December 21, 2012 class notes

Outline
1. Introduction: What is a species?
2. Taxonomic species: Amphipods in the Ryukyus.
3. Biological species: Fish species complex!
4. OTU & barcodes: ARMS and estimating coral reef biodiversity.
5. Conclusions.

1. Introduction: What is a species?
What is biodiversity? (Review)
Biodiversity = Number of taxa (species, genera).
OTUs = operational taxonomic units
Coral reefs are highly biodiverse, <0.2% of surface of Earth, >25% of marine species live there.
What is a species?
A species can be different, depending on who you talk to, or what meaning is implied.
Before we discuss species, we must be clear about what species concept we are discussing.
Three types are:
1. taxonomic species
A species with a scientific name.
Names are important for science & conservation.
Accuracy and authorship important.
Problems:
Naming species takes time & money.
Few experts.

2. Biological species
A species proven to reproduce only with itself.
Reproductive isolation.
Species concept important.
Problems:
Experiments take time & money.
Hybrids? Evolution is messy.

3. OTU/barcode species
A species defined by genetic differences.
Implies a threshold value.
Quick and easy.
Problems:
Sequencing species takes time & money.
Limited by previous knowledge.
Not always “true”, barcoding gap is problematic.

It is estimated we have described 1~25% of the total marine species.
Description of all species – possible?
However, describing is important.
1. Unknown species - What kind of undescribed species exist?
We have no idea what awaits discovery.
2. “Hidden” species
Hidden species may be hidden due to their cryptic nature, or due to researchers not being able to distinguish them from other, similar species. Usually small.
Often, there are large groups of “species complexes” that are hard to make sense of.

C. Known but not described species
We know this is a zoanthid. DNA has shown us how it is related to other zoanthids (=very unique).
We also know it is undescribed, and only on Okinawa.
It is waiting to be described.


Part 2: Taxonomic species
Commensal amphipods in Okinawa
White & Reimer 2011-2012
Taxonomic species
Can be detected through observation of morphology or classic diagnostic characteristics. DNA?
Compare with previous taxonomic literature.
Only way to name a species.

Leucothoidae (139 sp.) – one family of amphipods
Anamixid clade (pronounced sexual dimorphism):
• 22 Anamixis Stebbing, 1897
• 4 Nepanamixis Thomas, 1997a
• 13 Paranamixis Schellenberg, 1938
Leucothoid clade
(minimal to moderate sexual dimorphism):
• 98 Leucothoe Leach, 1814a
• 2 Paraleucothoe Stebbing, 1899
Ecologically unique
• Endocommensal associates of sponges, ascidians, and bivalve mollusks
• Extended parental care
• Social system
• Potential eusociality
• 
These are completely unexamined in Okinawa!
Contain two morphotypes, leucomorphs and anamorphs, previously thought to be different families of amphipods! DNA barcoding confirmed same species.
Materials and Methods
• Collect in-situ directly from host, take whole host, or coral rubble
• Traditional taxonomy
• Digital Inking
• Molecular DNA sequencing
Results 
25 new species from Okinawa in 1.5 years. More diverse in Okinawa than the GBR.


Part 3: Biological species
Fish species complex in the Pacific (Leray et al. 2010)
Biological species
Can be detected through observation of reproduction.
Also, reproductive experiments.
But these require extensive field work. Recently, molecular analyses usual, using phylogeny.
Background – Genus Dascyllus: Complex has 4 species:
1. D. trimaculatus (E. Africa to Central Pacific): 3 spots
2. D. albisella (Hawaii): white flanks
3. D. strasburgi (Marquesas Islands): gray
4. D. auripinnis (Line, Phoenix Islands): yellow fins
Each species has its own ecology and preferred habitats.
Materials and Methods
Specimens (n=563) from across the Indo-Pacific.
Microsatellite DNA data examined (data from previous research included).
Phylogenetic analyses and genotype assignment.
Results
Previous research showed 5 clades, not 4 (Bernadi et al. 2003).
This research showed 7 (!) groups of Dascyllus, not all with clear morphology.
Appears ancient history of Indo-Pacific combined with recent evolutionary events drives speciation.
Hybridization appears to be occuring.
NOTE: unknown species are not yet valid species, or new species. They are undescribed species.

So…. Biological species
Results could lead to “finding” undescribed species or groups
This leads to…
Taxonomic species
Describing a species.
Only way to give a scientific name.
New species.


Part 4: OTU/barcode species
ARMS and crustaceans
Plaisance et al. 2011;
Brainard et al. 2010
Background:
Coral reef monitoring of other species asides from fish/corals.
Establish systematic and consistent metric to assess and monitor change.
ARMS – manmade deployment devices to look at crustaceans/molluscs, etc., simulate dead coral heads.
Easy to build, 200USD each.
Rugged, look like plastic boxes/crates.
Prototypes tested in Northwestern Hawai’i. Seemed to work well.
Deployed worldwide, and retrieved. Then processed, samples preserved, DNA sequencing (DNA barcoding).

So…. OTU/barcode species
Results could lead to “finding” undescribed species or groups
This leads to…
Biological species
Results could lead to “finding” undescribed species or groups
This leads to…
Taxonomic species
Describing a species.
Only way to give a scientific name.
New species.

References cited:
1. CP Meyer, G Paulay. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3(12) e422.
2. KN White, JD Reimer – three papers (2011-2012). Commensal Leucothoidae in the Ryukyu Archipelago, Japan. ZooKeys (in press).
3. M Leray, R Beldade, SJ Holbrook, RJ Schmitt, S Planes, G Bernadi. 2010. Allopatric divergence and speciation in coral reef fish: the three spot dascyllus, Dascyllus trimaculatus, species complex. Evolution 64-5: 1218-1230.
4. L Plaisance, MJ Caley, R Brainard, N Knowlton. 2011. The diversity of coral reefs: what are we missing? PLoS One vol 6 issue 10 e25026.
5. R. Brainard et al. 2009. Autonomous Reef Monitoring Structures (ARMS): a tool for monitoring indices of biodiversity in the Pacific Islands. Pacific Science InterCongress, March 4, 2009.