Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species. Using improved comparative genomics methods for detecting readthrough, we identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector, Anopheles gambiae, and of 51 additional Drosophila melanogaster stop codons, including several cases of double and triple readthrough and of readthrough of two adjacent stop codons. We find that most differences between the readthrough repertoires of the two species arose from readthrough gain or loss in existing genes, rather than birth of new genes or gene death; that readthrough-associated RNA structures are sometimes gained or lost while readthrough persists; that readthrough is more likely to be lost at TAA and TAG stop codons; and that readthrough is under continued purifying evolutionary selection in mosquito, based on population genetic evidence. We also determine readthrough-associated gene properties that predate readthrough, and identify differences in the characteristic properties of readthrough genes between clades. We estimate more than 600 functional readthrough stop codons in mosquito and 900 in fruit fly, provide evidence of readthrough control of peroxisomal targeting, and refine the phylogenetic extent of abundant readthrough as following divergence from centipede.

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“…The non-metric phylogenetic tree shown in figure 5 was extracted from Version 3 Draft synthetic tree of life (Hinchliff et al 2015). …”

Section: Methodsmentioning

confidence: 99%

Evolutionary Dynamics of Abundant Stop Codon Readthrough

et al. 2016

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“…Obtaining a fully resolved phylogenetic tree with branch lengths for diverse taxa is notoriously difficult given that homologous character data are often not available across disparate lineages, and tree topology can be unresolved (Chamberlain et al, 2012;Hinchcliff et al, 2015). Nonetheless, ignoring phylogenetic relatedness among species can affect meta-analytic results (Chamberlain et al, 2012).…”

Section: (4) Meta-analysismentioning

confidence: 99%

Developmental temperatures and phenotypic plasticity in reptiles: a systematic review and meta‐analysis

2017

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Early environments can profoundly influence an organism in ways that persist over its life. In reptiles, early thermal environments (nest temperatures) can impact offspring phenotype and survival in important ways, yet we still lack an understanding of whether general trends exist and the magnitude of impact. Understanding these patterns is important in predicting how climate change will affect reptile populations and the role of phenotypic plasticity in buffering populations. We compiled data from 175 reptile studies to examine, and quantify, the effect of incubation temperature on phenotype and survival. Using meta-analytic approaches (standardized mean difference between incubation treatments, Hedges' g), we show that across all trait types examined there is, on average, a moderate to large magnitude of effect of incubation temperatures (absolute effect: |g| = 0.75). Unsurprisingly, this influence was extremely large for incubation duration, as predicted, with warmer temperatures decreasing incubation time overall (g = -8.42). Other trait types, including behaviour, physiology, morphology, performance, and survival experienced reduced, but still mostly moderate to large effects, with particularly strong effects on survival. Moreover, the impact of incubation temperature persisted at least one-year post-hatching, suggesting that these effects have the potential to impact fitness in the long term. The magnitude of effect increased as the change in temperature increased (e.g. 6°C versus 2°C) in almost all cases, and tended to decrease when temperatures of the treatments fluctuated around a mean temperature compared to when they were constant. The effect also depended on the mid-temperature of the comparison, but not in consistent ways, with some traits experiencing the greatest effects at extreme temperatures, while others did not. The highly heterogeneous nature of the effects we observe, along with a large amount of unexplained variability, indicates that the shape of reaction norms between phenotype and temperature, along with ecological and/or experimental factors, are important when considering general patterns. Our analyses provide new insights into the effects of incubation environments on reptile phenotype and survival and allow general, albeit coarse, predictions for taxa experiencing warming nest temperatures under climatic change.

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“…Guild data are from FUNGuild (Nguyen et al, 2016) and genus-to-order matching is from Index Fungorum (http://www.indexfungorum.org). The tree topology was constructed manually following Hinchliff et al (2015) and Open Tree of Life (https://tree.opentreeoflife.org/opentree/opentree10.4@ott352914/Fungi). The phylogeny is order level and branch lengths are not time calibrated.…”

Section: Figmentioning

confidence: 99%

“…The most recent effort to build a comprehensive fungal tree of life that includes all recognized species was conducted by the Open Tree of Life project (https://blog.opentreeoflife.org). An important innovation was synthesizing information from published phylogenies and taxonomic classifications including taxa never before incorporated into phylogenies (Hinchliff et al, 2015). Currently, however, the fungal tree, although taxonomically comprehensive, is highly unresolved including numerous redundant names.…”

Section: Linking Fungal Diversity To Taxonomic Names Within Systmentioning

confidence: 99%

Fungal functional ecology: bringing a trait‐based approach to plant‐associated fungi

et al. 2019

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Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro‐organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait‐based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and ‐omics‐based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait‐based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.

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Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cited by 73 publications

References 44 publications

Evolutionary Dynamics of Abundant Stop Codon Readthrough

Evolutionary Dynamics of Abundant Stop Codon Readthrough

Developmental temperatures and phenotypic plasticity in reptiles: a systematic review and meta‐analysis

Fungal functional ecology: bringing a trait‐based approach to plant‐associated fungi

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