EcoVirtual

Segue abaixo um e-mail que recebi a respeito do Portal EcoVirtual. Achei bem interessante a ferramenta.

Caros colegas,

Gostaríamos de convidá-lo a visitar o portal ECOVIRTUAL (http://ecovirtual.ib.usp.br), projeto que estamos desenvolvendo para o ensino de ecologia. O projeto está baseado na utilização de simulações computacionais para o aprendizado de modelos e conceitos em ecologia e matemática. São tratados temas em diferentes níveis de organização: população, metapopulações, comunidades e biogeografia, com simulações dos modelos clássicos acompanhados de roteiros. Para as simulações desenvolvemos uma interface gráfica de usuário para que possa ser utilizada por qualquer pessoa, sem a necessidade de treinamento em programação. A instalação é muito simples, veja como em: http://ecovirtual.ib.usp.br/doku.php?id=ecovirt:roteiro:soft:instalacaor.

Nosso objetivo é que este material seja utilizado e aperfeiçoado pelo máximo de colegas, e em breve teremos uma versão em inglês para ampliar o alcance. Sintam-se à vontade para usá-lo em suas disciplinas, e agradecemos qualquer contribuição ou sugestão (envie paraecovirtualpackage@gmail.com).

Para maiores informações veja nossa declaração de motivação e o vídeo explicando a filosofia do projeto em http://ecovirtual.ib.usp.br/doku.php?id=start#para_saber_mais.

Aproveito para convidar aqueles que querem se aventurar no aprendizado da linguagem R a visitarem o material online da nossa disciplina (http://ecologia.ib.usp.br/bie5782).

Um grande abraço a todos,

Alexandre Adalardo e Paulo Inácio Prado

Evaluation of GPS collar performance by stationary tests and fitting on free-ranging Japanese black bears

YAMAZAKI, K.; KASAI, S.; KOIKE, S.; GOTO, Y.; KOZAKAI, C.; FURUBAYASHI, K. 2008. Evaluation of GPS collar performance by stationary tests and fitting on free-ranging Japanese black bears. Mammal Study 33:131-142.

Abstract. We evaluated the performance of two GPS collars as a tool for studying Japanese black bears (Ursus thibetanus japonicus) in the Kanto region, Japan. Collars were placed at five stationary points to test the effects of GPS antenna orientation and degree of canopy closure on the fix rate and the positional error, and collars were deployed on 16 free-ranging bears to examine the fix rate and the effects of fix interval on fix rate. In the stationary tests, the proportions of no fix and of 2D fix (vs. 3D fix) increased as canopy closure increased and antenna orientation was further from vertical; at an antenna angle =90° from the vertical and canopy closure of 76.2–79.1%, the fix rate was <50%. The positional error for 3D fixes (ranged from 6.84 to 16.43 m) was significantly lower than that for 2D fixes (ranged from 30.74 to 43.45 m), and the positional error for both was affected by canopy closure and GPS antenna angle. An expected multipath effect on positional errors by rain was not statistically significant. Mean fix rates on collared bears ranged from 23.6% to 56.4% and were significantly lower than those in the stationary test. The fix rates at 5-min intervals were significantly higher than those at 4-hr intervals. Although our tests revealed some limitations and biases, GPS collar appears suitable for studying the movement and behavior of the bears.

geomorph: an R package for the collection and analysis of geometric morphometric shape data

ADAMS, D.C.; OTÁROLA-CASTILLO, E. 2013. geomorph: an R package for the collection and analysis of geometric morphometric shape data. Methods in Ecology and Evolution 4:393-399. doi: 10.1111/2041-210X.12035.

Abstract. Many ecological and evolutionary studies seek to explain patterns of shape variation and its covariation with other variables. Geometric morphometrics is often used for this purpose, where a set of shape variables are obtained from landmark coordenates following a Procruster superimaposition.
We introduce geomorph: a software package for performing geometric morphometric shape analysis in the R statistical computing environment.
Geomorph provides routines for all stages of landmark-based geometric morphometric analysis in two and three-dimensios. It is an open source package to read, manipulate, and digitize landmark data, generate shape variables via Procruster analysis for points, curves and surfaces, perform statistical analyses of shape variation and covariation, and to provide graphical depictions of shape and patterns of shape variation. An important contribution of geomorph is the ability to perform Procrustes superimposition on landmark points, as well as semilandmark from curves and surfaces.
A wide range of statistical methods germane to testing ecological and evolutionary hypotheses of shape variation are provided. These include standard multivariate methods such as principal components analysis, and approaches for multivariate regression and group comparison. Methods for more specialized analyses, such as for assessing shape allometry, comparing shape trajectories, examining morphological integration, and for assessing phylogenetic signal, are also included.
Several functions are provided to graphically visualize results, including routines for examining variation in shape space, visualizing allometric trajectories, comparing specific shapes to one another and for plotting phylogenetic changes in morphospace.
Finally, geomorph participates to make available advanced geometric morphometric analysis through the R statistical computing platform.

A demo-genetic analysis of a small reintroduced carnivore population: the otter (Lutra lutra) in the Netherlands

SEIGNOBOSC, M.; HEMERIK, L.; KOELEWIJN, H.P. 2011. A demo-genetic analysis of a small reintroduced carnivore population: the otter (Lutra lutra) in the Netherlands. International Journal of Ecology, v. 2011, Article ID 870853, 11 pages. doi: 10.1155/2011/870853.

Abstract. Assessing the viability of reintroduced animal populations is a complicated task. Reintroductions are usually carried out with a small number of individuals, thereby, limiting the possibilities for monitoring because of the possible negative effects of intensive monitoring on survival and reproduction. Moreover, reintroduction studies are part of a socioeconomic interplay of forces, thereby, also limiting monitoring possibilities. Also, knowledge of population demography and abundance can be incomplete or unattainable. Here, we illustrate how we combined traditional telemetry and novel non-invasive genetic methodology to construct a detailed life table of a small reintroduced otter population in The Netherlands. Combining an appropriate capture-mark-recapture framework with a matrix modelling approach provides, in general, useful insights for such populations. The data indicated that (i) male survival is lower than female survival, (ii) the reintroduced population is currently growing (estimated λ = 1.26: range [1.06, 1.42]) and seems viable, (iii) increasing adult survival is currently the critical stage at which efforts of field managers should concentrate, and (iv) the modelling framework allowed us to determine the boundary conditions for the vital rates under which the population would go extinct. The applied approach directs at measurements that help field managers to implement the right conservation strategy after reintroductions.

Influence of pitfall trap size and design on herpetofauna and small mammal studies in a Neotropical Forest

RIBEIRO-JÚNIOR, M.A.; ROSSI, R.V.; MIRANDA, C.L.; ÁVILA-PIRES, T.C.S. 2011. Influence of pitfall trap size and design on herpetofauna and small mammal studies in a Neotropical Forest. Zoologia 28(1):80-91. doi: 10.1590/S1984-46702011000100012.

Abstract. One of the most commonly used sampling techniques to capture leaf litter amphibians, lizards and small mammals is a set of pitfall traps with drift fences. However, there are still many speculations concerning the effectiveness of different designs of pitfall traps and the most adequate size of each trap. To address this problem, we conducted the first standardized comparison of patterns of species richness, rank-abundance, and community structure of leaf litter amphibians, lizards and small mammals for two trap designs (I and Y format) and three bucket sizes (35, 62, and 100 L) in a Neotropical forest. Results are very similar for the herpetofauna, regardless of the pitfall trap design or size used, while for small mammals values of species richness were higher for 100 L pitfall traps, as compared to the smaller traps. Therefore, the use of 100 L pitfall traps is recommended to sample the terrestrial vertebrate fauna, in multidisciplinary studies. For surveys aiming only the herpetofauna the use of smaller (35 L) traps is acceptable, taking into consideration the cost-benefits obtained by the smaller traps, in comparison to the larger ones.

rich: an R package to analyse species richness

ROSSI, J-P. 2011. rich: an R package to analyse species richness. Diversity 3(1):112-120. doi: 10.3390/d3010112.

Abstract. The paper describes rich, a new R package to perform species richness estimation and comparison. Species richness is the simplest surrogate for the more complex concept of species biodiversity. It is relatively easy to assess although estimations strongly depend on sampling intensity with the consequence that richness estimations should be standardized to perform valid comparisons. The R package rich allows such corrections as well as the computation of various statistics and implements different randomization tests to compare cumulative and average species richness of two communities. These tests are useful for ranking sites or communities which is a classical goal in restoration ecology and conservation biology.

Microhabitats in a forest-floor small mammal fauna

DUESER, R.D.; SHUGART JR., H.H. 1978. Microhabitats in a forest-floor small mammal fauna. Ecology 59(1):89-98.

Abstract. This study examines microhabitat  configurations for 3 small mammal species occupying second-growth mesic forest on Walker Branch Watershed in eastern Tennessee. Small mammal populations were sampled in oak-hickory, chestnut oak and pine forest types, with three 0.36-ha live-trapping grids per forest type. There were 255 total captures for 4 forest-floor species during 9,696 trap-nights between 1 May and 16 August 1973. These captures included 2% Blarina brevicauda, 66% Peromyscus  leucopus,  5% Ochrotomys  nuttalli  and 27% Tamias striatus.  Blarina was  captured most frequently in the pine forest type, Peromyscus and Tamias most frequently in the oak-hickory, and Ochrotomys exclusively in the pine. Twenty-nine variables describing proximate habitat structure were measured at each small mammal capture site. There were significant overall species differences on  18 of these  variables. A subset of variables was identified for each of the 3 most frequently observed species, consisting of only the variables of particular significance for distinguishing the capture sites of that species from those of the other species collectively. Discriminant analysis of these few variables both described the average microhabitat configuration for a species and indicated the relative importance of each variable for characterizing or describing that configuration, subject to the assumptions of the analysis. The observed differences between species in microhabitat  configuration are consistent with both the composition by  forest type of  each  species  sample and the  literature information for  each species. Microhabitat segregation among these species is discussed with reference to recent theories of habitat selection, ecological specialization and resource partitioning in equilibrium faunas.

A new study method of microhabitat structure of small mammals

CERQUEIRA, R.; FREITAS, S.R. 1999. A new study method of microhabitat structure of small mammals. Revista Brasileira de Biologia 59(2):219-223.

Abstract. The variables in habitat studies are usually transformed in such a way that they become abstractions and intuition is lost. We tested a new method for the analysis of habitat using data collected in a grid laid at the “restinga de Maricá”, in Rio de Janeiro State, Brazil. Thirty-seven microhabitat variables were measured at each trap station. We assume that these variables characterize the microhabitat structure at the moment when measurements were taken. The data are transformed in 3 ways: (1) the averages of the measured variables were calculated, as usual in habitat studies; (2) the data are transformed in densities per area in square meters without reduction in the number of variables; and (3) we calculated the natural logarithms of the data thus transformed. The 3 sets were analised through discriminant analysis. The logarithms of densities were the most efficient kind of transformation. This transformation resulted in a significance of p = 0.0001 with 39.72% of variance in the 1st discriminant function and of p = 0.0426 with 31.45% of variance in the 2nd function, and 84.62% of groups correctly classified. We obtained better classification results than previous similar works and we kept the intuition through the data analysis.

Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia)

BININDA-EMONDS, O.R.P.; GITTLEMAN, J.L.; PURVIS, A. 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biol. Rev. 74:143-175.

Abstract. One way to build large, more comprehensive phylogenies is to combine the vast amount of phylogenetic information already available. We review the two main strategies for accomplishing this (combining raw data versus combining trees), but employ a relatively new variant of the latter: supertree construction. The utility of one supertree technique, matrix representation using parsimony analysis (MRP), is demonstrated by deriving a complete phylogeny for all 271 extant species of the Carnivora from 177 literature sources. Beyond providing a 'consensus' estimate of carnivore phylogeny, the tree also indicates taxa for which the relationships remain controversial (e.g. herpestids, viverrids, and intrageneric relationships in the procyonids). Times of divergence throughout the tree were also estimated from 74 literature sources based on both fossil and molecular data. We use the phylogeny to show that some lineages within the Mustelinae and Canidae contain significantly more species than expected for their age, illustrating the tree's utility for studies of macroevolution. It will also provide a useful foundation for comparative and conservational studies involving the carnivores.

Ecological scale and habitat use

MORRIS, D.M. 1987. Ecological scale and habitat use. Ecology 68(2):362-369

Abstract. Population density can respond to habitat at different scales. If habitat selection occurs as a consequence of resource exploitation, the density of fine-grained consumers should reflect microhabitat variation. But if habitat use is controlled by a variety of selective pressured, it is no longer apparent whether density should respond to micro- or macrohabitat. These two alternatives can be tested simultaneously by multiple regression models where macrohabitat are represented by dummy variables. When the local densities of two Temperate Zone rodents were analyzed in this way, macrohabitat and temporal effects were consistent significant predictors of rodent density; microhabitat was not. This analysis suggests species whose patterns of resource and habitat use probably depart from classical interpretations of species coexistence. It is probably premature to assess the role of habitat selection in the structure of ecological systems until the results of further tests of habitat scaling are reported.

Pseudoreplication and the design of ecological field experiments

HULBERT, S.H. 1984. Pseudoreplication and the design of ecological field experiments. Ecological Monographs 54(2):187-211.

Abstract. Pseudoreplication is defined as the use of inferential statistics to test for treatment effects with data from experiments where either treatments are not replicated (though samples may be) or replicates are not statistically independent. In ANOVA terminology, it is the testing for treatment effects with and error term inappropriate to the hypothesis being considered. Scrutiny of 176 experimental studies published between 1960 and the present revealed that pseudoreplication occurred in 27% of them, or 48% of all such studies that applied inferential staticts. The incidence of pseudoreplication is especially high in studies of marine benthos and small mammals. The critical features of controlled experimentation are reviewed. Nondemonic intrusion is defined as the impingement of chance events on and experiment in progress. As a safeguard against both it and preexisting gradients, interspersion of treatments is argued to be an obligatory feature of good design. Especially in small experiments, adequate interspersion can sometimes be assumed only by dispensing with strict randomization procedures. Comprehension of this conflict between interspersion and randomization is aided by distinguishing pre-layout (or conventional) and layout-specific alpha (probability of tyme I error). Suggestions are offered to statisticians and editors of ecological journals as to how ecologists' understanding of experimental design and statistics might be improved.

Habitat fragmentation and movements of three small mammals (Sigmodon, Microtus, and Peromyscus)

DIFFENDORFER, J.E.; GAINES, M.S.; HOLT, R.D. 1995. Habitat fragmentation and movements of three small mammals (Sigmodon, Microtus, and Peromyscus). Ecology 76(3):827-839.

Abstract. We studied the effects of habitat fragmentation on the movements of cotton rats (Sigmodon hispidus), deer mice (Peromyscus maniculatus), and prairie voles (Microtus ochrogaster) living in a fragmented landscape using 7.7 yr (1984-1992) of mark-recapture data. The study area included three kinds of 0.5-ha blocks: single large patches (5000 m²), clusters of medium patches (288 m²), and clusters of small patches (32 m²). We tested three predictions regarding animal movements. First, animal should move longer distances as fragmentation increases. Second, the proportion of animals moving will decrease as fragmentation increases. Third, species will show more movement from putative sources to putative sinks. In support of our first two predictions, all species (except male cotton rats) moved farther, and lower proportions of animals moved, as fragmentation increased. In testing our third prediction, we found no trends, for all species, between patch size and the net number of animals a block either imported or exported, indicating source-sink dynamics were probably not occurring on our study site. Furthermore, animals of all species (except female deer mice) switched more frequently to blocks of larger patches. For prairie voles in the spring and deer mice in the summer, relative abundance among blocks predicted from a Markov matrix model of switching probabilities showed high congruence with the actual abundances, indicating movement and abundance were related. In both cotton rats and prairie voles but not in deer mice, more juveniles and nonreproductive animals switched between blocks than did adults or reproductive animals. Deer mice switched more frequently than did either cotton rats or prairie voles; the latter species switched in similar frequencies. We discuss the implications of our data for modeling and conservation.

The question of scale in threat analysis: a case study with Brazilian mammals

GRELLE, C.E.V.; FONSECA, G.A.B.; FONSECA, M.T.; COSTA, L.P. 1999. The question of scale in threat analysis: a case study with Brazilian mammals. Animal Conservation 2:149-152.

Abstract. Rates of biodiversity loss are clearly associated with a reduction in the extent of original habitat. The most frequently used method to derive such estimates comes from the well-known species–area relationship. We explored the relationship between habitat loss and area for the Brazilian mammal fauna on a biome level (Atlantic Forest, Cerrado and the Brazilian portion of the Amazon basin), as well as on a smaller regional scale (the Rio Doce Valley of the Atlantic Forest). Habitat loss overestimates the number of threatened species when the entire species pool is considered (endemics and wideranging species). Restricting the analyses to the endemic species, the predicted extinction as a function of habitat loss in the Atlantic Forest and in the Cerrado is found to be greater than the number of taxa actually listed as threatened. This relation is reversed in the Amazon. When considering only the localized species pool for the Rio Doce Valley region of the Atlantic Forest, the function accurately predicts the number of extinctions resulting from habitat loss. We suggest that there is both theoretical and empirical evidence to suggest that threat analysis will generate more accurate estimates of species loss when conducted on a more local scale, particularly for the fauna of non-insular, continental regions. Furthermore, other phenomena affecting the likelihood of extinction of certain groups of species, such as hunting, need to be taken into account in order to better understand the dynamics of biodiversity loss.

Spatial scale, species diversity, and habitat structure: small mammals in Australian Tropical Rain Forest

WILLIAMS, S.E.; MARSH, H.; WINTER, J. 2002. Spatial scale, species diversity, and habitat structure: small mammals in Australian Tropical Rain Forest. Ecology 83(5):1317-1329.

Abstract. We investigated patterns of mammal assemblage structure on the Atherton Tableland in the Wet Tropics biogeographic region of northeastern Australia. We used live trapping and quantitative estimates of stratified vegetation density to examine the relationships between the structure of the mammal assemblage and habitat structure over three nested spatial scales across a natural vegetation gradient from rain forest to dry, open forest. The narrow transition zone enabled us to examine the relationships between mammal assemblage structure and habitat structure while minimizing the confounding effects of distance, climate, and biogeographic history. The structure of the mammal assemblages was closely related to vegetation structure across and within habitats, and over all spatial scales examined. Vegetation complexity and heterogeneity both influenced assemblage structure, but the relationships varied with spatial scale. Species richness was highest in the open forest and decreased across the gradient into the rain forest. Point diversity was only weakly explained by vegetation structure, whereas .80% of the variation in species richness at the local scale could be explained by vegetation structure. Local-scale species richness of ground-dwelling mammals was mostly a product of the spatial variability in assemblage structure (b diversity), which was associated with the spatial variability in vegetation structure. Local-scale habitat heterogeneity thus promoted local-scale species richness via the close ecological interaction between mammals and habitat structure. The multiscale approach used here, and the nesting of spatial variability in within-habitat vegetation structure, enabled us to demonstrate the scale-dependent effects of spatial habitat heterogeneity and complexity on the structure and diversity of the small-mammal assemblage.

Scale-dependent habitat selection in three didelphid marsupials using the spool-and-line technique in the Atlantic forest of Brazil

MOURA, M.C.; CAPARELLI, A.C.; FREITAS, S.R.; VIEIRA, M.V. 2005. Scale-dependent habitat selection in three didelphid marsupials using the spool-and-line technique in the Atlantic forest of Brazil. Journal of Tropical Ecology 21:337-342.

Abstract. Habitat selection can be detected at different scales. For small mammals, habitat studies normally evaluate micro- or meso-habitat selection, but rarely are multiple scales analysed simultaneously. These studies use quantitative data of structural characteristics around the trap stations to evaluate selection. We test an alternative method to evaluate habitat selection in three didelphid marsupials (Didelphis aurita, Philander frenatus and Metachirus nudicaudatus), using a spool-and-line device, and measure habitat selection at two spatial scales. Habitat was characterized by seven habitat variables measured at ten points of direction change along the path traversed by each individual, and at 25 trap stations distributed in a 1-ha area. Micro-habitat selection was estimated at each point by comparing habitat measures between the direction selected against other directions. Meso-habitat selection was estimated by comparing habitat measurements on the whole path of an individual against habitat measures on the 25 trap stations. Patterns of selection for each species could only be detected at the meso-habitat scale, although a few individuals in each species were selective at the micro-habitat scale. Studies of habitat selection need to address the scale of study quantitatively, if possible comparing two or more scales to determine the scale of selection.

Movement distances and density estimation of small mammals using the spool-and-line technique

MENDEL, S.M.; VIEIRA, M.V. 2003. Movement distances and density estimation of small mammals using the spoll-and-line technique. Acta Theriologica 48(3):289-300.

Abstract. Edge effect is an inherent problem when using trapping grids to estimate density of small mammals, resulting in a sampling area larger than the area of the grid. Distances between captures of individuals are used to estimate A(W), the effective sampling area of a trapping grid, but grid size sets a limit for the largest detectable distance. The spool-and-line technique is proposed here as a new method to estimate A(W). Movement distances based on the spool-and-line technique were compared to similar movement distances based on capture-recapture of three spacies of marsupials of the Atlantic Forest of Brazil. Distances based on the two methos were uncorrelated, and only ln-transformed distances based on the spool-and-line were normally distributed. The maximum distance moved (MaxD) estimated by the spool-and-line was chosen as the more accurate and practical distance to estimate edge effect. Estimates of the effective sampling area and densities for the common opossum Didelphis aurita (Wied-Neuwied, 1826), were compared using MaxD based on spool-and-line (MaxDspool), capture-recapture (MaxDcap), and also the distance between traps (DT). MaxDspool reflected more accurately density variation between seasons. Movement distances of small mammals based on the spool-and-line technique permit more accurate estimates of density and its dynamics.

Estimating the abundance of mouse populations of known size: promises and pitfalls of new mothods

CONN, P.B.; ARTHUR, A.D.; BAILEY, L.L.; SINGLETON, G.R. 2006. Estimating the abundance of mouse populations of known size: promises and pitfalls of new mthods. Ecological Applications 16(2):829-837.

Abstract. Knowledge of animal abundance is fundamental to many ecological studies. Frequently, researchers cannot determine true abundance, and so must estimate it using a method such as mark–recapture or distance sampling. Recent advances in abundance estimation allow one to model heterogeneity with individual covariates or mixture distributions and to derive multimodel abundance estimators that explicitly address uncertainty about which model parameterization best represents truth. Further, it is possible to borrow information on detection probability across several populations when data are sparse. While promising, these methods have not been evaluated using mark–recapture data from populations of known abundance, and thus far have largely been overlooked by ecologists. In this paper, we explored the utility of newly developed mark–recapture methods for estimating the abundance of 12 captive populations of wild house mice (Mus musculus). We found that mark–recapture methods employing individual covariates yielded satisfactory abundance estimates for most populations. In contrast, model sets with heterogeneity formulations consisting solely of mixture distributions did not perform well for several of the populations. We show through simulation that a higher number of trapping occasions would have been necessary to achieve good estimator performance in this case. Finally, we show that simultaneous analysis of data from low abundance populations can yield viable abundance estimates.

ARCGIS aplicado à Biologia da Conservação

O CALBio (Centro Acadêmico Livre da Biologia) da Unisinos esta realizando mais um curso de extenção que deve interessar não apenas os mastozoólogos, mas qualquer profissional da área de biologia interessado em bons mapas para seus artigos. Ministrado por Msc. Rafael Gomes de Moura, o curso de ARCGis Aplicado à Biologia da Conservação será realizado na Unisinos, entre os dias 26 de junho e 8 de julho (período noturno, entre 19h e 22h, comduração de 30 horas).
Maiores informações no site: www.unisinos.br/eventos.