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Use of genetics in species-level taxonomy

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Use of genetics in species-level taxonomy

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  1. GCTTCACATTTTAACGCACATGACGTGTCACAGAACGAGTGCCTACGTCGAGCAATTAGATAATACGCTTCACATTTTAACGCACATGACGTGTCACAGAACGAGTGCCTACGTCGAGCAATTAGATAATAC GCTTCATACATTAACGCACATGACGTGTCACAGAACGAGTGCCTACGTCGAGCAATTAGAGAATAC GCTTCACACATTAACGCACATTTCGTGTCACAGAACGAGTGCCTACGTCGAGCAATTAGCCAATAC GCCTCACACATTAACGCACATTTCGTGTCACAGAACGAGTGCCTACGTCGAGCAATTAGAGAAGAC Use of genetics in species-level taxonomy Pete Hollingsworth Royal Botanic Garden Edinburgh

  2. The Problem......... • There are a lot of plant species........ • Species can be difficult to identify and delimit • Some plant groups are difficult • Some plant groups/geographical regions are under-studied • Shortage of botanical experts • Some material is suboptimal.........................

  3. ACGTGGGCTTGCATCGGGGAGTACATGCGTAACACTCGTTGCACGATCGATTGAAGCTACGTGCATGACGTGGGCTTGCATCGGGGAGTACATGCGTAACACTCGTTGCACGATCGATTGAAGCTACGTGCATG ACGTGGGCTTGCATCGGGGAGTACATGCGTAACACTCGTTGCACGATCGATTGAAGCTACGTGCATG ACGTAGGCTTGCATCGGGGAGTACATGCGTAACACTCGTTGCACGATCGATTGAAGCTACGTGCATG ACGTGCACATGCATCATGGTGTACATGTGTAACACACGATGCAGGATCGGTCGAAGCTACGTGCATG ACGTGCACATGCATCATGGTGTACATGTGTAACACACGATGCAGGATCGGTCGAAGCTACGTGCATG ACGTGCACATGCATCATAGTGTACATGTGTAACACACGATGCAGGATCGGTCGAAGCTACGTGCATG ACGTTTACATGCATCTGGGTGTACATGTGTAACTCCGATTGCACGAACGATCGAAGCTACGTGCATG ACGTTTACATGCATCTGGGTGTACATGTGTAACTCCGATTGCACGAACGATCGAAGCTACGTGCATG ACGTTTACATGCATCTGGGTGTACATGTGTATCTCCGATTGCACGAACGATCGAAGCTACGTGCATG ACGTGCATATGCATCGGTGTGTCCAGCCGTTACACCCGTTGCATGATCAATCGAAGCTA CGTGCATG ACGTGCATATGCATCGGTCTGTACAGCCGTTACATTCGTTGCATGATCAATCGAAGCTA CGTGCATG ACGTGCATATGCCTCGGTGTGTACAGCCGTTACACCCGTTGCATGATCAATCGAAGCTA CGTGCATG How can genetics help? • Comparability • Lack of environmental or developmental variation • Automateability/scaleability

  4. P. natans P. nodosus P. x schreberi

  5. Genetic markers support the recognition of two distinct taxa Ssp. germanicum Nothosspfoersteri Ssp. cespitosum Hollingsworth & Swan, Watsonia22, 235-242 (1999). Cryptic taxa Tricophorumcespitosum (Cyperaceae) One taxon recognised in UK, but subtle differences in leaf sheath morphology suggested two taxa

  6. Chloroplast sequence Type 1 & 2 Type 3 Type 3 Anacamptis fragrans Anacamptis robusta

  7. F1s Pure rivale Backcross rivale? Pure urbanum

  8. ACGTGGGCTTGCATCGGGGAGTACATGCGTAACACTCGTTGCACGATCGATTGAAGCTACGTGCATGACGTGGGCTTGCATCGGGGAGTACATGCGTAACACTCGTTGCACGATCGATTGAAGCTACGTGCATG ACGTGGGCTTGCATCGGGGAGTACATGCGTAACACTCGTTGCACGATCGATTGAAGCTACGTGCATG ACGTAGGCTTGCATCGGGGAGTACATGCGTAACACTCGTTGCACGATCGATTGAAGCTACGTGCATG ACGTGCACATGCATCATGGTGTACATGTGTAACACACGATGCAGGATCGGTCGAAGCTACGTGCATG ACGTGCACATGCATCATGGTGTACATGTGTAACACACGATGCAGGATCGGTCGAAGCTACGTGCATG ACGTGCACATGCATCATAGTGTACATGTGTAACACACGATGCAGGATCGGTCGAAGCTACGTGCATG ACGTTTACATGCATCTGGGTGTACATGTGTAACTCCGATTGCACGAACGATCGAAGCTACGTGCATG ACGTTTACATGCATCTGGGTGTACATGTGTAACTCCGATTGCACGAACGATCGAAGCTACGTGCATG ACGTTTACATGCATCTGGGTGTACATGTGTATCTCCGATTGCACGAACGATCGAAGCTACGTGCATG ACGTGCATATGCATCGGTGTGTCCAGCCGTTACACCCGTTGCATGATCAATCGAAGCTA CGTGCATG ACGTGCATATGCATCGGTGTGTACAGCCGTTACACCCGTTGCATGATCAATCGAAGCTA CGTGCATG ACGTGCATATGCATCGGTGTGTACAGCCGTTACACCCGTTGCATGATCAATCGAAGCTA CGTGCATG • Application of multiple techniques to solve taxonomic problems in difficult groups • Individual solutions for individual problems • Our capacity to do this is getting much better... • Can we use massive scale DNA sequencing of biodiversity to create a unified database of life?

  9. GCTTCACATTTTAACGCACATGACGTGTCACAGAACGAGTGCCTACGTCGAGCAATTAGATAATACGCTTCACATTTTAACGCACATGACGTGTCACAGAACGAGTGCCTACGTCGAGCAATTAGATAATAC DNA barcoding: sequence one (or a few) ‘standard’ short stretches of DNA Individuals of a species should be more similar in DNA sequence, than they are to individuals of other species Establish reference database of high quality sequences from well identified material (supported by voucher specimens) Take some tissue, sequence it, find out what it is, and what is known about it Provide a mechanism for speeding up the process of characterising biodiversity Identification of unknown specimens to known species Assist in the discovery of new species Approach not novel…..scale and coordination is…… DNA barcoding www.barcodinglife.org GCTTCATACATTAACGCACATGACGTGTCACAGAACGAGTGCCTACGTCGAGCAATTAGAGAATAC GCTTCACACATTAACGCACATTTCGTGTCACAGAACGAGTGCCTACGTCGAGCAATTAGCCAATAC GCCTCACACATTAACGCACATTTCGTGTCACAGAACGAGTGCCTACGTCGAGCAATTAGAGAAGAC

  10. This pioneering effort in DNA barcoding will set in motion the single most significant project in biology that I know today Dan Janzen (2003)

  11. “DNA barcoding generates information, not knowledge” “…..the practice is counterproductive to furthering our understanding of life” Ebach & Holdrege (2005) Nature 434, 697 “an excursion into futility” Wheeler (2005) Cladistics 21, 405–407 “the noisome weed of DNA barcoding” Will et al. (2005) Syst. Biol. 54, 844–851 • What are these objections based on? • It won’t work in all groups • A sequence from a single locus is inadequate for describing new species • It is not as intellectually ‘worthwhile’ as detailed taxonomic research • It might draw attention away from traditional taxonomy/understanding organisms

  12. Choosing a plant (chloroplast) barcode Proposed solutions: Chase et al (2007): rpoC1 + rpoB + matK (Taxon 56, 295-299)rpoC1 + matK + trnH-psbA Kim et al (2007): matK + atpF-H + psbK-I (unpublished)matK + atpF-H + trnH-psbA Kress/Erickson (2007): rbcL + trnH-psbA (PLoS ONE 2, e508 ) Lahayeet al. (2008): matK (PNAS 105, 2923–2928 Nature Precedings http://hdl.handle.net/10101/npre.2008.1896.1) Plant working group (2007) matK + trnH-psbA + atpF-H (minutes of Taipei meeting) TROUBLE AT MILL Reviewed by Ledford (2008) Nature 451, 616; Pennisi (2007) Science 318, 190-191.

  13. rbcL & matK selected as the core plant barcode Chloroplast barcode - will not discriminate between hybrids and their parents A broadly applicable tool, rather than targeted at complex groups RBGE Strategic Review November 2009

  14. What is the likely discriminatory power of a plant barcode? • Species discrimination asymptotes at ca 70-75% • Remaining species identified to “species groups” • Adding >2 chloroplast loci on average leads to diminishing returns of discrimination 80% 70% 60% 50% 40% 1 locus 2 locus 3 locus

  15. Predictions of plastid barcoding success High Low • Low • More ancient divergence • Sexuals • Not-over split • Herbs • Good • Hybridisation and/or polyploidy frequency • Species age • Reproductive mode • Taxonomic splitting • Life-history • Seed dispersal • (angiosperms) • High • Recent radiation • Agamosperms • Heavily split micro-species • Long-lived trees • Poor

  16. Using a plant barcode • LAND PLANTS • c. 400,000 species • VASCULAR PLANTS • > 350,000 species • c. 13,888 genera • c. 511 families

  17. Applications of plant barcoding • Identification of CITES protected materials • Ogden et al. (2008) Endang Species Res 9: 255–261 • Identification of plant material in diets • Jurado-Rivera et al. (2009) Proc R Soc BiolSciSerB276: 639-648 • Identification of fern gametophytes • Schneider et al. (2006) Molecular Ecology Resources 6: 989-991 • Squirrellet al. unpublished • Identification of invasive species • Van de Wielet al. (2009) Molecular Ecology Resources 9:1086-1091 • Identification of plants in horticultural trade • Pryeret al. (2010) Molecular Ecology Resources: online early • Identification of herbal medicine components • Baker and Little, Scientific American online ‘Observations’ 18/4/2010 • Cryptic species discovery in orchids • Lahayeet al. (2008) PNAS 105: 2923-2928 • Species identification and discovery in liverworts • Hollingsworth et al. (2009) Molecular Ecology Resources 9: 439-457 and unpublished

  18. Bryophyte identification is difficult and there is a shortage of experts Develop system for rapid low-cost identification and species discovery

  19. New species, Distinct ecology & morphology H. borealis Herbertus rbcL matK + trnH-psbA + ITS

  20. Aneura sp. nov. Cryptothallus (=Aneura) mirabilis Typical Aneura pinguis BarcodingAneura Barcoding of Aneura pinguis in UK has led to one new species being described, and identification of another four candidate new species

  21. Major Barcoding Projects • Many research groups with active plant barcoding projects • Tree-BoL: Barcoding all trees • Grass-BoL: Barcoding all grasses • Flora of Kruger National Park, • Flora of Area de Conservacion Guanacaste Costa Rica • British liverworts and UK BAP mosses • Flora of Korea • Plant barcoding China • Various medicinal plant projects • ‘All plant genera’ • iBoL • 500K species, 5 million specimens by 2015 • 100K species of plants

  22. Where we were (1990-2010) • Individual taxon studies • Small numbers of well-characterised genetic markers • Large numbers of poorly-characterised markers • Where we are • High throughput coordinated sequencing of a small number of DNA regions in lots of taxa(DNA barcoding) • Individual taxon studies using higher numbers of well characterised markers • Where we would like to be (2015 onwards) • High throughput sequencing of lots of well characterised DNA regions in lots of taxa

  23. Establishing the reference database (field collections, herbarium vouchers, determinations) will be the rate limiting step Important to commence this process now and establish “DNA ready” herbaria for future improvements in sequencing technologies Vast quantities of DNA sequence data divorced morphological and ecological information will be meaningless Integration with taxonomy and ecology, not replacement

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