DNA and pacific commensal models : applications, construction, limitations, and future prospects

Components of the Pacific transported landscape have been used as proxies to trace the prehistoric movement of humans across the Pacific for almost two decades. Analyses of archaeological remains and DNA sequences of plants, animals, and microorganisms moved by or with humans have contributed to understanding prehistoric migration, trade, exchange, and sometimes revealed the geographic origins of particular plants and animals. This paper presents the basic elements of a DNA-based commensal model and discusses the phylogenetic and population genetic approaches these models employ. A clear delineation of the underlying assumptions of these models and the background information required to construct them have yet to appear in the literature. This not only provides a framework with which to construct a commensal model but also highlights gaps in current knowledge. The ways in which commensal models have enriched archaeological reconstructions will be highlighted, as will their current limitations. With these limitations in mind, options will be outlined for augmenting commensal models through the application of established techniques and new technologies in order to provide the best tools for reconstructing ancient human mobility and behavior in the Pacific and beyond

A typology of laterals in twelve English dialects

Allophonic patterns of variation in English laterals have been well studied in phonetics and phonology for decades, but establishing broad generalizations across varieties has proven challenging. In this study, we advance a typology of onset/coda lateral distinctions in English, using crowdsourced recordings from 95 speakers across twelve dialects of Anglo (UK) English. Results confirm the existence of dialects with and without onset/coda distinctions, and conditional inference trees are used to identity three main patterns in the data: (1) clear onsets and dark codas; (2) intermediate/dark onsets and dark codas, but with a positional distinction intact; (3) dark onsets and dark codas, with minimal or no distinctions between positions

Automatic recognition of schwa variants in spontaneous Hungarian speech

This paper analyzes the nature of the process involved in optional vowel reduction in Hungarian, and the acoustic structure of schwa variants in spontaneous speech. The study focuses on the acoustic patterns of both the basic realizations of Hungarian vowels and their realizations as neutral vowels (schwas), as well as on the design, implementation, and evaluation of a set of algorithms for the recognition of both types of realizations from the speech waveform. The authors address the question whether schwas form a unified group of vowels or they show some dependence on the originally intended articulation of the vowel they stand for. The acoustic study uses a database consisting of over 4,000 utterances extracted from continuous speech, and recorded from 19 speakers. The authors propose methods for the recognition of neutral vowels depending on the various vowels they replace in spontaneous speech. Mel-Frequency Cepstral Coefficients are calculated and used for the training of Hidden Markov Models. The recognition system was trained on 2,500 utterances and then tested on 1,500 utterances. The results show that a neutral vowel can be detected in 72% of all occurrences. Stressed and unstressed syllables can be distinguished in 92% of all cases. Neutralized vowels do not form a unified group of phoneme realizations. The pronunciation of schwa heavily depends on the original articulation configuration of the intended vowel

Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders

<p>Abstract</p> <p>Background</p> <p>Among the surface antigens of <it>Mycoplasma hominis</it>, the P120' protein was previously shown to elicit a subtle antibody response and appears to be relatively conserved. To get better insight into the evolution of this protein, we analysed the genetic variability of its surface exposed region in 27 <it>M. hominis </it>isolates recovered from the genital tract of Tunisian patients with infertility disorders.</p> <p>Methods</p> <p>All specimens were processed for culture and PCR amplification of the N-terminal surface exposed region of p120' gene. PCR products were sequenced to evaluate the genetic variability, to test for adaptive selection, and to infer the phylogenetic relationship of the <it>M. hominis </it>isolates.</p> <p>Results</p> <p>Sequence analysis showed a total of 25 single nucleotide polymorphisms distributed through 23 polymorphic sites, yielding 13 haplotypes. All but one mutation were confined within three distinct regions. Analysis of the amino acid-based phylogenetic tree showed a predominant group of 17 closely related isolates while the remaining appear to have significantly diverged.</p> <p>Conclusion</p> <p>By analysing a larger sample of <it>M. hominis </it>recovered from patients with urogenital infections, we show here that the P120' protein undergoes substantial level of genetic variability at its surface exposed region.</p

The Role of Native Language and the Fundamental Design of the Auditory System in Detecting Rhythm Changes

Accepted December 13, 2018Purpose: We investigated whether rhythm discrimination is mainly driven by the native language of the listener or by the fundamental design of the human auditory system and universal cognitive mechanisms shared by all people irrespective of rhythmic patterns in their native language. Method: In multiple experiments, we asked participants to listen to 2 continuous acoustic sequences and to determine whether their rhythms were the same or different (AX discrimination). Participants were native speakers of 4 languages with different rhythmic properties (Spanish, French, English, and German) to understand whether the predominant rhythmic patterns of a native language affect sensitivity, bias, and reaction time in detecting rhythmic changes in linguistic (Experiment 2) and in nonlinguistic (Experiments 1 and 2) acoustic sequences. We examined sensitivity and bias measures, as well as reaction times. We also computed Bayes factors in order to assess the effect of native language. Results: All listeners performed better (i.e., responded faster and manifested higher sensitivity and accuracy) when detecting the presence or absence of a rhythm change when the 1st stimulus in an AX test pair exhibited regular rhythm (i.e., a syllable-timed rhythmic pattern) than when the 1st stimulus exhibited irregular rhythm (i.e., stress-timed rhythmic pattern). This result pattern was observed both on linguistic and nonlinguistic stimuli and was not modulated by the native language of the participant. Conclusion: We conclude that rhythm change detection is a fundamental function of a processing system that relies on general auditory mechanisms and is not modulated by linguistic experience.The authors acknowledge support from Spanish Ministry of Economy and Competitiveness Grant PSI2017-82563-P (awarded to A. G. S.), the “Severo Ochoa” Programme for Centres/Units of Excellence in R&D Grant SEV-2015-490 (BCBL), and the Basque Foundation for Science Grant IKERBASQUE (awarded to A. G. S. and M. O.). D. M. G. was supported by Grant PIA/Basal FB0003 from the Chilean Research Council. L. P. was supported by the Spanish Ministry of Economy and Competitiveness via Juan de la Cierva fellowship

Investigating the global dispersal of chickens in prehistory using ancient mitochondrial dna signatures

Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testingExcavations in Fais by MI were made possible by a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science. DB gratefully acknowledges support from the Marsden Fund, and the Allan Wilson Centre for Molecular Ecology and Evolution. During the course of this research AS was supported by a Postgraduate Scholarship from the University of Auckland and a Fellowship from the Allan Wilson Centre for Molecular Ecology and Evolutio

Comparing phoneme frequency, age of acquisition, and loss in aphasia:Implications for phonological universals

Phonological complexity may be central to the nature of human language. It may shape the distribution of phonemes and phoneme sequences within languages, but also determine age of acquisition and susceptibility to loss in aphasia. We evaluated this claim using frequency statistics derived from a corpus of phonologically transcribed Italian words (phonitalia, available at phonitalia,org), rankings of phoneme age of acquisition (AoA) and rate of phoneme errors in patients with apraxia of speech (AoS) as an indication of articulatory complexity. These measures were related to cross-linguistically derived markedness rankings. We found strong correspondences. AoA, however, was predicted by both apraxic errors and frequency, suggesting independent contributions of these variables. Our results support the reality of universal principles of complexity. In addition they suggest that these complexity principles have articulatory underpinnings since they modulate the production of patients with AoS, but not the production of patients with more central phonological difficulties

Linguistic Factors Affecting Moraic Duration in Spontaneous Japanese

Japanese is often referred to as a mora-timed language (Ladefoged 1975): the mora has been described as the psychological prosodic unit in the spoken language, and it is the metric unit of traditional poetry (Bloch 1950). However, it is clear that mo- rae are not strictly isochronous units (Beckman 1982). Thus, experimental studies have focused on detecting compensation effects that make average mora durations more equal through the modulation of the inherent duration of the segments involved (Han 1962; Port, Al-Ani, Maeda 1980; Homma 1981; Hoequist 1983a; 1983b; Warner, Arai 2001). Kawahara (2017) used the Corpus of Spontaneous Japanese to verify whether the dura- tional compensation effect within a /CV/ mora occurs in natural speech, in addition to read speech in the lab. He observed a statistically significant compensation effect of /CV/ morae, in which vowel duration tends to vary in response to the duration of the preced- ing consonant. However, as the same author has pointed out, the compensation is not absolute because there are several linguistic factors that potentially affect segments’ duration profiles. This study will support the idea that moraic isochrony does not occur in spontaneous Japanese by presenting empirical data on how linguistic factors can considerably affect variation in the average duration of morae

Life on Arginine for Mycoplasma hominis: Clues from Its Minimal Genome and Comparison with Other Human Urogenital Mycoplasmas

Mycoplasma hominis is an opportunistic human mycoplasma. Two other pathogenic human species, M. genitalium and Ureaplasma parvum, reside within the same natural niche as M. hominis: the urogenital tract. These three species have overlapping, but distinct, pathogenic roles. They have minimal genomes and, thus, reduced metabolic capabilities characterized by distinct energy-generating pathways. Analysis of the M. hominis PG21 genome sequence revealed that it is the second smallest genome among self-replicating free living organisms (665,445 bp, 537 coding sequences (CDSs)). Five clusters of genes were predicted to have undergone horizontal gene transfer (HGT) between M. hominis and the phylogenetically distant U. parvum species. We reconstructed M. hominis metabolic pathways from the predicted genes, with particular emphasis on energy-generating pathways. The Embden–Meyerhoff–Parnas pathway was incomplete, with a single enzyme absent. We identified the three proteins constituting the arginine dihydrolase pathway. This pathway was found essential to promote growth in vivo. The predicted presence of dimethylarginine dimethylaminohydrolase suggested that arginine catabolism is more complex than initially described. This enzyme may have been acquired by HGT from non-mollicute bacteria. Comparison of the three minimal mollicute genomes showed that 247 CDSs were common to all three genomes, whereas 220 CDSs were specific to M. hominis, 172 CDSs were specific to M. genitalium, and 280 CDSs were specific to U. parvum. Within these species-specific genes, two major sets of genes could be identified: one including genes involved in various energy-generating pathways, depending on the energy source used (glucose, urea, or arginine) and another involved in cytadherence and virulence. Therefore, a minimal mycoplasma cell, not including cytadherence and virulence-related genes, could be envisaged containing a core genome (247 genes), plus a set of genes required for providing energy. For M. hominis, this set would include 247+9 genes, resulting in a theoretical minimal genome of 256 genes