Individual-based population genomics reveal different drivers of adaptation in sympatric fish

Connectivity and local adaptation are two contrasting evolutionary forces highly influencing population structure. To evaluate the impact of early-life traits and environmental conditions on genetic structuring and adaptation, we studied two sympatric fish species in the Western Mediterranean Sea: Symphodus tinca and S. ocellatus. We followed an individual-based approach and measured early-life history traits from otolith readings, gathered information on environmental variables and obtained genome-wide markers from genotyping-by-sequencing (GBS). The two species presented contrasting population structure across the same geographic gradient, with high and significant population differentiation in S. ocellatus, mostly determined by oceanographic fronts, and low differentiation and no front effect in S. tinca. Despite their different levels of genetic differentiation, we identified in both species candidate regions for local adaptation by combining outlier analysis with environmental and phenotypic association analyses. Most candidate loci were associated to temperature and productivity in S. ocellatus and to temperature and turbulence in S. tinca suggesting that different drivers may determine genomic diversity and differentiation in each species. Globally, our study highlights that individual-based approach combining genomic, environmental and phenotypic information is key to identify signals of selection and the processes mediating them

Following the Phoenician example : Western Mediterranean colonization by Spirobranchus cf. tetraceros (Annelida:Serpulidae)

A newly established population of the fouling polychaete Spirobranchus cf. tetraceros is reported from the western Mediterranean (Valencia Port). Despite previous intensive surveys, this is the first record for the taxon in the Iberian Peninsula. Molecular analyses revealed that S. cf. tetraceros from Valencia are genetically identical to specimens from Heraklion, Crete, but different from those collected in the Red Sea and S. tetraceros sensu stricto from the type locality in Australia. Mediterranean and Red Sea S. cf. tetraceros form a well-supported monophyletic clade but are clearly distinct from New South Wales specimens of S. tetraceros. Our new molecular evidence supports the hypothesis that S. tetraceros is not a global invader of Australian origin but rather a large species complex in need of a comprehensive worldwide revision. These results highlight the importance of integrative taxonomic research for species with reported global distributions because these taxa may include cryptic invaders. An illustrated morphological account of the Valencia and Heraklion specimens and a taxonomic key for Spirobranchus species in the Mediterranean Sea are provided

BUENAS PRÁCTICAS APLICADAS A LA IMPLEMENTACION COLABORATIVO DE APLICATIVOS WEB

RESUMEN La implementación de buenas prácticas para el desarrollo de software, son una compilación de métodos o técnicas que permiten llevar a cabo de manera óptima el conjunto de actividades que comprenden el desarrollo de un sistema de información. En el campo de desarrollo de software colaborativo, estas prácticas son empleadas con el fin de que las actividades realizadas por cada miembro de un equipo de trabajo, y esté tengan concordancia con las actividades realizadas por los demás miembros. Esto se realiza mediante el seguimiento de las normas correspondientes, que al ser implementadas, generan un proyecto comprensible por quienes conforman el equipo de trabajo. El no seguimiento de las mismas, puede generar retrasos e incluso fracaso en un proyecto de desarrollo colaborativo, debido qué al no establecer una metodología específica para la solución de un problema, cada miembro del equipo puede tomar diferentes caminos para la solución del mismo, pudiendo las discrepancias entre los mismos, provocar futuros problemas de compatibilidad dentro del sistema a implementar. Este proyecto pretende llevar a cabo el establecimiento de una metodología de desarrollo, que involucre una serie de actividades para la implementación colaborativa de un aplicativo web en el entorno colaborativo cloud9, basada en las buenas prácticas, con la posterior aplicación y evaluación de la misma, de acuerdo con los resultados obtenidos

NeuroBoricuas: a novel approach for incorporating neuroscience education in schools of Puerto Rico

[EN] Puerto Rico is in dire need of transforming its education system to counter the current economic recession and ensure a future with talented Puerto Ricans at the forefront of scientific research and technology development.  Here we present a group of neuroscientists and educators, the NeuroBoricuas, committed to revolutionize the scientific culture of Puerto Rico by incorporating neuroscience research training and inquiry-based activities in public and private schools. We carry out our vision through diverse methods, such as community outreach activities, where we promote neuroscience literacy using diverse learning activities. In parallel, we are designing a neuroscience course and textbook with educators to be implemented in schools. We also established neuroscience laboratories in K-12 schools and trained science teachers to manage such laboratories, using equipment from the company “Backyard Brains”. These laboratory experiences are integrated into the academic curriculum in high schools and the equipment is also available for students interested in designing their independent research projects. Lastly, we are expanding a network of committed scientists who partner with educators to help nurture future neuroscientists early in their academic endeavors. Here, we describe our trajectory and our approach to transform scientific education in Puerto Rico.We thank Dr. Gregory J. Quirk, Dr. Daniel Colon-Ramos and Dr. Mark Miller for their support. We thank Tim Marzullo, from Backyard Brains, for supporting NeuroBoricuas. We also thank Palabreria, Digi-Serv and Puerto Rico 4.0 for their constant support. We thank all the NeuroBoricuas that selflessly work hard for a better Puerto Rico. This work has been supported by generous donations from the Puerto Rican people, a grant from the University of Puerto Rico Medical Sciences Campus’ Chancellor’s office, and the Grass Foundation.http://ocs.editorial.upv.es/index.php/HEAD/HEAD18Bravo-Rivera, C.; Díaz-Ríos, M.; Aldarondo-Hernández, A.; Santos-Vera, B.; Ramos-Medina, L.; De Jesús-Burgos, M.; Bravo-Rivera, H.... (2018). NeuroBoricuas: a novel approach for incorporating neuroscience education in schools of Puerto Rico. Editorial Universitat Politècnica de València. 1447-1455. https://doi.org/10.4995/HEAD18.2018.8223OCS1447145

De la genómica a la modelización: estudios poblacionales a nivel individual en peces litorales del Mediterráneo occidental

[spa] La conectividad y la adaptación local son dos fuerzas evolutivas contrastantes que influyen en la estructura poblacional. Debido a su complejo ciclo de vida, las especies de peces marinos tienden a estructurarse en metapoblaciones, conectadas casi exclusivamente por movimientos en la fase larvaria. En esta tesis estudiamos la estructura poblacional genómica de varios peces del litoral mediterráneo y los factores potenciales que afectan su distribución. Con este objetivo, combinamos un conjunto de diferentes metodologías que incluyen genómica de poblaciones, lectura de otolitos, modelos de dispersión oceanográfica y teoría de grafos. Mostramos un efecto negativo de la temperatura sobre la duración de la fase pelágica larval, pero ningún efecto sobre el tamaño del asentamiento, por lo que el aumento de las temperaturas reduciría la capacidad de dispersión de los peces. Con un modelo de dispersión oceanográfica individual, observamos un efecto tanto de la fecha de eclosión como de la duración de la fase pelágica en las distancias y orientaciones de dispersión, pero variable entre especies. Además, encontramos un claro efecto de los frentes oceanográficos en las capacidades de dispersión de nuestras especies, lo que nos permite identificar la presencia de tres unidades hidrodinámicas delimitadas por estos frentes en el Mediterráneo Occidental. Encontramos una estructura genómica diferente entre las especies simpátricas de Symphodus, a pesar de sus rasgos larvales similares. No obstante, en ambas especies identificamos regiones candidatas para la adaptación local mediante la combinación de análisis de valores atípicos con análisis de asociación ambientales y fenotípicos. Proporcionamos herramientas y pautas para análisis de laboratorio y bioinformáticos para optimizar los estudios utilizando la secuenciación 2b-RAD en diferentes organismos no modelo con diferentes tamaños de genoma. Además, encontramos en tres localidades diferentes tendencias claras de mortalidad selectiva para la fecha de nacimiento y, en menor medida, para la tasa de crecimiento y la duración de las larvas pelágicas en un pez litoral común. Confirmamos estos resultados con un estudio de asociación fenotipo-genotipo, encontrando loci relacionados con estos rasgos, lo que sugiere una base genética para esta mortalidad diferenciada entre colonos y supervivientes. Finalmente, definimos los principales grupos y los principales nodos de conectividad en tres especies de peces en el Mediterráneo Occidental. Con esta información evaluamos el estado de protección de las áreas de alta importancia para el mantenimiento de la conectividad presentes en la zona, encontrando una pequeña proporción de ellas protegidas. En conjunto, estos resultados proporcionan nueva y valiosa información sobre la conectividad, la estructura poblacional y la adaptación en los peces litorales del mar Mediterráneo.[eng] Connectivity and local adaptation are two contrasting evolutionary forces influencing population structure. Due to their complex life cycle, marine fish species tend to be structured in metapopulations, connected almost exclusively by movements in the larval phase. In this thesis, we study the population genomic structure of several Mediterranean littoral fishes and the potential factors affecting their distribution. To asses this goal, we combine a set of different methodologies including population genomics, otolith reading, oceanographical dispersion models and graph theory. We show a negative effect of temperature on pelagic larval duration but no effect on settlement size and thus raising temperatures would reduce dispersal capabilities of fishes. With an individual-based oceanographic dispersal model, we observed an effect of both hatching date and pelagic larval duration in the dispersal distances and orientations, but variable among species. Furthermore, we found a clear effect of the oceanographic fronts in dispersal capabilities of our species, allowing us to identify three hydrodynamic units in the Western Mediterranean delimited by these fronts. We found different genomic structuring between sympatric species of Symphodus despite their similar early life traits. Nonetheless, we identified in both species candidate regions for local adaptation by combining outlier analysis with environmental and phenotypic association analyses. We provided tools and guidelines for laboratory and bioinformatics analyses to optimise studies using 2b-RAD sequencing on different non-model organisms with different genome sizes. Additionally, we found in three different localities clear trends of selective mortality for hatch date and lower for growth rate and pelagic larval duration in a common littoral fish. We confirmed these results with a phenotype-genotype association study, finding loci related with these traits, suggesting a genetic basis of differential mortality between settlers and survivors. Finally, we defined the main clusters and the main nodes of connectivity in three fish species in the Western Mediterranean. With this information, we evaluated the protection state of the areas with high importance for connectivity maintenance, finding a small proportion of them protected. All together, these results provide new valuable information about connectivity, population structure and adaptation in littoral fishes of the Mediterranean Sea.[spa] La connectivitat i l’adaptació local són dues forces evolutives contrastants que influeixen en l’estructura poblacional. A causa del seu cicle de vida complex, les espècies de peixos marins tendeixen a estructurar-se en metapoblacions, connectades quasi exclusivament pels moviments en la fase larvària. En aquesta tesi, estudiem l’estructura poblacional genòmica de diversos peixos litorals mediterranis i els possibles factors que afecten la seva distribució. Per avaluar aquest objectiu, combinem un conjunt de metodologies diferents, inclosa la genòmica de la població, la lectura d’otòlits, els models de dispersió oceanogràfica i la teoria de grafs. Mostrem un efecte negatiu de la temperatura sobre la duració de la fase pelàgica larval, però cap efecte sobre la mida de l'assentament. Per tant, l’augment de les temperatures reduiria la capacitat de dispersió dels peixos. Amb un model de dispersió oceanogràfica individual, vam observar un efecte tant de la data d’eclosió com de la duració de la fase pelàgica larval en les distàncies i orientacions de dispersió, però variable entre les espècies. A més a més, vam trobat un clar efecte dels fronts oceanogràfics en la capacitat de dispersió de les nostres espècies, que ens permet identificar la presència de tres unitats hidrodinàmiques al Mediterrani occidental, delimitades per aquests fronts. Trobem estructuracions genòmiques diferents entre espècies simpàtriques de Symphodus, malgrat dels seus trets larvaris similars. No obstant això, vam identificar en ambdues espècies regions candidates a l’adaptació local, combinant anàlisis de valors atípics amb anàlisis d’associacions fenotípiques i ambientals. Vam proporcionar eines i directrius per a anàlisis de laboratori i bioinformàtica per optimitzar estudis mitjançant la tècnica de seqüenciació 2b-RAD en diferents organismes no models amb diferents mides de genoma. A més, hem trobat en tres localitats diferents tendències clares de mortalitat selectiva relacionada en la data d’eclosió i, de forma més feble, relacionada en la taxa de creixement i la durada larvària pelàgica d’un peix litoral comú. Vam confirmar aquests resultats amb un estudi d’associació fenotip-genotip, trobant loci relacionats amb aquests trets, suggerint per tant una base genètica d’aquesta mortalitat diferenciada entre colons i supervivents. Finalment, hem definit els principals grups i els principals nodes de connectivitat de tres espècies de peixos al Mediterrani occidental. Amb aquesta informació, hem avaluat l’estat de protecció de les àrees amb gran importància per al manteniment de la connectivitat, trobant una xicoteta proporció protegida. En conjunt, aquests resultats proporcionen una nova i valuosa informació sobre la connectivitat, estructura poblacional i adaptació en peixos litorals del mar Mediterrani

Temperature reduces fish dispersal as larvae grow faster to their settlement size

1. As species struggle to cope with rising ocean temperatures, temperate marine assemblages are facing major reorganization. Many benthic species have a brief but critical period dispersing through the plankton, when they are particularly susceptible to variations in temperature. Impacts of rising temperatures can thus ripple through the population with community‐wide consequences. However, responses are highly species‐specific, making it difficult to discern assemblage‐wide patterns in the life histories of different fish species. 2. Here, we evaluate the responses to temperature in the early life histories of several fish species using otolith reconstructive techniques. We also assess the consequences of future warming scenarios to this assemblage. 3. We sampled recent settlers of nine common species across a temperature gradient in the Mediterranean Sea and obtained environmental data for each individual. Using otolith microstructure, we measured early life traits including pelagic larval duration (PLD), growth rate, settlement size, hatching and settlement dates. We used a GLM framework to examine how environmental variables influenced early life‐history parameters. 4. We show that increasing temperature results in considerable reduction in the dispersal potential of temperate fish. We find a nearly universal, assemblage‐wide decline in pelagic larval duration (PLD) of between 10% and 25%. This was because, with increasing temperature, larvae grew quicker to their settlement size. Settlement size itself was less affected by temperature and appears to be an ontogenetically fixed process. 5. Given current estimates of ocean warming, there could be an assemblage‐wide reduction in larval dispersal of up to 50 km across the Mediterranean, reducing connectivity and potentially isolating populations as waters warm.The Spanish Ministry of Science and Innovation Funded this research (projects UMBRAL; CTM2017‐86695‐C3‐3‐R; ‘PopCOmics’ CTM2017‐88080 (MCIU, AEI/FEDER, UE) and project BBVA (PR17‐ECO‐0012)). The Spanish National Research Council supported R. Arthur's visitorship with the Memorandum of Understanding between CSIC and NCF. H.T. was supported by a PhD scholarship funded by the Spanish Ministry of Science, Innovation and Universities (FPU15/02390).Peer reviewe

Genomic basis for early‑life mortality in sharpsnout seabream

Este artículo contiene 11 páginas, 4 figuras.Mortality at early life stages of fishes is common in nature and can be shaped by stochastic and selective processes. Selective mortality has rarely been assessed in natural conditions but can now be studied by combining genomic data with information on different life stages that realates to fitness. Here we investigate selective mortality between settlers and six-month survivors of the sharpsnout seabream by genotype-phenotype/environmental association studies in three localities along a geographic gradient. We gathered information on 105 individuals at 85,031 SNPs, obtained from individual based 2b-RAD libraries, as well as 9 phenotypic and environmental variables derived from individual otolith readings. We found common signals across localities for potential selection, such as lower survival rates for individuals hatching earlier, growing faster and experiencing higher temperatures during their planktonic phase. We identified 122 loci with parallel significant association to phenotypic and environmental variables. Importantly, one of these loci mapped to the exonic region of the il20rb, a gene involved in immune response, in the phylogenetically closest reference genome, showing parallel frequency changes in non-synonymous mutations in the three studied populations. Further temporal assessments are needed to understand how polymorphisms that are key to selective mortality are maintained.This research was funded by projects PopCOmics (CTM2017-88080, funded by MCIN/ AEI/10.13039/501100011033 and by “ERDF A way of making Europe’’ of the European Union) and MarGeCh (PID2020-118550RB, funded by MCIN/AEI/10.13039/501100011033) from the Spanish Government. The authors CC and MP are members of the research group SGR2017-1120 and EM of SGR2017-378 (Catalan Government). HT was supported by a PhD scholarship funded by the Spanish Ministry of Science, Innovation and Universities (FPU15/02390).Peer reviewe

Impact of individual early life traits in larval dispersal: A multispecies approach using backtracking models

Este artículo contiene 13 páginas, 5 figuras, 2 tablas.Dispersal is a key process shaping species population structure. In demersal marine fishes, which usually have sedentary adult phases, dispersion relies on drifting larval stages. However, the dynamics and seasonal variability of seawater masses can greatly determine the connectivity patterns of these species along the same geographic gradient. For this reason, detailed information on the release moment of larvae is needed to obtain accurate patterns of connectivity. In this study, we performed backtracking Lagrangian particle dispersion simulations, with individual-based early life traits data, obtained from otolith reading for 1413 juveniles of nine fish species belonging to three families (Sparidae, Pomacentridae and Labridae). For each species, individuals had been sampled from four to seven localities in the western Mediterranean Sea between the Gulf of Lion to the Gibraltar Strait. These nine species reproduce in different seasons of the year and their pelagic larval duration (PLD) range from 7 to 43 days. We identified three hydrodynamic units separated by oceanographic discontinuities (Balearic Sea, West Algerian Basin and Alboran Sea) with low settler’s exchange according to our simulations, independently of the PLD and reproductive season of the species. Hatching date and PLD showed significant effects on larval dispersal distance and orientation, both at the intraspecific and interspecific levels, highlighting the importance of these variables in determining the geographic origin of individuals. Our multispecies modelling approach adds a step forward for an accurate description of larval dispersion and recruitment, key to understand population resilience and define management strategies.This work was supported by the Spanish Government project ‘Pop- COmics’ (CTM2017-88080) (MCIU, AEI/FEDER, UE) and by the European FP7 CoCoNet project (Ocean 2011-4, grant agreement #287844). The authors CC and MP are members of the research group SGR2017-1120 and EM of SGR2017-378 (Catalan Government). HT was supported by a PhD scholarship funded by the Spanish Ministry of Science, Innovation and Universities. The authors acknowledge the MEDCLIC project, funded by “La Caixa” Foundation, contributing to the development of the WMOP hydrodynamic model.Peer reviewe

Buenas prácticas aplicadas a la implementacion colaborativo de aplicativos web

La implementación de buenas prácticas para el desarrollo de software, son una compilación de métodos o técnicas que permiten llevar a cabo de manera óptima el conjunto de actividades que comprenden el desarrollo de un sistema de información. En el campo de desarrollo de software colaborativo, estas prácticas son empleadas con el fin de que las actividades realizadas por cada miembro de un equipo de trabajo, y esté tengan concordancia con las actividades realizadas por los demás miembros. Esto se realiza mediante el seguimiento de las normas correspondientes, que al ser implementadas, generan un proyecto comprensible por quienes conforman el equipo de trabajo. El no seguimiento de las mismas, puede generar retrasos e incluso fracaso en un proyecto de desarrollo colaborativo, debido qué al no establecer una metodología específica para la solución de un problema, cada miembro del equipo puede tomar diferentes caminos para la solución del mismo, pudiendo las discrepancias entre los mismos, provocar futuros problemas de compatibilidad dentro del sistema a implementar. Este proyecto pretende llevar a cabo el establecimiento de una metodología de desarrollo, que involucre una serie de actividades para la implementación colaborativa de un aplicativo web en el entorno colaborativo cloud9, basada en las buenas prácticas, con la posterior aplicación y evaluación de la misma, de acuerdo con los resultados obtenidos.The implementation of best practices for software development, is a compilation of methods or techni-ques to perform optimally the set of activities that include the development of an information system. In the field of collaborative software development, these practices are used in order that the activities of each member of a team, and is having consistent with the activities of the other members. This is done by tracking the relevant rules, which when implemented, produce a comprehensive project who make up the team. Failure to follow them, can cause delays and even failure in a collaborative development pro-ject, because by not establishing a specific methodology for solving a problem, each team member can take different paths to the solution thereof, may discrepancies between them, causing future problems of compatibility within the system to be implemented. This project aims to carry out the establishment of a development methodology that involves a series of activities for collaborative implementation of a web application in cloud9 collaborative environment based on best practices, with subsequent implementation and evaluation of it, according to the result

Genomic basis for early-life mortality in sharpsnout seabream

Mortality at early life stages of fishes is common in nature and can be shaped by stochastic and selective processes. Selective mortality has rarely been assessed in natural conditions but can now be studied by combining genomic data with information on different life stages that realates to fitness. Here we investigate selective mortality between settlers and six‑month survivors of the sharpsnout seabream by genotype‑phenotype/environmental association studies in three localities along a geographic gradient. We gathered information on 105 individuals at 85,031 SNPs, obtained from individual based 2b‑RAD libraries, as well as 9 phenotypic and environmental variables derived from individual otolith readings. We found common signals across localities for potential selection, such as lower survival rates for individuals hatching earlier, growing faster and experiencing higher temperatures during their planktonic phase. We identified 122 loci with parallel significant association to phenotypic and environmental variables. Importantly, one of these loci mapped to the exonic region of the il20rb, a gene involved in immune response, in the hylogenetically closest reference genome, showing parallel frequency changes in non‑synonymous mutations in the three studied populations. Further temporal assessments are needed to understand how polymorphisms that are key to selective mortality are maintained