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Article ; Online: The trichome pattern diversity of Cardamine shares genetic mechanisms with Arabidopsis but differs in environmental drivers.

Fuster-Pons, Alberto / Murillo-Sánchez, Alba / Méndez-Vigo, Belén / Marcer, Arnald / Pieper, Bjorn / Torres-Pérez, Rafael / Oliveros, Juan Carlos / Tsiantis, Miltos / Picó, Francisco Xavier / Alonso-Blanco, Carlos

Plant physiology

2024

Abstract: Natural variation in trichome pattern (amount and distribution) is prominent among populations of many angiosperms. However, the degree of parallelism in the genetic mechanisms underlying this diversity and its environmental drivers in different species ... ...

Abstract	Natural variation in trichome pattern (amount and distribution) is prominent among populations of many angiosperms. However, the degree of parallelism in the genetic mechanisms underlying this diversity and its environmental drivers in different species remain unclear. To address these questions, we analyzed the genomic and environmental bases of leaf trichome pattern diversity in Cardamine hirsuta, a relative of Arabidopsis (Arabidopsis thaliana). We characterized 123 wild accessions for their genomic diversity, leaf trichome patterns at different temperatures, and environmental adjustments. Nucleotide diversities and biogeographical distribution models identified two major genetic lineages with distinct demographic and adaptive histories. Additionally, C. hirsuta showed substantial variation in trichome pattern and plasticity to temperature. Trichome amount in C. hirsuta correlated positively with spring precipitation but negatively with temperature, which is opposite to climatic patterns in A. thaliana. Contrastingly, genetic analysis of C. hirsuta glabrous accessions indicated that, like for A. thaliana, glabrousness is caused by null mutations in ChGLABRA1 (ChGL1). Phenotypic genome-wide association studies (GWAS) further identified a ChGL1 haplogroup associated with low trichome density and ChGL1 expression. Therefore, a ChGL1 series of null and partial loss-of-function alleles accounts for the parallel evolution of leaf trichome pattern in C. hirsuta and A. thaliana. Finally, GWAS also detected other candidate genes (e.g. ChETC3, ChCLE17) that might affect trichome pattern. Accordingly, the evolution of this trait in C. hirsuta and A. thaliana shows partially conserved genetic mechanisms but is likely involved in adaptation to different environments.
Language	English
Publishing date	2024-04-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1093/plphys/kiae213
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Article ; Online: Spatiotemporal dynamics of genetic variation at the quantitative and molecular levels within a natural Arabidopsis thaliana population

Méndez‐Vigo, Belén / Castilla, Antonio R. / Gómez, Rocío / Marcer, Arnald / Alonso‐Blanco, Carlos / Picó, F. Xavier

Journal of Ecology. 2022 Nov., v. 110, no. 11 p.2701-2716

2022

Abstract: Evolutionary change begins at the population scale. Therefore, understanding adaptive variation requires the identification of the factors maintaining and shaping standing genetic variation at the within‐population level. Spatial and temporal ... ...

Abstract	Evolutionary change begins at the population scale. Therefore, understanding adaptive variation requires the identification of the factors maintaining and shaping standing genetic variation at the within‐population level. Spatial and temporal environmental heterogeneity represent ecological drivers of within‐population genetic variation, determining the evolutionary trajectory of populations along with random processes. Here, we focused on the effects of spatiotemporal heterogeneity on quantitative and molecular variation in a natural population of the annual plant Arabidopsis thaliana. We sampled 1093 individuals from a Spanish A. thaliana population across an area of 7.4 ha for 10 years (2012–2021). Based on a sample of 279 maternal lines, we estimated spatiotemporal variation in life‐history traits and fitness from a common garden experiment. We genotyped 884 individuals with nuclear microsatellites to estimate spatiotemporal variation in genetic diversity. We assessed spatial patterns by estimating spatial autocorrelation of traits and fine‐scale genetic structure. We analysed the relationships between phenotypic variation, geographical location and genetic relatedness, as well as the effects of environmental suitability and genetic rarity on phenotypic variation. The common garden experiment indicated that there was more temporal than spatial variation in life‐history traits and fitness. Despite the differences among years, genetic distance in ecologically relevant traits (e.g. flowering time) tended to be positively correlated to genetic distance among maternal lines, while isolation by distance was less important. Genetic diversity exhibited significant spatial structure at short distances, which were consistent among years. Finally, genetic rarity, and not environmental suitability, accounted for genetic variation in life‐history traits. Synthesis. Our study highlighted the importance of repeated sampling to detect the large amount of genetic diversity at the quantitative and molecular levels that a single A. thaliana population can harbour. Overall, population genetic attributes estimated from our long‐term monitoring scheme (genetic relatedness and genetic rarity), rather than biological (dispersal) or ecological (vegetation types and environmental suitability) factors, emerged as the most important drivers of within‐population structure of phenotypic variation in A. thaliana.
Keywords	Arabidopsis thaliana ; annuals ; autocorrelation ; ecology ; genetic distance ; genetic relationships ; genetic structure ; genetic variation ; life history ; microsatellite repeats ; phenotypic variation ; vegetation
Language	English
Dates of publication	2022-11
Size	p. 2701-2716.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	3023-5
ISSN	0022-0477
ISSN	0022-0477
DOI	10.1111/1365-2745.13981
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Article: Quantifying temporal change in plant population attributes: insights from a resurrection approach.

Gómez, Rocío / Méndez-Vigo, Belén / Marcer, Arnald / Alonso-Blanco, Carlos / Picó, F Xavier

AoB PLANTS

2018 Volume 10, Issue 5, Page(s) ply063

Abstract: Rapid evolution in annual plants can be quantified by comparing phenotypic and genetic changes between past and contemporary individuals from the same populations over several generations. Such knowledge will help understand the response of plants to ... ...

Abstract	Rapid evolution in annual plants can be quantified by comparing phenotypic and genetic changes between past and contemporary individuals from the same populations over several generations. Such knowledge will help understand the response of plants to rapid environmental shifts, such as the ones imposed by global climate change. To that end, we undertook a resurrection approach in Spanish populations of the annual plant
Language	English
Publishing date	2018-10-10
Publishing country	England
Document type	Journal Article
ISSN	2041-2851
ISSN	2041-2851
DOI	10.1093/aobpla/ply063
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Article ; Online: Ecological, genetic and evolutionary drivers of regional genetic differentiation in Arabidopsis thaliana.

Castilla, Antonio R / Méndez-Vigo, Belén / Marcer, Arnald / Martínez-Minaya, Joaquín / Conesa, David / Picó, F Xavier / Alonso-Blanco, Carlos

BMC evolutionary biology

2020 Volume 20, Issue 1, Page(s) 71

Abstract: Background: Disentangling the drivers of genetic differentiation is one of the cornerstones in evolution. This is because genetic diversity, and the way in which it is partitioned within and among populations across space, is an important asset for the ... ...

Abstract	Background: Disentangling the drivers of genetic differentiation is one of the cornerstones in evolution. This is because genetic diversity, and the way in which it is partitioned within and among populations across space, is an important asset for the ability of populations to adapt and persist in changing environments. We tested three major hypotheses accounting for genetic differentiation-isolation-by-distance (IBD), isolation-by-environment (IBE) and isolation-by-resistance (IBR)-in the annual plant Arabidopsis thaliana across the Iberian Peninsula, the region with the largest genomic diversity. To that end, we sampled, genotyped with genome-wide SNPs, and analyzed 1772 individuals from 278 populations distributed across the Iberian Peninsula. Results: IBD, and to a lesser extent IBE, were the most important drivers of genetic differentiation in A. thaliana. In other words, dispersal limitation, genetic drift, and to a lesser extent local adaptation to environmental gradients, accounted for the within- and among-population distribution of genetic diversity. Analyses applied to the four Iberian genetic clusters, which represent the joint outcome of the long demographic and adaptive history of the species in the region, showed similar results except for one cluster, in which IBR (a function of landscape heterogeneity) was the most important driver of genetic differentiation. Using spatial hierarchical Bayesian models, we found that precipitation seasonality and topsoil pH chiefly accounted for the geographic distribution of genetic diversity in Iberian A. thaliana. Conclusions: Overall, the interplay between the influence of precipitation seasonality on genetic diversity and the effect of restricted dispersal and genetic drift on genetic differentiation emerges as the major forces underlying the evolutionary trajectory of Iberian A. thaliana.
MeSH term(s)	Arabidopsis/genetics ; Environment ; Evolution, Molecular ; Genetic Drift ; Genetic Variation ; Genome, Plant/genetics ; Genotype
Language	English
Publishing date	2020-06-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041493-6
ISSN	1471-2148 ; 1471-2148
ISSN (online)	1471-2148
ISSN	1471-2148
DOI	10.1186/s12862-020-01635-2
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Article: An ecological history of the relict genetic lineage of Arabidopsis thaliana

Toledo, Bernardo / Alonso-Blanco, Carlos / Marcer, Arnald / Méndez-Vigo, Belén / Picó, F. Xavier

Environmental and experimental botany. 2019 June 24,

2019

Abstract: The combination of extensive population sampling with whole-genome sequencing in the annual plant Arabidopsis thaliana has recently allowed the identification of a genetically differentiated relict lineage. The most important nuclei of relict A. thaliana ...

Abstract	The combination of extensive population sampling with whole-genome sequencing in the annual plant Arabidopsis thaliana has recently allowed the identification of a genetically differentiated relict lineage. The most important nuclei of relict A. thaliana is found in the Iberian Peninsula and North Africa, although relict accessions have also been found scattered across Atlantic oceanic islands, eastern Mediterranean Basin, South and East Africa and China. We hypothesised that relict A. thaliana long survived and adapted to a wide array of environments in the Iberian Peninsula and North Africa due to the fact that the region repeatedly acted as glacial refugia. Given the lack of evidence to support this hypothesis, we addressed this issue by studying the ecological history of Iberian and North African relict A. thaliana. To this end, we analysed the relationship between the current habitat suitability of relict A. thaliana, estimated with species distribution models, and the vegetation dynamics in the region over the last millennia using pollen fossil data from sediment cores and reconstructions of past distribution ranges of the most important tree species occurring in the region. Overall, our results indicated that a higher current habitat suitability of relict A. thaliana was correlated with more stable vegetation dynamics since the Last Glacial Maximum and during the Holocene. Given that relict A. thaliana is known to harbour genetic variation specific to its relict nature, we also evaluated the differentiation between relict and non-relict A. thaliana accessions at the functional genetic level for the known flowering genes, CRY2 and TSF. Genomic surveys detected the existence of haplogroups of these genes occurring at very high frequency only among relict accessions. Overall, our study reinforced the relict character of this lineage thought to be at the base of the species' early history. We stress the need to sample in depth other geographic areas harbouring relict A. thaliana and conduct further functional genetic analyses between relict and non-relict accessions to keep disentangling the evolutionary trajectory of this annual plant.
Keywords	annuals ; Arabidopsis thaliana ; flowering ; fossils ; genes ; genetic analysis ; genetic variation ; genomics ; geographical distribution ; Holocene epoch ; islands ; models ; pollen ; refuge habitats ; sediments ; sequence analysis ; surveys ; trees ; vegetation ; China ; Eastern Africa ; Iberian Peninsula ; Mediterranean region ; Northern Africa
Language	English
Dates of publication	2019-0624
Publishing place	Elsevier B.V.
Document type	Article
Note	Pre-press version
ZDB-ID	195968-2
ISSN	0098-8472
ISSN	0098-8472
DOI	10.1016/j.envexpbot.2019.103800
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Article: Analytical methods in untargeted metabolomics: state of the art in 2015.

Alonso, Arnald / Marsal, Sara / Julià, Antonio

Frontiers in bioengineering and biotechnology

2015 Volume 3, Page(s) 23

Abstract: Metabolomics comprises the methods and techniques that are used to measure the small molecule composition of biofluids and tissues, and is actually one of the most rapidly evolving research fields. The determination of the metabolomic profile - the ... ...

Abstract	Metabolomics comprises the methods and techniques that are used to measure the small molecule composition of biofluids and tissues, and is actually one of the most rapidly evolving research fields. The determination of the metabolomic profile - the metabolome - has multiple applications in many biological sciences, including the developing of new diagnostic tools in medicine. Recent technological advances in nuclear magnetic resonance and mass spectrometry are significantly improving our capacity to obtain more data from each biological sample. Consequently, there is a need for fast and accurate statistical and bioinformatic tools that can deal with the complexity and volume of the data generated in metabolomic studies. In this review, we provide an update of the most commonly used analytical methods in metabolomics, starting from raw data processing and ending with pathway analysis and biomarker identification. Finally, the integration of metabolomic profiles with molecular data from other high-throughput biotechnologies is also reviewed.
Language	English
Publishing date	2015-03-05
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2015.00023
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Article ; Online: A hierarchical Bayesian Beta regression approach to study the effects of geographical genetic structure and spatial autocorrelation on species distribution range shifts.

Martínez-Minaya, Joaquín / Conesa, David / Fortin, Marie-Josée / Alonso-Blanco, Carlos / Picó, F Xavier / Marcer, Arnald

Molecular ecology resources

2019 Volume 19, Issue 4, Page(s) 929–943

Abstract: Global climate change (GCC) may be causing distribution range shifts in many organisms worldwide. Multiple efforts are currently focused on the development of models to better predict distribution range shifts due to GCC. We addressed this issue by ... ...

Abstract	Global climate change (GCC) may be causing distribution range shifts in many organisms worldwide. Multiple efforts are currently focused on the development of models to better predict distribution range shifts due to GCC. We addressed this issue by including intraspecific genetic structure and spatial autocorrelation (SAC) of data in distribution range models. Both factors reflect the joint effect of ecoevolutionary processes on the geographical heterogeneity of populations. We used a collection of 301 georeferenced accessions of the annual plant Arabidopsis thaliana in its Iberian Peninsula range, where the species shows strong geographical genetic structure. We developed spatial and nonspatial hierarchical Bayesian models (HBMs) to depict current and future distribution ranges for the four genetic clusters detected. We also compared the performance of HBMs with Maxent (a presence-only model). Maxent and nonspatial HBMs presented some shortcomings, such as the loss of accessions with high genetic admixture in the case of Maxent and the presence of residual SAC for both. As spatial HBMs removed residual SAC, these models showed higher accuracy than nonspatial HBMs and handled the spatial effect on model outcomes. The ease of modelling and the consistency among model outputs for each genetic cluster was conditioned by the sparseness of the populations across the distribution range. Our HBMs enrich the toolbox of software available to evaluate GCC-induced distribution range shifts by considering both genetic heterogeneity and SAC, two inherent properties of any organism that should not be overlooked.
MeSH term(s)	Africa, Northern ; Arabidopsis/classification ; Arabidopsis/genetics ; Genetics, Population/methods ; Peptides ; Phylogeography ; Plant Dispersal ; Portugal ; Spain ; Spatial Analysis
Chemical Substances	Peptides ; iberiotoxin (773HER9B6T)
Language	English
Publishing date	2019-05-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13024
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Article: A hierarchical Bayesian Beta regression approach to study the effects of geographical genetic structure and spatial autocorrelation on species distribution range shifts

Martínez‐Minaya, Joaquín / Conesa, David / Fortin, Marie‐Josée / Alonso‐Blanco, Carlos / Picó, F. Xavier / Marcer, Arnald

Molecular ecology resources. 2019 July, v. 19, no. 4

2019

Abstract	Global climate change (GCC) may be causing distribution range shifts in many organisms worldwide. Multiple efforts are currently focused on the development of models to better predict distribution range shifts due to GCC. We addressed this issue by including intraspecific genetic structure and spatial autocorrelation (SAC) of data in distribution range models. Both factors reflect the joint effect of ecoevolutionary processes on the geographical heterogeneity of populations. We used a collection of 301 georeferenced accessions of the annual plant Arabidopsis thaliana in its Iberian Peninsula range, where the species shows strong geographical genetic structure. We developed spatial and nonspatial hierarchical Bayesian models (HBMs) to depict current and future distribution ranges for the four genetic clusters detected. We also compared the performance of HBMs with Maxent (a presence‐only model). Maxent and nonspatial HBMs presented some shortcomings, such as the loss of accessions with high genetic admixture in the case of Maxent and the presence of residual SAC for both. As spatial HBMs removed residual SAC, these models showed higher accuracy than nonspatial HBMs and handled the spatial effect on model outcomes. The ease of modelling and the consistency among model outputs for each genetic cluster was conditioned by the sparseness of the populations across the distribution range. Our HBMs enrich the toolbox of software available to evaluate GCC‐induced distribution range shifts by considering both genetic heterogeneity and SAC, two inherent properties of any organism that should not be overlooked.
Keywords	Arabidopsis thaliana ; Bayesian theory ; annuals ; autocorrelation ; climate change ; computer software ; genetic heterogeneity ; geographical distribution ; georeferencing ; models ; regression analysis ; Iberian Peninsula
Language	English
Dates of publication	2019-07
Size	p. 929-943.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/1755-0998.13024
Database	NAL-Catalogue (AGRICOLA)

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Article: (with research data) Tackling intraspecific genetic structure in distribution models better reflects species geographical range.

Marcer, Arnald / Méndez-Vigo, Belén / Alonso-Blanco, Carlos / Picó, F Xavier

Ecology and evolution

2016 Volume 6, Issue 7, Page(s) 2084–2097

Abstract: 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 ... ...

Abstract	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.
Language	English
Publishing date	2016-02-26
Publishing country	England
Document type	Journal Article
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.2010
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Article: Genome‐wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana

Tabas‐Madrid, Daniel / Alberto Pascual‐Montano / Arnald Marcer / Belén Méndez‐Vigo / Carlos Alonso‐Blanco / Detlef Weigel / F. Xavier Picó / Noelia Arteaga

Plant, cell and environment. 2018 Aug., v. 41, no. 8

2018

Abstract: 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 ... ...

Abstract	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.
Keywords	alleles ; annuals ; Arabidopsis thaliana ; climatic factors ; flowering date ; genetic variation ; genomics ; global change ; mountains ; non-specific serine/threonine protein kinase ; phenotype ; plant adaptation ; single nucleotide polymorphism ; temperature ; temporal variation ; Iberian Peninsula
Language	English
Dates of publication	2018-08
Size	p. 1806-1820.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	391893-2
ISSN	1365-3040 ; 0140-7791
ISSN (online)	1365-3040
ISSN	0140-7791
DOI	10.1111/pce.13189
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