Semi‐automated workflows for acquiring specimen data from label images in herbarium collections

Computational workflow environments are an active area of computer science and informatics research; they promise to be effective for automating biological information processing for increasing research efficiency and impact. In this project, semi‐automated data processing workflows were developed to test the efficiency of computerizing information contained in herbarium plant specimen labels. Our test sample consisted of mexican and Central American plant specimens held in the University of michigan Herbarium (MICH). The initial data acquisition process consisted of two parts: (1) the capture of digital images of specimen labels and of full‐specimen herbarium sheets, and (2) creation of a minimal field database, or "pre‐catalog", of records that contain only information necessary to uniquely identify specimens. For entering "pre‐catalog" data, two methods were tested: key‐stroking the information (a) from the specimen labels directly, or (b) from digital images of specimen labels. In a second step, locality and latitude/longitude data fields were filled in if the values were present on the labels or images. If values were not available, geo‐coordinates were assigned based on further analysis of the descriptive locality information on the label. Time and effort for the various steps were measured and recorded. Our analysis demonstrates a clear efficiency benefit of articulating a biological specimen data acquisition workflow into discrete steps, which in turn could be individually optimized. First, we separated the step of capturing data from the specimen from most keystroke data entry tasks. We did this by capturing a digital image of the specimen for the first step, and also by limiting initial key‐stroking of data to create only a minimal "pre‐catalog" database for the latter tasks. By doing this, specimen handling logistics were streamlined to minimize staff time and cost. Second, by then obtaining most of the specimen data from the label images, the more intellectually challenging task of label data interpretation could be moved electronically out of the herbarium to the location of more highly trained specialists for greater efficiency and accuracy. This project used experts in the plants’ country of origin, mexico, to verify localities, geography, and to derive geo‐coordinates. Third, with careful choice of data fields for the "pre‐catalog" database, specimen image files linked to the minimal tracking records could be sorted by collector and date of collection to minimize key‐stroking of redundant data in a continuous series of labels, resulting in improved data entry efficiency and data quality.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146956/1/tax596014.pd

Contribución al conocimiento de la flora briológica de la ciudad de Ávila.

This paper presents a study on the urban bryoflora of Avila. It provides informa tion on the occurrence of Bryophyta ira 11w different habitats within iba town. A total list of 29 bryophytes (some of them never before mentioned to exist in ihis province) is given.Se han encontrado 29 briófitos en la ciudad de Avila. Se indican los hábitats y localizaciones de todos ellos y los que son novedades provinciales

Nicheâ based processes outperform neutral processes when predicting distance decay in coâ dominance along the Amazon â Andes rainforest gradient

QuestionDispersal limitation (neutral hypothesis) and deterministic factors (niche hypothesis) shape floristic gradients including betweenâ site patterns of speciesâ dominance (coâ dominance). Because their relative importance remains poorly known, we ask how their comparative contribution to coâ dominance changes with elevation and geographical extent.LocationMadidi region, NW Bolivia.MethodsWe analysed floristic composition and environmental factors of 90 plots spanning the gradient from Amazonian (<1,000 m) to montane forests at three elevations (1,200â 1,500; 2,000â 2,300; and 2,800â 3,200 m) and two geographical extents: local (plots <12 km apart) and regional (38â 120 km apart). We modelled distance decay within each elevational band with a neutral model, using two parameters (speciation rate and dispersal distance). Subsequently, we related the model’s residuals to environmental differences using flexible machine learning models.ResultsWe found that 5â 44% of the variability in floristic differences along the gradient studied can be explained by a neutral model of distance decay, while 18â 50% can be explained by environmental differences. Montane forests showed an overall gradient in floristic composition that is congruent with an increase in elevation for both dispersal limitation and environmental filtering. However, Amazonian forest was more nicheâ structured and more dispersalâ limited relative to its elevation and topography.ConclusionsEnvironmental differences explained floristic differences better than the neutral model, even giving preferential attribution to the more parsimonious neutral processes.We analysed 90 tree communities spanning the longest forested elevational gradient on Earth: the extraordinarily diverse Amazonian and Andean forests of the Madidi region (Bolivia). Dominant species vary more with greater barriers to dispersal and stronger environmental changes, increasingly so at higher elevations. Amazonian dominant species, however, change more than expected at their elevation and topography.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149700/1/jvs12761-sup-0003-AppendixS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149700/2/jvs12761-sup-0001-AppendixS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149700/3/jvs12761.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149700/4/jvs12761_am.pd

Trade-offs among aboveground, belowground, and soil organic carbon stocks along altitudinal gradients in Andean tropical montane forests

Tropical montane forests (TMFs) play an important role as a carbon reservoir at a global scale. However, there is a lack of a comprehensive understanding on the variation in carbon storage across TMF compartments [namely aboveground biomass (AGB), belowground biomass (BGB), and soil organic matter] along altitudinal and environmental gradients and their potential trade-offs. This study aims to: 1) understand how carbon stocks vary along altitudinal gradients in Andean TMFs, and; 2) determine the influence of climate, particularly precipitation seasonality, on the distribution of carbon stocks across different forest compartments. The study was conducted in sixty 0.1 ha plots along two altitudinal gradients at the Podocarpus National Park (Ecuador) and Río Abiseo National Park (Peru). At each plot, we calculated the amount of carbon in AGB (i.e. aboveground carbon stock, AGC), BGB (i.e. belowground carbon stock, BGC), and soil organic matter (i.e. soil organic carbon stock, SOC). The mean total carbon stock was 244.76 ± 80.38 Mg ha–1 and 211.51 ± 46.95 Mg ha–1 in the Ecuadorian and Peruvian plots, respectively. Although AGC, BGC, and SOC showed different partitioning patterns along the altitudinal gradient both in Ecuador and Peru, total carbon stock did not change with altitude in either site. The combination of annual mean temperature and precipitation seasonality explained differences in the observed patterns of carbon stocks across forest compartments between the two sites. This study suggests that the greater precipitation seasonality of colder, higher altitudes may promote faster turnover rates of organic matter and nutrients and, consequently, less accumulation of SOC but greater AGC and BGC, compared to those sites with lesser precipitation seasonality. Our results demonstrate the capacity of TMFs to store substantial amounts of carbon and suggest the existence of a trade-off in carbon stocks among forest compartments, which could be partly driven by differences in precipitation seasonality, especially under the colder temperatures of high altitudesAuthorizations to work in protected areas were granted by national authorities: Ecuador (MAE-DNB-CM2015-0016) and Perú (001-2016-SERNANP-PNRA-JEF

The Tree Biodiversity Network (BIOTREE-NET): prospects for biodiversity research and conservation in the Neotropics

Biodiversity research and conservation efforts in the tropics are hindered by the lack of knowledge of the assemblages found there, with many species undescribed or poorly known. Our initiative, the Tree Biodiversity Network (BIOTREE-NET), aims to address this problem by assembling georeferenced data from a wide range of sources, making these data easily accessible and easily queried, and promoting data sharing. The database (GIVD ID NA-00-002) currently comprises ca. 50,000 tree records of ca. 5,000 species (230 in the IUCN Red List) from \u3e2,000 forest plots in 11 countries. The focus is on trees because of their pivotal role in tropical forest ecosystems (which contain most of the world\u27s biodiversity) in terms of ecosystem function, carbon storage and effects on other species. BIOTREE-NET currently focuses on southern Mexico and Central America, but we aim to expand coverage to other parts of tropical America. The database is relational, comprising 12 linked data tables. We summarise its structure and contents. Key tables contain data on forest plots (including size, location and date(s) sampled), individual trees (including diameter, when available, and both recorded and standardised species name), species (including biological traits of each species) and the researchers who collected the data. Many types of queries are facilitated and species distribution modelling is enabled. Examining the data in BIOTREE-NET to date, we found an uneven distribution of data in space and across biomes, reflecting the general state of knowledge of the tropics. More than 90% of the data were collected since 1990 and plot size varies widely, but with most less than one hectare in size. A wide range of minimum sizes is used to define a \u27tree\u27. The database helps to identify gaps that need filling by further data collection and collation. The data can be publicly accessed through a web application at http://portal.biotreenet.com. Researchers are invited and encouraged to contribute data to BIOTREE-NET

Taking the pulse of Earth's tropical forests using networks of highly distributed plots

Tropical forests are the most diverse and productive ecosystems on Earth. While better understanding of these forests is critical for our collective future, until quite recently efforts to measure and monitor them have been largely disconnected. Networking is essential to discover the answers to questions that transcend borders and the horizons of funding agencies. Here we show how a global community is responding to the challenges of tropical ecosystem research with diverse teams measuring forests tree-by-tree in thousands of long-term plots. We review the major scientific discoveries of this work and show how this process is changing tropical forest science. Our core approach involves linking long-term grassroots initiatives with standardized protocols and data management to generate robust scaled-up results. By connecting tropical researchers and elevating their status, our Social Research Network model recognises the key role of the data originator in scientific discovery. Conceived in 1999 with RAINFOR (South America), our permanent plot networks have been adapted to Africa (AfriTRON) and Southeast Asia (T-FORCES) and widely emulated worldwide. Now these multiple initiatives are integrated via ForestPlots.net cyber-infrastructure, linking colleagues from 54 countries across 24 plot networks. Collectively these are transforming understanding of tropical forests and their biospheric role. Together we have discovered how, where and why forest carbon and biodiversity are responding to climate change, and how they feedback on it. This long-term pan-tropical collaboration has revealed a large long-term carbon sink and its trends, as well as making clear which drivers are most important, which forest processes are affected, where they are changing, what the lags are, and the likely future responses of tropical forests as the climate continues to change. By leveraging a remarkably old technology, plot networks are sparking a very modern revolution in tropical forest science. In the future, humanity can benefit greatly by nurturing the grassroots communities now collectively capable of generating unique, long-term understanding of Earth's most precious forests. Resumen Los bosques tropicales son los ecosistemas más diversos y productivos del mundo y entender su funcionamiento es crítico para nuestro futuro colectivo. Sin embargo, hasta hace muy poco, los esfuerzos para medirlos y monitorearlos han estado muy desconectados. El trabajo en redes es esencial para descubrir las respuestas a preguntas que trascienden las fronteras y los plazos de las agencias de financiamiento. Aquí mostramos cómo una comunidad global está respondiendo a los desafíos de la investigación en ecosistemas tropicales a través de diversos equipos realizando mediciones árbol por árbol en miles de parcelas permanentes de largo plazo. Revisamos los descubrimientos más importantes de este trabajo y discutimos cómo este proceso está cambiando la ciencia relacionada a los bosques tropicales. El enfoque central de nuestro esfuerzo implica la conexión de iniciativas locales de largo plazo con protocolos estandarizados y manejo de datos para producir resultados que se puedan trasladar a múltiples escalas. Conectando investigadores tropicales, elevando su posición y estatus, nuestro modelo de Red Social de Investigación reconoce el rol fundamental que tienen, para el descubrimiento científico, quienes generan o producen los datos. Concebida en 1999 con RAINFOR (Suramérica), nuestras redes de parcelas permanentes han sido adaptadas en África (AfriTRON) y el sureste asiático (T-FORCES) y ampliamente replicadas en el mundo. Actualmente todas estas iniciativas están integradas a través de la ciber-infraestructura de ForestPlots.net, conectando colegas de 54 países en 24 redes diferentes de parcelas. Colectivamente, estas redes están transformando nuestro conocimiento sobre los bosques tropicales y el rol de éstos en la biósfera. Juntos hemos descubierto cómo, dónde y porqué el carbono y la biodiversidad de los bosques tropicales está respondiendo al cambio climático y cómo se retroalimentan. Esta colaboración pan-tropical de largo plazo ha expuesto un gran sumidero de carbono y sus tendencias, mostrando claramente cuáles son los factores más importantes, qué procesos se ven afectados, dónde ocurren los cambios, los tiempos de reacción y las probables respuestas futuras mientras el clima continúa cambiando. Apalancando lo que realmente es una tecnología antigua, las redes de parcelas están generando una verdadera y moderna revolución en la ciencia tropical. En el futuro, la humanidad puede beneficiarse enormemente si se nutren y cultivan comunidades de investigadores de base, actualmente con la capacidad de generar información única y de largo plazo para entender los que probablemente son los bosques más preciados de la tierra. Resumo Florestas tropicais são os ecossistemas mais diversos e produtivos da Terra. Embora uma boa compreensão destas florestas seja crucial para o nosso futuro coletivo, até muito recentemente os esforços de medições e monitoramento foram amplamente desconexos. É essencial formarmos redes para obtermos respostas que transcendem fronteiras e horizontes de agências financiadoras. Neste estudo nós mostramos como uma comunidade global está respondendo aos desafios da pesquisa de ecossistemas tropicais, com equipes diversas medindo florestas, árvore por árvore, em milhares de parcelas monitoradas à longo prazo. Nós revisamos as maiores descobertas científicas deste trabalho, e mostramos também como este processo está mudando a ciência de florestas tropicais. Nossa abordagem principal envolve unir iniciativas de base a protocolos padronizados e gerenciamento de dados a fim de gerar resultados robustos em escalas ampliadas. Ao conectar pesquisadores tropicais e elevar seus status, nosso modelo de Rede de Pesquisa Social reconhece o papel-chave do produtor dos dados na descoberta científica. Concebida em 1999 com o RAINFOR (América do Sul), nossa rede de parcelas permanentes foi adaptada para África (AfriTRON) e Sudeste asiático (T-FORCES), e tem sido extensamente reproduzida em todo o mundo. Agora estas múltiplas iniciativas estão integradas através de uma infraestrutura cibernética do ForestPlots.net, conectando colegas de 54 países de 24 redes de parcelas. Estas iniciativas estão transformando coletivamente o entendimento das florestas tropicais e seus papéis na biosfera. Juntos nós descobrimos como, onde e por que o carbono e a biodiversidade da floresta estão respondendo às mudanças climáticas, e seus efeitos de retroalimentação. Esta duradoura colaboração pantropical revelou um grande sumidouro de carbono persistente e suas tendências, assim como tem evidenciado quais direcionadores são mais importantes, quais processos florestais são mais afetados, onde eles estão mudando, seus atrasos no tempo de resposta, e as prováveis respostas das florestas tropicais conforme o clima continua a mudar. Dessa forma, aproveitando uma notável tecnologia antiga, redes de parcelas acendem faíscas de uma moderna revolução na ciência das florestas tropicais. No futuro a humanidade pode se beneficiar incentivando estas comunidades basais que agora são coletivamente capazes de gerar conhecimentos únicos e duradouros sobre as florestas mais preciosas da Terra. Résume Les forêts tropicales sont les écosystèmes les plus diversifiés et les plus productifs de la planète. Si une meilleure compréhension de ces forêts est essentielle pour notre avenir collectif, jusqu'à tout récemment, les efforts déployés pour les mesurer et les surveiller ont été largement déconnectés. La mise en réseau est essentielle pour découvrir les réponses à des questions qui dépassent les frontières et les horizons des organismes de financement. Nous montrons ici comment une communauté mondiale relève les défis de la recherche sur les écosystèmes tropicaux avec diverses équipes qui mesurent les forêts arbre après arbre dans de milliers de parcelles permanentes. Nous passons en revue les principales découvertes scientifiques de ces travaux et montrons comment ce processus modifie la science des forêts tropicales. Notre approche principale consiste à relier les initiatives de base à long terme à des protocoles standardisés et une gestion de données afin de générer des résultats solides à grande échelle. En reliant les chercheurs tropicaux et en élevant leur statut, notre modèle de réseau de recherche sociale reconnaît le rôle clé de l'auteur des données dans la découverte scientifique. Conçus en 1999 avec RAINFOR (Amérique du Sud), nos réseaux de parcelles permanentes ont été adaptés à l'Afrique (AfriTRON) et à l'Asie du Sud-Est (T-FORCES) et largement imités dans le monde entier. Ces multiples initiatives sont désormais intégrées via l'infrastructure ForestPlots.net, qui relie des collègues de 54 pays à travers 24 réseaux de parcelles. Ensemble, elles transforment la compréhension des forêts tropicales et de leur rôle biosphérique. Ensemble, nous avons découvert comment, où et pourquoi le carbone forestier et la biodiversité réagissent au changement climatique, et comment ils y réagissent. Cette collaboration pan-tropicale à long terme a révélé un important puits de carbone à long terme et ses tendances, tout en mettant en évidence les facteurs les plus importants, les processus forestiers qui sont affectés, les endroits où ils changent, les décalages et les réactions futures probables des forêts tropicales à mesure que le climat continue de changer. En tirant parti d'une technologie remarquablement ancienne, les réseaux de parcelles déclenchent une révolution très moderne dans la science des forêts tropicales. À l'avenir, l'humanité pourra grandement bénéficier du soutien des communautés de base qui sont maintenant collectivement capables de générer une compréhension unique et à long terme des forêts les plus précieuses de la Terre. Abstrak Hutan tropika adalah di antara ekosistem yang paling produktif dan mempunyai kepelbagaian biodiversiti yang tinggi di seluruh dunia. Walaupun pemahaman mengenai hutan tropika amat penting untuk masa depan kita, usaha-usaha untuk mengkaji dan mengawas hutah-hutan tersebut baru sekarang menjadi lebih diperhubungkan. Perangkaian adalah sangat penting untuk mencari jawapan kepada soalan-soalan yang menjangkaui sempadan dan batasan agensi pendanaan. Di sini kami menunjukkan bagaimana sebuah komuniti global bertindak balas terhadap cabaran penyelidikan ekosistem tropika melalui penglibatan pelbagai kumpulan yang mengukur hutan secara pokok demi pokok dalam beribu-ribu plot jangka panjang. Kami meninjau semula penemuan saintifik utama daripada kerja ini dan menunjukkan bagaimana proses ini sedang mengubah bidang sains hutan tropika. Teras pendekatan kami memberi tumpuan terhadap penghubungan inisiatif akar umbi jangka panjang dengan protokol standar serta pengurusan data untuk mendapatkan hasil skala besar yang kukuh. Dengan menghubungkan penyelidik-penyelidik tropika dan meningkatkan status mereka, model Rangkaian Penyelidikan Sosial kami mengiktiraf kepentingan peranan pengasas data dalam penemuan saintifik. Bermula dengan pengasasan RAINFOR (Amerika Selatan) pada tahun 1999, rangkaian-rangkaian plot kekal kami kemudian disesuaikan untuk Afrika (AfriTRON) dan Asia Tenggara (T-FORCES) dan selanjutnya telah banyak dicontohi di seluruh dunia. Kini, inisiatif-inisiatif tersebut disepadukan melalui infrastruktur siber ForestPlots.net yang menghubungkan rakan sekerja dari 54 negara di 24 buah rangkaian plot. Secara kolektif, rangkaian ini sedang mengubah pemahaman tentang hutan tropika dan peranannya dalam biosfera. Kami telah bekerjasama untuk menemukan bagaimana, di mana dan mengapa karbon serta biodiversiti hutan bertindak balas terhadap perubahan iklim dan juga bagaimana mereka saling bermaklum balas. Kolaborasi pan-tropika jangka panjang ini telah mendedahkan sebuah sinki karbon jangka panjang serta arah alirannya dan juga menjelaskan pemandu-pemandu perubahan yang terpenting, di mana dan bagaimana proses hutan terjejas, masa susul yang ada dan kemungkinan tindakbalas hutan tropika pada perubahan iklim secara berterusan di masa depan. Dengan memanfaatkan pendekatan lama, rangkaian plot sedang menyalakan revolusi yang amat moden dalam sains hutan tropika. Pada masa akan datang, manusia sejagat akan banyak mendapat manfaat jika memupuk komuniti-komuniti akar umbi yang kini berkemampuan secara kolektif menghasilkan pemahaman unik dan jangka panjang mengenai hutan-hutan yang paling berharga di dunia

Sperm l1o~. o a dioleus pleurocarpous moss colonies, Anomodon virica¡osus (1-lech.) llook. & l’a~l., by a transplant experimení

. GRANZOW DE LA CERDA, 1. 1989. Flujo gamético en poblaciones de un musgo pleurocárpico dioico, Anomodon viticulosus (Hedw.) Hook. &amp; Tayl., mediante un exper¡niento de trasplantes. ¡lot Cotnp/utcn.sív 15: 91--lOO. Se reatizaron experimentos de trasplante entre colonias masculinas y femeninas del musgo pleurocárpico dioico Anomodon viticulosus (Hedw.) Hook. &amp; Tayl. enel Prepirineo de Gerona. Con ello se ha pretendido determinar las distancias a que pueden ser transportados, supuestamente por escorrentía, los anterozoides de esta especie. Se dispusieron bloques de 20-30 X 10-15cm provenientes de colonias con anteridios por encima de colonias con arquegonios exclusivamente y se observó que en éstas últimas se habian desarrollado por primera vez esporófitos al cabo de un año. Al medir las distancias entre dichos esporótitos y los bloques con plantas masculinas situados por encima, se obtuvo que estas eran de al menos 25 cm.. GRAN/OW DE LA CERDA. 1. 1989. Sperm 1kw a dioicus pleurocarpous rnoss colonies. Anomodon viticulosus (I-ledw.) Hook. &amp; Tayl., by a transplant experiment. flor. Complot cnsis 15: 91--100 ( in Spa ni sh). 92 Granzow de la Cerda, 1 Transplant experiments were carried out between male and female colonies of Ihe pleurocarpous moss Anomodon viticulosus (Hedw.) Hook. &amp; Tayl. in the eastern Pre-Pyrenees (Gerona, Spain). The purpose was to estimate the distance tbat sperm can be carried downwards by water down-flow or seepage. 20-30 &gt;&lt; 10-15 centimeter blocks of colonies witli antheridia were placed aboye unisexual female colonies. After a year, these had produced sporophytes for the fírst time. Ilie distance between the new sporophytes and the blocks with male plants, aboye, was found lo be at least 25 cm

Table S1

Country to whose institutions authors of papers belonged (A); total scientific production in tropical biology as number of returns for the text string “_tropic*’in ISI WoS (B); total scientific production under the ISI WoS category of ‘ecology and environmental science’ (C); total research and development (R&D) personnel (D); relative production in tropical biology (E); and ratio between tropical biological scientific production and number of researchers (F). Relative production in tropical biology is calculated as (B) divided by (C). The ratio between tropical biology scientific production and number of researchers is calculated as (B) divided by (D). Results are ordered in decreasing order of number of tropical papers (B)

Diversidad de espedes arbóreas en el bosque tropical humedo del Caribe nicaragüense siete años después del huracán Juana

Se prueba la hipótesis acerca del efecto que las perturbaciones catastróficas tienen sobre el incremento en diversidad de especies arbóreas usando el caso del Huracán Juana, de 1988, en el bosque tropical húmedo de tierras bajas de la costa caribeña de Nicaragua. Se censaron todos los árboles de más de 3.2 cm de DAP existentes en parcelas de estudio que suman un total de 1.17 distribuidas en seis localidades: cuatro que sufrieron el huracán y dos fuera del área de impacto. Se calcularon las curvas de especies/área para cada localidad. La riqueza de especies resultó estar directamente correlacionada con la intensidad del daño para todas las localidades. La de Bodega, en el Río Kukra, fue la que sufrió mayor daño, y tiene la máxima diversidad (128 especies en 0.3 ha), mientras que las del Río Kurinwás, no afectadas por el huracán, presentan la mínima de todas (total de 85 especies en 0.3 ha).Se prueba la hipótesis acerca del efecto que las perturbaciones catastróficas tienen sobre el incremento en diversidad de especies arbóreas usando el caso del Huracán Juana, de 1988, en el bosque tropical húmedo de tierras bajas de la costa caribeña de Nicaragua. Se censaron todos los árboles de más de 3.2 cm de DAP existentes en parcelas de estudio que suman un total de 1.17 distribuidas en seis localidades: cuatro que sufrieron el huracán y dos fuera del área de impacto. Se calcularon las curvas de especies/área para cada localidad. La riqueza de especies resultó estar directamente correlacionada con la intensidad del daño para todas las localidades. La de Bodega, en el Río Kukra, fue la que sufrió mayor daño, y tiene la máxima diversidad (128 especies en 0.3 ha), mientras que las del Río Kurinwás, no afectadas por el huracán, presentan la mínima de todas (total de 85 especies en 0.3 ha)