A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

Pavlidis, Pavlos; Jensen, Jeffrey D.; Stephan, Wolfgang; Stamatakis, Alexandros

doi:10.1093/molbev/mss136

Cited by 218 publications

(217 citation statements)

References 67 publications

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“…3B). These results provide an important negative control, validating our hypotheses regarding which classes of genes we expect to respond to ocean acidification (25).…”

Section: Resultssupporting

confidence: 74%

“…Ion and sterol categories together suggest selective survival of larvae with alleles that allow them to regulate internal pH in the face of elevated CO 2 . These results are in strong contrast to the absence of functional enrichment in control cultures (25). It remains to be determined whether these selected alleles have unmeasured future tradeoffs or costs (e.g., in terms of reduced larval tolerance of other stressors or altered juvenile performance).…”

Section: Discussionmentioning

confidence: 91%

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Evolutionary change during experimental ocean acidification

Pespeni

Sanford

Gaylord

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

297

296

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Rising atmospheric carbon dioxide (CO 2 ) conditions are driving unprecedented changes in seawater chemistry, resulting in reduced pH and carbonate ion concentrations in the Earth's oceans. This ocean acidification has negative but variable impacts on individual performance in many marine species. However, little is known about the adaptive capacity of species to respond to an acidified ocean, and, as a result, predictions regarding future ecosystem responses remain incomplete. Here we demonstrate that ocean acidification generates striking patterns of genome-wide selection in purple sea urchins (Strongylocentrotus purpuratus) cultured under different CO 2 levels. We examined genetic change at 19,493 loci in larvae from seven adult populations cultured under realistic future CO 2 levels. Although larval development and morphology showed little response to elevated CO 2 , we found substantial allelic change in 40 functional classes of proteins involving hundreds of loci. Pronounced genetic changes, including excess amino acid replacements, were detected in all populations and occurred in genes for biomineralization, lipid metabolism, and ion homeostasis-gene classes that build skeletons and interact in pH regulation. Such genetic change represents a neglected and important impact of ocean acidification that may influence populations that show few outward signs of response to acidification. Our results demonstrate the capacity for rapid evolution in the face of ocean acidification and show that standing genetic variation could be a reservoir of resilience to climate change in this coastal upwelling ecosystem. However, effective response to strong natural selection demands large population sizes and may be limited in species impacted by other environmental stressors.experimental evolution | population genomics | RNA sequencing | adaptation | environmental mosaic A ccelerating increases in ocean CO 2 concentrations and accompanying declines in pH are expected this century (1, 2), particularly in the California Current System (3). The negative impacts of ocean acidification have been seen in a broad range of species (4-8) and are predicted to lead to future populations of individuals with low growth, reproduction, or survival. However, the capacity of marine populations to adapt to these changes is unknown (9, 10), and, as a result, there may be circumstances in which natural selection could result in populations of individuals with better-than-expected fitness under acidified conditions. Until recently, the tools to scan for standing genetic variation with adaptive potential in the face of climate change have not been broadly available. Here we combine sequencing across the transcriptome of the purple sea urchin Strongylocentrotus purpuratus, growth measurements under experimental acidification, and tests of frequency shifts in 19,493 polymorphisms during development. We detect the widespread occurrence of genetic variation to tolerate ocean acidification.Rapid evolution in changing environments is likely to depend ...

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“…3B). These results provide an important negative control, validating our hypotheses regarding which classes of genes we expect to respond to ocean acidification (25).…”

Section: Resultssupporting

confidence: 74%

Section: Discussionmentioning

confidence: 91%

Evolutionary change during experimental ocean acidification

Pespeni

Sanford

Gaylord

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

297

296

View full text Add to dashboard Cite

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“…While acknowledging the dangers of post hoc interpretation of GO analysis (Pavlidis et al 2012), we note that within continents, terms such as GO:009416 (response to light) and GO:0045792 (negative regulation of cell size) are enriched because these could relate to phenotypic clines observed in traits that are influenced by circadian rhythm (Hut et al 2013;Svetec et al 2015) and body size (Zwaan et al 2000) in Drosophila.…”

Section: Patterns Of Parallel Differentiationmentioning

confidence: 99%

Genomic Patterns of Geographic Differentiation in Drosophila simulans

2016

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Geographic patterns of genetic differentiation have long been used to understand population history and to learn about the biological mechanisms of adaptation. Here we present an examination of genomic patterns of differentiation between northern and southern populations of Australian and North American Drosophila simulans, with an emphasis on characterizing signals of parallel differentiation. We report on the genomic scale of differentiation and functional enrichment of outlier SNPs. While, overall, signals of shared differentiation are modest, we find the strongest support for parallel differentiation in genomic regions that are associated with regulation. Comparisons to Drosophila melanogaster yield potential candidate genes involved in local adaptation in both species, providing insight into common selective pressures and responses. In contrast to D. melanogaster, in D. simulans we observe patterns of variation that are inconsistent with a model of temperate adaptation out of a tropical ancestral range, highlighting potential differences in demographic and colonization histories of this cosmopolitan species pair.KEYWORDS geographic variation; population genomics; Drosophila T HE geographic distribution of genetic or phenotypic variation can provide valuable insight into the process of adaptation. For example, consistent patterns of genetic variation across space have long been interpreted as evidence for local adaptation owing to spatially varying selection (Endler 1977; Adrion et al. 2015). This is well illustrated in populations of Drosophila melanogaster, a model system showing consistent phenotypic and molecular clines across environmental gradients (Hoffmann and Weeks 2007). Among these, the association of latitude with variation in ecologically relevant traits such as heat knockdown resistance, chill coma recovery, and diapause incidence Schmidt and Paaby 2008) provides strong support for local adaptation to climate.Despite efforts to understand the potential adaptive nature of molecular variation in populations of Drosophila, there remains some disconnect between our understanding of allele-frequency clines and phenotypic clines, of which the latter are more easily and intuitively interpretable. For the vast majority of clinal molecular polymorphisms in Drosophila, the mechanisms underlying their maintenance are poorly understood. Nevertheless, because gene flow in Drosophila is thought to be high, strong differentiation often can be argued as evidence of local adaptation. Moreover, because the physical scale of linkage disequilibrium (LD) in Drosophlia is often smaller than the size of genes (Langley et al. 2012), differentiation between populations generally is associated with hypotheses regarding individual genes as targets of selection.Observation of parallel patterns of differentiation furthers the argument for an adaptive basis to differentiation, and in general, comparisons of patterns of variation across independent replicate geographic transects may contribute to an understanding of...

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“…However, other approaches have also been used, such as Gene Ontology or pathway annotation, to detect enrichment in a given function (Amaral et al, 2011) or locate candidate genes associated with a trait of interest (a common method for selecting candidate genes in QTL studies). These other methods are more vulnerable to subjectivity and should be used carefully (Pavlidis et al, 2012).…”

Section: Moving Towards An Autosomal and Paternal Marker-based Definimentioning

confidence: 99%

Mining the pig genome to investigate the domestication process

et al. 2014

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Pig domestication began around 9000 YBP in the Fertile Crescent and Far East, involving marked morphological and genetic changes that occurred in a relatively short window of time. Identifying the alleles that drove the behavioural and physiological transformation of wild boars into pigs through artificial selection constitutes a formidable challenge that can only be faced from an interdisciplinary perspective. Indeed, although basic facts regarding the demography of pig domestication and dispersal have been uncovered, the biological substrate of these processes remains enigmatic. Considerable hope has been placed on new approaches, based on next-generation sequencing, which allow whole-genome variation to be analyzed at the population level. In this review, we provide an outline of the current knowledge on pig domestication by considering both archaeological and genetic data. Moreover, we discuss several potential scenarios of genome evolution under the complex mixture of demography and selection forces at play during domestication. Finally, we highlight several technical and methodological approaches that may represent significant advances in resolving the conundrum of livestock domestication.

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A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

Cited by 218 publications

References 67 publications

Evolutionary change during experimental ocean acidification

Evolutionary change during experimental ocean acidification

Genomic Patterns of Geographic Differentiation in Drosophila simulans

Mining the pig genome to investigate the domestication process

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