| 1. |
- Knape, Jonas
(författare)
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Estimability of density dependence in models of time series data
- 2008
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 89:11, s. 2994-3000
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Tidskriftsartikel (refereegranskat)abstract
- Estimation of density dependence from time series data on population abundance is hampered in the presence of observation or measurement errors. Fitting state-space models has been proposed as a solution that reduces the bias in estimates of density dependence caused by ignoring observation errors. While this is often true, I show that, for specific parameter values, there are identifiability issues in the linear state-space model when the strength of density dependence and the observation and process error variances are all unknown. Using simulation to explore properties of the estimators, I illustrate that, unless assumptions are imposed on the process or observation error variances, the variance of the estimator of density dependence varies critically with the strength of the density dependence. Under compensatory dynamics, the stronger the density dependence the more difficult it is to estimate in the presence of observation errors. The identifiability issues disappear when density dependence is estimated from the state-space model with the observation error variance known to the correct value. Direct estimates of observation variance in abundance censuses could therefore prove helpful in estimating density dependence but care needs to be taken to assess the uncertainty in variance estimates.
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| 2. |
- Knape, Jonas, et al.
(författare)
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Individual heterogeneity and senescence in Silvereyes on Heron Island
- 2011
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Ingår i: Ecology. - : John Wiley & Sons. - 0012-9658 .- 1939-9170. ; 92:4, s. 813-820
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Tidskriftsartikel (refereegranskat)abstract
- Individual heterogeneity and correlations between life history traits play a fundamental role in life history evolution and population dynamics. Unobserved individual heterogeneity in survival can be a nuisance for estimation of age effects at the individual level by causing bias due to mortality selection. We jointly analyze survival and breeding output from successful breeding attempts in an island population of Silvereyes (Zosterops lateralis chlorocephalus) by fitting models that incorporate age effects and individual heterogeneity via random effects. The number of offspring produced increased with age of parents in their first years of life but then eventually declined with age. A similar pattern was found for the probability of successful breeding. Annual survival declined with age even when individual heterogeneity was not accounted for. The rate of senescence in survival, however, depends on the variance of individual heterogeneity and vice versa; hence, both cannot be simultaneously estimated with precision. Model selection supported individual heterogeneity in breeding performance, but we found no correlation between individual heterogeneity in survival and breeding performance. We argue that individual random effects, unless unambiguously identified, should be treated as statistical nuisance or taken as a starting point in a search for mechanisms rather than given direct biological interpretation.
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| 3. |
- Knape, Jonas
(författare)
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Monte Carlo estimation of stage structured development from cohort data
- 2016
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 97, s. 992-1002
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Tidskriftsartikel (refereegranskat)abstract
- Cohort data are frequently collected to study stage-structured development and mortalities of many organisms, particularly arthropods. Such data can provide information on mean stage durations, among-individual variation in stage durations, and on mortality rates. Current statistical methods for cohort data lack flexibility in the specification of stage duration distributions and mortality rates. In this paper, we present a new method for fitting models of stage-duration distributions and mortality to cohort data. The method is based on a Monte Carlo within MCMC algorithm and provides Bayesian estimates of parameters of stage-structured cohort models. The algorithm is computationally demanding but allows for flexible specifications of stage-duration distributions and mortality rates. We illustrate the algorithm with an application to data from a previously published experiment on the development of brine shrimp from Mono Lake, California, through nine successive stages. In the experiment, three different food supply and temperature combination treatments were studied. We compare the mean duration of the stages among the treatments while simultaneously estimating mortality rates and among-individual variance of stage durations. The method promises to enable more detailed studies of development of both natural and experimental cohorts. An R package implementing the method and which allows flexible specification of stage duration distributions is provided.
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| 4. |
- Pärt, Tomas, et al.
(författare)
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Disentangling the effects of date, individual, and territory quality on the seasonal decline in fitness
- 2017
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 98, s. 2102-2110
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Tidskriftsartikel (refereegranskat)abstract
- The seasonal timing of reproduction is a major fitness factor in many organisms. Commonly, individual fitness declines with time in the breeding season. We investigated three suggested but rarely tested hypotheses for this seasonal fitness decline: (1) time per se (date hypothesis), (2) late breeders are of lower quality than early ones (individual quality hypothesis), and (3) late breeders are breeding at poorer territories than early breeders (territory quality hypothesis). We used Bayesian variance component analyses to examine reproductive output (breeding success, number fledged, and number of recruits) from repeated observations of female Northern Wheatears (Oenanthe oenanthe) and individual territories from a 20-yr population study. The major part of the observed seasonal decline in reproductive output seemed to be driven by date-related effects, whereas female age and territory type (i.e., known indicators of temporary quality) contributed to a smaller degree. Other, persistent effects linked to individual and territory identity did not show any clear patterns on the seasonal decline in reproductive output. To better disentangle the quality effects (persistent and temporary) of individual and territory from effects caused by the deterioration of the environment we suggest a protocol combining experimental manipulation of breeding time with a variance-covariance partitioning method used here.
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| 5. |
- Solbreck, Christer, et al.
(författare)
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Seed production and predation in a changing climate: new roles for resource and seed predator feedback?
- 2017
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 98, s. 2301-2311
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Tidskriftsartikel (refereegranskat)abstract
- Climate change may cause changes in the dynamics of populations beyond comparatively simple directional effects. To better understand complex effects on dynamics requires long-term studies of populations that experience changes in climatic conditions. We study the dynamics of a seed-production-seed-predation system, consisting of a perennial herb and its two seed predatory insects, over a 40-yr period during which climate change has caused the annual growing season to increase by 20 d. During this period, plant patches have increased almost threefold in size and seed production has slipped into a pattern of alternate high and low years with a higher variance than in the beginning of the period. We find that seed production is associated with precipitation of the present summer and a non-linear feedback from seed production of the previous year. When previous year's seed production is low, weather forcing and unexplained noise determine the extent of seed production. When previous seed production is high, depleted resources limit seed production. Resource depletion happened frequently in the latter parts of the study but rarely in the beginning. The changing patterns of seed production in turn affect the dynamics of seed predation, which is dominated by one of the seed predators. Its dynamics are strongly linked to seed density fluctuations, but its population growth rate is satiated when resource fluctuations become too large. In the latter part of the study period, when seed fluctuations were alternating between years of high and low density, satiation was common and there was a large increase in surviving seeds in good years. Our study illustrates that a changing climate can fundamentally influence patterns of long-term dynamics at multiple trophic levels.
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