Mehrdad Hajibabaei

Summary

Affiliation: University of Guelph
Country: Canada

Publications

  1. pmc A universal DNA mini-barcode for biodiversity analysis
    Isabelle Meusnier
    Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
    BMC Genomics 9:214. 2008
  2. pmc A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring
    Mehrdad Hajibabaei
    Centre for Biodiversity Genomics Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Ontario, Canada N1G 2W1
    Philos Trans R Soc Lond B Biol Sci 371:. 2016
  3. pmc Mitochondrial and nuclear phylogenetic analysis with Sanger and next-generation sequencing shows that, in Área de Conservación Guanacaste, northwestern Costa Rica, the skipper butterfly named Urbanus belli (family Hesperiidae) comprises three morphologica
    Claudia Bertrand
    Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
    BMC Evol Biol 14:153. 2014
  4. pmc Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    BMC Ecol 12:28. 2012
  5. doi request reprint The golden age of DNA metasystematics
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
    Trends Genet 28:535-7. 2012
  6. pmc DNA damage in preserved specimens and tissue samples: a molecular assessment
    Juergen Zimmermann
    New England Biolabs Inc, 240 County Rd, Ipswich, MA, 01938, USA
    Front Zool 5:18. 2008
  7. pmc Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    BMC Biol 5:24. 2007
  8. ncbi request reprint DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
    Trends Genet 23:167-72. 2007
  9. pmc Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    PLoS ONE 6:e17497. 2011
  10. pmc Critical factors for assembling a high volume of DNA barcodes
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
    Philos Trans R Soc Lond B Biol Sci 360:1959-67. 2005

Detail Information

Publications34

  1. pmc A universal DNA mini-barcode for biodiversity analysis
    Isabelle Meusnier
    Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
    BMC Genomics 9:214. 2008
    ..It may be difficult in practice, however, to retrieve a 650 bp fragment from archival specimens, (because of DNA degradation) or from environmental samples (where universal primers are needed)...
  2. pmc A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring
    Mehrdad Hajibabaei
    Centre for Biodiversity Genomics Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Ontario, Canada N1G 2W1
    Philos Trans R Soc Lond B Biol Sci 371:. 2016
    ....
  3. pmc Mitochondrial and nuclear phylogenetic analysis with Sanger and next-generation sequencing shows that, in Área de Conservación Guanacaste, northwestern Costa Rica, the skipper butterfly named Urbanus belli (family Hesperiidae) comprises three morphologica
    Claudia Bertrand
    Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
    BMC Evol Biol 14:153. 2014
    ..Here, we investigate three DNA barcode lineages of what has been identified as Urbanus belli (Hesperiidae, Eudaminae) in Área de Conservación Guanacaste (ACG), northwestern Costa Rica...
  4. pmc Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    BMC Ecol 12:28. 2012
    ..We also evaluate a multiplex PCR strategy, as compared to commonly used single amplicon workflow, using three newly designed primer sets targeting a wide array of benthic macroinvertebrate taxa...
  5. doi request reprint The golden age of DNA metasystematics
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
    Trends Genet 28:535-7. 2012
    ....
  6. pmc DNA damage in preserved specimens and tissue samples: a molecular assessment
    Juergen Zimmermann
    New England Biolabs Inc, 240 County Rd, Ipswich, MA, 01938, USA
    Front Zool 5:18. 2008
    ..We characterize the fragmentation state of the DNA and aim to identify abundant nucleoside lesions. Finally, simple models are introduced to describe the DNA fragmentation based on nicks and double-strand breaks...
  7. pmc Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    BMC Biol 5:24. 2007
    ..DNA arrays (micro and macro) and DNA barcodes are two molecular approaches that have recently garnered much attention. Here, we compare these two platforms for identification of an important group, the mammals...
  8. ncbi request reprint DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
    Trends Genet 23:167-72. 2007
    ....
  9. pmc Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    PLoS ONE 6:e17497. 2011
    ..Although considerable effort will be required to robustly optimize NGS tools to identify species from bulk environmental samples, our results indicate the potential of an environmental barcoding approach for biomonitoring programs...
  10. pmc Critical factors for assembling a high volume of DNA barcodes
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
    Philos Trans R Soc Lond B Biol Sci 360:1959-67. 2005
    ..Barcode analysis is already a cost-effective option for species identification in some situations and this will increasingly be the case as reference libraries are assembled and analytical protocols are simplified...
  11. pmc Googling DNA sequences on the World Wide Web
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
    BMC Bioinformatics 10:S4. 2009
    ..We have developed a novel algorithm and implemented it for searching species-specific genomic sequences, DNA barcodes, by using popular web-based methods such as Google...
  12. pmc DNA barcodes distinguish species of tropical Lepidoptera
    Mehrdad Hajibabaei
    Department of Integrative Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
    Proc Natl Acad Sci U S A 103:968-71. 2006
    ..If these results are general, DNA barcoding will significantly aid species identification and discovery in tropical settings...
  13. doi request reprint Spatial patterns of plant diversity below-ground as revealed by DNA barcoding
    Prasad R Kesanakurti
    Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    Mol Ecol 20:1289-302. 2011
    ..Our results provide insights into the role of environmental filtering and competitive interactions in the organization of plant diversity below-ground, and also demonstrate the utility of barcoding for the identification of plant roots...
  14. ncbi request reprint Assembling DNA barcodes. Analytical protocols
    Jeremy R deWaard
    Department of Integrative Biology, Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada
    Methods Mol Biol 410:275-93. 2008
    ..In this chapter, we detail the protocols involved in the assembly of DNA barcode records for members of the animal kingdom, but many of these approaches are of more general application...
  15. pmc Pyrosequencing for mini-barcoding of fresh and old museum specimens
    Shadi Shokralla
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    PLoS ONE 6:e21252. 2011
    ....
  16. doi request reprint Direct PCR amplification and sequencing of specimens' DNA from preservative ethanol
    Shadi Shokralla
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Ontario, Canada
    Biotechniques 48:233-4. 2010
    ....
  17. pmc iBarcode.org: web-based molecular biodiversity analysis
    Gregory A C Singer
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, N1G 2W1, Canada
    BMC Bioinformatics 10:S14. 2009
    ..Therefore, we have developed a web-based suite of tools to help the DNA barcode researchers analyze their vast datasets...
  18. pmc Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform
    Shadi Shokralla
    Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
    Sci Rep 5:9687. 2015
    ..In addition, the use of HTS allows the recovery of multiple sequences per specimen, for deeper analysis of genetic variation in target gene regions. ..
  19. pmc When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths
    John James Wilson
    Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
    BMC Ecol 11:18. 2011
    ..We simulated libraries with different levels of completeness (10-100% of the available species), and recorded assignments (positive or ambiguous) and their accuracy (true or false) under six criteria...
  20. doi request reprint Next-generation sequencing technologies for environmental DNA research
    Shadi Shokralla
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    Mol Ecol 21:1794-805. 2012
    ..Here, we review the advantages and limitations of current next-generation sequencing technologies in regard to their application for environmental DNA analysis...
  21. pmc Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing
    Joel F Gibson
    Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada Environment Canada, Canada Centre for Inland Waters, Burlington, Ontario, Canada
    PLoS ONE 10:e0138432. 2015
    ..The reduced cost and increased capacity of DNA sequence-based approaches will finally allow environmental monitoring programs to operate at the geographical and temporal scale required by industrial and regulatory end-users. ..
  22. pmc Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens
    Shadi Shokralla
    Department of Integrative Biology, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1 Department of Microbiology, Mansoura University, Egypt, 35516
    Mol Ecol Resour 14:892-901. 2014
    ..Next-generation sequencing is of great value because of its protocol simplicity, greatly reduced cost per barcode read, faster throughout and added information content. ..
  23. pmc Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics
    Joel Gibson
    Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada N1G 2W1
    Proc Natl Acad Sci U S A 111:8007-12. 2014
    ..This methodology opens the door to much cheaper and increased capacity for ecological and evolutionary studies applicable to a wide range of socio-economic issues, as well as a basic understanding of how the world works. ..
  24. ncbi request reprint Benchmarking DNA barcodes: An assessment using available primate sequences
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
    Genome 49:851-4. 2006
    ..As such, DNA barcoding provides enormous potential for use in global biodiversity studies...
  25. pmc Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well
    Aron J Fazekas
    Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
    PLoS ONE 3:e2802. 2008
    ....
  26. pmc Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers
    Nicole A Fahner
    Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
    PLoS ONE 11:e0157505. 2016
    ..Our work establishes the value of standard DNA barcodes for soil plant eDNA analysis in ecological investigations and biomonitoring programs and supports the collaborative development of DNA barcoding and metabarcoding. ..
  27. pmc Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas
    Teresita M Porter
    McMaster University, Biology Department, Hamilton, ON, L8S 4K1, Canada
    PLoS ONE 11:e0142759. 2016
    ..Conclusions drawn from the presence of even the most frequently observed taxa should be made with caution without corroborating lines of evidence. ..
  28. pmc Wolbachia and DNA barcoding insects: patterns, potential, and problems
    M Alex Smith
    Department of Integrative Biology and the Biodiversity, Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
    PLoS ONE 7:e36514. 2012
    ..While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region...
  29. doi request reprint DNA mini-barcodes
    Mehrdad Hajibabaei
    Biodiversity Institute of Ontario and Integrative Biology, University of Guelph, Guelph, ON, Canada
    Methods Mol Biol 858:339-53. 2012
    ....
  30. pmc A DNA Mini-Barcoding System for Authentication of Processed Fish Products
    Shadi Shokralla
    Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
    Sci Rep 5:15894. 2015
    ....
  31. pmc From writing to reading the encyclopedia of life
    Paul D N Hebert
    Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
    Philos Trans R Soc Lond B Biol Sci 371:. 2016
    ..J. C. Louden 1829. Magazine of natural history, vol. 1: This article is part of the themed issue 'From DNA barcodes to biomes'. ..
  32. pmc DNA barcodes and cryptic species of skipper butterflies in the genus Perichares in Area de Conservacion Guanacaste, Costa Rica
    John M Burns
    Department of Entomology, National Museum of Natural History, Smithsonian Institution, P O Box 37012, MRC 127, Washington, DC 20013 7012, USA
    Proc Natl Acad Sci U S A 105:6350-5. 2008
    ..This complex likely includes still more species, whose exposure may require barcoding. Barcoding ACG hesperiid morphospecies has increased their number by nearly 10%, an unexpectedly high figure for such relatively well known insects...
  33. pmc Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding
    Daniel H Janzen
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Philos Trans R Soc Lond B Biol Sci 360:1835-45. 2005
    ....
  34. ncbi request reprint Seed plant phylogeny: gnetophytes are derived conifers and a sister group to Pinaceae
    Mehrdad Hajibabaei
    Département de biologie et Centre de recherche avancée en génomique environnementale, Université d Ottawa, Ottawa, Ont, Canada, K1N 6N5
    Mol Phylogenet Evol 40:208-17. 2006
    ..The evolution of several morphological and molecular characters of gnetophytes and conifers will therefore need to be reinterpreted...