| 1. |
- Pontarp, Mikael, et al.
(författare)
-
Inferring community assembly processes from macroscopic patterns using dynamic eco-evolutionary models and Approximate Bayesian Computation (ABC)
- 2019
-
Ingår i: Methods in Ecology and Evolution. - : John Wiley & Sons. - 2041-210X. ; 10:4, s. 450-460
-
Forskningsöversikt (refereegranskat)abstract
- Statistical techniques exist for inferring community assembly processes from community patterns. Habitat filtering, competition, and biogeographical effects have, for example, been inferred from signals in phenotypic and phylogenetic data. The usefulness of current inference techniques is, however, debated as a mechanistic and causal link between process and pattern is often lacking, and evolutionary processes and trophic interactions are ignored.Here, we revisit the current knowledge on community assembly across scales and, in line with several reviews that have outlined challenges associated with current inference techniques, we identify a discrepancy between the current paradigm of eco-evolutionary community assembly and current inference techniques that focus mainly on competition and habitat filtering. We argue that trait-based dynamic eco-evolutionary models in combination with recently developed model fitting and model evaluation techniques can provide avenues for more accurate, reliable, and inclusive inference. To exemplify, we implement a trait-based, spatially explicit eco-evolutionary model and discuss steps of model modification, fitting, and evaluation as an iterative approach enabling inference from diverse data sources.Through a case study on inference of prey and predator niche width in an eco-evolutionary context, we demonstrate how inclusive and mechanistic approaches-eco-evolutionary modelling and Approximate Bayesian Computation (ABC)-can enable inference of assembly processes that have been largely neglected by traditional techniques despite the ubiquity of such processes.Much literature points to the limitations of current inference techniques, but concrete solutions to such limitations are few. Many of the challenges associated with novel inference techniques are, however, already to some extent resolved in other fields and thus ready to be put into action in a more formal way for inferring processes of community assembly from signals in various data sources.
|
|
| 2. |
- Jutfelt, Fredrik, et al.
(författare)
-
Two-current choice flumes for testing avoidance and preference in aquatic animals
- 2017
-
Ingår i: Methods in Ecology and Evolution. - : John Wiley & Sons. - 2041-210X. ; 8:3, s. 379-390
-
Forskningsöversikt (refereegranskat)abstract
- Aquatic chemical ecology is an important and growing field of research that involves understanding how organisms perceive and respond to chemical cues in their environment. Research assessing the preference or avoidance of a water source containing specific chemical cues has increased in popularity in recent years, and a variety of methods have been described in the scientific literature. Two-current choice flumes have seen the greatest increase in popularity, perhaps because of their potential to address the broadest range of research questions.Here, we review the literature on two-current choice flumes and show that there is a clear absence of standardized methodologies that make comparisons across studies difficult. Some of the main issues include turbulent flows that cause mixing of cues, inappropriate size of choice arenas for the animals, short experiments with stressed animals, failure to report how experiment and researcher biases were eliminated, general underreporting of methodological details, underutilization of collected data and inappropriate data analyses.In this review, we present best practice guidelines on how to build, test and use two-current choice flumes to measure the behavioural responses of aquatic animals to chemical cues, and provide blueprints for flume construction. The guidelines include steps that can be taken to avoid problems commonly encountered when using two-current choice flumes and analysing the resulting data.This review provides a set of standards that should be followed to ensure data quality, transparency and replicability in future studies in this field.
|
|
| 3. |
- Lennox, Robert J., et al.
(författare)
-
Positioning aquatic animals with acoustic transmitters
- 2023
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 14:10, s. 2514-2530
-
Forskningsöversikt (refereegranskat)abstract
- Geolocating aquatic animals with acoustic tags has been ongoing for decades, relying on the detection of acoustic signals at multiple receivers with known positions to calculate a 2D or 3D position, and ultimately recreate the path of an aquatic animal from detections at fixed stations.This method of underwater geolocation is evolving with new software and hardware options available to help investigators design studies and calculate positions using solvers based predominantly on time-difference-of-arrival and time-of-arrival.We provide an overview of the considerations necessary to implement positioning in aquatic acoustic telemetry studies, including how to design arrays of receivers, test performance, synchronize receiver clocks and calculate positions from the detection data. We additionally present some common positioning algorithms, including both the free open-source solvers and the ‘black-box’ methods provided by some manufacturers for calculating positions.This paper is the first to provide a comprehensive overview of methods and considerations for designing and implementing better positioning studies that will support users, and encourage further knowledge advances in aquatic systems.
|
|
| 4. |
|
|
| 5. |
- Skov Nielsen, Cecilie
(författare)
-
Isotopic methods for non-destructive assessment of carbon dynamics in shrublands under long-term climate change manipulation
- 2018
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 866-880
-
Forskningsöversikt (refereegranskat)abstract
- 1. Long-term climate change experiments are extremely valuable for studying ecosystem responses to environmental change. Examination of the vegetation and the soil should be non-destructive to guarantee long-term research. In this paper, we review field methods using isotope techniques for assessing carbon dynamics in the plant-soil-air continuum, based on recent field experience and examples from a European climate change manipulation network.2. Eight European semi-natural shrubland ecosystems were exposed to warming and drought manipulations. One field site was additionally exposed to elevated atmospheric CO2. We discuss the isotope methods that were used across the network to evaluate carbon fluxes and ecosystem responses, including: (1) analysis of the naturally rare isotopes of carbon (C-13 and C-14) and nitrogen (N-15); (2) use of in situ pulse labelling with (CO2)-C-13, soil injections of C-13- and N-15-enriched substrates, or continuous labelling by free air carbon dioxide enrichment (FACE) and (3) manipulation of isotopic composition of soil substrates (C-14) in laboratory-based studies.3. The natural C-14 signature of soil respiration gave insight into a possible long-term shift in the partitioning between the decomposition of young and old soil carbon sources. Contrastingly, the stable isotopes C-13 and N-15 were used for shorter-term processes, as the residence time in a certain compartment of the stable isotope label signal is limited. The use of labelled carbon-compounds to study carbon mineralisation by soil micro-organisms enabled to determine the long-term effect of climate change on microbial carbon uptake kinetics and turnover.4. Based on the experience with the experimental work, we provide recommendations for the application of the reviewed methods to study carbon fluxes in the plant-soil-air continuum in climate change experiments. C-13-labelling techniques exert minimal physical disturbances, however, the dilution of the applied isotopic signal can be challenging. In addition, the contamination of the field site with excess C-13 or C-14 can be a problem for subsequent natural abundance (C-14 and C-13) or label studies. The use of slight changes in carbon and nitrogen natural abundance does not present problems related to potential dilution or contamination risks, but the usefulness depends on the fractionation rate of the studied processes.
|
|
