Modelling Palaeoecological Time Series Using Generalised Additive Models

Simpson, Gavin L.

doi:10.3389/fevo.2018.00149

Cited by 372 publications

(343 citation statements)

References 59 publications

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“…Generalized additive mixed models (GAMMs) were used to test temporal trends in the δ 15 N and Suess corrected δ 13 C values of skull bone samples between 1990 and 2017 years. By using GAMMs, it is possible to observe the tendency of stable isotope ratios to change over time without defining a particular curve order a priori, while also accounting for temporal correlation (Wood, 2017;Simpson, 2018). GAMMs were fitted using a Gaussian distribution with an identity link function in the Mixed GAM Computation Vehicle (mgcv version 1.8-28) package with the restricted maximum likelihood (REML) smoothing method (Wood, 2017) in R 3.6.0 (R Development Core Team, 2019).…”

Section: Discussionmentioning

confidence: 99%

Long-Term Stability in the Trophic Ecology of a Pelagic Forager Living in a Changing Marine Ecosystem

et al. 2020

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Natural or human-induced environmental changes can modify the structure of ecological communities and thus alter food web interactions. After the collapse of hake stocks (Merluccius hubbsi) provoked by fisheries over the Patagonian shelf in 1997 profound changes have taken place in the community, including long-term dietary shifts in some marine vertebrate predators. Stable carbon (δ 13 C) and nitrogen (δ 15 N) isotope ratios in bone collagen of subadult and adult male South American fur seals (Arctocephalus australis) were measured for the period 1976-2017 to investigate if the changes occurred in the marine community from northern and central Patagonia affected the diet of this predator. Suess corrected δ 13 C values and δ 15 N values in bone collagen of fur seals did not change significantly over the study period. According to this, male fur seals have remained as pelagic foragers without changing their trophic position nor switching their main preys in the Patagonian food web over the last four decades. This longterm stability in the diet of fur seals contrasts with dietary changes reported for benthic foragers in the region. Although long-term diet studies are restricted to a few marine predators in the region, current evidence suggests that benthic-demersal foragers were more prone to dietary shifts than pelagic ones after perturbations that occurred in the marine community of northern and central Patagonia.

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Section: Discussionmentioning

confidence: 99%

Long-Term Stability in the Trophic Ecology of a Pelagic Forager Living in a Changing Marine Ecosystem

et al. 2020

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“…All statistical analyses were conducted in R, and levels were set to 0.05. All generalised α additive mixed-effects models ("GAMMs") were fit with restricted maximum likelihood ("REML") in the R package "mgcv" (Wood, 2011), as recommended by Simpson (2018).…”

Section: Statistical Analysesmentioning

confidence: 99%

A temperate endotherm trades thermoregulation for self-preservation: stress-induced changes in surface temperature as thermoregulatory trade-offs

Robertson

Mastromonaco

Burness

2020

Preprint

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1. Coping with stressors can require substantial energetic investment, and when resources are limited, such investment can preclude simultaneous expenditure on other biological processes. Among endotherms, energetic demands of thermoregulation can be immense, yet whether a stress response is sufficient to induce changes in thermoregulatory investment appears unexplored.2. We tested the hypothesis that stress-induced changes in surface temperature, a well-documented phenomenon across vertebrates, stem from a trade-off between thermoregulation and stress responsiveness, whereby individuals seek to reduce energetic expenditure on thermoregulation in challenging environments (the "Thermoprotective Hypothesis"). We predicted that surface temperature and dry heat loss of individuals that are resource-limited would fall under stress exposure at low ambient temperatures and rise under stress exposure at high ambient temperatures when compared with non-resource limited individuals.3. To test our predictions, we exposed Black-capped Chickadees to rotating stressors and control treatments (n days/treatment = 30; paired treatments) across an ambient temperature gradient whilst remotely monitoring both feeding behaviour and surface temperature. 4. Supporting the Thermoprotective Hypothesis, our results showed that: 1) social subordinates ( n = 12), who fed less than social dominants and alone suffered stress-induced declines in mass, displayed significantly larger changes in surface temperature following stress exposure than social dominants ( n = 8), and 2) stress-induced changes in surface temperature significantly increased heat conservation at low ambient temperature, and heat dissipation at high ambient temperature among social subordinates alone. 5. These results suggest that Black-capped Chickadees adjust their thermoregulatory strategies under stress when resources are limited and support the hypothesis that stress-induced changes in temperature are functionally significant.

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“…In all the cases, fitted GAMs were estimated using maximum likelihood-based smoothness selection procedures, in particular the restricted maximum likelihood (REML). A continuous time first-order autoregressive process (CAR(1)) was chosen to account for the correlation between residuals [35]. To identify periods of transition, we estimated simultaneous confidence intervals from the posterior distribution of the model (under an empirical Bayesian formulation), and the first derivative of the fitted trend [35].…”

Section: Data Analysesmentioning

confidence: 99%

“…A continuous time first-order autoregressive process (CAR(1)) was chosen to account for the correlation between residuals [35]. To identify periods of transition, we estimated simultaneous confidence intervals from the posterior distribution of the model (under an empirical Bayesian formulation), and the first derivative of the fitted trend [35]. Periods of significant change are identified as those time points where the simultaneous confidence interval on the first derivative bounded away from zero [35].…”

Section: Data Analysesmentioning

confidence: 99%

Changes in Planktivory and Herbivory Regimes in a Shallow South American Lake (Lake Blanca Chica, Argentina) Over the Last 250 Years

Carrozzo

Musazzi

Lami

et al. 2020

Water

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Shallow lakes are vulnerable ecosystems impacted by human activities and climate change. The Cladocera occupy a central role in food webs and are an excellent paleoecological indicator of food web structure and trophic status. We conducted a paleolimnological study in Lake Blanca Chica (Argentina) to detect changes on the planktivory and herbivory regimes over the last 250 years. Generalized additive models were fitted to the time series of fish predation indicators (ephippial abundance and size, mucrone size, fish scales, and the planktivory index) and pheophorbide a concentration. The cladoceran assemblage changed from littoral-benthic to pelagic species dominance and zooplankton switched from large-bodied (Daphnia) to small-bodied grazers (Bosmina) ca. 1900 due to increased predation. The shift in planktivory regime (ca. 1920–1930), indicated by fish scales and the planktivory index, as well as herbivory (ca. 1920–1950), was triggered by eutrophication. Changes in planktivory affected the size structure of Bosmina, reducing its body size. This study describes the baseline for the lake as well as the profound changes in the composition and size structure of the zooplankton community due to increased predation and the shift in the planktivory regime. These findings will provide a reference status for future management strategies of this ecosystem.

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Modelling Palaeoecological Time Series Using Generalised Additive Models

Cited by 372 publications

References 59 publications

Long-Term Stability in the Trophic Ecology of a Pelagic Forager Living in a Changing Marine Ecosystem

Long-Term Stability in the Trophic Ecology of a Pelagic Forager Living in a Changing Marine Ecosystem

A temperate endotherm trades thermoregulation for self-preservation: stress-induced changes in surface temperature as thermoregulatory trade-offs

Changes in Planktivory and Herbivory Regimes in a Shallow South American Lake (Lake Blanca Chica, Argentina) Over the Last 250 Years

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