Multimodal species abundance distributions: a deconstruction approach reveals the processes behind the pattern

Copyright © 2014 The Authors. Oikos © 2014 Nordic Society Oikos.

Deep ocean species. The little that is known mostly comes from collected specimens. Comment on L.A. Rocha et al. Letter "Specimen collection: An essential tool" (23 May, 344: 814).

Deep Ocean Species. The little that is known mostly comes from collected specimens. L.A. Rocha et al. Letter "Specimen collection: An essential tool" (23 May, 344: 814) brilliantly discuss the importance of specimen collection and present the evolution of collecting since the mid-19th century until our present strict codes and conducts. However, it is also important to emphasize the fact that the vast majority of deep ocean macro-organisms are only known to us because of collection and this is a strong argument that should be present in our actions as scientists. If the deep is considered the least known of Earth’s habitats (1% or so according to recent estimates) then what awesome collection of yet to discover species are still there to be properly described? As the authors point citing (1), something around 86% of species remain unknown. Voucher specimens are fundamental for the reasons pointed out and perhaps the vast depths of the World’s oceans are the best example of that importance. The resumed report of 2010 Census of Marine Life (2) showed that among the millions of specimens collected in both familiar and seldom-explored waters, the Census found more than 6,000 potentially new species and completed formal descriptions of more than 1,200 of them. It also found that a number of rare species are in fact common. Voucher specimens are essential and, again agreeing with L.A. Rocha et al. Letter (see above), the modern approach for collecting will not be a cause for extinctions but instead a valuable tool for knowledge, description and even, as seen above, a way to find out that supposed rare species may not be that rare and even prove to reach abundant populations.

Habitat predictive modelling of demersal fish species in the Azores

Dissertação de Mestrado, Estudos Integrados dos Oceanos, 25 de Março de 2013, Universidade dos Açores.

Caraterização dos habitats propícios à conservação da Estrelinha-de-Santa-Maria (Regulus regulus sanctaemariae)

Dissertação de Mestrado, Gestão e Conservação da Natureza, 11 de Junho de 2014, Universidade dos Açores.

Geographical, temporal and environmental determinants of bryophyte species richness in the Macaronesian Islands

Copyright: © 2014 Aranda et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

On three endemic species of the linyphiid spider genus Canariphantes Wunderlich, 1992 (Araneae, Linyphiidae) from the Azores archipelago

Copyright © 2014 Magnolia Press.

The gambin model provides a superior fit to species abundance distributions with a single free parameter : evidence, implementation and interpretation

The species abundance distribution (SAD) has been a central focus of community ecology for over fifty years, and is currently the subject of widespread renewed interest. The gambin model has recently been proposed as a model that provides a superior fit to commonly preferred SAD models. It has also been argued that the model's single parameter (α) presents a potentially informative ecological diversity metric, because it summarises the shape of the SAD in a single number. Despite this potential, few empirical tests of the model have been undertaken, perhaps because the necessary methods and software for fitting the model have not existed. Here, we derive a maximum likelihood method to fit the model, and use it to undertake a comprehensive comparative analysis of the fit of the gambin model. The functions and computational code to fit the model are incorporated in a newly developed free-to-download R package (gambin). We test the gambin model using a variety of datasets and compare the fit of the gambin model to fits obtained using the Poisson lognormal, logseries and zero-sum multinomial distributions. We found that gambin almost universally provided a better fit to the data and that the fit was consistent for a variety of sample grain sizes. We demonstrate how α can be used to differentiate intelligibly between community structures of Azorean arthropods sampled in different land use types. We conclude that gambin presents a flexible model capable of fitting a wide variety of observed SAD data, while providing a useful index of SAD form in its single fitted parameter. As such, gambin has wide potential applicability in the study of SADs, and ecology more generally.

Mutation accumulation in Tetrahymena

Background - The rate and fitness effects of mutations are key in understanding the evolution of every species. Traditionally, these parameters are estimated in mutation accumulation experiments where replicate lines are propagated in conditions that allow mutations to randomly accumulate without the purging effect of natural selection. These experiments have been performed with many model organisms but we still lack empirical estimates of the rate and effects of mutation in the protists. Results - We performed a mutation accumulation (MA) experiment in Tetrahymena thermophila, a species that can reproduce sexually and asexually in nature, and measured both the mean decline and variance increase in fitness of 20 lines. The results obtained with T. thermophila were compared with T. pyriformis that is an obligate asexual species. We show that MA lines of T. thermophila go to extinction at a rate of 1.25 clonal extinctions per bottleneck. In contrast, populations of T. pyriformis show a much higher resistance to extinction. Variation in gene copy number is likely to be a key factor in explaining these results, and indeed we show that T. pyriformis has a higher mean copy number per cell than T. thermophila. From fitness measurements during the MA experiment, we infer a rate of mutation to copy number variation of 0.0333 per haploid MAC genome of T. thermophila and a mean effect against copy number variation of 0.16. A strong effect of population size in the rate of fitness decline was also found, consistent with the increased power of natural selection. Conclusions - The rate of clonal extinction measured for T. thermophila is characteristic of a mutational degradation and suggests that this species must undergo sexual reproduction to avoid the deleterious effects detected in the laboratory experiments. We also suggest that an increase in chromosomal copy number associated with the phenotypic assortment of amitotic divisions can provide an alternative mechanism to escape the deleterious effect of random chromosomal copy number variation in species like T. pyriformis that lack the resetting mechanism of sexual reproduction. Our results are relevant to the understanding of cell line longevity and senescence in ciliates.

The Yellow-­crowned Night Heron Nyctanassa violacea (Aves: Pelecaniformes: Ardeidae) in the Azores and Madeira Archipelagos: a new species for the Western Palearctic

This paper presents and describes the first confirmed occurrence of the Yellow-crowned Night Heron Nyctanassa violacea in the Azores, which also represents the first record for Europe and the Western Palearctic. We also present and discuss subsequent reports of the species in Macaronesia. Several hypotheses may help to explain the occurrence of this species in this part of the Atlantic, including disorientation caused by strong winds and increasing observation pressure. However, further studies are necessary to assess the part played by the different factors in the occurrence of new vagrant individuals/species in Macaronesia.

Species composition of arbuscular mycorrhizal fungi differ in semi-natural and intensively managed pastures in an isolated oceanic island (Terceira, Azores)

Copyright © Springer Science+Business Media Dordrecht 2014.

A trophic analysis of target species of macrobenthos in a subtropical coast community: a taxa relationship essay

Studies on the feeding habits of aquatic organisms are a requirement for the management and sustainable use of marine ecosystems. The aim of the present research was to analyze the habits and trophic similarities of decapods, starfish and fish in order to propose trophic relationships between taxa, using Hennigian methods of phylogenetic systematics. This new grouping hypothesis, based on shared and exclusive food items and food types, corresponds to the broad taxonomic groups used in the analysis. Our results indicate that algae, Mollusca, Polychaeta, Crustacea, Echinodermata and Actinopterygii are the most exploited common resources among the species studied. Starfish were differentiated from other organisms for being stenophagic, and were grouped for feeding on bivalve mollusks. A larger group of fish and crustaceans shares algae and mainly crustaceans as food items. A third group united all eight species of Actinopterygii. This largest subgroup of fish is typically carnivorous, feeding on Anthozoa and a great quantity of Crustacea. Synodus foetens has a special position among fishes, due to its unique feeding on nematodes. A Euclidean distance dendrogram obtained in a previous publication grouped S. foetens with starfish. That result was based on a few non-exclusive shared similarities in feeding modes, as well as on shared absences of items, which are not an adequate grouping factor. Starfish are stenophagic, eating bivalves almost exclusively. Synodus foetens and Isopisthus parvipinnis have restricted food items, and are thus intermediary in relation to starfish, decapods, and other fish, which are euryphagous. The trophic cladogram displays details of food items, whether or not shared by all species. The resulting trophic analysis is consistent with known historical relationships.

A new species of Malacoctenus from the Cape Verde Islands, eastern Atlantic (Pisces Teleostei, Labrisomidae)

Malacoctenus carrowi is described on the basis of three specimens from the Cape Verde Islands. The species is most similar to the only other eastern Atlantic species of the same genus, Malacoctenus africanus Cadenat, 1951. M. carrowi differs in colouration, a more elongated body, longer snout length, lower lateral line scale count and the absence of scales on the breast and is probably endemic to the Cape Verde Islands. A key to the Atlantic species of Malacoctenus is provided.

First report of ciguatoxins in two starfish species : Ophidiaster ophidianus and Marthasterias glacialis

Ciguatera fish poisoning (CFP) is a syndrome caused by the ingestion of fish contaminated with Ciguatoxins (CTXs). These phycotoxins are produced mainly by dinoflagellates that belong to the genus Gambierdiscus that are transformed in more toxic forms in predatory fish guts, and are more present in the Indo-Pacific and Caribbean areas. It is estimated that CFP causes per year more than 10,000 intoxications worldwide. With the rise of water temperature and anthropogenic intervention, it is important to study the prevalence of CFP in more temperate waters. Through inter- and subtidal sampling, 22 species of organisms were collected, in Madeira and Azores archipelagos and in the northwestern Moroccan coast, during September of 2012 and June and July of 2013. A total of 94 samples of 22 different species of bivalves, gastropods, echinoderms and crustaceans where analyzed by Ultra Performance Liquid Chromatography-Mass Spectometry-Ion Trap-Time of Flight (UPLC-MS-IT-TOF) and Ultra Performance Chromatography- Mass Spectrometry (UPLC-MS). Our main aim was to detect new vectors and ascertain if there were some geographical differences. We detected for the first time putative CTXs in echinoderms, in two starfish species—M. glacialis and O. ophidianus. We detected differences regarding uptake values by organisms and geographical location. Toxin amounts were significant, showing the importance and the need for continuity of these studies to gain more knowledge about the prevalence of these toxins, in order to better access human health risk. In addition, we suggest monitoring of these toxins should be extended to other vectors, starfish being a good alternative for protecting and accessing human health risk.

Comparison of Aspergillus species-complexes detected in different environmental settings

Purpose: Samples from different environmental sources were screened for the presence of Aspergillus, and the distribution of the different species-complexes was determined in order to understand differences among that distribution in the several environmental sources and which of these species complexes are present in specific environmental settings. Methods: Four distinct environments (beaches, poultries, swineries and hospital) were studied and analyzed for which Aspergillus complexes were present in each setting. After plate incubation and colony isolation, morphological identification was done using macro- and microscopic characteristics. The universal fungal primers ITS1 and ITS4 were used to amplify DNA from all Aspergillus isolates, which was sequenced for identification to species complex level. SPSS v15.0 for Windows was used to perform the statistical analysis. Results: Thirty-nine isolates of Aspergillus were recovered from both the sand beach and poultries, 31 isolates from swineries, and 80 isolates from hospital environments, for a total 189 isolates. Eleven species complexes were found total. Isolates belonging to the Aspergillus Versicolores species-complex were the most frequently found (23.8%), followed by Flavi (18.0%), Fumigati (15.3%) and Nigri (13.2%) complexes. A significant association was found between the different environmental sources and the distribution of the several species-complexes (p<0.001); the hospital environment had a greater variability of species-complexes than other environmental locations (10 in hospital environment, against nine in swine, eight in poultries and seven in sand beach). Isolates belonging to Nidulantes complex were detected only in the hospital environment, whereas the other complexes were identified in more than one setting. Conclusion: Because different Aspergillus complexes have different susceptibilities to antifungal drugs, and different abilities in producing mycotoxins, knowledge of the species-complex epidemiology for each setting may allow preventive or corrective measures to be taken toward decreasing professional workers or patient exposure to those agents.

Efeito das condições ambientais na produtividade lipídica da Dunaliella tertiolecta

Este trabalho teve como objectivo a optimização das condições de crescimento de biomassa algal tendo em vista a sua utilização como fonte de lípidos para biocombustíveis. Assim, procedeu-se à inoculação de duas estirpes, a Dunaliella tertiolecta (água salgada) e a Tetraselmis subcordiformis (água salobra), seleccionando-se a Dunaliella tertiolecta uma vez que esta apresentou um crescimento mais rápido. Escolhida a estirpe a usar, avaliou-se a influência da composição do meio de cultura da espécie, variando-se a concentração de macronutrientes (Magnésio, Potássio, Azoto, Fósforo) e de micronutrientes (Manganês, Zinco, Ferro, Cobalto) presentes no meio em 10 e 20 vezes, comparativamente à do meio de cultura padrão, o meio Artificial Seawater Medium with Vitamins. Avaliou-se o crescimento algal, a uma temperatura de 25 ºC ± 2 ºC, com uma intensidade de iluminação de 5000 lux (lâmpadas luz dia) e fotoperíodos 12:12 h, controlando possíveis contaminações nas culturas em estudo. Para os ensaios realizados com a Dunaliella tertiolecta, os melhores resultados para a produtividade média e máxima de biomassa, 63,06 mgbiomassa seca/L.dia e 141,79 mgbiomassa seca/L.dia, respectivamente, foram obtidos no ensaio em que se fez variar 10 vezes a concentração de azoto (sob a forma de nitrato). Os resultados mais satisfatórios para o teor lípidico e para a produtividade lipídica máxima, 33,45% e 47,43 mgóleo/L.dia respectivamente, também foram obtidos no ensaio em que se fez variar 10 vezes a concentração de azoto (sob a forma de nitrato), (com extracção dos lípidos usando o método de Bligh e Dyer). Foram testados dois solventes para a extracção de lipídos, o clorofórmio e o hexano, tendose obtido resultados superiores com o clorofórmio, comparativamente aos obtidos quando se usou hexano, com excepção do ensaio em que se aumentou 20 vezes a concentração de fósforo no meio de cultura das microalgas. Verificou-se que, em todos os ensaios foi atingido o estado estacionário sensivelmente na mesma altura, isto é, decorridos cerca de 25 dias após o início do estudo, excepto os ensaios em que se fez variar a concentração de cobalto, para os quais as culturas não se adaptaram às alterações do meio, acabando por morrer passados 15 dias. A adição dos macronutrientes e micronutrientes usados nos ensaios, nas quantidades testadas, não influenciou significativamente a produtividade lipídica, com excepção do azoto e ferro. Conclui-se que o aumento da concentração de azoto para 10x o valor padrão potencia o aumento da produtividade lipídica máxima para mais do dobro (3,6 vezes – Padrão: 13,25 mgóleo/L.dia; 10x N: 47,43 mgóleo/L.dia) e que o aumento da concentração de ferro para 10x o valor padrão potencia o aumento da produtividade lipídica máxima para aproximadamente o dobro (1,9 vezes - Padrão: 14,61 mgóleo/L.dia; 10x Fe: 28,04 mgóleo/L.dia). Nos ensaios realizados com adição de azoto ou ferro, os resultados obtidos para a concentração, teor lípidico e produtividade lipídica máxima, foram sempre superiores aos do padrão correspondente, pelo que se pode concluir que estes ensaios se apresentam como os mais promissores deste estudo, embora o ensaio mais satisfatório tenha sido aquele em que se promoveu a alteração da concentração de azoto para 10 vezes o valor padrão.