Depolarizing metrics for plant samples imaging.

Optical methods, as fluorescence microscopy or hyperspectral imaging, are commonly used for plants visualization and characterization. Another powerful collection of optical techniques is the so-called polarimetry, widely used to enhance image contrast in multiple applications. In the botanical applications framework, in spite of some works have already highlighted the depolarizing print that plant structures left on input polarized beams, the potential of polarimetric methods has not been properly exploited. In fact, among the few works dealing with polarization and plants, most of them study light scattered by plants using the Degree of Polarization (DoP) indicator. Other more powerful depolarization metrics are nowadays neglected. In this context, we highlight the potential of different depolarization metrics obtained using the Mueller matrix (MM) measurement: the Depolarization Index and the Indices of Polarimetric Purity. We perform a qualitative and quantitative comparison between DoP- and MM-based images by studying a particular plant, the Hedera maroccana. We show how Mueller-based metrics are generally more suitable in terms of contrast than DoP-based measurements. The potential of polarimetric measurements in the study of plants is highlighted in this work, suggesting they can be applied to the characterization of plants, plant taxonomy, water stress in plants, and other botanical studies.

A critical review of the protracted domestication model for Near-Eastern founder crops: linear regression, long-distance gene flow, archaeological, and archaeobotanical evidence.

The recent review by Fuller et al. (2012a) in this journal is part of a series of papers maintaining that plant domestication in the Near East was a slow process lasting circa 4000 years and occurring independently in different locations across the Fertile Crescent. Their protracted domestication scenario is based entirely on linear regression derived from the percentage of domesticated plant remains at specific archaeological sites and the age of these sites themselves. This paper discusses why estimates like haldanes and darwins cannot be applied to the seven founder crops in the Near East (einkorn and emmer wheat, barley, peas, chickpeas, lentils, and bitter vetch). All of these crops are self-fertilizing plants and for this reason they do not fulfil the requirements for performing calculations of this kind. In addition, the percentage of domesticates at any site may be the result of factors other than those that affect the selection for domesticates growing in the surrounding area. These factors are unlikely to have been similar across prehistoric sites of habitation, societies, and millennia. The conclusion here is that single crop analyses are necessary rather than general reviews drawing on regression analyses based on erroneous assumptions. The fact that all seven of these founder crops are self-fertilizers should be incorporated into a comprehensive domestication scenario for the Near East, as self-fertilization naturally isolates domesticates from their wild progenitors.

Probability of identification: a statistical model for the validation of qualitative botanical identification methods.

A qualitative botanical identification method (BIM) is an analytical procedure that returns a binary result (1 = Identified, 0 = Not Identified). A BIM may be used by a buyer, manufacturer, or regulator to determine whether a botanical material being tested is the same as the target (desired) material, or whether it contains excessive nontarget (undesirable) material. The report describes the development and validation of studies for a BIM based on the proportion of replicates identified, or probability of identification (POI), as the basic observed statistic. The statistical procedures proposed for data analysis follow closely those of the probability of detection, and harmonize the statistical concepts and parameters between quantitative and qualitative method validation. Use of POI statistics also harmonizes statistical concepts for botanical, microbiological, toxin, and other analyte identification methods that produce binary results. The POI statistical model provides a tool for graphical representation of response curves for qualitative methods, reporting of descriptive statistics, and application of performance requirements. Single collaborator and multicollaborative study examples are given.

Determinants of scientific output: an in-depth view of the productivity of tropical botanist and conservationist, Luis Diego Gómez Pignataro

Bibliometric studies have found that male researchers have their greatest productivity around the age of 40, that female researchers produce less than their male colleagues, that incentives for collaboration are slow to affect productivity and that, just like humans, research institutes become larger, less productive, more expensive to maintain and less able to raise money as they grow old. Almost invariably, these conclusions come from statistical studies of large numbers of European and American scientists, and there are practically no studies about tropical researchers. We present an in-depth analysis of the productivity of an internationally recognized tropical botanist and conservationist, Luis Diego Gómez Pignataro, based on the totality of his published work and on our own knowledge, as co-workers and friends, of the life frame in which that scientific output was produced. His life output departs from the expected pattern in that he had the highest productivity before reaching the expected peak productivity age, and that when he reached it his productivity fell and never recovered. Furthermore, marriage did not produce the expected fall in productivity. A close analysis of his life indicates that in the middle of his career he switched to intense teaching and conservation activities, and this better explains why his output of scientific research articles was low afterwards. This switch may occur in other tropical scientists. Rev. Biol. Trop. 58 (4): 1093-1114. Epub 2010 December 01.

Los estudios bibliométricos han encontrado que los investigadores de sexo masculino tienen su mayor productividad aproximadamente a los 40 años; que las investigadoras producen menos que sus colegas masculinos, que los incentivos para la colaboración tardan en aumentar la productividad y que, al igual que los seres humanos, los institutos de investigación se hacen más grandes, menos productivos, más costosos y menos capaces de recaudar dinero a medida que envejecen. Casi siempre, estas conclusiones provienen de estudios de un gran número de científicos europeos y estadounidenses, y prácticamente no hay estudios sobre los investigadores tropicales. Aquí presentamos un análisis detallado de la productividad de un botánico y conservacionista tropical reconocido internacionalmente, Luis Diego Gómez Pignataro, basado en la totalidad de su obra publicada y en nuestro propio conocimiento de su vida como compañeros de trabajo y amigos. Su vida se aparta del patrón esperado en que tuvo su mayor productividad en los primeros 20 años de carrera y produjo comparativamente poco en los siguientes 20 años. Además, el matrimonio no produjo el descenso esperado en su productividad. Justo a la mitad de su carrera se dedicó intensamente a actividades de enseñanza y conservación, lo que explica esa baja en su producción. Este patrón podría darse en otros científicos tropicales.

La Revista Broteria, los jesuitas naturalistas y Gonçalo Sampaio. Intercambio de plantas e ideas y el desarrollo de la botánica en Portugal / The Journal Broteria, Jesuits Botanists and Gonçalo Sampaio. Exchange of plants and ideas and the development of the botany in Portugal

La revista Broteria recorrió un largo camino, desde su fundación en 1902, hasta mediados de la década de 1920, cuando se consolida como una de las mejores revistas de historia natural y una voz de la renovación de las Ciencias Naturales en Portugal. El éxito de Broteria se debió, principalmente, a las notables calidades de sus fundadores y principales redactores: capacidad de trabajo, nivel intelectual y perseverancia; capacidad para establecer una red de naturalistas que les enviaban colecciones biológicas de regiones mal conocidas; capacidad de adaptación en el exilio continuando su trabajo y enfocando sus estudios en la historia natural del país de exilio. La manutención, en regular funcionamiento, de sus colegios y la apertura a la colaboración de naturalistas no jesuitas, especialmente a los botánicos de Oporto, también contribuyeron al éxito de Broteria. Los documentos epistolares tratadosen este trabajo demuestran que A. Luisier, J.S. Tavares, y G. Sampaio lideraron una red de jesuitas naturalistas y botánicos de Oporto, que intercambiaron plantas e ideas. Este intercambio fue determinante en el estudio de la flora de musgos y plantas vasculares portuguesas y el progreso de los Herbarios de los colegios jesuitas y de la Academia Politécnica de Oporto (AU)

The journal Broteria has covered a long path, since its foundation in 1902 until the mid 20’s, when it stands as one of the best journals of natural history and a voice of the renewal of the natural sciences in Portugal. Broteria’s success was due, mainly, to the remarkable qualities of its founders and main editors: their working capacity, intellectual standards and perseverance as well as the ability to establish a network of naturalists who sent them biological collections from remote regions and the ability to adapt to exile, while continuing to work and focusing their studies on the natural history of the exile country. The maintenance, in regular functioning, of their schools, and the opening to the collaboration of non Jesuit naturalists, such as the botanists from Oporto, also contributed to the success of Broteria (AU)

Determinants of scientific output: an in-depth view of the productivity of tropical botanist and conservationist, Luis Diego Gómez Pignataro.

Bibliometric studies have found that male researchers have their greatest productivity around the age of 40, that female researchers produce less than their male colleagues, that incentives for collaboration are slow to affect productivity and that, just like humans, research institutes become larger, less productive, more expensive to maintain and less able to raise money as they grow old. Almost invariably, these conclusions come from statistical studies of large numbers of European and American scientists, and there are practically no studies about tropical researchers. We present an in-depth analysis of the productivity of an internationally recognized tropical botanist and conservationist, Luis Diego Gómez Pignataro, based on the totality of his published work and on our own knowledge, as co-workers and friends, of the life frame in which that scientific output was produced. His life output departs from the expected pattern in that he had the highest productivity before reaching the expected peak productivity age, and that when he reached it his productivity fell and never recovered. Furthermore, marriage did not produce the expected fall in productivity. A close analysis of his life indicates that in the middle of his career he switched to intense teaching and conservation activities, and this better explains why his output of scientific research articles was low afterwards. This switch may occur in other tropical scientists.

Accelerating global access to plant diversity information.

Botanic gardens play key roles in the development and dissemination of plant information resources. Drivers for change have included progress in information technology, growing public expectations of electronic access and international conservation policy. Great advances have been made in the quantity, quality and accessibility of plant information in digital form and the extent to which information from multiple providers can be accessed through a single portal. However, significant challenges remain to be addressed in making botanic gardens resources maximally accessible and impactful, not least the overwhelming volume of material which still awaits digitisation. The year 2010 represents an opportunity for botanic gardens to showcase their collaborative achievements in delivery of electronic plant information and reinforce their relevance to pressing environmental issues.

Plant science research productivity in Chile during the past 20 years.

The purpose of this study was to carry out a bibliometric analysis of the articles published in Chile during 1987-2006 that were categorized into the Plant Science discipline by ISI. The data was extracted from the Web of Science datábase, obtaining a total of 911 articles for analysis. Almost half of the articles were the outcome of an international collaboration, the United States being the country with more collaborative links with Chile within this discipline. A list was made with the 10 most-cited articles and 10 most frequently used journals. The analysis showed that almost 50% of the articles were concentrated in 10 different journals. The number of articles produced each year revealed a steady growth in scientific production since 1987. This is probably related to the progressive interaction between industry and public-research institutions.

Plant Science research productivity in Chile during the past 20 years

The purpose of this study was to carry out a bibliometric analysis of the articles published in Chile during 1987-2006 that were categorized into the Plant Science discipline by ISI. The data was extracted from the Web of Science datábase, obtaining a total of 911 articles for analysis. Almost half of the articles were the outcome of an international collaboration, the United States being the country with more collaborative links with Chile within this discipline. A list was made with the 10 most-cited articles and 10 most frequently used journals. The analysis showed that almost 50 percent of the articles were concentrated in 10 different journals. The number of articles produced each year revealed a steady growth in scientific production since 1987. This is probably related to the progressive interaction between industry and public-research institutions.

Redução de esforço amostral vs. retenção de informação em inventários de pteridófitas na Amazônia Central / Sample effort reduction vs. information retention in inventories of pteridophytes in Central Amazonia

A extensa área coberta pelo domínio amazônico e os recursos financeiros limitados para estudos da biodiversidade exigem programas de pesquisa que obtenham o máximo de informação com os menores custos. Com o objetivo de avaliar as conseqüências da redução do esforço amostral sobre a retenção da informação ecológica, testou-se como diferentes larguras de parcela afetam os resultados da relação entre variação ambiental e composição da comunidade de pteridófitas da Amazônia Central. Foram feitas medidas da inclinação do terreno, abertura do dossel e do teor de argila do solo, em 37 parcelas de floresta de terra-firme. Todos os indivíduos de pteridófitas foram identificados e mapeados com relação a três faixas de amostragem. Foram testados os efeitos das variáveis ambientais sobre a composição de pteridófitas em parcelas de 250 x 2,5 m e em sub-amostras com a largura da parcela reduzida. A redução de 2,5 para 1 m na largura da parcela (60 por cento de redução no esforço amostral) correspondeu a uma redução de 24 por cento no custo do projeto, considerado os custos das excursões à campo, e a uma redução no número de espécies amostradas de 52 para 44. A redução 2,5 para 2 m na largura da parcela causou redução de apenas duas (4 por cento) nas espécies amostradas e 8 por cento no custo do projeto. Para todas as larguras testadas, a composição da comunidade esteve associada ao teor de argila e não esteve associada à inclinação do terreno. O efeito de abertura de dossel sobre a composição de espécies de pteridófitas não foi coerente entre os diferentes tamanhos de amostra. Esta incoerência deve estar relacionada à importância relativamente menor da luz sobre a estruturação da comunidade. Concluímos que as amostras com menor tamanho foram suficientemente informativas para detectar os principais gradientes de composição e sua associação aos fatores ambientais. Isso permitiria a redução nos custos totais ou alocação de mais parcelas...

The large area covered by the Amazonian domain and the limited financial support for biodiversity studies demand efficient research programs. Aiming to evaluate the consequences of reduced sampling effort on the retention of ecological information, we tested how differences in plot width affect the perceived relationship between environmental variation and the composition of the pteridophyte community in Central Amazonia. Measures of slope, canopy openness and soil clay content were taken in 37 terra-firme forest plots. All pteridophyte individuals were identified and mapped according to three sample strips. We tested the effects of environmental variables on pteridophyte composition of 250 x 2.5 meters-plots and on sub-samples of reduced width. The reduction of plot width from 2.5 to 1 m (60 percent reduction in sampling effort) corresponded to a reduction of 24 percent of the project's costs concerning field work expenses. This would reduce the number of sampled species from 52 to 44. The reduction of 20 percent plot width (from 2.5 to 2 m) would cause a reduction of two (4 percent) sampled species and a reduction of 8 percent of the costs. For all tested plot widths, community composition was associated with soil clay content and was not associated with the terrain slope. The effect of canopy openness on pteridophyte species composition was not consistent among sample sizes. These may be related to the relatively lower importance of light availability in determining community structure at the studied spatial scale. We concluded that the smallest plots were informative enough to detect the main gradients of composition and their association to environmental factors. This would allow a reduction in total costs, or the allocation of available budget to more plots, which could increase the power of the statistical analyses, reduce the confidence intervals and increase probability of detecting more species.

O primeiro registro de Sinningia gigantifolia Chautems (Gesneriaceae) no estado de São Paulo / Sinningia gigantifolia Chautems (Gesneriaceae) first record in the São Paulo State

Sinningia gigantifolia Chautems é uma espécie rupícola restrita à Serra da Mantiqueira e partes altas da Serra do Mar, que ocorre principalmente em formações florestais. O presente trabalho apresenta o primeiro registro desta espécie para o Estado de São Paulo, na Serra do Baú, em São Bento do Sapucaí. Uma descrição completa da espécie, uma análise da sua distribuição e uma alteração na chave de identificação do gênero Sinningia da Flora Fanerogâmica do Estado de São Paulo são fornecidas.

Sinningia gigantifolia Chautems is a rupicolous species restricted to the Serra da Mantiqueira and higher parts of the Serra do Mar in SE Brazil, ocurring mainly in forest formations. This note presents the first record of this species for São Paulo State, from the Serra do Baú, in São Bento do Sapucaí. A full species description, an analysis of its distribution and a revised key to the genus Sinningia for the Flora Fanerogâmica do Estado de São Paulo are provided.

[Half century of botany publishing in Revista de Biologia Tropical]. / Medio Siglo de publicaciones botánicas en la Revista de Biología Tropical.

Over its first half century the Revista de Biología Tropical published many papers and supplements dealing with the botany. However, the Revista is not a primary botanical journal. A wide variety of topics and geographic sources have been included, taking into consideration species from the Neotropics, but also from India and Nigeria. A complete index of botanical papers is presented.

[Patterns of spiral phyllotaxy]. / Zakonomernosti spiral'nogo lisoraspolozheniia.

The author investigates theoretical variants of spiral phyllotaxy using structural coefficient--the distance between consequent members in genetic spiral, expressed in parts of circle. The meanings of structural coefficient in which parastichies change their isomerism are determined as critical points. The author describes the overlapping of parastichies of lower lane by higher lane parastichies and presents the methods of overlapping determination. Parastichies with minimal distance between members in lane are clearly determined on shoots. Methods and formulas for calculation of structural coefficient using the number of members in parastichy circle are presented. Orthostichy is considered as a special case of parastichy location. Orthostichies are equal to parastichies in maximum critical points.

Standard errors of heritabilities for forage breeding nurseries.

Estimators for standard errors of heritability for two typical and complex forage breeding models are illustrated with estimates of variance and covariance components from least-squares and restricted maximum likelihood methods. The first experiment (Model 1) is a factorial design (two grazing management factors) with two layers of split plots (populations and grazing periods) and with plants within populations nested beneath the first split. The second model is for a sites pooling of randomized complete block experiments, with plants nested inside plots and with a split in time. One definition of heritability was applied to the plant habit character for both models in a red clover germplasm. Heritability estimates were statistically the same for the two methods for both models.