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DNA barcoding British Euphrasia reveals deeply divergent polyploids but lack of species-level resolution

Xumei Wang, Galina Gussarova, Markus Ruhsam, Natasha de Vere, Chris Metherell, Peter M. Hollingsworth, View ORCID ProfileAlex D. Twyford
doi: https://doi.org/10.1101/164681
Xumei Wang
1School of Pharmacy, Xi’an Jiaotong University, 76 Yanta West Road, Xi’an, 710061,P.R.China
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Galina Gussarova
2Tromsø University Museum, UiT TheArctic University of Norway, PO box 6050 Langnes,NO-9037, Tromsø, Norway
3CEES-Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, PO BOX 1066, Blindern, NO-0316, Norway
4Dept. of Botany, Faculty of Biology, St Petersburg State University, Universitetskaya nab.7/9, 199034 St Petersburg, Russia
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Markus Ruhsam
5Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
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Natasha de Vere
6National Botanic Garden of Wales, Llanarthne, Carmarthenshire, SA32 8HG, UK and Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University,Penglais, Aberystwyth,Ceredigion, SY23 3DA, UK
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Chris Metherell
757 Walton Rd, Bristol BS11 9TA
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Peter M. Hollingsworth
5Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
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Alex D. Twyford
8University of Edinburgh, Institute of Evolutionary Biology, West Mains Road, Edinburgh,EH3 9JT, UK
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  • ORCID record for Alex D. Twyford
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ABSTRACT

Background and aims DNA barcoding is emerging as a useful tool not only for species identification but for studying evolutionary and ecological processes. Although plant DNA barcodes do not always provide species-level resolution, the generation of large DNA barcode datasets can provide insights into the mechanisms underlying the generation of species diversity. Here, we use DNA barcoding to study evolutionary processes in taxonomically complex British Euphrasia, a group with multiple ploidy levels, frequent self- fertilization, young species divergence and widespread hybridisation.

Methods We sequenced the core plant barcoding loci, supplemented with additional nuclear and plastid loci, in representatives of all 19 British Euphrasia species. We analyse these data in a population genetic and phylogenetic framework. We then date the divergence of haplotypes in a global Euphrasia dataset using a time-calibrated Bayesian approach implemented in BEAST.

Key results No Euphrasia species has a consistent diagnostic haplotype. Instead, haplotypes are either widespread across species, or are population specific. Nuclear genetic variation is strongly partitioned by ploidy levels, with diploid and tetraploid British Euphrasia possessing deeply divergent ITS haplotypes (DXY = 5.1%), with haplotype divergence corresponding to the late Miocene. In contrast, plastid data show no clear division by ploidy, and instead reveal weakly supported geographic patterns.

Conclusions Using standard DNA barcoding loci for species identification in Euphrasia will be unsuccessful. However, these loci provide key insights into the maintenance of genetic variation, with divergence of diploids and tetraploids suggesting that ploidy differences act as a barrier to gene exchange in British Euphrasia, with rampant hybridisation within ploidy levels. The scarcity of shared diploid-tetraploid ITS haplotypes supports the polyploids being allotetraploid in origin. Overall, these results show that even when lacking species-level resolution, DNA barcoding can reveal insightful evolutionary patterns in taxonomically complex genera.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted July 17, 2017.
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DNA barcoding British Euphrasia reveals deeply divergent polyploids but lack of species-level resolution
Xumei Wang, Galina Gussarova, Markus Ruhsam, Natasha de Vere, Chris Metherell, Peter M. Hollingsworth, Alex D. Twyford
bioRxiv 164681; doi: https://doi.org/10.1101/164681
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DNA barcoding British Euphrasia reveals deeply divergent polyploids but lack of species-level resolution
Xumei Wang, Galina Gussarova, Markus Ruhsam, Natasha de Vere, Chris Metherell, Peter M. Hollingsworth, Alex D. Twyford
bioRxiv 164681; doi: https://doi.org/10.1101/164681

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