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!
Wednesday, February 1, 2012
December 21st, 2011 class
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.
6. JCRS images.
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.
Part 6: Japan Coral Reef Society 14th Annual Symposium
Images from the conference.
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.
6. JCRS images.
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.
Part 6: Japan Coral Reef Society 14th Annual Symposium
Images from the conference.
Tuesday, January 31, 2012
January 25th, 2012 class
Presentations of applications by 15 groups. Overall, very well done; all groups passed.
Good job!
Good job!
January 18th, 2012 class
With Kimura-sensei.
Human evolution
“genjin” left Africa 20-10 man years ago.
Then “kyujin” (Neanderthal), and “shinjin” (us) – Neandethals expanded range a bit, but we expanded a lot. We were able to adapt to many environments, changing genotypes and phenotypes, lifestyles too.
Menu
1. Evolution
2. Pop gen
3. Genome analyses – tough, but can learn about genome analyses, don’t have to learn all!
1. Evolution
Darwin and Lamarck intro. Could be good to distinguish between the two.
Important points: a. DNA to RNA to proteins. DNA info.
b. cellular structure
c. gametes.
Discusses allele selection and natural mutations. Most mutations disappear, but a few stay. Stay by either selection or random!
Neutral evolution: random mutation, not directly apparent on selection.
Natural selection: of course, as explained.
1.5-3 mya, very diverse time. P. bosei, P. robustus, P. ethiopicus, A. africanus, H. habilus, H. ludorufeo. H. ergaster.
Order: Use of tools, then into Europe, then into Asia, then use of fire.
Maybe different theories on human evolution. Diverse ancestors, or all one group, or reticulate evolution, or half and half. Humans are one group, with some small reticulate evolution.
H. erectus was alive until recently, and also Neanderthal was in Europe same time as H. sapiens. "Heidelberg man" alive until recent in Mongolia/Tibet.
2. Pop gen.
Humans have 23 chromosomes. Ome=all (zentai). Genome, proteome, etc. 22 normal and 1 X/Y!
Chromosome structure. Chromatid, telomere, centromere, etc. Also introduce DNA base pairs, AGCT. A and G purines, C and T pyrimidines. A and T bond, etc.
Types of DNA mutation.
1. Translocation – multimegabase to chromosome, or monosomy, trisomy. Change in ploidy.
2. Kilobase to megabase: Tandem duplication, deletion, inversion
3. 10s to few kilobases: Alu element insertion, minisatellite, element insertion.
4. Few base pairs: substitution, single indels, microsats. E.g. SNPs. Transitions more common than transversions (C to T, G to A).
Discusses DNA and inheritance from each parent, plus mutations. Polymorphism, and how some stay in populations, and some disappear. How this can also lead to new species. Can compare number of changes with molecular clock.
Y and mtDNA do not recombine.
Genetic drift and founder effect. Uses example of alleles in population (gene pool) and how it can happen.
Small sizes can have harsh genetic drift much more easily. N=20 always rapidly fixes, n=1000 not much but changes. Bottleneck and founder event.
For humans, mtDNA has lots of mutations. Y chromosome too.
Y follows paternal, mtDNA follows maternal. Therefore can follow wide range of evolution. Be careful making assumptions using only one side of DNA, missing lots of the story!! By doing the genome, we can look at the rest of your ancestors. mtDNA’s Eve is the same thing – be careful! Y Adam is the same.
MRCA=most recent common ancestor.
Thus, much DNA has incomplete lineage sorting. Adding more DNA markers and you can get complete lineage sorting.
Genome:
2003 Human genome project finished.
Then, SNP project. HapMap.
Human Genome Gene Chip – 5man to 100 man SNPs (in one day). Next generation sequencer – soon a genome for 1000 USD.
Can envision reading all babies when born (!).
Genome-wide association study (GWAS); demography (pop movement etc/pop structure), natural selection, ancestral spp analyses.
a. GWAS: e.g. finding SNPs that link with human height. Weedon et al. 2008 etc. and related studies, now over 100 SNPs linked with height. Best to get all 100 SNP information, then calculate height.
b. Genome wide SNP, compare internal pop structure with distance from other populations. Infer pop history. E.g. Novembre et al. 2008 – mapping data fits with geographical history. Also migration in Polynesia; Tonga is mix of E Asia and PNG (Kimura et al. 2008; Price et al. 2008). Also examine admixed populations, understand how many generations have passed since admixing occurred.
c. Asia Pacific people came from E Asia. Several times of admixing/splitting.
Whole genome analyses:
Can use whole genome (n=2) of 1 person, can infer population size. With multiple people’s genomes, can infer sizes of populations in past. All infer serious bottleneck of 5000 people or so 50000 ybp. Do bottlenecks fit natural patterns? Usually to infer pop size, many samples, but can actually do this with whole genome! (Li et al. 2011).
Gronau et al. 201? – Bayesian inference from 6 genomes. All say humans evolved 50000 years ago. African populations split a long time ago.
Positive selection looks to fix must faster than neutral evolution (via selective sweep).
Population specific positive selection (selective sweep). Can look at human genotypes and phenotypes to examine this. Examples: Alcohol dehydrogenase, EDAR, etc.
Neanderthal genome – 1 to 4% in our genome!
Human evolution
“genjin” left Africa 20-10 man years ago.
Then “kyujin” (Neanderthal), and “shinjin” (us) – Neandethals expanded range a bit, but we expanded a lot. We were able to adapt to many environments, changing genotypes and phenotypes, lifestyles too.
Menu
1. Evolution
2. Pop gen
3. Genome analyses – tough, but can learn about genome analyses, don’t have to learn all!
1. Evolution
Darwin and Lamarck intro. Could be good to distinguish between the two.
Important points: a. DNA to RNA to proteins. DNA info.
b. cellular structure
c. gametes.
Discusses allele selection and natural mutations. Most mutations disappear, but a few stay. Stay by either selection or random!
Neutral evolution: random mutation, not directly apparent on selection.
Natural selection: of course, as explained.
1.5-3 mya, very diverse time. P. bosei, P. robustus, P. ethiopicus, A. africanus, H. habilus, H. ludorufeo. H. ergaster.
Order: Use of tools, then into Europe, then into Asia, then use of fire.
Maybe different theories on human evolution. Diverse ancestors, or all one group, or reticulate evolution, or half and half. Humans are one group, with some small reticulate evolution.
H. erectus was alive until recently, and also Neanderthal was in Europe same time as H. sapiens. "Heidelberg man" alive until recent in Mongolia/Tibet.
2. Pop gen.
Humans have 23 chromosomes. Ome=all (zentai). Genome, proteome, etc. 22 normal and 1 X/Y!
Chromosome structure. Chromatid, telomere, centromere, etc. Also introduce DNA base pairs, AGCT. A and G purines, C and T pyrimidines. A and T bond, etc.
Types of DNA mutation.
1. Translocation – multimegabase to chromosome, or monosomy, trisomy. Change in ploidy.
2. Kilobase to megabase: Tandem duplication, deletion, inversion
3. 10s to few kilobases: Alu element insertion, minisatellite, element insertion.
4. Few base pairs: substitution, single indels, microsats. E.g. SNPs. Transitions more common than transversions (C to T, G to A).
Discusses DNA and inheritance from each parent, plus mutations. Polymorphism, and how some stay in populations, and some disappear. How this can also lead to new species. Can compare number of changes with molecular clock.
Y and mtDNA do not recombine.
Genetic drift and founder effect. Uses example of alleles in population (gene pool) and how it can happen.
Small sizes can have harsh genetic drift much more easily. N=20 always rapidly fixes, n=1000 not much but changes. Bottleneck and founder event.
For humans, mtDNA has lots of mutations. Y chromosome too.
Y follows paternal, mtDNA follows maternal. Therefore can follow wide range of evolution. Be careful making assumptions using only one side of DNA, missing lots of the story!! By doing the genome, we can look at the rest of your ancestors. mtDNA’s Eve is the same thing – be careful! Y Adam is the same.
MRCA=most recent common ancestor.
Thus, much DNA has incomplete lineage sorting. Adding more DNA markers and you can get complete lineage sorting.
Genome:
2003 Human genome project finished.
Then, SNP project. HapMap.
Human Genome Gene Chip – 5man to 100 man SNPs (in one day). Next generation sequencer – soon a genome for 1000 USD.
Can envision reading all babies when born (!).
Genome-wide association study (GWAS); demography (pop movement etc/pop structure), natural selection, ancestral spp analyses.
a. GWAS: e.g. finding SNPs that link with human height. Weedon et al. 2008 etc. and related studies, now over 100 SNPs linked with height. Best to get all 100 SNP information, then calculate height.
b. Genome wide SNP, compare internal pop structure with distance from other populations. Infer pop history. E.g. Novembre et al. 2008 – mapping data fits with geographical history. Also migration in Polynesia; Tonga is mix of E Asia and PNG (Kimura et al. 2008; Price et al. 2008). Also examine admixed populations, understand how many generations have passed since admixing occurred.
c. Asia Pacific people came from E Asia. Several times of admixing/splitting.
Whole genome analyses:
Can use whole genome (n=2) of 1 person, can infer population size. With multiple people’s genomes, can infer sizes of populations in past. All infer serious bottleneck of 5000 people or so 50000 ybp. Do bottlenecks fit natural patterns? Usually to infer pop size, many samples, but can actually do this with whole genome! (Li et al. 2011).
Gronau et al. 201? – Bayesian inference from 6 genomes. All say humans evolved 50000 years ago. African populations split a long time ago.
Positive selection looks to fix must faster than neutral evolution (via selective sweep).
Population specific positive selection (selective sweep). Can look at human genotypes and phenotypes to examine this. Examples: Alcohol dehydrogenase, EDAR, etc.
Neanderthal genome – 1 to 4% in our genome!
January 11th, 2012 class
Conservation History on the Great Barrier Reef:
The Great Barrier Reef = GBR
Great Barrier Reef Marine Park
Outline
Background
Why was rezoning of GBR necessary?
Representative Areas Program (RAP) (only part of solution)
Phase 1 and 2
Final zoning plan
Implementation phase
Monitoring
Other actions
Reef Water Quality Plan
Reducing fishing and policing
The Great Barrier Reef = GBR
345,000 km2
> 2000 km long
2900 separate reefs
> 900 islands
Formation of the Park
Late 1960’s – early 1970’s—much agitation for a park, reinforced by plans to mine Ellison Reef (off Innisfail)
Politicians promised that the GBR should be protected as a Park
Park established in 1975, under Great Barrier Reef Marine Park Act (Federal Parliament Act)
Implementation
Park boundaries are non-negotiable, can only be changed by Act of Parliament
No mining within the Park
Development & implementation of zoning plans is a Federal responsibility
Day to day management is the responsibility of Queensland Parks & Wildlife Service
Zoning Plans
First areas to be zoned Capricorn and Bunker, finished in 1977
Subsequently the other regions were zoned
Zoning plans reviewed at regular intervals, with public participation, and plans changed over time and even the type of zones changed
GBRMPA
Based in Townsville
Responsible to Minister for Science
Issues permits and licences, including those for scientific research
GBR declared World Heritage Area in 1981— such listing requires regular report card to ensure the reef is being maintained
During the 1990’s
Increasing use of the reef by tourists
Increased scientific knowledge of the reef
Increasing awareness of the connectivity of reefs (mass spawning)
Increasing evidence of decline of some habitats, especially inshore
The Great Barrier Reef Is ‘Under Pressure’
Downstream effects of land use (water quality issues)
Coral bleaching
Coastal developments
Increasing fishing effort and impacts
Shipping & pollution incidents
Increasing tourism and recreation
Trends in Regional Biodiversity Are Negative
Fishing effort increasing substantially in intensity & spatial extent (coral trout fishery—effort x2 since 1995; shark catch x5 since 1991)
Turtles–all 6 species threatened; 2 are endangered (Loggerhead and Olive Ridley)
Dugong population south of Cooktown has declined >90% since mid-1980’s
Humpbacks listed as vulnerable; other cetaceans (Irrawaddy & Indo-Pacific hump-backed dolphins) listed as rare
Trends for most species unknown
GBR Is Not Isolated From World Trends
10% of world’s reefs destroyed or severely degraded
58% of world’s reefs potentially threatened
70% reefs already degraded in Indonesia & Philippines
On current trends 70% of the world’s reefs will have gone in 40 years
Minimising the
‘Pressures’
Downstream effects of land use ==> Reef Water Quality Action Plan (results not immediate)
Coastal developments ==> Aquaculture Regs; GBRMP permit requirements
Increasing fishing effort and impacts ==> Queensland FS fisheries management plans (ECTMP, Reef Line)
Minimising the
‘Pressures’
Shipping & pollution incidents ==> Australia Marine Shipping Authority shipping review, compulsory pilotage, mandatory reporting, etc
Increasing tourism and recreation ==> PoMs; new tourism framework
Threatened species ==> new policies; species recovery plans; seasonal closures, RAP
Protecting biodiversity ==> RAP
Why was rezoning of the GBR necessary?
Queenslanders depend on the GBR
Important for economy—tourism, commercial fishing, recreational fishing, shipping
Important for Traditional Owners—connection with Sea Country
Important for communities—relaxation, lifestyles
>90% Australians (including Queenslanders) wanted more no-take zones
Important for building knowledge—education, research
Better protection = insurance for all these values
Connectivity in the GBR
An overview of RAP
Representative examples of the entire diversity of habitats protected
RAP reviewed the existing zoning of the Marine Park
RAP attempted to minimise negative impacts for users and stakeholders while aiming to achieve protection of biodiversity
RAP has meant an increase in Green Zones to protect biodiversity
RAP is a crucial part of the solution to a complex problem
Other Issues Addressed During Rezoning
Some current zoning plans had been in existence for 16 years
Ensured consistent zone names and zone provisions throughout GBR
Coastal areas zoned for first time
Clearer delineation of zone boundaries (GPS co-ordinates)
Developing the Zoning Plan
The Zoning Plan was developed using environmental, economic, and social information
Clear Principles on how to use the environmental and social information were followed
These principles were set out in the first round of community participation (CP1)
Environmental Information
Bioregions
Bioregions were mapped between 1999 and 2002 using expert knowledge and best available data and methods
30 reef bioregions 40 non-reef bioregions
Many bioregions previously lacked adequate protection
At least 20% of each bioregion included in a no-take zone
The GBR Marine Park
Non reef bioregions
Environmental Information
Other key issues:
Special and unique places
Critical habitats such as turtle nesting sites
Deep & shallow water sea-grass, fish spawning sites etc.
Special and unique places
Critical turtle nesting areas
Environmental Information
Biophysical Principles guided selection and use of environmental information
The Principles :
were developed by independent reef scientists
published in CP1
said that at least 20% of each bioregion had to be in no-take zones
No-take zones must be
large
arranged to form viable network, allowing connectivity, provides insurance policy
Social & Economic Information
Sources:
Recreational fishing diaries, and tag and release records
Commercial fishing log-books
The location of boat-ramps and coastal developments
Historic ship-wrecks
Visitor use data
Over 10,000 submissions received in Phase 1 & >21,000 in Phase 2
All submissions read to identify community issues
All submissions were taken into account
Recreational fishing sites
Commercial fishing values
Using Social Information
Social, Economic, Cultural and Management Principles were:
developed by an independent panel of experts
published in Community Phase 1
The SEC Principles attempted to
minimise impact on existing users of the Marine Park
be fair—ie not impacting on one group or community more than another
but needed a Zoning plan easy to enforce
Previous Zoning
Previous Zoning, plus Trawl Plans
New green zones—environmental data only
Green zones—using economic data too
Green zones—revising boundaries
The Plan
What Does This Plan Do?
Provides strong, medium and long-term protection for future generations
Green zones mean more and bigger fish
Green zone spill-over, better fishing for reef communities
Natural values which attracts tourists and $ will be maintained
Protects at least 20% of each bioregion, special and unique areas, important habitats, and nesting areas—over 33% achieved
Phases of RAP
Classification (map biodiversity)
Reviewed existing protection
informal consultation with user groups
formal Community Participation phase 1
Identification of possible network options
Selection of most acceptable network
Draft zoning plan
formal Community Participation phase 2 (over 21,000 submissions)
Ministerial & parliamentary approval March 2004
Implemented July 1st 2004
Representative Areas Program
A new and effective network of ‘no-take’ areas representative of all bioregions helps to:
maintain biological diversity
maintain ecological processes and systems
provide an ecological safety margin, and if necessary, enable species and habitats to recover
ensure viable and sustainable industries
Current Status
Distribution of information and many maps to fishers, tourist operators, dive, boat and bait shops
Revised maps at boat ramps
Sorting out current permits in relation to new zoning, research stations issuing permits
Working with GPS manufacturers to incorporate zoning plans into charts, some available
Website available to download zoning plans for particular areas of interest
Related Activities
Reef Water Quality Protection Plan-implemented
Fisheries related: Reduction of number of fishing boats
Reduction in areas where trawling allowed
compensation being paid
Increased surveillance, penalties imposed
Dugong protected areas and reduce netting areas
Qld zoned adjacent coastal parks
Recognition of RAP
Authority awarded a Eureka Prize for Biodiversity Research and Banksia Environmental Award
WWF Australia acknowledges its importance for conserving biodiversity
Recognition overseas of importance of this approach to marine park management
Best practise
Relevance to Other Areas
Zoning with scientific basis
Problems facing the GBR faced by all reefal areas
Methods for zoning multi-use parks relevant to all areas in Australia and elsewhere
Such community involvement results in ownership and stewardship of the reef– schools adopting reefs, communities becoming effective policers
Other Management Strategies
Reef Water Quality Protection Plan
being implemented but ongoing and results will take years to be apparent
Reduction in number of fishing licences, compensation being paid
Increasing policing and enforcement
Global warming— the big question
increased rates of bleaching
increased cyclones activity
What is the long term future for the GBR?
Points to consider for Okinawa/Ryukyu Islands:
Only three major governments (National, 2 Prefectural).
However, management is very ambiguous.
Local fisheries have strong power; no no-take zones anywhere in Japan, aquaculture common.
Competing interests within national government have different agendas (Construction, Environment).
National laws for parks weak.
Okinawa Prefecture likely has strong wishes, but needs money from National government.
The Great Barrier Reef = GBR
Great Barrier Reef Marine Park
Outline
Background
Why was rezoning of GBR necessary?
Representative Areas Program (RAP) (only part of solution)
Phase 1 and 2
Final zoning plan
Implementation phase
Monitoring
Other actions
Reef Water Quality Plan
Reducing fishing and policing
The Great Barrier Reef = GBR
345,000 km2
> 2000 km long
2900 separate reefs
> 900 islands
Formation of the Park
Late 1960’s – early 1970’s—much agitation for a park, reinforced by plans to mine Ellison Reef (off Innisfail)
Politicians promised that the GBR should be protected as a Park
Park established in 1975, under Great Barrier Reef Marine Park Act (Federal Parliament Act)
Implementation
Park boundaries are non-negotiable, can only be changed by Act of Parliament
No mining within the Park
Development & implementation of zoning plans is a Federal responsibility
Day to day management is the responsibility of Queensland Parks & Wildlife Service
Zoning Plans
First areas to be zoned Capricorn and Bunker, finished in 1977
Subsequently the other regions were zoned
Zoning plans reviewed at regular intervals, with public participation, and plans changed over time and even the type of zones changed
GBRMPA
Based in Townsville
Responsible to Minister for Science
Issues permits and licences, including those for scientific research
GBR declared World Heritage Area in 1981— such listing requires regular report card to ensure the reef is being maintained
During the 1990’s
Increasing use of the reef by tourists
Increased scientific knowledge of the reef
Increasing awareness of the connectivity of reefs (mass spawning)
Increasing evidence of decline of some habitats, especially inshore
The Great Barrier Reef Is ‘Under Pressure’
Downstream effects of land use (water quality issues)
Coral bleaching
Coastal developments
Increasing fishing effort and impacts
Shipping & pollution incidents
Increasing tourism and recreation
Trends in Regional Biodiversity Are Negative
Fishing effort increasing substantially in intensity & spatial extent (coral trout fishery—effort x2 since 1995; shark catch x5 since 1991)
Turtles–all 6 species threatened; 2 are endangered (Loggerhead and Olive Ridley)
Dugong population south of Cooktown has declined >90% since mid-1980’s
Humpbacks listed as vulnerable; other cetaceans (Irrawaddy & Indo-Pacific hump-backed dolphins) listed as rare
Trends for most species unknown
GBR Is Not Isolated From World Trends
10% of world’s reefs destroyed or severely degraded
58% of world’s reefs potentially threatened
70% reefs already degraded in Indonesia & Philippines
On current trends 70% of the world’s reefs will have gone in 40 years
Minimising the
‘Pressures’
Downstream effects of land use ==> Reef Water Quality Action Plan (results not immediate)
Coastal developments ==> Aquaculture Regs; GBRMP permit requirements
Increasing fishing effort and impacts ==> Queensland FS fisheries management plans (ECTMP, Reef Line)
Minimising the
‘Pressures’
Shipping & pollution incidents ==> Australia Marine Shipping Authority shipping review, compulsory pilotage, mandatory reporting, etc
Increasing tourism and recreation ==> PoMs; new tourism framework
Threatened species ==> new policies; species recovery plans; seasonal closures, RAP
Protecting biodiversity ==> RAP
Why was rezoning of the GBR necessary?
Queenslanders depend on the GBR
Important for economy—tourism, commercial fishing, recreational fishing, shipping
Important for Traditional Owners—connection with Sea Country
Important for communities—relaxation, lifestyles
>90% Australians (including Queenslanders) wanted more no-take zones
Important for building knowledge—education, research
Better protection = insurance for all these values
Connectivity in the GBR
An overview of RAP
Representative examples of the entire diversity of habitats protected
RAP reviewed the existing zoning of the Marine Park
RAP attempted to minimise negative impacts for users and stakeholders while aiming to achieve protection of biodiversity
RAP has meant an increase in Green Zones to protect biodiversity
RAP is a crucial part of the solution to a complex problem
Other Issues Addressed During Rezoning
Some current zoning plans had been in existence for 16 years
Ensured consistent zone names and zone provisions throughout GBR
Coastal areas zoned for first time
Clearer delineation of zone boundaries (GPS co-ordinates)
Developing the Zoning Plan
The Zoning Plan was developed using environmental, economic, and social information
Clear Principles on how to use the environmental and social information were followed
These principles were set out in the first round of community participation (CP1)
Environmental Information
Bioregions
Bioregions were mapped between 1999 and 2002 using expert knowledge and best available data and methods
30 reef bioregions 40 non-reef bioregions
Many bioregions previously lacked adequate protection
At least 20% of each bioregion included in a no-take zone
The GBR Marine Park
Non reef bioregions
Environmental Information
Other key issues:
Special and unique places
Critical habitats such as turtle nesting sites
Deep & shallow water sea-grass, fish spawning sites etc.
Special and unique places
Critical turtle nesting areas
Environmental Information
Biophysical Principles guided selection and use of environmental information
The Principles :
were developed by independent reef scientists
published in CP1
said that at least 20% of each bioregion had to be in no-take zones
No-take zones must be
large
arranged to form viable network, allowing connectivity, provides insurance policy
Social & Economic Information
Sources:
Recreational fishing diaries, and tag and release records
Commercial fishing log-books
The location of boat-ramps and coastal developments
Historic ship-wrecks
Visitor use data
Over 10,000 submissions received in Phase 1 & >21,000 in Phase 2
All submissions read to identify community issues
All submissions were taken into account
Recreational fishing sites
Commercial fishing values
Using Social Information
Social, Economic, Cultural and Management Principles were:
developed by an independent panel of experts
published in Community Phase 1
The SEC Principles attempted to
minimise impact on existing users of the Marine Park
be fair—ie not impacting on one group or community more than another
but needed a Zoning plan easy to enforce
Previous Zoning
Previous Zoning, plus Trawl Plans
New green zones—environmental data only
Green zones—using economic data too
Green zones—revising boundaries
The Plan
What Does This Plan Do?
Provides strong, medium and long-term protection for future generations
Green zones mean more and bigger fish
Green zone spill-over, better fishing for reef communities
Natural values which attracts tourists and $ will be maintained
Protects at least 20% of each bioregion, special and unique areas, important habitats, and nesting areas—over 33% achieved
Phases of RAP
Classification (map biodiversity)
Reviewed existing protection
informal consultation with user groups
formal Community Participation phase 1
Identification of possible network options
Selection of most acceptable network
Draft zoning plan
formal Community Participation phase 2 (over 21,000 submissions)
Ministerial & parliamentary approval March 2004
Implemented July 1st 2004
Representative Areas Program
A new and effective network of ‘no-take’ areas representative of all bioregions helps to:
maintain biological diversity
maintain ecological processes and systems
provide an ecological safety margin, and if necessary, enable species and habitats to recover
ensure viable and sustainable industries
Current Status
Distribution of information and many maps to fishers, tourist operators, dive, boat and bait shops
Revised maps at boat ramps
Sorting out current permits in relation to new zoning, research stations issuing permits
Working with GPS manufacturers to incorporate zoning plans into charts, some available
Website available to download zoning plans for particular areas of interest
Related Activities
Reef Water Quality Protection Plan-implemented
Fisheries related: Reduction of number of fishing boats
Reduction in areas where trawling allowed
compensation being paid
Increased surveillance, penalties imposed
Dugong protected areas and reduce netting areas
Qld zoned adjacent coastal parks
Recognition of RAP
Authority awarded a Eureka Prize for Biodiversity Research and Banksia Environmental Award
WWF Australia acknowledges its importance for conserving biodiversity
Recognition overseas of importance of this approach to marine park management
Best practise
Relevance to Other Areas
Zoning with scientific basis
Problems facing the GBR faced by all reefal areas
Methods for zoning multi-use parks relevant to all areas in Australia and elsewhere
Such community involvement results in ownership and stewardship of the reef– schools adopting reefs, communities becoming effective policers
Other Management Strategies
Reef Water Quality Protection Plan
being implemented but ongoing and results will take years to be apparent
Reduction in number of fishing licences, compensation being paid
Increasing policing and enforcement
Global warming— the big question
increased rates of bleaching
increased cyclones activity
What is the long term future for the GBR?
Points to consider for Okinawa/Ryukyu Islands:
Only three major governments (National, 2 Prefectural).
However, management is very ambiguous.
Local fisheries have strong power; no no-take zones anywhere in Japan, aquaculture common.
Competing interests within national government have different agendas (Construction, Environment).
National laws for parks weak.
Okinawa Prefecture likely has strong wishes, but needs money from National government.
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