tRNA functional signatures classify plastids as late-branching cyanobacteria.

BackgroundEukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data.ResultsUsing Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies ("phyloclassifies") cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data.ConclusionsPhylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies

tRNA signatures reveal polyphyletic origins of streamlined SAR11 genomes among the alphaproteobacteria

Phylogenomic analyses are subject to bias from compositional convergence and noise from horizontal gene transfer (HGT). Compositional convergence is a likely cause of controversy regarding phylogeny of the SAR11 group of Alphaproteobacteria that have extremely streamlined, A+T-biased genomes. While careful modeling can reduce artifacts caused by convergence, the most consistent and robust phylogenetic signal in genomes may lie distributed among encoded functional features that govern macromolecular interactions. Here we develop a novel phyloclassification method based on signatures derived from bioinformatically defined tRNA Class-Informative Features (CIFs). tRNA CIFs are enriched for features that underlie tRNA-protein interactions. Using a simple tRNA-CIF-based phyloclassifier, we obtained results consistent with those of bias-corrected whole proteome phylogenomic studies, rejecting monophyly of SAR11 and affiliating most strains with Rhizobiales with strong statistical support. Yet SAR11 and Rickettsiales tRNA genes share distinct patterns of A+T-richness, as expected from their elevated genomic A+T compositions. Using conventional supermatrix methods on total tRNA sequence data, we could recover the artifactual result of a monophyletic SAR11 grouping with Rickettsiales. Thus tRNA CIF-based phyloclassification is more robust to base content convergence than supermatrix phylogenomics on whole tRNA sequences. Also, given the notoriously promiscuous HGT of aminoacyl-tRNA synthetases, tRNA CIF-based phyloclassification may be relatively robust to HGT of network components. We describe how unique features of tRNA-protein interaction networks facilitate the mining of traits governing macromolecular interactions from genomic data, and discuss why interaction-governing traits may be especially useful to solve difficult problems in microbial classification and phylogeny

Lexical stress and phonetic processing in word learning in 20- to 24-month-old English-learning children

PubMed ID: 2147719

Phonetic detail in the developing lexicon

Although infants show remarkable sensitivity to linguistically relevant phonetic variation in speech, young children sometimes appear not to make use of this sensitivity. Here, children's knowledge of the sound-forms of familiar words was assessed using a visual fixation task. Dutch 19-month-olds were shown pairs of pictures and heard correct pronunciations and mispronunciations of familiar words naming one of the pictures. Mispronunciations were word-initial in Experiment 1 and word-medial in Experiment 2, and in both experiments involved substituting one segment with [d] (a common sound in Dutch) or [g] (a rare sound). In both experiments, word recognition performance was better for correct pronunciations than for mispronunciations involving either substituted consonant. These effects did not depend upon children's knowledge of lexical or nonlexical phonological neighbors of the tested words. The results indicate the encoding of phonetic detail in words at 19 months

11-month-olds' knowledge of how familiar words sounds

During the first year of life, infants' perception of speech becomes tuned to the phonology of the native language, as revealed in laboratory discrimination and categorization tasks using syllable stimuli. However, the implications of these results for the development of the early vocabulary remain controversial, with some results suggesting that infants retain only vague, sketchy phonological representations of words. Five experiments using a preferential listening procedure tested Dutch 11-month-olds' responses to word, nonword and mispronounced-word stimuli. Infants listened longer to words than nonwords, but did not exhibit this response when words were mispronounced at onset or at offset. In addition, infants preferred correct pronunciations to onset mispronunciations. The results suggest that infants' encoding of familiar words includes substantial phonological detail

Lexical exposure and word-from encoding in 1.5-year-olds

In this study, 1.5-year-olds were taught a novel word. Some children were familiarized with the word's phonological form before learning the word's meaning. Fidelity of phonological encoding was tested in a picture-fixation task using correctly pronounced and mispronounced stimuli. Only children with additional exposure in familiarization showed reduced recognition performance given slight mispronunciations relative to correct pronunciations; children with fewer exposures did not. Mathematical modeling of vocabulary exposure indicated that children may hear thousands of words frequently enough for accurate encoding. The results provide evidence compatible with partial failure of phonological encoding at 19 months of age, demonstrate that this limitation in learning does not always hinder word recognition, and show the value of infants' word-form encoding in early lexical development

Making sense of infant familiarity and novelty responses to words at lexical onset

This study suggests that familiarity and novelty preferences in infant experimental tasks can in some instances be interpreted together as a single indicator of language advance. We provide evidence to support this idea based on our use of the auditory headturn preference paradigm to record responses to words likely to be either familiar or unfamiliar to infants. Fifty-nine 10-month-old infants were tested. The task elicited mixed preferences: Familiarity (longer average looks to the words likely to be familiar to the infants), novelty (longer average looks to the words likely to be unfamiliar) and no-preference (similar-length of looks to both type of words). The infants who exhibited either a familiarity or a novelty response were more advanced on independent indices of phonetic advance than the infants who showed no preference. In addition, infants exhibiting novelty responses were more lexically advanced than either the infants who exhibited familiarity or those who showed no-preference. The results provide partial support for Hunter and Ames' (1988) developmental model of attention in infancy and suggest caution when interpreting studies indexed to chronological age

Reverse production effect: Children recognize novel words better when they are heard rather than produced

This is the peer reviewed version of the following article: Tania S. Zamuner, Stephanie Strahm, Elizabeth Morin-Lessard, and Michael P. A. Page, 'Reverse production effect: children recognize novel words better when they are heard rather than produced', Developmental Science, which has been published in final form at DOI 10.1111/desc.12636. Under embargo until 15 November 2018. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.This research investigates the effect of production on 4.5- to 6-year-old children’s recognition of newly learned words. In Experiment 1, children were taught four novel words in a produced or heard training condition during a brief training phase. In Experiment 2, children were taught eight novel words, and this time training condition was in a blocked design. Immediately after training, children were tested on their recognition of the trained novel words using a preferential looking paradigm. In both experiments, children recognized novel words that were produced and heard during training, but demonstrated better recognition for items that were heard. These findings are opposite to previous results reported in the literature with adults and children. Our results show that benefits of speech production for word learning are dependent on factors such as task complexity and the developmental stage of the learner.Peer reviewedFinal Accepted Versio

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

OP9 is a yet-uncultivated bacterial lineage found in geothermal systems, petroleum reservoirs, anaerobic digesters and wastewater treatment facilities. Here we use single-cell and metagenome sequencing to obtain two distinct, nearly complete OP9 genomes, one constructed from single cells sorted from hot spring sediments and the other derived from binned metagenomic contigs from an in situ-enriched cellulolytic, thermophilic community. Phylogenomic analyses support the designation of OP9 as a candidate phylum for which we propose the name ‘Atribacteria’. Although a plurality of predicted proteins is most similar to those from Firmicutes, the presence of key genes suggests a diderm cell envelope. Metabolic reconstruction from the core genome suggests an anaerobic lifestyle based on sugar fermentation by Embden–Meyerhof glycolysis with production of hydrogen, acetate and ethanol. Putative glycohydrolases and an endoglucanase may enable catabolism of (hemi)cellulose in thermal environments. This study lays a foundation for understanding the physiology and ecological role of the ‘Atribacteria’.United States. National Aeronautics and Space Administration (Exobiology Grant EXO-NNX11AR78G)National Science Foundation (U.S.) (Grant MCB 0546865)National Science Foundation (U.S.) (Grant OISE 0968421)United States. Dept. of Energy (Grant DE-EE-0000716)Nevada Renewable Energy ConsortiumUnited States. Dept. of Energy. Office of Science. Joint Genome Institute (Contract DE-AC02-05CH11231