specific ecotypes, peacock fly Tephritis conura , a thistle bud specialist. By cross‐fostering larvae new buds their natal plant alternative, plant, uncover extensive especially genes associated with processing chemicals. However, evidence was minimal limited ancestral race. Genes race‐specific found more often than expected within large inversion T. genome, adding that inversions important diversification face flow underscores altered may key evolutionary consequences inversions.

Язык: Английский

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Inversions Dominate Evolution in the Highly Admixed European Sardine (Sardina pilchardus)

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 21, 2025

Abstract Inversions can play key roles in the genetic architecture of adaptation, but scale their effects across different species remains poorly understood. Here, we use whole- genome sequencing to investigate influence inversions on population genomics r-selected European sardine ( Sardina pilchardus ). Allele frequency differences from millions SNPs 34 populations spanning species’ range were analyzed. Genomic scans identified several extreme outlier regions overlapping chromosome-scale inversions, collectively representing over half genome. Our findings suggest these are associated with locally adapted life history strategies. First, within containing exhibited striking allele between Atlantic and Mediterranean sardines, which differ adaptive traits. In Atlantic, inversion frequencies varied latitudinally, while Mediterranean, they shifted longitudinally, aligning temperature oceanographic features that Moreover, adjacent contrasting environments displayed pronounced inversions. These spatial patterns sharply contrasted those based neutral loci, indicating driven by selection. After rigorously filtering affected selection showed high admixture significant structure isolation distance, especially Mediterranean. This study demonstrates shape genome-wide diversity highly admixed marine species. also offer crucial insights for stock delimitation management this commercially valuable face climate change.

Язык: Английский

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Inversions Can Accumulate Balanced Sexual Antagonism: Evidence from Simulations and Drosophila Experiments

Опубликована: Янв. 23, 2025

Chromosomal inversion polymorphisms can be common, but the causes of their persistence are often unclear. We propose a model for maintenance polymorphism, which requires that some variants contribute antagonistically to two phenotypes, one has negative frequency-dependent fitness. These conditions yield form disruptive selection, favoring predominant haplotypes segregating alleles favor opposing antagonistic phenotypes. An associated with haplotype reduce fitness load incurred by generating recombinant offspring, reinforcing its linkage and enabling both accumulate more than expected otherwise. develop apply forward simulator examine these dynamics under tradeoff between survival male display. simulations indeed generate inversion-associated sex-specific effects. Antagonism strengthens time, ultimately karyotypes at surprisingly predictable frequencies, striking genotype frequency differences sexes developmental stages. To test whether this may well-studied yet enigmatic in Drosophila melanogaster , we track frequencies laboratory crosses they influence reproductive success or survival. find four tested inversions show significant evidence examined, In(3R)K In(3L)Ok reproduction. In line apparent effects implied those inversions, was also found less costly viability and/or longevity males females, whereas beneficial female Based on work, expect balancing selection pleiotropic traits provide underappreciated contribution natural polymorphism.

Язык: Английский

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