marine molecular ecology for conservation and managements marine species

Question 1

Why do we need identifiable groups?

Answer 1

To enable us to describe, study, count, monitor and assess

To allow us to prioritise conservation issues by quantifying and qualifying management units

To be able to trace wildlife

Question 2

Biological species concept

Answer 2

“species are groups of actually and potentially interbreeding populations that are reproductively isolate from other such groups”

Question 3

problems with the “biological species concept”

Answer 3

not clear with hybridising species
Difficult to apply to fossils
Asexual organisms do not fit the criteria

Question 4

How can genetic tools help with the species question?

Answer 4

Genetic analysis can reveal the extent of population structuring and therefore give us an indication of subgroup effectiveness

Question 5

Ecotypes

Answer 5

genetically distinct group within species which is adapted to specific environmental conditions

Question 6

Evolutionary significant figures

Answer 6

populations or groups of populations that merit separate management or priority for conservation because of high distinctiveness (both genetic and ecological)

Question 7

Gene

Answer 7

defined sequence of DNA

Question 8

Locus

Answer 8

defined sequence of DNA, may or may not be a gene

Question 9

Allele

Answer 9

sequence variation at a locus

Question 10

Haptotype

Answer 10

set of alleles, e.g. individual collection of specific mutations within a given genetic segnment

Question 11

Micro satellites (micro stats)

Answer 11

locus with a simple sequences repeated several times e.g. -Di, -Tri or -Tetra

Question 12

types of Markers used

Answer 12

Microchondrial DNA (mtDNA)
Nuclear DNA
Micro satellites (Micro stats)
Allozymes
RFLPs & AFLPs

Question 13

Advantages of DNA barcoding

Answer 13

All aerobic organisms
High copy numbers per cell (mtDNA)
Considered a ‘neutral’ marker
Generally high inter specific but low intra specific variation

Question 14

Disadvantages of DNA Barcoding

Answer 14

Anaerobic organisms excluded
Too much or too little variation e.g. plants
Risk of errors

Question 15

risk of errors in DNA Barcoding

Answer 15

incomplete lineage sorting
Differences in morphology and ecology
Populations reproductively isolated

Question 16

what does low levels of sequence divergence indicate?

Answer 16

evolutionary changes occurred relatively rapidly and recently e.g. variation at neutral markers may not yet have had time to accumulate

Question 17

cryptic or sibling species

Answer 17

Pair or groups of closely related, frequently sympathetic species that are morphologically indistinguishable but which are reproductively isolated

Question 18

sub-species

Answer 18

Those species which are part way through the (very slow) speciation process

They often have a unique geographica range or habitat are distinguishable genetically

They do not normally exhibit reproduce isolation and can produce fertile offspring

Although there can be a reduction in fertility or survival of these offspring

Question 19

‘SUTURE ZONE’

Answer 19

cluster of hybrid zones formed when ‘paired’ species breed- often when regional biotas come into contact at biogeographical borders

Question 20

marine wildlife forensics (Cetaceans in Taiwan management)

Answer 20

Molecular techniques increasing used in wildlife forensics
Taiwan has 27 cetacean species
Protected by law
Cetacean meat suspected of being sold as ‘meat fritters’

Developed a set of COI cetacean primers
Used 2% threshold level for species delimitation
Checked sequences against GenBank
Of 4 fritters tested, 75% positive for cetacean and/or pinniped DNA
Cetacean DNA was from multiple individuals per species
Confirmed that marine mammals were illegally captured and/or illegally imported to Taiwan

Question 21

Environmental DNA (eDNA)

Answer 21

Genetic material obtained directly from environmental samples (seawater, sediment etc.) without an obvious signs of biological source material

Question 22

Advantages of eDNA

Answer 22

Avoids needs for physical/visual ID

Ensures identification of cryptic species/juvenile life stages

Alternate to taxonomic expertise

Efficient (sensitive, cost-efficient, ever-improving DNA sequencing technology)

Non-invasive

Easy-to-standardise sampling

Can be used on museum/extinct species

Question 23

Disadvantages of eDNA

Answer 23

Contamination

Inhibition

Not specific/too specific

High error rates

Dilution/dispersal in seawater

Maintaining reliable results over temporal and spatial scales

Question 24

whale shark example of eDNA use

Answer 24

Difficult to practically sample whale shark individuals/populations

Sampled seawater for whale shark DNA and compared with tissue samples