Opinion ID: 3040620
Heading Depth: 4
Heading Rank: 3

Heading: Marked Genetic Differences

Text: The third factor the Service considered was whether the Washington population’s genetic characteristics differ “markedly” from the remainder of the subspecies’ range. “Under the DPS Policy, ‘markedly’ is given its common meaning, which in this context is ‘appreciably.’ ” Nat’l Ass’n of Home Builders, 340 F.3d at 851. The parties do not dispute that some genetic differences exist between Washington gray squirrels and the rest of the taxon in Oregon and California. The question is whether their genetic profiles differ “markedly.” The Service based its decision on a peer-reviewed study of genetic differences among gray squirrel populations in Washington, Oregon, and California. Final Finding, 68 Fed. Reg. at 34,638. The study was carried out by Kenneth I. Warheit, a senior research scientist with the Washington Department of Fish and Wildlife. Dr. Warheit conducted microsatellite DNA analysis on samples from 3 California gray squirrels, 24 Oregon squirrels, and 101 Washington squirrels.13 He analyzed the samples’ alleles, which are series of two or more different genes that occupy the same position on a chromosome. He 13 “Microsatellites are short (no longer than six base pairs (nitrogenous bases that are part of the DNA molecule, such as cytosine and guanine)) tandemly repeated segments interspersed throughout the chromosome.” Final Finding, 68 Fed. Reg. at 34,638. 1240 NORTHWEST ECOYSTEM ALLIANCE v. USFWS found that each population in California and Oregon showed at least three “private alleles” that are present only in that population. In contrast, no Washington population had private alleles. In other words, “all alleles present in each of the Washington population are also present in at least one of the Oregon or California populations.” Id. At the same time, he found reduced genetic diversity in the Washington populations compared with Oregon and California, and “considerably more genetic differentiation between Washington and Oregon or California[ ] than there is between Oregon and California populations.” Id. He then conducted mitochondrial control region sequence analysis on a subset of 67 squirrels.14 He determined that no haplotype — which is the set of one allele of each gene, and which comprises the genetic constitution of an individual or taxon — was shared across the Columbia river. Mitochondrial DNA analysis also demonstrated that the Washington population had substantially less genetic diversity. Dr. Warheit found only 3 haplotypes from 40 Washington squirrels, compared with 14 haplotypes from 27 California and Oregon squirrels. After reviewing Dr. Warheit’s study, the Service concluded that “[w]hile there is clearly some genetic information that shows that the Washington populations are different from other populations . . . at this time we do not believe them to be markedly so.” Id. at 34,639. The Service explained that evidence of genetic differentiation is “counterbalanced” by the fact that the Washington population has no private alleles, “that some haplotypes in Washington are more closely related to haplotypes in Oregon than other haplotypes in Washington,” and “the fact that the Washington populations . . . show reduced genetic diversity.” Id. The Service further explained that the results of the study may have been confounded by 14 “Mitochondria are structures in the cell, but outside of the nucleus, which contains DNA inherited only from the mother.” Final Finding, 68 Fed. Reg. at 34638. In contrast, microsatellite DNA is inherited from both parents. NORTHWEST ECOYSTEM ALLIANCE v. USFWS 1241 “the effects of small population size and the consequent inbreeding and genetic drift” in Washington. Id. The Service also noted that the study used a small sample size for the California population. [12] The Alliance contends that the presence of unique haplotypes in the Washington population is sufficient to establish marked genetic differentiation, notwithstanding the fact that the population has no private alleles. However, we must defer to the agency’s interpretation of complex scientific data. United States v. Alpine Land and Reservoir Co., 887 F.2d 207, 213 (9th Cir. 1989) (“Deference to an agency’s technical expertise and experience is particularly warranted with respect to questions involving engineering and scientific matters.”). We decline the Alliance’s invitation to impose our own view on whether alleles or haplotypes constitute the best markers of genetic differentiation. Next, the Alliance maintains that reduced genetic diversity in Washington is itself evidence of the population’s genetic distinctiveness. Nothing in the DPS Policy or in the ESA compels the Service to focus on relative genetic diversity, rather than on the presence or absence of unique alleles, as the best indicators of genetic differentiation. As an internal Service memorandum explained, because “there was no evidence from the analysis that [Washington] populations possessed unique microsatellite alleles . . . most of the differentiation [between Washington and the rest of the range] comes from reduced numbers of alleles” in Washington. Whether the Service was correct to focus on the alleles is beside the point; interpretation of complex genetic data falls within the domain of the Service’s scientific discretion, to which we must defer so long as the Service has articulated a rational basis for its conclusion. Lastly, the Alliance argues that whether some haplotypes in Washington are closer to haplotypes in Oregon than to others in Washington is irrelevant for the question of overall genetic 1242 NORTHWEST ECOYSTEM ALLIANCE v. USFWS differences between Washington and Oregon. This argument ignores the inference that if all of the Washington haplotypes were closer to each other than to haplotypes in California and Oregon, the overall genetic profile of the Washington population would be more distinct. [13] Because the Service has articulated reasoned connections between the record and its conclusion, its genetic analysis was not arbitrary or capricious.