Simple models for scaling in phylogenetic trees

Many processes and models --in biological, physical, social, and other contexts-- produce trees whose depth scales logarithmically with the number of leaves. Phylogenetic trees, describing the evolutionary relationships between biological species, are examples of trees for which such scaling is not observed. With this motivation, we analyze numerically two branching models leading to non-logarithmic scaling of the depth with the number of leaves. For Ford's alpha model, although a power-law scaling of the depth with tree size was established analytically, our numerical results illustrate that the asymptotic regime is approached only at very large tree sizes. We introduce here a new model, the activity model, showing analytically and numerically that it also displays a power-law scaling of the depth with tree size at a critical parameter value.Comment: 7 pages, 4 figures. A new figure, with example trees, has been added. To appear in Int. J. Bifurcation and Chao

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

Universal scaling in the branching of the Tree of Life

Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and can be extended down to intra-specific relationships. Here we examine the topological properties of a large set of interspecific and intraspecific phylogenies and show that the branching patterns follow allometric rules conserved across the different levels in the Tree of Life, all significantly departing from those expected from the standard null models. The finding of non-random universal patterns of phylogenetic differentiation suggests that similar evolutionary forces drive diversification across the broad range of scales, from macro-evolutionary to micro-evolutionary processes, shaping the diversity of life on the planet.Comment: 6 pages + 19 of Supporting Informatio

A Complex Network Approach to Phylogenetic Trees: From Genes to the Tree of Life

Tesis leída en l´Universitat de les Illes Balears el 2 de noviembre de 2010The increasing interest during the last century in the study and comprehension of the evolutionary processes that govern biodiversity, as well as the huge expansion that the complex network approach has undergone in the last decade, has motivated us to address the interrelation of both scientific fields. In that sense, the main goal of this thesis is the application of the complex network theory to the inference of evolutionary patterns through the topological characterization of evolutionary tree.Peer reviewe

Pretty, but dangerous! Records of non-native Monk Parakeets (Myiopsitta monachus) in Mexico ¡Bonita pero peligrosa! Registros de la cotorra argentina (Myiopsitta monachus) en México

The Monk Parakeet (Myiopsitta monachus) is native to South America and has been introduced by the pet market to several countries around the world. In this note, we compiled records for this species in Mexico and report the first sight-recording of this species in the state of Michoacán and several nesting localities within the Metropolitan area of México City. Most records are of individuals escaped or released from captivity. Also, we review the negative effects that this species has had in invaded areas from around the world. Our analysis suggests the possible beginning of an invasion in Mexico that could have dramatic negative ecological and economic effects throughout this biodiverse country.<br>La cotorra argentina (Myiopsitta monachus) es nativa de Sudamérica y ha sido introducida a través del comercio de mascotas en diversos países del mundo. En esta nota compilamos los registros de esta especie para México, además de reportarla por primera vez para el estado de Michoacán y diversas localidades de anidación en la zona metropolitana de la ciudad de México. La mayoría de los registros son de individuos que han escapado o han sido liberados intencionalmente del cautiverio. Además, discutimos los efectos que ha tenido esta especie en otros lugares del mundo. Los registros compilados en esta nota sugieren el inicio de un proceso masivo de invasión por parte de la cotorra argentina, el cual podría tener efectos económicos y ecológicos dramáticos en un país biodiverso como México

Effect of Exenatide on Gastric Emptying and Graft Survival in Islet Allograft Recipients

OBJECTIVE: To evaluate the effect of exenatide on gastric emptying and long-term metabolic control. METHODS: Ten islet allograft recipients treated with exenatide up to 4 years. Data from a mixed meal test with (MMT+) versus without (MMT−) administration of exenatide before boost ingestion were analyzed at 6, 12, 24, 36, or 48 months after initiation of exenatide treatment. None of the subjects were symptomatic for gastroparesis before or during the study. The c-peptide, acetaminophen absorption and glucose responses to MMT were analyzed by Student t test and analysis of variance. RESULTS: Average exenatide dose was 12.75 ± 9.46 μg/dL. The MMT subjects included two groups those with acetaminophen peak ≤120 minutes (“good gastric emptying; n = 4”) versus those with an acetaminophen peak ≥180 minutes (“delayed gastric emptying”). Among the MMT+, acetaminophen absorption was the same in both groups (P = .27). Up to 48 months exenatide delayed time to peak of glucose, c-peptide, and acetaminophen as well as suppressed the glucagon response to MMT mean peak: 70.89 ± 12.45 versus 43.24 ± 4.67. The mean values of c-peptide and glucose responses to MMT were not significantly different. CONCLUSIONS: Long-term exenatide administration up to 4 years was safe in islet transplant recipients, even in the presence of delayed gastric emptying. The effects of exenatide were acute and reversible when the agent was withdrawn. The main difficulty with the use of exenatide in islet transplant subjects is their poor tolerability, although the physiological effects are clearly evident even at low doses. Approximately 63% of total subjects under exenatide treatment discontinued the drug due to nausea and vomiting. The use of new GLP1 analogs with longer half lives and fewer side effects may help to attain higher GLP1 levels, therefore improving islet function and survival

Effect of Exenatide on Gastric Emptying and Graft Survival in Islet Allograft Recipients

OBJECTIVE: To evaluate the effect of exenatide on gastric emptying and long-term metabolic control. METHODS: Ten islet allograft recipients treated with exenatide up to 4 years. Data from a mixed meal test with (MMT+) versus without (MMT−) administration of exenatide before boost ingestion were analyzed at 6, 12, 24, 36, or 48 months after initiation of exenatide treatment. None of the subjects were symptomatic for gastroparesis before or during the study. The c-peptide, acetaminophen absorption and glucose responses to MMT were analyzed by Student t test and analysis of variance. RESULTS: Average exenatide dose was 12.75 ± 9.46 μg/dL. The MMT subjects included two groups those with acetaminophen peak ≤120 minutes (“good gastric emptying; n = 4”) versus those with an acetaminophen peak ≥180 minutes (“delayed gastric emptying”). Among the MMT+, acetaminophen absorption was the same in both groups (P = .27). Up to 48 months exenatide delayed time to peak of glucose, c-peptide, and acetaminophen as well as suppressed the glucagon response to MMT mean peak: 70.89 ± 12.45 versus 43.24 ± 4.67. The mean values of c-peptide and glucose responses to MMT were not significantly different. CONCLUSIONS: Long-term exenatide administration up to 4 years was safe in islet transplant recipients, even in the presence of delayed gastric emptying. The effects of exenatide were acute and reversible when the agent was withdrawn. The main difficulty with the use of exenatide in islet transplant subjects is their poor tolerability, although the physiological effects are clearly evident even at low doses. Approximately 63% of total subjects under exenatide treatment discontinued the drug due to nausea and vomiting. The use of new GLP1 analogs with longer half lives and fewer side effects may help to attain higher GLP1 levels, therefore improving islet function and survival