Resultados de investigación

It is a contribution of the Marine Zooplankton Ecology Group (2017 SGR 87), Proper thermal adaptation is key to understanding how species respond to temperature. However, this is seldom considered in protozooplankton and mixoplankton experiments. In this work, we studied how two heterotrophic dinoflagellates (Gyrodinium dominans and Oxyrrhis marina), one heterotrophic ciliate (Strombidium arenicola), and one mixotrophic dinoflagellate (Karlodinium armiger) responded to warming, comparing strains adapted at 16, 19 and 22 °C and those adapted at 16 °C and exposed for 3 days at 19 and 22 °C (acclimated treatments). Neither CNP contents nor the corresponding elemental ratios showed straightforward changes with temperature, except for a modest increase in P contents with temperature in some grazers. In general, the performance of both acclimated and adapted grazers increased from 16 to 19 °C and then dropped at 22 °C, with a few exceptions. Therefore, our organisms followed the “hotter is better” hypothesis from 16 to 19 °C; above 19 °C, however, the results were variable. Despite the disparity in the responses between species and physiological rates, in general, it seems that 19 °C-adapted organisms performed better than acclimated-only organisms. However, at 22 °C, most species were at the limit of their metabolisms and were unable to fully adapt. Nevertheless, adaptation to higher temperatures conferred some advantages prior to sudden increases in temperature (up to 25 °C) that simulated a heatwave episode. In summary, adaptation to temperature seems to confer a selective advantage to protistan grazers within a narrow range (i.e., ca. 3 °C). Adaptation to much higher temperatures (i.e., 6 °C) does not confer any clear physiological advantage (with few exceptions; e.g., the mixotroph K. armiger), at least within the time frame of our experiments, This research was funded by Grant CTM2017-84288-R by Fondo Europeo de Desarrollo Regional (FEDER)/ Ministerio de Ciencia, Innovación y Universidades—Agencia Estatal de Investigación (AEI), and by Grant PID2020-118645RB-I00 by Ministerio de Ciencia e innovación (MCIN)/AEI/ 10.13039/501100011033 and by “ERDF A way of making Europe”. With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), Para 4 especies: Volumen (µm3/depredador), Tasa crecimiento (µ 1/d), Tasa de ingestion (cells/ind/d), Eficiencia bruta de crecimiento (GGE, %), Peer reviewed

Datos incluidos: Anexo 1. Selección bibliográfica Anexo 2. Selección bibliográfica / Extractos Anexo 3. Selección artículos publicaciones periódicas Anexo 4. Selección fuentes documentales Anexo 5. Índice temático Anexo 6. Fuentes documentales esenciales, El productor y distribuidor de cine, y gran aficionado a la historia, Javier de Garcillán, descubrió de manera fortuita, en un estudio sobre el geógrafo Alexander Dalrymple, la expedición capitaneada por Pedro Fernández de Quirós en 1605. Esta expedición, cuyo mando acabaría en manos del piloto de la segunda nave, Luis Báez de Torres, tras el abandono de Quirós y su regreso a Acapulco, conduciría al descubrimiento del estrecho en 1606, que posteriormente, tomaría el nombre del piloto, Estrecho de Torres. La extrañeza y sorpresa que produjo en Garcillán la intranscendencia de este hecho, junto a la casi ausencia de estudios de la historiografía española sobre esta “hazaña marinera”, estimularon la curiosidad del distribuidor. En torno a 1998, comenzó un trabajo de recopilación de fuentes que le llevó a visitar desde los grandes archivos, bibliotecas y librerías de nuestro país hasta los más importantes del continente australiano, pasando por todos aquellos de cualquier país (Italia, Estados Unidos, Gran Bretaña…) en los que pudiera “descubrir” nuevos documentos que arrojaran luz sobre este hecho histórico y que facilitaran el “acceso” al laberinto. Su objetivo “la publicación de un libro de gran formato y divulgación en una editorial comercial que sirviera de base a la elaboración y distribución de una película documental” quedó desgraciadamente cercenado con la muerte de Javier de Garcillán en el año 2007. En 2013, este extenso fondo documental llegó al CCHS - CSIC de la mano de la investigadora Ana Rodríguez y la productora López Li Films. En él hemos “buceado” con el objeto de destacar aquellas fuentes que “iluminen” el proceso del descubrimiento, “Esta investigación ha recibido financiada por el Ministerio de Economía y Competitividad (MINECO). Ref.: HAR2011-15924-E”, Peer reviewed

This study was part of the SoilClim project (https://www.biodiversa.org/976) and carried out in the DOK agricultural trial in Therwil, Switzerland. The DOK trial is an agricultural long-term farming system research that is comparing biodynamic, organic and conventional farming systems, under the same 7-year crop rotation and equal ploughing depth (20 cm), for more than 40 years. The soil is a Haplic Luvisol (16% clay, 72% silt and 12% sand) on deep deposits of alluvial loess. Mean annual precipitation is 842 mm, and mean annual temperature is 10.5°C. For the current study, winter wheat fields (Triticum aestivum L. cv. “Wiwa”) under biodynamic (organic) and conventional management were used with soybean as preceding crop. In fields under organic (biodynamic) management the guidelines for ‘Demeter’ food production were followed; while fields under conventional management were managed according to the Swiss Guidelines. For more information on the types of management and inputs applied during the experiment see Kundel et al. (2020), Birkhofer et al. (2021) and Meyer et al. (2021). + Experimental design The experiment consisted of four blocks (A–D), each one containing one organic (BIODYN) and one conventional (CONMIN) field. Every field included three plots with different precipitation treatments: a partial rainout shelter (Roof - 2.5 m × 2.5 m, 1.3–1.7 m height) that reduced precipitation by 65%; a rainout shelter control (Roof Control), which did not reduce precipitation, but allowed knowing possible artefacts derived from the shelters; and an open field (Control) without a shelter. In total, there were 24 experimental plots (i.e., four replicated fields in two farming systems with three precipitation treatments each). The rainout-shelters were installed from mid-March 2017 (during wheat tillering stage) until June of that same year (shortly before wheat harvesting). Details on the design and installation of the rainout shelters are available in Kundel et al. (2018)., The experiment consisted of four blocks (A–D), each one containing one organic (BIODYN) and one conventional (CONMIN) field. Every field included three plots with different precipitation treatments: a partial rainout shelter (Roof - 2.5 m × 2.5 m, 1.3–1.7 m height) that reduced precipitation by 65%; a rainout shelter control (Roof Control), which did not reduce precipitation, but allowed knowing possible artefacts derived from the shelters; and an open field (Control) without a shelter. In total, there were 24 experimental plots (i.e., four replicated fields in two farming systems with three precipitation treatments each). The rainout-shelters were installed from mid-March 2017 (during wheat tillering stage) until June of that same year (shortly before wheat harvesting). Details on the design and installation of the rainout shelters are available in Kundel et al. (2018, The SoilClim project was financed by the BiodivERsA COFUND (2015–2016 call), in concert with the following national funders: the Swiss National Science Foundation (SNSF), the German Research Foundation (DFG), the Swedish Research Council (Formas), the Estonian Research Council (ETAG), and the Spanish Ministry of Sciences and Innovation (MICINN, ref.: PCIN-2016-045). The DOK trial is funded through the Swiss Federal Office of Agriculture (FOAG)., 1_BaitLamina_Depth_Database_(GLMM)_Gavin-Centol_et_al_2022.xls 2_BaitLamina_RAI_Database_(GLM)_Gavin-Centol_et_al_2022.xls 3_BaitLamina_Database_(RF)_Gavin-Centol_et_al_2022.xls, Peer reviewed

Examination of relevant type materials and living plants reveals that Rungia axilliflora, R. densiflora and R. evrardii are conspecific with R. stolonifera. Lectotypes are designated for the names R. evrardii and R. stolonifera., Peer reviewed

Plants respond to shade-modulated light-signals, via the phytochrome (phy) system, by adaptive changes, collectively termed the shade avoidance syndrome (SAS). To examine the roles of the Phy-Interacting bHLH Factors, PIF1, 3, 4 and 5, in relaying this information to the transcriptional network, we compared the genome-wide expression profiles of wild-type and quadruple pif (pifq) mutants in response to shade. The data identify a subset of genes, enriched in transcription-factor-encoding loci, that respond rapidly (within 1 h), in a PIF-dependent manner, to the shade signal, and that contain promoter-located G-box-sequence motifs (CACGTG), known to be preferred PIF binding sites. These genes are thus potential direct targets of phy-PIF signaling that function in the primary transcriptional circuitry controlling downstream response-elaboration. A second subset of PIF-dependent, early-response genes, lacking G-box motifs, are enriched for auxin-responsive loci, suggestive of being indirect targets of phy-PIF signaling involved in the rapid cell-expansion known to be induced by shade. A meta-analysis comparing deetiolation- and shade-responsive transcriptomes identifies a further subset of G-box-containing genes that reciprocally display rapid repression and induction in response to light and shade signals at the inception of deetiolation and shade-avoidance, respectively. Collectively, these data define a core set of transcriptional and hormonal (auxin, cytokinin) processes that appear to be dynamically poised to react rapidly to changes in the light environment via perturbations in the mutually antagonistic actions of the phys and PIFs. Data from comparative analysis of the quadruple pifq and all triple pif-mutant combinations in response to light and shade, confirm that the PIF-quartet members act with overlapping redundancy on seedling morphogenesis and transcriptional regulation, but that the individual PIFs contribute differentially to these responses., Peer reviewed

Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds., Peer reviewed

Usage Notes Porcine APOA2 gene expression in liver Data from Analysis of the porcine APOA2 gene expression in liver, polymorphisms identification and association with fatty acid composition traits. Contains SNP genotypes for GWAS and eGWAS studies, mRNA expression of APOA2 in liver, and fatty acid composition in backfat and muscle, APOA2 is a protein implicated in triglyceride, fatty acid and glucose metabolism. In pigs, the APOA2 gene is located on pig chromosome 4 (SSC4) in a QTL region affecting fatty acid composition, fatness and growth traits. In this study, we evaluated APOA2 as a candidate gene for meat quality traits in an Iberian × Landrace backcross population. The APOA2:c.131T>A polymorphism, located in exon 3 of APOA2 and determining a missense mutation, was associated with the percentage of hexadecenoic acid [C16:1(n–9)], linoleic acid [C18:2(n–6)], α-linolenic acid [C18:3(n–3)], dihomo-gamma-linolenic acid [C20:3(n–6)] and polyunsaturated fatty acids (PUFAs) in backfat. Furthermore, this SNP was associated with the global mRNA expression levels of APOA2 in liver and was used as a marker to determine allelic expression imbalance by pyrosequencing. We determined an overexpression of the T allele in heterozygous samples with a mean ratio of 2.8 (T/A), observing a high variability in the allelic expression among individuals. This result suggests that complex regulatory mechanisms, beyond a single polymorphism (e.g. epigenetic effects or multiple cis-acting polymorphisms), may be regulating APOA2 gene expression., Peer reviewed

Usage Notes: Description_data_GSE_Global_pigs Table describing the samples. Note that the submitted data includes a few animals that were removed from the paper due to additional constraints applied in the review process. GSE_global_pigs.map PLINK MAP file, describing the SNPs used. GSE_global_pigs.ped Genotype data used in PLINK PED file format., [Background]: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection., [Results]: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection., [Conclusions]: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation., Peer reviewed

Software https://treeoflife.kew.org https://github.com/RBGKew/KewTreeOfLife, The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this paper are to (i) document our methods, (ii) describe our first data release and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). A “first pass” angiosperm tree of life was inferred from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections., Calleva Foundation. Sackler Trust. Garfield Weston Foundation, Peer reviewed

Genotypic data from 1,040 Murciano-Granadina female goats genotyped with the Goat SNP50 BeadChip, as well as milk production records of 817 Murciano-Granadina goats for the traits milk yield measured in kilograms at 210 days (MY210), 240 days (MY240) and 305 days (MY305), the natural logarithm of the somatic cell count divided by 1,000 (lnSCC, to convert this value into a somatic cell count please use the formula: elnSCC × 103 cells/mL), fat percentage (FP), protein percentage (PP) and lactose percentage (LP)., Peer reviewed