ARIP 2016

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Published Reference Sequences

Every ARIP 2016 intern succeeded in taking a biodiversity specimen all the way through from field collection to deposition in the international BOLD system for use by researchers around the world.

Links to each intern’s contributions are here:

A key goal of the ARIP program is to enable the participants to make real contributions to ongoing, cutting-edge science. For ARIP 2016, the target was contribution of DNA barcode sequences for select marine organisms collected from the Southern California coast. By collecting, identifying, sequencing, and depositing the DNA sequences for these specimens, the ARIP 2016 interns have made a substantive contribution to the international, professional working database of knowledge of marine biodiversity.

During the program, each intern had the opportunity to do the following:

ARIP in Action

How it looks collecting in the field at low tide, 6:30 AM.

Summary Agenda — ARIP 2016

DAY DATE

L = lecture
G = group discussion/activity
F = field collecting
T = tour/trip
R = research lab activity


ACTIVITY
On-Line Week Research paper reading
0 Su 17 July Arrivals in L.A.
Welcome dinner and orientation
1 Mo 18 July L: Biodiversity, evolution, phylogenetic trees, animal diversity
G: Research topic I discussion
T: Pterosaur exhibit and Crustacea collection tour at NHM
2 Tu 19 July F: Collecting at King Harbor floating dock
T: Seafood lunch and crustacea dissection
R: Sample sorting, identification, and processing
3 We 20 July R: DNA extraction from specimens
L: Ecology and the biosphere
T: California Science Center: ecosystems, space shuttle, IMAX movie
4 Th 21 July R: DNA amplification of specimen extracts
L: Introduction to using the scientific literature
G: The L.A. River; getting into U.S. colleges
5 Fr 22 July F: Intertidal field collecting trip to San Pedro
T: Exploration Vessel Nautilus tour at AltaSea
T: Beach time at Cabrillo Beach
T: Cabrillo Marine Aquarium visit
R: USC Nuzhdin Lab visit to clean amplified DNA
6 Sa 23 July T: La Brea Tar Pits visit
T: L.A. Farmers Market visit
T: Disney Downtown
7 Su 24 July T: Angeles National Forest — Mt. Wilson Observatories
T: Lunch barbecue at Switzer Falls
T: Afternoon kayaking on the L.A. River
8 Mo 25 July R: Molecular sequence editing
L: Science communication as storytelling
G: Presentation workshop
9 Tu 26 July T: Visit USC campus and admissions
R: Molecular sequence editing
10 We 27 July G: Presentation workshop
T: Visit UCLA campus and admissions
11 Th 28 July R: Molecular sequence posting to Barcode of Life Database
G: Research presentation I
G: Preparation for research presentation II
12 Fr 29 July G: Preparation for research presentation II
G: Final research presentations
G: Closing ceremonies and awards
G: Farewell dinner
13 Sa 30 July Departures

Daily Documents and Resources

Nearly every day of the internship program, new results emerged and new resources were made available. Below here are the day-by-day postings used by ARIP 2016 interns.

Day 11 (Thursday) documents

This PDF summarizes the primer information for the forward and reverse primers used for all the specimens you are posting to BOLD.

Following are the locality data and taxonomic data for each of the sequences you will be posting to BOLD:

USA, California, Los Angeles County, San Pedro, Inner Cabrillo Beach, 33.712°N 118.283°W, seine, depth 1.33 m. Preserved in 95% ethanol. 3 Mar 2016. MBPC 16874, Station 1. Coll. J. Wall and K. Omura. RW16.005
2432 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Decapoda: Pleocyemata: Brachyura: Eubrachyura: Heterotremata: Cancroidea: Cancridae: Romaleon antennarium

USA, California, Los Angeles County, San Pedro, Inner Cabrillo Beach, 33.712°N 118.283°W, seine, 1.33 m. Preserved in 95% ethanol. 4 Mar 2016. MBPC 16876, Station 1. Coll. N.D. Pentcheff. RW16.007
2430 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Decapoda: Pleocyemata: Anomura: Paguroidea: Paguridae: Pagurus sp.
2431 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Decapoda: Pleocyemata: Brachyura: Eubrachyura: Heterotremata: Cancroidea: Cancridae: Metacarcinus sp.
2434 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Decapoda: Pleocyemata: Brachyura: Eubrachyura: Thoracotremata: Grapsoidea: Grapsidae: Pachygrapsus crassipes

USA, California, Los Angeles County, Malibu, beneath Malibu pier, 34.037°N 118.676°W, sand swash zone, shoveled sand into sieve, depth 1.22 m. Preserved in 95% ethanol. 4 Apr 2016. MBPC 16902. Coll. A. Wall and J. Wall. RW16.017
2428 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Decapoda: Pleocyemata: Anomura: Hippoidea: Hippidae: Emerita analoga

USA, California, Los Angeles County, inside Los Angeles Harbor, 33.719°N 118.261°W, bio-dredge, depth 11.89 m. Preserved in 95% ethanol. 14 May 2016. MBPC 16910. Coll. R/V Yellowfin, R. Wetzer and N.D. Pentcheff. RW16.033
2429 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Decapoda: Pleocyemata: Anomura: Lithodidae: Lopholithodes sp.

Pacific, California, Los Angeles County, Palos Verdes Peninsula, Pelican Cove, 33.74°N 118.403°W, intertidal, hand. Preserved in 95% ethanol. 8 Jun 2016. MBPC 16918. Coll. R. Wetzer, K. Omura, L. Harris, A. Wall, J. Wall, N.D. Pentcheff. RW16.050
2437 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Peracarida: Mysida: Mysidae: Neomysis sp.
2459 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Peracarida: Mysida: Mysidae: Neomysis sp.

USA, California, Los Angeles County, Redondo Beach, King Harbor, 33.842°N 118.391°W, floating dock, scrapings. Preserved in 95% ethanol. 19 Jul 2016. MBPC 16925. Coll. I. Lee, G. Kim, J. Jang, J. Lee, G. Bae, E.Nam, Y. Lee, R. Wetzer, N.D. Pentcheff, A. Wall, K. Balakahovsky. RW16.056
2471 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Peracarida: Amphipoda: Senticaudata: Corophiida: Caprelloidea: Caprellidae: Caprella sp.
2472 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Peracarida: Amphipoda: Senticaudata: Corophiida: Corophioidea: Ampithoidae: Ampithoe sp.
2478 Annelida: Polychaeta: Nereididae: Nereis sp.
2481 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Peracarida: Amphipoda: Senticaudata: Corophiida: Corophioidea: Ampithoidae: Ampithoe sp. [CORRECTION:]
2481 Arthropoda: Crustacea: Malacostraca: Eumalacostraca: Decapoda: Pleocyemata: Brachyura: Eubrachyura: Thoracotremata: Grapsoidea: Grapsidae: Pachygrapsus crassipes

Day 10 (Wednesday) documents

Download this skeletal Powerpoint to use for your presentation. Rename the file with your name, so we know whose file is whose.

Day 9 (Tuesday) documents

Sample BOLD data submission form

This PDF file shows an example of filling out the BOLD specimen data form.

Sequence trace files

E. Nam
2469EN_HCO2198M13.ab1
2463EN_LCO1490M13.ab1
2469EN_LCO1490M13.ab1
2481EN_HCO2198M13.ab1
2462EN_LCO1490M13.ab1
2463EN_HCO2198M13.ab1
2462EN_HCO2198M13.ab1
2481EN_LCO1490M13.ab1

J. Lee
2476JL_LCO1490M13.ab1
2478JL_HCO2198M13.ab1
2479JL_HCO2198M13.ab1
2478JL_LCO1490M13.ab1
2476JL_HCO2198M13.ab1
2467JL_LCO1490M13.ab1
2477JL_HCO2198M13.ab1
2477JL_LCO1490M13.ab1
2479JL_LCO1490M13.ab1
2467JL_HCO2198M13.ab1

I. Lee
2469IL_LCO1490M13.ab1
2479IL_LCO1490M13.ab1
2479IL_HCO2198M13.ab1
2476IL_LCO1490M13.ab1
2462IL_LCO1490M13.ab1
2459IL_HCO2198M13.ab1
2476IL_HCO2198M13.ab1
2462IL_HCO2198M13.ab1
2469IL_HCO2198M13.ab1
2459IL_LCO1490M13.ab1

G. Bae
2478GB_LCO1490M13.ab1
2467GB_LCO1490M13.ab1
2474GB_HCO2198M13.ab1
2473GB_HCO2198M13.ab1
2475GB_HCO2198M13.ab1
2474GB_LCO1490M13.ab1
2481GB_HCO2198M13.ab1
2478GB_HCO2198M13.ab1
2467GB_HCO2198M13.ab1
2473GB_LCO1490M13.ab1
2481GB_LCO1490M13.ab1
2475GB_LCO1490M13.ab1

Y. Lee
2468YL_LCO1490M13.ab1
2482YL_HCO2198M13.ab1
2463YL_LCO1490M13.ab1
2479YL_HCO2198M13.ab1
2463YL_HCO2198M13.ab1
2481YL_LCO1490M13.ab1
2480YL_LCO1490M13.ab1
2479YL_LCO1490M13.ab1
2480YL_HCO2198M13.ab1
2481YL_HCO2198M13.ab1
2468YL_HCO2198M13.ab1
2482YL_LCO1490M13.ab1

G. Kim
2471GK_HCO2198M13.ab1
2470GK_LCO1490M13.ab1
2472GK_LCO1490M13.ab1
2466GK_LCO1490M13.ab1
2472GK_HCO2198M13.ab1
2474GK_HCO2198M13.ab1
2474GK_LCO1490M13.ab1
2471GK_LCO1490M13.ab1
2470GK_HCO2198M13.ab1
2465GK_HCO2198M13.ab1
2465GK_LCO1490M13.ab1
2466GK_HCO2198M13.ab1

J. Jang
2471JJ_LCO1490M13.ab1
2470JJ_LCO1490M13.ab1
2477JJ_LCO1490M13.ab1
2466JJ_LCO1490M13.ab1
2471JJ_HCO2198M13.ab1
2470JJ_HCO2198M13.ab1
2466JJ_HCO2198M13.ab1
2465JJ_LCO1490M13.ab1
2477JJ_HCO2198M13.ab1
2465JJ_HCO2198M13.ab1

Day 8 (Monday) documents

Here is a guide on how to download a trial version of Geneious, which we will use for sequence and tracefile editing.

A very brief worksheet to get us started on Randy Olson’s And, But, Therefore (ABT) concept for science communication.

Day 5 (Friday) documents

PCR Calculations Exercise

PCR calculation worksheet as: spreadsheet or PDF.

Day 4 (Thursday) documents

Tracing information through the scientific literature

Day 3 (Wednesday) documents

This is the manual for the DNA extraction kits we will be using. What we will do today (Wednesday) is on pages 28–30.

PDF of Wednesday’s presentation: Ecology and the Biosphere

Day 1 (Monday) documents

The Exploration Vessel Nautilus streams images and scientist commentary (whenever they have ROVs in the water) at: http://nautiluslive.org. Check it out before we visit them on Friday!

PDF's of Monday’s presentations:
Introduction
Biodiversity and Evolution
Trees
Animal Diversity

First week online activities

Our aim in this week is to familiarize you with the core concepts of genetic barcoding — the main activity you will be performing during the on-site weeks.

Most of the readings are peer-reviewed scientific publications. They will not be easy to read, if you have not encountered the scientific literature before.

The most important thing is to understand the main ideas of each paper. Do not expect to understand every detail. You will run across words (and acronyms) that you have not heard before. If the word seems important to the main ideas of the paper, try to find its meaning simply by using Google search to find a definition. Some complex details, however, may not be worth the time to track down. A mental test for that is to ask yourself: “Could I explain the meaning of this paragraph to someone else even if I don’t know what that one word means?” If you have a core understanding of the main point, the detail can probably be skipped.

If you find that there are important areas in these papers that you don’t understand, please email us and ask us about it. Please ask specific questions rather than just asking for a general interpretation. For example, this would be a good question: “In the ‘Samples’ section of the ‘Materials and methods’ in the paper by Radulovici, why would the authors have been unable to preserve vouchers for small animals?” An example of a question we’d prefer not to see would be: “Can you please explain the section on ‘Biodiversity assessment’ in the paper by Fišer Pečnikar?”

Also keep in mind that we will spend some time discussing these papers (and others that we will give you when you arrive) during the on-site session. For you to participate fully in the on-site discussions, you will need a good understanding of these papers. However, we will also be on hand to answer questions directly when you are on-site.

Contacting us: For questions, and for the writing assignments below, please email us at: mbc@nhm.org

Getting the papers: All the papers are available for download from the following web page: http://research.nhm.org/mbc/arip2016

Monday — Day 1: National Institute of General Medical Sciences. 2010. The New Genetics.

Download

Read the following sections of this short book to reinforce your understanding of central concepts in molecular genetics. You can read the other sections if you like, but they focus more on human and disease issues, rather than central concepts.

Chapter 1: How Genes Work — read all.
Chapter 2: RNA and DNA Revealed — read pages 36–37 “The other human genome”.
Chapter 3: Life’s Genetic Tree — read all.
Chapter 5: 21st Century Genetics — read pages 86–87 “The tools of genetics”.

The bad news: it’s quite a few pages to read. The good news: no writing assignment today! This reading is background that will help make the next several papers understandable.

Tuesday — Day 2: Savolainen, V. et al. 2005. Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society B 360: 1805–1811.

Download

This paper introduces the key concepts behind DNA barcoding — the technique we will involve you in during the on-site work. As described above, make sure you understand all the key ideas in this paper. You should be able to understand each paragraph’s main point.

For this paper, and each of the following days’ papers, we want you to do a short writing assignment. The length should be quite short: about 250 words or less. The short paper you write should answer this question: “What was the most surprising or exciting idea to you in this research paper, and why?” It is important that you complete your writing during this day and email it to us — we will critique your writing and return it to you. That won’t work well if you fall behind.

You may either put your writing directly into the text of an email, or attach a Word-format document to the email you send. In either case, make sure you begin your writing with:
   Your Name (so we can easily see who is sending us this work).
   The first author’s last name and the year of the paper you’re writing about.

An example of the beginning of an assignment (using my name):
   Dean Pentcheff
   Savolainen 2005
   Being able to use barcode sequences to…

Wednesday — Day 3: Fišer Pečnikar, Ž. and E. V. Buzan. 2013. 20 years since the introduction of DNA barcoding: from theory to application. Journal of Applied Genetics 55(1): 43–52.

Download

This paper documents some of the ways DNA barcoding has developed since it was first devised, and some of its more important applications.

As with the Day 2 paper, write up your answer to our question and email it to us.

Thursday — Day 4: Radulovici, A. E., B. Sainte-Marie, and F. Dufresne. 2009. DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach. Molecular Ecology Resources 9:181–187.

Download

This paper describes a project in Canada that is similar to the large-scale project you will be participating in at the Marine Biodiversity Center when you are here on-site.

As with the Day 2 paper, write up your answer to our question and email it to us.

Friday — Day 5: Cristescu, M. E. 2014. From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends in Ecology & Evolution 29:566–571.

Download

This paper gives a global context for the biodiversity applications of DNA barcoding.

As with the Day 2 paper, write up your answer to our question and email it to us. We understand that you may be travelling by this time, so you may not receive our critique of your writing on this paper until you are on-site.