Linguistic Phylogeny Research Articles

Self-supervised learning for Formosan speech representation and linguistic phylogeny

Formosan languages, spoken by the indigenous peoples of Taiwan, have unique roles in the reconstruction of Proto-Austronesian Languages. This paper presents a real-world Formosan language speech dataset, including 144 h of news footage for 16 Formosan languages, and uses self-supervised models to obtain and analyze their speech representations. Among the news footage, 13 h of the validated speech data of Formosan languages are selected, and a language classifier, based on XLSR-53, is trained to classify the 16 Formosan languages with an accuracy of 86%. We extracted and analyzed the speech vector representations learned from the model and compared them with 152 manually coded linguistic typological features. The comparison shows that the speech vectors reflect Formosan languages' phonological and morphological aspects. Furthermore, the speech vectors and linguistic features are used to construct a linguistic phylogeny, and the resulting genealogical grouping corresponds with previous literature. These results suggest that we can investigate the current real-world language usages through the speech model, and the dataset opens a window to look into the Formosan languages in vivo.

The time and place of origin of South Caucasian languages: insights into past human societies, ecosystems and human population genetics

This study re-examines the linguistic phylogeny of the South Caucasian linguistic family (aka the Kartvelian linguistic family) and attempts to identify its Urheimat. We apply Bayesian phylogenetics to infer a dated phylogeny of the South Caucasian languages. We infer the Urheimat and the reasons for the split of the Kartvelian languages by taking into consideration (1) the past distribution ranges of wildlife elements whose names can be traced back to proto-Kartvelian roots, (2) the distribution ranges of past cultures and (3) the genetic variations of past and extant human populations. Our best-fit Bayesian phylogenetic model is in agreement with the widely accepted topology suggested by previous studies. However, in contrast to these studies, our model suggests earlier mean split dates, according to which the divergence between Svan and Karto-Zan occurred in the early Copper Age, while Georgian and Zan diverged in the early Iron Age. The split of Zan into Megrelian and Laz is widely attributed to the spread of Georgian and/or Georgian speakers in the seventh-eighth centuries CE. Our analyses place the Kartvelian Urheimat in an area that largely intersects the Colchis glacial refugium in the South Caucasus. The divergence of Kartvelian languages is strongly associated with differences in the rate of technological expansions in relation to landscape heterogeneity, as well as the emergence of state-run communities. Neolithic societies could not colonize dense forests, whereas Copper Age societies made limited progress in this regard, but not to the same degree of success achieved by Bronze and Iron Age societies. The paper also discusses the importance of glacial refugia in laying the foundation for linguistic families and where Indo-European languages might have originated.

Detecting contact in language trees: a Bayesian phylogenetic model with horizontal transfer

Phylogenetic trees are a central tool for studying language evolution and have wide implications for understanding cultural evolution as a whole. For example, they have been the basis of studies on the evolution of musical instruments, religious beliefs and political complexity. Bayesian phylogenetic methods are transparent regarding the data and assumptions underlying the inference. One of these assumptions—that languages change independently—is incompatible with the reality of language evolution, particularly with language contact. When speakers interact, languages frequently borrow linguistic traits from each other. Phylogenetic methods ignore this issue, which can lead to errors in the reconstruction. More importantly, they neglect the rich history of language contact. A principled way of integrating language contact in phylogenetic methods is sorely missing. We present contacTrees, a Bayesian phylogenetic model with horizontal transfer for language evolution. The model efficiently infers the phylogenetic tree of a language family and contact events between its clades. The implementation is available as a package for the phylogenetics software BEAST 2. We apply contacTrees in a simulation study and a case study on a subset of well-documented Indo-European languages. The simulation study demonstrates that contacTrees correctly reconstructs the history of a simulated language family, including simulated contact events. Moreover, it shows that ignoring contact can lead to systematic errors in the estimated tree height, rate of change and tree topology, which can be avoided with contacTrees. The case study confirms that contacTrees reconstructs known contact events in the history of Indo-European and finds known loanwords, demonstrating its practical potential. The model has a higher statistical fit to the data than a conventional phylogenetic reconstruction, and the reconstructed tree height is significantly closer to well-attested estimates. Our method closes a long-standing gap between the theoretical and empirical models of cultural evolution. The implications are especially relevant for less documented language families, where our knowledge of past contacts and linguistic borrowings is limited. Since linguistic phylogenies have become the backbone of many studies of cultural evolution, the addition of this integral piece of the puzzle is crucial in the endeavour to understand the history of human culture.

Psycholinguistics of AI, Psycholinguistics versus Machine code

Abstract: I will examine the background of the language phylogeny in emerging Homo Sapiens as a fast, bipedal, long-distance runner in Black Africa;, followed by language psychogenesis in children from their gestation twenty-fourth week onward. I will concentrate on the audio-visual machiness impact, Lacan’s mirror stage, AV machines, the discontinuity between real and virtual realities, the remote control and AI machines as smart speakers and smart homes. In addition, I will discuss the following questions: Is the Machine beyond human intelligence? Is the human individual beyond Homo Sapiens? Is the human community beyond social contract? My working hypotheses on education within phylogenetic psycholinguistics are built on the following topics: Tomorrow’s AI class (unit and room); guided self-learning and who is the guide; can transference and countertransference take place in AI-guided self-learning? Can a human subject develop such transference/countertransference with a machine? Can a machine “play the game”? In conclusion, I will debate “The utopian vision of an improved human being versus the dystopic vision of human beings and human communities totally enslaved to AI machines. Keywords: AI; linguistic phylogeny; guided self-learning; (counter)-transference; enslaved-to-machines

Genetic substructure and complex demographic history of South African Bantu speakers

South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.

WOMEN’S ROLE AND POSITION IN THE EMERGENCE OF HOMO SAPIENS

Homo Sapiens (HS) started emerging around 300,000 BP. HS, a long-distance fast bipedal runner had a 29-year life expectancy. The ensuing physiological mutations caused the birth of long-dependent children. Their side-effect was enhanced vocal articulation. Linguistic phylogeny produced language with three time-ordered articulations: 1- rotation vowels-consonants into roots; 2- space- and timecategorization of roots into stems; 3- functional and temporal specifications of stems into fronds. Women henceforth developed as spiritual members in their communities, hereinafter their place in the production of symbolic cave and mobiliary art. The spiritual dimension of such symbolism must heavily be centered on women. Around 45,000 BCE all over the world, HS communities who had migrated out of Black Africa between 250,000 and 70,000 BP developed women-centered symbolism for the first time on durable media, though male-centered hunting weapons and tools had been produced even by previous Hominins.

Indo-European phylogenetics with R

Abstract The last twenty or so years have witnessed a dramatic increase in the use of computational methods for inferring linguistic phylogenies. Although the results of this research have been controversial, the methods themselves are an undeniable boon for historical and Indo-European linguistics, if for no other reason than that they allow the field to pursue questions that were previously intractable. After a review of the advantages and disadvantages of computational phylogenetic methods, I introduce the following methods of phylogenetic inference in R: maximum parsimony; distance-based methods (UPGMA and neighbor joining); and maximum likelihood estimation. I discuss the strengths and weaknesses of each of these methods and in addition explicate various measures associated with phylogenetic estimation, including homoplasy indices and bootstrapping. Phylogenetic inference is carried out on the Indo-European dataset compiled by Don Ringe and Ann Taylor, which includes phonological, morphological, and lexical characters.

Nonlinear diversification rates of linguistic phylogenies over the Holocene.

The expansion of the human species out of Africa in the Pleistocene, and the subsequent development of agriculture in the Holocene, resulted in waves of linguistic diversification and replacement across the planet. Analogous to the growth of populations or the speciation of biological organisms, languages diversify over time to form phylogenies of language families. However, the dynamics of this diversification process are unclear. Bayesian methods applied to lexical and phonetic data have created dated linguistic phylogenies for 18 language families encompassing ~3,000 of the world’s ~7,000 extant languages. In this paper we use these phylogenies to quantify how fast languages expand and diversify through time both within and across language families. The overall diversification rate of languages in our sample is ~0.001 yr-1 (or a doubling time of ~700 yr) over the last 6,000 years with evidence for nonlinear dynamics in language diversification rates over time, where both within and across language families, diversity initially increases rapidly and then slows. The expansion, evolution, and diversification of languages as they spread around the planet was a non-constant process.

Languages in Drier Climates Use Fewer Vowels.

This study offers evidence for an environmental effect on languages while relying on continuous linguistic and continuous ecological variables. Evidence is presented for a positive association between the typical ambient humidity of a language’s native locale and that language’s degree of reliance on vowels. The vowel-usage rates of over 4000 language varieties were obtained, and several methods were employed to test whether these usage rates are associated with ambient humidity. The results of these methods are generally consistent with the notion that reduced ambient humidity eventually yields a reduced reliance of languages on vowels, when compared to consonants. The analysis controls simultaneously for linguistic phylogeny and contact between languages. The results dovetail with previous work, based on binned data, suggesting that consonantal phonemes are more common in some ecologies. In addition to being based on continuous data and a larger data sample, however, these findings are tied to experimental research suggesting that dry air affects the behavior of the larynx by yielding increased phonatory effort. The results of this study are also consistent with previous work suggesting an interaction of aridity and tonality. The data presented here suggest that languages may evolve, like the communication systems of other species, in ways that are influenced subtly by ecological factors. It is stressed that more work is required, however, to explore this association and to establish a causal relationship between ambient air characteristics and the development of languages.

New Evidence from Linguistic Phylogenetics Identifies Limits to Punctuational Change.

Since the early 1970s, biologists have debated whether evolution is punctuated by speciation events with bursts of cladogenetic changes, or whether evolution tends to be of a more gradual, anagenetic nature. A similar discussion among linguists has barely begun, but the present results suggest that there is also room for controversy over this issue in linguistics. The only previous study correlated the number of nodes in linguistic phylogenies with branch lengths and found support for punctuated equilibrium. We replicate this result for branch lengths, but find no support for punctuated equilibrium using a different, automated measure of linguistic divergence and a much larger data set. With the automated measure, segments of trees containing more nodes show no greater divergence from an outgroup than segments containing fewer nodes.

Phylogenetics: Tracing the Evolutionary Legacy of Organisms, Metastatic Clones, Bioactive Compounds and Languages

Since its inception seventy-five years ago, the field of phylogenetics has steadily been expanding to contribute in a number of scientific fields including biogeography, medicinal chemistry, forensics, transcriptomics, cancer biology and even linguistics, in addition to systematic biology -for which it was originally erupted by Willi Hennig. In this invited editorial contributed to the Journal of Phylogenetics and Evolutionary Biology a big picture of this ever evolving field is expounded. Application of phylogenetic inference in biosystematics, phylogeography, phylogenetic selection of target taxa in medicinal chemistry, cancer phylogenetics, and linguistic phylogeny are reviewed with a personal perspective summarizing contribution to this interdisciplinary field from my group. Parametric methods such as Maximum Likelihood and Bayesian Inference have dramatically improved for last one decade, yet empirical solutions to some of the most fundamental issues, including homoplasmy and lineage sorting, remains to be materialized.

Linguistic Phylogenies Support Back-Migration from Beringia to Asia

Recent arguments connecting Na-Dene languages of North America with Yeniseian languages of Siberia have been used to assert proof for the origin of Native Americans in central or western Asia. We apply phylogenetic methods to test support for this hypothesis against an alternative hypothesis that Yeniseian represents a back-migration to Asia from a Beringian ancestral population. We coded a linguistic dataset of typological features and used neighbor-joining network algorithms and Bayesian model comparison based on Bayes factors to test the fit between the data and the linguistic phylogenies modeling two dispersal hypotheses. Our results support that a Dene-Yeniseian connection more likely represents radiation out of Beringia with back-migration into central Asia than a migration from central or western Asia to North America.

Reply to comments on “Surname distribution in population genetics and in statistical physics”

I can only agree with almost all the observations made in the Comments, and I will only stress some points complementing my review or suggesting new promising lines of investigation. I will also quote the most relevant recent contributions, missing in the review and suggested by the comments. Baek and Kim correctly point out the heterogeneity of surname distributions, and suggest that in general scaling laws must be seen as the most random outcome under certain constraints; hence the analysis should focus on the constraints and not on the specific dynamics [1]. In the RG approach this would correspond to focussing on the relevant field operator associated with the introduction of new surnames. Boattini and Pettner offer a convincing explaination of the relative decline of biodemography in the last decade (based especially on the advent of easier end cheaper technologies for DNA typing, and partially on the difficulties raised by polyphyletism). However they stress that there is still much interest in comparing surnames and Y-chromosome haplotypes and indicate the existence of several possible directions for a fruitful interdisciplinary approach (among them anthropology, forensics [2], genetic genealogy [3] and especially linguistics [4]). Maruvka and Shnerb underline the connection of the statistical approach to surname studies with many other developments, not only in population dymamics, but also in the theory of scale-free networks. However they raise a number of technical problems that should be the object of further analysis, among them the limiting assumptions of fixed size or fixed growth rate of the population, and the difficult comparison of theoretical models with empirical data generated by sampling [5]. As a side comment I would like to stress that the application of surname statistics to the study of nepotism in the academia has been the object also of one of the references quoted in my review [6]. Also Manrubia stresses the importance of shifting the attention from the commonalities to the dissimilarities. She also underlines the relevance of surname patterns to solve questions in history and anthropology (migratory phenomena, transmission of cultural traits) and suggests the possibility of deriving a ”surname phylogenies” in analogy with linguistic phylogenies, and exploring second and higher order contributions to the composition of human groups. Zanette emphasizes the problems raised by polyphyletism, and suggests an extensive analysis of this aspect of surname dynamics, as well as a better exploration of the mechanisms of surname mutation, possibly in connection with the study of linguistic evolution. He also stresses the lack of a rigorous analysis of the mutual compatibility of the theoretical methods applied to the study of surname dynamics. To this purpose I would like to notice that one of the aims of my review was to show that many of the results presented in the literature are substantially equivalent since they basically derive from different representations of the same Yule-Simon process.

An experimental study comparing linguistic phylogenetic reconstruction methods

This paper reports a simulation study comparing and evaluating the performance of different linguistic phylogeny reconstruction methods on model datasets for which the true trees are known. UPGMA performed least well, then (in ascending order) neighbor joining, the method of Gray & Atkinson and finally maximum parsimony. Weighting characters greatly improves the accuracy of maximum parsimony and maximum compatibility if the characters with high weights exhibit low homoplasy.

On the disintegration of (proto-)languages

AbstractDo languages split into dialects and subsequently into new languages at regular rates? Does such a regular splitting rate also apply to speech communities ancestral to the world's current language families? Do linguistic phylogenies exhibit intermediate levels (“genera”) which are somehow objectively identifiable? These questions are rarely raised, much less answered. In this article we present a simple method that provides insights into all the questions, drawing upon data from a world-wide sample of languages. It will be shown that splitting rates are approximately regular even if the languages studied are proto-languages spoken at very different points in prehistory and different places in the world. Ancestors of the world's linguistic families tend to have similar life-times. An intermediate transitional level corresponding to the point where genera appear can be objectively inferred from differences among descendant languages even without previously having established the structure of the phylogenetic tree.

Investigating cultural evolution using phylogenetic analysis: the origins and descent of the southeast Asian tradition of warp ikat weaving.

The warp ikat method of making decorated textiles is one of the most geographically widespread in southeast Asia, being used by Austronesian peoples in Indonesia, Malaysia and the Philippines, and Daic peoples on the Asian mainland. In this study a dataset consisting of the decorative characters of 36 of these warp ikat weaving traditions is investigated using Bayesian and Neighbornet techniques, and the results are used to construct a phylogenetic tree and taxonomy for warp ikat weaving in southeast Asia. The results and analysis show that these diverse traditions have a common ancestor amongst neolithic cultures the Asian mainland, and parallels exist between the patterns of textile weaving descent and linguistic phylogeny for the Austronesian group. Ancestral state analysis is used to reconstruct some of the features of the ancestral weaving tradition. The widely held theory that weaving motifs originated in the late Bronze Age Dong-Son culture is shown to be inconsistent with the data.

Cultural phylogenetics of the Tupi language family in lowland South America.

BackgroundRecent advances in automated assessment of basic vocabulary lists allow the construction of linguistic phylogenies useful for tracing dynamics of human population expansions, reconstructing ancestral cultures, and modeling transition rates of cultural traits over time.MethodsHere we investigate the Tupi expansion, a widely-dispersed language family in lowland South America, with a distance-based phylogeny based on 40-word vocabulary lists from 48 languages. We coded 11 cultural traits across the diverse Tupi family including traditional warfare patterns, post-marital residence, corporate structure, community size, paternity beliefs, sibling terminology, presence of canoes, tattooing, shamanism, men's houses, and lip plugs.Results/DiscussionThe linguistic phylogeny supports a Tupi homeland in west-central Brazil with subsequent major expansions across much of lowland South America. Consistently, ancestral reconstructions of cultural traits over the linguistic phylogeny suggest that social complexity has tended to decline through time, most notably in the independent emergence of several nomadic hunter-gatherer societies. Estimated rates of cultural change across the Tupi expansion are on the order of only a few changes per 10,000 years, in accord with previous cultural phylogenetic results in other language families around the world, and indicate a conservative nature to much of human culture.

Ideologies of descent in linguistics and law

Contemporary jurisprudence of self-determination draws on a trope of European conjectural anthropology, the Stammbaum, as it surfaces in documentary linguistics. This essay traces the work of linguist Ken Hale in Australia, first in linguistic phylogeny, later in endangered language documentation. It argues that linguists’ linguistic ideology supports multiple metaphysics of collective legal persona: one in which shared speakership is diacritic of group cohesion, two in which possession of language as a kind of property is central to collective flourishing. It juxtaposes linguists’ interventions in Australian indigenous land claims with recent debates among cultural property theorists as to the limits of property, and it proposes that linguists take a more active role in these debates. [Stammbaum; Australia; native title; cultural environmentalism; Locke, Kenneth Hale (1934–2001)]

Correlates of Reticulation in Linguistic Phylogenies

AbstractThis paper discusses phylogenetic reticulation using linguistic data from the Automated Similarity Judgment Program or ASJP (Holman et al., 2008; Wichmann et al., 2010a). It contributes methodologically to the examination of two measures of reticulation in distance-based phylogenetic data, specifically the δ score of Holland et al. (2002) and the more recent Q-residuals of Gray et al. (2010). It is shown that the δ score is a more adequate measure of reticulation. Our empirical analyses examine possible correlations between δ and (a) the size (number of languages), (b) age, and (c) heterogeneity of language groups, (d) linguistic isolation of individual languages within their respective phylogenies, and (e) the status of speech forms as dialects or recently emerged languages. Among these, only (d) is significantly correlated with δ. Our interpretation is that δ is a realistic measure of reticulation and sensitive to effects of socio-historical events such as language extinction. Finally, we correlate average δ scores for different language families with the goodness of fit between ASJP and expert classifications, showing that the δ scores explain much of the variance.

Farming and Language in Island Southeast Asia

Current portrayals of Island Southeast Asia (ISEA) over the past 5,000 years are dominated by discussion of the Austronesian “farming/language dispersal,” with associated linguistic replacement, genetic clines, Neolithic “packages,” and social transformations. The alternative framework that we present improves our understanding of the nature of the Austronesian language dispersal from Taiwan and better accords with the population genetics, archaeological evidence, and crop domestication histories for ISEA. Genetic studies do not demonstrate that the dispersal of Austronesian languages through ISEA was associated with large‐scale displacement, replacement, or absorption of preexisting populations. Linguistic phylogenies for Austronesian languages do not support staged movement from Taiwan through the Philippines into Indo‐Malaysia; in addition, the lexical and grammatical structure of many Austronesian languages suggests significant interaction with pre‐Austronesian languages and cultures of the region. Ar...