Browsing by Author "Santos, Juan Carlos"
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Item The implementation of phylogenetic structural equation modeling for biological data from variance-covariance matrices, phylogenies, and comparative analyses(2009-12) Santos, Juan Carlos; Wilke, Claus O.; Bryant, JamesOne statistical approach with a long history in the social sciences is a multivariate method called Structural Equation Modeling (SEM). The development of SEM followed the evolution of factor and path analyses, multiple regression analysis and MACOVA. One of the key innovations of factor analysis and SEM is that they group a set of multivariate statistical approaches that condense variability among a set of variables in fewer latent (unobserved) factors. Most biological systems are multivariate, which are not easily dissected into their component parts. However, most biologists use only univariate statistical methods, which have definitive limitations in accounting for more than a few variables simultaneously. Therefore, the implementation of methodologies like SEM into biological research is necessary. However, SEM cannot be applied directly to most biological datasets or generalized across species because of the hierarchical pattern of evolutionary history (i.e., phylogenetic non-independence or signal). This report includes the theoretical grounds for the development of Phylogenetic SEM in preparation of the development of utilitarian algorithms. I have divided this report in six parts: (1) a brief introduction to factor analysis and SEM from historical perspective and a brief description of its utility; (2) a summary of the implications of using biological data and the underlying hierarchical structure due to shared common ancestry or phylogeny; (3) a summary of the two most common comparative methods to incorporate the phylogeny in univariate analyses (i.e., phylogenetic independent contrasts and phylogenetic generalized least squares); (4) I describe how some intermediate output from both comparative methods can be used to estimate the variance–covariance matrix that has been corrected for phylogenetic signal; (5) I describe how to perform a exploratory factor analysis, specifically principal component analysis, with the corrected variance–covariance matrix; and (6) I describe the development of the phylogenetic confirmatory factor analysis and phylogenetic SEM. I hope that this report encourages other researchers to develop adequate multivariate analysis that incorporate the evolutionary principles in its analyses.Item Phylogeography and the evolution of correlated traits under multiple origins of aposematism in the poison frog family(2009-08) Santos, Juan Carlos; Cannatella, David C.Living organisms are under selection not only for one, but also for several inheritable characters at the same time. Well-sampled and well-supported phylogenies are necessary for the studies of character evolution and their history. The poison frogs (Dendrobatidae) are a well-known example of aposematism in anurans. They include ~270 species of Neotropical frogs with aposematic (toxic and conspicuous) and non-defended (palatable and cryptic) species. The origin of aposematism in poison frogs is puzzling, because of its predicted low probability of establishment due to the prey's increased conspicuousness. Previous studies suggested a single origin of toxicity and warning coloration. By expanding taxon sampling of the group, I reexamined the phylogenetic correlation between the origins of toxicity and warning coloration. I found four or five independent origins of aposematism; by using simulations, I rejected hypotheses of one, two, or three origins of aposematism (P < 0.002). I also found that diet specialization is linked with the evolution of aposematism and has evolved independently at least two times. Poison frogs are endemic to the Neotropic, which is one of the Earth's largest reservoir of biodiversity. I reconstructed the biogeography of the poison frog clade and rejected an Amazonian center-of-origin in favor of a model expanding over the Neotropics. I inferred 14 dispersals into and 18 out of Amazonia to adjacent regions; the Andes were the major source of dispersals into Amazonia. Significant percentage of dendrobatid diversity in Amazonia and Chocó resulted from repeated immigrations, with radiations at <10.0 million years ago. In contrast, the Andes, Venezuelan Highlands, and Guiana Shield have undergone extended in situ diversification at near constant rate since the Oligocene. Poison frogs have significant variation on their physiological characteristics. I measured resting and active metabolic rates of 54 species. I traced metabolic measurements along aposematism, diet specialization, molecular rates, and body mass. I found a synergistic and co-adapted functionality of active metabolic rates with all previous traits that is perhaps the consequence of the increase in complexity in most biological systems. My thesis has expanded the knowledge of the biology, phylogenetic history, and biogeography of the poison frogs.