Temporal variability in effective size (Ne) identifies potential sources of discrepancies between mark recapture and close kin mark recapture estimates of population abundance

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 in their
ratio. 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 (Nb) using individuals aged 1+. We
then adjusted these estimates using two life history traits, to obtain
Nb(adj2) and subsequently Ne(adj2),  following Waples et al.
(2013). Ne(adj2) was estimated for the years 2014 to 2019. Census
size was estimated by mark recapture using double-pass electrofishing
(Nc(MR)) (years 2014-2018) as well as by the Close Kin Mark Recapture
approach (Nc(CKMR)) (years 2015-2017). Within populations, annual
variation in Ne(adj2), (ratio of maximum to minimum
Ne(adj2) ranged from 1.6-fold to 58-fold. Over all 7 populations,
the median annual variation in Ne(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
Nc(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 Ne(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 Nc(MR) to Nc(CKMR). For five of the seven
populations, the estimates of population abundance based on mark recapture
(Nc(MR) ) were indistinguishable from those based on close kin mark
recapture (Nc(CKMR)). The two populations with discordant Nc(MR) and
Nc(CKMR) exhibited extremely low Ne(adj2) /
Nc(MR)  ratios and the largest annual variation in
(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 the
estimate of Ne can be used to identify potential sources of
discrepancies between the estimates of Nc(MR) and  those of
Nc(CKMR).