Ecologists have debated the nature of density dependence in natural populations for decades, and efforts to detect density dependence from time series of abundance data have paralleled these debates. ...Yet due to the correlative nature of time series data, these undertakings have been statistically problematic. Most analyses of density dependence have focused on simple population models (i.e., non-overlapping generations), but in reality most vertebrates exhibit more complex life histories, and this complexity has been incorporated into population models in a variety of ways. Unfortunately, adding complexity to population models can further exacerbate efforts to detect density dependence. We examined the effect of adding age structure when inadequate data exist in support; to demonstrate this effect, we adopted Pacific salmon (Oncorhynchus spp.) as our study organism. Most salmon populations are semelparous and have variable age at maturity. Salmon populations (and many other fish species populations) are typically modeled in terms of numbers of recruits arising from spawners in a given brood year. Recruits are enumerated as they return as adults to spawn, and proper assignment of recruits to brood year requires age information. Unfortunately, while adult counts are common, detailed age information is not. A common practice is to apply long-term averages of age composition to returning adults to "reconstruct" time series of recruits. Here, by conducting simulations and analyzing data from natural populations, we demonstrated that this practice leads to a biased portrayal of density dependence by overestimating recruits from small spawning classes and underestimating recruits from large spawning classes. Also, productivity was overestimated and variance was underestimated, which could lead to overly optimistic predictions of extinction risk or overharvesting.
Environmental change can shift the phenotype of an organism through either evolutionary or nongenetic processes. Despite abundant evidence of phenotypic change in response to recent climate change, ...we typically lack sufficient genetic data to identify the role of evolution. We present a method of using phenotypic data to characterize the hypothesized role of natural selection and environmentally driven phenotypic shifts (plasticity). We modeled historical selection and environmental predictors of interannual variation in mean population phenotype using a multivariate state-space model framework. Through model comparisons, we assessed the extent to which an estimated selection differential explained observed variation better than environmental factors alone. We applied the method to a 60-year trend toward earlier migration in Columbia River sockeye salmon Oncorhynchus nerka, producing estimates of annual selection differentials, average realized heritability, and relative cumulative effects of selection and plasticity. We found that an evolutionary response to thermal selection was capable of explaining up to two-thirds of the phenotypic trend. Adaptive plastic responses to June river flow explain most of the remainder. This method is applicable to other populations with time series data if selection differentials are available or can be reconstructed. This method thus augments our toolbox for predicting responses to environmental change. PUBLICATION ABSTRACT
While many recovery programs for threatened species focus on acute sources of mortality, understanding some of the evolutionary processes of these species may lead to more effective recovery efforts, ...especially in cases where human-induced disturbances have resulted in artificial selection pressures. We developed a Monte Carlo test to determine whether Snake River spring/summer chinook salmon (Oncorhynchus tshawytscha) experienced selective mortality as a function of their juvenile length and timing of downstream migration. Actively migrating juvenile fish (smolts) were captured, tagged, and released in 1995 and 1996 approximately 700 km upstream from the Pacific Ocean, and returning adults were detected at the same location. We analyzed data from two groups of fish: those that migrated downstream in-river and those that were barged downstream as part of the juvenile-salmon transportation program. These groups were further separated into wild and hatchery fish. Length at release was significantly greater in returning adults than in the general population for fish that migrated downstream in-river (both wild and hatchery) or were transported (hatchery only). From the 1995 seaward migration, adult returns of both wild and hatchery fish that migrated in-river were composed of fish released significantly earlier than the general population. In contrast, the opposite trend existed for wild and hatchery transported fish. From the 1996 seaward migration, no significant difference in release date was found between returning adults and the original population for any of the groups analyzed. Fish length at migration is a result of factors encountered in early life stages but selectively determines mortality in the smolt-to-adult stage. Thus freshwater habitat improvements, such as salmon carcass supplementation, directed at increasing nutrient levels and thus fish length may result in an increase in overall survival. The development of hydroelectric dams in the migratory corridors of these fish has disrupted their arrival timing to the estuary. Mitigation efforts designed to shift arrival timing toward that experienced prior to impoundment may confer considerable survival benefits.
Capture-recapture studies are powerful tools for studying animal population dynamics, providing information on population abundance, survival rates, population growth rates, and selection for ...phenotypic traits. In these studies, the probability of observing a tagged individual reflects both the probability of the individual surviving to the time of recapture and the probability of recapturing an animal, given that it is alive. If both of these probabilities are related to the same phenotypic trait, it can be difficult to distinguish effects on survival probabilities from effects on recapture probabilities. However, when animals are individually tagged and have multiple opportunities for recapture, we can properly partition observed trait-related variability into survival and recapture components. We present an overview of capture-recapture models that incorporate individual variability and develop methods to incorporate results from these models into estimates of population survival and selection for phenotypic traits. We conducted a series of simulations to understand the performance of these estimators and to assess the consequences of ignoring individual variability when it exists. In addition, we analyzed a large data set of > 153 000 juvenile chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) of known length that were PIT-tagged during their seaward migration. Both our simulations and the case study indicated that the ability to precisely estimate selection for phenotypic traits was greatly compromised when differential recapture probabilities were ignored. Estimates of population survival, however, were far more robust. In the chinook salmon and steelhead study, we consistently found that smaller fish had a greater probability of recapture. We also uncovered length-related survival relationships in over half of the release group/river segment combinations that we observed, but we found both positive and negative relationships between length and survival probability. These results have important implications for the management of salmonid populations.
Abstract
In recent years, returns of adult sockeye salmon
O
ncorhynchus nerka
to the
C
olumbia
R
iver
B
asin have reached numbers not observed since the 1950s. To understand factors related to these ...increased returns, we first looked for changes in freshwater production and survival of juvenile migrants. We then evaluated productivity changes by estimating smolt‐to‐adult return rates (
SAR
) for juvenile migration years 1985–2010. We found
SAR
varied between 0.2 and 23.5%, with the highest values coinciding with recent large adult returns. However, the largest adult return, in 2012, resulted not from increased survival, but from increased smolt production. We evaluated 19 different variables that could influence
SAR
s, representing different facets of freshwater and ocean conditions. We used model selection criteria based on small‐sample corrected
AIC
to evaluate the relative performance of all two‐ and three‐variable models. The model with
A
pril upwelling,
P
acific
N
orthwest
I
ndex (
PNI
) in the migration year, and
PNI
in the year before migration had 10 times the
AIC
c
weight as the second‐best‐supported model, and
R
2
= 0.82. The variables of
A
pril ocean upwelling and
PNI
in the migration year had high weights of 0.996 and 0.927, respectively, indicating they were by far the best of the candidate variables to explain variations in
SAR
. While our analyses were primarily correlative and limited by the type and amount of data currently available, changes in ocean conditions in the northern
C
alifornia Current system, as captured by April upwelling and
PNI
, appeared to play a large role in the variability of
SAR
.
An ordered NotI fragment map containing over 60 loci and encompassing approximately 17 Mb has been constructed for human chromosome band 11p15. Forty-two probes, including 11 NotI-linking cosmids, ...were subregionally mapped to 11p15 using a subset of the J1-deletion hybrids. These and 23 other probes defining loci previously mapped to 11p15 were hybridized to genomic DNA digested with NotI and 5 other infrequently cleaving restriction enzymes and separated by pulsed-field gel electrophoresis. Thirty-nine distinct NotI fragments were detected encompassing approximately 85% of the estimated length of 11p15. The predicted order of the gene loci used is cen-MYOD1-PTH-CALCA-ST5-RBTN1-HPX-HBB-RRM1 -TH/INS/IGF2-H19-CTSD-MUC2-DRD4-HRAS - RNH-tel. This map will allow higher resolution mapping of new 11p15 markers, facilitate positional cloning of disease genes, and provide a framework for the physical mapping of 11p15 in clone contigs.
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