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opencc-zeroAug 2020View details →

Data from: Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon

A major goal in biology is to understand how evolution shapes variation in individual life histories. Genome-wide association studies have been successful in uncovering genome regions linked with traits underlying life history variation in a range of species. However, lack of functional studies of the discovered genotype-phenotype associations severely restrains our understanding how alternative life history traits evolved and are mediated at the molecular level. Here, we report a cis-regulatory mechanism whereby expression of alternative isoforms of the transcription co-factor vestigial-like 3 (vgll3) associate with variation in a key life history trait, age at maturity, in Atlantic salmon (Salmo salar). Using a common-garden experiment, we first show that vgll3 genotype associates with puberty timing in one-year-old salmon males. By way of temporal sampling of vgll3 expression in ten tissues across the first year of salmon development, we identify a pubertal transition in vgll3 expression where maturation coincided with a 66% reduction in testicular vgll3 expression. The late maturation allele was not only associated with a tendency to delay puberty, but also with expression of a rare transcript isoform of vgll3 pre-puberty. By comparing absolute vgll3 mRNA copies in heterozygotes we show that the expression difference between the earlyand late maturity alleles is largely cis-regulatory. We propose a model whereby expression of a rare isoform from the late allele shifts the liability of its carriers towards delaying puberty. These results exemplify the potential importance of regulatory differences as a mechanism for the evolution of life history traits.

opencc-zeroFeb 2020View details →

Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features

Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act is still an open question in evolutionary developmental biology. We use high-resolution Quantitative Trait Locus (QTL) mapping in the F34 generation of an advanced intercross experiment (LG,SM-G34) to characterize the genetic architecture of the mouse pelvis. We test the prediction that genomic features linked to developmental patterning and differentiation of the hind limb and pelvis and the regulation of chondrogenesis are overrepresented in QTL. We find 31 single QTL-trait associations at the genome- or chromosome-wise significance level coalescing to 27 pleiotropic loci. We recover further QTL at a more relaxed significance threshold replicating locations found in a previous experiment in an earlier generation of the same population. QTL were more likely than chance to harbor Pitx1 and Sox9 Class II ChIP-seq features active during development of skeletal features. There was weak or no support for the enrichment of seven more categories of developmental features drawn from the literature. Our results suggest genotypic variation is channeled through a subset of developmental processes involved in the generation of phenotypic variation in the pelvis. This finding indicates the evolvability of complex traits may be subject to biases not evident from patterns of covariance among morphological features or developmental patterning when either is considered in isolation.

publicFeb 2020View details →

Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features

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publicAug 2020View details →

Data from: Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon

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publicFeb 2024View details →

Data from: Among-population variation in telomere regulatory proteins and their potential role as hidden drivers of intraspecific variation in life history

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opencc-zeroDec 2020View details →

Cis-regulatory variation in the shavenbaby gene underlies intraspecific phenotypic variation, mirroring interspecific divergence in the same trait

Despite considerable progress in recent decades in dissecting the genetic causes of natural morphological variation, there is limited understanding of how variation within species ultimately contributes to species differences. We have studied patterning of the non-sensory hairs, commonly known as "trichomes," on the dorsal cuticle of first-instar larvae of Drosophila. Most Drosophila species produce a dense lawn of trichomes, but a subset of dorsal trichomes were lost in D. sechellia and D. ezoana due entirely to regulatory evolution of the shavenbaby (svb) gene. Here we describe intraspecific variation in dorsal trichome patterns of first-instar larvae of D. virilis that is similar to the trichome pattern variation identified previously between species. We found that 67% of this difference is explained by a QTL that contains svb and that svb expression correlates with trichome variation within D. virilis . Despite using an experimental design with reasonable power to detect a second locus accounting for the remainder of the variance in trichome number, only a single QTL could be mapped, suggesting that multiple other loci each make a small contribution to trichome patterning. Thus, the genetic architecture of intraspecific variation and interspecific differences exhibit similarities and differences that may reflect differences between short-term and long-term evolutionary processes.

opencc-zeroDec 2012View details →

Data from: The impact of gene expression variation on robustness and evolvability of a developmental gene regulatory network

Regulatory interactions buffer development against genetic and environmental perturbations, but adaptation requires phenotypes to change. We investigated the relationship between robustness and evolvability within the gene regulatory network underlying development of the larval skeleton in the sea urchin Strongylocentrotus purpuratus. We find extensive variation in gene expression in this network throughout development in a natural population, some of which has a heritable genetic basis. Switch-like regulatory interactions predominate during early development, buffer expression variation, and may promote the accumulation of cryptic genetic variation affecting early stages. Regulatory interactions during later development are typically more sensitive (linear), allowing variation in expression to affect downstream target genes. Variation in skeletal morphology is associated primarily with expression variation of a few, primarily structural, genes at terminal positions within the network. These results indicate that the position and properties of gene interactions within a network can have important evolutionary consequences independent of their immediate regulatory role.

opencc-zeroDec 2018View details →

Data from: Standing genomic variation within coding and regulatory regions contributes to the adaptive capacity to climate in a foundation tree species

Global climate is rapidly changing and the ability for tree species to adapt is dependent on standing genomic variation; however the distribution and abundance of functional and adaptive variants are poorly understood in natural systems. We test key hypotheses regarding the genetics of adaptive variation in a foundation tree: genomic variation is associated with climate and genomic variation is more likely to be associated with temperature than precipitation or aridity. To test these hypotheses, we used 9,593 independent, genomic single‐nucleotide polymorphisms (SNPs) from 270 individuals sampled from Corymbia calophylla's entire distribution in southwestern Western Australia, spanning orthogonal temperature and precipitation gradients. Environmental association analyses returned 537 unique SNPs putatively adaptive to climate. We identified SNPs associated with climatic variation (i.e. temperature (458), precipitation (75) and aridity (78)) across the landscape. Of these, 78 SNPs were non-synonymous (NS), while 26 SNPs were found within gene regulatory regions. The NS and regulatory candidate SNPs associated with temperature explained more deviance (27.35%) then precipitation (5.93%) and aridity (4.77%), suggesting that temperature provides stronger adaptive signals than precipitation. Genes associated with adaptive variants include functions important in stress responses to temperature and precipitation. Patterns of allelic turnover of NS and regulatory SNPs show small patterns of change through climate space with the exception of an aldehyde dehydrogenase gene variant with 80% allelic-turnover with temperature. Together, these findings provide evidence for the presence of adaptive variation to climate in a foundation species and provide critical information to guide adaptive management practices.

opencc-zeroDec 2014View details →

Data from: Sexual fidelity trade-offs promote regulatory variation in the prairie vole brain

Individual variation in social behavior seems ubiquitous, but we know little about how it relates to brain diversity. Among monogamous prairie voles, levels of vasopressin receptor (encoded by the gene avpr1a) in brain regions related to spatial memory predict male space use and sexual fidelity in the field. We find that trade-offs between the benefits of male fidelity and infidelity are reflected in patterns of territorial intrusion, offspring paternity, avpr1a expression, and the evolutionary fitness of alternative avpr1a alleles. DNA variation at the avpr1a locus includes polymorphisms that reliably predict the epigenetic status and neural expression of avpr1a, and patterns of DNA diversity demonstrate that avpr1a regulatory variation has been favored by selection. In prairie voles, trade-offs in the fitness consequences of social behaviors seem to promote neuronal and molecular diversity.

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Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity

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opencc-by-4.0Feb 2023View details →

publicMar 2019View details →

Data from: Standing genomic variation within coding and regulatory regions contributes to the adaptive capacity to climate in a foundation tree species

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publicApr 2013View details →

Data from: Recent ecological selection on regulatory divergence is shaping clinal variation in Senecio on Mount Etna

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publicNov 2016View details →

Data from: Sexual fidelity trade-offs promote regulatory variation in the prairie vole brain

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publicOct 2014View details →

Data from: The impact of gene expression variation on robustness and evolvability of a developmental gene regulatory network

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publicDec 2020View details →

Cis-regulatory variation in the shavenbaby gene underlies intraspecific phenotypic variation, mirroring interspecific divergence in the same trait

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opencc-zeroDec 2014View details →

Data from: Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster

Pigmentation traits in adult Drosophila melanogaster were used in this study to investigate how phenotypic variations of continuous ecological traits can be maintained in a natural population. First, pigmentation variation in the adult female was measured at seven different body positions in 20 strains from the Drosophila melanogaster Genetic Reference Panel (DGRP) originating from a natural population in North Carolina. Next, to assess the contributions of cis-regulatory polymorphisms of the genes involved in the melanin biosynthesis pathway, allele-specific expression levels of four genes were quantified by amplicon sequencing using a 454 GS Junior. Among those genes, ebony was significantly associated with pigmentation intensity of the thoracic segment. Detailed sequence analysis of the gene regulatory regions of this gene indicated that many different functional cis-regulatory alleles are segregating in the population and that variations outside the core enhancer element could potentially play important roles in the regulation of gene expression. In addition, a slight enrichment of distantly associated SNP pairs was observed in the ~10 kb cis-regulatory region of ebony, which suggested the presence of interacting elements scattered across the region. In contrast, sequence analysis in the core cis-regulatory region of tan indicated that SNPs within the region are significantly associated with allele-specific expression level of this gene. Collectively, the data suggest that the underlying genetic differences in the cis-regulatory regions that control intraspecific pigmentation variation can be more complex than those of interspecific pigmentation trait differences, where causal genetic changes are typically confined to modular enhancer elements.

opencc-zeroDec 2015View details →

Data from: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations

The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.

publicOct 2015View details →

Data from: Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster

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