Inferring linguistic transmission between generations at the scale of individuals

AbstractHistorical linguistics highly benefited from recent methodological advances inspired by phylogenetics. Nevertheless, no currently available method uses contemporaneous within-population linguistic diversity to reconstruct the history of human populations. Here, we develop an approach inspired from population genetics to perform historical linguistic inferences from linguistic data sampled at the individual scale, within a population. We built four demographic models of linguistic transmission at this scale, each model differing by the number of teachers involved during the language acquisition, and the relative roles of these teachers. We then compared the simulated data obtained with these models with real contemporaneous linguistic data sampled in Tajik speakers in Central Asia, an area known for its high within-population linguistic diversity, using approximate Bayesian computation methods. With these statistical methods, we were able to select the models that best explained the data, and inferred the best-fitting parameters under these selected models, demonstrating the feasibility of using contemporaneous within-population linguistic diversity to infer historical features of human cultural evolution.

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Genetic and linguistic histories in Central Asia inferred using approximate Bayesian computations

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2017.0706 ◽

2017 ◽

Vol 284 (1861) ◽

pp. 20170706 ◽

Cited By ~ 7

Author(s):

Valentin Thouzeau ◽

Philippe Mennecier ◽

Paul Verdu ◽

Frédéric Austerlitz

Keyword(s):

Central Asia ◽

Linguistic Diversity ◽

Past History ◽

Genetic Data ◽

Human Populations ◽

Language Diversity ◽

Methodological Framework ◽

The Past ◽

Approximate Bayesian ◽

Future Work

Linguistic and genetic data have been widely compared, but the histories underlying these descriptions are rarely jointly inferred. We developed a unique methodological framework for analysing jointly language diversity and genetic polymorphism data, to infer the past history of separation, exchange and admixture events among human populations. This method relies on approximate Bayesian computations that enable the identification of the most probable historical scenario underlying each type of data, and to infer the parameters of these scenarios. For this purpose, we developed a new computer program PopLingSim that simulates the evolution of linguistic diversity, which we coupled with an existing coalescent-based genetic simulation program, to simulate both linguistic and genetic data within a set of populations. Applying this new program to a wide linguistic and genetic dataset of Central Asia, we found several differences between linguistic and genetic histories. In particular, we showed how genetic and linguistic exchanges differed in the past in this area: some cultural exchanges were maintained without genetic exchanges. The methodological framework and the linguistic simulation tool developed here can be used in future work for disentangling complex linguistic and genetic evolutions underlying human biological and cultural histories.

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Helicobacter pylori’s historical journey through Siberia and the Americas

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2015523118 ◽

2021 ◽

Vol 118 (25) ◽

pp. e2015523118

Author(s):

Yoshan Moodley ◽

Andrea Brunelli ◽

Silvia Ghirotto ◽

Andrey Klyubin ◽

Ayas S. Maady ◽

...

Keyword(s):

Native Americans ◽

Ethnically Diverse ◽

Northern Eurasia ◽

Human Populations ◽

Bering Strait ◽

Demographic Bottleneck ◽

History Of ◽

Low Levels ◽

Approximate Bayesian ◽

H Pylori

The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.

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Lexicostatistics avant la lettre

Language or Dialect? ◽

10.1093/oso/9780198845713.003.0014 ◽

2020 ◽

pp. 183-192

Author(s):

Raf Van Rooy

Keyword(s):

Eighteenth Century ◽

Linguistic Diversity ◽

Linguistic Distance ◽

Linguistic Data ◽

Limited Success ◽

Innovative Methodology ◽

History Of ◽

Basic Vocabulary

Chapter 14 presents a case study from an angle different from that of philology, taking the historian Johann Christoph Gatterer’s ideas on linguistic diversity as its object. It not only serves as another telling example of the tendency towards systematization, but also, and especially, represents a climax in eighteenth-century attempts at rationalizing the language / dialect distinction. Proposing an embryonic lexicostatistic method, Gatterer tried to find an objective way to use linguistic data in writing an encompassing history of tribes and nations, in particular their prehistory. Starting from a basic vocabulary set, Gatterer attempted to quantify linguistic distance. In doing so, he divided the kinship continuum into four sections: unrelated languages, related languages, dialects, and closely related dialects. His innovative methodology, prefiguring modern lexicostatistic approaches, had only limited success, however. Gatterer failed to put it into practice, and the historian was criticized for his ahistorical method by the grammarian Johann Christoph Adelung.

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Comparison of single genome and allele frequency data reveals discordant demographic histories

10.1101/182899 ◽

2017 ◽

Author(s):

Annabel C. Beichman ◽

Tanya N. Phung ◽

Kirk E. Lohmueller

Keyword(s):

Statistical Power ◽

Empirical Test ◽

Demographic History ◽

Empirical Studies ◽

Simulated Data ◽

Wide Distribution ◽

Model Organisms ◽

Human Populations ◽

Whole Genome ◽

Demographic Models

ABSTRACTInference of demographic history from genetic data is a primary goal of population genetics of model and non-model organisms. Whole genome-based approaches such as the Pairwise/Multiple Sequentially Markovian Coalescent (PSMC/MSMC) methods use genomic data from one to four individuals to infer the demographic history of an entire population, while site frequency spectrum (SFS)-based methods use the distribution of allele frequencies in a sample to reconstruct the same historical events. Although both methods are extensively used in empirical studies and perform well on data simulated under simple models, there have been only limited comparisons of them in more complex and realistic settings. Here we use published demographic models based on data from three human populations (Yoruba (YRI), descendants of northwest-Europeans (CEU), and Han Chinese (CHB)) as an empirical test case to study the behavior of both inference procedures. We find that several of the demographic histories inferred by the whole genome-based methods do not predict the genome-wide distribution of heterozygosity nor do they predict the empirical SFS. However, using simulated data, we also find that the whole genome methods can reconstruct the complex demographic models inferred by SFS-based methods, suggesting that the discordant patterns of genetic variation are not attributable to a lack of statistical power, but may reflect unmodeled complexities in the underlying demography. More generally, our findings indicate that demographic inference from a small number of genomes, routine in genomic studies of nonmodel organisms, should be interpreted cautiously, as these models cannot recapitulate other summaries of the data.

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Reconstructing contact network parameters from viral phylogenies

10.1101/050435 ◽

2016 ◽

Author(s):

Rosemary M. McCloskey ◽

Richard H. Liang ◽

Art F.Y. Poon

Keyword(s):

Sequential Monte Carlo ◽

Preferential Attachment ◽

Structural Parameters ◽

Simulated Data ◽

Network Models ◽

Similarity Score ◽

Contact Network ◽

Parameter Estimates ◽

Human Populations ◽

Approximate Bayesian

AbstractModels of the spread of disease in a population often make the simplifying assumption that the population is homogeneously mixed, or is divided into homogeneously mixed compartments. However, human populations have complex structures formed by social contacts, which can have a significant influence on the rate of epidemic spread. Contact network models capture this structure by explicitly representing each contact which could possibly lead to a transmission. We developed a method based on kernel approximate Bayesian computation (kernel-ABC) for estimating structural parameters of the contact network underlying an observed viral phylogeny. The method combines adaptive sequential Monte Carlo for ABC, Gillespie simulation for propagating epidemics though networks, and a kernel-based tree similarity score. We used the method to fit the Barabási-Albert network model to simulated transmission trees, and also applied it to viral phylogenies estimated from five published HIV sequence datasets. On simulated data, we found that the preferential attachment power and the number of infected nodes in the network can often be accurately estimated. On the other hand, the mean degree of the network, as well as the total number of nodes, were not estimable with kernel-ABC. We observed substantial heterogeneity in the parameter estimates on real datasets, with point estimates for the preferential attachment power ranging from 0.06 to 1.05. These results underscore the importance of considering contact structures when performing phylodynamic inference. Our method offers the potential to quantitatively investigate the contact network structure underlying viral epidemics.

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Complex genetic admixture histories reconstructed with Approximate Bayesian Computations

10.1101/761452 ◽

2019 ◽

Author(s):

Cesar A. Fortes-Lima ◽

Romain Laurent ◽

Valentin Thouzeau ◽

Bruno Toupance ◽

Paul Verdu

Keyword(s):

Maximum Likelihood ◽

Evolutionary Process ◽

Genetic Admixture ◽

Human Populations ◽

Model Parameter ◽

Parameter Estimations ◽

Maximum Likelihood Methods ◽

History Of ◽

Approximate Bayesian ◽

Parameter Values

ABSTRACTAdmixture is a fundamental evolutionary process that has influenced genetic patterns in numerous species. Maximum-likelihood approaches based on allele frequencies and linkage-disequilibrium have been extensively used to infer admixture processes from dense genome-wide datasets mostly in human populations. Nevertheless, complex admixture histories, beyond one or two pulses of admixture, remain methodologically challenging to reconstruct, especially when large datasets are unavailable. We develop an Approximate Bayesian Computations (ABC) framework to reconstruct complex admixture histories from independent genetic markers. We built the software package MetHis to simulate independent SNPs in a two-way admixed population for scenarios with multiple admixture pulses, or monotonically decreasing or increasing admixture at each generation; drawing model-parameter values from prior distributions set by the user. For each simulated dataset, we calculate 24 summary statistics describing genetic diversity and moments of individual admixture fraction. We coupled MetHis with existing ABC algorithms and investigate the admixture history of an African American and a Barbadian population. Results show that Random-Forest ABC scenario-choice, followed by Neural-Network ABC posterior parameter estimation, can distinguish most complex admixture scenarios and provide accurate model-parameter estimations. For both admixed populations, we find that monotonically decreasing contributions over time, from the European and African sources, explain the observed data more accurately than multiple admixture pulses. Furthermore, we find contrasted trajectories of introgression decay from the European and African sources between the two admixed populations. This approach will allow for reconstructing detailed admixture histories in numerous populations and species, particularly when maximum-likelihood methods are intractable.

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Strontium isotopes as an indicator of human migration – easy questions, difficult answers

Anthropological Review ◽

10.1515/anre-2015-0010 ◽

2015 ◽

Vol 78 (2) ◽

pp. 133-156 ◽

Cited By ~ 13

Author(s):

Krzysztof Szostek ◽

Katarzyna Mądrzyk ◽

Beata Cienkosz-Stepańczak

Keyword(s):

Strontium Isotopes ◽

Climatic Changes ◽

Human Migration ◽

Human Populations ◽

Animal Tissues ◽

Human Species ◽

Trace Back ◽

History Of ◽

The Individual ◽

Isotope Analyses

AbstractIsotope analyses of bones and teeth allow us to study phenomena which occurred in the history of human species and which are difficult to capture by traditional anthropological methods. Measuring oxygen, nitrogen and carbon isotope levels in the skeleton makes it possible to reconstruct climatic changes, diet and/or the weaning process. Among isotopes used in such analyses are strontium isotopes, helpful in analysing migration and studying the mobility of historical and prehistoric human populations. In this respect, the proportion of two isotopes, the heavier87Sr and the lighter86Sr, is measured, following their extraction from the bioapatite of the bone mineral. Released from rocks in the weathering process, strontium permeates individual components of inanimate and animate environments, and then finds its way, together with food, to the human body. Thanks to comprehensive environmental studies and the measurement of the strontium ratio87Sr/86Sr in various animal tissues it is possible to determine the local isotope background for the environment. Values obtained by analysing human skeletons referenced against the range of environmental isotope variability enable researchers to trace back the location inhabited by the individual or group.

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Cattle demographic history modelled from autosomal sequence variation

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2010.0103 ◽

2010 ◽

Vol 365 (1552) ◽

pp. 2531-2539 ◽

Cited By ~ 41

Author(s):

Caitriona Murray ◽

Emilia Huerta-Sanchez ◽

Fergal Casey ◽

Daniel G. Bradley

Keyword(s):

South Asian ◽

Sequence Variation ◽

Bos Taurus ◽

Demographic History ◽

Bos Indicus ◽

Frequency Spectra ◽

Demographic Models ◽

History Of ◽

Best Fitting ◽

Fitting Model

The phylogeography of cattle genetic variants has been extensively described and has informed the history of domestication. However, there remains a dearth of demographic models inferred from such data. Here, we describe sequence diversity at 37 000 bp sampled from 17 genes in cattle from Africa, Europe and India. Clearly distinct population histories are suggested between Bos indicus and Bos taurus , with the former displaying higher diversity statistics. We compare the unfolded site frequency spectra in each to those simulated using a diffusion approximation method and build a best-fitting model of past demography. This implies an earlier, possibly glaciation-induced population bottleneck in B. taurus ancestry with a later, possibly domestication-associated demographic constriction in B. indicus . Strikingly, the modelled indicine history also requires a majority secondary admixture from the South Asian aurochs, indicating a complex, more diffuse domestication process. This perhaps involved multiple domestications and/or introgression from wild oxen to domestic herds; the latter is plausible from archaeological evidence of contemporaneous wild and domestic remains across different regions of South Asia.

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Accent Policy and Accent Modification Enterprises as Potential Indicators of Intercultural Power Relations: A Call for an Updated Research Agenda

Perspectives on Global Issues in Communication Sciences and Related Disorders ◽

10.1044/gics3.1.22 ◽

2013 ◽

Vol 3 (1) ◽

pp. 22-33 ◽

Cited By ~ 1

Author(s):

Brynne D. Ovalle ◽

Rahul Chakraborty

Keyword(s):

International Relations ◽

Identity Construction ◽

Social Theory ◽

Power Relations ◽

Linguistic Diversity ◽

Cultural Organization ◽

Using Data ◽

The Individual ◽

The Impact ◽

The Relationship

This article has two purposes: (a) to examine the relationship between intercultural power relations and the widespread practice of accent discrimination and (b) to underscore the ramifications of accent discrimination both for the individual and for global society as a whole. First, authors review social theory regarding language and group identity construction, and then go on to integrate more current studies linking accent bias to sociocultural variables. Authors discuss three examples of intercultural accent discrimination in order to illustrate how this link manifests itself in the broader context of international relations (i.e., how accent discrimination is generated in situations of unequal power) and, using a review of current research, assess the consequences of accent discrimination for the individual. Finally, the article highlights the impact that linguistic discrimination is having on linguistic diversity globally, partially using data from the United Nations Educational, Scientific and Cultural Organization (UNESCO) and partially by offering a potential context for interpreting the emergence of practices that seek to reduce or modify speaker accents.

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Investigating the Relationship Between Self-Esteem and Stigma Among Young Adults With History of Suicide Attempts

Crisis ◽

10.1027/0227-5910/a000399 ◽

2016 ◽

Vol 37 (4) ◽

pp. 265-270 ◽

Cited By ~ 10

Author(s):

Meshan Lehmann ◽

Matthew R. Hilimire ◽

Lawrence H. Yang ◽

Bruce G. Link ◽

Jordan E. DeVylder

Keyword(s):

Young Adults ◽

Suicide Attempts ◽

Self Esteem ◽

High Risk Population ◽

High Functioning ◽

People With Mental Illness ◽

History Of ◽

The Individual ◽

The Impact ◽

The Relationship

Abstract. Background: Self-esteem is a major contributor to risk for repeated suicide attempts. Prior research has shown that awareness of stigma is associated with reduced self-esteem among people with mental illness. No prior studies have examined the association between self-esteem and stereotype awareness among individuals with past suicide attempts. Aims: To understand the relationship between stereotype awareness and self-esteem among young adults who have and have not attempted suicide. Method: Computerized surveys were administered to college students (N = 637). Linear regression analyses were used to test associations between self-esteem and stereotype awareness, attempt history, and their interaction. Results: There was a significant stereotype awareness by attempt interaction (β = –.74, p = .006) in the regression analysis. The interaction was explained by a stronger negative association between stereotype awareness and self-esteem among individuals with past suicide attempts (β = –.50, p = .013) compared with those without attempts (β = –.09, p = .037). Conclusion: Stigma is associated with lower self-esteem within this high-functioning sample of young adults with histories of suicide attempts. Alleviating the impact of stigma at the individual (clinical) or community (public health) levels may improve self-esteem among this high-risk population, which could potentially influence subsequent suicide risk.

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