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  • 1. Blair, M. W.
    et al.
    Soler, A.
    Cortés, Andrés J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Diversification and Population Structure in Common Beans (Phaseolus vulgaris L.)2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 11, p. e49488-Article in journal (Refereed)
    Abstract [en]

    Wild accessions of crops and landraces are valuable genetic resources for plant breeding and for conserving alleles and gene combinations in planta. The primary genepool of cultivated common beans includes wild accessions of Phaseolus vulgaris. These are of the same species as the domesticates and therefore are easily crossable with cultivated accessions. Molecular marker assessment of wild beans and landraces is important for the proper utilization and conservation of these important genetic resources. The goal of this research was to evaluate a collection of wild beans with fluorescent microsatellite or simple sequence repeat markers and to determine the population structure in combination with cultivated beans of all known races. Marker diversity in terms of average number of alleles per marker was high (13) for the combination of 36 markers and 104 wild genotypes that was similar to the average of 14 alleles per marker found for the 606 cultivated genotypes. Diversity in wild beans appears to be somewhat higher than in cultivated beans on a per genotype basis. Five populations or genepools were identified in structure analysis of the wild beans corresponding to segments of the geographical range, including Mesoamerican (Mexican), Guatemalan, Colombian, Ecuadorian-northern Peruvian and Andean (Argentina, Bolivia and Southern Peru). The combined analysis of wild and cultivated accessions showed that the first and last of these genepools were related to the cultivated genepools of the same names and the penultimate was found to be distinct but not ancestral to the others. The Guatemalan genepool was very novel and perhaps related to cultivars of race Guatemala, while the Colombian population was also distinct. Results suggest geographic isolation, founder effects or natural selection could have created the different semi-discrete populations of wild beans and that multiple domestications and introgression were involved in creating the diversity of cultivated beans.

  • 2.
    Blair, Matthew W.
    et al.
    Department of Plant Breeding and Genetics, Cornell University.
    Cortés, Andres J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Penmetsa, R.Varma
    University of California, Davis.
    Farmer, Andrew
    National Center for Genomic Research, Albuquerque.
    Carrasquilla-Garcia, Noelia
    University of California, Davis.
    Cook, Doug R.
    University of California, Davis.
    A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.)2013In: Theoretical and Applied Genetics, ISSN 0040-5752, E-ISSN 1432-2242, Vol. 126, no 2, p. 535-548Article in journal (Refereed)
    Abstract [en]

    Single nucleotide polymorphism (SNP) detection has become a marker system of choice, because of the high abundance of source polymorphisms and the ease with which allele calls are automated. Various technologies exist for the evaluation of SNP loci and previously we validated two medium throughput technologies. In this study, our goal was to utilize a 768 feature, Illumina GoldenGate assay for common bean (Phaseolus vulgaris L.) developed from conserved legume gene sequences and to use the new technology for (1) the evaluation of parental polymorphisms in a mini-core set of common bean accessions and (2) the analysis of genetic diversity in the crop. A total of 736 SNPs were scored on 236 diverse common bean genotypes with the GoldenGate array. Missing data and heterozygosity levels were low and 94 % of the SNPs were scorable. With the evaluation of the parental polymorphism genotypes, we estimated the utility of the SNP markers in mapping for inter-genepool and intra-genepool populations, the latter being of lower polymorphism than the former. When we performed the diversity analysis with the diverse genotypes, we found Illumina GoldenGate SNPs to provide equivalent evaluations as previous gene-based SNP markers, but less fine-distinctions than with previous microsatellite marker analysis. We did find, however, that the gene-based SNPs in the GoldenGate array had some utility in race structure analysis despite the low polymorphism. Furthermore the SNPs detected high heterozygosity in wild accessions which was probably a reflection of ascertainment bias. The Illumina SNPs were shown to be effective in distinguishing between the genepools, and therefore were most useful in saturation of inter-genepool genetic maps. The implications of these results for breeding in common bean are discussed as well as the advantages and disadvantages of the GoldenGate system for SNP detection.

  • 3. Blair, Matthew W.
    et al.
    Cortés, Andrés J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    This, Dominique
    Identification of an ERECTA gene and drought adaptation associations in wild and cultivated common bean2016In: Plant Science, ISSN 0168-9452, E-ISSN 1873-2259, Vol. 242, p. 250-259Article in journal (Refereed)
    Abstract [en]

    In this research, we cloned and accessed nucleotide diversity in the common beanERECTA gene which has been implicated in drought tolerance and stomatal patterning.The homologous gene segment was isolated with degenerate primer and was found to be located on Chromosome 1. The gene had at least one paralog on Chromosome 9 and duplicate copies in soybean for each homolog. ERECTA-like genes were also discovered but the function of these was of less interest due to low similarity with the ERECTA gene from Arabidopsis. The diversity of the 5’ end of the large Chr. 1 PvERECTA gene was evaluated in a collection of 145 wild and cultivated common beans that were also characterized by geographic source and drought tolerance, respectively. Our wild population sampled a range of wet to dry habitats, while our cultivated samples were representative of landrace diversity and the patterns of nucleotide variation differed between groups. The 5’ region exhibited lower levels of diversity in the cultivated collection, which was indicative of population bottlenecks associated with the domestication process, compared to the wild collection where diversity was associated with ecological differences. We discuss associations of nucleotide diversity at PvERECTA with drought tolerance prediction for the genotypes.

  • 4.
    Cortes, Andres J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Monserrate, Fredy A.
    Ramirez-Villegas, Julian
    Madrinan, Santiago
    Blair, Matthew W.
    Drought Tolerance in Wild Plant Populations: The Case of Common Beans (Phaseolus vulgaris L.)2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 5, p. e62898-Article in journal (Refereed)
    Abstract [en]

    Reliable estimations of drought tolerance in wild plant populations have proved to be challenging and more accessible alternatives are desirable. With that in mind, an ecological diversity study was conducted based on the geographical origin of 104 wild common bean accessions to estimate drought tolerance in their natural habitats. Our wild population sample covered a range of mesic to very dry habitats from Mexico to Argentina. Two potential evapotranspiration models that considered the effects of temperature and radiation were coupled with the precipitation regimes of the last fifty years for each collection site based on geographical information system analysis. We found that wild accessions were distributed among different precipitation regimes following a latitudinal gradient and that habitat ecological diversity of the collection sites was associated with natural sub-populations. We also detected a broader geographic distribution of wild beans across ecologies compared to cultivated common beans in a reference collection of 297 cultivars. Habitat drought stress index based on the Thornthwaite potential evapotranspiration model was equivalent to the Hamon estimator. Both ecological drought stress indexes would be useful together with population structure for the genealogical analysis of gene families in common bean, for genome-wide genetic-environmental associations, and for postulating the evolutionary history and diversification processes that have occurred for the species. Finally, we propose that wild common bean should be taken into account to exploit variation for drought tolerance in cultivated common bean which is generally considered susceptible as a crop to drought stress.

  • 5.
    Cortes, Andres J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    This, Dominique
    Chavarro, Carolina
    Madrinan, Santiago
    Blair, Matthew W.
    Nucleotide diversity patterns at the drought-related DREB2 encoding genes in wild and cultivated common bean (Phaseolus vulgaris L.)2012In: Theoretical and Applied Genetics, ISSN 0040-5752, E-ISSN 1432-2242, Vol. 125, no 5, p. 1069-1085Article in journal (Refereed)
    Abstract [en]

    Common beans are an important food legume faced with a series of abiotic stresses the most severe of which is drought. The crop is interesting as a model for the analysis of gene phylogenies due to its domestication process, race structure, and origins in a group of wild common beans found along the South American Andes and the region of Mesoamerica. Meanwhile, the DREB2 transcription factors have been implicated in controlling non-ABA dependent responses to drought stress. With this in mind our objective was to study in depth the genetic diversity for two DREB2 genes as possible candidates for association with drought tolerance through a gene phylogenetic analysis. In this genetic diversity assessment, we analyzed nucleotide diversity at the two candidate genes Dreb2A and Dreb2B, in partial core collections of 104 wild and 297 cultivated common beans with a total of 401 common bean genotypes from world-wide germplasm analyzed. Our wild population sample covered a range of semi-mesic to very dry habitats, while our cultivated samples presented a wide spectrum of low to high drought tolerance. Both genes showed very different patterns of nucleotide variation. Dreb2B exhibited very low nucleotide diversity relative to neutral reference loci previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, Dreb2A exhibited higher levels of nucleotide diversity, which is indicative of adaptive selection and population expansion. These patterns were more distinct in wild compared to cultivated common beans. These approximations suggested the importance of Dreb2 genes in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits. We discuss the utility of allele mining in the DREB gene family for the discovery of new drought tolerance traits from wild common bean.

  • 6.
    Cortes, Andres J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Waeber, S.
    Lexer, C.
    Sedlacek, J.
    Wheeler, J. A.
    van Kleunen, M.
    Bossdorf, O.
    Hoch, G.
    Rixen, C.
    Wipf, S.
    Karrenberg, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Small-scale patterns in snowmelt timing affect gene flow and the distribution of genetic diversity in the alpine dwarf shrub Salix herbacea2014In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 113, no 3, p. 233-239Article in journal (Refereed)
    Abstract [en]

    Current threats to biodiversity, such as climate change, are thought to alter the within-species genetic diversity among microhabitats in highly heterogeneous alpine environments. Assessing the spatial organization and dynamics of genetic diversity within species can help to predict the responses of organisms to environmental change. In this study, we evaluated whether small-scale heterogeneity in snowmelt timing restricts gene flow between microhabitats in the common long-lived dwarf shrub Salix herbacea L. We surveyed 273 genets across 12 early-and late-snowmelt sites (that is, ridges and snowbeds) in the Swiss Alps for phenological variation over 2 years and for genetic variation using seven SSR markers. Phenological differentiation triggered by differences in snowmelt timing did not correlate with genetic differentiation between microhabitats. On the contrary, extensive gene flow appeared to occur between microhabitats and slightly less extensively among adjacent mountains. However, ridges exhibited significantly lower levels of genetic diversity than snowbeds, and patterns of effective population size (Ne) and migration (Nem) between microhabitats were strongly asymmetric, with ridges acting as sources and snowbeds as sinks. As no recent genetic bottlenecks were detected in the studied sites, this asymmetry is likely to reflect current metapopulation dynamics of the species dominated by gene flow via seeds rather than ancient re-colonization after the last glacial period. Overall, our results suggest that seed dispersal prevents snowmelt-driven genetic isolation, and snowbeds act as sinks of genetic diversity. We discuss the consequences of such small-scale variation in gene flow and diversity levels for population responses to climate change.

  • 7. Cortes, Andrés J
    et al.
    Chavarro, MC
    Blair, MW
    SNP marker diversity in common bean (Phaseolus vulgaris L.)2011In: Theoretical and Applied Genetics, ISSN 0040-5752, E-ISSN 1432-2242, Vol. 123, no 5, p. 827-845Article in journal (Refereed)
  • 8.
    Cortés, Andres J,
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    On the origin of the Common Bean (Phaseolus vulgaris L.)2013In: American Journal of Plant Sciences, ISSN 2158-2742, E-ISSN 2158-2750, Vol. 4, no 10, p. 1998-2000Article in journal (Refereed)
    Abstract [en]

    Phylogeographic methods provide the tools to accurately access the geographic origin and diversification of crop species. In the present commentary, I urge the common bean community to face those methods and a tree-thinking mentality with regards to the long standing debate of the origin of common bean. Such efforts will ultimately bring back interest into wild bean studies and reinforce the uniqueness of this species as a system to study diversification, domestication and adaptive processes across the two most diverse hotspots in the world.

  • 9.
    Cortés, Andrés J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    On The Big Challenges of a Small Shrub: Ecological Genetics of Salix herbacea L2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The response of plants to climate change is among the main questions in ecology and evolution. Faced with changing conditions, populations may respond by adapting, going extinct or migrating. Fine-scale environmental variation offers a unique mosaic to explore these alternatives. In this thesis, I used ecological surveys, field experiments and molecular methods to study the range of possible responses at a very local scale in the alpine dwarf willow Salix herbacea L. Since gene flow may impact the potential for adaptation and migration, I first explored whether phenological divergence driven by snowmelt patterns impacts gene flow. I found that sites with late snowmelt work as sinks of the genetic diversity, as compared to sites with early snowmelt. I also used a combined approach that looked at the selection, heritability and genomic architecture of ecologically-relevant traits, as well as genomic divergence across the snowmelt mosaic. In this way, I was able to understand which genomic regions may relate to phenological, growth and fitness traits, and which regions in the genome harbor genetic variation associated with late- and early- snowmelt sites. I found that most of the genomic divergence driven by snowmelt is novel and is localized in few regions. Also, Salix herbacea has a strong female bias. Sex bias may matter for adaptation to climate change because different sexes of many dioecious species differ in several functions that may fluctuate with changing conditions. I found that the bias is uniform across environments and is already present at seeds and seedlings. A polygenic sex determination system together with transmission distortion may be maintaining the bias. Overall, fast-evolving microhabitat-driven genomic divergence and, at the same time, genetically-based trait variation at a larger scale may play a role for the ability of S. herbacea to persist in diverse and variable conditions.

    List of papers
    1. Small-scale patterns in snowmelt timing affect gene flow and the distribution of genetic diversity in the alpine dwarf shrub Salix herbacea
    Open this publication in new window or tab >>Small-scale patterns in snowmelt timing affect gene flow and the distribution of genetic diversity in the alpine dwarf shrub Salix herbacea
    Show others...
    2014 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 113, no 3, p. 233-239Article in journal (Refereed) Published
    Abstract [en]

    Current threats to biodiversity, such as climate change, are thought to alter the within-species genetic diversity among microhabitats in highly heterogeneous alpine environments. Assessing the spatial organization and dynamics of genetic diversity within species can help to predict the responses of organisms to environmental change. In this study, we evaluated whether small-scale heterogeneity in snowmelt timing restricts gene flow between microhabitats in the common long-lived dwarf shrub Salix herbacea L. We surveyed 273 genets across 12 early-and late-snowmelt sites (that is, ridges and snowbeds) in the Swiss Alps for phenological variation over 2 years and for genetic variation using seven SSR markers. Phenological differentiation triggered by differences in snowmelt timing did not correlate with genetic differentiation between microhabitats. On the contrary, extensive gene flow appeared to occur between microhabitats and slightly less extensively among adjacent mountains. However, ridges exhibited significantly lower levels of genetic diversity than snowbeds, and patterns of effective population size (Ne) and migration (Nem) between microhabitats were strongly asymmetric, with ridges acting as sources and snowbeds as sinks. As no recent genetic bottlenecks were detected in the studied sites, this asymmetry is likely to reflect current metapopulation dynamics of the species dominated by gene flow via seeds rather than ancient re-colonization after the last glacial period. Overall, our results suggest that seed dispersal prevents snowmelt-driven genetic isolation, and snowbeds act as sinks of genetic diversity. We discuss the consequences of such small-scale variation in gene flow and diversity levels for population responses to climate change.

    National Category
    Genetics Ecology
    Identifiers
    urn:nbn:se:uu:diva-232992 (URN)10.1038/hdy.2014.19 (DOI)000341087900006 ()
    Available from: 2014-10-13 Created: 2014-09-29 Last updated: 2017-12-05Bibliographically approved
    2. Evolutionary potential in the Alpine: trait heritabilities and performance variation of the dwarf willow Salix herbacea from different elevations and microhabitats
    Open this publication in new window or tab >>Evolutionary potential in the Alpine: trait heritabilities and performance variation of the dwarf willow Salix herbacea from different elevations and microhabitats
    Show others...
    2016 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 6, no 12, p. 3940-3952Article in journal (Refereed) Published
    Abstract [en]

    Alpine ecosystems are seriously threatened by climate change. One of the key mechanisms by which plants can adapt to changing environmental conditions is through evolutionary change. However, we still know little about the evolutionary potential in wild populations of long-lived alpine plants. Here, we investigated heritabilities of phenological traits, leaf size, and performance traits in natural populations of the long-lived alpine dwarf shrub Salix herbacea using relatedness estimates inferred from SSR (Simple Sequence Repeat) markers. Salix herbacea occurs in early-and late-snowmelt microhabitats (ridges and snowbeds), and we assessed how performance consequences of phenological traits and leaf size differ between these microhabitats in order to infer potential for evolutionary responses. Salix herbacea showed low, but significant, heritabilities of leaf size, clonal and sexual reproduction, and moderate heritabilities of phenological traits. In both microhabitats, we found that larger leaves, longer intervals between snowmelt and leaf expansion, and longer GDD (growing-degree days) until leaf expansion resulted in a stronger increase in the number of stems (clonal reproduction). In snowbeds, clonal reproduction increased with a shorter GDD until flowering, while the opposite was found on ridges. Furthermore, the proportion of flowering stems increased with GDD until flowering in both microhabitats. Our results suggest that the presence of significant heritable variation in morphology and phenology might help S. herbacea to adapt to changing environmental conditions. However, it remains to be seen if the rate of such an evolutionary response can keep pace with the rapid rate of climate change.

    Keywords
    Adaptive evolution; alpine ecosystem; animal model; long-lived plants; snowmelt microhabitats; SSR markers
    National Category
    Botany
    Identifiers
    urn:nbn:se:uu:diva-262237 (URN)10.1002/ece3.2171 (DOI)000379342900008 ()
    Available from: 2015-09-10 Created: 2015-09-10 Last updated: 2017-12-05Bibliographically approved
    3. Genome-wide patterns of microhabitat-driven divergence in the alpine dwarf shrub Salix herbacea L.
    Open this publication in new window or tab >>Genome-wide patterns of microhabitat-driven divergence in the alpine dwarf shrub Salix herbacea L.
    (English)Manuscript (preprint) (Other academic)
    National Category
    Botany
    Identifiers
    urn:nbn:se:uu:diva-262229 (URN)
    Available from: 2015-09-10 Created: 2015-09-10 Last updated: 2015-11-23
    4. Maintenance of female-bias in a polygenic sex determination system is consistent with genomic conflict
    Open this publication in new window or tab >>Maintenance of female-bias in a polygenic sex determination system is consistent with genomic conflict
    (English)Manuscript (preprint) (Other academic)
    National Category
    Botany
    Identifiers
    urn:nbn:se:uu:diva-262230 (URN)
    Available from: 2015-09-10 Created: 2015-09-10 Last updated: 2015-11-23
  • 10.
    Cortés, Andrés J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Carolina Chavarro, M.
    Madrinan, Santiago
    This, Dominique
    Blair, Matthew W.
    Molecular ecology and selection in the drought-related Asr gene polymorphisms in wild and cultivated common bean (Phaseolus vulgaris L.)2012In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 13, p. 58-Article in journal (Refereed)
    Abstract [en]

    Background: The abscisic acid (ABA) pathway plays an important role in the plants' reaction to drought stress and ABA-stress response (Asr) genes are important in controlling this process. In this sense, we accessed nucleotide diversity at two candidate genes for drought tolerance (Asr1 and Asr2), involved in an ABA signaling pathway, in the reference collection of cultivated common bean (Phaseolus vulgaris L.) and a core collection of wild common bean accessions. Results: Our wild population samples covered a range of mesic (semi-arid) to very dry (desert) habitats, while our cultivated samples presented a wide spectrum of drought tolerance. Both genes showed very different patterns of nucleotide variation. Asr1 exhibited very low nucleotide diversity relative to the neutral reference loci that were previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, Asr2 exhibited higher levels of nucleotide diversity, which is indicative of adaptive selection. These patterns were more notable in wild beans than in cultivated common beans indicting that natural selection has played a role over long time periods compared to farmer selection since domestication. Conclusions: Together these results suggested the importance of Asr1 in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits. Furthermore, one of our major successes was to find that wild common bean is a reservoir of genetic variation and selection signatures at Asr genes, which may be useful for breeding drought tolerance in cultivated common bean.

  • 11. Galeano, C.H.
    et al.
    Cortés, Andres J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Fernandez, A.C.
    Soler, A.
    Franco-Herrera, N.
    Makunde, G.
    Vanderleyden, J.
    Blair, M.W.
    Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean2012In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 12, article id 48Article in journal (Refereed)
    Abstract [en]

    Background: In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. 

    Results: In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 x G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 x JALO EEP558 and DOR364 x BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. 

    Conclusions: In short, this study illustrates the power of intron-based markers for linkage and association mapping in common bean. The utility of these markers is discussed in relation with the usefulness of microsatellites, the molecular markers by excellence in this crop.

  • 12. Kelleher, CT
    et al.
    Wilkin, J
    Zhuang, J
    Cortés, Andrés Javier
    School of Biology and Environmental Science, University College Dublin, Ireland.
    Perez, AL
    Gallagher, TF
    Bohlmann, J
    Douglas, CJ
    Ritland, K
    SNP discovery, gene diversity, and linkage disequilibrium in wild populations of Populus tremuloides2012In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 8, no 4, p. 821-829Article in journal (Refereed)
    Abstract [en]

    The use of single-nucleotide polymorphisms (SNPs) as molecular markers in plant studies has become increasingly common. With the development of these markers, there is an interest in determining levels of variation in natural populations. Here, we identify and characterize levels of SNPs in wild populations of aspen ( Populus tremuloides Michx.). Four populations were sampled from Alberta and British Columbia in Western Canada. A total of 35 gene regions were selected for analysis. The loci selected are mainly involved in wood formation and include regions from genes for lignin biosynthesis, cellulose biosynthesis, and other cell wall compounds and a number of transcription factors. Other genes included those coding for growth hormones, disease resistance, and light responses. Primers were developed from conserved regions in multi-species EST alignments. Regions were PCR amplified, and products (approximately 500 to 1,000 bp) were assessed for levels of SNPs using Ecotilling. From a total of approximately 25 kb 462 SNPs were identified, over 18 SNPs/kb. Thus, SNPs are an abundant and potentially useful molecular marker in aspen. Gene diversity (heterozygosity) varied in the gene regions, with an overall average of H = 0.18. Although gene diversity was considerable, genetic differentiation was low with the overall F value being 0.004. A surrogate measure of linkage disequilibrium (LD) was calculated, and overall, the LD was shown to decay relatively rapidly with distance along the gene region. The results obtained from the wood formation genes in this study will enable further targeting of regions for association studies on lignin and cellulose variation in aspen and other Populus species.

  • 13. Little, CJ
    et al.
    Wheeler, JA
    Sedlacek, J
    Cortés, Andrés J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Rixen, C
    Small-scale drivers: the importance of nutrient availability and snowmelt timing on performance of the alpine shrub Salix herbacea2016In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 180, no 4, p. 1015-1024Article in journal (Refereed)
    Abstract [en]

    Alpine plant communities are predicted to face range shifts and possibly extinctions with climate change. Fine-scale environmental variation such as nutrient availability or snowmelt timing may contribute to the ability of plant species to persist locally; however, variation in nutrient availability in alpine landscapes is largely unmeasured. On three mountains around Davos, Switzerland, we deployed Plant Root Simulator probes around 58 Salix herbacea plants along an elevational and microhabitat gradient to measure nutrient availability during the first 5 weeks of the summer growing season, and used in situ temperature loggers and observational data to determine date of spring snowmelt. We also visited the plants weekly to assess performance, as measured by stem number, fruiting, and herbivory damage. We found a wide snowmelt gradient which determined growing season length, as well as variations of an order of magnitude or more in the accumulation of 12 nutrients between different microhabitats. Higher nutrient availability had negative effects on most shrub performance metrics, for instance decreasing stem number and the proportion of stems producing fruits. High nutrient availability was associated with increased herbivory damage in early-melting microhabitats, but among late-emerging plants this pattern was reversed. We demonstrate that nutrient availability is highly variable in alpine settings, and that it strongly influences performance in an alpine dwarf shrub, sometimes modifying the response of shrubs to snowmelt timing. As the climate warms and human-induced nitrogen deposition continues in the Alps, these factors may contribute to patterns of local plants persistence.

  • 14. Madrinan, Santiago
    et al.
    Cortés, Andres
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Richardson, James E.
    Páramo is the world’s fastest evolving and coolest biodiversity hotspot2013In: Frontiers in Genetics, ISSN 1664-8021, E-ISSN 1664-8021, Vol. 4, p. 192-Article in journal (Refereed)
    Abstract [en]

    Understanding the processes that cause speciation is a key aim of evolutionary biology. Lineages or biomes that exhibit recent and rapid diversification are ideal model systems for determining these processes. Species rich biomes reported to be of relatively recent origin, i.e., since the beginning of the Miocene, include Mediterranean ecosystems such as the California Floristic Province, oceanic islands such as the Hawaiian archipelago and the Neotropical high elevation ecosystem of the Páramos. Páramos constitute grasslands above the forest tree-line (at elevations of c. 2800–4700 m) with high species endemism. Organisms that occupy this ecosystem are a likely product of unique adaptations to an extreme environment that evolved during the last three to five million years when the Andes reached an altitude that was capable of sustaining this type of vegetation. We compared net diversification rates of lineages in fast evolving biomes using 73 dated molecular phylogenies. Based on our sample, we demonstrate that average net diversification rates of Páramo plant lineages are faster than those of other reportedly fast evolving hotspots and that the faster evolving lineages are more likely to be found in Páramos than the other hotspots. Páramos therefore represent the ideal model system for studying diversification processes. Most of the speciation events that we observed in the Páramos (144 out of 177) occurred during the Pleistocene possibly due to the effects of species range contraction and expansion that may have resulted from the well-documented climatic changes during that period. Understanding these effects will assist with efforts to determine how future climatic changes will impact plant populations.

  • 15.
    Sedlacek, Janosch
    et al.
    Univ Konstanz, Dept Biol, Ecol, Univ Str 10, D-78457 Constance, Germany.
    Cortés, Andrés
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Swedish Agr Univ, Dept Plant Biol, Undervisningsplan 7E, S-75007 Uppsala, Sweden.
    Wheeler, Julia
    WSL Inst Snow & Avalanche Res SLF, Fluelastr 11, CH-7260 Davos, Switzerland;Univ Basel, Inst Bot, Schonbeinstr 6, CH-4056 Basel, Switzerland;Univ Massachusetts, Dept Environm Conservat, Amherst, MA 01003 USA.
    Bossdorf, Oliver
    Univ Tubingen, Plant Evolutionary Ecol, Inst Evolut & Ecol, Morgenstelle 5, D-72076 Tubingen, Germany.
    Hoch, Guenter
    Univ Basel, Inst Bot, Schonbeinstr 6, CH-4056 Basel, Switzerland.
    Klapste, Jaroslav
    Univ British Columbia, Dept Forest & Conservat Sci, Fac Forestry, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada;Czech Univ Life Sci Prague, Dept Genet & Physiol Forest Trees, Fac Forestry & Wood Sci, Kamycka 129, Prague 16521 6, Czech Republic;Univ Massachusetts, Dept Environm Conservat, Amherst, MA 01003 USA.
    Lexer, Christian
    Univ Vienna, Dept Bot & Biodivers Res, Rennweg 14, A-1030 Vienna, Austria.
    Rixen, Christian
    WSL Inst Snow & Avalanche Res SLF, Fluelastr 11, CH-7260 Davos, Switzerland.
    Wipf, Sonja
    WSL Inst Snow & Avalanche Res SLF, Fluelastr 11, CH-7260 Davos, Switzerland.
    Karrenberg, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    van Kleunen, Mark
    Univ Konstanz, Dept Biol, Ecol, Univ Str 10, D-78457 Constance, Germany.
    Evolutionary potential in the Alpine: trait heritabilities and performance variation of the dwarf willow Salix herbacea from different elevations and microhabitats2016In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 6, no 12, p. 3940-3952Article in journal (Refereed)
    Abstract [en]

    Alpine ecosystems are seriously threatened by climate change. One of the key mechanisms by which plants can adapt to changing environmental conditions is through evolutionary change. However, we still know little about the evolutionary potential in wild populations of long-lived alpine plants. Here, we investigated heritabilities of phenological traits, leaf size, and performance traits in natural populations of the long-lived alpine dwarf shrub Salix herbacea using relatedness estimates inferred from SSR (Simple Sequence Repeat) markers. Salix herbacea occurs in early-and late-snowmelt microhabitats (ridges and snowbeds), and we assessed how performance consequences of phenological traits and leaf size differ between these microhabitats in order to infer potential for evolutionary responses. Salix herbacea showed low, but significant, heritabilities of leaf size, clonal and sexual reproduction, and moderate heritabilities of phenological traits. In both microhabitats, we found that larger leaves, longer intervals between snowmelt and leaf expansion, and longer GDD (growing-degree days) until leaf expansion resulted in a stronger increase in the number of stems (clonal reproduction). In snowbeds, clonal reproduction increased with a shorter GDD until flowering, while the opposite was found on ridges. Furthermore, the proportion of flowering stems increased with GDD until flowering in both microhabitats. Our results suggest that the presence of significant heritable variation in morphology and phenology might help S. herbacea to adapt to changing environmental conditions. However, it remains to be seen if the rate of such an evolutionary response can keep pace with the rapid rate of climate change.

  • 16. Sedlacek, Janosch F.
    et al.
    Bossdorf, Oliver
    Cortes, Andres J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wheeler, Julia A.
    van Kleunen, Mark
    What role do plant-soil interactions play in the habitat suitability and potential range expansion of the alpine dwarf shrub Salix herbacea?2014In: Basic and Applied Ecology, ISSN 1439-1791, E-ISSN 1618-0089, Vol. 15, no 4, p. 305-315Article in journal (Refereed)
    Abstract [en]

    Mountain plants may respond to warming climates by migrating along altitudinal gradients or, because climatic conditions on mountain slopes can be locally very heterogeneous, by migrating to different microhabitats at the same altitude. However, in new environments, plants may also encounter novel soil microbial communities, which might affect their establishment success. Thus, biotic interactions could be a key factor in plant responses to climate change. Here, we investigated the role of plant soil feedback for the establishment success of the alpine dwarf shrub Salix herbacea L. across altitudes and late- and early snowmelt microhabitats. We collected S. herbacea seeds and soil from nine plots on three mountain-slope transects near Davos, Switzerland, and we transplanted seeds and seedlings to substrate inoculated with soil from the same plot or with soils from different microhabitats, altitudes and mountains under greenhouse conditions. We found that, on average, seeds from higher altitudes (2400-2700 m) and late-exposed snowbeds germinated better than seeds from lower altitudes (2200-2300 m) and early-exposed ridges. However, despite these differences in germination, growth was generally higher for plants from low altitudes, and there were no indications for a an home-soil advantage within the current range of S. herbacea. Interestingly, seedlings growing on soil from above the current altitudinal distribution of S. herbacea grew on average less well than on their own soil. Thus, although the lack of a home-soil advantage in the current habitat might be beneficial for S. herbacea in a changing environment, migration to habitats beyond the current altitudinal range might be limited, probably due to missing positive soil-feedback.

  • 17. Sedlacek, Janosch
    et al.
    Wheeler, Julia A.
    Cortes, Andres J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bossdorf, Oliver
    Hoch, Guenter
    Lexer, Christian
    Wipf, Sonja
    Karrenberg, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    van Kleunen, Mark
    Rixen, Christian
    The Response of the Alpine Dwarf Shrub Salix herbacea to Altered Snowmelt Timing: Lessons from a Multi-Site Transplant Experiment2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 4, article id e0122395Article in journal (Refereed)
    Abstract [en]

    Climate change is altering spring snowmelt patterns in alpine and arctic ecosystems, and these changes may alter plant phenology, growth and reproduction. To predict how alpine plants respond to shifts in snowmelt timing, we need to understand trait plasticity, its effects on growth and reproduction, and the degree to which plants experience a home-site advantage. We tested how the common, long-lived dwarf shrub Salix herbacea responded to changing spring snowmelt time by reciprocally transplanting turfs of S. herbacea between early-exposure ridge and late-exposure snowbed microhabitats. After the transplant, we monitored phenological, morphological and fitness traits, as well as leaf damage, during two growing seasons. Salix herbacea leafed out earlier, but had a longer development time and produced smaller leaves on ridges relative to snowbeds. Longer phenological development times and smaller leaves were associated with reduced sexual reproduction on ridges. On snowbeds, larger leaves and intermediate development times were associated with increased clonal reproduction. Clonal and sexual reproduction showed no response to altered snowmelt time. We found no home-site advantage in terms of sexual and clonal reproduction. Leaf damage probability depended on snowmelt and thus exposure period, but had no short-term effect on fitness traits. We conclude that the studied populations of S. herbacea can respond to shifts in snowmelt by plastic changes in phenology and leaf size, while maintaining levels of clonal and sexual reproduction. The lack of a home-site advantage suggests that S. herbacea may not be adapted to different microhabitats. The studied populations are thus unlikely to react to climate change by rapid adaptation, but their responses will also not be constrained by small-scale local adaptation. In the short term, snowbed plants may persist due to high stem densities. However, in the long term, reduction in leaf size and flowering, a longer phenological development time and increased exposure to damage may decrease overall performance of S. herbacea under earlier snowmelt.

  • 18. Wheeler, J. A.
    et al.
    Hoch, G.
    Cortes, Andres J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Sedlacek, J.
    Wipf, S.
    Rixen, C.
    Increased spring freezing vulnerability for alpine shrubs under early snowmelt2014In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 175, no 1, p. 219-229Article in journal (Refereed)
    Abstract [en]

    Alpine dwarf shrub communities are phenologically linked with snowmelt timing, so early spring exposure may increase risk of freezing damage during early development, and consequently reduce seasonal growth. We examined whether environmental factors (duration of snow cover, elevation) influenced size and the vulnerability of shrubs to spring freezing along elevational gradients and snow microhabitats by modelling the past frequency of spring freezing events. We sampled biomass and measured the size of Salix herbacea, Vaccinium myrtillus, Vaccinium uliginosum and Loiseleuria procumbens in late spring. Leaves were exposed to freezing temperatures to determine the temperature at which 50 % of specimens are killed for each species and sampling site. By linking site snowmelt and temperatures to long-term climate measurements, we extrapolated the frequency of spring freezing events at each elevation, snow microhabitat and per species over 37 years. Snowmelt timing was significantly driven by microhabitat effects, but was independent of elevation. Shrub growth was neither enhanced nor reduced by earlier snowmelt, but decreased with elevation. Freezing resistance was strongly species dependent, and did not differ along the elevation or snowmelt gradient. Microclimate extrapolation suggested that potentially lethal freezing events (in May and June) occurred for three of the four species examined. Freezing events never occurred on late snow beds, and increased in frequency with earlier snowmelt and higher elevation. Extrapolated freezing events showed a slight, non-significant increase over the 37-year record. We suggest that earlier snowmelt does not enhance growth in four dominant alpine shrubs, but increases the risk of lethal spring freezing exposure for less freezing-resistant species.

  • 19. Wheeler, J. A.
    et al.
    Schnider, F.
    Sedlacek, J.
    Cortés, Andrés J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wipf, S.
    Hoch, G.
    Rixen, C.
    With a little help from my friends: community facilitation increases performance in the dwarf shrub Salix herbacea2015In: Basic and Applied Ecology, ISSN 1439-1791, E-ISSN 1618-0089, Vol. 16, no 3, p. 202-209Article in journal (Refereed)
    Abstract [en]

    Shifts between positive and negative plant interactions along environmental stress gradients can affect alpine plant performance. We removed neighbours around Salix herbacea, a common arctic and alpine dwarf shrub, along elevational and snowmelt gradients on three mountains in Switzerland. The objectives of our study were to determine the effect of neighbours on phenological, morphological, and fitness traits ofS. herbacea, and to determine whether neighbour interactions shift from competition to facilitation along environmental stress gradients.

    Target plants without neighbours required less time for fruit production; however, they also were more likely to be damaged by caterpillar herbivory. Effects of neighbour removal changed along the environmental gradients: plants without neighbours had smaller leaves on earlier snowmelt sites, and increased fungal damage with increasing elevation. Without neighbour removal, damage generally led to reduced female flowering under later snowmelt conditions in the following summer.

    Our results indicate that the majority of neighbour interactions influencing S. herbacea are facilitative, particularly at stressful early snowmelt and high elevation sites. We suggest that neighbours moderate environmental conditions by protecting plants from temperature extremes, and reduce plant apparency to caterpillars. Neighbours also indirectly increase fitness by reducing damage. Facilitation by neighbours may become more important under climate change, as early snowmelt may increase stress.

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