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A review of techniques for spatial modeling in geographical, conservation and landscape genetics Genet. Mol. Biol.
Diniz-Filho,José Alexandre Felizola; Nabout,João Carlos; Telles,Mariana Pires de Campos; Soares,Thannya Nascimento; Rangel,Thiago Fernando L.V.B..
Most evolutionary processes occur in a spatial context and several spatial analysis techniques have been employed in an exploratory context. However, the existence of autocorrelation can also perturb significance tests when data is analyzed using standard correlation and regression techniques on modeling genetic data as a function of explanatory variables. In this case, more complex models incorporating the effects of autocorrelation must be used. Here we review those models and compared their relative performances in a simple simulation, in which spatial patterns in allele frequencies were generated by a balance between random variation within populations and spatially-structured gene flow. Notwithstanding the somewhat idiosyncratic behavior of the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Autocorrelation; Geographical genetics; Isolation-by-distance; Landscape genetics; Spatial regression.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000200001
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Agriculture, habitat loss and spatial patterns of human occupation in a biodiversity hotspot Scientia Agricola
Diniz-Filho,José Alexandre Felizola; Oliveira,Guilherme de; Lobo,Fábio; Ferreira,Laerte Guimarães; Bini,Luis Mauricio; Rangel,Thiago Fernando Lopes Valle Brito.
The Cerrado biome, the second largest biome in Neotropical region, consists of a mosaic of different habitat types, ranging from open grasslands to dense woodlands and dry forests. An intensive recent occupation process has transformed it into the most important region for cattle ranching and intensive commodity crops in Brazil. In this study, a macroecological approach was used to evaluate broad-scale spatial patterns of habitat loss in the Brazilian Cerrado, applying a series of spatial autocorrelation and partial regression analyses to understand how the proportion of remaining natural habitats is correlated with socio-economic variables, expressing different dimensions of human occupation and climatic variation. On average, 59% of the area is occupied...
Tipo: Info:eu-repo/semantics/article Palavras-chave: MODIS; Brazilian Cerrado; Spatial autocorrelation.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162009000600007
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Distribuição de abundância e tamanho do corpo de invertebrados do folhiço em uma floresta de terra firme na Amazônia Central, Brasil Rev. Bras. entomol.
Cunha,Hélida Ferreira da; Diniz-Filho,José Alexandre Felizola; Brandão,Divino.
Abundace and body size distribution of invertebrates of leaf litter in Amazonian forest, Brazil. Based on 605 invertebrates sampled of the litter in an Amazonian Forest, some basic macroecological patterns for this assemblage were described. The relationship between abundance and body size, at logarithmic scale, was triangular, and the distribution of species was constrained in an asymmetric triangular envelope, that was tested using null model procedures in ECOSIM (P= 0,0002). The most abundant species were at an intermediated body size. The relationship between maximum abundance with different mean body size classes confirmed the Energetic Equivalent Rule (b = -1,069; t-0,75 = -2,13; P = 0.079). This way, species tend to consume energy from the community...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Abundance; Body size; Energetic Equivalence Rule; Invertebrates; Triangular pattern.
Ano: 2003 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0085-56262003000100009
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Distribuição espacial da variabilidade genética intrapopulacional de Dipteryx alata PAB
Soares,Thannya Nascimento; Chaves,Lázaro José; Telles,Mariana Pires de Campos; Diniz-Filho,José Alexandre Felizola; Resende,Lucileide Vilela.
O objetivo deste trabalho foi avaliar o padrão espacial da variabilidade genética entre plantas, dentro de três populações naturais de barueiro (Dipteryx alata Vogel), pela genotipagem por RAPD e técnicas de autocorrelação espacial. Os cinco iniciadores RAPD permitiram a codificação de 45 locos, utilizados nas análises de diversidade, estrutura e distribuição espacial da variabilidade genética entre populações. As populações apresentaram diversidade genética (Hs) com valor médio 0,314. Verificou-se que 12% da variação total se encontra entre as populações, o que indica que estas mantêm um considerável nível de variabilidade genética. Foi observada tendência de autocorrelação espacial positiva nas primeiras classes de distâncias, nas três populações, o que...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Autocorrelação espacial; Baru; Conservação; Estrutura familiar; Fluxo gênico; RAPD.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2008000900008
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Extinction of canid populations by inbreeding depression under stochastic environments in Southwestern Goiás State: a simulation study Genet. Mol. Biol.
Rodrigues,Flávia Melo; Diniz-Filho,José Alexandre Felizola.
A frequently addressed question in conservation biology is what is the chance of survival for a population for a given number of years under certain conditions of habitat loss and human activities. This can be estimated through an integrated analysis of genetic, demographic and landscape processes, which allows the prediction of more realistic and precise models of population persistence. In this study, we modeled extinction in stochastic environments under inbreeding depression for two canid species, the maned wolf (Chrysocyon brachiurus) and the crab-eating fox (Cerdocyon thous), in southwest Goiás State. Genetic parameters were obtained from six microsattelite loci (Short Tandem Repeats - STR), which allowed estimates of inbreeding levels and of the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Population persistence; Population viability analysis; Canids; STR markers; Parque Nacional das Emas.
Ano: 2007 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000100021
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Extinction of mammalian populations in conservation units of the Brazilian Cerrado by inbreeding depression in stochastic environments Genet. Mol. Biol.
Silva,Marcel Müller Fernandes Pereira da; Diniz-Filho,José Alexandre Felizola.
Despite methodological and theoretical advances in conservation genetics, data on genetic variation on broad regional spatial scales are still scarce, leading conservation planners to use general heuristic or simulation models for an integrated analysis of genetic, demographic and landscape parameters. Here, we extended previous results by evaluating spatial patterns of extinction by inbreeding depression under stochastic variation of environments for mammalian populations in 31 conservation units of the Brazilian Cerrado. We observed a large spatial variation of times to extinction, for different conservation units and body-size classes of species. For small-bodied species (500 g), the population times to extinction in the conservation units were usually...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Population persistence; Population viability analysis; Mammals; Cerrado; Conservation units.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000400030
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Hierarchical structure of genetic distances: Effects of matrix size, spatial distribution and correlation structure among gene frequencies Genet. Mol. Biol.
Rodrigues,Flávia Melo; Diniz-Filho,José Alexandre Felizola.
Geographic structure of genetic distances among local populations within species, based on allozyme data, has usually been evaluated by estimating genetic distances clustered with hierarchical algorithms, such as the unweighted pair-group method by arithmetic averages (UPGMA). The distortion produced in the clustering process is estimated by the cophenetic correlation coefficient. This hierarchical approach, however, can fail to produce an accurate representation of genetic distances among populations in a low dimensional space, especially when continuous (clinal) or reticulate patterns of variation exist. In the present study, we analyzed 50 genetic distance matrices from the literature, for animal taxa ranging from Platyhelminthes to Mammalia, in order...
Tipo: Info:eu-repo/semantics/article
Ano: 1998 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47571998000200010
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Hypothesis testing of genetic similarity based on RAPD data using Mantel tests and model matrices Genet. Mol. Biol.
Rodrigues,Flávia Melo; Diniz-Filho,José Alexandre Felizola; Bataus,Luiz Artur Mendes; Bastos,Rogério Pereira.
Clustering and ordination procedures in multivariate analyses have been widely used to describe patterns of genetic distances. However, in some cases, such as when dealing with Jaccard coefficients based on RAPD data, these techniques may fail to represent genetic distances because of the high dimensionality of the genetic distances caused by stochastic variation in DNA fragments among the units analyzed (species or populations). In this note, we show how Mantel tests can be used to test hypotheses about genetic distances and avoid problems with multivariate data representation. The procedure is illustrated with RAPD data comparing 20 anuran species from the cerrado, in which Jaccard genetic distances were compared to three model matrices linking the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Anura; Clustering; Genetic distances; Mantel test; RAPD.
Ano: 2002 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572002000400013
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Macroecologia de mamíferos neotropicais com ocorrência no Cerrado Zoologia
Vieira,Cleiber Marquez; Diniz-Filho,José Alexandre Felizola.
The macroecological approach has been used recently to analyze correlations between ecological variables in large taxonomic groups, at continental scales. A positive relationship between body weight and geographic range size has been described as a poligonal space envelope form, that can be explained by ecological and evolutionary constraints. However, these variables can be disturbed by spatial and phylogenetic autocorrelation effects. In this work, the relationship between body weight and geographic range size was analyzed for 80 species of Neotropical mammals present in the Brazilian "cerrado". Spatial and taxonomic effects were tested using a linear trend surface analysis and an ANOVA (at level of order), combined in a generalized model. Around 61% of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Macroecology; "Cerrado" mammals; Geographic range size; Ecological and evolutionary constraints; Spatial and phylogenetic autocorrelation.
Ano: 2000 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0101-81752000000400008
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Modeling body size evolution in Felidae under alternative phylogenetic hypotheses Genet. Mol. Biol.
Diniz-Filho,José Alexandre Felizola; Nabout,João Carlos.
The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Autocorrelation; Body size; Felidae; Phylogenetic eigenvector regression; Phylogenies.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000100026
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Null expectation of spatial correlograms under a stochastic process of genetic divergence with small sample sizes Genet. Mol. Biol.
Telles,Mariana Pires de Campos; Diniz-Filho,José Alexandre Felizola.
An Ornstein-Uhlenbeck process was used to simulate the exponential relationship between genetic divergence and geographic distances, as predicted by stochastic processes of population differentiation, such as isolation-by-distance, stepping-stone or coalescence models. These simulations were based only on the spatial coordinates of the local populations that defined a spatial unweighted pair-group method using arithmetic averages (UPGMA) link among them. The simulated gene frequency surfaces were then analyzed using spatial autocorrelation procedures and Nei's genetic distances, constructed with different numbers of variables (gene frequencies). Stochastic divergence in space produced strong spatial patterns at univariate and mutivariate levels. Using a...
Tipo: Info:eu-repo/semantics/article
Ano: 2000 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572000000400007
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Phylogenetic autocorrelation and evolutionary diversity of Carnivora (Mammalia) in Conservation Units of the New World Genet. Mol. Biol.
Tôrres,Natália Mundim; Diniz-Filho,José Alexandre Felizola.
One of the main concerns of Conservation Biology is the identification of priority areas for conservation, and the development of quantitative methods is important to achieve this task. Many phylogenetic diversity indexes and higher-taxon approaches have been used in this context. In this study, Faith's phylogenetic indexes and the number of evolutionary independent lineages of Carnivora were calculated at the average patch level based on phylogenetic autocorrelation analysis of phenotypic traits, in 18 conservation units in America (frequently National Parks). Despite controversies about the hierarchical level to be adopted, the characters included in this study suggest that the family level produces independent units for the analysis of phenotypic...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Phylogenetic autocorrelation; Carnivora; Conservation units; New World.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400008
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Phylogenetic correlograms and the evolution of body size in South American owls (Strigiformes) Genet. Mol. Biol.
Diniz-Filho,José Alexandre Felizola; Sant'Ana,Carlos Eduardo Ramos de.
During the last few years, many models have been proposed to link microevolutionary processes to macroevolutionary patterns, defined by comparative data analysis. Among these, Brownian motion and Ornstein-Uhlenbeck (O-U) processes have been used to model, respectively, genetic drift or directional selection and stabilizing selection. These models produce different curves of pairwise variance between species against time since divergence, in such a way that different profiles appear in phylogenetic correlograms. We analyzed variation in body length among 19 species of South American owls, by means of phylogenetic correlograms constructed using Moran's I coefficient in four distance classes. Phylogeny among species was based on DNA hybridization. The...
Tipo: Info:eu-repo/semantics/article
Ano: 2000 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572000000200008
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Population structure of Eupemphix nattereri (Amphibia, Anura, Leiuperidae) from Central Brazil Genet. Mol. Biol.
Silva,Daniela de Melo e; Cruz,Aparecido Divino da; Bastos,Rogério Pereira; Reis,Raquel Loren; Telles,Mariana Pires de Campos; Diniz-Filho,José Alexandre Felizola.
This study reports on 156 specimens of the amphibian Eupemphix nattereri, a widely distributed leiuperid, obtained from 11 municipalities of central Brazil. The extent of genetic variation was quantified by determining the mean number of alleles per locus and the proportion of polymorphic loci. An analysis of molecular variance (AMOVA) was performed on the random amplified polymorphic DNA (RAPD) haplotypes. The genetic distances obtained by calculating pairwise phist among local samples were used to determine population relationships using the unweighted pair-group method (UPGMA) and non-metric multidimensional scaling (NMDS). The cophenetic correlation was calculated to confirm agreement between the genetic matrix and the unweighted pair group method with...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Eupemphix nattereri; Gene flow; Population structure; RAPD markers.
Ano: 2007 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000600022
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Spatial pattern and genetic diversity estimates are linked in stochastic models of population differentiation Genet. Mol. Biol.
Diniz-Filho,José Alexandre Felizola; Telles,Mariana Pires de Campos.
In the present study, we used both simulations and real data set analyses to show that, under stochastic processes of population differentiation, the concepts of spatial heterogeneity and spatial pattern overlap. In these processes, the proportion of variation among and within a population (measured by G ST and 1 - G ST, respectively) is correlated with the slope and intercept of a Mantel's test relating genetic and geographic distances. Beyond the conceptual interest, the inspection of the relationship between population heterogeneity and spatial pattern can be used to test departures from stochasticity in the study of population differentiation.
Tipo: Info:eu-repo/semantics/article
Ano: 2000 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572000000300007
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