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.
sábado, 30 de novembro de 2013
Journals: Marine Mammal Science
Marine
Mammal Science
-
Abreviatura: Mar. Mammal Sci.
- Qualis
CAPES: A2 (Biodiversidade), B2 (Ciências Biológicas I).
- Taxa
de Publicação: Não há.
-
Idiomas: Inglês.
-
Disponibilidade: Restrito. Apenas os artigos do fascículo
mais recente estão disponíveis na home page.
-
Submissão: Online, pelo sistema ScholarOne, com acesso na home page
da revista.
O periódico Marine Mammal Science publica significativos novos achados em
mamíferos marinhos resultantes de pesquisas originais em sua forma e função,
evolução, sistemática, fisiologia, bioquímica, comportamento, biologia
populacional, história de vida, genética, ecologia e conservação. Extensão de
distribuição, observações incomuns de comportamento, e estudos preliminares de
poucos indivíduos são publicados apenas quando há informação nova suficiente
para tornar o manuscrito de interesse geral. Baixa prioridade será dada a
confirmação de investigações de interesse local ou regional.
O periódico endossa o princípio de que
experimentos utilizando animais vivos devem ser empreendidos apenas para
propósitos de avanço do conhecimento. Considerações devem ser dadas aos
procedimentos experimentais apropriados, espécies animais utilizadas, e número
de animais necessários. Todos os experimentos com animais relatados no Marine Mammal Science devem ser
conduzidos em conformidade com as regras de cuidado animal relevantes do país
de origem. O Editor irá recusar manuscritos cujas evidências de adesão a estas
regras não sejam aparentes.
sábado, 23 de novembro de 2013
An introduction to Marmosops (Marsupialia: Didelphidae), with the description of a new species from Bolivia and notes on the taxonomy and distribution of other bolivian forms
VOOS, R.S.; TARIFA, T.; YENSEN, E. 2004. An introduction to Marmosops (Marsupialia: Didelphidae), with the description of a new species from Bolivia and notes on the taxonomy and distribution of other bolivian forms. American Museum Novitates 3466:1-40.
Abstract. In order to facilitate much-needed revisionary research on Marmosops, we summarize the currently accepted species-level taxonomy, provide full bibliographic citations for original descriptions of all 36 included nominal taxa, map their type localities, and list their type material (if known). We rediagnose the genus Marmosops, compare it with three other didelphid genera to which misidentified specimens of Marmosops have often been referred, and review the phylogenetic evidence that Marmosops is monophyletic. After describing a new species from the eastern-slope montane forest of Bolivia, we review the taxonomy of other Bolivian congeners based on morphological characters and published cytochrome-b gene sequences. Among our taxonomic results, we synonymize albiventris Tate (1931), dorothea Thomas (1911), and yungasensis Tate (1931) with M. noctivagus (Tschudi, 1845). By contrast, M. ocellatus (Tate, 1931), currently considered a synonym of dorothea, appears to be a valid species. Whereas published range maps of Bolivian species of Marmosops are demonstrably based on misidentified material and show little correspondence with known environmental factors, locality records based on specimens examined for this report make much more eco-geographic sense.
Abstract. In order to facilitate much-needed revisionary research on Marmosops, we summarize the currently accepted species-level taxonomy, provide full bibliographic citations for original descriptions of all 36 included nominal taxa, map their type localities, and list their type material (if known). We rediagnose the genus Marmosops, compare it with three other didelphid genera to which misidentified specimens of Marmosops have often been referred, and review the phylogenetic evidence that Marmosops is monophyletic. After describing a new species from the eastern-slope montane forest of Bolivia, we review the taxonomy of other Bolivian congeners based on morphological characters and published cytochrome-b gene sequences. Among our taxonomic results, we synonymize albiventris Tate (1931), dorothea Thomas (1911), and yungasensis Tate (1931) with M. noctivagus (Tschudi, 1845). By contrast, M. ocellatus (Tate, 1931), currently considered a synonym of dorothea, appears to be a valid species. Whereas published range maps of Bolivian species of Marmosops are demonstrably based on misidentified material and show little correspondence with known environmental factors, locality records based on specimens examined for this report make much more eco-geographic sense.
sábado, 16 de novembro de 2013
Rural roads as barriers to the movements of small mammals
MACPHERSON, D.; MACPHERSON, J.L.; MORRIS, P. 2011. Rural roads as barriers to the movements of small mammals. Applied Ecology and Environmental Research 9(2):167-180.
Abstract. Over the last 50 years increasing fragmentation of habitats has occurred due to road building. Fragmenting a large population into smaller ones can have a negative effect on population demography. In England much small mammal habitat occurs in suburban and rural areas where the majority of roads are either single track or two lanes, and traffic density is light. This study investigated the effect of minor roads on the movements of two small mammals, the wood mouse (Apodemus sylvaticus) and bank vole (Myodes glareolus). Capture-Mark-Recapture was used to study movements beside and across rural roads of two different widths. The results suggest that even small roads less than 6metres wide, with relatively little traffic, do act as partial barriers for these small mammals, reducing their movement between habitats on either side of the road. It is evident that island populations are being created as a result of road construction, even access roads within nature reserves.
Abstract. Over the last 50 years increasing fragmentation of habitats has occurred due to road building. Fragmenting a large population into smaller ones can have a negative effect on population demography. In England much small mammal habitat occurs in suburban and rural areas where the majority of roads are either single track or two lanes, and traffic density is light. This study investigated the effect of minor roads on the movements of two small mammals, the wood mouse (Apodemus sylvaticus) and bank vole (Myodes glareolus). Capture-Mark-Recapture was used to study movements beside and across rural roads of two different widths. The results suggest that even small roads less than 6metres wide, with relatively little traffic, do act as partial barriers for these small mammals, reducing their movement between habitats on either side of the road. It is evident that island populations are being created as a result of road construction, even access roads within nature reserves.
sexta-feira, 15 de novembro de 2013
Journals: Mammal Study
Mammal Study
- Abreviatura: Mamm. Stud.
- Home Page: http://www.mammalogy.jp/journals/MammalStudy_e.html
- Qualis
CAPES: Não cadastrado. Fator de Impacto 0,581.
- Taxa
de Publicação: Não há.
-
Idiomas: Inglês.
- Disponibilidade: Restrito.
Não há artigos disponíveis no site.
-
Submissão: Online, pelo sistema ScholarOne, com acesso na home page
da revista.
Mammal
Study é o periódico oficial da Sociedade de Mamíferos do Japão
(Mammal Society of Japan). Ela
publica artigos originais, comunicações curtas e revisões em todos os aspectos
da mastozoologia, trimestralmente. Segundo a revista, os autores são
notificados, com comentários dos revisores, aceitação, rejeição ou necessidade
de revisão em três meses.
O periódico Mammal Study não está cadastrado no qualis da CAPES (talvez por ser
uma revista japonesa). O fato de impacto é 0,581, o que resultado em um qualis
bastante baixo (B3 ou B4).
sábado, 2 de novembro de 2013
The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals
COSTA, L.P. 2003. The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals. Journal of Biogeography 30:71-86.
Abstract.
Aim. To examine how the genetic diversity of selected taxa of forest-dwelling small mammals is distributed between and within the major rain forest domains of Amazonia and Atlantic Forest and the intervening interior forests of Brazil, as inferred by the relationships between gene genealogies and geography. I also addressed the historical importance of the central Brazilian forests in connecting Amazon and Atlantic Forest populations of rodents and marsupials.
Methods. I evaluated variation in the mitochondrial cytochrome b gene to estimate the levels of sequence divergence between those taxa occurring throughout the Amazon, Atlantic Forest, and forests in the Cerrado and Caatinga regions. I inferred the hierarchical relationships between haplotypes, populations and formal taxa using the cladistic approach of maximum parsimony. I compared areas and the clades identified by superimposing cladograms on the geographical distribution of samples. The degree of concordance both in phylogeny and the depth of the nodes in these phylogenies, in addition to patterns of geographical distribution of clades, permitted me to make inferences on how, when and where the taxa differentiated.
Results. Sequence similarity is often greater between samples from the Atlantic Forest and either Amazon or central Brazilian forests than it is within each of the two rain forest domains. The Atlantic Forest clades are either not reciprocally monophyletic or are the sister group to all the other clades. There is some indication of northern and southern components in the Atlantic Forest. Given the geographical distribution of clades and the relatively deep levels of divergence, the central Brazilian area does not behave as a separate region but is complementary to either Amazon or Atlantic Forest. Patterns of area relationships differ across taxa, suggesting that different processes and ⁄or historic events affected the diversification within each lineage.
Main conclusions. The Amazon and the Atlantic forests are not exclusive in terms of their small mammal faunas; both overlap broadly with taxa occurring in gallery forests and dry forests in central Brazil. Central Brazilian forests are an integral part of the evolutionary scenario of lowland small mammals, playing an important role as present and past habitats for rain forest species. Therefore, representatives from this area should always be included in analyses of the evolutionary history of lowland rain forest faunas. The incongruence of branching patterns among areas is in agreement with recent results presented for Neotropical passerine birds and indicates that a single hypothesis of Neotropical area relationships is unlikely. These findings reinforce the idea that speciation in the Neotropics will not be explained by any single model of vicariance or climatic changes.
Abstract.
Aim. To examine how the genetic diversity of selected taxa of forest-dwelling small mammals is distributed between and within the major rain forest domains of Amazonia and Atlantic Forest and the intervening interior forests of Brazil, as inferred by the relationships between gene genealogies and geography. I also addressed the historical importance of the central Brazilian forests in connecting Amazon and Atlantic Forest populations of rodents and marsupials.
Methods. I evaluated variation in the mitochondrial cytochrome b gene to estimate the levels of sequence divergence between those taxa occurring throughout the Amazon, Atlantic Forest, and forests in the Cerrado and Caatinga regions. I inferred the hierarchical relationships between haplotypes, populations and formal taxa using the cladistic approach of maximum parsimony. I compared areas and the clades identified by superimposing cladograms on the geographical distribution of samples. The degree of concordance both in phylogeny and the depth of the nodes in these phylogenies, in addition to patterns of geographical distribution of clades, permitted me to make inferences on how, when and where the taxa differentiated.
Results. Sequence similarity is often greater between samples from the Atlantic Forest and either Amazon or central Brazilian forests than it is within each of the two rain forest domains. The Atlantic Forest clades are either not reciprocally monophyletic or are the sister group to all the other clades. There is some indication of northern and southern components in the Atlantic Forest. Given the geographical distribution of clades and the relatively deep levels of divergence, the central Brazilian area does not behave as a separate region but is complementary to either Amazon or Atlantic Forest. Patterns of area relationships differ across taxa, suggesting that different processes and ⁄or historic events affected the diversification within each lineage.
Main conclusions. The Amazon and the Atlantic forests are not exclusive in terms of their small mammal faunas; both overlap broadly with taxa occurring in gallery forests and dry forests in central Brazil. Central Brazilian forests are an integral part of the evolutionary scenario of lowland small mammals, playing an important role as present and past habitats for rain forest species. Therefore, representatives from this area should always be included in analyses of the evolutionary history of lowland rain forest faunas. The incongruence of branching patterns among areas is in agreement with recent results presented for Neotropical passerine birds and indicates that a single hypothesis of Neotropical area relationships is unlikely. These findings reinforce the idea that speciation in the Neotropics will not be explained by any single model of vicariance or climatic changes.
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