Networks of lexical borrowing and lateral gene transfer in language and genome evolution.
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ABSTRACT:
SUBMITTER: List JM
PROVIDER: S-EPMC3910147 | biostudies-literature | 2014 Feb
REPOSITORIES: biostudies-literature
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Project description:Lateral gene transfer is an important mechanism of natural variation among prokaryotes, but the significance of its quantitative contribution to genome evolution is debated. Here, we report networks that capture both vertical and lateral components of evolutionary history among 539,723 genes distributed across 181 sequenced prokaryotic genomes. Partitioning of these networks by an eigenspectrum analysis identifies community structure in prokaryotic gene-sharing networks, the modules of which do not correspond to a strictly hierarchical prokaryotic classification. Our results indicate that, on average, at least 81 +/- 15% of the genes in each genome studied were involved in lateral gene transfer at some point in their history, even though they can be vertically inherited after acquisition, uncovering a substantial cumulative effect of lateral gene transfer on longer evolutionary time scales.
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| S-EPMC2628915 | biostudies-literature
Project description:BackgroundLarge scale genome arrangement, such as whole gene insertion/deletion, plays an important role in bacterial genome evolution. Various methods have been employed to study the dynamic process of gene insertions and deletions, such as parsimony methods and maximum likelihood methods. Previous maximum likelihood studies have assumed that the rate of gene insertions/deletions is constant over different genes. This assumption is unrealistic. For instance, it has been shown that informational genes are less likely to be laterally transferred than non-informational genes. However, how much of the variation in gene transfer rates is due to the difference between informational genes and non-informational genes is unclear. In this study, a Gamma-distribution was incorporated in the likelihood estimation by considering rate variation for gene insertions/deletions between genes. This makes it possible to address whether a difference between informational genes and non-informational genes is the main contributor to rate variation of lateral gene transfers.ResultsThe results show that models incorporating rate variation fit the data better than do constant rate models in many phylogenetic groups. Even though informational genes are less likely to be laterally transferred than non-informational genes, the degree of rate variation for insertions/deletions did not change dramatically and remained high even when informational genes were excluded from the study. This suggests that the variation in rate of insertions/deletions is not due mainly to the simple difference between informational genes and non-informational genes. Among genes that are not classified as informational and among the informational genes themselves, there are still large differences in the rates that these genes are inserted and deleted.ConclusionWhile the difference in informational gene rates contributes to rate variation, it is only a small fraction of the variation present; instead, a substantial amount of rate variation for insertions/deletions remains among both informational genes and among non-informational genes.
| S-EPMC2426709 | biostudies-literature
Project description:When describing variation at the lexical level in sign languages, researchers often distinguish between phonological and lexical variants, using the following principle: if two signs differ in only one of the major phonological components (handshape, orientation, movement, location), then they are considered phonological variants, otherwise they are considered separate lexemes. We demonstrate that this principle leads to contradictions in some simple and more complex cases of variation. We argue that it is useful to visualize the relations between variants as graphs, and we describe possible networks of variants that can arise using this visualization tool. We further demonstrate that these scenarios in fact arise in the case of variation in color terms and kinship terms in Russian Sign Language (RSL), using a newly created database of lexical variation in RSL. We show that it is possible to develop a set of formal rules that can help distinguish phonological and lexical variation also in the problematic scenarios. However, we argue that it might be a mistake to dismiss the actual patterns of variant relations in order to arrive at the binary lexical vs. phonological variant opposition.
| S-EPMC8766300 | biostudies-literature
Project description:The amount of lateral gene transfer (LGT) that has occurred in microbial evolution is heavily debated. Efforts to quantify LGT through gene-tree comparisons have delivered estimates that between 2% and 60% of all prokaryotic genes have been affected by LGT, the 30-fold discrepancy reflecting differences among gene samples studied and uncertainties inherent in phylogenetic reconstruction. Here we present a simple method that is independent of gene-tree comparisons to estimate the LGT rate among sequenced prokaryotic genomes. If little or no LGT has occurred during evolution, ancestral genome sizes would become unrealistically large, whereas too much LGT would render them far too small. We determine the amount of LGT that is necessary and sufficient to bring the distribution of inferred ancestral genome sizes into agreement with that observed among modern microbes. Rather than testing for phylogenetic congruence or lack thereof across genes, we assume that all gene trees are compatible; hence, our method delivers very conservative lower-bound estimates of the average LGT rate. The results indicate that among 57,670 gene families distributed across 190 sequenced genomes, at least two-thirds and probably all, have been affected by LGT at some time in their evolutionary past. A component of common ancestry nonetheless remains detectable in gene distribution patterns. We estimate the minimum lower bound for the average LGT rate across all genes as 1.1 LGT events per gene family and gene family lifespan and this minimum rate increases sharply when genes present in only a few genomes are excluded from the analysis.
| S-EPMC1783406 | biostudies-literature
Project description:All languages borrow words from other languages. Some languages are more prone to borrowing, while others borrow less, and different domains of the vocabulary are unequally susceptible to borrowing. Languages typically borrow words when a new concept is introduced, but languages may also borrow a new word for an already existing concept. Linguists describe two causalities for borrowing: need, i.e., the internal pressure of borrowing a new term for a concept in the language, and prestige, i.e., the external pressure of borrowing a term from a more prestigious language. We investigate lexical loans in a dataset of 104 concepts in 115 Eurasian languages from 7 families occupying a coherent contact area of the Eurasian landmass, of which Indo-European languages from various periods constitute a majority. We use a cognacy-coded dataset, which identifies loan events including a source and a target language. To avoid loans for newly introduced concepts in languages, we use a list of lexical concepts that have been in use at least since the Chalcolithic (4000-3000 BCE). We observe that the rates of borrowing are highly variable among concepts, lexical domains, languages, language families, and time periods. We compare our results to those of a global sample and observe that our rates are generally lower, but that the rates between the samples are significantly correlated. To test the causality of borrowing, we use two different ranks. Firstly, to test need, we use a cultural ranking of concepts by their mobility (of nature items) or their labour intensity and "distance-from-hearth" (of culture items). Secondly, to test prestige, we use a power ranking of languages by their socio-cultural status. We conclude that the borrowability of concepts increases with increasing mobility (nature), and with increased labour intensity and "distance-from-hearth" (culture). We also conclude that language prestige is not correlated with borrowability in general (all languages borrow, independently of prestige), but prestige predicts the directionality of borrowing, from a more prestigious language to a less prestigious one. The process is not constant over time, with a larger inequality during the ancient and modern periods, but this result may depend on the status of the data (non-prestigious languages often remain unattested). In conclusion, we observe that need and prestige compete as causes of lexical borrowing.
| S-EPMC6821065 | biostudies-literature
Project description:BackgroundThe Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan.ResultsAc encodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms.ConclusionsOur analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.
| S-EPMC4053784 | biostudies-literature
Project description:Knowledge in the human mind exhibits a dualistic vector/network nature. Modelling words as vectors is key to natural language processing, whereas networks of word associations can map the nature of semantic memory. We reconcile these paradigms-fragmented across linguistics, psychology and computer science-by introducing FEature-Rich MUltiplex LEXical (FERMULEX) networks. This novel framework merges structural similarities in networks and vector features of words, which can be combined or explored independently. Similarities model heterogenous word associations across semantic/syntactic/phonological aspects of knowledge. Words are enriched with multi-dimensional feature embeddings including frequency, age of acquisition, length and polysemy. These aspects enable unprecedented explorations of cognitive knowledge. Through CHILDES data, we use FERMULEX networks to model normative language acquisition by 1000 toddlers between 18 and 30 months. Similarities and embeddings capture word homophily via conformity, which measures assortative mixing via distance and features. Conformity unearths a language kernel of frequent/polysemous/short nouns and verbs key for basic sentence production, supporting recent evidence of children's syntactic constructs emerging at 30 months. This kernel is invisible to network core-detection and feature-only clustering: It emerges from the dual vector/network nature of words. Our quantitative analysis reveals two key strategies in early word learning. Modelling word acquisition as random walks on FERMULEX topology, we highlight non-uniform filling of communicative developmental inventories (CDIs). Biased random walkers lead to accurate (75%), precise (55%) and partially well-recalled (34%) predictions of early word learning in CDIs, providing quantitative support to previous empirical findings and developmental theories.
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Project description:Bacteriophages are recognized DNA vectors and transduction is considered as a common mechanism of lateral gene transfer (LGT) during microbial evolution. Anecdotal events of phage-mediated gene transfer were studied extensively, however, a coherent evolutionary viewpoint of LGT by transduction, its extent and characteristics, is still lacking. Here we report a large-scale evolutionary reconstruction of transduction events in 3982 genomes. We inferred 17 158 recent transduction events linking donors, phages and recipients into a phylogenomic transduction network view. We find that LGT by transduction is mostly restricted to closely related donors and recipients. Furthermore, a substantial number of the transduction events (9%) are best described as gene duplications that are mediated by mobile DNA vectors. We propose to distinguish this type of paralogy by the term autology. A comparison of donor and recipient genomes revealed that genome similarity is a superior predictor of species connectivity in the network in comparison to common habitat. This indicates that genetic similarity, rather than ecological opportunity, is a driver of successful transduction during microbial evolution. A striking difference in the connectivity pattern of donors and recipients shows that while lysogenic interactions are highly species-specific, the host range for lytic phage infections can be much wider, serving to connect dense clusters of closely related species. Our results thus demonstrate that DNA transfer via transduction occurs within the context of phage-host specificity, but that this tight constraint can be breached, on rare occasions, to produce long-range LGTs of profound evolutionary consequences.
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Project description:Mycobacterium tuberculosis is a high GC Gram-positive member of the actinobacteria. The mycobacterial cell wall is composed of a complex assortment of lipids and is the interface between the bacterium and its environment. The biosynthesis of fatty acids plays an essential role in the formation of cell wall components, in particular mycolic acids, which have been targeted by many of the drugs used to treat M. tuberculosis infection. M. tuberculosis has approximately 250 genes involved in fatty acid metabolism, a much higher proportion than in any other organism. In silico methods have been used to compare the genome of M. tuberculosis CDC1551 to a database of 58 complete bacterial genomes. The resulting alignments were scanned for genes specifically involved in fatty acid biosynthetic pathway I. Phylogenetic analysis of these alignments was used to investigate horizontal gene transfer, gene duplication, and adaptive evolution. It was found that of the eight gene families examined, five of the phylogenies reconstructed suggest that the actinobacteria have a closer relationship with the alpha-proteobacteria than expected. This is either due to either an ancient transfer of genes or deep paralogy and subsequent retention of the genes in unrelated lineages. Additionally, adaptive evolution and gene duplication have been an influence in the evolution of the pathway. This study provides a key insight into how M. tuberculosis has developed its unique fatty acid synthetic abilities.
| S-EPMC193559 | biostudies-literature