Estimating monotonic rates from biological data using local linear regression

Olito, Colin; White, Craig R.; Marshall, Dustin J.; Barneche, Diego R.

doi:10.1242/jeb.148775

Cited by 42 publications

(39 citation statements)

References 20 publications

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“…We used the r package LoLinR (Olito, White, Marshall, & Barneche, ), which implements local linear regression techniques for estimating monotonic biological rates from time‐series or trace data, to determine the optimal measurement interval (i.e., the most linear part of the measurement curve). We excluded the first 30 min of the 3‐h measurement period (during which colonies might show oxygen consumption patterns that reflect recovery from handling procedures).…”

Section: Methodsmentioning

confidence: 99%

Influence of food, body size, and fragmentation on metabolic rate in a sessile marine invertebrate

Schuster

White

Marshall

2019

Invertebrate Biology

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Metabolic rates vary among individuals according to food availability and phenotype, most notably body size. Disentangling size from other factors (e.g., age, reproductive status) can be difficult in some groups, but modular organisms may provide an opportunity for manipulating size experimentally. While modular organisms are increasingly used to understand metabolic scaling, the potential of feeding to alter metabolic scaling has not been explored in this group. Here, we perform a series of experiments to examine the drivers of metabolic rate in a modular marine invertebrate, the bryozoan Bugula neritina. We manipulated size and examined metabolic rate in either fed or starved individuals to test for interactions between size manipulation and food availability. Field collected colonies of unknown age showed isometric metabolic scaling, but those colonies in which size was manipulated showed allometric scaling. To further disentangle age effects from size effects, we measured metabolic rate of individuals of known age and again found allometric scaling. Metabolic rate strongly depended on access to food: starvation decreased metabolic rate by 20% and feeding increased metabolic rate by 43%. In comparison to other marine invertebrates, however, the increase in metabolic rate, as well as the duration of the increase (known as specific dynamic action, SDA), were both low. Importantly, neither starvation nor feeding altered the metabolic scaling of our colonies. Overall, we found that field‐collected individuals showed isometric metabolic scaling, whereas metabolic rate of size‐manipulated colonies scaled allometrically with body size. Thus, metabolic scaling is affected by size manipulation but not feeding in this colonial marine invertebrate.

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Section: Methodsmentioning

confidence: 99%

Influence of food, body size, and fragmentation on metabolic rate in a sessile marine invertebrate

Schuster

White

Marshall

2019

Invertebrate Biology

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“…Rates of Oxygen flux were extracted using repeated local linear regressions with the package LoLinR (Olito et al, 2017) in R (R Core Team, 2013), corrected for chamber volume, blank rates, and normalized to coral surface area calculated by tracing of planar area of the flat O. franksi samples using ImageJ (Schneider et al, 2012). LoLinR was run with the parameters of L pc for linearity metric (L pc = the sum of the percentile-ranks of the Zmin scores for each component metric) and alpha = 0.2 (minimum window size for fitting the local regressions, which is the proportion of the total observations in the data set) for observations, and thinning of the data from every second to every 20 seconds.…”

Section: Methodsmentioning

confidence: 99%

Comparative thermal performance ofOrbicella franksiat its latitudinal range limits

Silbiger

Goodbody‐Gringley

Bruno

et al. 2019

Preprint

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22 23 24 Summary statement: We apply a thermal performance curve approach to a variety of fitness 25 related parameters in a reef building coral across its geographic range and various functions to 26 improve our understanding of the inherent variability in thermal tolerance.Abstract 32 Temperature drives biological responses that scale from the cellular to ecosystem levels 33 and thermal sensitivity will shape organismal functions and population dynamics as the world 34 warms. Reef building corals are sensitive to temperature due to their endosymbiotic relationship 35 with single celled dinoflagellates, with mass mortality events increasing in frequency and 36 magnitude. The purpose of this study was to quantify the thermal sensitivity of important 37 physiological functions of a Caribbean reef-building coral, Orbicella franksi through the 38 measurement of thermal performance curves (TPCs). We compared TPC metrics (thermal 39 optimum, critical maximum, activation energy, deactivation energy, and rate at a standardized 40 temperature) between two populations at the northern and southern extent of the geographic range 41 of this species. We further compared essential coral organismal processes (gross photosynthesis, 42 respiration, and calcification) within a site to determine which function is most sensitive to thermal 43 stress using a hierarchical Bayesian modeling approach. We found evidence for differences in 44 thermal performance, which could be due to thermal adaptation or acclimatization, with higher 45 TPC metrics (thermal optimum and critical maximum) in warmer Panama, compared to cooler 46 Bermuda. We also documented the hierarchy in thermal sensitivity of essential organismal 47 functions within a population, with respiration less sensitive than photosynthesis, which was less 48 sensitive than calcification. Understanding thermal performance of corals is essential for 49 projecting coral reef futures, given that key biological functions necessary to sustain coral reef 50 ecosystems are thermally-mediated. 51 52 53 89 worldwide over the last 30 years (from ~60% to <20% on some reefs), in large part due to ocean 90warming (Bruno and Selig, 2007; De'ath et al., 2012; Gardner et al., 2003; Hughes et al., 2018a) 91 causing mass bleaching, or the loss of the corals' symbiotic dinoflagellates and their nutritional 92 4 benefits to the host (Oakley and Davy, 2018). While there are numerous local causes of coral loss 93 (e.g., pollution, destructive fishing practices, tourism, etc.), the single most detrimental stressor to 94 date is thermal stress from anomalous heating events (i.e., heatwaves) and its associated 95 complications (i.e., bleaching, disease, reduced calcification etc.; (DeCarlo et al., 2017; Harvell et 96 al., 2002; Hughes et al., 2017)). Reef building corals and their dinoflagellate symbionts live close 97 to their physiological thermal maximum and, as a result, warming of 1°C or more above local 98 mean monthly maxima can reduce fitness and cause tissue loss or whole-colony...

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“…Truncating the data to exclude these nonlinearities manually is subjective and difficult to reproduce. Therefore, we recommend using the “ LoLinR ” package for r (Olito, White, Marshall, & Barneche, ), which provides a flexible toolkit to implement local linear regression techniques to estimate biological rates from linear and nonlinear time‐series data. Local linear regressions enhance the accuracy by estimating the slope of a linear subset of the time series as defined by linearity metrics underpinning the function (details in Olito et al., ).…”

Section: Methodsmentioning

confidence: 99%

An in situ approach for measuring biogeochemical fluxes in structurally complex benthic communities

et al. 2019

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1. The exchange of energy and nutrients are integral components of ecological functions of benthic shallow-water ecosystems and are directly dependent on in situ environmental conditions. Traditional laboratory experiments cannot account for the multidimensionality of interacting processes when assessing metabolic rates and biogeochemical fluxes of structurally complex benthic communities. Current in situ chamber systems are expensive, limited in their functionality and the deployment is often restricted to planar habitats (e.g. sediments or seagrass meadows) only.2. To overcome these constraints, we describe a protocol to build and use non-invasive, cost-effective and easy to handle in situ incubation chambers that provide reproducible measurements of biogeochemical processes in simple and structurally complex benthic shallow-water communities. Photogrammetry tools account for the structural complexity of benthic communities, enabling to calculate accurate community fluxes.We tested the performance of the system in laboratory assays and various benthic habitats (i.e. algae growing on rock, coral assemblages, sediments and seagrass meadows). In addition, we estimated community budgets of photosynthesis and respiration by corals, rock with algae and carbonate sediments, which were subsequently compared to budgets extrapolated from conventional ex situ single-organism incubations. The tests highlight the transparency (>90% light transmission) of the chambersand minimal water exchange with the surrounding medium on most substrates.Linear dissolved oxygen fluxes in dependence to incubation time showed sufficient mixing of the water by circulation pumps and no organismal stress response.The comparison to single-organism incubations showed that ex situ measurements might overestimate community-wide net primary production and underestimate respiration and gross photosynthesis by 20%-90%. 4. The proposed protocol overcomes the paucity of observational and manipulative studies that can be performed in in situ native habitats, thus producing widely applicable and realistic assessments on the community level. Importantly, the tool provides a standardized approach to compare community functions across a wide This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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Estimating monotonic rates from biological data using local linear regression

Cited by 42 publications

References 20 publications

Influence of food, body size, and fragmentation on metabolic rate in a sessile marine invertebrate

Influence of food, body size, and fragmentation on metabolic rate in a sessile marine invertebrate

Comparative thermal performance ofOrbicella franksiat its latitudinal range limits

An in situ approach for measuring biogeochemical fluxes in structurally complex benthic communities

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