Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal

Background: Myotragus balearicus was an endemic bovid from the Balearic Islands (Western Mediterranean) that became extinct around 6,000-4,000 years ago. The Myotragus evolutionary lineage became isolated in the islands most probably at the end of the Messinian crisis, when the desiccation of the Mediterranean ended, in a geological date established at 5.35 Mya. Thus, the sequences of Myotragus could be very valuable for calibrating the mammalian mitochondrial DNA clock and, in particular, the tree of the Caprinae subfamily, to which Myotragus belongs. Results: We have retrieved the complete mitochondrial cytochrome b gene (1,143 base pairs), plus fragments of the mitochondrial 12S gene and the nuclear 28S rDNA multi-copy gene from a well preserved Myotragus subfossil bone. The best resolved phylogenetic trees, obtained with the cytochrome b gene, placed Myotragus in a position basal to the Ovis group. Using the calibration provided by the isolation of Balearic Islands, we calculated that the initial radiation of caprines can be dated at 6.2 ± 0.4 Mya. In addition, alpine and southern chamois, considered until recently the same species, split around 1.6 ± 0.3 Mya, indicating that the two chamois species have been separated much longer than previously thought. Conclusion: Since there are almost no extant endemic mammals in Mediterranean islands, the sequence of the extinct Balearic endemic Myotragus has been crucial for allowing us to use the Messinian crisis calibration point for dating the caprines phylogenetic tree

Enhancers with tissue-specific activity are enriched in intronic regions

Tissue function and homeostasis reflect the gene expression signature by which the combination of ubiquitous and tissue-specific genes contribute to the tissue maintenance and stimuli-responsive function. Enhancers are central to control this tissue-specific gene expression pattern. Here, we explore the correlation between the genomic location of enhancers and their role in tissue-specific gene expression. We find that enhancers showing tissue-specific activity are highly enriched in intronic regions and regulate the expression of genes involved in tissue-specific functions, whereas housekeeping genes are more often controlled by intergenic enhancers, common to many tissues. Notably, an intergenic-to-intronic active enhancers continuum is observed in the transition from developmental to adult stages: the most differentiated tissues present higher rates of intronic enhancers, whereas the lowest rates are observed in embryonic stem cells. Altogether, our results suggest that the genomic location of active enhancers is key for the tissue-specific control of gene expression

Towards a new biological science of language

Science is the human activity aimed at acquiring knowledge by means of a very specific method, the scientific method, in which logical reasoning is put at the service of empirical and observable evidence. We perfectly understand what it means to be able to focus our scientific perspective on a problem: we want to understand it reasonably, according to the observation, and different observers will obtain an equivalent result. More and more fields of knowledge are diving into scientific analysis. Experimental sciences are based on it, but other fields of knowledge have also found themselves needing it in order to gain social acceptance and recognised explanatory possibilities

Aproximació molecular a l'estudi de l'home

The application of molecular studies to reconstruct the history of the human species has become a powerful to01 for ascertaining either the evolutionary pathway or the timing of evolutionary events. Both long term and short term evolutionary problems may be analyzed, although only the long term, the human lineage, is treated here. Several levels of analysis allow us to compare among related species or different human populations in order to ascertain their degree of similarity from which an evolutionary tree may be reconstructed. These levels include, with increasing closeness to the genetic infomation (DNA), comparison using blood groups, immunological techniques, polymorphisms, sequence of aminoacids of proteins, sequence of nucleotides of DNA, and DNA hybridation. Since the complexity and diversity of techniques and of the mathematical treatment of results provided is very powerful in ascertaining the date of human origin, those and other molecular methods are being employed successfully to understand the problems related to migration and composition of ancient human populations

Monograph: assembled life: a natural history of societies

La biología evolutiva sugiere explicaciones de los orígenes naturales y remotos de la cooperación, así como de la revolución cognitiva asociada al surgimiento de la especie humana y de la organización social que la caracteriza. Para entender los cimientos de esta organización social humana necesitamos buscar las ventajas adaptativas que quizás han supuesto, en la historia de la vida, las estructuras sociales y entender qué cualidades parecen seguir vectores biológicos genuinos. Sin duda, las aptitudes cognitivas humanas nos han permitido ir todavía más allá y el incremento de la complejidad de las estructuras sociales ha seguido también un proceso independiente, basado en lo que más tarde se llamará economía y estructuras de poder y que inicialmente se basa en un rasgo distintivamente humano, la cultura acumulativa. Hoy es materia de debate si los comportamientos que van de los primeros asentamientos de cazadores-recolectores hasta las grandes estructuras urbanas actuales tienen un verdadero arraigo biológico. Partiendo de las bases evolutivas de la cooperación, en este monográfico nos adentramos en las estructuras sociales humanas, desde las más simples hasta la complejidad de las sociedades modernas.; La biologia evolutiva suggereix explicacions dels orígens naturals i remots de la cooperació, com també de la revolució cognitiva associada al sorgiment de l’espècie humana i de l’organització social que la caracteritza. Per entendre els fonaments d’aquesta organització social humana ens cal buscar els avantatges adaptatius que potser han suposat, en la història de la vida, les estructures socials i entendre quines qualitats semblen seguir vectors biològics genuïns. Sense dubte, les aptituds cognitives humanes ens han permès anar encara més enllà i l’increment de la complexitat de les estructures socials ha seguit també un procés independent, basat en el que més tard se’n dirà economia i estructures de poder i que inicialment es basa en un tret distintivament humà, la cultura cumulativa. Avui és matèria de debat si els comportaments que van des dels primers assentaments de caçadors-recol·lectors fins a les grans estructures urbanes actuals tenen un veritable arrelament biològic. Partint de les bases evolutives de la cooperació, en aquest monogràfic ens endinsem en les estructures socials humanes, des de les més simples fins a la complexitat de les societats modernes.; Evolutionary biology provides explanations for the natural and remote origins of cooperation, as well as for the cognitive revolution associated with the emergence of the human species and its characterising social organisation. To understand the foundations of this human social organisation, we need to look for the adaptive advantages that social structures may have provided in the history of life, and understand which of these qualities appear to follow genuine biological vectors. Undoubtedly, human cognitive skills have allowed us to go even further and the increase in the complexity of social structures also followed an independent process, based on what would later be called economics and power structures, and initially rooted in a distinctively human trait, cumulative culture. It is now a matter of debate whether the behaviours from the earliest hunter-gatherer settlements to today’s large urban structures are truly biologically rooted. Building on the evolutionary basis of cooperation, this monograph looks at human social structures, from the most ancient and simple to the most complex of modern societies

Cosmic phylogeny: reconstructing the chemical history of the solar neighbourhood with an evolutionary tree

Using 17 chemical elements as a proxy for stellar DNA, we present a full phylogenetic study of stars in the solar neighbourhood. This entails applying a clustering technique that is widely used in molecular biology to construct an evolutionary tree from which three branches emerge. These are interpreted as stellar populations that separate in age and kinematics and can be thus attributed to the thin disc, the thick disc and an intermediate population of probable distinct origin. We further find six lone stars of intermediate age that could not be assigned to any population with enough statistical significance. Combining the ages of the stars with their position on the tree, we are able to quantify the mean rate of chemical enrichment of each of the populations, and thus show in a purely empirical way that the star formation rate in the thick disc is much higher than that in the thin disc. We are also able to estimate the relative contribution of dynamical processes such as radial migration and disc heating to the distribution of chemical elements in the solar neighbourhood. Our method offers an alternative approach to chemical tagging methods with the advantage of visualizing the behaviour of chemical elements in evolutionary trees. This offers a new way to search for ‘common ancestors’ that can reveal the origin of solar neighbourhood stars.The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement nos 320360 and 321067, as well as King's College Cambridge CRA programme

Dynamic sensitivity and nonlinear interactions influence the system-level evolutionary patterns of phototransduction proteins

Determining the influence of complex, molecular-system dynamics on the evolution of proteins is hindered by the significant challenge of quantifying the control exerted by the proteins on system output. We have employed a combination of systems biology and molecular evolution analyses in a first attempt to unravel this relationship. We employed a comprehensive mathematical model of mammalian phototransduction to predict the degree of influence that each protein in the system exerts on the high-level dynamic behaviour. We found that the genes encoding the most dynamically sensitive proteins exhibit relatively relaxed evolutionary constraint. We also investigated the evolutionary and epistatic influences of the many nonlinear interactions between proteins in the system and found several pairs to have coevolved, including those whose interactions are purely dynamical with respect to system output. This evidence points to a key role played by nonlinear system dynamics in influencing patterns of molecular evolution.This work was supported by the Ministerio de Economia y Competitividad, Spain (grant no. BFU2013-43726-P, subprogram BMC) and the María de Maez to Program for Units of Excellence in R&D (MDM-2014-0370); the Departament d'Economia i Coneixement de la Generalitat de Catalunya (Grup de Recerca Consolidat GRC 2014 SGR 866); AGAUR, Generalitat de Catalunya (2011 FI BI 00275 to B.M.I.); and the Spanish Ministry of Science and Innovation (MICINN) (Juan de la Cierva Program to L.M.

Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania

Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.M.M was supported by the European Union through the European Regional Development Fund (Project No. 2014-2020.4.01.16-0030). For J.B, this study has been possible thanks to grant BFU2016-77961-P (AEI/FEDER, UE) awarded by the Agencia Estatal de Investigación (MINECO, Spain) and with the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 702). Part of the “Unidad de Excelencia María de Maeztu”, funded by the MINECO (ref: MDM-2014-0370). O.L. was supported by a Ramón y Cajal grant from the Spanish Ministerio de Economia y Competitividad (MINECO) with reference RYC-2013-14797, a BFU2015-68759-P (MINECO/FEDER) grant and the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 937)

Dynamic sensitivity and nonlinear interactions influence the system-level evolutionary patterns of phototransduction proteins

Determining the influence of complex, molecular-system dynamics on the evolution of proteins is hindered by the significant challenge of quantifying the control exerted by the proteins on system output. We have employed a combination of systems biology and molecular evolution analyses in a first attempt to unravel this relationship. We employed a comprehensive mathematical model of mammalian phototransduction to predict the degree of influence that each protein in the system exerts on the high-level dynamic behaviour. We found that the genes encoding the most dynamically sensitive proteins exhibit relatively relaxed evolutionary constraint. We also investigated the evolutionary and epistatic influences of the many nonlinear interactions between proteins in the system and found several pairs to have coevolved, including those whose interactions are purely dynamical with respect to system output. This evidence points to a key role played by nonlinear system dynamics in influencing patterns of molecular evolution.This work was supported by the Ministerio de Economia y Competitividad, Spain (grant no. BFU2013-43726-P, subprogram BMC) and the María de Maez to Program for Units of Excellence in R&D (MDM-2014-0370); the Departament d'Economia i Coneixement de la Generalitat de Catalunya (Grup de Recerca Consolidat GRC 2014 SGR 866); AGAUR, Generalitat de Catalunya (2011 FI BI 00275 to B.M.I.); and the Spanish Ministry of Science and Innovation (MICINN) (Juan de la Cierva Program to L.M.