Genomic insights on the ethno-history of the Maya and the ‘Ladinos’ from Guatemala

Background

Guatemala is a multiethnic and multilingual country located in Central America. The main population groups separate ‘Ladinos’ (mixed Native American-African-Spanish), and Native indigenous people of Maya descent. Among the present-day Guatemalan Maya, there are more than 20 different ethnic groups separated by different languages and cultures. Genetic variation of these communities still remains largely unexplored. The principal aim of this study is to explore the genetic variability of the Maya and ‘Ladinos’ from Guatemala by means of uniparental and ancestry informative markers (AIMs).

Results

Analyses of uniparental genetic markers indicate that Maya have a dominant Native American ancestry (mitochondrial DNA [mtDNA]: 100%; Y-chromosome: 94%). ‘Ladino’, however, show a clear gender-bias as indicated by the large European ancestry observed in the Y-chromosome (75%) compared to the mtDNA (0%). Autosomal polymorphisms (AIMs) also mirror this marked gender-bias: (i) Native American ancestry: 92% for the Maya vs. 55% for the ‘Ladino’, and (ii) European ancestry: 8% for the Maya vs. 41% for the ‘Ladino’. In addition, the impact of the Trans-Atlantic slave trade on the present-day Guatemalan population is very low (and only occurs in the ‘Ladino’; mtDNA: 9%; AIMs: 4%), in part mirroring the fact that Guatemala has a predominant orientation to the Pacific Ocean instead of a Caribbean one. Sequencing of entire Guatemalan mitogenomes has led to improved Native American phylogeny via the addition of new haplogroups that are mainly observed in Mesoamerica and/or the North of South America.

Conclusions

The data reveal the existence of a fluid gene flow in the Mesoamerican area and a predominant unidirectional flow towards South America, most likely occurring during the Pre-Classic (1800 BC-200 AD) and the Classic (200–1000 AD) Eras of the Mesoamerican chronology, coinciding with development of the most distinctive and advanced Mesoamerican civilization, the Maya. Phylogenetic features of mtDNA data also suggest a demographic scenario that is compatible with moderate local endogamy and isolation in the Maya combined with episodes of gene exchange between ethnic groups, suggesting an ethno-genesis in the Guatemalan Maya that is recent and supported on a cultural rather than a biological basis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1339-1) contains supplementary material, which is available to authorized users.     

Effects of inoculation methods on the incidence of ear-cockle and ‘tundu’ on wheat under field conditions

Wheat,Triticum aestivum L. cv. Mexipak was artificially inoculated withAnguina tritici (Steinb.) under field conditions. Nematode inocula: 0, 0.1, 0.2 and 0.3 g of seed galls/50 seeds or, germinated seeds of wheat (sown in a 1-m long row) were either added as intact seed galls or as a suspension of 2nd stage juveniles. Inoculation of ungerminated seeds with juveniles produced the highest incidence of ear-cockle disease. Whereas, intact seed galls inocula produced the highest incidence of tundu disease. Ear-cockle incidence was always greater than that of tundu at all treatments. The highest reduction in grain yield was associated with the treatments that caused the highest incidence of tundu disease.     

‘Placebos’ and the logic of placebo comparison

Robin Nunn has argued that we should stop using the terms ‘placebo’ and ‘placebo effect’. I argue in support of Nunn’s position by considering the logic of why we perform placebo comparisons. Like all comparisons, placebo comparison is just a case of comparing one thing with another, but it is a mistake, I argue, to think of placebo comparison as a case where something is compared to ‘a placebo’. Rather, placebo comparison should be understood as a situation which sets-up the treatment and control groups in a particular way; not as a case involving objects or procedures called ‘placebos’ employed in order to control for ‘placebo effects’.     

Phylogeny and taxonomy of the ‘manna lichens’

We present ataxonomic revision of the ‘manna lichens’ based on morphological, chemical, ecological and molecular data. A large number of herbarium specimens and fresh collections were examined. Phylogenetic analyses were performed using nuclear ribosomal (nrITS, nrLSU) and mitochondrial small subunit (mtSSU) sequences. Some notable phenotypic characters were plotted on the phylogenetic tree, and the analysis reveals that some of these characters are useful for genus and species level distinction of certain ‘manna lichens.’ Phylogeny of the Megasporaceae was revised using a combined data set of nrLSU and mtSSU and performing parsimony and Bayesian analyses. Five genera (Aspicilia, Circinaria, Lobothallia, Megaspora and Sagedia) are recognized. Further, the relationships of five presumably closely related genera of ‘manna lichens’, namely Agrestia (vagrant), Aspicilia (crustose) Circinaria (crustose), Chlorangium (vagrant) and Sphaerothallia (vagrant) with different growth forms were analysed. The analyses revealed that ‘manna lichens’ do not form a monophyletic group but occur in different clades within the genus Circinaria. The genera Agrestia, Chlorangium and Sphaerothallia are assigned as new synonyms under the genus Circinaria and no vagrant or erratic species remain in the genus Aspicilia. The analyses also show that five new erratic, vagrant and crustose species can be recognized. In this study two ‘manna lichens’, viz. Circinaria rostamii sp. nov. (Azerbaijan, Iran and Turkey), and Circinaria gyrosa sp. nov. (Armenia, Azerbaijan, Iran, Turkey, Turkmenistan and Spain) are described as new to science. Three potentially new species with crustose and erratic forms need additional study. Aspicilia fruticolosofoliacea is reduced to synonymy under C. alpicola, and a lectotype is designated for C. aspera. Thirteen new combinations in Circinaria are presented. The phenomenon of vagrancy is briefly discussed, and the biogeography of the ‘manna lichens’ is outlined. Illustrations, distribution maps, and an identification key to the species are provided.     

‘Gender’ and the Concerns of Carnal Self-Consumption

This article analyses the co-occurrence of two concerns often expressed by indigenous leaders involved with reparations for victims of paramilitaries in Colombia. These concerns revolve around discomfort with the intense use of hegemonic ‘gender’ discourses in the context of the reparations, and a feeling that leaders' involvement in the latter brings about a betrayal of the family and of themselves. By engaging with the local category of eirruku (flesh), I argue that ways of engaging women in reparations entail the commoditisation of caring relationships. This article, based on 13 months of fieldwork with an indigenous organisation and the communities integrated into it between 2007 and 2008, contributes to the understanding of the articulation of gender and ethnic/racial identification in the context of contemporary forms of governance of indigenous peoples, while delving into ‘carnality’ as a concept to understand gendered forms of reproduction, reparation and selfhood.     

Making sense of ‘mixture’: states and the classification of ‘mixed’ people

Caribbean diaspora intellectuals have contributed significantly to African-American political struggles over the years, despite arguments by some African-American intellectuals about what they discern as West Indian negativism, extremism, and divisiveness in American political life. This essay examines the legacy of a representative sample of diasporic Caribbean intellectuals since the time of the Harlem Renaissance in the 1920s and culminating in the 1970s, notably, Garvey, members of the African Blood Brotherhood [ABB], C.L.R. James, and Walter Rodney, to demonstrate the phenomenal ideological vision, organizational capability, and political activism they have brought into fostering solidarity with African Americans in the struggle for fundamental change. The focus here is on their respective contributions to the debate on the relationship between class and race in America and the black diaspora generally, which has helped to shape the form, and orient the direction of African-American and Caribbean diasporic struggles for the better part of the twentieth century.     

Influence of Prohexadione-Calcium on the Growth and Quality of Summer ‘Jen-Ju Bar’ Guava Fruit

A 2-year trial was conducted to investigate the influence of prohexadione-calcium (ProCa) on the fruit quality of summer ‘Jen-Ju Bar’ guava (Psidium guajava L.). ‘Jen-Ju Bar’ trees were treated with various concentrations of ProCa: 0 (as control), 125, 250, and 500 mg L^?1, which significantly inhibited spring shoot growth. Summer guava fruits of the trees subjected to ProCa exhibited higher levels of total soluble solids and higher values of total soluble solids to titratable acidity ratio compared with control fruits. Summer guava fruits from trees treated with ProCa were firmer than those from untreated trees. ProCa sprays significantly affected pulp weight, core weight, pulp thickness, and pulp-to-core ratio. No other fruit quality characteristics were significantly affected by ProCa treatment.     

Ethnocentricity and the social construction of ‘mass hysteria’

This study provides a critical historical review and analysis of the variety of human expressions which have been erroneously labeled under the grandiose category mass hysteria. It is argued that Western science reductionist approaches to the classification of mass hysteria treat it as an entity to be discovered transculturally, and in their self-fulfilling search for universals systematically exclude what does not fit within the autonomous parameters of its Western-biased culture model, exemplifying what Kleinman (1977) terms a category fallacy. As a result of objectivist methodologies, the etiology of actions labeled as mass hysteria is typically viewed as deviant, irrational or abnormal behavior resulting from a malfunctioning proper social order. However, what constitutes the correct social order is a function of a researcher's historical sociocultural and/or scientific milieu. This study reviews the problem, advocating Geertz's (1973) culturally relativistic approach to understanding various cross-cultural behavior that is sensitive to and tolerant of the unique context and milieu of participants. Mass or epidemic hysteria is viewed as an invention of Western psychiatry and should be abandoned and replaced with the term collective exaggerated emotions. Instead of attempting to discover a neatly packaged, unitary external disease entity, the focus of a meaning-oriented approach emphasizes the deciphering of foreign realities, semantic networks and symbol systems.     

Special Issue on‘‘Metagenomics of Marine Environments’’

<正>We are pleased to announce a special issue on‘‘Metagenomics of Marine Environments’’of the journal Genomics,ProteomicsBioinformatics(GPB),aiming to provide a platform for high-quality papers focusing on the topic and we invite submissions for this special issue(to be published in the fall of 2015).With most microbes being difficult or impossible to culture     

Comparison of ‘ignition’ and ‘extraction’ methods for the determination of organic phosphate in rocks and soils

Summary Ignition markedly increased the solubility in dilute acid of iron- and aluminium-bound inorganic phosphate in samples of weathered New Zealand greywacke rock. This observation supports the view that ignition methods may sometimes overestimate the total organic phosphate of soils.     

Labour's ‘strange blindness’ and the end of Jubilee

ABSTRACT

This essay responds to David Roediger's Seizing Freedom: Slave Emancipation and Liberty for All. After a brief examination of the central themes of the book, I turn to the author's emphasis upon political agency. I argue that this emphasis is necessary, given the political and scholarly aims of the book. At the same time, I suggest that the agency depicted in Seizing Freedom was simultaneously constrained by the cultural, political, and social forces discussed in Roediger's earlier companion volume, The Wages of Whiteness. I end the essay with a short discussion of the labour leader William Sylvis that attempts to synthesize insights from Seizing Freedom and The Wages of Whiteness in order to explain the ‘strange blindness’ that led white labour to systematically ignore and repress the activity of black workers.     

Official statement of the Japan Monkey Centre on the ‘Shimokita incident’

The Japan Monkey Centre issued the following official statement concerning the aerial spraying of herbicide which was carried out at the end of June on the Shimokita Peninsula. It invites all who are interested in the research of nature to understand and support its aim for the conservation of wild Japanese monkeys and the protection of nature from artificial destruction. Copies of the statement (in Japanese) have been sent to a number of inland individuals and organizations concerned.     

Effect of cysteine modifications on the activity of the ‘small’ Clostridium perfringens sialidase

The small (43 kDa) sialidase of Clostridium perfringens is inhibited by low concentrations of mercury ions. For the investigation of possible functional roles of the enzyme's four cysteine residues at the amino acid positions 2, 282, 333 and 349, they were separately altered to serine by site-directed mutagenesis. The four mutant sialidases expressed in E. coli and purified by metal chelate chromatography were markedly reduced in specific activity when compared to the wild-type enzyme but with the exception of C282S exhibited similar KM-values indicating an unchanged mode of substrate binding. The substrate specificity was also conserved for C2S, C282S, and C333S. Only the C349S sialidase exhibited a higher relative activity with colominic acid and the 2,6-linked sialic acid of sialyllactose compared to the 2,3-linked isomer than the other mutants. Chemical modifications with the thiol-blocking reagents N-ethylmaleimide (NEM), p-chloromercuribenzoate (pCMB) and HgCl2 had little effect on the C282S sialidase, e.g., 6% inhibition by 5 m M NEM compared to reductions in activity between 65 and 90% for the wild-type and other mutant enzymes, supporting the idea that among the enzyme's cysteines, Cys-282 has the highest structural or functional significance. The results also explain the higher mercury tolerance of Salmonella typhimurium and Clostridium tertium sialidases, which have the positions equivalent to Cys-282 altered to Val and Thr, respectively, indicating that the thiol group of Cys-282, despite being situated near the active site, is not involved in catalysis.     

‘Ins’ and ‘outs’ of triple therapy

Chronic oral anticoagulant treatment is obligatory in patients (class I) with mechanical heart valves and in patients with atrial fibrillation with CHADS2 score >1. When these patients undergo percutaneous coronary intervention with placement of a stent, there is also an indication for treatment with aspirin and clopidogrel. Unfortunately, triple therapy is known to increase the bleeding risk. For this group of patients, the bottom line is to find the ideal therapy in patients with indications for both chronic anticoagulation therapy and percutaneous intervention to prevent thromboembolic complications such as stent thrombosis without increasing the risk of bleeding. (Neth Heart J 2010;18:444-50.)     

Comprehensive analysis of the roles of ‘black’ and ‘gray’ clusters in structure and function of rat β-parvalbumin

Recently we found two highly conserved structural motifs in the proteins of the EF-hand calcium binding protein family. These motifs provide a supporting scaffold for the Ca²⁺ binding loops and contribute to the hydrophobic core of the EF-hand domain. Each structural motif forms a cluster of three amino acids called cluster I (‘black’ cluster) and cluster II (‘grey’ cluster). Cluster I is much more conserved and mostly incorporates aromatic amino acids. In contrast, cluster II includes a mix of aromatic, hydrophobic, and polar amino acids. The ‘black’ and ‘gray’ clusters in rat β-parvalbumin consist of F48, A100, F103 and G61, L64, M87, respectively. In the present work, we sequentially substituted these amino acids residues by Ala, except Ala100, which was substituted by Val. Physical properties of the mutants were studied by circular dichroism, scanning calorimetry, dynamic light scattering, chemical crosslinking, and fluorescent probe methods. The Ca²⁺ and Mg²⁺ binding affinities of these mutants were evaluated by intrinsic fluorescence and equilibrium dialysis methods. In spite of a rather complicated pattern of contributions of separate amino acid residues of the ‘black’ and ‘gray’ clusters into maintenance of rat β-parvalbumin structural and functional status, the alanine substitutions in the cluster I cause noticeably more pronounced changes in various structural parameters of proteins, such as hydrodynamic radius of apo-form, thermal stability of Ca²⁺/Mg²⁺-loaded forms, and total energy of Ca²⁺ binding in comparison with the changes caused by amino acid substitutions in the cluster II. These findings were further supported by the outputs of computational analysis of the effects of these mutations on the intrinsic disorder predisposition of rat β-parvalbumin, which also indicated that local intrinsic disorder propensities and the overall levels of predicted disorder were strongly affected by mutations in the cluster I, whereas mutations in cluster II had less pronounced effects. These results demonstrate that amino acids of the cluster I provide more essential contribution to the maintenance of structuraland functional properties of the protein in comparison with the residues of the cluster II.     

Microbiology of the fermentation of ‘iru pete’ and ‘iru woro’ obtained from local producers

Summary The microorganisms responsible for the fermentation of iru, obtained from local producers, were isolated and identified. Only bacteria were involved in the fermentation; the species areMicrococcus luteus, Staphylococcus aureus, Bacillus subtilis, Lactobacillus plantarum, Citrobacter freundii, Lactobacillus salivarius andStreptococcus pyogenes. Microbial population, temperature, pH and moisture content increased with increase in period of fermentation. A progressive in titratable acidity accompanied the fermentation.

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Resumen Se aislaron e identificaron los microorganismos responsables de la fermentación de iru obtenido de productores locales. En el proceso de fermentación unicamente estaban implicadas bacterias que se identificaron como:Micrococcus luteus, Staphylococcus aureus, Bacillus subtilis, Lactobacillus plantarum, Citrobacter freundii, Lactobacillus salivarius yStreptococcus pyogenes. La población microbiana, la temperatura, el pH y el contenido en humedad se incrementaron al aumentar el periodo de fermentación. Se observó un decremento progresivo del título de acidez a lo largo de la fermentación.

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Résumé Les microorganismes responsables de la fermentation des iru obtenus de producteurs locaux ont été isolés et identifiés. Seules des bactéries sont impliquées dans la fermentation. Les espèces sontMicrococcus luteus, Staphylococcus aureus, Bacillus subtilis, Lactobacillus plantarum, Citrobacter freundii, Lactobacillus salivarius etStreptococcus pyogenes. La population microbienne, la température, le pH et la teneur en eau agumentent avec l'augmentation du temps de fermentation. Une baisse progressive de l'acidité titrable accompagne la fermentation.

     

‘Good-genes’ and ‘compatible-genes’ effects in an Alpine whitefish and the information content of breeding tubercles over the course of the spawning season

Some models of sexual selection predict that individuals vary in their genetic quality and reveal some of this variation in their secondary sexual characteristics. Alpine whitefish (Coregonus sp.) develop breeding tubercles shortly before their spawning season. These tubercles are epidermal structures that are distributed regularly along the body sides of both males and females. There is still much unexplained variation in the size of breeding tubercles within both sexes and with much overlap between the sexes. It has been suggested that breeding tubercles function to maintain body contact between the mating partners during spawning, act as weapons for defence of spawning territories, or are sexual signals that reveal aspects of genetic quality. We took two samples of whitefish from their spawning place, one at the beginning and one around the peak of spawning season. We found that females have on average smaller breeding tubercles than males, and that tubercle size partly reveals the stage of gonad maturation. Two independent full-factorial breeding experiments revealed that embryo mortality was significantly influenced by male and female effects. This finding demonstrates that the males differed in their genetic quality (because offspring get nothing but genes from their fathers). Tubercle size was negatively linked to some aspects of embryo mortality in the first breeding experiment but not significantly so in the second. This lack of consistency adds to inconsistent results that were reported before and suggests that (i) some aspects of genetic quality are not revealed in breeding tubercles while others are, or (ii) individuals vary in their signaling strategies and the information content of breeding tubercles is not always reliable. Moreover, the fact that female whitefish have breeding tubercles of significant size while males seem to have few reasons to be choosy suggests that the tubercles might also serve some functions that are not linked to sexual signaling.