528 
Abstract — Mitochondria] DNA(mtDNA) 
haplotypes of coho salmon ( Oncorhyn - 
chus kisutch) sampled from northern 
Pacific Ocean and Bering Sea drain- 
ages formed two monophyletic clades 
between which nucleotide divergences 
averaged 2.95 substitutions per 1000 
nucleotides. These data were obtained 
from restriction endonuclease diges- 
tions of PCR products that included 
over 97% of the mtDNA genome and 
resolved 16 different haplotypes in 258 
fish from 13 locations. Comparisons of 
haplotype compositions of populations 
indicated that the Bering Sea drain- 
ages and one Kodiak Island population 
clustered separately from nine other 
Gulf of Alaska populations, including 
one from Asia. Rates of gene flow among 
populations estimated from haplotype 
frequencies (assuming an equilibrium 
between gene flow and random drift) 
were low (about one female per genera- 
tion between drainages within regions) 
in relation to allozyme-based estimates 
of gene flow for other Pacific salmon spe- 
cies. Much of the haplotype frequency 
variation was within-region variation. 
Haplotypes from both clades occur in 
many extant populations, suggesting 
that gene flow, population movements, 
or recolonization followed divergence of 
refugial isolates. Nested clade analysis 
of the geographic distribution of mtDNA 
haplotypes indicated that coho salmon 
demographic history has been influ- 
enced by recent isolation by distance 
and that historic population fragmen- 
tation was preceded by range expan- 
sion. These observations are consistent 
with effects expected from Pleistocene 
glacial advances and retreats. 
Manuscript accepted 19 March 2001. 
Fish. Bull. 99:528-544 (2001). 
Phylogeographic analysis of mitochondrial 
DNA variation in Alaskan coho salmon, 
Oncorhynchus kisutch 
Anthony J. Gharrett 
Andrew K. Gray 
Fisheries Division, School of Fisheries and Ocean Sciences 
University of Alaska Fairbanks 
1 1 120 Glacier Highway 
Juneau, Alaska 99801 
E-mail address (for Anthony J. Gharrett): ffajg@uaf.edu 
Vladimir Brykov 
Institute of Marine Biology 
Russian Academy of Science, Far East Branch 
690041 Vladivostok, Russia 
In drainages flowing into the Gulf of 
Alaska and Bering Sea, coho salmon 
( Oncorhyjichus kisutch) are the least 
numerous and their population struc- 
ture the least understood of Pacific 
salmon species (Oncorhynchus spp.). 
Many populations spawn in late fall 
or winter in remote drainages that are 
difficult to access. Spawning popula- 
tions are often small and separated 
widely (Sandercock, 1991). In larger 
rivers spawning adults may return 
to small, often transient, headwater 
streams. After emergence, fry and juve- 
niles may move to rearing areas, usually 
much lower in the river (Sandercock, 
1991), forming complex admixtures 
from spawning populations in large 
drainages. 
Studies of allozyme variation have 
provided insight into the population 
structure of Pacific salmon species (e.g. 
Zhivotovsky et al., 1994, and references 
therein). Patterns of genetic variability 
often provide evidence of relationships 
between populations resulting from 
coancestry or gene flow, and genetic 
divergence among populations may be 
used for stock identification (Shaklee et 
al., 1999). In coho salmon, the low level 
of allozyme variation resolves relatively 
little population genetic structure (Rei- 
senbichler and Phelps, 1987; Wehrhahn 
and Powell, 1987; Bartley et al., 1992; 
Pustavoit, 1995). This low level of al- 
lozyme variation is consistent with nu- 
merous spawning populations that have 
small effective sizes and low levels of 
gene flow, such as that of coho salmon. 
Analysis of DNA variation adds di- 
mensions of interpretation not possible 
with allozyme data (Avise et al., 1988; 
Avise, 1989). “Gene trees” for mitochon- 
drial DNA (mtDNA) haplotypes are es- 
pecially informative. The mitochondrial 
genome is transmitted (primarily) ma- 
ternally (Gyllensten et al., 1991), and 
mtDNA is haploid and clonally inherit- 
ed with no recombination. Consequently, 
mutations accumulate over time within 
a clonal mtDNA line or haplotype. Com- 
parison of different haplotypes provides 
a basis for reconstruction of matriarchal 
genealogies. There is also evidence that 
mtDNA sequences may diverge (evolve) 
faster than many nuclear sequences 
(Brown et al., 1982). The extent of nu- 
cleotide divergence provides a temporal 
basis for comparing haplotype lineages. 
The rates of divergence of mtDNA have 
been roughly estimated for a number of 
species pairs by comparing observed nu- 
cleotide sequence divergence with fossil 
records that document the emergence of 
those species (Brown et al., 1979; Shields 
and Wilson, 1987 and references there- 
in). Although applications of these mo- 
lecular “clocks” are questionable when 
extended to species for which the fossil 
record is poor or missing, deductions 
about relative (as opposed to absolute) 
divergence times can be made from the 
extent of nucleotide change within a spe- 
cies. Furthermore, the geographic distri- 
