Cultural phylogenetics of the Tupi language family in lowland South America

Hunter-gatherer genetics research: Importance and avenues

Major developments in the field of genetics in the past few decades have revolutionised notions of what it means to be human. Although currently only a few populations around the world practise a hunting and gathering lifestyle, this mode of subsistence has characterised members of our species since its very origins and allowed us to migrate across the planet. Therefore, the geographical distribution of hunter-gatherer populations, dependence on local ecosystems and connections to past populations and neighbouring groups have provided unique insights into our evolutionary origins. However, given the vulnerable status of hunter-gatherers worldwide, the development of the field of anthropological genetics requires that we reevaluate how we conduct research with these communities. Here, we review how the inclusion of hunter-gatherer populations in genetics studies has advanced our understanding of human origins, ancient population migrations and interactions as well as phenotypic adaptations and adaptability to different environments, and the important scientific and medical applications of these advancements. At the same time, we highlight the necessity to address yet unresolved questions and identify areas in which the field may benefit from improvements.

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

Tupí-Guaraní is one of the largest branches of the Tupían 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 Tapajós-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.

Predicting the geographic distribution of ancient Amazonian archaeological sites with machine learning

Amazonia has as least two major centers of ancient human social complexity, but the full geographic extents of these centers remain uncertain. Across the southern rim of Amazonia, over 1,000 earthwork sites comprised of fortified settlements, mound villages, and ditched enclosures with geometric designs known as geoglyphs have been discovered. Qualitatively distinct and densely located along the lower stretches of major river systems and the Atlantic coast are Amazonian Dark Earth sites (ADEs) with deep anthropogenic soils enriched by long-term human habitation. Models predicting the geographic extents of earthworks and ADEs can assist in their discovery and preservation and help answer questions about the full degree of indigenous landscape modifications across Amazonia. We classify earthworks versus ADEs versus other non-earthwork/non-ADE archaeological sites with multi-class machine learning algorithms using soils, climate, and distances to rivers of different types and sizes as geospatial predictors. Model testing is done with spatial cross-validation, and the best model at the optimal spatial scale of 1 km has an Area Under the Curve of 0.91. Our predictive model has led to the discovery of 13 new geoglyphs, and it pinpoints specific areas with high probabilities of undiscovered archaeological sites that are currently hidden by rainforests. The limited, albeit impressive, predicted extents of earthworks and ADEs means that other non-ADE/non-earthwork sites are expected to predominate most of Western and Northern Amazonia.

A genomic perspective on South American human history

It has generally been accepted that the current indigenous peoples of the Americas are derived from ancestors from northeastern Asia. The latter were believed to have spread into the American continent by the end of the Last Glacial Maximum. In this sense, a joint and in-depth study of the earliest settlement of East Asia and the Americas is required to elucidate these events accurately. The first Americans underwent an adaptation process to the Americas' vast environmental diversity, mediated by biological and cultural evolution and niche construction, resulting in enormous cultural diversity, a wealth of domesticated species, and extensive landscape modifications. Afterward, in the Late Holocene, the advent of intensive agricultural food production systems, sedentism, and climate change significantly reshaped genetic and cultural diversity across the continent, particularly in the Andes and Amazonia. Furthermore, starting around the end of the 15th century, European colonization resulted in massive extermination of indigenous peoples and extensive admixture. Thus, the present review aims to create a comprehensive picture of the main events involved in the formation of contemporary South American indigenous populations and the dynamics responsible for shaping their genetic diversity by integrating current genetic data with evidence from archeology, linguistics and other disciplines.

Maize dispersal patterns associated with different types of endosperm and migration of indigenous groups in lowland South America

BACKGROUND AND AIMS

The lowlands of South America appear to be remarkably important in the evolutionary history of maize, due to new evidence that suggests that maize dispersed from Mexico and arrived in this region in a state of partial domestication. This study aimed to identify dispersal patterns of maize genetic diversity in this part of the continent.

METHODS

A total of 170 maize accessions were characterized with 4398 single nucleotide polymorphisms (SNPs) and analysed to determine if maize dispersal was associated with types of endosperm and indigenous language families.

KEY RESULTS

Four genetic groups were identified in the discriminant analysis of principal components and five groups in the cluster analysis (neighbour-joining method). The groups were structured according to the predominance of endosperm types (popcorn, floury, flint/semi-flint). Spatial principal component analysis of genetic variation suggests different dispersal patterns for each endosperm type and can be associated with hypotheses of expansions of different indigenous groups.

CONCLUSIONS

From a possible origin in Southwestern Amazonia, different maize dispersal routes emerged: (1) towards Northern Amazonia, which continued towards the Caatinga and south-eastern Atlantic Forest (Floury); (2) towards Southern Brazil, passing through the Cerrado and Southern Atlantic Forest reaching the Pampa region (Floury); and (3) along the Atlantic Coast, following Tupi movements originating from two separate expansions: one (Tupinamba) from north to south, and the other (Guarani) in the opposite direction, from south to north (flint, floury and popcorn).

Food storage facilitates professional religious specialization in hunter-gatherer societies

Professional religious specialists centralised religious authority in early human societies and represented some of the earliest instances of formalised social leadership. These individuals played a central role in the emergence of organised religion and transitions to more stratified human societies. Evolutionary theories highlight a range of environmental, economic and social factors that are potentially causally related to the emergence of professional religious specialists in human history. There remains little consensus over the relative importance of these factors and whether professional religious specialists were the outcome or driver of increased socio-cultural complexity. We built a global dataset of hunter-gatherer societies and developed a novel method of exploratory phylogenetic path analysis. This enabled us to systematically identify the factors associated with the emergence of professional religious specialists and infer the directionality of causal dependencies. We find that environmental predictability, environmental richness, pathogen load, social leadership and food storage systems are all correlated with professional religious specialists. However, only food storage is directly related to the emergence of professional religious specialists. Our findings are most consistent with the claim that the early stages of organised religion were the outcome rather than driver of increased socio-economic complexity.

TuLeD (Tupían lexical database): introducing a database of a South American language family

The last two decades witnessed a rapid growth of publicly accessible online language resources. This has allowed for valuable data on lesser known languages to become available. Such resources provide linguists with opportunities for advancing their research. Yet despite the proliferation of lexical and morphological databases, the ca. 456 languages spoken in South America are poorly represented, particularly the Tupían family, which is the largest on the continent. This paper therefore introduces and discusses TuLeD, a lexical database exclusively devoted to a South American language family. It provides a comprehensive list of lexical items presented in a unified transcription for all languages with cognacy assignment and relevant (cultural or linguistic) notes. One of the main goals of TuLeD is to become a full-fledged database and a benchmark for linguistic studies on South American languages in general and the Tupían family in particular.

Reassessing the role of climate change in the Tupi expansion (South America, 5000-500 BP)

The expansion of forest farmers across tropical lowland South America during the Late Holocene has long been connected to climate change. The more humid conditions established during the Late Holocene are assumed to have driven the expansion of forests, which would have facilitated the dispersal of cultures that practised agroforestry. The Tupi, a language family of widespread distribution in South America, occupies a central place in the debate. Not only are they one of the largest families in the continent, but their expansion from an Amazonian homeland has long been hypothesized to have followed forested environments wherever they settled. Here, we assess that hypothesis using a simulation approach. We employ equation-based and cellular automaton models, simulating demic-diffusion processes under two different scenarios: a null model in which all land cells can be equally settled, and an alternative model in which non-forested cells cannot be settled or delay the expansion. We show that including land cover as a constraint to movement results in a better approximation of the Tupi expansion as reconstructed by archaeology and linguistics.

Diversity begets diversity in mammal species and human cultures

Across the planet the biogeographic distribution of human cultural diversity tends to correlate positively with biodiversity. In this paper we focus on the biogeographic distribution of mammal species and human cultural diversity. We show that not only are these forms of diversity similarly distributed in space, but they both scale superlinearly with environmental production. We develop theory that explains that as environmental productivity increases the ecological kinetics of diversity increases faster than expected because more complex environments are also more interactive. Using biogeographic databases of the global distributions of mammal species and human cultures we test a series of hypotheses derived from this theory and find support for each. For both mammals and cultures, we show that (1) both forms of diversity increase exponentially with ecological kinetics; (2) the kinetics of diversity is faster than the kinetics of productivity; (3) diversity scales superlinearly with environmental productivity; and (4) the kinetics of diversity is faster in increasingly productive environments. This biogeographic convergence is particularly striking because while the dynamics of biological and cultural evolution may be similar in principle the underlying mechanisms and time scales are very different. However, a common currency underlying all forms of diversity is ecological kinetics; the temperature-dependent fluxes of energy and biotic interactions that sustain all forms of life at all levels of organization. Diversity begets diversity in mammal species and human cultures because ecological kinetics drives superlinear scaling with environmental productivity.

The emergence of locally adaptive institutions: Insights from traditional social structures of East African pastoralists

Humans inhabit the widest range of ecological and social niches of any mammal. Yet each ecological and social environment presents a set of challenges that we must solve in order to successfully inhabit it. We are able to do so by building institutions that can flexibly respond to changing circumstances. Institutions that solve adaptive challenges necessary for human sociality, such as how to resolve conflicts, find mates, and extract and distribute resources, are termed locally adaptive institutions. The design of locally adaptive institutions promotes coordination and cooperation among unrelated individuals, reflecting the constraints of the particular ecological and social challenges to which they are responsive. Institutions generally are enabled by a suite of social and psychological mechanisms, including norm compliance, self-interested design, selective imitation, and cultural group selection among others. The development of locally adaptive institutions are likely to be especially shaped by self-interested design in which agents are sensitive to the payoffs from various norms and choose to enforce and follow those which they anticipate to be most beneficial to themselves. Exogenous shocks, including the advent of material and cultural technologies, population pressures, or even group conflict can contribute to the modification of existing social institutions and the development of new social structures. Using several case examples from traditional east African pastoralist societies, I illustrate how ecological and social pressures shape the development of social norms that underlie locally adaptive social institutions and facilitate continued cooperation in the face of change at scales ranging from local to global.

Archaeological expansions in tropical South America during the late Holocene: Assessing the role of demic diffusion

Human expansions motivated by the spread of farming are one of the most important processes that shaped cultural geographies during the Holocene. The best known example of this phenomenon is the Neolithic expansion in Europe, but parallels in other parts of the globe have recently come into focus. Here, we examine the expansion of four archaeological cultures of widespread distribution in lowland South America, most of which originated in or around the Amazon basin and spread during the late Holocene with the practice of tropical forest agriculture. We analyze spatial gradients in radiocarbon dates of each culture through space-time regressions, allowing us to establish the most likely geographical origin, time and speed of expansion. To further assess the feasibility of demic diffusion as the process behind the archaeological expansions in question, we employ agent-based simulations with demographic parameters derived from the ethnography of tropical forest farmers. We find that, while some expansions can be realistically modeled as demographic processes, others are not easily explainable in the same manner, which is possibly due to different processes driving their dispersal (e.g. cultural diffusion) or problematic/incomplete archaeological data.

Identifying post-marital residence patterns in prehistory: A phylogenetic comparative analysis of dwelling size

Post-marital residence patterns are an important aspect of human social organization. However, identifying such patterns in prehistoric societies is challenging since they leave almost no direct traces in archaeological records. Cross-cultural researchers have attempted to identify correlates of post-marital residence through the statistical analysis of ethnographic data. Several studies have demonstrated that, in agricultural societies, large dwellings (over ca. 65 m²) are associated with matrilocality (spouse resides with or near the wife’s family), whereas smaller dwellings are associated with patrilocality (spouse resides with or near the husband’s family). In the present study, we tested the association between post-marital residence and dwelling size (average house floor area) using phylogenetic comparative methods and a global sample of 86 pre-industrial societies, 22 of which were matrilocal. Our analysis included the presence of agriculture, sedentism, and durability of house construction material as additional explanatory variables. The results confirm a strong association between matrilocality and dwelling size, although very large dwellings (over ca. 200 m²) were found to be associated with all types of post-marital residence. The best model combined dwelling size, post-marital residence pattern, and sedentism, the latter being the single best predictor of house size. The effect of agriculture on dwelling size becomes insignificant once the fixity of settlement is taken into account. Our results indicate that post-marital residence and house size evolve in a correlated fashion, namely that matrilocality is a predictable response to an increase in dwelling size. As such, we suggest that reliable inferences about the social organization of prehistoric societies can be made from archaeological records.

Genomic insight into the origins and dispersal of the Brazilian coastal natives

In the 15th century, ∼900,000 Native Americans, mostly Tupí speakers, lived on the Brazilian coast. By the end of the 18th century, the coastal native populations were declared extinct. The Tupí arrived on the east coast after leaving the Amazonian basin ∼2,000 y before present; however, there is no consensus on how this migration occurred: toward the northern Amazon and then directly to the Atlantic coast, or heading south into the continent and then migrating to the coast. Here we leveraged genomic data from one of the last remaining putative representatives of the Tupí coastal branch, a small, admixed, self-reported Tupiniquim community, as well as data of a Guaraní Mbyá native population from Southern Brazil and of three other native populations from the Amazonian region. We demonstrated that the Tupiniquim Native American ancestry is not related to any extant Brazilian Native American population already studied, and thus they could be considered the only living representatives of the extinct Tupí branch that used to settle the Atlantic Coast of Brazil. Furthermore, these data show evidence of a direct migration from Amazon to the Northeast Coast in pre-Columbian time, giving rise to the Tupí Coastal populations, and a single distinct migration southward that originated the Guaraní people from Brazil and Paraguay. This study elucidates the population dynamics and diversification of the Brazilian natives at a genomic level, which was made possible by recovering data from the Brazilian coastal population through the genomes of mestizo individuals.

Environmental conditions do not predict diversification rates in the Bantu languages

The global distribution of language diversity mirrors that of several variables related to ecosystem productivity. It has been argued that this is driven by the size of social networks, which tend to be larger in harsher climates to ensure food security, leading to reduced language divergence. Is this pattern purely synchronic, or is there also a quantifiable relationship between environmental conditions and language diversification over time? We used a spatio-temporal phylogeny of the Bantu language family to estimate local diversification rates at the times and locations of language divergence. We compared these data against spatially-explicit reconstructions of several palaeoclimate and palaeovegetation variables (mean annual temperature and the temperature of the coldest and warmest quarter, annual precipitation and the precipitation of the wettest and driest quarter, growing degree days, the length of the growing season, and net primary production), to investigate a potential link between local environmental factors and diversification rates in the Bantu languages. A regression analysis does not suggest a statistically significant relationship between climatic or ecological variables and linguistic diversification over time. We find a strong positive correlation between pairwise linguistic and geographic distances in the Bantu languages, arguing for a dominant role of isolation as a result of the rapid Bantu expansion that might have overwhelmed any potential influence of local environmental factors.

On 'lost' indigenous etymological origins with the specific case of the name Ameiva

Modern biology builds upon the historic exploration of the natural world. Recognizing the origin of a species’ name is one path to honor the historic exploration and description of the natural world and the indigenous peoples that lived closely with organisms prior to their description. While digitization of historic papers catalogued in databases such as the Biodiversity Heritage Library (BHL) allows for searching of the first use and origin of names, the rapid pace of taxonomic publishing can occlude a thorough search for etymologies. The etymological origin of the genus name Ameiva is one such case; while unattributed in multiple recent works, it is of Tupí language origin. The first description was in the Historiae Rerum Naturalium Brasiliae by George Marcgrave (1648). Ameiva was the name used by Marcgrave’s Amerindian hosts in 17^th century Dutch Brazil, where local people spoke the now extinct language Tupí. The Tupí origin was not lost, however, until as recently as the 2000s. Herein, the pre- and post-Linnaean use of the name Ameiva is traced and when the name is attributed to the Tupí language and to Marcgrave through time it is noted. The opportunity to discover and/or recover etymological origins, especially names from extinct and indigenous languages, provides insight into the early Western sciences. Careful study of etymology by naturalists is consistent with the idea that science is an evolving process with many predecessors to appreciate.

On ‘lost’ indigenous etymological origins with the specific case of the name Ameiva

Modern biology builds upon the historic exploration of the natural world. Recognizing the origin of a species’ name is one path to honor the historic exploration and description of the natural world and the indigenous peoples that lived closely with organisms prior to their description. While digitization of historic papers catalogued in databases such as the Biodiversity Heritage Library (BHL) allows for searching of the first use and origin of names, the rapid pace of taxonomic publishing can occlude a thorough search for etymologies. The etymological origin of the genus name Ameiva is one such case; while unattributed in multiple recent works, it is of Tupí language origin. The first description was in the Historiae Rerum Naturalium Brasiliae by George Marcgrave (1648). Ameiva was the name used by Marcgrave’s Amerindian hosts in 17th century Dutch Brazil, where local people spoke the now extinct language Tupí. The Tupí origin was not lost, however, until as recently as the 2000s. Herein, the pre- and post-Linnaean use of the name Ameiva is traced and when the name is attributed to the Tupí language and to Marcgrave through time it is noted. The opportunity to discover and/or recover etymological origins, especially names from extinct and indigenous languages, provides insight into the early Western sciences. Careful study of etymology by naturalists is consistent with the idea that science is an evolving process with many predecessors to appreciate.

The cultural evolution of shamanism

Shamans, including medicine men, mediums, and the prophets of religious movements, recur across human societies. Shamanism also existed among nearly all documented hunter-gatherers, likely characterized the religious lives of many ancestral humans, and is often proposed by anthropologists to be the "first profession," representing the first institutionalized division of labor beyond age and sex. In this article, I propose a cultural evolutionary theory to explain why shamanism consistently develops and, in particular, (1) why shamanic traditions exhibit recurrent features around the world; (2) why shamanism professionalizes early, often in the absence of other specialization; and (3) how shifting social conditions affect the form or existence of shamanism. According to this theory, shamanism is a set of traditions developed through cultural evolution that adapts to people's intuitions to convince observers that a practitioner can influence otherwise unpredictable, significant events. The shaman does this by ostensibly transforming during initiation and trance, violating folk intuitions of humanness to assure group members that he or she can interact with the invisible forces that control uncertain outcomes. Entry requirements for becoming a shaman persist because the practitioner's credibility depends on his or her "transforming." This contrasts with dealing with problems that have identifiable solutions (such as building a canoe), in which credibility hinges on showing results and outsiders can invade the jurisdiction by producing the outcome. Shamanism is an ancient human institution that recurs because of the capacity of cultural evolution to produce practices adapted to innate psychological tendencies.

Hunter-Gatherers and the Origins of Religion

Recent studies of the evolution of religion have revealed the cognitive underpinnings of belief in supernatural agents, the role of ritual in promoting cooperation, and the contribution of morally punishing high gods to the growth and stabilization of human society. The universality of religion across human society points to a deep evolutionary past. However, specific traits of nascent religiosity, and the sequence in which they emerged, have remained unknown. Here we reconstruct the evolution of religious beliefs and behaviors in early modern humans using a global sample of hunter-gatherers and seven traits describing hunter-gatherer religiosity: animism, belief in an afterlife, shamanism, ancestor worship, high gods, and worship of ancestors or high gods who are active in human affairs. We reconstruct ancestral character states using a time-calibrated supertree based on published phylogenetic trees and linguistic classification and then test for correlated evolution between the characters and for the direction of cultural change. Results indicate that the oldest trait of religion, present in the most recent common ancestor of present-day hunter-gatherers, was animism, in agreement with long-standing beliefs about the fundamental role of this trait. Belief in an afterlife emerged, followed by shamanism and ancestor worship. Ancestor spirits or high gods who are active in human affairs were absent in early humans, suggesting a deep history for the egalitarian nature of hunter-gatherer societies. There is a significant positive relationship between most characters investigated, but the trait “high gods” stands apart, suggesting that belief in a single creator deity can emerge in a society regardless of other aspects of its religion.

The Origins and Maintenance of Female Genital Modification across Africa : Bayesian Phylogenetic Modeling of Cultural Evolution under the Influence of Selection

We present formal evolutionary models for the origins and persistence of the practice of Female Genital Modification (FGMo). We then test the implications of these models using normative cross-cultural data on FGMo in Africa and Bayesian phylogenetic methods that explicitly model adaptive evolution. Empirical evidence provides some support for the findings of our evolutionary models that the de novo origins of the FGMo practice should be associated with social stratification, and that social stratification should place selective pressures on the adoption of FGMo; these results, however, are tempered by the finding that FGMo has arisen in many cultures that have no social stratification, and that forces operating orthogonally to stratification appear to play a more important role in the cross-cultural distribution of FGMo. To explain these cases, one must consider cultural evolutionary explanations in conjunction with behavioral ecological ones. We conclude with a discussion of the implications of our study for policies designed to end the practice of FGMo.

The domestication of Amazonia before European conquest

During the twentieth century, Amazonia was widely regarded as relatively pristine nature, little impacted by human history. This view remains popular despite mounting evidence of substantial human influence over millennial scales across the region. Here, we review the evidence of an anthropogenic Amazonia in response to claims of sparse populations across broad portions of the region. Amazonia was a major centre of crop domestication, with at least 83 native species containing populations domesticated to some degree. Plant domestication occurs in domesticated landscapes, including highly modified Amazonian dark earths (ADEs) associated with large settled populations and that may cover greater than 0.1% of the region. Populations and food production expanded rapidly within land management systems in the mid-Holocene, and complex societies expanded in resource-rich areas creating domesticated landscapes with profound impacts on local and regional ecology. ADE food production projections support estimates of at least eight million people in 1492. By this time, highly diverse regional systems had developed across Amazonia where subsistence resources were created with plant and landscape domestication, including earthworks. This review argues that the Amazonian anthrome was no less socio-culturally diverse or populous than other tropical forested areas of the world prior to European conquest.

Are Isolated Indigenous Populations Headed toward Extinction?

At least 50 indigenous groups spread across lowland South America remain isolated and have only intermittent and mostly hostile interactions with the outside world. Except in emergency situations, the current policy of governments in Brazil, Colombia, and Peru towards isolated tribes is a “leave them alone” strategy, in which isolated groups are left uncontacted. However, these no-contact policies are based on the assumption that isolated populations are healthy and capable of persisting in the face of mounting external threats, and that they can maintain population viability in the long-term. Here, we test this assumption by tracking the sizes and movements of cleared horticultural areas made by 8 isolated groups over the last 10–14 years. We used deforestation data derived from remote sensing Landsat satellite sensors to identify clearings, and those were then validated and assessed with high-resolution imagery. We found only a single example of a relatively large and growing population (c. 50 cleared ha and 400 people), whereas all of the other 7 groups exhibited much smaller villages and gardens with no sizable growth through time. These results indicated that the smaller groups are critically endangered, and it prompts an urgent re-thinking of policies toward isolated populations, including plans for well-organized contacts that may help save lives and rescue isolated indigenous populations from imminent extinction.

Cultural group selection plays an essential role in explaining human cooperation: A sketch of the evidence

Human cooperation is highly unusual. We live in large groups composed mostly of non-relatives. Evolutionists have proposed a number of explanations for this pattern, including cultural group selection and extensions of more general processes such as reciprocity, kin selection, and multi-level selection acting on genes. Evolutionary processes are consilient; they affect several different empirical domains, such as patterns of behavior and the proximal drivers of that behavior. In this target article, we sketch the evidence from five domains that bear on the explanatory adequacy of cultural group selection and competing hypotheses to explain human cooperation. Does cultural transmission constitute an inheritance system that can evolve in a Darwinian fashion? Are the norms that underpin institutions among the cultural traits so transmitted? Do we observe sufficient variation at the level of groups of considerable size for group selection to be a plausible process? Do human groups compete, and do success and failure in competition depend upon cultural variation? Do we observe adaptations for cooperation in humans that most plausibly arose by cultural group selection? If the answer to one of these questions is "no," then we must look to other hypotheses. We present evidence, including quantitative evidence, that the answer to all of the questions is "yes" and argue that we must take the cultural group selection hypothesis seriously. If culturally transmitted systems of rules (institutions) that limit individual deviance organize cooperation in human societies, then it is not clear that any extant alternative to cultural group selection can be a complete explanation.

tqDist: a library for computing the quartet and triplet distances between binary or general trees

tqDist is a software package for computing the triplet and quartet distances between general rooted or unrooted trees, respectively. The program is based on algorithms with running time [Formula: see text] for the triplet distance calculation and [Formula: see text] for the quartet distance calculation, where n is the number of leaves in the trees and d is the degree of the tree with minimum degree. These are currently the fastest algorithms both in theory and in practice.

AVAILABILITY AND IMPLEMENTATION

tqDist can be installed on Windows, Linux and Mac OS X. Doing this will install a set of command-line tools together with a Python module and an R package for scripting in Python or R. The software package is freely available under the GNU LGPL licence at http://birc.au.dk/software/tqDist.

Algorithms for computing the triplet and quartet distances for binary and general trees

Distance measures between trees are useful for comparing trees in a systematic manner, and several different distance measures have been proposed. The triplet and quartet distances, for rooted and unrooted trees, respectively, are defined as the number of subsets of three or four leaves, respectively, where the topologies of the induced subtrees differ. These distances can trivially be computed by explicitly enumerating all sets of three or four leaves and testing if the topologies are different, but this leads to time complexities at least of the order n³ or n⁴ just for enumerating the sets. The different topologies can be counted implicitly, however, and in this paper, we review a series of algorithmic improvements that have been used during the last decade to develop more efficient algorithms by exploiting two different strategies for this; one based on dynamic programming and another based on coloring leaves in one tree and updating a hierarchical decomposition of the other.

GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework

GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis.

Evidence of traditional knowledge loss among a contemporary indigenous society

As biological and linguistic diversity, the world's cultural diversity is on decline. However, to date there are no estimates of the rate at which the specific cultural traits of a group disappear, mainly because we lack empirical data to assess how the cultural traits of a given population change over time. Here we estimate changes in cultural traits associated to the traditional knowledge of wild plant uses among an Amazonian indigenous society. We collected data among 1151 Tsimane' Amerindians at two periods of time. Results show that between 2000 and 2009, Tsimane' adults experienced a net decrease in the report of plant uses ranging from 9% (for the female subsample) to 26% (for the subsample of people living close to towns), equivalent to a 1 to 3 % per year. Results from a Monte Carlo simulation show that the observed changes were not the result of randomness. Changes were more acute for men than for women and for informants living in villages close to market towns than for informants settled in remote villages. The Tsimane' could be abandoning their traditional knowledge as they perceive that this form of knowledge do not equip them well to deal with the new socio-economic and cultural conditions they face nowadays.