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Crepaz H, Quaglia E, Lombardi G, Lonati M, Rossi M, Ravetto Enri S, Dullinger S, Tappeiner U, Niedrist G. Phenological responses of alpine snowbed communities to advancing snowmelt. Ecol Evol 2024; 14:e11714. [PMID: 39005886 PMCID: PMC11246788 DOI: 10.1002/ece3.11714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Climate change is leading to advanced snowmelt date in alpine regions. Consequently, alpine plant species and ecosystems experience substantial changes due to prolonged phenological seasons, while the responses, mechanisms and implications remain widely unclear. In this 3-year study, we investigated the effects of advancing snowmelt on the phenology of alpine snowbed species. We related microclimatic drivers to species and ecosystem phenology using in situ monitoring and phenocams. We further used predictive modelling to determine whether early snowmelt sites could be used as sentinels for future conditions. Temperature during the snow-free period primarily influenced flowering phenology, followed by snowmelt timing. Salix herbacea and Gnaphalium supinum showed the most opportunistic phenology, while annual Euphrasia minima struggled to complete its phenology in short growing seasons. Phenological responses varied more between years than sites, indicating potential local long-term adaptations and suggesting these species' potential to track future earlier melting dates. Phenocams captured ecosystem-level phenology (start, peak and end of phenological season) but failed to explain species-level variance. Our findings highlight species-specific responses to advancing snowmelt, with snowbed species responding highly opportunistically to changes in snowmelt timings while following species-specific developmental programs. While species from surrounding grasslands may benefit from extended growing seasons, snowbed species may become outcompeted due to internal-clock-driven, non-opportunistic senescence, despite displaying a high level of phenological plasticity.
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Affiliation(s)
- Harald Crepaz
- Institute for Alpine EnvironmentEurac ResearchBozenItaly
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | | | - Giampiero Lombardi
- Department of Agricultural, Forest and Food Sciences, University of TorinoUniversità degli Studi di TorinoGrugliascoItaly
- NBFC, National Biodiversity Future CenterPalermoItaly
| | - Michele Lonati
- Department of Agricultural, Forest and Food Sciences, University of TorinoUniversità degli Studi di TorinoGrugliascoItaly
| | - Mattia Rossi
- European CommissionIspraItaly
- Institute for Earth ObservationEurac ResearchBozenItaly
| | - Simone Ravetto Enri
- Department of Agricultural, Forest and Food Sciences, University of TorinoUniversità degli Studi di TorinoGrugliascoItaly
| | - Stefan Dullinger
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Ulrike Tappeiner
- Institute for Alpine EnvironmentEurac ResearchBozenItaly
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Georg Niedrist
- Institute for Alpine EnvironmentEurac ResearchBozenItaly
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Brown MR, Becher H, Williams S, Twyford AD. Is there hybridization between diploid and tetraploid Euphrasia in a secondary contact zone? AMERICAN JOURNAL OF BOTANY 2023; 110:e16100. [PMID: 36371731 PMCID: PMC10107515 DOI: 10.1002/ajb2.16100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Strong postzygotic reproductive isolating barriers are usually expected to limit the extent of natural hybridization between species with contrasting ploidy. However, genomic sequencing has revealed previously overlooked examples of natural cross-ploidy hybridization in some flowering plant genera, suggesting that the phenomenon may be more common than once thought. We investigated potential cross-ploidy hybridization in British eyebrights (Euphrasia, Orobanchaceae), a group from which 13 putative cross-ploidy hybrid combinations have been reported based on morphology. METHODS We analyzed a contact zone between diploid Euphrasia rostkoviana and tetraploid E. arctica in Wales. We sequenced part of the internal transcribed spacer (ITS) of nuclear ribosomal DNA and used genotyping by sequencing (GBS) to look for evidence of cross-ploidy hybridization and introgression. RESULTS Common variant sites in the ITS region were fixed between diploids and tetraploids, indicating a strong barrier to hybridization. Clustering analyses of 356 single-nucleotide polymorphisms (SNPs) generated using GBS clearly separated samples by ploidy and revealed strong genetic structure (FST = 0.44). However, the FST distribution across all SNPs was bimodal, indicating potential differential selection on loci between diploids and tetraploids. Demographic inference suggested potential gene flow, limited to around one or fewer migrants per generation. CONCLUSIONS Our results suggest that recent cross-ploidy hybridization is rare or absent in a site of secondary contact in Euphrasia. While a strong ploidy barrier prevents hybridization over ecological timescales, such hybrids may form in stable populations over evolutionary timescales, potentially allowing cross-ploidy introgression to take place.
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Affiliation(s)
- Max R. Brown
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
- Wellcome Sanger InstituteWellcome Genome Campus, HinxtonCambridgeCB10 1SAUK
| | - Hannes Becher
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
| | - Sebastian Williams
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
| | - Alex D. Twyford
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
- Royal Botanic Garden Edinburgh, 20a Inverleith RowEdinburghEH3 5LRUK
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Gawenda-Kempczyńska D, Olech M, Balcerek M, Nowak R, Załuski T, Załuski D. Phenolic acids as chemotaxonomic markers able to differentiate the Euphrasia species. PHYTOCHEMISTRY 2022; 203:113342. [PMID: 35948137 DOI: 10.1016/j.phytochem.2022.113342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 07/17/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
The objective of this study was to get the answer on the question, which phenolic compounds may serve as chemical markers in taxonomy of Euphrasia spp. (E. nemorosa, E. rostkoviana, E. stricta) collected from the wild. Moreover, it is still unknown how and which environmental parameters can impact on the quantity of polyphenols, flavonoids and phenolic acids. To the authors' knowledge, this is the first study that analyses such a broad spectrum of phenolic compounds in the genus Euphrasia and takes into account the habitat conditions of their synthesis. The species of Euphrasia differ significantly in the content of phenolic compounds. Euphrasia rostkoviana has the highest total content of polyphenols and flavonoids. Euphrasia stricta contains the largest amounts of phenolic acids, such as 5-O-caffeoylquinic, p-coumaric, protocatechuic and salicylic acid. It has been evidenced that the content of metabolites in the Euphrasia herb depends on a number of habitat parameters. The increased content of phenolic acids in E. stricta can be attributed to the fact that this species occupies drier habitats, with lower content of nitrogen and organic carbon compared to E. nemorosa and E. rostkoviana. The compounds that can be considered as chemotaxonomic markers are salicylic and protocatechuic acid for E. stricta, 5-O-caffeoylquinic acid for E. rostkoviana and ferulic acid for E. nemorosa. These findings provide theoretical and empirical basis for a chemotaxonomic classification of those species, which taken together with morphological characteristics should prevent misidentification.
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Affiliation(s)
- Dorota Gawenda-Kempczyńska
- Department of Pharmaceutical Botany and Pharmacognosy, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 Marie Curie-Skłodowska Street, 85-094, Bydgoszcz, Poland.
| | - Marta Olech
- Department of Pharmaceutical Botany, Medical University of Lublin, 1 Chodźki Street, 20-093, Lublin, Poland.
| | - Maciej Balcerek
- Department of Pharmaceutical Botany and Pharmacognosy, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 Marie Curie-Skłodowska Street, 85-094, Bydgoszcz, Poland.
| | - Renata Nowak
- Department of Pharmaceutical Botany, Medical University of Lublin, 1 Chodźki Street, 20-093, Lublin, Poland.
| | - Tomasz Załuski
- Department of Pharmaceutical Botany and Pharmacognosy, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 Marie Curie-Skłodowska Street, 85-094, Bydgoszcz, Poland.
| | - Daniel Załuski
- Department of Pharmaceutical Botany and Pharmacognosy, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 Marie Curie-Skłodowska Street, 85-094, Bydgoszcz, Poland.
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Garrett P, Becher H, Gussarova G, dePamphilis CW, Ness RW, Gopalakrishnan S, Twyford AD. Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights ( Euphrasia, Orobanchaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:869583. [PMID: 35720561 PMCID: PMC9197813 DOI: 10.3389/fpls.2022.869583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Disentangling the phylogenetic relationships of taxonomically complex plant groups is often mired by challenges associated with recent speciation, hybridization, complex mating systems, and polyploidy. Here, we perform a phylogenomic analysis of eyebrights (Euphrasia), a group renowned for taxonomic complexity, with the aim of documenting the extent of phylogenetic discordance at both deep and at shallow phylogenetic scales. We generate whole-genome sequencing data and integrate this with prior genomic data to perform a comprehensive analysis of nuclear genomic, nuclear ribosomal (nrDNA), and complete plastid genomes from 57 individuals representing 36 Euphrasia species. The species tree analysis of 3,454 conserved nuclear scaffolds (46 Mb) reveals that at shallow phylogenetic scales postglacial colonization of North Western Europe occurred in multiple waves from discrete source populations, with most species not being monophyletic, and instead combining genomic variants from across clades. At a deeper phylogenetic scale, the Euphrasia phylogeny is structured by geography and ploidy, and partially by taxonomy. Comparative analyses show Southern Hemisphere tetraploids include a distinct subgenome indicative of independent polyploidy events from Northern Hemisphere taxa. In contrast to the nuclear genome analyses, the plastid genome phylogeny reveals limited geographic structure, while the nrDNA phylogeny is informative of some geographic and taxonomic affinities but more thorough phylogenetic inference is impeded by the retention of ancestral polymorphisms in the polyploids. Overall our results reveal extensive phylogenetic discordance at both deeper and shallower nodes, with broad-scale geographic structure of genomic variation but a lack of definitive taxonomic signal. This suggests that Euphrasia species either have polytopic origins or are maintained by narrow genomic regions in the face of extensive homogenizing gene flow. Moreover, these results suggest genome skimming will not be an effective extended barcode to identify species in groups such as Euphrasia, or many other postglacial species groups.
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Affiliation(s)
- Phen Garrett
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Becher
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Galina Gussarova
- Natural History Museum, University of Oslo, Oslo, Norway
- Botany Department, Faculty of Biology and Soil Science, St Petersburg State University, St Petersburg, Russia
- Tromsø University Museum, University of Tromsø, Tromsø, Norway
| | - Claude W. dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Rob W. Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | | | - Alex D. Twyford
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
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Brown MR, Moore PGP, Twyford AD. Performance of generalist hemiparasitic Euphrasia across a phylogenetically diverse host spectrum. THE NEW PHYTOLOGIST 2021; 232:2165-2174. [PMID: 34555197 DOI: 10.1111/nph.17752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 09/11/2021] [Indexed: 05/14/2023]
Abstract
Generalist hemiparasites may attach to many different host species and experience complex parasite-host interactions. How these parasite-host interactions impact on the fitness of hemiparasitic plants remain largely unknown. We used experimentally tractable eyebrights (Euphrasia, Orobanchaceae) to understand parasite-host species interactions affecting the performance of a generalist hemiparasitic plant. Common garden experiments were carried out measuring Euphrasia performance across 45 diverse hosts and in different parasite-host combinations. We show that variation in hemiparasite performance can be attributed mainly to host species and host phylogenetic relationships (λ = 0.82; 0.17-1.00 CI). When variation in performance is considered temporally, annual host species cause earlier flowering, and lead to poorer performance late in the season. While Euphrasia species typically perform similarly on a given host species, some eyebrights show more specialized parasite-host species interactions. Our results show that generalist hemiparasites only benefit from attaching to a limited, but phylogenetically divergent, subset of hosts. The conserved responses of divergent Euphrasia species suggest hemiparasite performance is affected by common host attributes. However, evidence for more complex parasite-host species interactions show that a generalist hemiparasite can potentially respond to individual host selection pressures and may adapt to local host communities.
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Affiliation(s)
- Max R Brown
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | | | - Alex D Twyford
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
- Royal Botanical Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
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Becher H, Powell RF, Brown MR, Metherell C, Pellicer J, Leitch IJ, Twyford AD. The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights. ANNALS OF BOTANY 2021; 128:639-651. [PMID: 34318876 PMCID: PMC8422891 DOI: 10.1093/aob/mcab102] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species. METHODS We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples. KEY RESULTS We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small. CONCLUSIONS We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.
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Affiliation(s)
- Hannes Becher
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Max R Brown
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Wellcome Trust Genome Campus, Hinxton, Saffron Walden, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, Harpenden, Hertfordshire, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | | | - Alex D Twyford
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
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Becher H, Brown MR, Powell G, Metherell C, Riddiford NJ, Twyford AD. Maintenance of Species Differences in Closely Related Tetraploid Parasitic Euphrasia (Orobanchaceae) on an Isolated Island. PLANT COMMUNICATIONS 2020; 1:100105. [PMID: 33367265 PMCID: PMC7748025 DOI: 10.1016/j.xplc.2020.100105] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/24/2020] [Accepted: 08/27/2020] [Indexed: 05/02/2023]
Abstract
Polyploidy is pervasive in angiosperm evolution and plays important roles in adaptation and speciation. However, polyploid groups are understudied due to complex sequence homology, challenging genome assembly, and taxonomic complexity. Here, we study adaptive divergence in taxonomically complex eyebrights (Euphrasia), where recent divergence, phenotypic plasticity, and hybridization blur species boundaries. We focus on three closely related tetraploid species with contrasting ecological preferences that are sympatric on Fair Isle, a small isolated island in the British Isles. Using a common garden experiment, we show a genetic component to the morphological differences present between these species. Using whole-genome sequencing and a novel k-mer approach we call "Tetmer", we demonstrate that the species are of allopolyploid origin, with a sub-genome divergence of approximately 5%. Using ∼2 million SNPs, we show sub-genome homology across species, with a very low sequence divergence characteristic of recent speciation. This genetic variation is broadly structured by species, with clear divergence of Fair Isle heathland Euphrasia micrantha, while grassland Euphrasia arctica and coastal Euphrasia foulaensis are more closely related. Overall, we show that tetraploid Euphrasia is a system of allopolyploids of postglacial species divergence, where adaptation to novel environments may be conferred by old variants rearranged into new genetic lineages.
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Affiliation(s)
- Hannes Becher
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
- Corresponding author
| | - Max R. Brown
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Gavin Powell
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, 4 High Firs Crescent, Harpenden, Hertfordshire AL5 1NA, UK
| | | | - Alex D. Twyford
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
- Corresponding author
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