Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae)

© 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution. Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic-niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic-niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic-niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic-niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined

Disentangling the effects of geographic and ecological isolation on genetic differentiation

Populations can be genetically isolated both by geographic distance and by differences in their ecology or environment that decrease the rate of successful migration. Empirical studies often seek to investigate the relationship between genetic differentiation and some ecological variable(s) while accounting for geographic distance, but common approaches to this problem (such as the partial Mantel test) have a number of drawbacks. In this article, we present a Bayesian method that enables users to quantify the relative contributions of geographic distance and ecological distance to genetic differentiation between sampled populations or individuals. We model the allele frequencies in a set of populations at a set of unlinked loci as spatially correlated Gaussian processes, in which the covariance structure is a decreasing function of both geographic and ecological distance. Parameters of the model are estimated using a Markov chain Monte Carlo algorithm. We call this method Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology (BEDASSLE), and have implemented it in a user-friendly format in the statistical platform R. We demonstrate its utility with a simulation study and empirical applications to human and teosinte datasets

Patterns of Diversification in a Neotropical Radiation of Birds (Aves: Furnariidae)

Ecology and the role of natural selection in lineage diversification has been a central topic in evolutionary biology since Darwin. At the macroevolutionary scale, this idea is embodied in the ecological theory of adaptive radiation, which posits that rapid diversification is driven by ecological adaptive radiation in which speciation is coupled with niche divergence. Within species, the theory of ecological speciation proposes that local adaptation drives speciation by reducing gene flow among populations occupying different environments either by directly reducing migration or by reducing the fitness of migrants. Much progress has been made testing these predictions in a multitude of organisms, but there remains a lack of studies addressing the role of ecology in diversification at multiple evolutionary scales within the same lineage. Herein, I use the Neotropical bird radiation of ovenbirds (Passeriformes: Furnariidae) as a model system to examine the role of ecology in speciation and lineage diversification. I show that, across furnariid subclades, rates of lineage diversification are best predicted by the rate of climatic-niche evolution rather than ecomorphological evolution, although both are clearly important. This result is consistent with a role for environmental gradients in driving speciation through the process of isolation-by-adaptation (IBA). I then compared the relative support for IBA against the null model of isolation-by-distance (IBD) in a species of furnariid, Cranioleuca antisiensis, that shows signs of incipient speciation and is distributed across a broad environmental gradient. Using genetic, phenotypic, and environmental data from across its distribution, I found evidence of local adaptation in body size. However, I found that IBD was the best explanation for genetic differentiation along the cline, suggesting a limited role for the environmental gradient in reducing gene flow among populations of C. antisiensis. Finally, I explore the properties of the speciation mechanism ‘speciation-by-extinction’. Speciation-by-extinction (SBE) is an alternative to the standard model of allopatric speciation where speciation results from divergence accrued following the isolation of two undifferentiated populations. SBE, in contrast, proposes that speciation can result from the partitioning of standing phenotypic or genetic variation through the local extinction of intermediate populations

Climate constrains the evolutionary history and biodiversity of crocodylians

The fossil record of crocodylians and their relatives (pseudosuchians) reveals a rich evolutionary history, prompting questions about causes of long-term decline to their present-day low biodiversity. We analyse climatic drivers of subsampled pseudosuchian biodiversity over their 250 million year history, using a comprehensive new data set. Biodiversity and environmental changes correlate strongly, with long-term decline of terrestrial taxa driven by decreasing temperatures in northern temperate regions, and biodiversity decreases at lower latitudes matching patterns of increasing aridification. However, there is no relationship between temperature and biodiversity for marine pseudosuchians, with sea-level change and post-extinction opportunism demonstrated to be more important drivers. A ‘modern-type' latitudinal biodiversity gradient might have existed throughout pseudosuchian history, and range expansion towards the poles occurred during warm intervals. Although their fossil record suggests that current global warming might promote long-term increases in crocodylian biodiversity and geographic range, the 'balancing forces' of anthropogenic environmental degradation complicate future predictions

Improving the accuracy and realism of Bayesian phylogenetic analyses

textCentral to the study of Life is knowledge both about the underlying relationships among living things and the processes that have molded them into their diverse forms. Phylogenetics provides a powerful toolkit for investigating both aspects. Bayesian phylogenetics has gained much popularity, due to its readily interpretable notion of probability. However, the posterior probability of a phylogeny, as well as any dependent biological inferences, is conditioned on the assumed model of evolution and its priors, necessitating care in model formulation. In Chapter 1, I outline the Bayesian perspective of phylogenetic inference and provide my view on its most outstanding questions. I then present results from three studies that aim to (i) improve the accuracy of Bayesian phylogenetic inference and (ii) assess when the model assumed in a Bayesian analysis is insufficient to produce an accurate phylogenetic estimate. As phylogenetic data sets increase in size, they must also accommodate a greater diversity of underlying evolutionary processes. Partitioned models represent one way of accounting for this heterogeneity. In Chapter 2, I describe a simulation study to investigate whether support for partitioning of empirical data sets represents a real signal of heterogeneity or whether it is merely a statistical artifact. The results suggest that empirical data are extremely heterogeneous. The incorporation of heterogeneity into inferential models is important for accurate phylogenetic inference. Bayesian phylogenetic estimates of branch lengths are often wildly unreasonable. However, branch lengths are important input for many other analyses. In Chapter 3, I study the occurrence of this phenomenon, identify the data sets most likely to be affected, demonstrate the causes of the bias, and suggest several solutions to avoid inaccurate inferences. Phylogeneticists rarely assess absolute fit between an assumed model of evolution and the data being analyzed. While an approach to assessing fit in a Bayesian framework has been proposed, it sometimes performs quite poorly in predicting a model’s phylogenetic utility. In Chapter 4, I propose and evaluate new test statistics for assessing phylogenetic model adequacy, which directly evaluate a model’s phylogenetic performance.Biological Sciences, School o

PATTERNS AND CORRELATES OF ECOMORPHOLOGICAL DIVERSIFICATION IN BIRDS

A fundamental theme in macroevolution is understanding the origin and drivers behind the accumulation of phenotypic diversity in deep-time. Specifically, we want to describe and explain the mode (how) and tempo (at what speed) of morphological differentiation between species. Here, I investigate the patterns and correlates of ecomorphological diversification across the most diverse radiation among the tetrapods - birds. First, I investigated how variation in evolutionary rates impacts inferences from models of trait evolution. I show that rate-static models can produce spurious interpretations regarding the process of trait evolution in the presence of rate-heterogeneity, whereas robust conclusions can be drawn by co-utilizing rate-variable approaches and tests for absolute model adequacy. Second, I use a multipredictor approach to investigate correlates for the tempo of beak shape evolution across more than a half of bird species. I find high rates of evolution in morphologically-distinct clades as well as in species-rich groups, showing that ecological opportunity and species-packing impact the tempo of ecomorphological diversification in deep-time. Thirdly, I apply trait evolutionary models with competition alongside ecologically-neutral models to investigate the mode of beak shape, beak size and body mass evolution across birds. I show that models with species-interactions are not uncommonly the best fit for the data in clades, and thus ecological selection pressures can impact the accumulation of morphological diversity at deep-time scales. Lastly, I investigated how competition affects the process of ecomorphological evolution in sympatric avian granivorous assemblages. I find that species-interactions contribute to increased morphological diversity across the globe, however, the strength of competition signal is mediated by the negative association with the tempo of trait evolution. Taken together, these results explore how key ecological processes (the presence and absence of ecological opportunity, niche packing, the strength and resolution of competition) can explain variation in how biodiversity accumulates in deep time

Growth patterns of medium-sized, fast-growing firms

This report examines rapidity of business expansion, by analysing potential organisational growth patterns, as well as potential theories explaining these patterns. Besides, the study examines sources of importance during the various growth phases. Finally, emphasis is put on the issue as to whether strategy and sources affect growth.

Interacting populations in heterogeneous environments

To optimally manage a metapopulation, managers and conservation biologists can favor a type of habitat spatial distribution (e.g. aggregated or random). However, the spatial distribution that provides the highest habitat occupancy remains ambiguous and numerous contradictory results exist. Habitat occupancy depends on the balance between local extinction and colonization. Thus, the issue becomes even more puzzling when various forms of relationships - positive or negative co-variation - between local extinction and colonization rate within habitat types exist. Using an analytical model we demonstrate first that the habitat occupancy of a metapopulation is significantly affected by the presence of habitat types that display different extinction-colonization dynamics, considering: (i) variation in extinction or colonization rate and (ii) positive and negative co-variation between the two processes within habitat types. We consequently examine, with a spatially explicit stochastic simulation model, how different degrees of habitat aggregation affect occupancy predictions under similar scenarios. An aggregated distribution of habitat types provides the highest habitat occupancy when local extinction risk is spatially heterogeneous and high in some places, while a random distribution of habitat provides the highest habitat occupancy when colonization rates are high. Because spatial variability in local extinction rates always favors aggregation of habitats, we only need to know about spatial variability in colonization rates to determine whether aggregating habitat types increases, or not, metapopulation occupancy. From a comparison of the results obtained with the analytical and with the spatial-explicit stochastic simulation model we determine the conditions under which a simple metapopulation model closely matches the results of a more complex spatial simulation model with explicit heterogeneity