Evolution of Gene Expression and Splicing in Parallel Cold-Adapted Fly Populations

AbstractChanges in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find significant although somewhat limited evidence for parallel expression evolution between them, and less evidence for parallel splicing evolution. We find that genes with mitochondrial functions are particularly enriched among candidates for adaptive expression evolution. We also develop a method to estimate cis-versus trans-encoded contributions to expression or splicing differences that does not rely on the presence of fixed differences between parental strains. Applying this method, we infer important roles of both cis-and trans-regulation among our putatively adaptive expression and splicing differences. The apparent contributions of cis-versus trans-regulation to adaptive evolution vary substantially among population pairs, with an Ethiopian pair showing pervasive trans-effects, suggesting that basic characteristics of regulatory evolution may depend on biological context. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.

Download Full-text

Parallel and Population-specific Gene Regulatory Evolution in Cold-Adapted Fly Populations

Genetics ◽

10.1093/genetics/iyab077 ◽

2021 ◽

Author(s):

Yuheng Huang ◽

Justin B Lack ◽

Grant T Hoppel ◽

John E Pool

Keyword(s):

Adaptive Evolution ◽

Parallel Evolution ◽

Natural Populations ◽

Population Variation ◽

Specific Gene ◽

Regulatory Evolution ◽

Cold Adapted ◽

Thermal Environments ◽

Gene Regulatory ◽

Trans Regulation

Abstract Changes in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find evidence for parallel expression evolution between them, with stronger parallelism at larval and adult stages than for pupae. We also implement a flexible method to estimate cis- versus trans-encoded contributions to expression or splicing differences at the adult stage. The apparent contributions of cis- versus trans-regulation to adaptive evolution vary substantially among population pairs. While two of three population pairs show a greater enrichment of cis-regulatory differences among adaptation candidates, trans-regulatory differences are more likely to be implicated in parallel expression changes between population pairs. Genes with significant cis-effects are enriched for signals of elevated genetic differentiation between cold- and warm-adapted populations, suggesting that they are potential targets of local adaptation. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.

Download Full-text

Gene regulatory evolution in cold-adapted fly populations neutralizes plasticity and may undermine genetic canalization

10.1101/2022.01.14.476421 ◽

2022 ◽

Author(s):

Yuheng Huang ◽

Justin Lack ◽

Grant Hoppel ◽

John E Pool

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Adaptive Evolution ◽

Empirical Studies ◽

Natural Populations ◽

Plastic Response ◽

Cold Adapted ◽

Thermal Environments ◽

Gene Regulatory ◽

Transcriptomic Level

The relationships between adaptive evolution, phenotypic plasticity, and canalization remain incompletely understood. Theoretical and empirical studies have made conflicting arguments on whether adaptive evolution may enhance or oppose the plastic response. Gene regulatory traits offer excellent potential to study the relationship between plasticity and adaptation, and they can now be studied at the transcriptomic level. Here we take advantage of three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. We measure the transcriptome-wide plasticity in gene expression levels and alternative splicing (intron usage) between warm and cold laboratory environments. We find that suspected adaptive changes in both gene expression and alternative splicing tend to neutralize the ancestral plastic response. Further, we investigate the hypothesis that adaptive evolution can lead to decanalization of selected gene regulatory traits. We find strong evidence that suspected adaptive gene expression (but not splicing) changes in cold-adapted populations are more vulnerable to the genetic perturbation of inbreeding than putatively neutral changes. We find some evidence that these patterns may reflect a loss of genetic canalization accompanying adaptation, although other processes including hitchhiking recessive deleterious variants may contribute as well. Our findings augment our understanding of genetic and environmental effects on gene regulation in the context of adaptive evolution.

Download Full-text

Contributions of cis- and trans-Regulatory Evolution to Transcriptomic Divergence across Populations in the Drosophila mojavensis Larval Brain

Genome Biology and Evolution ◽

10.1093/gbe/evaa145 ◽

2020 ◽

Vol 12 (8) ◽

pp. 1407-1418

Author(s):

Kyle M Benowitz ◽

Joshua M Coleman ◽

Carson W Allan ◽

Luciano M Matzkin

Keyword(s):

Gene Expression ◽

Population Level ◽

F1 Hybrids ◽

Evolutionary Divergence ◽

Drosophila Mojavensis ◽

Regulatory Evolution ◽

Larval Brain ◽

Expression Evolution ◽

Trans Regulation ◽

In Cis

Abstract Natural selection on gene expression was originally predicted to result primarily in cis- rather than trans-regulatory evolution, due to the expectation of reduced pleiotropy. Despite this, numerous studies have ascribed recent evolutionary divergence in gene expression predominantly to trans-regulation. Performing RNA-seq on single isofemale lines from genetically distinct populations of the cactophilic fly Drosophila mojavensis and their F1 hybrids, we recapitulated this pattern in both larval brains and whole bodies. However, we demonstrate that improving the measurement of brain expression divergence between populations by using seven additional genotypes considerably reduces the estimate of trans-regulatory contributions to expression evolution. We argue that the finding of trans-regulatory predominance can result from biases due to environmental variation in expression or other sources of noise, and that cis-regulation is likely a greater contributor to transcriptional evolution across D. mojavensis populations. Lastly, we merge these lines of data to identify several previously hypothesized and intriguing novel candidate genes, and suggest that the integration of regulatory and population-level transcriptomic data can provide useful filters for the identification of potentially adaptive genes.

Download Full-text

Evolved Differences in cis and trans Regulation Between the Maternal and Zygotic mRNA Complements in the Drosophila Embryo

Genetics ◽

10.1534/genetics.120.303626 ◽

2020 ◽

Vol 216 (3) ◽

pp. 805-821

Author(s):

Emily L. Cartwright ◽

Susan E. Lott

Keyword(s):

Gene Expression ◽

Developmental Stages ◽

Transcript Level ◽

Drosophila Embryo ◽

Gene Products ◽

Regulatory Evolution ◽

Transcript Levels ◽

Maternal Transcript ◽

Zygotic Transcription ◽

Trans Regulation

How gene expression can evolve depends on the mechanisms driving gene expression. Gene expression is controlled in different ways in different developmental stages; here we ask whether different developmental stages show different patterns of regulatory evolution. To explore the mode of regulatory evolution, we used the early stages of embryonic development controlled by two different genomes, that of the mother and that of the zygote. During embryogenesis in all animals, initial developmental processes are driven entirely by maternally provided gene products deposited into the oocyte. The zygotic genome is activated later, when developmental control is handed off from maternal gene products to the zygote during the maternal-to-zygotic transition. Using hybrid crosses between sister species of Drosophila (D. simulans, D. sechellia, and D. mauritiana) and transcriptomics, we find that the regulation of maternal transcript deposition and zygotic transcription evolve through different mechanisms. We find that patterns of transcript level inheritance in hybrids, relative to parental species, differ between maternal and zygotic transcripts, and maternal transcript levels are more likely to be conserved. Changes in transcript levels occur predominantly through differences in trans regulation for maternal genes, while changes in zygotic transcription occur through a combination of both cis and trans regulatory changes. Differences in the underlying regulatory landscape in the mother and the zygote are likely the primary determinants for how maternal and zygotic transcripts evolve.

Download Full-text

The importance of alternative splicing in adaptive evolution

10.32942/osf.io/wak9g ◽

2021 ◽

Author(s):

Pooja Singh ◽

Ehsan Pashay Ahi

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Adaptive Evolution ◽

Adaptive Divergence ◽

Mrna Isoforms ◽

Evolutionary Transitions ◽

Splice Variation ◽

Gene Regulatory ◽

Splice Forms

Although alternative splicing is a ubiquitous gene regulatory mechanism in plants and animals, its contribution to evolutionary transitions is understudied. Splicing enables different mRNA isoforms to be generated from the same gene, expanding transcriptomic and proteomic diversity. While the role of gene expression in adaptive evolution is widely accepted, biologists still debate the functional impact of alternative isoforms on phenotype. In light of recent empirical research linking splice variation to ecological adaptations, we propose that alternative splicing is an important substrate for adaptive evolution and speciation, particularly at short timescales. We synthesise what is known about the role of splicing in adaptive evolution. We discuss the contribution of standing splice variation to phenotypic plasticity and how hybridisation can produce novel splice forms. Going forwards, we propose that splicing be included as a standard analysis alongside gene expression analysis so we can better understand of how splicing contributes to adaptive divergence at the micro- and macroevolutionary levels.

Download Full-text

Evolved differences in cis and trans regulation between the maternal and zygotic mRNA complements in the Drosophila embryo

10.1101/737536 ◽

2019 ◽

Author(s):

Emily L. Cartwright ◽

Susan E. Lott

Keyword(s):

Gene Expression ◽

Developmental Stages ◽

Transcript Level ◽

Drosophila Embryo ◽

Gene Products ◽

Regulatory Evolution ◽

Transcript Levels ◽

Maternal Transcript ◽

Zygotic Transcription ◽

Trans Regulation

ABSTRACTHow gene expression can evolve depends on the mechanisms driving gene expression. Gene expression is controlled in different ways in different developmental stages; here we ask whether different developmental stages show different patterns of regulatory evolution. To explore the mode of regulatory evolution, we used the early stages of embryonic development controlled by two different genomes, that of the mother and that of the zygote. During embryogenesis in all animals, initial developmental processes are driven entirely by maternally provided gene products deposited into the oocyte. The zygotic genome is activated later, when developmental control is handed off from maternal gene products to the zygote during the maternal-to-zygotic transition. Using hybrid crosses between sister species of Drosophila (D. simulans, D. sechellia, and D. mauritiana) and transcriptomics, we find that the regulation of maternal transcript deposition and zygotic transcription evolve through different mechanisms. We find that patterns of transcript level inheritance in hybrids, relative to parental species, differ between maternal and zygotic transcripts, and maternal transcript levels are more likely to be conserved. Changes in transcript levels occur predominantly through differences in trans regulation for maternal genes, while changes in zygotic transcription occur through a combination of both cis and trans regulatory changes. Differences in the underlying regulatory landscape in the mother and the zygote are likely the primary determinants for how maternal and zygotic transcripts evolve.

Download Full-text

Dense encoding of developmental regulatory information may constrain evolvability

10.1101/2020.04.17.046052 ◽

2020 ◽

Cited By ~ 1

Author(s):

Timothy Fuqua ◽

Jeff Jordan ◽

Maria Elize van Breugel ◽

Aliaksandr Halavatyi ◽

Christian Tischer ◽

...

Keyword(s):

Gene Expression ◽

Drosophila Melanogaster ◽

Natural Variation ◽

Phenotypic Evolution ◽

Evolutionary Potential ◽

Regulatory Evolution ◽

Regulatory Changes ◽

Regulatory Information ◽

Gene Regulatory ◽

Gene Expression Levels

AbstractGene regulatory changes underlie much of phenotypic evolution. However, the evolutionary potential of regulatory evolution is unknown, because most evidence comes from either natural variation or limited experimental perturbations. Surveying an unbiased mutation library for a developmental enhancer in Drosophila melanogaster using an automated robotics pipeline, we found that most mutations alter gene expression. Our results suggest that regulatory information is distributed throughout most of a developmental enhancer and that parameters of gene expression—levels, location, and state—are convolved. The widespread pleiotropic effects of most mutations and the codependency of outputs may constrain the evolvability of developmental enhancers. Consistent with these observations, comparisons of diverse drosophilids reveal mainly stasis and apparent biases in the phenotypes influenced by this enhancer. Developmental enhancers may encode a much higher density of regulatory information than has been appreciated previously, which may impose constraints on regulatory evolution.Quote“Rock, robot rockRock, robot rockRock, robot rock”Daft Punk (2005)

Download Full-text

Widespread misregulation of inter-species hybrid transcriptomes due to sex-specific and sex-chromosome regulatory evolution

10.1101/2020.05.04.076505 ◽

2020 ◽

Cited By ~ 2

Author(s):

Santiago Sánchez-Ramírez ◽

Jörg G. Weiss ◽

Cristel G. Thomas ◽

Asher D. Cutter

Keyword(s):

Gene Expression ◽

Sex Differences ◽

Regulatory Networks ◽

Genetic Networks ◽

Stabilizing Selection ◽

Species Hybrid ◽

Regulatory Evolution ◽

Speciation Process ◽

Gene Regulatory ◽

Species Hybrids

AbstractWhen gene regulatory networks diverge between species, their dysfunctional expression in inter-species hybrid individuals can create genetic incompatibilities that generate the developmental defects responsible for intrinsic post-zygotic reproductive isolation. Both cis- and trans-acting regulatory divergence can be hastened by directional selection through adaptation, sexual selection, and inter-sexual conflict, in addition to inconspicuous evolution under stabilizing selection. Dysfunctional sex-biased gene expression, in particular, may provide an important source of sexually-dimorphic genetic incompatibilities. Here, we characterize and compare male and female/hermaphrodite transcriptome profiles for sibling nematode species Caenorhabditis briggsae and C. nigoni, along with allele-specific expression in their F1 hybrids, to deconvolve features of expression divergence and regulatory dysfunction. Despite evidence of widespread stabilizing selection on gene expression, misexpression of sex-biased genes pervades F1 hybrids of both sexes. This finding implicates greater fragility of male genetic networks to produce dysfunctional organismal phenotypes. Spermatogenesis genes are especially prone to high divergence in both expression and coding sequences, consistent with a “faster male” model for Haldane’s rule and elevated sterility of hybrid males. Moreover, underdominant expression pervades male-biased genes compared to female-biased and sex-neutral genes and an excess of cis-trans compensatory regulatory divergence for X-linked genes underscores a “large-X effect” for hybrid male expression dysfunction. Extensive regulatory divergence in sex determination pathway genes likely contributes to feminization of XX hybrids. The evolution of genetic incompatibilities due to regulatory versus coding sequence divergence, however, are expected arise in an uncorrelated fashion. This study identifies important differences between the sexes in how regulatory networks diverge to contribute to sex-biases in how genetic incompatibilities manifest during the speciation process.Author’s summaryAs species diverge, many mutations that affect traits do so by altering gene expression. Such gene regulatory changes also accumulate in the control of static traits, due to compensatory effects of mutation on multiple regulatory elements. Theory predicts many of these changes to cause inter-species hybrids to experience dysfunctional gene expression that leads to reduced fitness, disproportionately affecting genes biased toward expression in one sex and that localize to sex chromosomes. Our analyses of genome-wide gene expression from Caenorhabditis nematode roundworms support these predictions. We find widespread rewiring of gene regulation, despite the extensive morphological stasis and conserved expression profiles that are hallmarks of these animals. Misregulation of expression in inter-species hybrids of both sexes is most severe for genes linked to the X-chromosome, but male organismal phenotypes are most disrupted in hybrids. This fragility of male genetic networks and sex differences in regulatory evolution of local versus distant elements may underlie feminized and sterile phenotypes among hybrids. Our work clarifies how distinct components of regulatory networks evolve and contribute to sex differences in the manifestation of genetic incompatibilities in the speciation process.

Download Full-text