Early Siberians from Lake Baikal and Alaskan population affinities

Among the materials excavated by the 1975 joint USSR–USA team in Siberia are two burials from Shaman's Cape, Olkhon Island, Lake Baikal. One is a middle-aged male of the Serovo culture, 6,000 B.C. , and the other is a young male of the Glaskovo culture of 2,000 B.C. This later burial displays an unusual pathology affecting the nose and post-cranial regions of the pelvic girdle and lower limbs. Osteon analysis confirms the determination of age at death and illustrates the difference between normal and pathological bone. Numerous cultural materials were associated with these burials, including harpoon heads, knives, a compound fishhook and a pestle with the Serovo man, and nephrite ornaments with the Glaskovo man. The skulls, though far apart in time, are pronouncedly Mongoloid and alike in their low cranial vaults. A low, broad and inclined ascending ramus resembles Chukchi, Eskimos and Aleuts. These two specimens document the Mongoloid character of the early inhabitants of Lake Baikal.     

Ethnobotany of the Rama of Southeastern Nicaragua and Comparisons with Miskitu Plant Lore<Superscript>1</Superscript>

Ethnobotany of the Rama of Southeastern Nicaragua and Comparisons with Miskitu Plant Lore. The Rama are one of the three Amerindian groups of eastern Nicaragua. This is the first systematic study of Rama ethnobotany. A total of 249 plant species, in 190 genera and 78 families, were documented as useful. Included are 190 species used as medicinals, 80 as food plants, and 99 for other uses. The ethnobotanical lore of two distinct indigenous groups, the Rama and Miskitu, were compared. Out of 249 species used by the Rama, 171, or 69%, were used by both groups, and 78 unique species were used by the Rama. These results have important implications for the understanding of ethnobotany as they demonstrate how unrelated indigenous groups sharing the same ecosystem, though separated by some physical distance, can have significantly similar ethnobotanical lore.

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Resumen   Etnobotánica de los Ramas del Oriente Nicaragüense y Comparasiones con el Saber Etnobotánico de los Miskitus. Los Ramas constituyen uno de los tres grupos Amerindios del oriente Nicaragüense. Este es el primer studio sistemático de la etnobotánica Rama. Se documentó un total de 249 especies de plantas útiles en 190 géneros y 78 familias. Incluyendo 190 especies medicinales, 80 especies alimenticias y 99 especies para usos auxiliares. La erudición etnobotánica de los Ramas y los Miskitus fueron comparados. Un total de 171 de 249 especies documentadas son usados por ambos grupos y 78 especies solo por los Ramas. Estos resultados tienen implicaciones importantes para el entendimiento de la etnobotánica porque demuestran que grupos sin parentesco alguno que comparten el mismo ecosistema aunque separados por cierta distancia pueden tener una similitud significativa en la erudición etnobotánica.

     

Microbial diversity in marine biofilms along a water quality gradient on the Great Barrier Reef

Microbial communities are potential indicators for water quality as they respond rapidly to environmental changes. In the Whitsunday Islands, Australia, microbial biofilm communities from two offshore islands were compared to those from two inshore islands subjected to poor water quality. Biofilm community composition was characterized using three culture-independent molecular techniques. The clone libraries indicated high genetic diversity, with somewhat higher scores in the offshore sites (57%) compared to the inshore sites (41%). The majority of microbes in the biofilms were related to Alphaproteobacteria (39.8%), Gammaproteobacteria (14.1%), Bacteroidetes (13.2%), diatoms (8.3%) and Cyanobacteria (3.9%). Redundancy analysis (RDA) for the CARD-FISH data showed distinct microbial assemblages between offshore and inshore communities. Additionally, 5 out of 13 water quality parameters (DIN, Chla, POP, TSS and POC) explained a significant amount of variation in the microbial communities and high values of these were associated with inshore communities. Analysis of variance (ANOVA) indicated that Cyanobacteria (p = 0.01), Bacteroidetes (p = 0.04) and to some extent Alphaproteobacteria (p = 0.07), were significantly more abundant in the offshore biofilm communities. Principal Component Analysis (PCA) of DGGE data showed clear grouping of cyanobacterial communities into inshore and offshore communities. Reasons for community shifts in the bacterial lineages are currently not resolved. One possible causative factor may be that autotrophic primary producers are more dominant in offshore sites due to the higher light availability as well as the limitation by DIN. The trends found in this study are the bases for more detailed research on microbial indicator species for changes in water quality.     

Evolution of parallel β/α-barrel enzyme family lightened by structural data on starch-processing enzymes

The parallel /-barrel domain consisting of eight parallel -sheets surrounded by eight -helices has been currently identified in crystal structures of more than 20 enzymes. This type of protein folding motif makes it possible to catalyze various biochemical reactions on a variety of substrates (i.e., it seems to be robust enough so that different enzymatic functionalities could be designed on it). In spite of many efforts aimed at elucidation of evolutionary history of the present-day /-barrels, a challenging question remains unanswered: How has the parallel /-barrel fold arisen? Although the complete sequence comparison of all /-barrel amino acid sequences is not yet available, several sequence similarities have been revealed by using the highly conserved regions of -amylase as structural templates. Since many starch-processing enzymes adopt the parallel /-barrel structure these enzymes might be useful in the search for evolutionary relationships of the whole parallel eight-folded /-barrel enzyme family.     

Identification of visual paternity cues in humans

Understanding how individuals identify their relatives has implications for the evolution of social behaviour. Kinship cues might be based on familiarity, but in the face of paternity uncertainty and costly paternal investment, other mechanisms such as phenotypic matching may have evolved. In humans, paternal recognition of offspring and subsequent discriminative paternal investment have been linked to father–offspring facial phenotypic similarities. However, the extent to which paternity detection is impaired by environmentally induced facial information is unclear. We used 27 portraits of fathers and their adult sons to quantify the level of paternity detection according to experimental treatments that manipulate the location, type and quantity of visible facial information. We found that (i) the lower part of the face, that changes most with development, does not contain paternity cues, (ii) paternity can be detected even if relational information within the face is disrupted and (iii) the signal depends on the presence of specific information rather than their number. Taken together, the results support the view that environmental effects have little influence on the detection of paternity using facial similarities. This suggests that the cognitive dispositions enabling the facial detection of kinship relationships ignore genetic irrelevant facial information.     

The effects of forest conversion to oil palm on ground‐foraging ant communities depend on beta diversity and sampling grain

Beta diversity – the variation in species composition among spatially discrete communities – and sampling grain – the size of samples being compared – may alter our perspectives of diversity within and between landscapes before and after agricultural conversion. Such assumptions are usually based on point comparisons, which do not accurately capture actual differences in total diversity. Beta diversity is often not rigorously examined. We investigated the beta diversity of ground‐foraging ant communities in fragmented oil palm and forest landscapes in Sabah, Malaysia, using diversity metrics transformed from Hill number equivalents to remove dependences on alpha diversity. We compared the beta diversities of oil palm and forest, across three hierarchically nested sampling grains. We found that oil palm and forest communities had a greater percentage of total shared species when larger samples were compared. Across all grains and disregarding relative abundances, there was higher beta diversity of all species among forest communities. However, there were higher beta diversities of common and very abundant (dominant) species in oil palm as compared to forests. Differences in beta diversities between oil palm and forest were greatest at the largest sampling grain. Larger sampling grains in oil palm may generate bigger species pools, increasing the probability of shared species with forest samples. Greater beta diversity of all species in forest may be attributed to rare species. Oil palm communities may be more heterogeneous in common and dominant species because of variable community assembly events. Rare and also common species are better captured at larger grains, boosting differences in beta diversity between larger samples of forest and oil palm communities. Although agricultural landscapes support a lower total diversity than natural forests, diversity especially of abundant species is still important for maintaining ecosystem stability. Diversity in agricultural landscapes may be greater than expected when beta diversity is accounted for at large spatial scales.     

连续13年稻鸭共作兼秸秆还田的稻麦连作麦田杂草种子库物种多样性变化

稻鸭共作能有效控制稻田杂草的危害, 但是它对后茬小麦田杂草的影响及其控制作用尚没有详细的报道。我们于2000-2012年对江苏丹阳稻鸭共作兼秸秆还田的有机稻麦连作田土壤杂草种子库进行了连续13年的观察实验。结果显示, 稻鸭共作兼秸秆还田的措施使看麦娘(Alopecurus aequalis)、通泉草(Mazus japonicus)、碎米荠(Cardamine hirsuta)等18种麦田主要杂草的种子库均有较大幅度的降低, 总体的降低幅度高达97%。除了Pielou指数处于小幅波动状态外, 麦田杂草群落多样性指数整体呈下降趋势。丰富度下降表明杂草种子库向种类少、多样性低的方向演变。从Bray-Curtis指数和Jaccard相似性指数也可以得到同样的结论。可见, 连续稻鸭共作兼秸秆还田能够降低下茬的麦田土壤里杂草种子密度及多样性, 控制杂草危害。     

Comparative influence of spatial scale on beta diversity within regional assemblages of birds and butterflies

Aim We examined whether variation in species composition of breeding birds and resident butterflies in the Great Basin of North America depended on sampling grain (the smallest resolvable unit of study) and on the relative proximity of sampling units across the landscape. We also compared patterns between the two taxonomic groups with reference to their life‐history characteristics. Location Data for our analyses were collected from 1996 to 2003 in three adjacent mountain ranges in the central Great Basin (Lander and Nye counties, Nevada, USA): the Shoshone Mountains, Toiyabe Range and Toquima Range. Methods Data on species composition for both taxonomic groups were collecting using standard inventory methods for birds and butterflies in temperate regions. Data were compiled at three sampling grains, sites (average 12 ha), canyons (average 74 ha) and mountain ranges. For each sampling grain in turn, we calculated similarity of species composition using the Jaccard index. First, we investigated whether mean similarity of species composition among the three ranges differed as a function of the grain size at which data were compiled. Secondly, we explored whether mean similarity of species composition was greater for canyons within the same mountain range than for canyons within different mountain ranges. Thirdly, we examined whether mean similarity of species composition at the site level was different for sites within the same canyon, sites within different canyons in the same mountain range, and sites within canyons in different mountain ranges. We used a Bayesian model to analyse these comparisons. Results For both taxonomic groups, mean similarity of species composition increased as the sampling grain increased. The effect of spatial grain was somewhat greater for birds than for butterflies, especially when the intermediate sampling grain was compared with the smallest sampling grain. Similarity of species composition of butterflies at each sampling grain was greater than similarity of species composition of birds at the same grain. Mean similarity of species composition of both birds and butterflies at the canyon level and site level was affected by relative proximity of sampling locations; beta diversity increased as the relative isolation of sampling locations increased. Main conclusions The sensitivity of beta diversity to sampling grain likely reflects the effect of local environmental heterogeneity: as sampling grain increases, biotic assemblages appear more homogeneous. Although breeding birds in our study system have larger home ranges than resident butterflies, birds may have more specialized resource requirements related to vegetation structure and composition, especially at small sampling scales. The degree of variation in species composition of both taxonomic groups suggests that spatially extensive sampling will be more effective for drawing inferences about regional patterns of species diversity than intensive sampling at relatively few, smaller sites.     

The Search for the Spatial and Electronic Requirements of a Drug

A new program called GAMMA (genetic algorithm for multiple molecule alignment) has been developed for the superimposition of several three-dimensional chemical structures. Superimposition of molecules and evaluation of structural similarity is an important task in drug design and pharmaceutical research. Similarities of compounds are determined by this program either based on their structural or their physicochemical properties by defining different matching criteria. These matching criteria are atomic properties such as atomic number or partial atomic charges. The program is based on a combination of a genetic algorithm with a numerical optimization process. A major goal of this hybrid procedure is to address the conformational flexibility of ligand molecules adequately. Thus, only one conformation per structure is necessary and the program can work even when only one conformation of a compound is stored in a database. The genetic algorithm optimizes in a nondeterministic process the size and the geometric fit of the overlay. The geometric fit of the conformations is further improved by changing torsional angles combining the genetic algorithm and the directed tweak method. The determination of the fitness of a superimposition is based on the Pareto optimization. As an application the superimposition of a set of Cytochrome P450c17 enzyme inhibitors has been performed.Electronic Supplementary Material available.     

Enzyme-mononucleotide interactions: three different folds share common structural elements for ATP recognition

Three ATP-dependent enzymes with different folds, cAMP-dependent protein kinase, D-Ala:D-Ala ligase and the alpha-subunit of the alpha2beta2 ribonucleotide reductase, have a similar organization of their ATP-binding sites. The most meaningful similarity was found over 23 structurally equivalent residues in each protein and includes three strands each from their beta-sheets, in addition to a connecting loop. The equivalent secondary structure elements in each of these enzymes donate four amino acids forming key hydrogen bonds responsible for the common orientation of the "AMP" moieties of their ATP-ligands. One lysine residue conserved throughout the three families binds the alpha-phosphate in each protein. The common fragments of structure also position some, but not all, of the equivalent residues involved in hydrophobic contacts with the adenine ring. These examples of convergent evolution reinforce the view that different proteins can fold in different ways to produce similar structures locally, and nature can take advantage of these features when structure and function demand it, as shown here for the common mode of ATP-binding by three unrelated proteins.