Genome-wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana

Tabas-Madrid D., Méndez-Vigo B., Arteaga N., Marcer A., Pascual-Montano A., Weigel D., Xavier Picó F., Alonso-Blanco C. (2018) Genome-wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana. Plant Cell and Environment. 41: 1806-1820.
Enlace
Doi: 10.1111/pce.13189

Resumen:

Current global change is fueling an interest to understand the genetic and molecular mechanisms of plant adaptation to climate. In particular, altered flowering time is a common strategy for escape from unfavourable climate temperature. In order to determine the genomic bases underlying flowering time adaptation to this climatic factor, we have systematically analysed a collection of 174 highly diverse Arabidopsis thaliana accessions from the Iberian Peninsula. Analyses of 1.88 million single nucleotide polymorphisms provide evidence for a spatially heterogeneous contribution of demographic and adaptive processes to geographic patterns of genetic variation. Mountains appear to be allele dispersal barriers, whereas the relationship between flowering time and temperature depended on the precise temperature range. Environmental genome-wide associations supported an overall genome adaptation to temperature, with 9.4% of the genes showing significant associations. Furthermore, phenotypic genome-wide associations provided a catalogue of candidate genes underlying flowering time variation. Finally, comparison of environmental and phenotypic genome-wide associations identified known (Twin Sister of FT, FRIGIDA-like 1, and Casein Kinase II Beta chain 1) and new (Epithiospecifer Modifier 1 and Voltage-Dependent Anion Channel 5) genes as candidates for adaptation to climate temperature by altered flowering time. Thus, this regional collection provides an excellent resource to address the spatial complexity of climate adaptation in annual plants. © 2018 John Wiley & Sons Ltd

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Temperature fine-tunes Mediterranean Arabidopsis thaliana life-cycle phenology geographically

Marcer, A., Vidigal, D.S., James, P.M.A., Fortin, M.-J., Méndez-Vigo, B., Hilhorst, H.W.M., Bentsink, L., Alonso-Blanco, C., Picó, F.X. (2017) Temperature fine-tunes Mediterranean Arabidopsis thaliana life-cycle phenology geographically. Plant Biology. : 0-0.
Enlace
Doi: 10.1111/plb.12558

Resumen:

Tackling intraspecific genetic structure in distribution models better reflects species geographical range

Marcer A., Méndez-Vigo B., Alonso-Blanco C., Picó F.X. (2016) Tackling intraspecific genetic structure in distribution models better reflects species geographical range. Ecology and Evolution. 6: 2084-2097.
Enlace
Doi: 10.1002/ece3.2010

Resumen:

Genetic diversity provides insight into heterogeneous demographic and adaptive history across organisms' distribution ranges. For this reason, decomposing single species into genetic units may represent a powerful tool to better understand biogeographical patterns as well as improve predictions of the effects of GCC (global climate change) on biodiversity loss. Using 279 georeferenced Iberian accessions, we used classes of three intraspecific genetic units of the annual plant Arabidopsis thaliana obtained from the genetic analyses of nuclear SNPs (single nucleotide polymorphisms), chloroplast SNPs, and the vernalization requirement for flowering. We used SDM (species distribution models), including climate, vegetation, and soil data, at the whole-species and genetic-unit levels. We compared model outputs for present environmental conditions and with a particularly severe GCC scenario. SDM accuracy was high for genetic units with smaller distribution ranges. Kernel density plots identified the environmental variables underpinning potential distribution ranges of genetic units. Combinations of environmental variables accounted for potential distribution ranges of genetic units, which shrank dramatically with GCC at almost all levels. Only two genetic clusters increased their potential distribution ranges with GCC. The application of SDM to intraspecific genetic units provides a detailed picture on the biogeographical patterns of distinct genetic groups based on different genetic criteria. Our approach also allowed us to pinpoint the genetic changes, in terms of genetic background and physiological requirements for flowering, that Iberian A. thaliana may experience with a GCC scenario applying SDM to intraspecific genetic units. © 2016 Published by John Wiley & Sons Ltd.

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Deciphering the adjustment between environment and life history in annuals: Lessons from a geographically-explicit approach in Arabidopsis thaliana

Manzano-Piedras E., Marcer A., Alonso-Blanco C., Pico F.X. (2014) Deciphering the adjustment between environment and life history in annuals: Lessons from a geographically-explicit approach in Arabidopsis thaliana. PLoS ONE. 9: 0-0.
Enlace
Doi: 10.1371/journal.pone.0087836

Resumen:

The role that different life-history traits may have in the process of adaptation caused by divergent selection can be assessed by using extensive collections of geographically-explicit populations. This is because adaptive phenotypic variation shifts gradually across space as a result of the geographic patterns of variation in environmental selective pressures. Hence, large-scale experiments are needed to identify relevant adaptive life-history traits as well as their relationships with putative selective agents. We conducted a field experiment with 279 geo-referenced accessions of the annual plant Arabidopsis thaliana collected across a native region of its distribution range, the Iberian Peninsula. We quantified variation in life-history traits throughout the entire life cycle. We built a geographic information system to generate an environmental data set encompassing climate, vegetation and soil data. We analysed the spatial autocorrelation patterns of environmental variables and life-history traits, as well as the relationship between environmental and phenotypic data. Almost all environmental variables were significantly spatially autocorrelated. By contrast, only two life-history traits, seed weight and flowering time, exhibited significant spatial autocorrelation. Flowering time, and to a lower extent seed weight, were the life-history traits with the highest significant correlation coefficients with environmental factors, in particular with annual mean temperature. In general, individual fitness was higher for accessions with more vigorous seed germination, higher recruitment and later flowering times. Variation in flowering time mediated by temperature appears to be the main life-history trait by which A. thaliana adjusts its life history to the varying Iberian environmental conditions. The use of extensive geographically-explicit data sets obtained from field experiments represents a powerful approach to unravel adaptive patterns of variation. In a context of current global warming, geographically-explicit approaches, evaluating the match between organisms and the environments where they live, may contribute to better assess and predict the consequences of global warming. © 2014 Manzano-Piedras et al.

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Using species distribution modelling to disentangle realised versus potential distributions for rare species conservation

Marcer A., Saez L., Molowny-Horas R., Pons X., Pino J. (2013) Using species distribution modelling to disentangle realised versus potential distributions for rare species conservation. Biological Conservation. 166: 221-230.
Enlace
Doi: 10.1016/j.biocon.2013.07.001

Resumen:

Range maps provide important information in species conservation management, specially in the case of rare species of conservation interest. For the vast majority of cases, this information can only be estimated by means of species distribution modelling. When absence data is unavailable, modelled distribution maps represent the spatial variation of the degree of suitability for the species rather than their realised distribution. Although discerning potentially suitable areas for a given species is an important asset in conservation, it is necessary to estimate current distributions in order to preserve current populations. This work explores the use of species distribution modelling (Maxent) for species of conservation interest when their Extent of Occurrence (EOO) is well-known and there is quality occurrence data. In this case, derived binary maps of potentially suitable areas can be obtained and used to assess the conservation and protection status of a given species in combination with the EOO and existing protected area networks. Seven species, which are rare and endemic to the Western Mediterranean, have been used as an example. Valuable information for conservation assessment such as potentially suitable areas, EOO, Areas of Occupancy (AOO) and degree of protection is provided for this set of species. In addition, the existing informal view that among experts these species have range sizes much smaller than their potentially suitable area is confirmed. This could probably be attributed to important but currently unknown predictor variables and to historical phylogeographic factors. © 2013 Elsevier Ltd.

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IberiAt. An Information System on Natural Variation of the Annual Plant Arabidopsis thaliana in the Iberian Peninsula.

Marcer A, Alonso-Blanco C, Escobar A, Garcia V, Picó X (2012) IberiAt. An Information System on Natural Variation of the Annual Plant Arabidopsis thaliana in the Iberian Peninsula.  Biodiversity Technologies Symposium. University of Oxford, UK, September 27-28.  pòster i comunicació oral.

Modelling invasive alien species distributions from digital biodiversity atlases. Model upscaling as a means of reconciling data at different scales

Marcer A., Pino J., Pons X., Brotons L. (2012) Modelling invasive alien species distributions from digital biodiversity atlases. Model upscaling as a means of reconciling data at different scales. Diversity and Distributions. 18: 1177-1189.
Enlace
Doi: 10.1111/j.1472-4642.2012.00911.x

Resumen:

Aim: There is a wealth of information on species occurrences in biodiversity data banks, albeit presence-only, biased and scarce at fine resolutions. Moreover, fine-resolution species maps are required in biodiversity conservation. New techniques for dealing with this kind of data have been reported to perform well. These fine-resolution maps would be more robust if they could explain data at coarser resolutions at which species distributions are well represented. We present a new methodology for testing this hypothesis and apply it to invasive alien species (IAS). Location: Catalonia, Spain. Methods: We used species presence records from the Biodiversity data bank of Catalonia to model the distribution of ten IAS which, according to some recent studies, achieve their maximum distribution in the study area. To overcome problems inherent with the data, we prepared different correction treatments: three for dealing with bias and five for autocorrelation. We used the MaxEnt algorithm to generate models at 1-km resolution for each species and treatment. Acceptable models were upscaled to 10 km and validated against independent 10 km occurrence data. Results: Of a total of 150 models, 20 gave acceptable results at 1-km resolution and 12 passed the cross-scale validation test. No apparent pattern emerged, which could serve as a guide on modelling. Only four species gave models that also explained the distribution at the coarser scale. Main conclusions: Although some techniques may apparently deliver good distribution maps for species with scarce and biased data, they need to be taken with caution. When good independent data at a coarser scale are available, cross-scale validation can help to produce more reliable and robust maps. When no independent data are available for validation, however, new data gathering field surveys may be the only option if reliable fine-scale resolution maps are needed. © 2012 Blackwell Publishing Ltd.

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Handling historical information on protected-area systems and coverage. An information system for the Natura 2000 European context

Marcer A., Garcia V., Escobar A., Pons X. (2010) Handling historical information on protected-area systems and coverage. An information system for the Natura 2000 European context. Environmental Modelling and Software. 25: 956-964.
Enlace
Doi: 10.1016/j.envsoft.2010.03.011

Resumen:

Protected-area coverage is an internationally-recognized surrogate indicator for measuring biodiversity conservation. To measure trends in biodiversity conservation over time, historical records on protected-area boundaries are needed. Protected-area systems represent a challenge in information management for public environmental organizations. Protected areas may be subjected to changes which must follow a mandatory multiple-step administrative process. A wealth of information is generated which needs to be stored in a way that eases the handling process and for future reference. We present an information system which handles both change on protected-area boundaries over time and their related administrative processes. It also provides distributed data maintenance functionality as well as integrated alphanumeric, file and cartographic information handling. We discuss the actual implementation of the system for handling Natura 2000 sites in the Catalan and Spanish contexts. The designed system is applicable to other European Union member states. © 2010 Elsevier Ltd. All rights reserved.

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ISOMDE: Una nueva aproximación a la generación de modelos digitales del terreno.

Pons X, Dalmases C, Pesquer L, Marcer A, Masó J (2004) ISOMDE: Una nueva aproximación a la generación de modelos digitales del terreno. In Conesa C, Martínez JB (eds) Territorio y Medio Ambiente: Métodos Cuantitativos y Técnicas de Información Geográfica. Grupo de Métodos Cuantitativos, SIG y Teledetección (Asociación de Geógrafos Españoles) y Departamento de Geografía, Universidad de Mu rcia, pp. 27-38.

Inventarios Forestales y sistemas de información geográfica en la gestión forestal de áreas protegidas.

Marcer A, Ibàñez JJ, Vayreda J, Pons X (2001) Inventarios Forestales y sistemas de información geográfica en la gestión forestal de áreas protegidas. In Actas del Congreso de Ordenación y Gestión Sostenible de Montes. Tomo I:239-247.

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