Wednesday, February 1, 2012

February 1st, 2012 class

Outline
1. Introduction: Problems facing taxonomy and diversity.
2. Accelerating “taxonomy”: DNA barcoding.
3. Promoting taxonomy: Census of Marine Life.
4. Images from one CoML Project (Creefs).
5. Conclusions.
6. Test advice.

1. Introduction: Problems facing taxonomy and diversity.
Problems facing taxonomy 1
Too many species! Diversity confounds our best efforts to examine it.
Keep finding new species.
Extinction rates increasing.
Problems facing taxonomy 2
Not enough taxonomists.
Pay poor, work long.
Everyone says “important” but not considered essential.
Many groups have no active workers.
Potential solutions 1
Increasing technology and information available.
Global information systems.
Molecular experiment techniques.
Potential solutions 2
Increasing international research collaboration.
Growing awareness of biodiversity and importance.


2. Accelerating “taxonomy”: DNA barcoding.
What is “DNA barcoding”?
遺伝子バーコードというのは?
A DNA barcode is a short sequence, taken from standardized portions of the genome,used to identify species.
遺伝子バーコードとはひとつの配列を利用して、全生物の種類区別を行うこと。
If a genome project is deep and narrow, DNA barcoding is broad and shallow.
Genome projectは深くて、狭いが、遺伝子バーコードは浅くて、広い。
Requirements of a DNA barcoding marker
A sequence/marker used to barcode should:
be easy to amplify
not possess paralogues
have conserved regions to design primers efficiently for a broad taxonomic sampling
be variable enough to distinguish species
but conserved enough within species
Choosing the correct DNA marker is critical.
Point:
Barcoding does not aim to solve phylogeny!
Reasons for DNA barcoding
1. Works with fragments.
2. Works with all stages of life: Can link male/females. Different stages of same organism. E.g. Amphipods (White & Reimer 2012)
3. Cryptic species detection. E.g. Astraptes
4. Reduces ambiguity (set DNA code).
5. Makes expertise go further.
6. Democratizes access to data. E.g. Barcode of Life project
7. Opens the way for handheld barcoders.
8. Finds new diversity.
9. Demonstrates value of museum collections. Sequencing of collections vital.
10. Speeds up discovery of new species.
Additional strong point
Does not need expert knowledge.
Weak points
1. DNA (specifically COI) does not always work for each group of organisms.
2. Handheld technology has not succeeded, despite many advances.
3. Different taxa have different DNA protocols, so standardization is difficult.
4. The “barcoding gap”
Barcoding implies that the level of DNA divergence between and within species is different.
But evolution not neat - hybrids, incomplete lineage sorting, etc.
This gap is not always present – so taxonomy comes back to “judgement”.

Results
DNA barcoding proposed in 2003 as a “solution” to taxonomy.
Two large projects: Barcode of Life and Ocean Genome Legacy.
Encyclopedia of Life on the internet.
Common method of identification.
Gaining acceptance as a practical method to obtain much data.
But has not solved taxonomy, instead a new approach or “sub-field”.

For zoanthids (and corals), > 1 DNA marker is needed.
mt DNA evolves very slowly.
Still, better than no experts at all!

3. Promoting taxonomy: Census of Marine Life.

Scientific Framework
What has lived in the oceans?
What does live in the oceans?
What will live in the oceans?
The Census consisted of four major component programs organized around these questions.
1. Investigating the Past
Census researchers undertook the challenge of constructing the history of marine animal populations since human predation became important, roughly the last 500 years. This program component was called HMAP.
Teams of fisheries scientists, historians, economists and others conducted case studies in southern Africa, Australia, and approximately a dozen other regions.
Together, these case studies created the first reliable picture of life in the oceans before fishing.
The long historical records of marine populations help distinguish the contributions of natural fluctuations in the environment from the effects of human activities.
2. Assessing the Present
The largest component of the Census involved investigating what now lives in the world's oceans through 14 field projects.
Each sampled important kinds of biota in one of six realms of the global oceans using a range of technologies.
This included CReefs.
3. Forecasting the Future
To speak about what will live in the oceans required numerical modeling and simulation. This component program is the Future of Marine Animal Populations (FMAP).
Integrating data from many different sources and creating new statistical and analytical tools to predict marine populations and composition of ecosystems in the future
4. Living Legacy
Such a global initiative required a state-of-the-art data assimilation framework, and this is:Ocean Biogeographic Information System (OBIS).

Numbers
2,700 scientists
80+ nations
540 expeditions
US$ 650 million
2,600+ scientific publications
6,000+ potential new species
30 million distribution records and counting

Example: CReefs:
Heron Island Trip
November 8th – December 1st, 2010
Census of Coral Reef Ecosystems (www.creefs.org), part of Census of Marine Life (CoML – www.coml.org).
Large international effort to understand biodiversity, use data for conservation.
Many researchers from different institutions, focused on different taxa, many “ignored”.
I focused on zoanthids (of course)!
Location:
Heron Island
Many seabirds nest here. Always noisy, and dangerous to walk without a hat!
Rails also live on the island.
The island is an important nesting site for green and loggerhead sea turtles.
Heron Island Research Station is run by the University of Queensland. Most of the station is very new.
There are excellent facilities for experiments, sample collection, and analyses, indoors and outside.
Scientists from all over the world, most based in Australia, but others from USA, Japan, Iceland, etc.
Most scientists had much field experience, and were good divers. Many also had boat licenses and first aid training.
There were also dive officers, who acted as boat captains, guides, diving assistants, etc.
Outreach included a professional photographer, and a professional blogger with stories and images posted every day.
A professional chef ensured everyone was well-fed. The food was amazing!
Every night at dinner, based on everyone’s ideas, weather conditions, and tides, the next day’s schedule was decided.
Boats were launched from the harbor, 3-10 people per boat. Often boats were out for over 7 hours.
Diving was always done under the buddy system, with very strict guidelines on diving protocol.
Special permits were obtained to allow specimen collection. Work underwater was intense and focused.
I was able to collect 270 specimens in 33 dives. Other groups collected up to >2000 specimens!
Samples were also collected on reef walks, and by snorkeling. Other groups used ARMS and the “carpet of death”.
Some groups found many new species, others new records for the southern GBR. This genus was found in the southern Pacific Ocean for the 1st time, likely a new species.
Another potential new species of zoanthid.
Many people also collected for other groups.
Back in the lab, data were collected, and specimens numbered. All data were given to the CReefs data manager as well.
All sites were assigned numbers, and all had GPS coordinates. 130 sites were visited in 3 weeks!
Samples will be shipped to institutions all over the world and analyzed further.
Of course, work was not 24 hours a day…
Sunset drinks were the one time of day when everyone would relax and take a break.
And the sunsets were amazing…

References cited:
1. CP Meyer, G Paulay. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3(12) e422.
2. Consortium for Barcoding of Life homepage.
3. Census of Marine Life homepage.
4. OBIS homepage.

Test
Wednesday, February 8th; 8:30-10:00.
10 questions, choose 7.
Open book, no cellphones, etc.
Must pass to pass class.
Arrive after 9 a.m. – out.
Advice: study!

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