1 Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
2 Department of Biology, Concordia University, Montreal, Quebec, Canada.
3 Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture, Halifax, Nova Scotia, Canada.
4 Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada.

Although efforts to estimate effective population size, census size and their ratio in wild populations are expanding, few empirical studies investigate interannual changes in these parameters. Hence, we do not know how repeatable or representative many estimates may be. Answering this question requires studies of long-term population dynamics. Here we took advantage of a rich dataset of seven brook trout (Salvelinus fontinalis) populations, 5 consecutive years and 5400 individuals genotyped at 33 microsatellites to examine variation in estimates of effective and census size and in their ratio. We first estimated the annual effective number of breeders ( ˆN b) using individuals aged 1+. We then adjusted these estimates using two life history traits, to obtain ˆNb(adj2) and subsequently, ˆNe(adj2) following Waples et al. (2013). ˆNe(adj2) was estimated for the years 2014 to 2019. Census size was estimated by mark recapture using double-pass electrofishing ( ˆNc(MR) ) (years 2014-2018) as well as by the Close Kin Mark Recapture approach ( ˆNc(CKMR) ) (years 2015-2017). Within populations, annual variation in ˆNe(adj2) (ratio of maximum to minimum ˆNe(adj2) ) ranged from 1.6-fold to 58-fold. Over all 7 populations, the median annual variation in ˆNe(adj2) was around 5-fold. These results reflect important interannual changes in the variance in reproductive success and more generally in population dynamics. Within population ˆNc(MR) varied between years by a (median) factor of 2.7 with a range from 2 to 4.3. Thus, estimated effective size varied nearly twice as much as did estimated census size. Our results therefore suggest that, at least in small populations like those examined in the present study, any single annual estimate of ˆNe(adj2) is unlikely to be representative of long-term dynamics. At least 3-4 annual estimates may be required for an estimate of contemporary effective size to be truly representative. We then compared ˆNc(MR) to ˆNc(CKMR) . For five of the seven populations, the estimates of population abundance based on mark recapture ( ˆNc(MR) ) were indistinguishable from those based on close kin mark recapture ( ˆNc(CKMR) ). The two populations with discordant ˆNc(MR) and ˆNc(CKMR) exhibited extremely low ˆNe(adj2)/ˆNc(MR) ratios and the largest annual variation in ˆNe(adj2) (58-fold and 35.4-fold respectively). These results suggest that sampling effort in these two streams may have been insufficient to properly capture the genetic diversity of the entire population and that individuals sampled were not representative of the population. Our study further validates CKMR as a method for estimating abundance in wild populations and it demonstrates how knowledge of the temporal variation in ˆNe can be used to identify potential sources of discrepancies between ˆNc(MR) and ˆNc(CKMR) .