Tables with the results of two alternative methods of type II regression (Tables A1 and A2), info... more Tables with the results of two alternative methods of type II regression (Tables A1 and A2), information on the range in body size of the analyzed taxa (Table A3), and a figure showing relationships between the log(body mass) of predators and prey for subsets at the class level (Fig. A1).
Schematic depictions of (1) the Chesapeake Bay (USA) food web and (2) three hypothetical food web... more Schematic depictions of (1) the Chesapeake Bay (USA) food web and (2) three hypothetical food webs illustrating various measures of link density (LD).
Networks play a prominent role in the study of complex systems of interacting entities in biology... more Networks play a prominent role in the study of complex systems of interacting entities in biology, sociology, and economics. Despite this diversity, we demonstrate here that a statistical model decomposing networks into matching and centrality components provides a comprehensive and unifying quantification of their architecture. The matching term quantifies the assortative structure in which node makes links with which other node, while the centrality term quantifies the number of links that nodes make. We show, for a diverse set of networks, that this decomposition can provide a tight fit to observed networks. Then we provide three applications. First, we show that the model allows very accurate prediction of missing links in partially known networks. Second, when node characteris- tics are known, we show how the matching-centrality decomposition can be related to this external information. Consequently, it offers a simple and versatile tool to explore how node characteristics ex- plain network architecture. Finally, we demonstrate the efficiency and flexibility of the model to forecast the links that a novel node would create if it were to join an existing network
1. Studies on biodiversity and ecosystem functioning (BEF) have elicited debate over the interpre... more 1. Studies on biodiversity and ecosystem functioning (BEF) have elicited debate over the interpretation of the positive relationship between species richness and plant productivity. Manipulating richness cannot be achieved without affecting composition; it is thus essential to consider the latter in statistical models. 2. We firstly review existing approaches that use species richness as an explanatory variable and propose modifications to improve their performance. We use an original dataset to illustrate the analyses. The classical method where composition is coded as a factor with a level for each different species mixture can be improved by defining the levels using clustering. Methods based on ordinations reduce the dimensionality of plant composition and use the new coordinates as fixed effects; they provide a much better fit to our observations. 3. Secondly, we develop a new method where composition is included as a similarity matrix affecting the residual variance-covariance. Similarity in composition between plots is treated in the same way as shared evolutionary history between species in phylogenetic regression. We find that it outperforms the other models. 4. We discuss the different approaches and suggest that our method is particularly suited for observational studies or for manipulative studies where plant diversity is not kept constant by weeding. By treating species composition in an intuitive and sensible way, it offers a valuable and powerful complement to existing models
Background/Question/Methods Food webs are complex objects and models have been devised to capture... more Background/Question/Methods Food webs are complex objects and models have been devised to capture the basic processes underlying their structure. While these approaches are interesting, one drawback is that models based on different assumptions can lead to very similar structures. To solve this problem, we introduce statistical approaches to study food-web structure. The models we present are based on the estimation of latent traits, which represents variables that are thought to be important, but not measured. However, they can be estimated directly from the food-web matrix with MCMC or Simulated annealing methods. Results/Conclusions First, we use a simple logistic regression, with body size in terms of an optimal ratio between prey and predator as explanatory variable, to study the interactions in a food web. Such a model is able to predict on average 20% of the observed interactions in a dataset of 12 food webs. We show that introducing latent traits can improve substantially th...
Speciation is facilitated if ecological adaptation directly causes assortative mating, but few na... more Speciation is facilitated if ecological adaptation directly causes assortative mating, but few natural examples are known. Here we show that a shift in colour pattern mimicry was crucial in the origin of two butterfly species. The sister species Heliconius melpomene and Heliconius cydno recently diverged to mimic different model taxa, and our experiments show that their mimetic coloration is also
Speciation is facilitated if ecological adaptation directly causes assortative mating, but few na... more Speciation is facilitated if ecological adaptation directly causes assortative mating, but few natural examples are known. Here we show that a shift in colour pattern mimicry was crucial in the origin of two butterfly species. The sister species Heliconius melpomene and Heliconius cydno recently diverged to mimic different model taxa, and our experiments show that their mimetic coloration is also important in choosing mates. Assortative mating between the sister species means that hybridization is rare in nature, and the few hybrids that are produced are non-mimetic, poorly adapted intermediates. Thus, the mimetic shift has caused both pre-mating and post-mating isolation. In addition, individuals from a population of H. melpomene allopatric to H. cydno court and mate with H. cydno more readily than those from a sympatric population. This suggests that assortative mating has been enhanced in sympatry.
Tables with the results of two alternative methods of type II regression (Tables A1 and A2), info... more Tables with the results of two alternative methods of type II regression (Tables A1 and A2), information on the range in body size of the analyzed taxa (Table A3), and a figure showing relationships between the log(body mass) of predators and prey for subsets at the class level (Fig. A1).
Schematic depictions of (1) the Chesapeake Bay (USA) food web and (2) three hypothetical food web... more Schematic depictions of (1) the Chesapeake Bay (USA) food web and (2) three hypothetical food webs illustrating various measures of link density (LD).
Networks play a prominent role in the study of complex systems of interacting entities in biology... more Networks play a prominent role in the study of complex systems of interacting entities in biology, sociology, and economics. Despite this diversity, we demonstrate here that a statistical model decomposing networks into matching and centrality components provides a comprehensive and unifying quantification of their architecture. The matching term quantifies the assortative structure in which node makes links with which other node, while the centrality term quantifies the number of links that nodes make. We show, for a diverse set of networks, that this decomposition can provide a tight fit to observed networks. Then we provide three applications. First, we show that the model allows very accurate prediction of missing links in partially known networks. Second, when node characteris- tics are known, we show how the matching-centrality decomposition can be related to this external information. Consequently, it offers a simple and versatile tool to explore how node characteristics ex- plain network architecture. Finally, we demonstrate the efficiency and flexibility of the model to forecast the links that a novel node would create if it were to join an existing network
1. Studies on biodiversity and ecosystem functioning (BEF) have elicited debate over the interpre... more 1. Studies on biodiversity and ecosystem functioning (BEF) have elicited debate over the interpretation of the positive relationship between species richness and plant productivity. Manipulating richness cannot be achieved without affecting composition; it is thus essential to consider the latter in statistical models. 2. We firstly review existing approaches that use species richness as an explanatory variable and propose modifications to improve their performance. We use an original dataset to illustrate the analyses. The classical method where composition is coded as a factor with a level for each different species mixture can be improved by defining the levels using clustering. Methods based on ordinations reduce the dimensionality of plant composition and use the new coordinates as fixed effects; they provide a much better fit to our observations. 3. Secondly, we develop a new method where composition is included as a similarity matrix affecting the residual variance-covariance. Similarity in composition between plots is treated in the same way as shared evolutionary history between species in phylogenetic regression. We find that it outperforms the other models. 4. We discuss the different approaches and suggest that our method is particularly suited for observational studies or for manipulative studies where plant diversity is not kept constant by weeding. By treating species composition in an intuitive and sensible way, it offers a valuable and powerful complement to existing models
Background/Question/Methods Food webs are complex objects and models have been devised to capture... more Background/Question/Methods Food webs are complex objects and models have been devised to capture the basic processes underlying their structure. While these approaches are interesting, one drawback is that models based on different assumptions can lead to very similar structures. To solve this problem, we introduce statistical approaches to study food-web structure. The models we present are based on the estimation of latent traits, which represents variables that are thought to be important, but not measured. However, they can be estimated directly from the food-web matrix with MCMC or Simulated annealing methods. Results/Conclusions First, we use a simple logistic regression, with body size in terms of an optimal ratio between prey and predator as explanatory variable, to study the interactions in a food web. Such a model is able to predict on average 20% of the observed interactions in a dataset of 12 food webs. We show that introducing latent traits can improve substantially th...
Speciation is facilitated if ecological adaptation directly causes assortative mating, but few na... more Speciation is facilitated if ecological adaptation directly causes assortative mating, but few natural examples are known. Here we show that a shift in colour pattern mimicry was crucial in the origin of two butterfly species. The sister species Heliconius melpomene and Heliconius cydno recently diverged to mimic different model taxa, and our experiments show that their mimetic coloration is also
Speciation is facilitated if ecological adaptation directly causes assortative mating, but few na... more Speciation is facilitated if ecological adaptation directly causes assortative mating, but few natural examples are known. Here we show that a shift in colour pattern mimicry was crucial in the origin of two butterfly species. The sister species Heliconius melpomene and Heliconius cydno recently diverged to mimic different model taxa, and our experiments show that their mimetic coloration is also important in choosing mates. Assortative mating between the sister species means that hybridization is rare in nature, and the few hybrids that are produced are non-mimetic, poorly adapted intermediates. Thus, the mimetic shift has caused both pre-mating and post-mating isolation. In addition, individuals from a population of H. melpomene allopatric to H. cydno court and mate with H. cydno more readily than those from a sympatric population. This suggests that assortative mating has been enhanced in sympatry.
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