An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae

Aim  Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony-based approaches. Here, we compare a parametric method, dispersal-extinction-cladogenesis (DEC), against a parsimony-based method, dispersal-vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes-DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study.Location  World-wide.Methods  Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes-DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years.Results  Despite differences in the underlying biogeographical model, Bayes-DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events - which in Bayes-DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node.Main conclusions  By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes-DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide-spanning spatial and temporal model proposed here could prove useful for testing large-scale biogeographical patterns in plants.

Influence of a lifestyle intervention in preschool children on physiological and psychological parameters (Ballabeina): study design of a cluster randomized controlled trial.

Childhood obesity and physical inactivity are increasing dramatically worldwide. Children of low socioeconomic status and/or children of migrant background are especially at risk. In general, the overall effectiveness of school-based programs on health-related outcomes has been disappointing. A special gap exists for younger children and in high risk groups. This paper describes the rationale, design, curriculum, and evaluation of a multicenter preschool randomized intervention study conducted in areas with a high migrant population in two out of 26 Swiss cantons. Twenty preschool classes in the German (canton St. Gallen) and another 20 in the French (canton Vaud) part of Switzerland were separately selected and randomized to an intervention and a control arm by the use of opaque envelopes. The multidisciplinary lifestyle intervention aimed to increase physical activity and sleep duration, to reinforce healthy nutrition and eating behaviour, and to reduce media use. According to the ecological model, it included children, their parents and the teachers. The regular teachers performed the majority of the intervention and were supported by a local health promoter. The intervention included physical activity lessons, adaptation of the built infrastructure; promotion of regional extracurricular physical activity; playful lessons about nutrition, media use and sleep, funny homework cards and information materials for teachers and parents. It lasted one school year. Baseline and post-intervention evaluations were performed in both arms. Primary outcome measures included BMI and aerobic fitness (20 m shuttle run test). Secondary outcomes included total (skinfolds, bioelectrical impedance) and central (waist circumference) body fat, motor abilities (obstacle course, static and dynamic balance), physical activity and sleep duration (accelerometry and questionnaires), nutritional behaviour and food intake, media use, quality of life and signs of hyperactivity (questionnaires), attention and spatial working memory ability (two validated tests). Researchers were blinded to group allocation. The purpose of this paper is to outline the design of a school-based multicenter cluster randomized, controlled trial aiming to reduce body mass index and to increase aerobic fitness in preschool children in culturally different parts of Switzerland with a high migrant population. Trial Registration: (clinicaltrials.gov) NCT00674544.

Optimal Design of Permit Markets with an Ex Ante Pollution Target, August 2006

In this paper, we examine the design of permit trading programs when the objective is to minimize the cost of achieving an ex ante pollution target, that is, one that is defined in expectation rather than an ex post deterministic value. We consider two potential sources of uncertainty, the presence of either of which can make our model appropriate: incomplete information on abatement costs and uncertain delivery coefficients. In such a setting, we find three distinct features that depart from the well-established results on permit trading: (1) the regulator’s information on firms’ abatement costs can matter; (2) the optimal permit cap is not necessarily equal to the ex ante pollution target; and (3) the optimal trading ratio is not necessarily equal to the delivery coefficient even when it is known with certainty. Intuitively, since the regulator is only required to meet a pollution target on average, she can set the trading ratio and total permit cap such that there will be more pollution when abatement costs are high and less pollution when abatement costs are low. Information on firms’ abatement costs is important in order for the regulator to induce the optimal alignment between pollution level and abatement costs.

The role of gene duplication in the origin and evolution of new biological functions

Abstract : Gene duplication is an essential source of material for the origin of genetic novelty and the evolution of lineage- or species-specific phenotypic traits. The reverse transcription of source gene mRNA followed by the genomic insertion of the resulting cDNA - retroposition - has provided the human genome with a significant number of gene copies during the last ~63 million years (MYA) of primate evolution. We estimated that at least 1 new functional gene (retrogene) per MYA emerged by retroposition in the primate lineage leading to humans. Using a combination of comparative sequencing and evolutionary simulations, we obtained strong evidence of functionality for 7 primate specific retrogenes. Most of these genes are specifically expressed in testis suggesting that retroposition has contributed with genetic raw material necessary for the evolution ofmale-specific functions in primates. We characterized CDC14Bretro (identified in the previous survey) that originated from the retroposition of a cell cycle gene - CDC14B - in the common ancestor of humans and apes. We demonstrate that CDC14Bretro experienced a period of intense positive selection in the African ape ancestor. By virtue of the amino acid substitutions that occurred during this period CDC 14Bretro adapted to a new subcellular compartment in African apes. Further analyses indicate that this subcellular shift reflects the evolution of anew functional role of CDC 14Bretro. Prompted by this result, we used yeast (Saccharomyces cerevisiae) to investigate on a global scale the extent of functional diversification of duplicate genes through the subcellular adaptation of their encoded proteins. We found that duplicate proteins frequently evolved new cellular localization patterns, either by partitioning of ancestral localizations ("sublocalization"), or more frequently by relocalization to previously unoccupied compartments ("neolocalization"). Interestingly, proteins involved in processes with a wider subcellular distribution more frequently evolved new localization patterns suggesting that subcellular localization changes are dependent on progenitor gene functions. Relocated proteins adapted to their new subcellular environments and evolved new functional roles through changes of their physio-chemical properties, expression levels, and interaction partners. Our work suggests an important role of subcellular adaptation for the emergence of new gene functions.

Description of a new genus and new species of New World Phlebotominae (Diptera, Psychodidae)

A new genus and new species of Phlebotominae, Edentomyia piauiensis (Diptera, Psychodidae) from a cave in Piauí State, Brazil, are described. This new genus belongs to Phlebotomini, but its inclusion in any subdivision of this tribe depends on further study.

Hybotinae (Diptera, Empidoidea, Hybotidae) from the Dominican Republic: new records and description of new species

Hybotinae is being recorded for the first time to Dominican Republic where the subfamily becomes represented by the genera Euhybus Coquillett, 1895, Neohybos Ale-Rocha & Carvalho, 2003 and Syneches Walker, 1852. Euhybus and Neohybos occur exclusively in the Americas, and Syneches is cosmopolitan. Six new species are described and illustrated: Euhybus martiniensis sp. nov., Neohybos cinereus sp. nov., N. longicornis sp. nov., N. pruinosus sp. nov., N. setosus sp. nov. and Syneches dominicanus sp. nov.. Identification keys are provided for the species of the three hybotine genera registered in West Indies. The following species are recorded for the first time from the Dominican Republic: Syneches inversus Curran, 1928, S. pallidus Wilder, 1974 and S. vineus Wilder, 1974. The previously unknown female of S. inversus is described.

Descriptions of new species with a key to identification of the genus Neodexiopsis Malloch (Diptera, Muscidae) in Brazil

Nine new species of Neodexiopsis Malloch from Paraná, southern Brazil, are described: Neodexiopsis cinerea sp. nov. and N. paranaensis sp. nov. from Ponta Grossa; N. facilis sp. nov., N. legitima sp. nov., N. similis sp. nov. and N. uber sp. nov. from Guarapuava; N. erecta sp. nov., N. pura sp. nov. and N. rara sp. nov. from Colombo. A key to the identification of the Brazilian species of Neodexiopsis is also presented.

15 years of new growth economics: What have we learnt?

This paper evaluates the empirical and theoretical contributions of theEconomic Growth Literature since the publication of Paul Romer s seminalpaper in 1986.

The genus Lycoderides Sakakibara, stat. nov., its composition and descriptions of new species (Hemiptera, Membracidae, Stegaspidinae)

The genus Lycoderides Sakakibara, stat. nov. , its composition and descriptions of new species (Hemiptera, Membracidae, Stegaspidinae).The subgenus Lycoderes (Lycoderides) Sakakibara, 1972 is raised to the genus category - Lycoderides stat. nov.. - : and it now includes: Lycoderides amazonicus (Sakakibara, 1991), comb. nov. , Lycoderides brevilobus (Sakakibara, 1972), comb. nov. , Lycoderides burmeisteri (Fairmaire, 1846), comb. nov. , Lycoderides cultratus (Sakakibara, 1991), comb. nov. , Lycoderides fernandezi (Strümpel, 1988), comb. nov. , Lycoderides fuscus (Amyot & Serville, 1843), comb. nov. , Lycoderides gradatus (Sakakibara, 1972), comb. nov. , Lycoderides hippocampus (Fabricius, 1803), comb. nov. , Lycoderides luteus (Funkhouser, 1940), comb. nov. , Lycoderides marginalis (Walker, 1851), comb. nov. , Lycoderides nathanieli (Cryan, 1999), comb. nov. , Lycoderides obtusus (Sakakibara, 1991), comb. nov. , Lycoderides pennyi (Sakakibara, 1991), comb. nov. , Lycoderides phasianus (Fowler, 1896), comb. nov. (= Enchenopa minamen Buckton, 1901,SYN. NOV: ), Lycoderides protensus (Sakakibara, 1991), comb. nov. , Lycoderides serraticornis (Fowler, 1896), comb. nov. , and Lycoderides strumpeli (Sakakibara, 1991), comb. nov. The following new species are described: Lycoderides abditus, sp. nov. , Lycoderides brulei,SP. NOV. (: both from French Guiana), Lycoderides capixaba, sp. nov. (from Brazil, Espírito Santo), Lycoderides cavichiolii, sp. nov. (from Brazil, Rio de Janeiro), Lycoderides meloi, sp. nov. (from Brazil, Bahia), and Lycoderides oliviae, sp. nov. (from Brazil, Minas Gerais). Other nomenclatural change: Stegaspis bracteata (Fabricius, 1787) = Lycoderes capitata Buckton, 1903, syn. nov. New records of geographical distribution and a key to the species are provided.

You’re the COACH!: A Guide for Parents of New Drivers, June 23, 2008

This publication is a guide for parents and guardians of teenagers learning to drive. It should be used with the Iowa Driver’s Manual to aid you in instructing your new driver about how to safely and responsibly operate a motor vehicle. Since the task of driving is affected by changing conditions, this manual does not attempt to cover all situations that may arise. Under Iowa’s graduated driver licensing system young drivers must complete 20 hours of supervised drive time with their parents or guardians during the instruction permit stage and 10 hours during the intermediate license stage. Even though your teenager is taking or has completed driver education in school, there is a great deal of benefit to be obtained from you providing this additional practice time. Learning from your experience and under your guidance, your teenager will apply the rules of the road and more fully understand the risks involved in driving. This will require time and patience on your part, but the effort will result in you knowing that your teenager will be better able to cope with the demands of safe driving. In the back of this manual you will find several pages of diagrams. Use these diagrams to illustrate different driving situations for your teenage driver. Consider taking a notepad and pencil along during your practice sessions for additional drawings. This manual also contains a chart to log your supervised drive time. As your new driver advances through the graduated system you will be required to certify to an Iowa driver’s license examiner that you completed the minimum number of hours of supervised drive time. By becoming involved in the learning driver’s educational process, you are contributing to Iowa’s overall highway safety effort and helping your teenager develop safe driving habits that will last a lifetime.

Escherchia coli ribose binding protein based bioreporters revisited.

Bioreporter bacteria, i.e., strains engineered to respond to chemical exposure by production of reporter proteins, have attracted wide interest because of their potential to offer cheap and simple alternative analytics for specified compounds or conditions. Bioreporter construction has mostly exploited the natural variation of sensory proteins, but it has been proposed that computational design of new substrate binding properties could lead to completely novel detection specificities at very low affinities. Here we reconstruct a bioreporter system based on the native Escherichia coli ribose binding protein RbsB and one of its computationally designed variants, reported to be capable of binding 2,4,6-trinitrotoluene (TNT). Our results show in vivo reporter induction at 50 nM ribose, and a 125 nM affinity constant for in vitro ribose binding to RbsB. In contrast, the purified published TNT-binding variant did not bind TNT nor did TNT cause induction of the E. coli reporter system.

Establishment of new crops for the production of natural rubber.

Natural rubber is a unique biopolymer of strategic importance that, in many of its most significant applications, cannot be replaced by synthetic alternatives. The rubber tree Hevea brasiliensis is the almost exclusive commercial source of natural rubber currently and alternative crops should be developed for several reasons, including: a disease risk to the rubber tree that could potentially decimate current production, a predicted shortage of natural rubber supply, increasing allergic reactions to rubber obtained from the Brazilian rubber tree and a general shift towards renewables. This review summarizes our knowledge of plants that can serve as alternative sources of natural rubber, of rubber biosynthesis and the scientific gaps that must be filled to bring the alternative crops into production.