Publications

A chronological list of GrAToL project publications. Names in bold are GrAToL participants or collaborators.

  1. Hall JDK Fuč­íková, C Lo, LA Lewisand KG Karol (2010) Assessing proposed DNA barcodes in the green algae. Cryptogamie, Algologie 31: 529-555.
  2. Lewis PO (2011) MCMC Robot: A Markov chain Monte Carlo Teaching Tool. iOS Universal App published on Apple iTunes Store 13 August 2011.
  3. Ayres DL, A Darling, DJ Zwickl, P Beerli, MT Holder, PO Lewis, JP Huelsenbeck, F Ronquist, DL Swofford, MP Cummings, A Rambaut, and MA Suchard (2011) BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Systematic Biology. In review.
  4. Lewis LAJD Hall, and FW Zechman (2011) Green Algae. In: Encyclopedia of Life Sciences. John Wiley and Sons, Ltd, Chichester.
  5. Rindi F, TI Mikhailyuk, HJ Sluiman, T Friedl, and JM López-Bautista (2011) Phylogenetic relationships in Interfilum and Klebsormidium (Klebsormidiophyceae, Streptophyta). Molecular Phylogenetics and Evolution 58: 218-231.
  6. Letsch MR and LA Lewis (2012) Four gene arrangements within the chloroplast genome of a closely related group of green algae (Trebouxiophyceae, Chlorophyta). Molecular Phylogenetics and Evolution 64: 524-532.
  7. Rodrí­guez-Salinas E, H Riveros-Rosas, Z Li, K Fuč­íková, JJ Brand, LA Lewis and D González-Halphen (2012) Lineage-specific fragmentation and nuclear relocation of the mitochondrial cox2 gene in chlorophycean green algae (Chlorophyta). Molecular Phylogenetics and Evolution 64: 166-176.
  8. McManus HA, P Haugen, K Fuč­íková and LA Lewis (2012) Invasion of protein coding genes by green algal ribosomal group I introns. Molecular Phylogenetics and Evolution 62: 109-116.
  9. Tippery NP, K Fuč­íková, PO Lewis, and LA Lewis (2012) Probing the monophyly of the directly opposite flagellar apparatus group in Chlorophyceae using data from five genes. Journal of Phycology 48: 1482-1493.DOI: 10.1111/jpy.12003
  10. Wolf, PG and KG Karol (2012) Plastomes of bryophytes, lycophytes and ferns. In: Bock, R & V Knoop (eds.). Genomics of Chloroplasts and Mitochondria. Advances in Photosynthesis and Respiration 35, pp. 89-102.
  11. López-Bautista, JM and MS DePriest (2012)  In Fredericks S, L Shen, S Thompson & D Vasey (Eds.), The Encyclopedia of Sustainability: Vol. 4. Natural Resources and Sustainability, pp. 25–29. Great Barrington, MA: Berkshire Publishing.
  12. Allali H, F Rindi and JM López-Bautista (2013) Biodiversity of Trentepohliales (Ulvophyceae, Chlorophyta) in Gabon, central Africa. Nova Hedwigia 96(3-4):309-324.
  13. Stancheva, R, JD Hall, RM McCourt and RG Sheath (2013) Identity and phylogenetic placement of Spirogyra species (Zygnematophyceae, Charophyta) from California streams and elsewhere. Journal of Phycology 49:588-607.  (10.1111/jpy.12070)
  14. Allali H, D Ward and JM López-Bautista (2014) The use of metagenomics to infer algal diversity in a subaerial community from an African tropical rainforest, “Les Monts de Cristal” national park, Gabon. Bol. Soc. Mex. Ficologia 3:6-19.
  15. Casanova MT and KG Karol (2014) A revision of Chara sect. Protochara, comb et stat nov. (Characeae: Charophyceae). Australian Systematic Botany 27: 23-37.
  16. Cooper ED, B Bentlage, TR Gibbons, TR Bachvaroff and CF Delwiche (2014) Metatranscriptome profiling of a harmful algal bloom. Harmful Algae 37: 75-83.
  17. Fuč­íková K, PO Lewis and LA Lewis (2014) Putting incertae sedis taxa in their place: a proposal for nine new families and three new genera in Sphaeropleales (Chlorophyceae, Chlorophyta). Journal of Phycology 50:14-25.
  18. Graham LE, LA Lewis, W Taylor, C Wellman and M Cook (2014) Early terrestrialization: transition from algal to bryophyte grade. In: D. Hanson and S. Rice (eds.) Advances in Photosynthesis and Respiration, Vol. 37: Photosynthesis in Early Land Plants, pp. 9-28. Springer, Dordrecht.
  19. Holder MT, PO Lewis, DL Swofford and D Bryant (2014) Variable tree topology stepping-stone marginal likelihood estimation. Pp. 95-112 in: Chen, M-H, L Kuo and PO Lewis (eds.). 2014. Bayesian phylogenetics: methods, algorithms, and applications. Chapman & Hall/CRC Mathematical and Computational Biology. ISBN 9781466500792
  20. Leliaert F, H Verbruggen, P Vanormelingen, F Steen, JM López-Bautista, GC Zuccarello, & O De Clerck (2014) DNA-based species delimitation in algae. European J. Phycol. 49(2):179-196.
  21. Lewis PO, W Xie, M-H Chen, Y Fan, & L Kuo (2014) Posterior predictive Bayesian phylogenetic model selection. Systematic Biology 63: 309-321. DOI: 10.1093/sysbio/syt068
  22. Perez W, JD Hall, RM McCourt and KG Karol (2014) Phylogeny of North American Tolypella (Charophyceae, Charophyta) based on plastid DNA sequences with a description of Tolypella ramosissima sp. nov. Journal of Phycology.
  23. Rui W, M-H Chen, L Kuo and PO Lewis (2014) Consistency of marginal likelihood estimation when topology varies. Pp. 113-128 in: Chen, M-H, L Kuo & PO Lewis (eds.). 2014. Bayesian phylogenetics: methods, algorithms, and applications. Chapman & Hall/CRC Mathematical and Computational Biology.
  24. Fuč­íková K, PO Lewis and LA Lewis (2014). Widespread desert affiliations of trebouxiophycean algae (Trebouxiophyceae, Chlorophyta) including discovery of three new desert genera. Phycological Research 62: 294-305. [cover image] DOI: 10.1111/pre.12062
  25. Fučíková K, PO Lewis, D González-Halphen and LA Lewis (2014) Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of Sphaeropleales (Chlorophyta). Genome Biology and Evolution 6: 2170-2180. doi: 10.1093/gbe/evu172
  26. Ju C, B Van de Poel, EC Cooper, J Thierer, TR Gibbons, CF Delwiche and C Chang (Submitted) The plant hormone ethylene has been conserved over 450 million years of evolution. Nature Plants.
  27. Fučíková K, F Leliaert, ED Cooper, P Škaloud, S D’Hondt, O De Clerck, CFD Gurgel, LA Lewis, PO Lewis, JM Lopez-Bautista, CF Delwiche & H Verbruggen (2014) New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data. Frontiers in Ecology and Evolution 2: 63. doi: 10.3389/fevo.2014.00063
  28. Stancheva R, JD Hall, K Herburger, LA Lewis, RM McCourt, RG Sheath & A Holzinger (2014) Phylogenetic position of Zygogonium ericetorum Kütz. (Zygnematophyceae, Charophyta) from a high alpine habitat and ultrastructural characterization of unusual aplanospores. Journal of Phycology 50: 790-803. [cover image]  doi: 10.1111/jpy.12229
  29. Herburger K, LA Lewis & A Holzinger (2015) Photosynthetic efficiency, desiccation tolerance and ultrastructure in two phylogenetically distinct strains of alpine Zygnema sp. (Zygnematophyceae, Streptophyta): Role of akinete formation. [cover image] Protoplasma 252: 571-589. doi: 10.1007/s00709-014-0703-3
  30. Sciuto K, LA Lewis, E Verleyen, I. Moro & N. LaRocca (2015) Chodatodesmus australis sp. nov. (Scenedesmaceae, Chlorophyta) from Antarctica, with the emended description of the genus Chodatodesmus, and circumscription of Flechtneria rotunda gen. et sp. nov.  Journal of Phycology 51: 1172-1188. doi: 10.1111/jpy.12355
  31. Holzinger A, K Herburger, F Kaplan & LA Lewis (2015) Desiccation tolerance in the chlorophyte green alga Ulva compressa: Does cell wall architecture contribute to its ecological success? Planta 242: 477-492. doi: 10.1007/s00425-015-2292-6
  32. Fučíková K, PO Lewis & LA Lewis (2016) Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution. Molecular Phylogenetics and Evolution 98: 176-183. doi: 10.1016/j.ympev.2016.01.022
  33. Watanabe S, K. Fučíková, PO Lewis & LA Lewis (in press) Koshicola spirodelophila gen. et sp. nov. (Chaetopeltidales, Chlorophyceae), a novel green alga associated with the aquatic angiosperm Spirodela polyrhiza. American Journal of Botany.