Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution

Manda, Prashanti; Balhoff, James P.; Lapp, Hilmar; Mabee, Paula M.

doi:10.1002/dvg.22878

Cited by 23 publications

(26 citation statements)

References 72 publications

(81 reference statements)

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“…We also looked for overlap between introgressed candidate regions be-tween tests involving S. galilaeus MM and S. galilaeus CR, another pattern suggestive of a hybrid swarm after initial colonization. For each of these regions, we looked for annotated genes using the well annotated NCBI Oreochromis Annotation Release 102 and searched their gene ontology in the phenotype database Phenoscape (Mabee et al 2012;Midford et al 2013;Manda et al 2015;Edmunds et al 2016) and AmiGO2 (Balsa-Canto et al 2016) for functions related to the trophic specializations and observed morphological differences among specialist species, such as skeletal system, circulatory system, metabolism, or pigmentation. It is possible that some of the topologies consistent with introgression with outgroups and introgressed regions from f d tests stem from introgression from unsampled or extinct populations rather than S. galilaeus MM or S.galilaeus CR directly; however, this should not change the overall conclusion that secondary gene flow events occurred in the history of the radiation or the functional support for the importance of the introgressed regions that we detected.…”

Section: Across the Genomementioning

confidence: 99%

Don't throw out the sympatric speciation with the crater lake water: fine-scale investigation of introgression provides equivocal support for causal role of secondary gene flow in one of the clearest examples of sympatric speciation

2018

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Genomic data has revealed complex histories of colonization and repeated gene flow previously unrecognized in some of the most celebrated examples of sympatric speciation and radiation. However, much of the evidence for secondary gene flow into these radiations comes from summary statistics calculated from sparse genomic sampling without knowledge of which specific genomic regions introgressed. This tells us little about how gene flow potentially influenced sympatric diversification. Here, we investigated whole genomes of Barombi Mbo crater lake cichlids for fine‐scale patterns of introgression with neighboring riverine cichlid populations. We found evidence of secondary gene flow into the radiation scattered across <0.24% of the genome; however, from our analyses, it is not clear if the functional diversity in these regions contributed to the ecological, sexual, and morphological diversity found in the lake. Unlike similar studies, we found no obvious candidate genes for adaptive introgression and we cannot rule out that secondary gene flow was predominantly neutral with respect to the diversification process. We also found evidence for differential assortment of ancestral polymorphisms found in riverine populations between sympatric sister species, suggesting the presence of an ancestral hybrid swarm. Although the history of gene flow and colonization is more complicated than previously assumed, the lack of compelling evidence for secondary gene flow's role in species diversification suggests that we should not yet rule out one of the most celebrated examples of sympatric speciation in nature without a more thorough investigation of the timing and functional role of each introgressed region.

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Section: Across the Genomementioning

confidence: 99%

Don't throw out the sympatric speciation with the crater lake water: fine-scale investigation of introgression provides equivocal support for causal role of secondary gene flow in one of the clearest examples of sympatric speciation

2018

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“…26 In future work, we intend to explore the impact of homology reasoning on measurement of semantic similarity for phenotypes that vary naturally among vertebrate lineages, such as those in the Phenoscape Knowledgebase. 27 Independent of the use of homology axioms, some of the semantic similarity statistics that we examined showed relatively poor discrimination between orthologs and non-orthologs, suggesting the need to take a critical look at the biological accuracy of different phenotype semantic similarity measures.…”

Section: Discussionmentioning

confidence: 92%

Investigating the Importance of Anatomical Homology for Cross-Species Phenotype Comparisons Using Semantic Similarity

Manda¹,

Mungall²,

Balhoff

et al. 2015

Biocomputing 2016

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There is growing use of ontologies for the measurement of cross-species phenotype similarity. Such similarity measurements contribute to diverse applications, such as identifying genetic models for human diseases, transferring knowledge among model organisms, and studying the genetic basis of evolutionary innovations. Two organismal features, whether genes, anatomical parts, or any other inherited feature, are considered to be homologous when they are evolutionarily derived from a single feature in a common ancestor. A classic example is the homology between the paired fins of fishes and vertebrate limbs. Anatomical ontologies that model the structural relations among parts may fail to include some known anatomical homologies unless they are deliberately added as separate axioms. The consequences of neglecting known homologies for applications that rely on such ontologies has not been well studied. Here, we examine how semantic similarity is affected when external homology knowledge is included. We measure phenotypic similarity between orthologous and non-orthologous gene pairs between humans and either mouse or zebrafish, and compare the inclusion of real with faux homology axioms. Semantic similarity was preferentially increased for orthologs when using real homology axioms, but only in the more divergent of the two species comparisons (human to zebrafish, not human to mouse), and the relative increase was less than 1% to non-orthologs. By contrast, inclusion of both real and faux random homology axioms preferentially increased similarities between genes that were initially more dissimilar in the other comparisons. Biologically meaningful increases in semantic similarity were seen for a select subset of gene pairs. Overall, the effect of including homology axioms on cross-species semantic similarity was modest at the levels of divergence examined here, but our results hint that it may be greater for more distant species comparisons.

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“…Moving on to the pink cluster, we see "data integration", "database", "semantic web", and ontologies being used for the study of phenotypes, evolution, and phylogenies. This cluster points to the increasing applications of ontologies and data integration for the study of evolutionary phenotypes [16]. The grey cluster is largely related to proteomics, systems biology, functional genomics, analysis of microrna etc.…”

Section: Keyword-based Analysismentioning

confidence: 99%

What’s Hot and What’s Not? - Exploring Trends in Bioinformatics Literature Using Topic Modeling and Keyword Analysis

Hahn¹,

Mohanty²,

Manda³

2017

Bioinformatics Research and Applications

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Abstract. Scientists exploring a new area of research are interested to know the "hot" topics in that area in order to make informed choices. With exponential growth in scientific literature, identifying such trends manually is not easy. Topic modeling has emerged as an effective approach to analyze large volumes of text. While this approach has been applied on literature in other scientific areas, there has been no formal analysis of bioinformatics literature.Here, we conduct keyword and topic model-based analysis on bioinformatics literature starting from 1998 to 2016. We identify top keywords and topics per year and explore temporal popularity trends of those keywords/areas. Network analysis was conducted to identify clusters of sub-areas/topics in bioinformatics. We found that "big-data", "next generation sequencing", and "cancer" all experienced exponential increase in popularity over the years. On the other hand, interest in drug discovery has plateaued after the early 2000s.

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Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution

Cited by 23 publications

References 72 publications

Don't throw out the sympatric speciation with the crater lake water: fine-scale investigation of introgression provides equivocal support for causal role of secondary gene flow in one of the clearest examples of sympatric speciation

Don't throw out the sympatric speciation with the crater lake water: fine-scale investigation of introgression provides equivocal support for causal role of secondary gene flow in one of the clearest examples of sympatric speciation

Investigating the Importance of Anatomical Homology for Cross-Species Phenotype Comparisons Using Semantic Similarity

What’s Hot and What’s Not? - Exploring Trends in Bioinformatics Literature Using Topic Modeling and Keyword Analysis

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