Population genetic structure and colonisation history of the tool-using New Caledonian crow

New Caledonian crows exhibit considerable variation in tool making between populations. Here, we present the first study of the species' genetic structure over its geographical distribution. We collected feathers from crows on mainland Grande Terre, the inshore island of Toupéti, and the nearby island of Maré where it is believed birds were introduced after European colonisation. We used nine microsatellite markers to establish the genotypes of 136 crows from these islands and classical population genetic tools as well as Approximate Bayesian Computations to explore the distribution of genetic diversity. We found that New Caledonian crows most likely separate into three main distinct clusters: Grande Terre, Toupéti and Maré. Furthermore, Toupéti and Maré crows represent a subset of the genetic diversity observed on Grande Terre, confirming their mainland origin. The genetic data are compatible with a colonisation of Maré taking place after European colonisation around 1900. Importantly, we observed (1) moderate, but significant, genetic differentiation across Grande Terre, and (2) that the degree of differentiation between populations on the mainland increases with geographic distance. These data indicate that despite individual crows' potential ability to disperse over large distances, most gene flow occurs over short distances. The temporal and spatial patterns described provide a basis for further hypothesis testing and investigation of the geographical variation observed in the tool skills of these crows.     

Bringing together linguistic and genetic evidence to test the Bantu expansion

The expansion of Bantu languages represents one of the most momentous events in the history of Africa. While it is well accepted that Bantu languages spread from their homeland (Cameroon/Nigeria) approximately 5000 years ago (ya), there is no consensus about the timing and geographical routes underlying this expansion. Two main models of Bantu expansion have been suggested: The 'early-split' model claims that the most recent ancestor of Eastern languages expanded north of the rainforest towards the Great Lakes region approximately 4000 ya, while the 'late-split' model proposes that Eastern languages diversified from Western languages south of the rainforest approximately 2000 ya. Furthermore, it is unclear whether the language dispersal was coupled with the movement of people, raising the question of language shift versus demic diffusion. We use a novel approach taking into account both the spatial and temporal predictions of the two models and formally test these predictions with linguistic and genetic data. Our results show evidence for a demic diffusion in the genetic data, which is confirmed by the correlations between genetic and linguistic distances. While there is little support for the early-split model, the late-split model shows a relatively good fit to the data. Our analyses demonstrate that subsequent contact among languages/populations strongly affected the signal of the initial migration via isolation by distance.     

Linguistic Magic Bullets in the Making of a Modernist Anthropology

This article engages current debates about concepts of culture in U.S. anthropology by examining how assumptions about language shape them. Characterizing linguistic patterns as particularly inaccessible to conscious introspection, Franz Boas suggested that culture is similarly automatic and unconscious—except for anthropologists. He used this notion in attempting to position the discipline as the obligatory passage point for academic and public debate about difference. Unfortunately, this mode of inserting linguistics in the discipline, which has long outlived Boas, reifies language ideologies by promoting simplistic models that belie the cultural complexity of human communication. By pointing to the way that recent work in linguistic anthropology has questioned key assumptions that shaped Boas's concept of culture, the article urges other anthropologists to stop asking their linguistic colleagues for magic bullets and to appreciate the critical role that examining linguistic ideologies and practices can play in discussions of the politics of culture. [Keywords: Franz Boas, culture concept, linguistic anthropology, language ideologies, scientific authority]     

Modelling the Geographical Origin of Rice Cultivation in Asia Using the Rice Archaeological Database

We have compiled an extensive database of archaeological evidence for rice across Asia, including 400 sites from mainland East Asia, Southeast Asia and South Asia. This dataset is used to compare several models for the geographical origins of rice cultivation and infer the most likely region(s) for its origins and subsequent outward diffusion. The approach is based on regression modelling wherein goodness of fit is obtained from power law quantile regressions of the archaeologically inferred age versus a least-cost distance from the putative origin(s). The Fast Marching method is used to estimate the least-cost distances based on simple geographical features. The origin region that best fits the archaeobotanical data is also compared to other hypothetical geographical origins derived from the literature, including from genetics, archaeology and historical linguistics. The model that best fits all available archaeological evidence is a dual origin model with two centres for the cultivation and dispersal of rice focused on the Middle Yangtze and the Lower Yangtze valleys.     

Influence of the geographical locations on the agronomical and technological potentialities of the olive tree (Olea europaea L.) in Tunisia

This study aims at characterization four cultivars of the olive trees, Chétoui, Chemlali, Gerboui, and Cha?bi, cultivated in three different geographical locations, from pomological and technological points of view. The pomological characters of the fruit are influenced by the geographical location. Each individual of the same cultivar expresses different pomological characters. We have noted a significant fluctuation of the flush percentage in three Cha?bi individuals according to their geographical site; it varies from 49.06 to 82.19%. The three Gerboui individuals showed a significant variability of the fruit weight (from 1.13 to 3.17 g). Fluctuations of olive oil contents were also observed. Several fatty acid compositions showed some variation. The oleic and linoleic acid contents varied among individuals from Chétoui and Cha?bi. Moreover, the individuals of the cultivar Chemlali showed a variation of their content in palmitic and palmitoleic acids. Indeed, each individual of a cultivar showed its own potentialities, which are reflected by its pomological and technological characters. According to their geographical location, individuals from a given cultivar displayed diverse potentialities.     

Climate and habitat barriers to dispersal in the highly mobile grey wolf

We reanalysed published data to evaluate whether climate and habitat are barriers to dispersal in one of the most mobile and widely distributed mammals, the grey wolf (Canis lupus). Distance-based redundancy analysis (dbRDA) was used to examine the amount of variation in genetic distances that could be explained by an array of environmental factors, including geographical distance. Patterns in genetic variation were also examined using MDS plots among populations and relationships between genetic structure and individual environmental variables were further explored using the BIOENV procedure. We found that, contrary to a previous report, a pattern of isolation with distance is evident on a continental scale in the North American wolf population. This pattern is apparently related to climate and habitat. Specifically, vegetation types appear to play a role in the genetic dissimilarities among populations. When we controlled for the effect of spatial variation, climate was still associated with genetic distance. Further, partitioning of geographical distances into latitudinal and longitudinal axes revealed that the east-west gradient had the strongest relationship with genetic distance. We suggest two possible mechanisms by which environmental conditions may influence the dispersal decisions made by wolves.     

Phylin 2.0: Extending the phylogeographical interpolation method to include uncertainty and user‐defined distance metrics

Estimating geographical ranges of intra‐specific evolutionary lineages is crucial to the fields of biogeography, evolution, and biodiversity conservation. Models of isolation mechanisms often consider multiple distances in order to explain genetic divergence. Yet, the available methods to estimate the geographical ranges of lineages are based on direct geographical distances, neglecting other distance metrics that can better explain the spatial genetic structure. We extended the phylogeographical interpolation method (phylin ) in order to accommodate user‐defined distance metrics and to incorporate the uncertainty associated with genetic distance calculation. These new features were tested with simulated and empirical data sets. Multiple distance matrices were generated including geographical, resistance, and environmental distances to derive maps of lineage occurrence. The new additions to this method improved the ability to predict lineage occurrence, even with low sample size. We used a regression framework to quantify the relationship between the genetic divergence and competing distance matrices representing potential isolation processes that are subsequently used in the interpolation process. Including uncertainty in tree topology and the different distance matrices improved the robustness of the variograms, allowing a better fit of the theoretical model of spatial dependence. The improvements to the method increase its potential application in other fields. Accurately mapping genetic divergence can help to locate potential contact zones between lineages as well as barriers to gene flow, which has a broad interest in biogeographical and evolutionary studies. Additionally, conservation efforts could benefit from the integration of genetic variation and landscape features in a spatially explicit framework.     

Quantitative social dialectology: explaining linguistic variation geographically and socially

In this study we examine linguistic variation and its dependence on both social and geographic factors. We follow dialectometry in applying a quantitative methodology and focusing on dialect distances, and social dialectology in the choice of factors we examine in building a model to predict word pronunciation distances from the standard Dutch language to 424 Dutch dialects. We combine linear mixed-effects regression modeling with generalized additive modeling to predict the pronunciation distance of 559 words. Although geographical position is the dominant predictor, several other factors emerged as significant. The model predicts a greater distance from the standard for smaller communities, for communities with a higher average age, for nouns (as contrasted with verbs and adjectives), for more frequent words, and for words with relatively many vowels. The impact of the demographic variables, however, varied from word to word. For a majority of words, larger, richer and younger communities are moving towards the standard. For a smaller minority of words, larger, richer and younger communities emerge as driving a change away from the standard. Similarly, the strength of the effects of word frequency and word category varied geographically. The peripheral areas of the Netherlands showed a greater distance from the standard for nouns (as opposed to verbs and adjectives) as well as for high-frequency words, compared to the more central areas. Our findings indicate that changes in pronunciation have been spreading (in particular for low-frequency words) from the Hollandic center of economic power to the peripheral areas of the country, meeting resistance that is stronger wherever, for well-documented historical reasons, the political influence of Holland was reduced. Our results are also consistent with the theory of lexical diffusion, in that distances from the Hollandic norm vary systematically and predictably on a word by word basis.     

Spatial Variations in the Abundance of Sporophila Seedeaters in the Southern Neotropics: Contrasting the Effects of Agricultural Development and Geographical Position

Human alterations of the habitat may interfere with the natural processes that determine spatial patterns of species abundance. We examine the geographical position hypothesis and the agricultural transformation hypothesis to explain spatial patterns in the abundance of seedeater species (Sporophila spp.) in the southern Neotropics. The geographical position hypothesis predicts decreasing abundance with increasing distance from the center to the edge of a species' geographical range, and the agricultural transformation hypothesis predicts changing abundance as a response of variations in agricultural intensity. Bird abundance and the proportion of agricultural land were estimated for 16 transects covering 500 km along a gradient of both increasing agricultural intensity and increasing distance from the center of the species' geographical ranges. We found no evidence of distance effects on seedeater abundance. Responses to agricultural intensity varied among species. Neither the geographical position nor the agricultural transformation seemed to explain the pattern of abundance of Double-collared seedeaters (S. caerulescens). Agricultural intensity accounted for 63% and 99% of the spatial variation in the abundance of Dark-throated (S. ruficollis) and Tawny-bellied (S. hypoxantha) seedeaters, supporting the agricultural transformation hypothesis. The Dark-throated seedeater seem to be more tolerant to agricultural transformation than the Tawny-bellied seedeater, as they were not recorded in areas with more than 60% and 20% of agricultural lands, respectively. Our results indicate that the Dark-throated seedeater and the Tawny-bellied seedeater will most likely face (or may be already facing) a reduction in the southern part of their geographical range due to habitat loss to agriculture.     

Genetic and linguistic coevolution in Northern Island Melanesia

Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain). There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast, global patterns may emphasize more ancient demographic events, including population splits associated with the early colonization of major world regions.     

Secretion of type III effectors into host cells in real time

Type III secretion (T3S) systems are key features of many gram-negative bacteria that translocate T3S effector proteins directly into eukaryotic cells. There, T3S effectors exert many effects, such as cellular invasion or modulation of host immune responses. Studying spatiotemporal orchestrated secretion of various effectors has been difficult without disrupting their functions. Here we developed a new approach using Shigella flexneri T3S as a model to investigate bacterial translocation of individual effectors via multidimensional time-lapse microscopy. We demonstrate that direct fluorescent labeling of tetracysteine motif-tagged effectors IpaB and IpaC is possible in situ without loss of function. Studying the T3S kinetics of IpaB and IpaC ejection from individual bacteria, we found that the entire pools of IpaB and IpaC were released concurrently upon host cell contact, and that 50% of each effector was secreted in 240 s. This method allows an unprecedented analysis of the spatiotemporal events during T3S.     

Oceanic barriers promote language diversification in the Japanese Islands

Good barriers make good languages. Scholars have long speculated that geographical barriers impede linguistic contact between speech communities and promote language diversification in a manner similar to the process of allopatric speciation. This hypothesis, however, has seldom been tested systematically and quantitatively. Here, we adopt methods from evolutionary biology and attempt to quantify the influence of oceanic barriers on the degree of lexical diversity in the Japanese Islands. Measuring the degree of beta diversity from basic vocabularies, we find that geographical proximity and, more importantly, isolation by surrounding ocean, independently explains a significant proportion of lexical variation across Japonic languages. Further analyses indicate that our results are neither a by‐product of using a distance matrix derived from a Bayesian language phylogeny nor an epiphenomenon of accelerated evolutionary rates in languages spoken by small communities. Moreover, we find that the effect of oceanic barriers is reproducible with the Ainu languages, indicating that our analytic approach as well as the results can be generalized beyond Japonic language family. The findings we report here are the first quantitative evidence that physical barriers formed by ocean can influence language diversification and points to an intriguing common mechanism between linguistic and biological evolution.     

Review of the Palaearctic members of the Lispe tentaculata species-group (Diptera, Muscidae): revised key, synonymy and notes on ecology

The taxonomic reasons for regarding Lispe draperi Séguy, 1933, sp. rev., as a valid species instead of a synonym of Lispe tentaculata (De Geer, 1776) and for treating Lispe quaerens Villeneuve, 1936, syn. n., as a junior synonym of Lispe sericipalpis Stein, 1904 are given. A revised key for the Palaearctic members of the Lispe tentaculata species-group is given. Data on ecology, distribution and feeding preferences are provided.     

Investigating Individual Vocal Signatures and Small-Scale Patterns of Geographic Variation in Female Bornean Gibbon (<Emphasis Type="Italic">Hylobates muelleri</Emphasis>) Great Calls

Quantifying patterns of variation in primate vocalizations has important implications for understanding the evolutionary processes that lead to variation in phenotypic traits more broadly. Here, we investigated individuality and patterns of geographic variation across a small geographic scale (ca. 10 km) in female Bornean gibbon (Hylobates muelleri) great calls. We analyzed calls recorded from wild, unhabituated gibbon groups at the Stability of Altered Forest Ecosystems site in Sabah, Malaysia. We estimated 23 acoustic features in 376 great calls from 33 different females. We used linear discriminant function analysis to investigate intra- and interindividual variation in great calls. To examine small-scale patterns of geographic variation great calls we investigated measures of acoustic dissimilarity as a function of distance. We found that temporal features (such as the duration of the notes and the duration of rest between notes) contributed substantially to individuality. We were able to identify females based on their calls with 95.7% accuracy using leave-one-out cross-validation. We found no discernible patterns of geographic variation at our site; females with neighboring territories were just as likely to have similar calls as females with more distant territories. It is possible that we did not sample across a large enough geographic range, or that substantial interindividual variation effectively swamped across-site patterns of variation. Our findings add to the growing body of evidence for individual vocal signatures in primates and mammals, but further research is needed to understand the evolutionary mechanisms that contribute to individuality in gibbon calls.     

Situational Designations in "Glossoethnographic" Perspective

Soviet and foreign linguists and educators continually stress the importance of studying a foreign language within its cultural context. Accordingly, a new field of applied linguistics has emerged, at the borderline between linguistics and foreign language instruction, that we have termed "glossoethnography" [see 1, 2, 4, 61. This new area of linguistics has not yet sufficiently delimited i t s subject matter: it abuts on other areas that are also relatively new and as yet ill defined, such as sociolinguistics, ethnolinguistics, linguistic anthropology, linguistic typology (for the various definitions of these disciplines, see reference 7). The many interesting examples adduced in studies in this new area all deal with specific national features of linguistic means of expression (sometimes in combination with paralinguistic means). However, these specific features exist on different levels: there are the specific features of the real objects expressed in language, and then there are those of the linguistic forms themselves, which are independent of the properties of the real objects to which they refer.     

Temporal and Spectral Analyses Reveal Individual Variation in a Non‐Vocal Acoustic Display: The Drumming Display of the Ruffed Grouse (Bonasa umbellus,L.)

Individual variation in vocalizations is a common feature of many forms of long‐distance communication in vertebrates. The extent to which individual variation occurs in non‐vocal, long‐distance acoustic communication has not, however, been tested. Here, we examine the spectral and temporal characteristics of a non‐vocal acoustic signal, the wing‐beating drumming display of the male Ruffed Grouse (Bonasa umbellus, L.), and test whether its structure varies more among individuals than within them. Drumming displays were recorded over two field seasons, and we measured several temporal and spectral features of these recordings. Each drumming display consists of 39–50 pulses produced over a period of 9–10 s with most of the energy concentrated at frequencies below 100 Hz. We calculated the potential for individual coding of several temporal and spectral features, and both the number of pulses and pulse rate were highly individually specific. This was corroborated by analyses of variance, bivariate plots of pulse number and rate, and discriminant function analyses. Overall, we conclude that male Ruffed Grouse produce individually specific drumming displays in a similar fashion to vocal individuality in other birds. The extent to which these individual differences persist from one season to the next is unclear, but individual differences in the number of pulses and pulse rate could provide information on individual identity to conspecifics.     

Mitochondrial DNA variation and GIS analysis confirm a secondary origin of geographical variation in the bushcricket Ephippiger ephippiger (Orthoptera: Tettigonioidea), and resurrect two subspecies

Geographic variation within species can originate through selection and drift in situ (primary variation) or from vicariant episodes (secondary variation). Most patterns of subspecific variation within European flora and fauna are thought to have secondary origins, reflecting isolation in refugia during Quaternary ice ages. The bushcricket Ephippiger ephippiger has an unusual pattern of geographical variability in morphology, behaviour and allozymes in southern France, which has been interpreted as reflecting recent primary origins rather than historical isolation. Re-analysis of this variation using Geographical Information Systems (GIS) suggests a possible zone of hybridization within a complex pattern of geographical variation. Here we produce a genetic distance matrix from restriction fragment length polymorphism (RFLP) bandsharing of an approximately 4.5 kb fragment of mitochondrial DNA (mtDNA), and compare this with predictions resulting from the GIS analysis. The mtDNA variation supports a postglacial origin of geographical variation. Partial Mantel test comparisons of genetic distances with matrices of geographical distance, relevant environmental characteristics and possible refugia show refugia to be the best predictors of genetic distance. There is no evidence to support isolation by distance. However, environmental contrasts do explain significant variation in genetic distance after allowing for the effect of refugial origin. Also, a neighbour-joining tree has a major division separating eastern and western forms. We conclude that the major source of variation within the species is historical isolation in glacial refugia, but that dispersal, hybridization and selection associated with environmental features has influenced patterns of mtDNA introgression. At least two valid subspecies can be defined.     

Quantitative trait, genetic, environmental, and geographical distances among populations of the C4 grass Trachypogon plumosus in Neotropical savannas

Venezuelan savannas are exposed to land‐use changes and biological invasions which compromise their persistence and function. The native C₄ grass Trachypogon plumosus is the most important component of the savannas under diverse combinations of climate and soils, suggesting substantial interpopulation variation. We examined quantitative traits and isozyme variation of nine populations of this grass and related these estimates to geographical and environmental features of sampled locations. Isozyme diversity estimates were based on 10 polymorphic enzyme systems whereas 21 quantitative traits, from field and controlled growth conditions, were evaluated. Distance matrices for quantitative traits, isozyme, geographical and environmental data were subjected to clustering analysis. Correspondence between quantitative trait distance and genetic distance, and their association to geographical and environmental distances were analysed with Mantel tests. All quantitative traits differed significantly among populations. The average Q_ST calculated for eight quantitative traits measured in the greenhouse was 0.157. Isozyme diversity differed significantly among populations. About 28% of total isozyme variation occurred among populations. Significant positive associations were detected between environmental, quantitative field traits, and geographical distance as well as between the later and genetic distances. Genetic distances did not correspond significantly with quantitative traits nor did environmental distances. Ecologically meaningful associations were detected between field quantitative traits, environmental, and geographical data using cluster analysis. Our results support the hypothesis that processes of the neutral type are mainly responsible for the variation patterns observed in T. plumosus populations in Venezuelan savannas. Variation observed for quantitative traits among populations seems to be due to the effect of environmental conditions on phenotypically plastic traits, and not the result of directional selection favouring different phenotypes in different populations.     

Genetic structures and linguistic boundaries in Italy: a microregional approach.

The amount of genetic data (sequences, gene frequencies, and isonymy) available for the Province of Ferrara, Italy, makes this area one of the world's best known. In an effort to infer the underlying demographic processes, we studied the province's population structure by comparing geological, palaeoclimatic, archeological, historical, and linguistic data. This multilevel approach allowed us to date some characteristics of the population structure from prehistoric times to the Roman and Middle Ages, and to detect overlapping biological, cultural, and geographic boundaries. To detect linguistic boundaries within this area we turned pronunciation differences into phonetic notation. We then computed pairwise distances by using methods for multiple genetic sequence analysis, in order to obtain a distance matrix of the overall pronunciation variability. This approach enabled us to test the association among linguistic, geographical, and genetic distance matrices using the same statistical tests. Results indicate that demographic phenomena can be traced in an area as small as the Province of Ferrara and that, on a microregional scale, recent events may have influenced important aspects of the overall genetic variation.     

Testing hierarchical levels of population sub-structuring: the Azores islands (Portugal) as a case study

The Azores archipelago (Portugal) is formed by nine islands whose relative positions define them as three geographical groups: Eastern (S. Miguel and Sta. Maria), Central (Terceira, Faial, Pico, Graciosa and S. Jorge) and Western (Flores and Corvo). Using the father's surname of 187,398 individuals living on the nine Azorean Islands, a population analysis based on inter-island relationship and hierarchical organization was conducted. The relation between islands was investigated using summary statistics, analysis of molecular variance (AMOVA) as well as graphical methods. When the values of heteronymy were contrasted with values of gene diversity based on haplogroup frequencies of the Y chromosome, it was possible to verify that Graciosa and Sta. Maria appeared to have the least diverse populations, and that Flores, despite its smaller population size and geographical isolation, has considerably higher levels of diversity. As for inter-island relationships, the difficulty of directly interpreting summary statistics values was evidenced. The AMOVA revealed that only 0.77% of the variation in surnames can be attributed to among-island variation, a value that, although small, can be considered significant. Application of Malécot's model revealed that geographic distance has an important impact in the genetic structure of the archipelago. Monmonier's maximum-difference algorithm demonstrated that the most isolated island of the archipelago appears to be Graciosa, followed by the islands of the Western group and by Sta. Maria. After integrating values of summary statistics with results from AMOVA and graphical methods, a more accurate genetic profile of the Azores, highly supported by genetic data, has emerged.