FISH 475 Lecture Notes - Lecture 20: Southern Resident Killer Whales, Polymerase Chain Reaction, Biopsy
10 Jun 2018
School
Department
Course
Professor
Cetacean genetics & genomics
Genetic Sex
-
Relatedness
-
Pedigree Construction
Looking at individuals between populations
○
-
Population Assignment
-
Stock Structure
-
Sequencing the Gene from within the nucleus from within a cell
Species ID
-
Individual ID
-
Phylogenetic analysis
-
Population genetics
-
Polymerase Chain Reaction
A technique to make many copies of a particular section of DNA.
-
Regents mixed with the nucleus will break the cell wall
-
Go from one copy (original) to 16 copies after fourth cycle
-
Sources of DNA:
Carcasses
-
Skin/Blubber Biopsy
-
Sloughed Skin
Sperm Whales are "really good" at sloughing skin
○
-
Feces
Also get prey information
○
-
Killer Whales
Southern Resident Killer Whales
Targeted for removal for captivity in the early 60s
○
Early 70s, photo-ID study, to better understand the population and the
affects of removing animals from the population
○
1972 population at all time low - 66 animals
○
Photo-Id studied emigration and immigration
○
Over-time there was a recovery, mid-90s saw steep decline in population
○
Listed as endangered in 2005, distinct population segment
○
-
Individual Recognition
"open" saddle patches are far more common among southern residents
than northerns
○
Right side often differs from the left side
○
Social Structure
Matrilineal Structure
§
Stable Social Units
§
Paternities?
Never see the actual mating□
Paternity Assignment
Taking samples from males in the area
®
Nuclear Genotypes
SNPs - single nucleotide polymorphism
◊
One difference in one location - distributed
throughout the genome
◊
The most common type of individual genetic
variation
◊
Biparentally inherited
◊
®
Paternity Patterns
Individual genotypes (genetic fingerprints)
◊
Skew in paternity assignments
◊
No evidence of gene flow from outside SRKWs
◊
No evidence that they are avoiding in-breeding
◊
®
□
§
Immigration/Emigration?
§
○
-
Three primary threats identified:
Prey availability
Evidence from stomach contents
§
Prey metabarcoding from whale feces
Library generation --> Barcoding --> Amplification -->
Consensus sequence generation
□
§
Over 100 samples
Mid-Summer Diet: Mostly Chinook, as well as other salmonid
species
□
Late Summer Diet: Almost equal Chinook and Coho, as well as
other salmonid species
□
Now looking at Winter Diet… TBD□
§
○
High levels of contaminants
○
Disturbance from vessels and sound
○
-
Harbor Porpoise
SE Alaska porpoise
Abundance Trends (1991-2012)
○
Decline in abundance in mid-1990s
○
Contrasting trends by region
○
Multiple populations
If there is more than one stock, that could lead to completely
different management strategies
§
○
-
Fst - Population Genetic Differentiation
Fst is a measure of population differentiation based on shared genetic
markers
○
Fst is a metric measured on a scale of 0 to 1.
○
Fst = 1.0 indicates that the two populations are fixed for different alleles
○
Fst = 0.0 indicates that the two populations are mixing and have
combinations of different alleles
○
-
eDNA
Hair cells, gametes, mucus, anything
○
Process:
Scoop 3L of water from the fluke print on the water
§
Filter through a skimmer
§
Extract DNA
§
Amplify mtDNA markers
§
qPCR & high throughput sequencing
§
Bioinformatic processing of sequence data
§
Species/Haplotype Identification
§
○
Phylogenetic clustering of porpoise mtDNA haplotypes
9 unique haplotypes (379bp)
§
7 haplotypes found previously in Alaska harbor porpoise
§
2 'new' haplotypes
§
3 eDNA samples contained two haplotypes
§
○
Alternative method of sample collection
○
Generation of population-level sequence data from eDNA
○
Novel approach to address data gaps in contemporary stock structure
○
-
Lecture 20: Cetacean genetics & genomics (Guest
Lecture)
Friday, May 11, 2018
9:33 AM
Cetacean genetics & genomics
Genetic Sex
-
Relatedness
-
Pedigree Construction
Looking at individuals between populations
○
-
Population Assignment
-
Stock Structure
-
Sequencing the Gene from within the nucleus from within a cell
Species ID
-
Individual ID
-
Phylogenetic analysis
-
Population genetics
-
Polymerase Chain Reaction
A technique to make many copies of a particular section of DNA.
-
Regents mixed with the nucleus will break the cell wall
-
Go from one copy (original) to 16 copies after fourth cycle
-
Sources of DNA:
Carcasses
-
Skin/Blubber Biopsy
-
Sloughed Skin
Sperm Whales are "really good" at sloughing skin
○
-
Feces
Also get prey information
○
-
Killer Whales
Southern Resident Killer Whales
Targeted for removal for captivity in the early 60s
○
Early 70s, photo-ID study, to better understand the population and the
affects of removing animals from the population
○
1972 population at all time low - 66 animals
○
Photo-Id studied emigration and immigration
○
Over-time there was a recovery, mid-90s saw steep decline in population
○
Listed as endangered in 2005, distinct population segment
○
-
Individual Recognition
"open" saddle patches are far more common among southern residents
than northerns
○
Right side often differs from the left side
○
Social Structure
Matrilineal Structure
§
Stable Social Units
§
Paternities?
Never see the actual mating□
Paternity Assignment
Taking samples from males in the area
®
Nuclear Genotypes
SNPs - single nucleotide polymorphism
◊
One difference in one location - distributed
throughout the genome
◊
The most common type of individual genetic
variation
◊
Biparentally inherited
◊
®
Paternity Patterns
Individual genotypes (genetic fingerprints)
◊
Skew in paternity assignments
◊
No evidence of gene flow from outside SRKWs
◊
No evidence that they are avoiding in-breeding
◊
®
□
§
Immigration/Emigration?
§
○
-
Three primary threats identified:
Prey availability
Evidence from stomach contents
§
Prey metabarcoding from whale feces
Library generation --> Barcoding --> Amplification -->
Consensus sequence generation
□
§
Over 100 samples
Mid-Summer Diet: Mostly Chinook, as well as other salmonid
species
□
Late Summer Diet: Almost equal Chinook and Coho, as well as
other salmonid species
□
Now looking at Winter Diet… TBD□
§
○
High levels of contaminants
○
Disturbance from vessels and sound
○
-
Harbor Porpoise
SE Alaska porpoise
Abundance Trends (1991-2012)
○
Decline in abundance in mid-1990s
○
Contrasting trends by region
○
Multiple populations
If there is more than one stock, that could lead to completely
different management strategies
§
○
-
Fst - Population Genetic Differentiation
Fst is a measure of population differentiation based on shared genetic
markers
○
Fst is a metric measured on a scale of 0 to 1.
○
Fst = 1.0 indicates that the two populations are fixed for different alleles
○
Fst = 0.0 indicates that the two populations are mixing and have
combinations of different alleles
○
-
eDNA
Hair cells, gametes, mucus, anything
○
Process:
Scoop 3L of water from the fluke print on the water
§
Filter through a skimmer
§
Extract DNA
§
Amplify mtDNA markers
§
qPCR & high throughput sequencing
§
Bioinformatic processing of sequence data
§
Species/Haplotype Identification
§
○
Phylogenetic clustering of porpoise mtDNA haplotypes
9 unique haplotypes (379bp)
§
7 haplotypes found previously in Alaska harbor porpoise
§
2 'new' haplotypes
§
3 eDNA samples contained two haplotypes
§
○
Alternative method of sample collection
○
Generation of population-level sequence data from eDNA
○
Novel approach to address data gaps in contemporary stock structure
○
-
Lecture 20: Cetacean genetics & genomics (Guest
Lecture)
Friday, May 11, 2018
9:33 AM
