Showing papers by "Richard J. Ladle published in 2014"

Frequently asked questions about in vivo chlorophyll fluorescence: Practical issues

Abstract: The aim of this educational review is to provide practical information on the hardware, methodology, and the hands on application of chlorophyll (Chl) a fluorescence technology. We present the paper in a question and answer format like frequently asked questions. Although nearly all information on the application of Chl a fluorescence can be found in the literature, it is not always easily accessible. This paper is primarily aimed at scientists who have some experience with the application of Chl a fluorescence but are still in the process of discovering what it all means and how it can be used. Topics discussed are (among other things) the kind of information that can be obtained using different fluorescence techniques, the interpretation of Chl a fluorescence signals, specific applications of these techniques, and practical advice on different subjects, such as on the length of dark adaptation before measurement of the Chl a fluorescence transient. The paper also provides the physiological background for some of the applied procedures. It also serves as a source of reference for experienced scientists.

Functional biogeography of oceanic islands and the scaling of functional diversity in the Azores

Abstract: Analyses of species-diversity patterns of remote islands have been crucial to the development of biogeographic theory, yet little is known about corresponding patterns in functional traits on islands and how, for example, they may be affected by the introduction of exotic species. We collated trait data for spiders and beetles and used a functional diversity index (FRic) to test for nonrandomness in the contribution of endemic, other native (also combined as indigenous), and exotic species to functional-trait space across the nine islands of the Azores. In general, for both taxa and for each distributional category, functional diversity increases with species richness, which, in turn scales with island area. Null simulations support the hypothesis that each distributional group contributes to functional diversity in proportion to their species richness. Exotic spiders have added novel trait space to a greater degree than have exotic beetles, likely indicating greater impact of the reduction of immigration filters and/or differential historical losses of indigenous species. Analyses of species occurring in native-forest remnants provide limited indications of the operation of habitat filtering of exotics for three islands, but only for beetles. Although the general linear (not saturating) pattern of trait-space increase with richness of exotics suggests an ongoing process of functional enrichment and accommodation, further work is urgently needed to determine how estimates of extinction debt of indigenous species should be adjusted in the light of these findings.

Tropical Artisanal Coastal Fisheries: Challenges and Future Directions

Abstract: Artisanal fisheries occur all over the tropics and provide an important source of protein and income for many coastal communities However, varied types and magnitudes of anthropogenic impacts threaten the environmental, economic, and socio-cultural sustainability of this poorly studied fishing practice This article reviews the scattered literature on tropical artisanal coastal fisheries, identifying key challenges to ensure future sustainability Despite huge data shortfalls, there is considerable evidence that artisanal fisheries have a significant influence on the distribution and abundance of target and by-catch species, in addition to wider impacts on biodiversity, biomass, assemblage structure, community dynamics, and ecosystem functioning Despite these immediate and considerable threats, regulation and management of artisanal fisheries are problematic Local communities in the coastal tropics are frequently very poor, and families frequently rely on fishing for food security and income Ensuring

The Use of Chlorophyll Fluorescence Kinetics Analysis to Study the Performance of Photosynthetic Machinery in Plants

Abstract: Plants under natural conditions experience unfavorable growth conditions. These can cause a reduction of their photosynthetic rate or even damage the photosynthetic apparatus, which can lead to a serious decrease of plant productivity and yield. Photosynthesis is sensitive to environmental limitations, which means that photosynthetic measurement is an important tool for plant stress studies. Nevertheless, classic methods, such as the measurement of photosynthetic rates through gas exchange (CO2, H2O, and O2), are time-consuming and give incomplete information about photosynthetic function. Thus, the introduction of methods based on chlorophyll a fluorescence has led to a significant breakthrough in photosynthesis research. In this chapter we discuss the wide range of chlorophyll a fluorescence applications to understand the response of the photosynthetic apparatus to various stress conditions. We concentrate on demonstrating the so-called “OJIP test” as a good tool to explore the response of photosystem II (PSII). In addition, we discuss the issue of PSII heterogeneity under unfavorable growth conditions.

Complexity for Artificial Substrates (CASU): Software for Creating and Visualising Habitat Complexity

Abstract: Physical habitat complexity regulates the structure and function of biological communities, although the mechanisms underlying this relationship remain unclear. Urbanisation, pollution, unsustainable resource exploitation and climate change have resulted in the widespread simplification (and loss) of habitats worldwide. One way to restore physical complexity to anthropogenically simplified habitats is through the use of artificial substrates, which also offer excellent opportunities to explore the effects of different components (variables) of complexity on biodiversity and community structure that would be difficult to separate in natural systems. Here, we describe a software program (CASU) that enables users to visualise static, physical complexity. CASU also provides output files that can be used to create artificial substrates for experimental and/or restoration studies. It has two different operational modes: simple and advanced. In simple mode, users can adjust the five main variables of informational complexity (i.e. the number of object types, relative abundance of object types, density of objects, variability and range in the objects' dimensions, and their spatial arrangement) and visualise the changes as they do so. The advanced mode allows users to design artificial substrates by fine-tuning the complexity variables as well as alter object-specific parameters. We illustrate how CASU can be used to create tiles of different designs for application in a marine environment. Such an ability to systematically influence physical complexity could greatly facilitate ecological restoration by allowing conservationists to rebuild complexity in degraded and simplified habitats.

Geographic and Temporal Trends in Amazonian Knowledge Production

Abstract: The presence of researchers from Western (i.e., developed world) institutions in Amazonia has frequently been contentious due to fears of ‘scientific imperialism’ or suspicions that they may be exerting undue influence over research agendas and knowledge production to the detriment of local researchers. Such negative perceptions are widespread, but not well substantiated. A more nuanced understanding of these issues requires information on who is conducting research in Amazonia and how knowledge production has changed over time. We performed a bibliometric analysis on Thomson Reuters’ISI Web of Science of all research articles about the Amazon published in three time periods: 1986–1989, 1996–1999, and 2006–2009. We found that the number of articles published and the diversity of countries involved in Amazonian research increased dramatically over the three time periods. The representation of several Amazonian countries—especially Brazil—increased, while the proportion of articles without a single author from an Amazonian country also increased. The results indicate that the research capacity of Amazonian countries has increased, but that leadership of high-impact projects may still largely reside with researchers from developed countries.

Invasive house (Rattus rattus) and brown rats (Rattus norvegicus) threaten the viability of red-billed tropicbird (Phaethon aethereus) in Abrolhos National Park, Brazil.

Abstract: Destruction of nests and predation by introduced species are among the main factors responsible for seabird declines. The red-billed tropicbird (Phaethon aethereus) is a tropical, colonially nestin...

Bromeliad Selection by Two Salamander Species in a Harsh Environment

Abstract: Bromeliad phytotelmata are frequently used by several Neotropical amphibian taxa, possibly due to their high humidity, microclimatic stability, and role as a refuge from predators. Indeed, the ability of phytotelmata to buffer against adverse environmental conditions may be instrumental in allowing some amphibian species to survive during periods of environmental change or to colonize sub-optimal habitats. Association between bromeliad traits and salamanders has not been studied at a fine scale, despite the intimate association of many salamander species with bromeliads. Here, we identify microhabitat characteristics of epiphytic bromeliads used by two species of the Bolitoglossa morio group (B. morio and B. pacaya) in forest disturbed by volcanic activity in Guatemala. Specifically, we measured multiple variables for bromeliads (height and position in tree, phytotelma water temperature and pH, canopy cover, phytotelma size, leaf size, and tree diameter at breast height), as well as salamander size. We employed a DNA barcoding approach to identify salamanders. We found that B. morio and B. pacaya occurred in microsympatry in bromeliads and that phytotelmata size and temperature of bromeliad microhabitat were the most important factors associated with the presence of salamanders. Moreover, phytotelmata with higher pH contained larger salamanders, suggesting that larger salamanders or aggregated individuals might modify pH. These results show that bromeliad selection is nonrandom with respect to microhabitat characteristics, and provide insight into the relationship between salamanders and this unique arboreal environment.

Private protected areas: three key challenges.

Abstract: Private protected areas (PPAs) are a board category that includes reserves established and managed by non-government entities, including civil society organizations, businesses and private individuals. It was recently suggested that the creation of a system of PPAs in Brazil may act as a useful model for extending protected area systems internationally. While it is clear that RPPNs have an important role to play in the future development of Brazil's protected area system, there are several significant challenges that need to be overcome if they are fulfil their potential: (1) ensuring that RPPNs contribute to coverage and representation; (2) ensuring adequate governance; and (3) increasing the attractiveness of the RPPN model. While it is still too early to determine whether RPPNs constitute a robust PPA model that could (or should) be exported to other countries, they are creating new opportunities for innovation and novel management strategies that might eventually lead to a vibrant and distinctly Brazilian protected area movement.

Multilinguismo nas ciências ambientais: Ahora ya! (Multilingualism in environmental sciences: it's about time!).

Abstract: Comment to: Bortolus, A. 2012. Running like Alice and losing good ideas: On the quasi-compulsive use of English by non-native English speaking scientists. AMBIO 41: 769–772. doi:10.1007/s13280-012-0339-5. Writing in Ambio, Bortolus (2012) recently argued that many non-native English-speaking environmental scientists invest a disproportionate amount of time in over-coming language barriers, limiting the impact of their research, and constraining their productivity. While it may be inevitable and possibly desirable that one language dominates academic communication, most native English-speaking academics never need to adapt to a work environment dominated by another language, and may not appreciate the magnitude of this problem. We are both English language native speakers (US and UK) who have lived and worked for several years in South America (Chile and Brazil). Like many “expat scientists,” our experiences have given us new perspectives on the importance of language in science. Specifically, we have come to believe that universities in all countries (English and non-English speaking) are missing out on remarkable opportunities by failing to take advantage of the latent scientific capacity in non-English-speaking countries. Indeed, some of the policy challenges are surprisingly similar in English-speaking (ES) and non-English-speaking (NES) countries, with both needing trained personnel who can bridge the language gap. For scientists in NES countries, the most pressing need is usually to convert their research into high quality English language manuscripts that will be judged purely on the basis of scientific merit. Currently, many of these scientists pay large amounts for private translation services—many of which provide poor value for money because they do not clearly understand the science, the structure of scientific papers, or the terminology. Alternatively, bilingual colleagues provide correction and translation services at discount rates or, more typically, as a favor; the first option is a waste of scarce funding resources, while the second is often a waste of bilingual researchers’ time. One obvious solution would be for departments (or universities) in NES countries to hire professional translators with a background in the subject. Alternatively, and more radically, departments could offer attractive positions for bilingual or native English-speaking researchers, where a percentage of their time is earmarked for capacity raising with colleagues. Such positions could be permanent or implemented through offering positions to visiting academics. More radically, journals could take on some of the burden of translation by providing them as a free part of the publishing service. The impacts of such a strategy in terms of attracting new readership and increasing submissions could be considerable. For example, Ambio translated all issues into Chinese (Mandarin) as part of its publishing service for more than 15 years (1993–2008), reporting many benefits to the journal (Kessler 2009) including a marked increase in articles submitted by Chinese researchers (Soderstrom, personal communication). Translators also have a potentially important role in universities in ES countries. Scientific production is growing throughout the developing world, notably in Brazil and China. Translating research papers into any of the main languages spoken internationally (e.g., Mandarin, Spanish, Portuguese, French, Russian) could significantly boost a scientist’s citation rate. The capacity for foreign-language citation generating and publishing is enormous. Data from Google Metrics indicate that the top ten current h5 indices for journals publishing in Mandarin, Portuguese, Spanish, and French languages are an order of magnitude smaller than the top journals in English. At the same time, the total productivity in environmental, biological, and agricultural sciences for countries speaking those four languages currently accounts for a fifth of global publishing (Table 1). Table 1 Potential for publication in four major non-English languages, 1996–2012. Documents published in the categories of earth sciences, environmental sciences, agriculture, evolutionary biology, and molecular biology in countries among the top 50 most ... One way to productively take advantage of this gap is to fill it with multiple translations into target languages (English to non-English and vice versa). This will raise the h indices and impact factors of non-English publications—a situation which benefits both journals and researchers under current productivity metric regimes. Arguably, it is also good for science due to the greater sharing of ideas and the more rapid accumulation of support/refutation of hypotheses. Such a strategy would also increase the knowledge sharing of publications originally in English, especially in applied areas (such as agronomy) where English language publishing, citing, and language competency may be low. There are already multiple models for publishing translations. Some of these can be implemented already, although many researchers are likely to be unaware of them. Some English language journals currently publish abstracts in Spanish or French (e.g., Conservation Biology, Journal of Mammalogy and Canadian Journal of Zoology). Other journals, such as the Natureza e Conservacao (The Brazilian Journal of Nature Conservation), publish papers in multiple languages. There seems to be little reason why in the future online-only versions of full translations could not be provided by the same journals that publish the original papers. This especially makes sense under the rapidly expanding pay-to-publish open access model. In addition, there are some journals that sometimes publish translations of papers originally published in other journals, e.g., Iberoamerican Communication Review. A more straightforward option is to post a translation of an article on a personal website or under “unpublished materials” on scientific social networks such as ResearchGate (www.researchgate.net). Another forward-looking approach to disseminating material in multiple languages would be for major universities to develop online, freely available archives of their research publications translated into targeted foreign languages. This could be an exciting way for universities to increase their profiles in other countries, and has the power to generate new citations and collaborations by breaking down existing academic networks. Thus, rather than relying on personal interactions with bilingual researchers to exchange ideas, universities could extend their international networks by the simple expedient of making their researchers’ papers available in the native languages of major scientific nations. Scientific communication in a variety of media is increasingly valued. Communication in other languages should be considered an aspect of this trend and should be incentivized and rewarded. Even if scientific publishing moves toward the decontextualized database model advocated by some commentators (e.g., Priem 2013), science will remain a social activity. The language in which we communicate affects the confidence with which we express ourselves, our ability to convey complex and appropriately nuanced ideas, our snap judgments of how intelligent other people are, and even our personalities. Ipso facto, we need good translators for good science.