Temporal variability in effective size (N _e) identifies sampling bias in close kin mark recapture estimate of population abundance (Nc(CKMR))

Although efforts to estimate Ne, Nc, and their ratio in wild populations are expanding, few empirical studies investigate interannual changes in these parameters. Hence, we do not know how representative many estimates may be. Answering this question requires studies of long-term population dynamics. We non-lethally sampled N=5400 brook trout (Salvelinus fontinalis) from seven populations during 6 consecutive years (2014-2019) and genotyped them at 33 microsatellites to examine variation in Ne, Nc and their ratio. Nc was estimated by Mark-Recapture (Nc(MR)) (2014-2018) as well as by Close-Kin-Mark-Recapture (Nc(CKMR)) (2015-2017). Within populations, annual variation in Ne (max/min Ne) ranged from 1.6-fold to 58-fold. Over all 7 populations, median annual variation in Ne was 5-fold. These results reflect important interannual changes in reproductive success variance. Within population Nc(MR) varied by a median of 2.7. Thus, Ne varied nearly twice as much as did Nc(MR) . Our results suggest that, at least in small populations, any single annual estimate of Ne is unlikely to be representative of long-term dynamics. At least 3-4 annual estimates may be required for an estimate of contemporary Ne to be representative. For five of the seven populations, Nc(MR) was indistinguishable from Nc(CKMR). The two populations with discordant estimates exhibited the largest annual Ne variation (58-fold and 35.4-fold). These results suggest sampling effort in these two streams may have been insufficient to capture the genetic diversity of the entire population. Our study demonstrates how knowledge of temporal variation in Ne can be used to identify potential biases in Nc(CKMR).