Transcript Slide 1

Population and Evolutionary Genetic Analyses Using
Multiple Nuclear and Mitochondrial Loci in Steller Sea
Lions.
John W. Bickham, Ryan M. Huebinger, Thomas R. Gelatt, Greg
O’Corry-Crowe, and Joseph I. Hoffman
ACKNOWLEDGEMENTS
Project began in 1992
I thank the following for providing
samples:
T. Loughlin, T. Gelatt, V. Burkanov
and D. Calkins
Southeastern Alaska and PWSADF&G
Gulf of Alaska and Aleutian Is.-NOAA
sponsored cruises
ACKNOWLEDGEMENTS
Russia: Vladimir Burkanov, Nikolay Pavlov,
Vladimir Vertynkin, Evgeny Mamaev.
The Alaska SeaLife Center, Don Calkins
For help in the laboratory and for data
analysis I thank Alyson Baker, Robert
Trujillo, John Patton, Cole Matson and
Dmitri Politov.
200
Eastern Stock
East of 144°W
Population Estimates in Thousands
180
160
Western Stock
West of 144°W
140
120
100
80
60
40
20
0
1960s
1970s
1980s
1990s
1994
Population Estimates for Steller Sea Lions
(1960-1994)
Population Trends
 The total SSL population numbered between 240,000 and 300,000
during the late 1950’s and early 1960’s.
 Only 116,000 were estimated range-wide in 1989.
-1969-
-1979-
-1989-
RUSSIA
ALASKA
PWS
60°
BER
OKH
KAM
CGA
SEA
COM
WGA
EAL
WAL
45°
CAL
BRC
KUR
Sampled Rookeries
ORE
NCA
JAPAN
30°
135°E
180°
135°W
Previous Genetic Studies
Bickham et al. (1996):


Discovered high genetic differentiation
between populations on either side of 144˚W;
subsequently recognized an eastern stock
(threatened) and western stock (endangered)
Also found high diversity of “mtDNA
haplotypes and a clear pattern of
macrogeographic variation”
The Western and Eastern Stocks
RUSSIA
ALASKA
PWS
Cape Suckling
60°
BER
OKH
KAM
CGA
SEA
COM
WGA
EAL
WAL
45°
CAL
BRC
KUR
Sampled Rookeries
ORE
144°W
NCA
JAPAN
WESTERN
STOCK
30°
135°E
180°
EASTERN
STOCK
135°W
Previous Genetic Studies (cont)
Bickham et al. (1998)


Found evidence for three possible groups:
Asian and central groups within the western
stock and an eastern stock
Could have arisen due to two, possibly three,
glacial refugia that separated the populations
during the Pleistocene era
A Third Stock?
 Previous research suggests that animals sampled from Russian rookeries are
genetically distinct from other western stock sea lions.
RUSSIA
ALASKA
PWS
Cape Suckling
60°
BER
OKH
KAM
CGA
SEA
COM
WGA
EAL
WAL
45°
CAL
BRC
KUR
Sampled Rookeries
ORE
144°W
NCA
JAPAN
30°
135°E
ASIAN
STOCK
WESTERN
STOCK
180°
EASTERN
STOCK
135°W
Previous Genetic Studies (cont)
Baker et al. (2005)

Subdivided the Western Stock into Asian
Stock (OKH, KUR, KAM) and Western Stock
(COM east through PWS)
In this presentation we will:
Summarize a 14-year range-wide populationgenetic analysis based upon the mtDNA control
region of Steller sea lions.
Present preliminary results from an ongoing
complementary study of cytochrome b
sequences.
Compare phylogeographic and population
genetic patterns for control region vs. cyt b
sequences.
Present data from nuclear microsatellite loci that
corroborate some of the findings of stock
structure in Steller sea lions.
Control Region Sample Sizes
Stock
Region
EASTERN STOCK
NCA (1 ROOKERY)
51
ORE (1 ROOKERY)
85
BRC (2 ROOKERIES)
23
SEA (3 ROOKERIES)
76
WESTERN STOCK
TOTAL
235
PWS (2 ROOKERIES)
153
BER (1 ROOKERY)
42
CGA (6 ROOKERIES)
197
WGA (5 ROOKERIES)
108
EAL (6 ROOKERIES)
275
CAL (10 ROOKERIES)
247
WAL (3 ROOKERIES)
98
COM (1 ROOKERY)
TOTAL
ASIAN STOCK
Sample Size
126
1246
KAM (2 ROOKERIES)
71
KUR (5 ROOKERIES)
207
OKH (2 ROOKERIES)
237
TOTAL
515
GRAND TOTAL
1,710
Cytochrome b Sample Sizes
Stock
Region
EASTERN STOCK
NCA (1 ROOKERY)
27
ORE (1 ROOKERY)
32
BRC (2 ROOKERIES)
15
SEA (3 ROOKERIES)
341
TOTAL
415
WESTERN STOCK
PWS (2 ROOKERIES)
27
BER (1 ROOKERY)
21
CGA (7 ROOKERIES)
114
WGA (5 ROOKERIES)
32
EAL (6 ROOKERIES)
84
CAL (9 ROOKERIES)
73
WAL (3 ROOKERIES)
51
COM (1 ROOKERY)
46
TOTAL
ASIAN STOCK
Sample Size
448
KAM (2 ROOKERIES)
63
KUR (5 ROOKERIES)
74
OKH (2 ROOKERIES)
133
TOTAL
165
GRAND TOTAL
878
Microsatellite Sample Sizes
Stock
Region
EASTERN STOCK
NCA (1 ROOKERY)
25
ORE (1 ROOKERY)
25
BRC (2 ROOKERIES)
18
SEA (3 ROOKERIES)
45
TOTAL
WESTERN STOCK
113
PWS (2 ROOKERIES)
75
BER (1 ROOKERY)
13
CGA (3 ROOKERIES)
43
WGA (3 ROOKERIES)
30
EAL (4 ROOKERIES)
172
CAL (3 ROOKERIES)
70
WAL (1 ROOKERY)
12
COM (1 ROOKERY)
25
TOTAL
ASIAN STOCK
Sample Size
440
KAM (1 ROOKERY)
25
KUR (4 ROOKERIES)
40
OKH (2 ROOKERIES)
50
TOTAL
115
GRAND TOTAL
668
L-shaped distribution of control-region haplotypes
No evidence of a significant bottleneck or reduction in variation
Individual Haplotype Totals
N= 1,433 Individuals
N= 132 Haplotypes
50
40
30
20
10
Number of Individuals per Haplotype
10
5
12
8
18
2
25
2
86
31
35
36
51
16
17
21
22
6
7
8
10
11
12
13
3
4
5
0
1
2
Number of Haplotypes
60
Control Region Haplotype Distributions
Haplotype LLL
Haplotype Frequency
Haplotype Frequency
Haplotype BB
0.50
0.40
0.30
0.20
0.10
0.00
0.10
0.08
0.06
0.04
0.02
0.00
0.12
0.10
0.08
0.06
0.04
0.02
0.00
Haplotype H
Haplotype Frequency
Haplotype Frequency
Haplotype E
0.50
0.40
0.30
0.20
0.10
0.00
Cytochrome b Haplotype Distributions
Haplotype 4
1.00
0.90
0.90
Haplotype Frequency
Haplotype Frequency
Haplotype 1
1.00
0.80
0.70
0.60
0.50
0.40
0.30
0.20
0.10
0.00
0.80
0.70
0.60
0.50
0.40
0.30
0.20
0.10
0.00
Haplotype 10
1.00
0.90
0.90
0.80
0.70
0.60
0.50
0.40
0.30
0.20
0.10
0.00
Haplotype Frequency
Haplotype Frequency
Haplotype 2
1.00
0.80
0.70
0.60
0.50
0.40
0.30
0.20
0.10
0.00
NJ Tree for Rookeries
Based on Fst Estimates
Control Region
Legend
Asian Stock
Western Stock
Eastern Stock
Adak Island CAL
Akun Island EAL
Seal Rocks PWS
Clubbing Rocks WGA
Yunaska Island CAL
Ugamak Island EAL
Chirikof Island CGA
Amak Island EAL
Bogoslof Island EAL
Pinnacle Rock WGA
Chowiet Island CGA
Marmot Island CGA
Adugak Island EAL
Attu Island WAL
Amchitka Island CAL
Seguam Island CAL
Medney Island COM
Kasatoshi Island CAL
Sugarloaf Island CGA
Akutan Island EAL
Agattu Island WAL
Kozlova Cape RUS
Walrus Island BER
Fish Island PWS
Kiska Island Lief Cove CAL
Kiska Island Cape St. Stephen CAL
Buldir Island WAL
Gramp Rock CAL
Atkins Island WGA
Tag Island CAL
Ogchul Island EAL
Antsiferova Island KUR
Zheleznaya Bay KAM
Raykoke Island KUR
Iony Island OKH
Tuleniy Island OKH
Srednego Island KUR
Yamsky Island OKH
Lovushki Island KUR
Chernyye Bratya KUR
Forrester Island SEA
North Danger Rocks BRC
St. George Reef NCA
Triangle Island BRC
Hazy Islands SEA
Rogue Reef ORE
White Sisters Islands SEA
0.005 changes
NJ Tree Regions
OKH
Based on Fst Estimates
Control Region
KUR
KAM
COM
CAL
EAL
CGA
WGA
PWS
BER
WAL
Legend
Eastern Stock
Western Stock
Asian Stock
SEA
BRC
ORE
NCA
0.005 changes
NJ
Zalophus
A
XXXX
UUUUU
IIII
EEEEE
NNN
TTTTT
E
NJ tree of control region
haplotypes shows two distinct
eastern stock haplotype lineages.
F
XX
VV
AAAAA
B
R
FFFF
XXXXX
ZZZ
FFFFF
RRRR
UU
P
SSSS
III
C
YYYYY
H
Q
D
GGGG
BBBBB
SS
YY
LL
M
DDDDD
KKK
JJJJ
SSS
HHHH
MMMMM
OOOOO
Y
NNNNN
QQQ
OOOO
KKKK
PPPPP
LLLL
KKKKK
LLLLL
W
PPP
X
HH
II
JJJJJ
NN
U
SSSSS
0.001 substitutions/site
DDDD
EEEE
QQQQ
ZZZZZ
XXX
WWW
MMMM
TTTT
MM
KK
HHHHH
DD
HHH
NNNN
AAAAAA
T
EE
UUU
AAA
FF
V
BBB
GG
TT
JJ
PPPP
OOO
VVV
CC
G
QQ
YYY
RRRRR
GGG
YYYY
LLL
TTT
BBBB
MMM
RRR
VVVVV
AAAA
RR
S
O
WWWW
JJJ
FFF
DDD
QQQQQ
PP
BB
EEE
CCCC
WWWWW
IIIII
GGGGG
L
VVVV
K
AA
J
ZZ
BBBBBB
CCC
N
UUUU
OO
WW
Z
CCCCC
I
ZZZZ
16
29
5
Minimum Spanning
Network of Steller Sea Lion
Cytochrome b haplotypes
n = 878, 1040 bp
34
33
28
18
20
22
1
?
24
7
19
9
29 Variable Positions
Ti/Tv = 26/3
13 Silent, 13 Nonsynonymous Transitions
1 Silent, 2 Nonsynonymous Transversions
1st Position: 10 (9 AAS)
2nd Position: 6 (6 AAS)
3rd Position: 13 (0 AAS)
14 Total Variable Amino Acids
25
17
21
23
8
27
11
12
3
4
14
13
32
200+
15
25-50
26
100-200
WEST
2
31
EAST
10-25
50-100
30
?
10
ASIAN
6
White Line: Silent Mutation
Red Line: Amino Acid Shift
2-10
ALL
1
Regional Cytochrome b Slatkin’s Linearized FST
Midpoint Rooted NJ Phylogram
OKH
KUR
KAM
COM
CAL
CGA
WAL
WGA
BER
EAL
PWS
Legend
Eastern Stock
Western Stock
Asian Stock
BRC
OR
E
SEA
NCA
0.05 changes
NJ Phylogram of Rookeries
Based on Microsatellite Data
Yamsky Island -OKH
Srednego Island -KUR
Raykoke Island -KUR
Kozlova Cape -KAM
Iony Island -OKH
Lovushki Island -KUR
Kiska Island -CAL
Seguam Island -CAL
Sugarloaf Island -CGA
Yunaska Island -CAL
Akutan Island -EAL
Chirikof Island -CGA
Ogchul Island -EAL
Ugamak Island -EAL
Pinnacle Rocks -WGA
Medny Island -COM
Adugak Island -EAL
Antsiferova Island -KUR
Clubbing Rocks -WGA
Walrus Island -BER
Seal Rocks -PWS
Buldir Island -WAL
Chowiet Island -CGA
Fish Island -PWS
Atkins Island -WGA
Rogue Reef -ORE
St. George Island -NCA
North Danger Rocks -BRC
Triangle Island -BRC
Forrester Island -SEA
White Sisters Island -SEA
Hazy Island -SEA
0.01
Asian
Stock
Asian
Stock
Western
Stock
Eastern
Stock
Legend
Eastern Stock
Western Stock
Asian Stock
NJ Phylogram of Regions
Based on Microsatellite Data.
OKH
Asian
Stock
KAM
KUR
WAL
CAL
COM
EAL
Western
Stock
BER
WGA
CGA
Legend
Eastern Stock
Western Stock
Asian Stock
PWS
ORE
NCA
BRC
0.01
SEA
Eastern
Stock
Conclusions
Control Region Phylogeography
 Despite the generally high sample sizes in this study, resolution of
population substructure increased when rookeries were grouped into their
respective regions.
Control region sequences clearly support the recognition of three stocks.
Cytochrome b Phylogeography
• Clearly differentiates the eastern and western stocks but does not
resolve the Asian stock.
Microsatellite Analysis
•
Nuclear microsatellites show a pattern nearly the same as for the
cytochrome b gene.
• Clearly differentiates the eastern and western stocks but does not
resolve the Asian stock.
The Asian Stock
 The recognition of three management units may be appropriate for Steller sea
lion conservation.
RUSSIA
ALASKA
PWS
Cape Suckling
60°
BER
OKH
KAM
CGA
SEA
COM
WGA
EAL
WAL
45°
CAL
BRC
KUR
Sampled Rookeries
ORE
144°W
NCA
JAPAN
30°
135°E
ASIAN
STOCK
WESTERN
STOCK
180°
EASTERN
STOCK
135°W