fuzzySim: Fuzzy similarity in species distributions

fuzzySim is an R package for calculating fuzzy similarity in species occurrence patterns. It includes functions for data preparation, such as converting species lists (long format) to presence-absence tables (wide format), obtaining unique abbreviations of species names, or transposing (parts of) complex data frames; and sample data sets for providing practical examples. It can convert binary presence-absence to fuzzy occurrence data, using e.g. trend surface analysis, inverse distance interpolation or prevalence-independent environmental favourability modelling, for multiple species simultaneously. It then calculates fuzzy similarity among (fuzzy) species distributions and/or among (fuzzy) regional species compositions. Currently available similarity indices are Jaccard, Sørensen, Simpson, and Baroni-Urbani & Buser.

Aves da Estação Ecológica de Itirapina, estado de São Paulo, Brasil

O cerrado é um dos biomas mais ameaçados no mundo, apresentando algumas das maiores taxas de destruição causadas principalmente pela agropecuária. Poucos estudos têm avaliado a diversidade local de aves no cerrado, especialmente em áreas marginais desse bioma. A Estação Ecológica de Itirapina (EEI) contém um dos últimos remanescentes de campos naturais e cerrados do estado de São Paulo. Um levantamento das aves desta unidade de conservação, feito tanto por observações casuais como sistemáticas entre 1998 e 2007, e complementado por revisão de literatura, revelou que 231 espécies apresentaram ocorrência recente na área. Desse total, 38 espécies (16,4%) encontram-se na lista de espécies ameaçadas para o estado de São Paulo e/ou são endêmicas do Cerrado, um alto número quando comparado com outras áreas de cerrados paulistas ou mesmo em relação ao Brasil Central. Tal fato reforça a importância da EEI em relação à conservação da avifauna e demonstra que a mesma está mantendo sua função de conservar a biodiversidade. Adicionalmente, ao longo dos 10 anos de estudo foram detectadas várias ameaças à EEI, e neste sentido são recomendadas aqui algumas sugestões de manejo que consideramos essenciais para essa unidade de conservação manter ou mesmo aumentar sua diversidade de aves.

Mamíferos não voadores (Mammalia) da Estação Ecológica Serra Geral do Tocantins

A comunidade de mamíferos terrestres foi amostrada em três localidades (1-Mateiros, TO; 2- Rio da Conceição, TO e 3- Formosa do Rio Preto, BA) no interior da Estação Ecológica Serra Geral do Tocantins. Para o registro dos marsupiais e pequenos roedores foram utilizadas armadilhas convencionais (5.396 armadilhas.noite) e armadilhas de queda (5.300 pitfalls.noite) nas diferentes fitofisionomias encontradas, entre elas: campo úmido, campo limpo, campo sujo, campo cerrado, cerrado sensu stricto, cerrado com afloramentos rochosos, mata de galeria e mata de galeria úmida. No caso dos mamíferos de médio e grande porte, foram obtidos registros casuais através de observação direta e evidências indiretas (rastros, fezes, crânios e carcaças de animais encontrados mortos). Foram amostradas 24 espécies de pequenos mamíferos e 17 espécies de mamíferos de médio e grande porte, totalizando 41 espécies para a região. Considerando-se os pequenos mamíferos, a comunidade foi representada por várias espécies raras e de abundância intermediária, e poucas espécies muito abundantes. Os roedores cricetídeos dominaram tanto em número de espécies (14) quanto em abundância (50% da comunidade). As espécies se distribuíram, basicamente, em dois tipos de fisionomias: um grupo esteve restrito aos ambientes florestais, e outro às formações abertas, demonstrando a grande seletividade de hábitats e a importância de se amostrar o mosaico de hábitats presente na região para uma melhor caracterização da diversidade deste grupo de mamíferos. Em termos biogeográficos, a fauna de pequenos mamíferos amostrada apresentou certa sobreposição com a fauna da Caatinga e da Amazônia, evidenciando a importância destes domínios para a composição de espécies das comunidades que habitam a porção norte do Cerrado, além da presença de espécies endêmicas e de distribuição geográfica restrita ao norte do domínio, caracterizando uma comunidade distinta de outras regiões do Cerrado. Em relação aos mamíferos de médio e grande porte, a presença de um elevado número de espécies ameaçadas de extinção (10) também ressalta a importância da preservação desta região.

Vertebrados da Estação Ecológica Serra Geral do Tocantins: faunística, biodiversidade e conservação no Cerrado brasileiro

Inventários e estudos faunísticos detalhados sobre vertebrados são uma das fontes mais relevantes de dados para interpretações de padrões detalhados de diversidade biológica. Dados básicos e de boa qualidade sobre faunística são ainda mais urgentes em regiões pouco estudadas e sob intensa ameaça antrópica, tais como a região do Cerrado, um dos 34 hotspots globais para a conservação da biodiversidade. Apresentamos aqui uma síntese dos resultados dos inventários de vertebrados na Estação Ecológica Serra Geral do Tocantins (~716.000 ha), a segunda maior unidade de conservação em todo o Cerrado. Foram registradas 450 espécies de vertebrados na EESGT e entorno imediato, incluindo 17 espécies ameaçadas, 50 espécies endêmicas do Cerrado e 11 espécies com distribuição potencialmente restrita. Do total de espécies amostradas, 180 são novos registros para a região do Jalapão. Ao menos 12 espécies amostradas foram consideradas potenciais espécies novas, das quais quatro foram descritas recentemente, a partir do material obtido no inventário. Os resultados evidenciam que a EESGT é uma das mais importantes áreas protegidas no Brasil central, contribuindo para a persistência de espécies ameaçadas, dependentes dos últimos grandes blocos contínuos de vegetação nativa de Cerrado. Nossos resultados indicam ainda que a conservação da EESGT e suas principais subunidades é crucial para a representatividade do sistema de áreas protegidas do Cerrado, protegendo potenciais endemismos restritos que aliam alta vulnerabilidade intrínseca e valor como indicadores de padrões e processos biogeográficos formadores da rica e cada vez mais ameaçada fauna Neotropical.

Exploring the use of Viagra in place of animal and plant potency products in traditional Chinese medicine

Recently, conservationists have debated whether consumers of animal and plant potency products used to treat erectile dysfunction (ED) in traditional Chinese medicine (TCM) might be switching to Viagra, consequently consuming fewer of these animals and plants. To address this question, a survey examined the medical decisions of male consumers of TCM in Hong Kong who were over the age of 50. As predicted, these consumers reported selectively switching to Western medicines to treat ED, but not to treat other health ailments. These findings provide support for the possibility that Viagra may have conservation benefits for certain species.

Foraging by the endangered black-breasted button-quail (Turnix melanogaster) within fragmented rainforest of an agricultural landscape

We studied the foraging habitat of the endangered black-breasted button-quail (Turnix melanogaster) in 13 rainforest patches of an agricultural landscape (23.4 km(2)) in eastern Australia to assess its use of fragmented habitats outside conservation reserves. The species foraged only in the three largest patches (17.4, 40.0, 63.8 ha in size), all of which were connected to open eucalypt forest, and in intact rainforest. Occurrence of birds was greatest in the largest patch. The maximum number of individuals within the study area was estimated to be 22. Radio-tracking of nine birds revealed that three were resident in the largest patch for periods of over 100 days; no movements between patches were detected. Three radio-tagged birds were taken by avian and mammalian predators. Our results indicated that the long-term future of the species in agricultural landscapes is bleak and that management action is urgently needed to arrest its decline in these ecosystems, (C) 2001 Elsevier Science Ltd. All rights reserved.

The use of stochastic dynamic programming in optimal landscape reconstruction for metapopulations

A decision theory framework can be a powerful technique to derive optimal management decisions for endangered species. We built a spatially realistic stochastic metapopulation model for the Mount Lofty Ranges Southern Emu-wren (Stipiturus malachurus intermedius), a critically endangered Australian bird. Using diserete-time Markov,chains to describe the dynamics of a metapopulation and stochastic dynamic programming (SDP) to find optimal solutions, we evaluated the following different management decisions: enlarging existing patches, linking patches via corridors, and creating a new patch. This is the first application of SDP to optimal landscape reconstruction and one of the few times that landscape reconstruction dynamics have been integrated with population dynamics. SDP is a powerful tool that has advantages over standard Monte Carlo simulation methods because it can give the exact optimal strategy for every landscape configuration (combination of patch areas and presence of corridors) and pattern of metapopulation occupancy, as well as a trajectory of strategies. It is useful when a sequence of management actions can be performed over a given time horizon, as is the case for many endangered species recovery programs, where only fixed amounts of resources are available in each time step. However, it is generally limited by computational constraints to rather small networks of patches. The model shows that optimal metapopulation, management decisions depend greatly on the current state of the metapopulation,. and there is no strategy that is universally the best. The extinction probability over 30 yr for the optimal state-dependent management actions is 50-80% better than no management, whereas the best fixed state-independent sets of strategies are only 30% better than no management. This highlights the advantages of using a decision theory tool to investigate conservation strategies for metapopulations. It is clear from these results that the sequence of management actions is critical, and this can only be effectively derived from stochastic dynamic programming. The model illustrates the underlying difficulty in determining simple rules of thumb for the sequence of management actions for a metapopulation. This use of a decision theory framework extends the capacity of population viability analysis (PVA) to manage threatened species.

Ecological criteria for evaluating candidate sites for marine reserves

Several schemes have been developed to help select the locations of marine reserves. All of them combine social, economic, and biological criteria, and few offer any guidance as to how to prioritize among the criteria identified. This can imply that the relative weights given to different criteria are unimportant. Where two sites are of equal value ecologically; then socioeconomic criteria should dominate the choice of which should be protected. However, in many cases, socioeconomic criteria are given equal or greater weight than ecological considerations in the choice of sites. This can lead to selection of reserves with little biological value that fail to meet many of the desired objectives. To avoid such a possibility, we develop a series of criteria that allow preliminary evaluation of candidate sites according to their relative biological values in advance of the application of socioeconomic criteria. We include criteria that,. while not strictly biological, have a strong influence on the species present or ecological processes. Out scheme enables sites to be assessed according to their biodiversity, the processes which underpin that diversity, and the processes that support fisheries and provide a spectrum of other services important to people. Criteria that capture biodiversity values include biogeographic representation, habitat representation and heterogeneity, and presence of species or populations of special interest (e.g., threatened species). Criteria that capture sustainability of biodiversity and fishery values include the size of reserves necessary to protect viable habitats, presence of exploitable species, vulnerable life stages, connectivity among reserves, links among ecosystems, and provision of ecosystem services to people. Criteria measuring human and natural threats enable candidate sites to be eliminated from consideration if risks are too great, but also help prioritize among sites where threats can be mitigated by protection. While our criteria can be applied to the design of reserve networks, they also enable choice of single reserves to be made in the context of the attributes of existing protected areas. The overall goal of our scheme is to promote the development of reserve networks that will maintain biodiversity and ecosystem functioning at large scales. The values of eco-system goods and services for people ultimately depend on meeting this objective.

Planeamento espacial marinho das áreas marinhas protegidas: o caso de estudo da ára protegida de gestão de recursos: Caloura - ilhéu de Vila Franca do Campo

Tese de Doutoramento, Ciências do Mar (Ecologia Marinha), 26 de Novembro de 2013, Universidade dos Açores.

Assessing the conservation status of the strict endemic Desertas wolf spider, Hogna ingens (Araneae, Lycosidae)

The Desertas Islands (Madeira, Portugal) are the sole home of one of the largest and rarest wolf spiderspecies, Hogna ingens (Blackwall 1857) (Araneae, Lycosidae). Despite its size, it inhabits a single valleyin the North of the Deserta Grande Island, Vale da Castanheira, currently invaded by the herb Phalarisaquatica. This invasive species competes with the native flora and was subject to several eradicationexperiments, namely through fire and chemicals. The objectives of this work were to: (1) estimate thecurrent distribution and abundance of H. ingens and respective trends; (2) evaluate the impact of theinvasive plant and eradication methods on the spider population; (3) suggest future measures for therecovery of the species; and (4) evaluate its conservation status according to the IUCN criteria. The current distribution of H. ingens covers 23 ha, a recent reduction from its original 83 ha, correspond-ing to the entire Vale da Castanheira. A total of 4447 and 4086 adults and 71,832 and 24,635 juvenileswere estimated to live in the valley during 2011 and 2012, respectively. We found a significant negativeimpact of P. aquatica cover on the presence and abundance of H. ingens and that chemical treatmentspecifically directed towards the invasive plant species may be the only way to effectively recover thespider's habitat. We suggest (1) regular monitoring; (2) extend chemical treatments; (3) ex-situ conserva-tion with future reintroduction of adults. Based on the current area of occupancy (AOO) of H. ingens and itsrecent decline in both AOO and number of individuals, it was recently classified as Critically Endangeredby IUCN and we suggest its urgent inclusion in the Habitats Directive species lists.

Effects of forest structure components on the occurence, group size and density of groups of bare-face tamarin (Saguinus bicolor - primates: Callitrichinae) in Central Amazonia

This study analyzed the influence of forest structural components on the occurence, size and density of groups of Bare-face Tamarin (Saguinus bicolor) - the most threatened species in the Amazon - and produced the first map of distribution of groups in large-scale spatial within the area of continuous forest. Population censuses were conducted between November 2002 and July 2003, covering 6400 hectares in the Ducke Reserve, Manaus-AM, Brazil. Groups of S. bicolor were recorded 41 times accordingly distributed in the environments: plateau (20); slopes (12); and lowlands (09). The mean group size was 4.8 indiv./group, and ranged from 2 to 11 individuals. In the sites where the groups were recorded, and in an equivalent number of sites where no tamarins were found located at least 500 m from those where they had been recorded, we placed 50 m x 50 m plots to record the following forest structural components: abundance of trees; abundance of lianas; abundance of fruiting trees and lianas; abundance of snags; abundance of logs; percentage of canopy opening; leaf litter depth; and altitude. Bare-face Tamarin more often uses areas with lower abundance of forest logs, smaller canopy opening and with higher abundance of snags, areas in the forest with smaller canopy opening present higher density of S. bicolor groups. Apparently this species does not use the forest in a random way, and may select areas for its daily activities depending on the micro-environmental heterogeneity produced by the forest structural components.

Conservation status assessment of the amphibians and reptiles of Uruguay

The native species of amphibians and reptiles of Uruguay were categorized according to the IUCN Red List criteria. Out of 47 amphibian species, seven are listed as Critically Endangered (CR), five as Endangered (EN), one as Vulnerable (VU), three as Near Threatened (NT), and two as Data Deficient (DD); the remaining species are considered to be Least Concern (LC). Among the 64 species of reptiles evaluated, one is listed as Critically Endangered (CR), seven as Endangered (EN), two as Vulnerable (VU), one as Near Threatened (NT) and seven as Data Deficient (DD); the rest are considered to be Least Concern (LC). The use of these results as an additional criterion in the definition of protected areas in Uruguay will contribute towards the conservation of the aforementioned threatened species and their associated ecosystems.

Bird communities in three forest types in the Pernambuco Centre of Endemism, Alagoas, Brazil

The Pernambuco Center of Endemism (PCE) in northeastern Brazil is highly fragmented and degraded. Despite its potential conservation importance the bird fauna in this area is still relatively unknown and there are many remnant fragments that have not been systematically surveyed. Here, we report the results of bird surveys in five forest fragments (one pioneer, two ombrophilous and two seasonal). In total, 162 taxa were recorded, 12 of which are endemic to the PCE. The frequency of endangered species was lower than what has been reported in studies from the same area and most of the taxa considered to be at risk of extinction were sub-species of uncertain taxonomic validity. The comparatively low number of endemic/threatened species may be due to the small size of the fragments in the present study - a consequence of the high levels of habitat loss in this region. Analysis of species richness patterns indicates that ombrophilous forest fragments are acting as refuges for those bird species that are most sensitive to environmental degradation.

Bird-habitat associations in coastal rangelands of southern Brazil

Nearly all remnants of temperate grasslands in southeastern South America are used for livestock ranching and are subject to habitat degradation resulting from this activity. Exploring how habitat features affect the composition of grassland avifaunal communities is a first step to understand how current cattle-ranching management practices impact avian diversity. We used canonical ordination to test for relationships between five habitat variables and the composition of the bird community in coastal grasslands in southern Brazil. We sampled pastures with different heights, from overgrazed short-grass to tall herbaceous vegetation. We recorded 1,535 individuals and 27 species of birds. The first ordination axis indicated a strong contribution of mean vegetation height on the composition of the bird community, whereas the second axis revealed the influence of herbaceous vegetation patchiness and woody vegetation cover. Three groups of species were revealed by the ordination: one more diffuse associated with intermediate and tall herbaceous vegetation, another with short grass, and a third with vegetation patchiness and woody vegetation. Species restricted to tall herbaceous vegetation are negatively impacted from habitat degradation resulting from overgrazing and trampling by livestock, and mowing and burning of tall plants. Occurrence of these species in our study area is related with the presence of swales immediately behind the dune system and where remnants of tall vegetation persist. Birds of pastures with ample cover of short herbaceous plants, including one globally threatened species and six other restricted to short-grass habitat, apparently benefit from local livestock management practices. Woody vegetation possibly functions as a keystone structure, enabling the occurrence in grasslands of avian species that rely on shrubby habitat. Although livestock ranching promotes the diversity of habitats by creating distinct patches of vegetation height in grasslands, current management practices directed to the maintenance of short grass pastures may eliminate an entire subset of species, including regionally threatened taxa, and reduce avian diversity. The maintenance of large patches of tall herbaceous plants is needed to ensure the survival of species reliant on this type of grassland structure in our study area.