Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa.

Clines in life history traits, presumably driven by spatially varying selection, are widespread. Major latitudinal clines have been observed, for example, in Drosophila melanogaster, an ancestrally tropical insect from Africa that has colonized temperate habitats on multiple continents. Yet, how geographic factors other than latitude, such as altitude or longitude, affect life history in this species remains poorly understood. Moreover, most previous work has been performed on derived European, American and Australian populations, but whether life history also varies predictably with geography in the ancestral Afro-tropical range has not been investigated systematically. Here, we have examined life history variation among populations of D. melanogaster from sub-Saharan Africa. Viability and reproductive diapause did not vary with geography, but body size increased with altitude, latitude and longitude. Early fecundity covaried positively with altitude and latitude, whereas lifespan showed the opposite trend. Examination of genetic variance-covariance matrices revealed geographic differentiation also in trade-off structure, and QST -FST analysis showed that life history differentiation among populations is likely shaped by selection. Together, our results suggest that geographic and/or climatic factors drive adaptive phenotypic differentiation among ancestral African populations and confirm the widely held notion that latitude and altitude represent parallel gradients.

Influence of floral structure and flower bud quality on productivity and fruit shape in different apple cultivars

This study examines the relationship between floral structure and bud quality with the productivity and fruit shape of Gala, Fuji and Daiane apple cultivars under the mild winter conditions in Southern Brazil. Six different types of floral structures were characterized in field growing plants, according to their nature and bud size: spurs, short and long twigs with weak and vigorous buds. Variables related to the phenology and the productivity for these different structures were evaluated. Gala and Fuji cvs. showed earlier phenological development in the twigs, and cv. Daiane in the spurs. For the three cvs. the highest percentage of buds in each phenological phase was observed in the long twigs. The long twigs also showed the highest sprout and fruit set index, floral number per cluster, and leaf area in the three cvs., while the bud abortion was higher in the spurs than in the twigs. No difference was observed among the structures in cvs. Gala and Fuji regarding to the fruit shape. In the cv. Daiane, however, a tendency to higher length diameter ratio of the fruits produced by the long twigs was observed.

Diversity and genetic structure in natural populations of Hancornia speciosa var. speciosa Gomes in northeastern Brazil

Hancornia speciosa Gomes is a fruit tree native from Brazil that belongs to Apocinaceae family, and is popularly known as Mangabeira. Its fruits are widely consumed raw or processed as fruit jam, juices and ice creams, which have made it a target of intense exploitation. The extractive activities and intense human activity on the environment of natural occurrence of H. speciosa has caused genetic erosion in the species and little is known about the ecology or genetic structure of natural populations. The objective of this research was the evaluation of the genetic diversity and genetic structure of H. speciosa var. speciosa. The genetic variability was assessed using 11 allozyme loci with a sample of 164 individuals distributed in six natural populations located in the States of Pernambuco and Alagoas, Northeastern Brazil. The results showed a high level of genetic diversity within the species (e= 0.36) seeing that the most of the genetic variability of H. speciosa var. speciosa is within its natural populations with low difference among populations ( or = 0.081). The inbreeding values within ( = -0.555) and among populations ( =-0.428) were low showing lacking of endogamy and a surplus of heterozygotes. The estimated gene flow ( m ) was high, ranging from 2.20 to 13.18, indicating to be enough to prevent the effects of genetic drift and genetic differentiation among populations. The multivariate analyses indicated that there is a relationship between genetic and geographical distances, which was confirmed by a spatial pattern analysis using Mantel test (r = 0.3598; p = 0.0920) with 1000 random permutations. The high genetic diversity index in these populations indicates potential for in situ genetic conservation.

3-D density structure and geological evolution of Stromboli volcano (Aeolian Islands, Italy) inferred from land-based and sea-surface gravity data

We present the first density model of Stromboli volcano (Aeolian Islands, Italy) obtained by simultaneously inverting land-based (543) and sea-surface (327) relative gravity data. Modern positioning technology, a 1 x 1 m digital elevation model, and a 15 x 15 m bathymetric model made it possible to obtain a detailed 3-D density model through an iteratively reweighted smoothness-constrained least-squares inversion that explained the land-based gravity data to 0.09 mGal and the sea-surface data to 5 mGal. Our inverse formulation avoids introducing any assumptions about density magnitudes. At 125 m depth from the land surface, the inferred mean density of the island is 2380 kg m(-3), with corresponding 2.5 and 97.5 percentiles of 2200 and 2530 kg m-3. This density range covers the rock densities of new and previously published samples of Paleostromboli I, Vancori, Neostromboli and San Bartolo lava flows. High-density anomalies in the central and southern part of the island can be related to two main degassing faults crossing the island (N41 and NM) that are interpreted as preferential regions of dyke intrusions. In addition, two low-density anomalies are found in the northeastern part and in the summit area of the island. These anomalies seem to be geographically related with past paroxysmal explosive phreato-magmatic events that have played important roles in the evolution of Stromboli Island by forming the Scari caldera and the Neostromboli crater, respectively. (C) 2014 Elsevier B.V. All rights reserved.

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori.

Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tipα) and hitherto unknown functional genes.

Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis

Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population.

GENETIC DIVERSITY AND STRUCTURE OF Oenocarpus mapora GERMPLASM CONSERVED AT EASTERN AMAZON

ABSTRACT The aim of this study was to evaluate the genetic diversity and structure in the germoplasm of Oenocarpus mapora conserved at Eastern Amazon. Thus, 88 individuals were genotyped with five microsatellite loci. These individuals belong to 24 accessions that were sampled in eight sample places of three Brazilian Amazon states conserved at the Active Germplasm Bank (AGB) of Embrapa Eastern Amazon. All loci were polymorphic and they generated 85 alleles with an average of 17 alleles per loci. Total genetic diversity (HE) was 0.48. Sample places were considered genetically distinct, with ?p = 0.354. The analysis of molecular variance (AMOVA) identified that the genetic portion among areas was of 36.14% and within 63.86%. The Nei distances varied from 0.091 between Abaetetuba and Santo Antônio do Tauá, both in the state of Pará (PA), to 4.18, between Parintins, AM and Rio Branco, AC. By means of Bayesian analysis, it was identified nine clusters that compose the accessions of the germplasm bank, with different distributions among individuals. The study showed high fixation rates per sample area, which indicates that there may have been significant inbreeding or crossing among parental individuals. It suggests that future samples should be made of different plants in natural populations. Even though, it was verified that there is considerable genetic variation in the germplasm of O. mapora.

What can ecosystems learn? Expanding evolutionary ecology with learning theory.

BACKGROUND: The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have shaped this architecture is vital for understanding system responses to change at scales from the microbial upwards. However, in the absence of a group selection process, the collective behaviours and ecosystem functions exhibited by the whole community cannot be organised or adapted in a Darwinian sense. A long-standing open question thus persists: Are there alternative organising principles that enable us to understand and predict how the coevolution of the component species creates and maintains complex collective behaviours exhibited by the ecosystem as a whole? RESULTS: Here we answer this question by incorporating principles from connectionist learning, a previously unrelated discipline already using well-developed theories on how emergent behaviours arise in simple networks. Specifically, we show conditions where natural selection on ecological interactions is functionally equivalent to a simple type of connectionist learning, 'unsupervised learning', well-known in neural-network models of cognitive systems to produce many non-trivial collective behaviours. Accordingly, we find that a community can self-organise in a well-defined and non-trivial sense without selection at the community level; its organisation can be conditioned by past experience in the same sense as connectionist learning models habituate to stimuli. This conditioning drives the community to form a distributed ecological memory of multiple past states, causing the community to: a) converge to these states from any random initial composition; b) accurately restore historical compositions from small fragments; c) recover a state composition following disturbance; and d) to correctly classify ambiguous initial compositions according to their similarity to learned compositions. We examine how the formation of alternative stable states alters the community's response to changing environmental forcing, and we identify conditions under which the ecosystem exhibits hysteresis with potential for catastrophic regime shifts. CONCLUSIONS: This work highlights the potential of connectionist theory to expand our understanding of evo-eco dynamics and collective ecological behaviours. Within this framework we find that, despite not being a Darwinian unit, ecological communities can behave like connectionist learning systems, creating internal conditions that habituate to past environmental conditions and actively recalling those conditions. REVIEWERS: This article was reviewed by Prof. Ricard V Solé, Universitat Pompeu Fabra, Barcelona and Prof. Rob Knight, University of Colorado, Boulder.

Structure-Based, Rational Design of T Cell Receptors.

Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce T cell receptor (TCR) modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction with peptides (p) bound to major histocompatibility complexes (MHC). Using the well-characterized 2C TCR/SIYR/H-2K(b) structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157-165 cancer-testis epitope. Fifty-four percent of the designed sequence replacements exhibited improved pMHC binding as compared to the native TCR, with up to 150-fold increase in affinity, while preserving specificity. Genetically engineered CD8(+) T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity, K D = ∼1 - 5 μM. Beyond the affinity threshold at K D < 1 μM we observed an attenuation in cellular function, in line with the "half-life" model of T cell activation. Our computer-aided protein-engineering approach requires the 3D-structure of the TCR-pMHC complex of interest, which can be obtained from X-ray crystallography. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes when experimental data is not available. Since the accuracy of the models depends on the prediction of the TCR orientation over pMHC, we have complemented the approach with a simplified rigid method to predict this orientation and successfully assessed it using all non-redundant TCR-pMHC crystal structures available. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of stage IV melanoma.

Linking brain structure and activation in the temporoparietal junction to explain the neurobiology of human altruism

Human altruism shaped our evolutionary history and pervades social and political life. There are, however, enormous individual differences in altruism. Some people are almost completely selfish, while others display strong altruism, and the factors behind this heterogeneity are only poorly understood. We examine the neuroanatomical basis of these differences with voxel-based morphometry and show that gray matter (GM) volume in the right temporoparietal junction (TPJ) is strongly associated with both individuals' altruism and the individual-specific conditions under which this brain region is recruited during altruistic decision making. Thus, individual differences in GM volume in TPJ not only translate into individual differences in the general propensity to behave altruistically, but they also create a link between brain structure and brain function by indicating the conditions under which individuals are likely to recruit this region when they face a conflict between altruistic and selfish acts.

The composition of airborne and grain-dust fungal communities is shaped at regional scale by plant genotypes and farming practices

Chronic exposure to airborne fungi has been associated with different respiratory symptoms and pathologies in occupational populations, such as grain workers. However, the homogeneity in the fungal species composition of these bioaerosols on a large geographical scale and the different drivers that shape these fungal communities remain unclear. In this study, the diversity of fungi in grain dust and in the aerosols released during harvesting was determined across 96 sites at a geographical scale of 560 km(2) along an elevation gradient of 500 m by tag-encoded 454-pyrosequencing of the internal transcribed spacer (ITS) sequences. Associations between the structure of fungal communities in the grain dust and different abiotic (farming system, soil characteristics, geographic and climatic parameters) and biotic (wheat cultivar, previous crop culture) factors were explored. These analyses revealed a strong relationship between the airborne and grain dust fungal communities and showed the presence of allergenic and mycotoxigenic species in most samples, which highlights the potential contribution of these fungal species to work-related respiratory symptoms of grain workers. The farming system was the major driver of the alpha and beta phylogenetic diversity of fungal communities. In addition, elevation and soil CaCO3 concentrations shaped the alpha diversity whereas wheat cultivar, cropping history and the number of freezing days per year shaped the taxonomic beta diversity of these communities.

Trophic versus geographic structure in stable isotope signatures of pelagic seabirds breeding in the northeast Atlantic

Feeding ecology and geographic location are 2 major factors influencing animal stable isotope signatures, but their relative contributions are poorly understood, which limits the usefulness of stable isotope analysis in the study of animal ecology. To improve our knowledge of the main sources of isotopic variability at sea, we determined δ15N and δ13C signatures in the first primary feather of adult birds from 11 Procellariiform species (n = 609) across 16 northeast Atlantic localities, from Cape Verde (20°N) to Iceland (60°N). Post-breeding areas (where the studied feather is thought to be grown) were determined using light-level geolocation for 6 of the 11 species. Isotopic variability was geographically unstructured within the mid-northeast Atlantic (Macaronesian archipelagos), but trophically structured according to species and regardless of the breeding location, presumably as a result of trophic segregation among species. Indeed, the interspecific isotopic overlap resulting from combining δ15N and δ13C signatures of seabirds was low, which suggests that most species exploited exclusive trophic resources consistently across their geographic range. Species breeding in north temperate regions (Iceland, Scotland and Northern Ireland) showed enriched δ15N compared to the same or similar species breeding in tropical and subtropical regions, suggesting some differences in baseline levels between these regions. The present study illustrates a noticeable trophic segregation of northeast Atlantic Procellariiformes. Our results show that the isotopic approach has limited applicability for the study of animal movements in the northeast Atlantic at a regional scale, but is potentially useful for the study of long-distance migrations between large marine systems

Haja-asutusalueiden sähkönjakelujärjestelmien kehittäminen – erityisesti 1000 V jakelujännitteen käyttömahdollisuudet

Yhteiskunnan riippuvuus sähköstä on lisääntynyt voimakkaasti viime vuosikymmenien aikana. Sähkönjakelussa esiintyneet lyhyet ja pitkät keskeytykset ovat osoittaneet yhteiskunnan haavoittuvuuden ja yhteiskunta kestää entistä vähemmän sähkönjakelussa tapahtuvia häiriöitä. Keskeytyksistä aiheutuneiden haittojen arvostus on kasvanut ja tämä on luonut taloudelliset perusteet sähkön laatua parantaville investoinneille. Haja-asutusalueiden keskijänniteverkon johdot on rakennettu avojohtoina ja siten ne ovat alttiita sääolosuhteista johtuville myrsky- ja lumikuormavaurioille. Ilmastomuutoksen ennustetaan lisäävän tuulisuutta ja siten ongelmat sähkönjakelussa mahdollisesti lisääntyvät. Taajamissa käytetään enemmän kaapeleita ja johtolähdöt ovat lyhyitä, joten myrskyistä aiheutuvia keskeytyksiä on vähemmän kuin haja-asutusalueella. Olemassa olevat jakeluverkot ovat käytössä vielä vuosikymmeniä, joten uuden tekniikan kehittämisen rinnalla on kehitettävä myös olemassa olevaa jakeluverkkoa ja sen ylläpitoa. Ylläpidon tavoitteena on käyttövarmuuden parantamisen lisäksi huolehtia siitä, että jakeluverkkoihin sitoutunut omaisuus säilyttää arvonsa mahdollisimman hyvin pitoajan loppuun saakka. Jakeluverkkoihin investoitiin paljon 1950–70-luvuilla. Tältä ajalta on yhä käytössä puupylväitä, joiden ikääntymisen takia korvausinvestointien tarve kasvaa. Hyvänä puolena tässä on että käyttövarmuuden parantamiseksi olemassa olevaa jakeluverkkoa ei tarvitse uusia ennenaikaisesti. Tutkimuksessa päähuomio on haja-asutusalueiden 20 kV keskijänniteverkon kehittämisessä, sillä yli 90 % asiakkaiden kokemista keskeytyksistä johtuu keskijänniteverkon vioista. Erityisesti johtorakenteisiin ja johtojen sijoittamiseen on kiinnitettävä huomiota. Käyttövarmuuden lisäksi jakeluverkkojen kehittämistä ohjaavia tekijöitä ovat taloudellisuus, ympäristön huomioiminen, viranomaisvalvonta sekä asiakkaiden ja omistajien odotukset. Haja-asutusalueilla taloudelliset haasteet ovat suuret vakituisen väestön vähenemisen ja mahdollisesti sähköntarpeen pienenemisen takia. Taloudellisuus korostuu ja riskit kasvavat, kun tuottojen määrä supistuu tarvittaviin jakeluverkon investointeihin ja ylläpitokustannuksiin verrattuna. Ristiriitaa aiheuttaa se, että asiakkaat odottavat sähkönjakelulta parempaa luotettavuutta, mutta paremmasta sähkönlaadusta ei olla valmiita maksamaan juurikaan nykyistä enempää. Jakeluverkkojen kehittämistä voi hidastaa myös viranomaisvalvonta, jos tuottoja ei voida lisätä investointien lisätarpeiden suhteessa. Tutkimuksessa on analysoitu yleisellä tasolla kaapeloinnin lisäämistä, korkeiden pylväiden käyttämistä, leveitä johtokatuja, edullisten ja yksinkertaisten sähköasemien rakentamista haja-asutusalueille ja automaatioasemien lisäämistä keskijänniteverkon solmupisteisiin. Erityisesti tutkimuksessa on analysoitu uutena tekniikkana 1000 V jännitteen käyttömahdollisuutta jakeluverkkojen kehittämisessä. Sähköjohtojen siirtäminen teiden varsiin parantaa käyttövarmuutta, vaikka johdot rakennetaan samalla tekniikalla kuin olemassa olevat johdot. Hajaasutusalueille rakennettavilla sähköasemilla pitkät syöttöjohdot voidaan jakaa pienemmiksi syöttöalueiksi, jolloin keskeytyksistä aiheutuvat haitat koskettavat kerrallaan pienempää asiakasmäärää. Samaan tulokseen päästään oikein sijoitetuilla ja toteutetuilla automaatioasemilla. Tutkimuksen mukaan lupaavaksi tekniikaksi jakeluverkkojen kehittämisessä on osoittautumassa 1000 V jänniteportaan ottaminen 400 V pienjännitteen lisäksi. 1000 V verkoilla voidaan korvata häiriöherkkiä 20 kV keskijänniteverkon lyhyitä, alle viiden kilometrin pituisia haarajohtoja ja haarajohtojen jatkeita, missä siirrettävät tehot ovat pieniä. Uudessa jakelujärjestelmässä sähkö tuodaan 1000 V jännitteellä lähelle asiakasta, jossa jännite muunnetaan normaaliksi asiakkaille soveltuvaksi 400/230 V jännitteeksi. Edullisuus perustuu siihen, että rakentamisessa käytetään samoja pienjännitejohtoja kuin asiakkaille menevässä 400 V pienjänniteverkossa. 1000 V jakelutekniikassa sekä investointikustannukset että ylläpitokustannukset ovat pienemmät kuin perinteisessä 20 kV ilmajohtotekniikassa. 1000 V johdot säästävät maisemaa, sillä ne eivät tarvitse leveää johtokatua kuten 20 kV keskijännitejohdot. 1000 V verkkojen käyttö soveltuukin erityisesti vapaa-ajanasuntojen sähköistykseen herkissä ranta- ja järvimaisemissa. 1000 V verkot mahdollistavat kaapeliauraamisen lisäämisen ja näin voidaan vähentää ympäristöä haittaavien kyllästettyjen pylväiden käyttöä. 1000 V jakeluverkkojen osalta tutkimustyön tuloksia on sovellettu suomalaisessa Suur-Savon Sähkö Oy:ssä. Käytännön kokemuksia 1000 V jakelujärjestelmästä on useista kymmenistä kohteista. Tutkimustulokset osoittavat, ettei keskijänniteverkon maakaapelointi hajaasutusalueilla ole taloudellisesti kannattavaa nykyisillä keskeytyksistä aiheutuvilla haitta-arvoilla, mutta jos keskeytyskustannusten arvostus kasvaa, tulee kaapelointi kannattavaksi monissa paikoissa. Myös myrskyisyyden ja myrskyistä aiheutuvien jakelukeskeytysten lisääntyminen tekisi kaapeloinnista kannattavan. Tulevaisuudessa jakeluverkkojen rakentaminen on entistä monimuotoisempi tehtävä, jossa taloudellisuuden ja käyttövarmuuden lisäksi on huomioitava asiakkaat, omistajat, viranomaiset ja ympäristö. Tutkimusta jakelutekniikan kehittämiseksi tarvitaan edelleen. Tulevaisuuden osalta haja-asutusalueiden jakeluverkkojen kehittämiseen liittyy paljon epävarmuuksia. Hajautetun kiinteistökohtaisen sähköntuotannon lisääntyminen voi tehdä jakeluverkoista nykyistä tarpeettomampia, mutta esimerkiksi liikenteen sähköistyminen voi kasvattaa jakeluverkkojen merkitystä. Tästä syystä jakeluverkkojen rakentamisessa tarvitaan joustavuutta, jotta tarvittaessa voidaan helposti sopeutua erilaisiin kehityssuuntiin.