Supporting Information
Table S1. Number of reads (following quality filtering) and loci (with >15 reads per locus)
generated by RAD sequencing of pooled common bottlenose dolphin samples from the Florida
Panhandle and central-west Florida. Samples represent coastal and estuarine (St. Joseph Bay &
Sarasota Bay) populations and multiple unusual mortality events (UMEs) associated with red
tides. Sample accession numbers reference pooled sample sequences within NCBI Short Read
Archive project SRP040141.
Sample
Accession
Collection
Years
DNA
Quality
N
Reads
Loci
Read Depth
(avg ± sd)
SRX492615
SRX492615
SRX492616
SRX492617
SRX492618
2004-2005
2004-2005
2004-2006
1999
2004
Excellent
Good
Excellent
Good
Good
9
8
12
16
35
14,880,205
13,889,991
16,594,432
9,236,187
13,896,773
118,299
116,659
118,030
110,902
119,743
103.35 ± 64.54
98.46 ± 61.85
114.08 ± 73.78
59.37 ± 39.17
80.16 ± 54.99
SRX492613
SRX490773
SRX492614
SRX492614
1999-2000
2009-2011
1992-2006
1992-2006
Good
26
Excellent 25
Excellent
13
Good
12
Total 156
a
includes 9 samples collected from other HABs between 1992-2003.
3,073,044
17,269,321
15,101,244
15,386,415
119,327,612
62,391
119,823
119,454
120,991
129,594
34.79 ± 25.96
112.4 ± 73.46
100.60 ± 63.76
97.05 ± 61.48
88.69 ± 63.45
Sample Pool
Florida Panhandle
Live coastal
Live coastal
Live estuarine
1999 UME
2004 UME
Central-west Florida
Live coastal
Live estuarine
2005-2006 UMEa
2005-2006 UMEa
1
Table S2. Full gene names for annotated genes found in the common bottlenose dolphin genome
within 200 Kb of three loci that were identified as significant BayeScan outliers in at least three
comparisons of allele frequency between live and dead dolphins (Fig. 4). Relative position
describes distance (bp) between RAD locus and annotated gene.
Relative pos. (bp)
Locus 127758
111,241
Locus 134756
-150,545
-128,503
-98,139
-92,826
-77,612
-71,168
-50,468
-49,678
-34,134
-6,700
31,618
81,239
97,912
112,799
117,363
127,314
142,714
149,268
183,168
193,347
Locus 134756
-105,324
-10,064
6,241
66,715
89,088
119,602
Gene Symbol
Gene Name
KAZN
kazrin, periplakin interacting protein
PRDM7
GAS8
AFG3L1
AFG3L1L
TIGD1L
DEF8
MC1R
na
TCF25
SPIRE2
FANCA
ZNF276
VPS9D1
SPATA2L
CDK10
SPATA33
CHMP1A
DPEP1
CPNE7
RPL13
PR domain containing 7
growth arrest-specific 8
AFG3-like protein 1
AFG3-like protein 1-like
tigger transposable element-derived protein 1-like
differentially expressed in FDCP 8 homolog
Melanocortin-1 receptor
novel miRNA
transcription factor 25
spire-type actin nucleation factor 2
Fanconi anemia, complementation group A
zinc finger protein 276
VPS9 domain containing 1
spermatogenesis associated 2-like
cyclin-dependent kinase 10
spermatogenesis associated 33
charged multivesicular body protein 1A
dipeptidase 1 (renal)
copine VII
ribosomal protein L13
ELOVL5
MHC-DQB
MHC-DQA2
MHC-DRB
MHC-DRA
BTNL2
ELOVL fatty acid elongase 5
Major histocompatibility complex, class II DQ beta
major histocompatibility complex, class II DQ alpha 2
Major histocompatibility complex, class II DR beta
major histocompatibility complex, class II DR alpha
butyrophilin-like 2 (MHC class II associated)
2
Table S3. Full gene names for annotated genes found in the common bottlenose dolphin genome
surrounding two genomic regions that were identified as significant across multiple live-dead
comparisons using the sliding window FST approach (Fig. 5). Location describes approximate
location along the corresponding killer whale scaffold.
Location (Mb)
Gene Symbol Gene Name
Oo_Scaffold22
8.21
SLC25A46
solute carrier family 25, member 46
8.47
TSLP
thymic stromal lymphopoietin
8.49
WDR36
WD repeat domain 36
9.04
MCC
mutated in colorectal cancers
9.40
DCP2
decapping mRNA 2
9.48
REEP5
receptor accessory protein 5
9.53
SRP19
signal recognition particle 19kDa
9.55
APC
adenomatous polyposis coli
16.17
TNFAIP8
tumor necrosis factor, alpha-induced protein 8
16.24
HSD17B4
hydroxysteroid (17-beta) dehydrogenase 4
16.40
FAM170A
family with sequence similarity 170, member A
17.13
PRR16
proline rich 16
Oo_Scaffold60
3.77
C15orf52
chromosome 15 open reading frame 52
3.80
PLCB2
phospholipase C, beta 2
3.88
BUB1B
BUB1 mitotic checkpoint serine/threonine kinase B
3.97
BMF
Bcl2 modifying factor
4.04
EIF2AK4
eukaryotic translation initiation factor 2 alpha kinase 4
4.28
GPR176
G protein-coupled receptor 176
4.39
FSIP1
fibrous sheath interacting protein 1
4.56
THBS1
thrombospondin 1
7.21
C15orf41
chromosome 15 open reading frame 41
8.59
DPH6
diphthamine biosynthesis 6
9.14
AQR
aquarius intron-binding spliceosomal factor
9.30
ACTC
Cardiac muscle alpha actin 1
9.33
GJD2
gap junction protein, delta 2, 36kDa
9.49
ARHGAP11A Rho GTPase activating protein 11A
9.52
SCG5
secretogranin V (7B2 protein)
9.69
FMN1
formin 1
10.44
RYR3
ryanodine receptor 3
10.82
AVEN
apoptosis, caspase activation inhibitor
3