Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most widely spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here, we explore the genetic structure of 176 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, including a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long-distance genetic connections between speakers of the same language family suggest that indigenous languages here were spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including understudied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional-scale analysis.

The Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs. We report a high indigenous component, which stands apart from the network of intense genetic exchange in the core central zone of Andean civilization, and is also distinct from neighbouring populations. This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas. Furthermore, speakers of Chachapoyas Quechua are found to share no particular genetic similarity or gene-flow with Quechua speakers elsewhere, suggesting that here the language spread primarily by cultural diffusion, not migration. Our results demonstrate how population genetics, when fully guided by the archaeological, historical and linguistic records, can inform multiple disciplines within anthropology.

The Yanesha are a Peruvian population who inhabit an environment transitional between the Andes and Amazonia. They present cultural traits characteristic of both regions, including in the language they speak: Yanesha belongs to the Arawak language family (which very likely originated in the Amazon/Orinoco lowlands), but has been strongly influenced by Quechua, the most widespread language family of the Andes. Given their location and cultural make-up, the Yanesha make for an ideal case study for investigating language and population dynamics across the Andes-Amazonia divide.In this study, we analyze data from high and mid-altitude Yanesha villages, both Y chromosome (17 STRs and 16 SNPs diagnostic for assigning haplogroups) and mtDNA data (control region sequences and 3 SNPs and one INDEL diagnostic for assigning haplogroups). We uncover sex-biased genetic trends that probably arose in different stages: first, a male-biased gene flow from Andean regions, genetically consistent with highland Quechua-speakers and probably dating back to Inca expansion; and second, traces of European contact consistent with Y chromosome lineages from Italy and Tyrol, in line with historically documented migrations. Most research in the history, archaeology and linguistics of South America has long been characterized by perceptions of a sharp divide between the Andes and Amazonia; our results serve as a clear case-study confirming demographic flows across that 'divide'. Am J Phys Anthropol 155:600-609,

The genetic affinities that characterize Central Andean populations are highly consistent with the succession of expansive polities in the region, culminating with the Incas. In the environs of Lake Titicaca, however, one subset of the present day Aymara-speaking population exhibits a peculiar position: perhaps a genetic correlate to their original Uro linguistic lineage (now extinct in the area), tallying with ethnohistorical claims for the distinctiveness of the Uro population. Our results emphasize the need for genetic descriptions to consider the widespread phenomenon of language shift.

Linguists are able to describe, transcribe, and classify the differences and similarities between accents formally and precisely, but there has until very recently been no reliable and objective way of measuring degrees of difference. It is one thing to say how varieties are similar, but quite another to assess how similar they are. On the other hand, there has recently been a strong focus in historical linguistics on the development of quantitative methods for comparing and classifying languages; but these have tended to be applied to problems of language family membership, at rather high levels in the family tree, not down at the level of individual accents. In this article, we outline our attempts to address the question of relative similarity of accents using quantitative methods. We illustrate our method for measuring phonetic similarity in a sample of cognate words for a number of (mainly British) varieties of English, and show how these results can be displayed using newer and more innovative network diagrams, rather than trees. We consider some applications of these methods in tracking ongoing changes in English and beyond, and discuss future prospects.1 How are accents different; and how different are accents?In November 2004, the BBC commissioned an online poll on attitudes to accents, as part of the 'Voices' project (which more generally explored 'how we speak in the UK now'). The fact that over 5,000 responses were received shows how interested speakers of English are in each others' accents; and the results and comments make fascinating reading (http://www.bbc.co.uk/voices/yourvoice/poll_results.shtml, accessed 13 September 2006). Part of the fascination, however, lies in the opacity of many of the comments, which are difficult to interpret in phonetic terms, as shown in (1).(1) (a) I don't really like the Birmingham accent that much (even though I've got one), but I do like the Black Country Accent . . . It sounds singy and old-fashioned. (S. Murphy, Birmingham) (b) Yorksher accent and more specifically 'ull accent rules!. (red badger, 'ull) (c) I never notice my accent until someone points it out and the way we shorten words and the rs we sound here in Bristol. (Debbie Smith, Bristol) Many of these comments are straightforwardly attitudinal, and are expressed in terms of liking one accent and not liking another; and typically respondents are positive about their own varieties (though with distressing frequency this is not the case for the denizens of Birmingham). More interesting are the cases where respondents attempt to ground their comments with reference to particular phonetic or phonological characteristics of varieties, as shown in (1) by 'red badger', who encodes [h]-dropping in his/her response, and in Debbie Smith's comment on Bristol 'r'. These mentions, however, are hardly very specific, and are consequently hard to interpret. What is the issue with 'r' in Bristol here? For instance, is it the phonetic quality that counts, or its distribution? And does it matter whether someone is co...

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Linguists have traditionally represented patterns of divergence within a language family in terms of either a 'splits' model, corresponding to a branching family tree structure, or the wave model, resulting in a (dialect) continuum. Recent phylogenetic analyses, however, have tended to assume the former as a viable idealization also for the latter. But the contrast matters, for it typically reflects different processes in the real world: speaker populations either separated by migrations, or expanding over continuous territory. Since history often leaves a complex of both patterns within the same language family, ideally we need a single model to capture both, and tease apart the respective contributions of each. The 'network' type of phylogenetic method offers this, so we review recent applications to language data. Most have used lexical data, encoded as binary or multi-state characters. We look instead at continuous distance measures of divergence in phonetics. Our output networks combine branch-and continuum-like signals in ways that correspond well to known histories (illustrated for Germanic, and particularly English). We thus challenge the traditional insistence on shared innovations, setting out a new, principled explanation for why complex language histories can emerge correctly from distance measures, despite shared retentions and parallel innovations.

Although borrowing and contact are recognised as important factors in language histories, there is no clear and agreed way of dealing with their effects on methods like traditional lexicostatistics. We argue that one promising approach involves subdividing standard meaning‐lists into more and less conservative sublists. Differences between trees or networks generated from these sublists may then indicate borrowing. This approach has been tested on Indo‐European, but here we apply it to languages of the Andes in an attempt to answer the vexed Quechumara question: are Quechua and Aymara genetically related, or linked only by contact? Our evidence suggests that contact is the more likely explanation for parallels between Quechua and Aymara.