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GO'Mez-DIaz E.,Institute Of Biologia Evolutiva | Sindaco R.,Museo Civico di Storia Naturale | Pupin F.,MdS Museo di Science | Fasola M.,University of Pavia | Carranza S.,Institute Of Biologia Evolutiva
Molecular Ecology | Year: 2012

The Socotra Archipelago is an ancient continental fragment of Gondwanan origin and one of the most isolated landforms on Earth and a biodiversity hot spot. Yet, the biogeography and evolutionary history of its endemic fauna still remain largely overlooked. We investigate the origin, tempo and mode of diversification in the Hemidactylus geckos of the Socotra Archipelago. Concatenated and multilocus species coalescent analyses of Hemidactylus from Arabia and North Africa indicate that the Hemidactylus from Socotra do not form a monophyletic group and branch as three independent and well-supported clades instead. Both the chronogram inferred using the gene tree approach of BEAST and the age-calibrated multilocus species tree obtained using*BEAST suggest that the origin of Hemidactylus from Socotra may have involved a first vicariance event that occurred in the Early Miocene, followed by two independent transoceanic dispersal events that occurred more recently, during the Pliocene. Within Socotra, we analysed patterns of genetic diversity, the phylogeography and the demographic history in all seven nonintroduced species of Hemidactylus. Results based on two mitochondrial and two nuclear loci from 144 individuals revealed complex patterns of within-island diversification and high levels of intra-species genetic divergence. The interplay of both historical and ecological factors seems to have a role in the speciation process of this group of geckos. Interestingly, the case of H. forbesii and H. oxyrhinus, which inhabit the island of Abd al Kuri with an area of 133 km2, may represent one of the most extreme cases of intra-island speciation in reptiles ever reported. © 2012 Blackwell Publishing Ltd.


Heyn H.,08908 Lhospitalet Of Llobregat | Moran S.,08908 Lhospitalet Of Llobregat | Hernando-Herraez I.,08908 Lhospitalet Of Llobregat | Sayols S.,Institute Of Biologia Evolutiva | And 10 more authors.
Genome Research | Year: 2013

DNA methylation patterns are important for establishing cell, tissue, and organism phenotypes, but little is known about their contribution to natural human variation. To determine their contribution to variability, we have generated genomescale DNA methylation profiles of three human populations (Caucasian-American, African-American, and Han Chinese-American) and examined the differentially methylated CpG sites. The distinctly methylated genes identified suggest an influence of DNA methylation on phenotype differences, such as susceptibility to certain diseases and pathogens, and response to drugs and environmental agents. DNA methylation differences can be partially traced back to genetic variation, suggesting that differentially methylated CpG sites serve as evolutionarily established mediators between the genetic code and phenotypic variability. Notably, one-third of the DNA methylation differences were not associated with any genetic variation, suggesting that variation in population-specific sites takes place at the genetic and epigenetic levels, highlighting the contribution of epigenetic modification to natural human variation. © 2013, Published by Cold Spring Harbor Laboratory Press.


Fort J.,University of Girona | Sole R.V.,University Pompeu Fabra | Sole R.V.,Institute Of Biologia Evolutiva | Sole R.V.,Santa Fe Institute
New Journal of Physics | Year: 2013

Glioblastomas are highly diffuse, malignant tumors that have so far evaded clinical treatment. The strongly invasive behavior of cells in these tumors makes them very resistant to treatment, and for this reason both experimental and theoretical efforts have been directed toward understanding the spatiotemporal pattern of tumor spreading. Although usual models assume a standard diffusion behavior, recent experiments with cell cultures indicate that cells tend to move in directions close to that of glioblastoma invasion, thus indicating that a biased random walk model may be much more appropriate. Here we show analytically that, for realistic parameter values, the speeds predicted by biased dispersal are consistent with experimentally measured data. We also find that models beyond reaction-diffusion-advection equations are necessary to capture this substantial effect of biased dispersal on glioblastoma spread. © IOP Publishing and Deutsche Physikalische Gesellschaft.


Corominas-Murtra B.,University Pompeu Fabra | Corominas-Murtra B.,Institute Of Biologia Evolutiva | Fortuny J.,Autonomous University of Barcelona | Sole R.V.,Santa Fe Institute | Sole R.V.,Institute Of Biologia Evolutiva
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2011

Zipf's law seems to be ubiquitous in human languages and appears to be a universal property of complex communicating systems. Following the early proposal made by Zipf concerning the presence of a tension between the efforts of speaker and hearer in a communication system, we introduce evolution by means of a variational approach to the problem based on Kullback's Minimum Discrimination of Information Principle. Therefore, using a formalism fully embedded in the framework of information theory, we demonstrate that Zipf's law is the only expected outcome of an evolving communicative system under a rigorous definition of the communicative tension described by Zipf. © 2011 American Physical Society.


Sole R.,University Pompeu Fabra | Sole R.,Institute Of Biologia Evolutiva | Sole R.,Santa Fe Institute
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2016

The evolution of life in our biosphere has been marked by several major innovations. Such major complexity shifts include the origin of cells, genetic codes or multicellularity to the emergence of non-genetic information, language or even consciousness. Understanding the nature and conditions for their rise and success is a major challenge for evolutionary biology. Along with data analysis, phylogenetic studies and dedicated experimental work, theoretical and computational studies are an essential part of this exploration. With the rise of synthetic biology, evolutionary robotics, artificial life and advanced simulations, novel perspectives to these problems have led to a rather interesting scenario, where not only the major transitions can be studied or even reproduced, but even new ones might be potentially identified. In both cases, transitions can be understood in terms of phase transitions, as defined in physics. Such mapping (if correct) would help in defining a general frame- work to establish a theory of major transitions, both natural and artificial. Here, we review some advances made at the crossroads between statistical physics, artificial life, synthetic biology and evolutionary robotics. © 2016 The Author(s) Published by the Royal Society. All rights reserved.


Macia J.,University Pompeu Fabra | Macia J.,Institute Of Biologia Evolutiva | Sole R.,University Pompeu Fabra | Sole R.,Institute Of Biologia Evolutiva | Sole R.,Santa Fe Institute
PLoS ONE | Year: 2014

Biological systems perform computations at multiple scales and they do so in a robust way. Engineering metaphors have often been used in order to provide a rationale for modeling cellular and molecular computing networks and as the basis for their synthetic design. However, a major constraint in this mapping between electronic and wet computational circuits is the wiring problem. Although wires are identical within electronic devices, they must be different when using synthetic biology designs. Moreover, in most cases the designed molecular systems cannot be reused for other functions. A new approximation allows us to simplify the problem by using synthetic cellular consortia where the output of the computation is distributed over multiple engineered cells. By evolving circuits in silico, we can obtain the minimal sets of Boolean units required to solve the given problem at the lowest cost using cellular consortia. Our analysis reveals that the basic set of logic units is typically non-standard. Among the most common units, the so called inverted IMPLIES (N-Implies) appears to be one of the most important elements along with the NOT and AND functions. Although NOR and NAND gates are widely used in electronics, evolved circuits based on combinations of these gates are rare, thus suggesting that the strategy of combining the same basic logic gates might be inappropriate in order to easily implement synthetic computational constructs. The implications for future synthetic designs, the general view of synthetic biology as a standard engineering domain, as well as potencial drawbacks are outlined. © 2014 Macia, Sole.


Macia J.,University Pompeu Fabra | Macia J.,Institute Of Biologia Evolutiva | Posas F.,University Pompeu Fabra | Sole R.V.,University Pompeu Fabra | And 2 more authors.
Trends in Biotechnology | Year: 2012

Synthetic biology (SB) offers a unique opportunity for designing complex molecular circuits able to perform predefined functions. But the goal of achieving a flexible toolbox of reusable molecular components has been shown to be limited due to circuit unpredictability, incompatible parts or random fluctuations. Many of these problems arise from the challenges posed by engineering the molecular circuitry: multiple wires are usually difficult to implement reliably within one cell and the resulting systems cannot be reused in other modules. These problems are solved by means of a nonstandard approach to single cell devices, using cell consortia and allowing the output signal to be distributed among different cell types, which can be combined in multiple, reusable and scalable ways. © 2012 Elsevier Ltd.


Corominas-Murtra B.,University Pompeu Fabra | Sole R.V.,University Pompeu Fabra | Sole R.V.,Santa Fe Institute | Sole R.V.,Institute Of Biologia Evolutiva
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2010

Zipf's law is the most common statistical distribution displaying scaling behavior. Cities, populations or firms are just examples of this seemingly universal law. Although many different models have been proposed, no general theoretical explanation has been shown to exist for its universality. Here, we show that Zipf's law is, in fact, an inevitable outcome of a very general class of stochastic systems. Borrowing concepts from Algorithmic Information Theory, our derivation is based on the properties of the symbolic sequence obtained through successive observations over a system with an ubounded number of possible states. Specifically, we assume that the complexity of the description of the system provided by the sequence of observations is the one expected for a system evolving to a stable state between order and disorder. This result is obtained from a small set of mild, physically relevant assumptions. The general nature of our derivation and its model-free basis would explain the ubiquity of such a law in real systems. © 2010 The American Physical Society.


Belles X.,Institute Of Biologia Evolutiva
Annual Review of Entomology | Year: 2010

The increasing availability of insect genomes has revealed a large number of genes with unknown functions and the resulting problem of how to discover these functions. The RNA interference (RNAi) technique, which generates loss-of-function phenotypes by depletion of a chosen transcript, can help to overcome this challenge. RNAi can unveil the functions of new genes, lead to the discovery of new functions for old genes, and find the genes for old functions. Moreover, the possibility of studying the functions of homologous genes in different species can allow comparisons of the genetic networks regulating a given function in different insect groups, thereby facilitating an evolutionary insight into developmental processes. RNAi also has drawbacks and obscure points, however, such as those related to differences in species sensitivity. Disentangling these differences is one of the main challenges in the RNAi field. © 2010 by Annual Reviews All rights reserved.


Montelongo T.,Institute Of Biologia Evolutiva | Gomez-Zurita J.,Institute Of Biologia Evolutiva
Proceedings of the Entomological Society of Washington | Year: 2013

In this study we use a combination of morphological, molecular (mtDNA cytochrome c oxidase subunit 1 gene), geographic and ecological (field observations and cpDNA sequences from ingested plant tissue) data to describe and diagnose a new southern Nearctic leaf beetle species of Calligrapha Chevrolat, 1836 (Chrysomelidae: Chrysomelinae): Calligrapha thermalis Gómez-Zurita, sp. nov., associated to Perymenium mendezii De Candolle (Asteraceae). This new species, restricted to the Sierra Madre Occidental, is closely related to the Texan endemic Calligrapha wickhami Bowditch, 1911 associated to Viguiera stenoloba Blake (Asteraceae) in the northern foothills of the Sierra Madre Oriental ecoregion. The evolutionary scenarios explaining this recent taxonomic split, dated in the Pleistocene, are laid out and discussed.

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