ibol 2017 Pre-conference Workshop DNA Barcoding Natural History Collections

Transcription

1 ibol 2017 Pre-conference Workshop DNA Barcoding Natural History Collections

2 2 Schedule 09:00-09:45 Lecture Theme Welcome and Introduction Natural History Collection Harvesting Strategies & Logistics Lecturer/Speaker Jeremy dewaard 09:45-10:30 Sample Harvesting in Natural History Collections Valerie Levesque-Beaudin 10:30-11:00 Coffee Break 11:00-11:45 Specimen Digitization Jayme Sones 11:45-12:30 Pre-lab Processing Labelling, Imaging and Tissue sampling Monica Young and Kate Perez 12:30-13:30 Lunch 13:30-14:15 Standard Protocols for Natural History Collection Barcoding Suresh Naik 14:15-15:00 BOLD Data Analysis and Archiving Chris Ho 15:00-15:30 Coffee Break 15:30-16:15 New Developments for Natural History Collection Barcoding Sean Prosser 16:15-16:45 Workflow Overview and Open Discussion Jeremy dewaard and Jayme Sones

3 3 Introduction to DNA Barcoding 09:00-09:30 Lecture Theme Welcome and introduction Enabling scientific discovery through DNA Barcodes Lecturer/Speaker Michelle van der Bank 09:30-10:00 Building a barcode reference library Monica Young 10:00-10:30 Beyond the bench Suresh Naik 10:30-11:00 Coffee Break 11:00-11:45 Beyond the bench Suresh Naik 11:45-12:30 Data analytics and the integrity of a barcode record Thomas Braukmann and Megan Milton 12:30-13:30 Lunch 13:30-14:15 14:15-15:00 When species identification matters Wildlife and environmental applications of DNA barcoding When species identification matters DNA barcoding and the integrity of food supply chain Sean Prosser Natalia Ivanova 15:00-15:30 Coffee Break 15:30-16:15 DNA Barcoding and the new frontiers Evgeny Zakharov 16:30-16:45 Closing remarks, questions and discussion Evgeny Zakharov, Michelle van der Bank

4 4 DNA Metabarcoding Lecture Theme Lecturer/Speaker 09:00-09:30 Introduction to DNA Metabarcoding & Genomic Approaches Mehrdad Hajibabaei 09:30-10:00 10:00-10:10 Sampling and Sample Prep Questions Natalia Ivanova 10:15-10:45 Coffee Break 10:40-11:20 11:20-11:30 DNA Marker Selection: Recovery, Resolution and Annotation Questions Nicole Fahner 11:30-12:00 Microbial biodiversity analysis through HTS Linda Amaral Zettler 12:15-13:15 Lunch 13:30-14:15 13:30-13:40 13:40-14:20 14:20-14:30 14:30-15:00 15:00-15:10 HTS Platforms Questions Primary Data Analysis Questions Biodiversity/Ecological and Statistical Interpretation Questions Thomas Braukmann Nicole Fahner Mehrdad Hajibabaei & Nicole Fahner 15:10-15:30 Final Discussion Panel

5 5 Schedule Morning 9:00-9:45 - Jeremy dewaard: Natural History Collection Harvesting Strategies & Logistics Considerations for Museum Selection Considerations for Harvesting Strategy Sampling On Site vs. Off Site Import/Export Permits BMTA/Museum Agreements Transportation Jeremy dewaard Director of Collections dewaardj@uoguelph.ca

6 6 Schedule Morning 9:45-10:30 Valerie Levesque- Beaudin: Sample Harvesting in Natural History Collections Before arriving the museum (checklists, picklists) At the museum (specimen selection, specimen array, what to pack) Before leaving the museum (loan forms, other duties) Valerie Levesque-Beaudin Senior Collections Technician

7 7 Schedule Morning 10:30-11:00 Coffee Break

8 Schedule Morning 11:00-11:45 Jayme Sones: Specimen Digitization BOLD Specimen Data & Spreadsheets Interpreting Museum Data Labels Museum Data Protocols & Formatting Accessioning & CIMS BOLD Projects & Uploads Creating Plate Records & Plate Maps Jayme Sones Collections Manager 8

9 9 Summary Schedule Morning Kate Perez Field Operations Lead Collections Monica Young Taxonomic Lead Collections / PhD Student (P. Hebert) 1:45 12:30 - Kate Perez and Monica Young: Pre-lab Processing Specimen Labelling Specimen Imaging Image Upload Tissue Sampling Lab Submission Voucher Recovery s: myoung02@uoguelph.ca kperez@uoguelph.ca

10 10 Schedule Afternoon 12:30-13:30 Lunch

11 11 Schedule Afternoon Suresh Naik Research Scientist / Curator of DNA Archive Genomics 13:30-14:15 Suresh Naik: Standard Protocols for Natural History Collection Barcoding CCDB Workflow Lysis & Extraction PCR Amplification Taxon Specific Protocols Sequencing Failure Tracking DNA Archiving Quality Control snaik@uoguelph.ca

12 Schedule Afternoon Chris Ho Data Manager-Informatics 14:15-15:00 - Chris Ho: Data Analysis & Archiving Overview of a Digital Specimen Record Validation of Barcode Data Integrity Tools for Validation Visualization & Analysis Tools Trees for Publication Geological Distribution Publication: Datasets & Sharing Submission to Genbank Publication Association hoc@uoguelph.ca 12

13 13 Schedule Afternoon 15:00-15:30 Coffee Break

14 Schedule Afternoon 15:30-16:15 Sean Prosser: New Developments for Natural History Collection Barcoding Primers PCR Protocols MID-Tagging NGS Data Assembly & Analysis NGS Platforms Sean Prosser Research Analyst Genomics 14

15 Schedule Afternoon 16:15 16:45 - Jeremy dewaard and Jayme Sones Workflow Overview & Open Discussion s: dewaardj@uoguelph.ca jsones@uoguelph.ca 15

16 16 Special Thanks to Meredith Miller, Crystal Sobel, Jaclyn McKeown

17 Workshop Materials & Misc. Items Workshop materials available online /resources/ibol-2017/ Wifi access Questions Audience poll 17

18 18 Introduction Reference Library Building Ideal: maintain permanent link to authoritativelyidentified voucher specimens Canada Two approaches: 1. 1 Barcode freshly-collected material, worry about identifications later 2. 2 Barcode specimens held in national and regional natural history collections Vascular Plants: 6K Other Plants: 3K Invertebrates: 70K Vertebrates: 2K

19 Fresh collections offer ease and numbers various ways to identify after barcoding Introduction Reference Library Building 19

20 20 Introduction Reference Library Building Museum harvesting offers well-prepared, curated, and identified specimens

21 21 Introduction Reference Library Building Advantages: Fresh Specimens Little to nil DNA degradation Can choose DNA friendly preservation Large abundances/series Control ownership of specimens, data, images, etc. Low assembly and analytical costs Build library for encountered spp. Museum Harvesting Expert identifications Type material Rare and rarely-collected specimens Can easily target your group Specimens from across species range, including restrictive countries Value-added specimens

22 22 Disadvantages: Introduction Reference Library Building Fresh Specimens Not identified sorting to higher taxonomy usually possible, but difficult beyond Large quantities to sort through Hollow-curve species abundance pattern Taxonomic impediment for some taxa Museum Harvesting DNA degradation due to age/preservation/other May be restrictions on access and sharing data/images/dna High assembly and analytical costs Travel and specimen transport costs

23 23 Single sample approach Introduction Throughput and Scale NOT SCALABLE! Core labs operate in 96-well plate format Requires compatible front-end solutions

24 24 Introduction Throughput and Scale

25 Specimens Introduction CBG s Work with Museums Museum harvesting by our team: > 172,000 specimens Major BOLD contributors Top 5 Museums CNC ANIC NMNH Lyman RBCM 25

26 26 Introduction CBG s Work with Museums

27 27 Introduction CBG s Services for Reference Library Building

28 Post- Processing Laboratory BOLD Workbench Harvesting BOLD Upload Prep Museum selection Harvesting strategy Permits Museum BMTA Transport Eois burla 15-Jun-1937 Eois burla 31-Aug-1995 Eois burla 26-Jul-1997 Eois burla 3-Jul-1943 Eois burla 28-Jun-2005 Picklist Selection criteria Array Digitization Data + Image Tissue sample Plate record CCDB BMTA Imaging Label Trace + Sequence Tissue lysis DNA extraction + PCR Sanger sequencing Manual assembly Sequences Auto validation DNA archiving Degraded DNA NGS sequencing Auto assembly User validation BIN designation Transport Voucher recovery DNA repatriation Sample return Permits Data release

29 9:15-9:45 Jeremy dewaard Natural History Collection Harvesting Strategies & Logistics DNA Barcoding Natural History Collections

30 Post- Processing Laboratory BOLD Workbench Harvesting BOLD Upload Prep Museum selection Harvesting strategy Permits Museum BMTA Transport Eois burla 15-Jun-1937 Eois burla 31-Aug-1995 Eois burla 26-Jul-1997 Eois burla 3-Jul-1943 Eois burla 28-Jun-2005 Picklist Selection criteria Array Digitization Data + Image Tissue sample Plate record CCDB BMTA Imaging Label Trace + Sequence Tissue lysis DNA extraction + PCR Sanger sequencing Manual assembly Sequences Auto validation DNA archiving Degraded DNA NGS sequencing Auto assembly User validation BIN designation Transport Voucher recovery DNA repatriation Sample return Permits Data release

31 Harvesting Strategies & Logistics Considerations for Museum Selection Considerations for Harvesting Strategy Sampling On Site vs. Off Site Import/Export Permits BMTA/Museum Agreements Transportation

32 32 Considerations for Museum Selection Depends on several factors: 1) 1 Strength of collection in target taxon or region 2) 2 One or more steps completed (i.e. databased, imaged, sub-sampled) 3) 3 Collection database online or available 4) 4 Actively researched, recently curated or visited by taxonomic expert(s) 5) 5 Permanence of collection 6) 6 Access to DNA or frozen tissue archive

33 33 Considerations for Museum Selection Depends on several factors: 7) 7 Infrastructure and space for various steps 8) 8 Policies on destructive sampling 9) 9 Policies on biological material transfer 10 Restrictions placed on image and data accessibility Contact the directors/curators/collection managers Generally glad to highlight the advantages of their collection Often have to defend the value of their collection for continued funding/support/existence

34 Considerations for Harvesting Strategy Broad or specific taxonomic coverage Targeting species missing from a checklist Targeting species without DNA barcode representation Databased or not databased collections Preservation methods Permit and shipping restrictions 34

35 35 Sampling On Site vs. Off Site Choose the approach for your situation/needs On Site Off Site

36 Sampling On Site vs. Off Site On Site May be necessary for sampling restricted specimens Time-consuming stages limits what can be processed Reduces risk of damage to specimens Direct curator knowledge about collection 36

37 Sampling On Site vs. Off Site Off Site (Borrowing Specimens) Lab space and equipment needs met Time commitment can be lengthened Increases risk of damage to specimens Loan documents and permits needed 37

38 Import/Export Permits Requirements Depends on taxon (invertebrates/plants/vertebrates) CITES permits for threatened species Government regulations Border inspections and declarations 38

39 Import/Export Permits Make a plan with museum you are visiting Discuss with curators permit requirements Requirements Apply for permits promptly with governing body 39

40 Import/Export Permits Approved permits can be used for: Crossing country borders with specimens Sending specimens from museum to your institution Returning specimens from your institution to museum 40

41 BMTA/Museum Agreements Museum Agreements Agreement between museum and collaborator Determine use and ownership of specimens, DNA, sharing of information Destructive or non-destructive sampling If borrowing specimens time table for completion of work 41

42 BMTA/Museum Agreements 3 rd Party Transfer Agreement between collaborator and molecular lab Determine use and ownership of specimens, DNA, sharing of information Ensure third party use does not violate original agreement with donor institution As with all steps, it s important to discuss thoroughly with directors/curators/collection managers 42

43 43 Transportation Shipping Customs Declaration

44 Transportation Shipping Dry Invertebrate Specimens 1. 1 Ensure pins are firmly in foam and cross pin any specimens/labels that may rotate 2. 2 Add cardboard toppers to boxes 3. 3 Pack specimen boxes securely inside another box 4. 4 Include documentation for customs declaration Mark as Scientific research specimens, no commercial value

45 Transportation Shipping Invertebrate Specimens in Fluid Each vial/jar cannot exceed 30mL Max 1L of fluid per box When possible, wrap and heat seal all containers Pack specimen boxes securely inside another box with bubble wrap Include documentation for customs declaration Mark as Scientific research specimens, not restricted Special Provision A180 applies Plastic wrap the flat to limit movement of vials Add the wrapped flat in a Ziploc bag with absorbent paper and heat seal it. 45

46 46 Transportation Shipping Invertebrate Specimens in Fluid International Air Transport Association Dangerous Goods Regulations, 52 nd Edition

47 47 Transportation Shipping Herbarium Specimens

48 Transportation Shipping Herbarium Specimens Pack specimens securely Include documentation for customs declaration Mark as Scientific research specimens, no commercial value Include scientific names and preservation method Specimen Sheets Wrapped in paper Wrapped these bundles with more layers of bubble wrap and foam peanuts within a box Bundle 2-3 in bubble wrap 48

49 Transportation Shipping Tissue Plates Ensure caps/lids are securely fastened Seal microplates in ziplock bag Follow shipping requirements for Special Provision A180 Mark as Scientific research specimens, not restricted Special Provision A180 applies 49

50 Pack specimen containers in large bins with bubble wrap to absorb shock Secure bins in vehicle so there is no movement No limitations on fluid specimens May require Transportation of Dangerous Goods training in your country May require cooler with ice or electric cooling container for tissues, DNA and PCR products Have loan and permit documentation readily available Transportation Transporting by Vehicle 50

51 After completion of all analyses, return any borrowed vouchers and required derivatives Voucher specimens and/or tissue DNA extracts Some museums require copies of all digital metadata Specimen data Image files Trace files/sequences Transportation Return of Vouchers and Derivatives Keep museum informed of taxonomic revisions or associated publications 51