Lexical phylogenetics of the Tupí-Guaraní family: Language, archaeology, and the problem of chronology

RESEARCH ARTICLE Lexical phylogenetics of the Tupı ´ -Guaranı ´ family: Language, archaeology, and the problem of chronology Fabrı ´cio Ferraz Gerardi 1 *, Tiago TresoldiID 2 , Carolina Coelho Aragon 3 , Stanislav Reichert 1 , Jonas Gregorio de Souza 4 , Francisco Silva NoelliID 5 1SfS, Eberhard Karls Universita ¨t Tu¨bingen, Tu¨bingen, Germany, 2Department of Linguistics and Philology, Uppsala Universitet, Uppsala, Sweden, 3DLPL, Universidade Federal da Paraı ´ba, João Pessoa, Brazil, 4Department of Humanities, Universitat Pompeu Fabra, Barcelona, Spain, 5Centro de Arqueologia, Universidade de Lisboa, Lisboa, Portugal *[email protected] Abstract Tupı ´-Guaranı ´is one of the largest branches of the Tupı ´an language family, but despite its relevance there is no consensus about its origins in terms of age, homeland, and expansion. Linguistic classifications vary significantly, with archaeological studies suggesting incompatible date ranges while ethnographic literature confirms the close similarities as a result of continuous inter-family contact. To investigate this issue, we use a linguistic database of cognate data, employing Bayesian phylogenetic methods to infer a dated tree and to build a phylogeographic expansion model. Results suggest that the branch originated around 2500 BP in the area of the upper course of the Tapajo ´s-Xingu basins, with a split between Southern and Northern varieties beginning around 1750 BP. We analyse the difficulties in reconciling archaeological and linguistic data for this group, stressing the importance of developing an interdisciplinary unified model that incorporates evidence from both disciplines. 1 Introduction The problem of establishing the internal relations and chronology of the Tupı ´-Guaranı ´language family (henceforth TG) has been a long-standing one. Ideally, there should be a unified model explaining the language expansion and incorporating data from both linguistics and archaeology [1]. The consideration of archaeological data is crucial for establishing the precolonial geography of TG populations, which would be very incomplete if based only on historical records, as shown by Fig 1. To achieve it, we began by revising arguments built without considering the archaeological data, especially those developed before the 1960s [2–6], in order to contrast them with other evidence to build our models. As far as linguistic classifications are concerned, the internal relations of the TG branch of the Tupı ´an family have received much scholarly attention, with different approaches employed to establish them from linguistic data alone. Phonological criteria have been put to use alongside grammatical properties and lexical cognacy, both in “traditional” [7–12] and “quantitative” approaches [13–17]. Although these studies agree to a large extent on the topology of the PLOS ONE PLOS ONE | https://doi.org/10.1371/journal.pone.0272226 June 15, 2023 1 / 25 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Ferraz Gerardi F, Tresoldi T, Coelho Aragon C, Reichert S, de Souza JG, Silva Noelli F (2023) Lexical phylogenetics of the Tupı ´-Guaranı ´ family: Language, archaeology, and the problem of chronology. PLoS ONE 18(6): e0272226. https:// doi.org/10.1371/journal.pone.0272226 Editor: Søren Wichmann, Kiel University, GERMANY Received: October 29, 2021 Accepted: July 14, 2022 Published: June 15, 2023 Peer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here: https://doi.org/10.1371/journal.pone.0272226 Copyright: ©2023 Ferraz Gerardi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: The supplementary material is available in an anonymous online repository hosted at OpenScienceFramework at the address: https://osf.io/afsyk. shallower splits, there are still irreconcilable differences in terms of the deepest ones, and much disagreement about their dating. Previous studies using reduced datasets not designed for phylogenetic analysis [8–10] are still the most commonly referenced ones. The otherwise thorough studies by [11,12] contained errors in the data that may have influenced the results. [15] is the first Bayesian phylogenetic classification, but neither the underlying data nor the model are public. [18] has several issues, such as low posterior support in branches for well-known cases of relationship (e.g., between Yuki and Siriono, or among Apiaka and Kawahiv languages), analyses including parameters with very low coverage, and the position of some languages (e.g., Kamajura ´), besides errors in cognacy judgment. In this study, we make all our data and models available, following the principles of FAIR data [19], and prepare multiple phylogenetic models. Besides providing a phylogeny based on open data, our results are the first to offer a dating of the splits through relaxed molecular clocks. Considering how the question of the root age and the order of splits is a dividing point among specialists, the prospect of building a unified interdisciplinary theory involving linguistic, historical, genetic, archaeological, and ethnographic evidence is considered in the discussion while presenting new groupings. 2 Tupı ´-Guaranı ´languages and the related archaeology 2.1 Languages TG is the largest branch of the Tupı ´an linguistic family [14,20,21], with about 40 living languages (here excluding Piripkura [22]) and at least 9 extinct ones [16]. The number of speakers ranges from less than a hundred (e.g., Amondawa and Juma) to over 6 million (Paraguayan Guaranı ´) [23]. The geographic distribution, with most TG subgroups found in Southeastern Amazon, points to an origin in this area due to its greater linguistic diversity [24–26]. Such hypothesis contrasts with common interpretations of the archaeological records (pointing to an origin closer to the area between the upper Tapajo ´s and Xingu rivers, further to the west [6]), ethnographic sources, and indigenous cultural repertoire. A clear example of the latter are the foundation myths and legends of the Ka’apor, carrying various hints that they were once located to the west of their present territory [27,28]. No matter the location of the homeland, the expansion of TG is among the largest in the world, spreading across over 4000 km in both latitude and longitude [33] (see Fig 1), with its driving forces a matter of intense debate [6,13,21,34–42]. Archaeological research suggests that demographic growth was propelled by the rise of agriculture, coupled with a strong sense of territoriality supported by long-range political networks and by an expansionist warlike ideology [6]. An increasing area of forested landscape that could be used for agriculture might have contributed to this expansion [33,43]. Due to substantial similarities and affinities, material evidence suggests a different scenario and a chronology in line with what one would expect based on linguistic and ethnographic grounds. This is illustrated by the rates of shared cognates, as shown in Fig 2 (also in Fig 7 in Appendix C of S1 File), which are relatively high when compared with those observed in other groups with supposedly comparable dates for their most recent common ancestor, such as Uralic at 43% and Romance at 93% [44]. Archaeological dates considered too ancient have often been discarded, based on the view that the TG dispersal is a recent one. However, over time the accumulation of dates close to ca. 2000 BP in different regions led to a questioning of this premise. Glottochronological estimates of ca. 2500 BP for the initial split of the TG languages [45] have been used to support the archaeological dates. Nonetheless, the discrepancy between such an early chronology and the obvious proximity between the TG languages was never left unnoticed [3,4]. Any model seeking to explain the evolution of TG needs to account for these facts when proposing language phylogenies [43]. Originally, two such models were put forward. The first PLOS ONE Lexical phylogenetics of the Tupı ´-Guaranı ´family PLOS ONE | https://doi.org/10.1371/journal.pone.0272226 June 15, 2023 2 / 25 Funding: FFG and SR were supported by the by European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 834050). TT was supported by Cultural Evolution of Texts project, with funding from the Riksbankens Jubileumsfond (grant agreement ID: MXM19-1087:1). Competing interests: The authors have declared that no competing interests exist. [34] sees the fluvial network as the main enabler of a rapid expansion, an idea further developed by [37,46], in which the causes of the dispersal are related to climatic factors. The other model finds the key driver in population increase, with the growing need for more cultivation areas (floodplain agriculture) and slower movements of expansion [6,35,38,47,48]. More recently, a compromise has been found by explicitly testing demographic models against simulated climate change scenarios for the late Holocene [43]. These models show that a combination of demic-diffusion processes and the preference for a particular environmental niche (tropical moist forests) best explains the archaeological chronology and the general Fig 1. The Tupı ´-Guaranı ´languages used in this study (in green) and the Tupı ´an (non-TG) Awetı ´(in blue), and Mawe ´(in red), along with the distribution of the TG archaeological record (black dots). Prepared by the authors with QGIS 3 [29], based on based on public domain data and raster images from “Natural Earth”, including data from [30–32] and an unpublished database by Corrêa and Noelli. https://doi.org/10.1371/journal.pone.0272226.g001 PLOS ONE Lexical phylogenetics of the Tupı ´-Guaranı ´family PLOS ONE | https://doi.org/10.1371/journal.pone.0272226 June 15, 2023 3 / 25 reconstruction of historical linguistics: a long stasis in the Amazon, with the emergence and development of the main Tupı ´branches, followed by a rapid expansion to other parts of South America (corresponding to the TG expansion) [43]. [34] concludes that the most likely center of the dispersion of the TG is the Upper Tapajo ´s. [49] proposes a southwestern Amazonian homeland for Proto-Tupı ´-Guaranı ´(PTG), lying near the Arinos and upper Juruena river basins. Using the Linguistics Migration Theory and motivated by the classification in [15,50] posits the homeland of PTG in the lower Xingu. The location of the center of expansion is, as expected, dependent of the topology for the family. The Mawe ´-Awetı ´-Tupı ´-Guaranı ´hypothesis [21,51–56] states that a single ancestor for these three groups branched off from the rest of the Tupı ´an family [14] (see Fig 3). The split of the branch today composed by Mawe ´would have been followed by that of the ancestor of Awetı ´and PTG. Cognates shared by Awetı ´and TG languages but not present in Mawe ´support this hypothesis, showing that Mawe ´had already branched off while the ancestors of Awetı ´and Fig 2. Cognacy for each language pair used in the main analysis, ranging from 0 (full difference) to 1 (identity). The cognacy diversity [44] for all languages is 15%. If Mawe ´and Awetı ´are excluded, the value is 14%. https://doi.org/10.1371/journal.pone.0272226.g002 PLOS ONE Lexical phylogenetics of the Tupı ´-Guaranı ´family PLOS ONE | https://doi.org/10.1371/journal.pone.0272226 June 15, 2023 4 / 25 PTG formed single group which heavily borrowed lexical material of Cariban origin [49,57]. We present some of these cases in Table 1, with cognacy judgment based on [16]. 2.2 Archaeology The dispersal of TG languages has a clear material correlate in the spread throughout eastern South America of a package that includes a particular type of ceramics, plant management, Fig 3. The Tupı ´an languages with the sub-branches of the Mawe ´-Awetı ´-Tupı ´-Guaranı ´branch emphasized. Adapted from [21]. https://doi.org/10.1371/journal.pone.0272226.g003 Table 1. Cognates shared by Mawe ´and Awetı ´not present in TG (in yellow) and cognates shared by Awetı ´and TG (in blue) not present in Mawe ´.Tupinamba ´is taken as a representative of the PTG descendants. The numbers in the last column refer to TG languages whose concepts are cognates with the Tupinamba ´word provided, illustrating cognates in other branches of TG: Ava ´-Canoeiro (1), Wayampi (2), Guajajara (3), Parakanã(4), Asurinı ´Xingu (5), Kamajura ´(6). Mawe ´Awetı ´Tupinamba ´ Leg ʔup ʔup etɨmã(1,2,3,5,6) Sing mepɨtepɨ ɲeʔeɲgar (2,4) Come back aipok ʔajpog jeβi (1,2,3,5,6) Hoplias (genus) (n)ipiuta piuta ´taeʔia (1,2,3,4) Fly (insect) win tin meu (2,3,4,5,6) Jaguar awɨato tawat jawa (1,2,3,4,5,6) Anteater arihı ˜tamajua tamandwa (1,2,3,4,6) Grandfather aseʔi amu ˜j amı ˜ja (2,3,4,5,6) Wound pihi peʐep peɾeb – Tapir wewato tapiʔit tapiʔiɾ(1,2,3,4,5,6) Sky atipɨ ɨwak ɨβak (1,2,3,4,5,6) Genipa wããhop tẽtɨpap janɨpab (2,3,4,5,6) Bat hakiʔi tatiʔa anɨra (1,2,3,4,5) Sieve (tool) panane kurupem urupem (2,4,5,6) Burn (something) wuk apɨapɨ(1,2,3,4,5,6) Bow moreawat ʒapat ɨβɨɾapaɾ(1,2,3,4,5,6) Star wajkiru tatɨaɁɨt jasɨtata (1,2,3,4,5,6) https://doi.org/10.1371/journal.pone.0272226.t001 PLOS ONE Lexical phylogenetics of the Tupı ´-Guaranı ´family PLOS ONE | https://doi.org/10.1371/journal.pone.0272226 June 15, 2023 5 / 25 and cultivation of a variety of crops [6,38], as shown in Fig 1. This is often cited as one of the few cases where an obvious correlation exists between an archaeological culture and a language family, to the point where the name “Tupiguarani” (no hyphen) was applied to the archaeological tradition (for a criticism of this concept see [47,58]). Admittedly, correlating a material culture style with the speakers of a single language or language family is in most cases a problematic, if not naïve, approach. Similarly, material culture changes may precede or postdate related changes in society and language [59–61]. Nevertheless, there is overwhelming evidence to support the association between the ceramics conventionally called “Tupiguarani” and the spread of the Tupı ´-Guaranı ´language family. Of particular interest is the notable homogeneity of the material culture throughout the Tupı ´-Guaranı ´territory [31]. This conservatism is seen even in areas historically occupied by linguistically distinct groups such as the Tupiniquim and Tupinamba ´[62]. The high standardization in ceramic styles across time and space—accompanied by the maintenance of a specific vocabulary to describe vessel shapes [63]—is a testimony to the conservatism found in other spheres of the Tupı ´-Guaranı ´cultures [64]. Ultimately, the ceramics recognized as “Tupiguarani” by archaeologists can be traced back to the Tupı ´an homeland in southwestern Amazon, where its stylistic components, such as polychrome painting, can be found among other ceramic traditions [65]. In what follows, we summarize the earliest radiocarbon dates available for Tupiguarani sites. The dates are divided according to five regions: Eastern Amazon, Bolivia, Atlantic Coast, Northern Brazil, and the Parana ´Basin. All dates are calibrated with the southern hemisphere curve [66] and reported in the 2-sigma interval. Eastern Amazon An early presence in the Xingu-Tocantins interfluve is supported by the available radiocarbon dates. A date of 2430 ±20 BP (cal BP 2680–2340) from a site in the Tocantins-Araguaia confluence is still seen with caution, as it is considerably older than all other dates from the same region [67,68]. The accepted Tupiguarani chronology for the eastern Amazon starts at 1670 ±80 BP (cal BP 1700–1350) between the Tapajo ´s and Tocantins rivers [68]. Bolivia The earliest potential TG site in pre-Andean Bolivia has a date of 1680 ±90 BP (cal BP 1730–1320, UA-10240), which, if confirmed, would imply an arrival of the Guaranı ´-speaking Guarayo and Chiriguano in the region earlier than commonly thought [69]. Atlantic coast In the region historically occupied by the Tupinamba ´, a controversial early chronology has been proposed by Scheel-Ybert et al. [70], based on dates reaching 2920 ±70 BP (cal BP 3220–2790, Gif-11045) from sites in the state of Rio de Janeiro. These predate the TG expansion out of the Amazon by any estimate. Excluding those outliers, the earliest date for the Atlantic forest is of 1740 ±90 BP (cal BP 1825–1380, Beta-84333) [70], which is in line with the chronology of other parts of the TG territory. Most dates are considerably more recent, later than 1055 ±80 BP (cal BP 1060–740, SI-828) [71]. Northeastern Brazil Few dates are available for northeastern Brazil. In the semi-arid hinterland, a date of 1690 ±110 BP (cal BP 1810–1315, GIF-3225) is sometimes attributed to a TG occupation, but the cultural affiliation of the dated site is not a consensus [38,72]. Discounting dates with excessively large standard deviations [73], the occupation of the coast possibly extends back to 1880 ±60 BP (cal BP 1920–1590, Beta-118818) [31], with most dates being considerably later. Parana ´Basin The southernmost region of Tupı ´-Guaranı ´occupation, where Guaranı ´and related languages were dominant, has the most complete and reliable chronology [32]. The earliest date, 2010 ±75 BP (cal BP 2090–1740, SI-5028), comes from the middle Parana ´river [74]. Between that date and the second millennium, multiple sites are attested in the São Paulo highlands, southernmost Brazil, and the Parana ´-Uruguay interfluve in Argentina [74]. PLOS ONE Lexical phylogenetics of the Tupı ´-Guaranı ´family PLOS ONE | https://doi.org/10.1371/journal.pone.0272226 June 15, 2023 6 / 25 3 Materials and methods 3.1 Data We followed the current best practices for linguistic phylogenetics (“phylolinguistics”), where cognate gain and loss in basic vocabulary are the evolutionary characters used to infer a dated tree [75–77]. The complete dataset used in this study is derived from [16] and is publicly available, along with the phylogenetic models, at https://osf.io/afsyk. For better integration with other linguistic resources, we standardized the data following the formats and catalogues of [78]. Cognate set assignment, following the principle of root-meaning traits [79], was first performed with the automatic methods implemented in LingPy [44,77,80,81] and later manually reviewed by experts in its entirety. Table 2 shows a sample of cognacy assignment from [16]. The data in our study comprises lexica from 40 “doculects” [82] (i.e., language varieties). Mawe ´and Awetı ´were included in the analyses, with the split of the Mawe ´ancestor serving as the root and reflecting the aforementioned and well established Mawe ´-Awetı ´-TG hypothesis. We also included Omagua and Kokama due to a high portion of their lexicon being of TG origin, despite their non-TG origin [83,84], a hypothesis rejected by [85]. Some TG languages available in our source were excluded from the analyses due to an excessively low coverage. The list of concepts is provided in Appendix A of S1 File, along with the corresponding Concepticon cognate set ids and glosses [86] when available. The choice of concepts relied on the following criteria: concepts from the Swadesh [87] and Leipzig-Jakarta [88] lists, the Swadesh list extended by [89], and culturally relevant TG concepts taken from [90] and expanded by the authors. The concept coverage for each language is given in Table 3. We used 415 concepts from an upcoming version of [16]. We assessed the degree of tree-likeliness by computing the concepts’ TIGER scores [91,92] with the implementation by [93], obtaining a mean score of 0.14 (±0.14) (individual scores are reported in Appendix K of S1 File). This value suggests a comparatively high level of non-vertical transmission, being lower than the lowest score reported in [93] of 0.20 for Dravidian, and supports the qualitative assessment that “there is an overall absence of well-delimited lexical clusters inside [TG]” [13]. 3.2 Phylogenetic reconstruction and dating Data was prepared with the state-of-the-art software tools for computer-assisted pipelines in computational historical linguistics [80,94] and exported in the extended NEXUS format [95]. The files produced by this pipeline were processed and normalized with Python scripts developed for this research. Since the evolutionary history of the TG languages is not completely tree-like, as per [13] and measures in Section 3.1, we first generated a distance matrix to build a NeighborNet network using SplitsTree version 4.17.1 [96] to visualize the conflicting signal and calculate the Qresiduals and the δ-scores. Different phylogenetic models were then explored in terms of subsets of concepts, languages, molecular clocks, calibration dates, substitution models, rate variation, and Table 2. Cognacy sample from our database. Language Concept Phonetic form Cognate set Tupinamba ´BAT anɨra 171 Wayampi BAT anɨla 171 Guaranı ´BAT mopi 172 Kaiowa ´BAT m bopiri 172 Mawe ´BAT hakiɁi 4513 https://doi.org/10.1371/journal.pone.0272226.t002 PLOS ONE Lexical phylogenetics of the Tupı ´-Guaranı ´family PLOS ONE | https://doi.org/10.1371/journal.pone.0272226 June 15, 2023 7 / 25 monophyletic constraints. We decided in favor of the simplest and most common practices whenever possible and sensible, following the principle that we should begin with more approachable studies before venturing into more complex scenarios. The initial exploration, partly published in [97], was relevant for the authors to discuss the concepts that were deemed less reliable, and the problems that could arise from the analysis. These studies also served to evaluate the feasibility and robustness of our approach. Table 3. Concept coverage for the languages used in this study from [16]. Language Glottocode ISO 639–3 Code Coverage Ache ache1246 guq 80% Amondawa amun1246 adw 74% Anambe anam1249 aan 49% Apiaka apia1248 api 65% Arawete araw1273 awt 71% Asurinı ´Tocantins toca1235 asu 84% Asurinı ´Xingu xing1248 asn 63% Ava-Canoeiro avac1239 avv 79% Aweti awet1244 awe 93% Chiriguano east2555 gui 90% Guaja guaj1256 gvj 80% Guajajara guaj1255 gub 97% Guaranı ´para1311 gnn 99% Guarayo guar1292 gyr 89% Ka’apor urub1250 urb 95% Kaiowa kaiw1246 kgk 51% Kamajura kama1373 kay 68% Kayabi kaya1329 kyz 63% Kokama coca1259 cod 82% Mawe sate1243 mav 88% Mbya mbya1239 gun 84% Nheengatu nhen1239 yrl 91% Old Guaranı ´oldp1258 grn 83% Omagua omag1248 omg 80% Parakanãpara1312 pak 83% Parintintin tenh1241 pah 96% Siriono siri1273 srq 94% Surui-Aikewara suru1262 mdz 83% Tapiete tapi1253 tpj 77% Tapirape tapi1254 taf 68% Teko emer1243 eme 96% Tembe temb1276 tqb 93% Tenharim nucl1663 pah 76% Tupinamba tupi1273 tpw 99% Urueuwauwau urue1240 urz 60% Warazu paus1244 psm 85% Wayampi waya1270 oym 99% Xeta xeta1241 xet 61% Yuki yuqu1240 yuq 64% Zo’e zoee1240 pto 82% https://doi.org/10.1371/journal.pone.0272226.t003 PLOS ONE Lexical phylogenetics of the Tupı ´-Guaranı ´family PLOS ONE | https://doi.org/10.1371/journal.pone.0272226 June 15, 2023 8 / 25 We structured the research into two rounds, the first one designed to obtain summary trees given different scenarios of analysis and the second one using these results to perform a phylogeographic study. The first round was composed of two studies that differ in the subset of concepts used: a “full” study, with all concepts described above filtered to ensure they were missing at most in 20% of the languages, and a “swadesh” study using the list of [87] (see Appendix C in S1 File) as close as possible, filtered to ensure they were missing in at most 30% of the cases. Such thresholds were necessary due to the high level of sparsity of the data. In both cases concepts were grouped in two equal-sized partitions based on the overall number of cognates in each. Besides simpler strict-clock models, which are comparable to glottochronological approaches, all analyses also used uncorrelated relaxed-clock models sampled from a lognormal distribution [98,99]. In the latter, each branch of a tree has its own clock rate, with parameters that are independent from those of the mother and sister branches, allowing abrupt changes in evolutionary rates. These are considered compatible with both the evolution of TG, given its relatively recent and rapid expansion, and South American languages in general, particularly due to the impact of European colonization in terms of population size, displacement, and replacement [100,101]. We performed phylogenetic reconstruction using BEAST2 version 2.6.6 [102], fitting different binary covarion models [103], where the transition between “presence” and “absence” of a cognate in a language is assumed to be symmetric and equally probable, along with a latent variable modeling whether each cognate switches between presence and absence at a “fast” or “slow” rate. Ascertainment correction was performed according to practices described in [76]. Considering how our data only offers two historical languages that could be used for temporal calibration (Tupinamba ´and Old Guaranı ´), both of which are to some extent composed from multiple sources diverging in provenance and date (each spanning over more than a hundred years), we decided to guide the inference only by setting a uniform distribution for the root, in agreement with all sensible archaeological and linguistic hypotheses, and by establishing monophyletic groups accepted by virtually all experts, also adjusting tip dates for languages collected more than 50 years ago (detailed in Appendix D of S1 File). We used a Birth-Death model [104], performing 25 7 MCMC iterations, sampling trees from the posterior distribution to obtain a maximum clade credibility tree (MCC) based on common ancestor heights after a 50% burn-in, using TreeAnnotator version 2.6.4 [105]. We plotted trees with [106] and FigTree version 1.4.4; the trees, including for the supplementary models, are presented in Figs 8–11, all in Appendix E of S1 File. The results in Section 4 are those of the “full” study using a relaxed clock. The decision in favor of this model as our main result is based on the set of concepts it involves, which, despite a higher reticulation signal, includes family-specific concepts that were deemed relevant for studying the vertical transmission. It is necessary to note that the logmarginal likelihood (see Appendix L in S1 File), computed with nested samples [107], not only favored the “swadesh” dataset, as expected in face of its lower data complexity, but it also yielded a better score for the strict molecular clock in the case of the “full” dataset. Our decision in favor of the relaxed clock model was due to an expert analysis of the resulting topology and dates, as it was far more compatible with the literature, and by the fact that most unexpected results, such as the position of the Anambe ´-Arawete ´clade or the branch length of Tupinamba ´, can be explained by differences in concept coverage. The complete studies are presented in the supplementary material and should guide future research and refinements to cognate judgments. The phylogeographic study used the topology of the MCC tree of the “full” study as a set of monophyletic constraints wherever we had obtained a posterior support of at least 0.70, along with the 95% height range for each such split, focusing on having the model search for dates PLOS ONE Lexical phylogenetics of the Tupı ´-Guaranı ´family PLOS ONE | https://doi.org/10.1371/journal.pone.0272226 June 15, 2023 9 / 25 6 Concluding remarks Most cases of lower posterior support in our tree can be explained, at least in part, by missing data. The low confidence in some of the splits within individual groups, such as among the Guaranı ´languages, might be due to both technical aspects, like an unequal level of sampling, and the actual history of the languages, involving dialect chains, admixture both at the linguistic and genetic levels, etc. These issues are heightened by the lack of calibration data of temporal and geographic matter that can be applied directly, as well as by our decision to begin this research path by using models which are simpler to understand and less susceptible to prior hypotheses specified by us. The topology and the posterior support are expected to improve as we extend the data, employ more complex models (which tend to involve different types of calibrations), and, potentially, the direct or indirect usage of additional linguistic evidence to allow the a priori definition of monophyletic groups, aiming for more precise parameters of local evolution. The historical-anthropological survey work presented in the previous sections, in particular, may prove to be extremely valuable in future research, provided that it is used with the due caution (see [159]). It is essential to emphasize that the classification presented here is exclusively based on lexical changes, although for most of the clades there is a significant agreement with Rodrigues’ taxonomy based on phonology [10], and even with the cultural classification in [42]. A caveat is necessary here: linguistic classifications based exclusively on phonological changes, such as the one by [10], are generally considered to be more susceptible to common independent innovations, that is, cases in which the same character (a sound change) independently arises more than once in different branches, leading to “homoplasy”. This is one of the main reasons for the suggestion that most phylolinguistic studies should involve exclusively or majorly characters based on lexical innovations, which can be assumed to be independent and arise only once. Likewise, when considering differences with archaeological datings, it is worth noting that such phylolinguistic models consider, and by extension date, splits as the moment when the first disjunctive lexical innovation in the basic vocabulary takes place. Such event does not necessarily imply a degradation of mutual intelligibility, nor can it be automatically associated with either population displacement or changes in archeological packages. In terms of routes of expansion, we believe that the ancestors of Tupinamba ´took different directions, traveling eastwards, while the rest of the group traveled westwards first and then northwards. Paralleling Rodrigues’ Group VIII (which includes Guaja ´), the group containing Ka’apor, Teko ´, Wayampi, and Zo’e is clearly supported by phonological and lexical innovations alike, despite the presence of the Teko ´in the French Guiana already in the 1500s [160]. Since Zo’e is phonologically closer to Teko ´than to Wayampi [161], it is possible that the ancestors of the Zo’e, as those of the Teko ´, had already separated from the ancestors of Wayampi, whose migration northwards from the lower Xingu river only began in the early 1600s [154, 155,162]. The late split of Wayampi and Teko ´in our tree is probably caused by innovations common to both groups and borrowings of Cariban origin not present in Zo’e, exemplified in Table 5. It is unknown whether the Tupı ´an group referred to as “Apama” [144,163] and described in 1691 between the Curua and Maicuru are ancestors of the Zo’e, who in 1600 were still located in Lower Xingu. If the identification of this group with the Zo’e is correct, we could infer their movements based on additional, non-linguistic evidence. The migration of multiple groups towards Rondo ˆnia during the colonial period is not only acknowledged by multiple sources [123,139,140,143,164], but can also be demonstrated linguistically on the basis of the abovementioned Carib loans in PTG [124], not found in Mawe ´ or Awetı ´. These loans are also found in the Kawahiv languages. Of all conjectures regarding how the Kamajura ´reached their current location [126,132,165], an attractive one is told by PLOS ONE Lexical phylogenetics of the Tupı ´-Guaranı ´family PLOS ONE | https://doi.org/10.1371/journal.pone.0272226 June 15, 2023 16 / 25 the Kuikuro, according to whom they came from the North, passing via the Araguaia river through the Karaja ´territories, entering the Xingu basin via the Suya ´-Missu ´river [166]. However, there is no archaeological sign of such an entrance of a TG group in the Upper Xingu. In conclusion, a thorough history of the formation and development of TG languages, including the distinction between vertical, in-family, and out-family horizontal transmission, is yet to be written, reviewing everything that has been proposed so far. A unified interdisciplinary theory must give weight to data from linguistics, archaeology, ethnology, as well as genetics and the approach proposed in this article collaborates towards such an enterprise. We must also consider that the presence of material that is not vertically transmitted does not mean only that a tree will be distorted: it also means that even a “perfect” tree, one correctly capturing all relationships of descent, will mirror only a part of the history, especially if the spread of “horizontal” innovations was much faster than that of the “vertical” descent. A tree of lexical innovations is not a narrative of the history of the languages involved, but a means to tell one. Although a critical review of the entire radiocarbon record associated with the TG dispersal is beyond the scope of this work, the quick assessment of the earliest regional dates summarized in this paper illustrates the difficulty of conciliating archaeological and linguistic data. In the future, strict criteria of chronometric hygiene should be applied to the published TG chronology to ascertain the reliability of each date [167]. For now, even if the long chronology proposed for some regions is discarded [70], the chronology available for the Parana ´basin makes it difficult to argue for a recent arrival in the region. Numerous sites in southern Brazil and Argentina predate the second millennium [32], which is impossible to conciliate with an estimate of around 1750 years BP for the beginning of the TG dispersal to those regions. In terms of phylogenetic studies based on linguistic data, besides incorporating expediencies from archaeology as priors, future work might investigate combining non-partial cognacy data with other features, such as partial cognacy sets, morphology, and phonology. For example, due to the strong composite character of TG lexicon, we decided not to use information on partial cognacy, despite its limited availability in [16]. Despite the source data carrying information on partial cognacy, we decided to employ exclusively simple cognates, also in consideration of how the substitution models available in Bayesian frameworks still demand nonstandard configurations to use them in an adequate way [81,168]. Also deserving more consideration are TG practices that resulted in the conservancy of part of the language and its meanings observed in their material culture and environmental management. These are facts often historically, ethnographically, linguistically, and archaeologically recorded in different times and places by people with different expertise and objectives Table 5. Lexical innovations in our Group Ib (Wayampi, Teko ´, and Zo’e). Some, not shared by Zo’e, took place when Wayampi and Teko ´were already in the French Guiana, as the source of the borrowings indicates. The word for ‘timbo liana’ and the plural marker are exclusive to these languages. Concept Wayampi Teko ´Zo’e Borrowed from Timbo ´liana ɨmeku beku meku ˜Wayana Plural marker ku ˜kom kãCariban language Pan patu patu tapimãFrom Portuguese through Wayana Milk tile direr tɨCreole Mirror warua waruwa poroesake Lı ´ngua Geral Knife marija m b ariʤe boke Wayana Salt sautu sautu jukɨt From English through Wayana 3 rd pl. kupa kupa – Cariban language Hen masakala masakala ɲarı ˜Wayana https://doi.org/10.1371/journal.pone.0272226.t005 PLOS ONE Lexical phylogenetics of the Tupı ´-Guaranı ´family PLOS ONE | https://doi.org/10.1371/journal.pone.0272226 June 15, 2023 17 / 25 who perceived various “empirical” and “theoretical” aspects of the TG peoples, as shown in [169]. Both ways lead to understanding the relations between the TG and other cultures, which included the appropriation and transformation of people, objects and language [170, 171], in processes characterized by “changes within continuities”. 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