Scaling properties of protein family phylogenies

One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of balance) of a large set of protein phylogenies with a set of species phylogenies. The comparative analysis shows that both sets of phylogenies share remarkably similar scaling behavior, suggesting the universality of branching rules and of the evolutionary processes that drive biological diversification from gene to species level. In order to explain such generality, we propose a simple model which allows us to estimate the proportion of evolvability/robustness needed to approximate the scaling behavior observed in the phylogenies, highlighting the relevance of the robustness of a biological system (species or protein) in the scaling properties of the phylogenetic trees. Thus, the rules that govern the incapability of a biological system to diversify are equally relevant both at the gene and at the species level.Comment: Replaced with final published versio

A model of macro-evolution as a branching process based on innovations

We introduce a model for the evolution of species triggered by generation of novel features and exhaustive combination with other available traits. Under the assumption that innovations are rare, we obtain a bursty branching process of speciations. Analysis of the trees representing the branching history reveals structures qualitatively different from those of random processes. For a tree with n leaves, the average distance of leaves from root scales as (log n)^2 to be compared to log n for random branching. The mean values and standard deviations for the tree shape indices depth (Sackin index) and imbalance (Colless index) of the model are compatible with those of real phylogenetic trees from databases. Earlier models, such as the Aldous' branching (AB) model, show a larger deviation from data with respect to the shape indices.Comment: 16 pages, 8 figures, 1 table, v2: minor corrections and addition

Phylogenetic analysis of stemmed points from Patagonia: Shape change and morphospace evolution

This work is focused in the study of Patagonian lithic projectile points shape variation from a phylogenetic perspective pursuing three main aims: first, generate a model of projectile point shape diversification and morphospace evolution; second, estimate shape variation through time, and finally, assess the robustness of previous results using the same methods but in a larger sample with better spatial coverage. A previous work using geometric morphometric and cladistic methods suggested a pattern of general morphological diversification across Patagonia related, at least in part, to the spatial distance between cases, distinguishing two main clades in northern (43-45° S) and southern (50-52° S) Patagonia. In the present work to study this pattern in a more detailed level, a sample of ca. 1200 projectile points was used to obtain statistically different morphological classes performing unsupervised K-means searching. Shape characters were used to describe the different taxonomic units and to perform the phylogenetic analysis (through the Neighbor Joining and Maximun Parsimony methods) using as an ancestor the earliest point type known to the region (Fishtail point). The new results suggest that projectile points with longer and narrow blades and smaller stems evolved later in Patagonia and occupy a different sector of morphospace that could be related to the emergence of different technical systems, like the bow and arrow. However, these results do not support the previous ones of a projectile point diversification pattern mediated by spatial distance, maybe due to the reduction of contrast between the extreme north and south of Patagonia by the larger spatial coverage used in the present analysis.En un trabajo previo se estudió la variación morfológica de las puntas de projectil líticas de Patagonia desde una perspectiva filogenética. A través de los métodos de morfometría geométrica se obtuvieron clases en base a la forma media (forma consenso) de las puntas pedunculadas según franjas latitudinales. Los resultados mostraron un patrón general de diversificación morfológica a lo largo de Patagonia que se encuentra en parte relacionado a la distanica espacial entre casos. Para estudiar el patrón de diversificación morfológica en mayor detalle, en el presente trabajo se usó una muestra de puntas de proyectil más grande para obtener clases morfológicas diferentes estadísticamente mediante los procedimientos de búsqueda automáticos (machine learning). Los caracteres morfológicos fueron usados para describir las diferentes unidades taxonómicas y para realizar el análisis filogenérico (mediante el método de Neighbor-Joining) usando como ancestro el tipo de punta de proyectil más antiguo conocido para la región (Cola de Pescado). Nuestro objetivo principal es evaluar la robustez de la hipótesis cladística sobre la existencia de una señal filogenética en el diseño de las puntas de proyectil. Para ello se evalúa el ajuste entre el patrón de diversificación y el espacio morfológico generado por el método Generalizado de Procrustes. Los resultados obtenidos sirven para discutir el tempo y modo de la evolución de las diferentes clases morfológicas, como así también la incidencia de la morfología y la historia de vida en la convergencia o divergencia de las puntas de proyectil patagónicas a través del tiemp

Historical Ecology as a Research Program

Modern evolutionary biology is the descendant of two theories proposed by Darwin. First, all organisms are connected by common genealogy, and second, the form and function of organisms is closely tied to the environments in which they live. Of these two theories, the role of the first (phylogeny) in evolutionary explanations has been diminishing in some fields, most notably in ecology and ethology. However, the last ten years have witnessed the beginning of a reversal in this trend. With increasing frequency, ecologists (Wanntorp et aI., 1990; Maurer and Brooks, submitted), ethologists (Dobson, 1985; Huey and Bennett, 1987; Mclennan et aI., 1988), functional morphologists (Lauder, 1982), and other evolutionary biologists (Ridley, 1983; Clutton-Brock and Harvey, 1984; Endler and McLellan, 1988) are accepting the proposition that some innovations that arose in the past have been integrated into the phenotype and function today as constraints on the evolution of other characters

Historical Ecology as a Research Program

Modern evolutionary biology is the descendant of two theories proposed by Darwin. First, all organisms are connected by common genealogy, and second, the form and function of organisms is closely tied to the environments in which they live. Of these two theories, the role of the first (phylogeny) in evolutionary explanations has been diminishing in some fields, most notably in ecology and ethology. However, the last ten years have witnessed the beginning of a reversal in this trend. With increasing frequency, ecologists (Wanntorp et aI., 1990; Maurer and Brooks, submitted), ethologists (Dobson, 1985; Huey and Bennett, 1987; Mclennan et aI., 1988), functional morphologists (Lauder, 1982), and other evolutionary biologists (Ridley, 1983; Clutton-Brock and Harvey, 1984; Endler and McLellan, 1988) are accepting the proposition that some innovations that arose in the past have been integrated into the phenotype and function today as constraints on the evolution of other characters

Urban road networks -- Spatial networks with universal geometric features? A case study on Germany's largest cities

Urban road networks have distinct geometric properties that are partially determined by their (quasi-) two-dimensional structure. In this work, we study these properties for 20 of the largest German cities. We find that the small-scale geometry of all examined road networks is extremely similar. The object-size distributions of road segments and the resulting cellular structures are characterised by heavy tails. As a specific feature, a large degree of rectangularity is observed in all networks, with link angle distributions approximately described by stretched exponential functions. We present a rigorous statistical analysis of the main geometric characteristics and discuss their mutual interrelationships. Our results demonstrate the fundamental importance of cost-efficiency constraints for in time evolution of urban road networks.Comment: 16 pages; 8 figure

From Genes to Communities: An Integrative Approach to the Evolution of Varanidae

Why do organisms look the way they do? Why do they live where they do? Why are some groups more diverse than others? These basic questions are often addressed at different scales using a particular set of methods. For example, the first question could be addressed by either looking at phenotypes across a phylogeny in a comparative framework or by looking at fine scale variation across the landscape within a species. However, it has been challenging to build a conceptual and methodological bridge linking ecological processes and population dynamics with evolutionary and biogeographic patterns above the species level. In this thesis, I present research spanning a broad range in the continuum between micro- and macroevolution. Appropriately, my study system is monitor lizards (Squamata: Varanidae), the terrestrial vertebrate genus showing the largest disparity in body size. These charismatic reptiles display notable variation in species richness, morphology, and ecology across the three continents and numerous oceanic islands they call home. I gathered large molecular, morphological, and environmental datasets and analysed them using process-based methods linking ecological and population-level processes with speciation and macroevolutionary patterns. I used this integrative approach to identify the drivers of genetic, phenotypic, and lineage diversification in Varanidae at different evolutionary scales. In Chapter I, I show that the diversification dynamics of three endemic varanid radiations in Indo-Australasia have been dictated by a combination of geography and interspecific interactions. In Chapter II, I demonstrate that ontogenetic lability is behind morphological diversification in varanids and their kin, and that ontogenetic ecological shifts in ecology explain some of the ontogenetic variation in the group. In Chapter III, I used a comprehensive approach to uncover signs of ancient hybridization between the iconic Komodo dragon and a group of Australian varanids, corroborating the Australian origin of the former. In Chapter IV, I evaluate species limits in spiny-tailed monitors and present genomic and phenotypic evidence for local adaptation despite extensive gene flow. Together, these chapters show how the integration of multiple sources of evidence can offer insight into the long-term evolutionary consequences of developmental, ecological, and population-level processes

Limitations of Climatic Data for Inferring Species Boundaries: Insights from Speckled Rattlesnakes

Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the "climatic niche"); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs and mitochondrial DNA), phenotypic, and climatic data for objective species delimitation in the speckled rattlesnake (Crotalus mitchellii) complex. Ordination and clustering patterns were largely congruent among intrinsic (heritable) traits (nDNA, mtDNA, phenotype), and discordance is explained by biological processes (e.g., ontogeny, hybridization). In contrast, climatic data did not produce biologically meaningful clusters that were congruent with any intrinsic dataset, but rather corresponded to regional differences in atmospheric circulation and climate, indicating an absence of inherent taxonomic signal in these data. Surrogating climate for physiological tolerances adds artificial weight to evidence of species boundaries, as these data are irrelevant for that purpose. Based on the evidence from congruent clustering of intrinsic datasets, we recommend that three subspecies of C. mitchellii be recognized as species: C. angelensis, C. mitchellii, and C. Pyrrhus