scholarly journals How molecular tools can help understanding species interactions to improve restoration outcomes

2016 ◽  
Author(s):  
Stéphane Boyer ◽  
Benjamin R Waterhouse ◽  
Steve D Wratten
Keyword(s):  
Species Interactions ◽  
Restoration Ecology ◽  
Environmental Dna ◽  
Ecological Interactions ◽  
Molecular Tools ◽  
Predator Prey ◽  
Prey Animal ◽  
Restoration Practice ◽  
High Throughput Dna Sequencing ◽  
The Cost

Preserving species interactions should be a key desired outcome in restoration ecology. With progress in environmental DNA techniques and the dramatic reduction in the cost of high-throughput DNA sequencing, large amounts of information can be gathered on how species interact with little to no disturbance to ecosystems. Here, we argue that the use of molecular tools to study ecological interactions will become increasingly important in restoration projects. We describe specific examples where recent advances in genetics allow for a better understanding of predator-prey, animal-plant, plant-microbe and trophic cascade interactions, which can inform restoration practice and substantially improve our capacity to restore functioning ecosystems.

scholarly journals How molecular tools can help understanding species interactions to improve restoration outcomes

2016 ◽  
Author(s):  
Stéphane Boyer ◽  
Benjamin R Waterhouse ◽  
Steve D Wratten
Keyword(s):  
Species Interactions ◽  
Restoration Ecology ◽  
Environmental Dna ◽  
Ecological Interactions ◽  
Molecular Tools ◽  
Predator Prey ◽  
Prey Animal ◽  
Restoration Practice ◽  
High Throughput Dna Sequencing ◽  
The Cost

Preserving species interactions should be a key desired outcome in restoration ecology. With progress in environmental DNA techniques and the dramatic reduction in the cost of high-throughput DNA sequencing, large amounts of information can be gathered on how species interact with little to no disturbance to ecosystems. Here, we argue that the use of molecular tools to study ecological interactions will become increasingly important in restoration projects. We describe specific examples where recent advances in genetics allow for a better understanding of predator-prey, animal-plant, plant-microbe and trophic cascade interactions, which can inform restoration practice and substantially improve our capacity to restore functioning ecosystems.

scholarly journals Anthropogenic noise impairs foraging for cryptic prey via cross-sensory interference

2020 ◽  
Vol 287 (1924) ◽  
pp. 20192951 ◽  
Author(s):  
Wouter Halfwerk ◽  
Kees van Oers
Keyword(s):  
Species Interactions ◽  
Visual Information ◽  
Acoustic Noise ◽  
Parus Major ◽  
Anthropogenic Noise ◽  
Ecological Interactions ◽  
Noise Levels ◽  
Predator Prey ◽  
As Species ◽  
Processing Of Visual Information

Anthropogenic noise levels are globally rising with profound impacts on ecosystems and the species that live in them. Masking or distraction by noise can interfere with relevant sounds and thereby impact ecological interactions between individuals of the same or different species. Predator–prey dynamics are particularly likely to be influenced by rising noise levels, with important population- and community-level consequences, as species may differentially adapt to noise disturbance. Acoustic noise can, however, also impair the use of visual information by animals through the process of cross-sensory interference, possibly impacting species interactions that have so far been largely ignored by noise impact studies. Here, we assessed how noise affected the performance of great tit ( Parus major ) foraging on cryptic prey. Birds trained individually to search for paper moths differing in the level of camouflage with the test background were tested in the presence and absence of noise. We found that noise significantly increased approach and attack latencies, but that the effect depended on the level of crypsis. Noise increased latencies for cryptic prey targets, but not for conspicuous and colour-matched prey targets. Our results show that noise can interfere with the processing of visual information, particularly in difficult tasks such as separating objects from a similar looking background. These results have important ecological and evolutionary implications as they demonstrate how globally rising anthropogenic noise levels can influence the arms race between predators and prey across sensory domains.

Evolutionary community ecology

2019 ◽  
pp. 307-333
Author(s):  
Gary G. Mittelbach ◽  
Brian J. McGill
Keyword(s):  
Population Dynamics ◽  
Community Ecology ◽  
Species Interactions ◽  
Evolutionary Dynamics ◽  
Ecological Interactions ◽  
Predator Prey ◽  
Evolutionary Rescue ◽  
Species Pools ◽  
Laboratory Populations ◽  
Long Time

Ecology and evolution go hand in hand. However, since evolution occurs over relatively long time scales, ecologists had long thought it unlikely that evolutionary events could affect population dynamics or species interactions in ecological time. This view is changing. Today, there are multiple areas of research examining how evolutionary processes feedback directly on ecology. For example, eco-evolutionary dynamics focus on the cyclical interaction between ecology and adaptive evolution, such that changes in ecological interactions drive selection on organismal traits that, in turn, alter the outcome of ecological interactions. Striking examples of eco-evolutionary feedbacks are found in predator–prey interactions of laboratory populations. However, less is known about eco-evolutionary feedbacks in nature. Evolutionary rescue describes a process whereby rapid adaptation may prevent extinction in a changing environment. Other topics covered in this chapter are community phylogenetics and the evolution of regional species pools.

Past and recent biodiversity profiling in ancient Lake Chalco Mexico by a metagenomics analysis

2021 ◽  
Author(s):  
Bárbara Moguel ◽  
Liseth Pérez ◽  
Luis David Alcaraz ◽  
Socorro Lozano-García ◽  
Luis Herrera-Estrella ◽  
...  
Keyword(s):  
Volcanic Belt ◽  
Environmental Dna ◽  
Radiocarbon Dates ◽  
The Past ◽  
Mexican Volcanic Belt ◽  
History Of ◽  
High Throughput Dna Sequencing ◽  
High Altitude Lake ◽  
Taxonomic Groups ◽  
The Relationship

<p>For decades, paleoecological studies in lake sediments have focused on reconstructing the environments of the past and explaining phenomena linked to climatic variations. Recent advances in high-throughput DNA sequencing have allowed access to environmental DNA (eDNA) and ancient sedimentary DNA (sedaDNA) as a new and efficient proxy for past and present biodiversity. The basin of Mexico (BM) is located in the central part of the Trans-Mexican Volcanic Belt at 2,200 m a.s.l.; with the southern portion harboring the Chalco sub-basin. Lake Chalco is one of the last remaining natural aquatic ecosystems within the ever-expanding urban area surrounding Mexico City. The paleoenvironmental history of this lake has been previously characterized using sedimentological and geochemical proxies, as well as preserved microfossils (diatoms, pollen) with a temporal framework based on multiple radiocarbon dates. However, information for the remaining taxonomic groups and metabolic pathways remained unexplored. Here, we present the first metagenomics-based study for the Holocene in a high-altitude lake in Central Mexico –Lake Chalco. We explored the relationship between the lake’s paleoenvironmental condition and estimations of taxonomic and metabolic profiles across the sedimentary sequence (2.5 meters long). Multiple biological and abiotic variables revealed three main environmental phases: 1) a cool freshwater lake (FW1: 11,500-11,000 cal years BP), 2) a warm hyposaline lake (HS2: 11,000-6,000 cal years BP), and 3) a temperate, subsaline lake (SS3, <6,000 cal years BP). We describe the structure of the microbiota community and taxonomy richness turnover in the three Holocene paleoenvironmental phases. During the past 12 000 years BP the most abundant domains in Lake Chalco sediments were Bacteria, followed by Archaea, and Eukarya (36,722 genera). The analysis of functional proteins showed high biodiversity with a total of 27,636,243 proteins identified, but it was only possible to annotate 3,227,398 of them. Also, we identified several genes associated with some relevant pathways, such as methanogenesis. Altogether, this study allowed us to reconstruct the natural history of lake Chalco and its surroundings.</p>

scholarly journals Impacts of predator-mediated interactions along a climatic gradient on the population dynamics of an alpine bird

2020 ◽  
Author(s):  
Diana E. Bowler ◽  
Mikkel A. J. Kvasnes ◽  
Hans C. Pedersen ◽  
Brett K. Sandercock ◽  
Erlend B. Nilsen
Keyword(s):  
Population Dynamics ◽  
Species Interactions ◽  
Climatic Conditions ◽  
Boreal Ecosystems ◽  
Prey Switching ◽  
Predator Prey ◽  
Classic Theory ◽  
Species Population ◽  
Cyclic Dynamics ◽  
Ground Nesting

AbstractAccording to classic theory, species’ population dynamics and distributions are less influenced by species interactions under harsh climatic conditions compared to under more benign climatic conditions. In alpine and boreal ecosystems in Fennoscandia, the cyclic dynamics of rodents strongly affect many other species, including ground-nesting birds such as ptarmigan. According to the ‘alternative prey hypothesis’ (APH), the densities of ground-nesting birds and rodents are positively associated due to predator-prey dynamics and prey-switching. However, it remains unclear how the strength of these predator-mediated interactions change along a climatic harshness gradient in comparison with the effects of climatic variation. We built a hierarchical Bayesian model to estimate the sensitivity of ptarmigan populations to interannual variation in climate and rodent occurrence across Norway during 2007–2017. Ptarmigan abundance was positively linked with rodent occurrence, consistent with the APH. Moreover, we found that rodent dynamics had stronger effects on ptarmigan in colder regions. Our study highlights how species interactions play an important role for the population dynamics of species at higher latitudes and suggests that they can become even more important in the most climatically harsh regions.

scholarly journals Ecological Interactions and the Netflix Problem

2016 ◽  
Author(s):  
Philippe Desjardins-Proulx ◽  
Idaline Laigle ◽  
Timothée Poisot ◽  
Dominique Gravel
Keyword(s):  
Machine Learning ◽  
Supervised Learning ◽  
Random Forests ◽  
Species Interactions ◽  
Similarity Measures ◽  
Theoretical Models ◽  
Machine Learning Techniques ◽  
Nearest Neighbour ◽  
Ecological Interactions ◽  
Learning Techniques

0AbstractSpecies interactions are a key component of ecosystems but we generally have an incomplete picture of who-eats-who in a given community. Different techniques have been devised to predict species interactions using theoretical models or abundances. Here, we explore the K nearest neighbour approach, with a special emphasis on recommendation, along with other machine learning techniques. Recommenders are algorithms developed for companies like Netflix to predict if a customer would like a product given the preferences of similar customers. These machine learning techniques are well-suited to study binary ecological interactions since they focus on positive-only data. We also explore how the K nearest neighbour approach can be used with both positive and negative information, in which case the goal of the algorithm is to fill missing entries from a matrix (imputation). By removing a prey from a predator, we find that recommenders can guess the missing prey around 50% of the times on the first try, with up to 881 possibilities. Traits do not improve significantly the results for the K nearest neighbour, although a simple test with a supervised learning approach (random forests) show we can predict interactions with high accuracy using only three traits per species. This result shows that binary interactions can be predicted without regard to the ecological community given only three variables: body mass and two variables for the species’ phylogeny. These techniques are complementary, as recommenders can predict interactions in the absence of traits, using only information about other species’ interactions, while supervised learning algorithms such as random forests base their predictions on traits only but do not exploit other species’ interactions. Further work should focus on developing custom similarity measures specialized to ecology to improve the KNN algorithms and using richer data to capture indirect relationships between species.

scholarly journals Multispecies integrated population model reveals bottom-up dynamics in a seabird predator-prey system

2020 ◽  
Author(s):  
Maud Quéroué ◽  
Christophe Barbraud ◽  
Frédéric Barraquand ◽  
Daniel Turek ◽  
Karine Delord ◽  
...  
Keyword(s):  
Breeding Success ◽  
Species Interactions ◽  
Interspecific Interactions ◽  
Demographic Parameters ◽  
Multiple Sources ◽  
Bottom Up ◽  
Climate Conditions ◽  
Predator Prey ◽  
Relative Contribution ◽  
Prey System

AbstractAssessing the effects of climate and interspecific relationships on communities is challenging because of the complex interplay between species population dynamics, their interactions, and the need to integrate information across several biological levels (individuals – populations – communities). Usually used to quantify species interactions, integrated population models (IPMs) have recently been extended to communities. These models allow fitting multispecies matrix models to data from multiple sources while simultaneously accounting for various sources of uncertainty in each data source. We used multispecies IPMs accommodating climate conditions to quantify the relative contribution of climate vs. interspecific interactions on demographic parameters, such as survival and breeding success, in the dynamics of a predator-prey system. We considered a stage-structured predator–prey system combining 22 years of capture–recapture data and population counts of two seabirds, the Brown Skua (Catharacta lönnbergi) and its main prey the Blue Petrel (Halobaena caerulea) both breeding on the Kerguelen Islands in the Southern Ocean. Our results showed that climate and predator-prey interactions drive the demography of skuas and petrels in different ways. The breeding success of skuas appeared to be largely driven by the number of petrels and to a lesser extent by intraspecific density-dependence. In contrast, there was no evidence of predation effects on the demographic parameters of petrels, which were affected by oceanographic factors (chlorophyll a and sea surface temperature anomalies). We conclude that bottom-up mechanisms are the main drivers of this skua-petrel system. We discuss the mechanisms by which climate variability and predator-prey relationships may affect the demographic parameters of these seabirds. Taking into account both species interactions and environmental covariates in the same analysis improved our understanding of species dynamics.

Predator–prey interactions and climate change

2019 ◽  
pp. 199-220 ◽  
Author(s):  
Vincent Bretagnolle ◽  
Julien Terraube
Keyword(s):  
Climate Change ◽  
Species Interactions ◽  
Experimental Studies ◽  
Trophic Levels ◽  
Generalist Predators ◽  
Top Down ◽  
Predator Prey ◽  
Key Topics ◽  
Available Information

Climate change is likely to impact all trophic levels, although the response of communities and ecosystems to it has only recently received considerable attention. Further, it is expected to affect the magnitude of species interactions themselves. In this chapter, we summarize why and how climate change could affect predator–prey interactions, then review the literature about its impact on predator–prey relationships in birds, and provide prospects for future studies. Expected effects on prey or predators may include changes in the following: distribution, phenology, population density, behaviour, morphology, or physiology. We review the currently available information concerning particular key topics: top-down versus bottom-up control, specialist versus generalist predators, functional versus numerical responses, trophic cascades and regime shifts, and lastly adaptation and selection. Finally, we focus our review on two well-studied bird examples: seabirds and raptors. Key future topics include long-term studies, modelling and experimental studies, evolutionary questions, and conservation issues.

scholarly journals Diversity and coexistence are influenced by time‐dependent species interactions in a predator–prey system

2020 ◽  
Vol 23 (6) ◽  
pp. 983-993 ◽  
Author(s):  
Canan Karakoç ◽  
Adam Thomas Clark ◽  
Antonis Chatzinotas
Keyword(s):  
Species Interactions ◽  
Time Dependent ◽  
Predator Prey ◽  
Prey System

scholarly journals Analysis of productivity and stability of synthetic microbial communities

2019 ◽  
Vol 16 (150) ◽  
pp. 20180859 ◽  
Author(s):  
Sihao Di ◽  
Aidong Yang
Keyword(s):  
Species Interactions ◽  
Feedback Loop ◽  
Single Species ◽  
System Structure ◽  
Negative Feedback Loop ◽  
Positive Feedback Loop ◽  
Trade Off ◽  
The Cost ◽  
Synthetic Microbial Communities ◽  
Generic System

Bioreactors that employ a synthetic microbial community hold potential to overcome limitations of those based on a single species, which embrace a higher level of complexity due to the inter-species interactions. In this work, a number of generic system structures involving two cross-feeding species and various types of inhibition have been studied, together with two three-species cases where a third species is introduced to fulfil a specific function. These cases are represented by mathematical models and inspected through bifurcation analysis and numerical simulation to reveal how the system structure and parametrization affect stability and productivity of the bioreactor. The results show that inhibitions generally lead to reduction in both productivity and stability, and that the presence of a negative feedback loop and a positive feedback loop may give rise to oscillation and bi-stability, respectively, depending on the strength of the inhibitions involved. The intended gains by the introduction of a third species may be achieved when its negative side-effect is sufficiently moderate, and at the cost of reduced stability. As observed in several cases, the changes in stability and productivity do not always follow the same trend, implying trade-off between the two objectives in the engineering of such bioreactors.

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