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08 Aug 2020
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Trophic cascade driven by behavioural fine-tuning as naïve prey rapidly adjust to a novel predator

While the quoll’s away, the mice will play… and the seeds will pay

Recommended by based on reviews by 2 anonymous reviewers

A predator can strongly influence the demography of its prey, which can have profound carryover effects on the trophic network; so-called density-mediated indirect interactions (DMII; Werner and Peacor 2003; Schmitz et al. 2004; Trussell et al. 2006). Furthermore, a novel predator can alter the phenotypes of its prey for traits that will change prey foraging efficiency. These trait-mediated indirect interactions may in turn have cascading effects on the demography and features of the basal resources consumed by the intermediate consumer (TMIII; Werner and Peacor 2003; Schmitz et al. 2004; Trussell et al. 2006), but very few studies have looked for these effects (Trusell et al. 2006). The study “Trophic cascade driven by behavioural fine-tuning as naïve prey rapidly adjust to a novel predator”, by Jolly et al. (2020) is therefore a much-needed addition to knowledge in this field. The authors have profited from a rare introduction of Northern quolls (Dasyurus hallucatus) on an Australian island, to examine both the density-mediated and trait-mediated indirect interactions with grassland melomys (Melomys burtoni) and the vegetation of their woodland habitat.
Jolly et al. (2020) compared melomys populations in four quoll-invaded and three quoll-free sites on the same island. Using capture-mark-recapture methods, they found a lower survival and decreased population size in quoll-invaded sites compared to quoll-free sites. Although they acknowledge that this decline could be attributable to either the direct effects of the predator or to a wildfire that occurred early in the experiment in the quoll-invaded sites, the authors argue that the wildfire alone cannot explain all of their results.
Beyond demographic effects, Jolly et al. (2020) also examined risk taking, foraging behaviour, and predator avoidance in melomys. Quoll presence was first associated with a strong decrease in risk taking in melomys, but the difference disappeared over the three years of study, indicating a possible adjustment by the prey. In quoll-invaded sites, though, melomys continued to be more neophobic than in the quoll-free sites throughout the study. Furthermore, in a seed (i.e. wheat) removal experiment, Jolly et al. (2020) measured how melomys harvested seeds in the presence or absence of predator scents. In both quoll-invaded and quoll-free sites, melomys density increased seed harvest efficiency. Melomys also removed less seeds in quoll-invaded sites than in quoll-free sites, supporting both the DMII and TMII hypotheses. However, in the quoll-invaded sites only, melomys foraged less on predator-scented seed patches than on unscented ones, trading foraging efficiency for an increased safety against predators, and this effect increased across the years. This last result indicates that predators can indirectly influence seed consumption through the trade-off between foraging and predator avoidance, strongly supporting the TMII hypothesis.
Ideally, the authors would have run a nice before-after, impact-control design, but nature does not always allow for ideal experimental designs. Regardless, the results of such an “experiment in the wild” predation study are still valuable, as they are very rare (Trussell et al. 2006), and they provide crucial information on the direct and indirect interactions along a trophic cascade. Furthermore, the authors have effectively addressed any concerns about potential confounding factors, and thus have a convincing argument that their results represent predator-driven demographic and behavioural changes.
One important question remains from an evolutionary ecology standpoint: do the responses of melomys to the presence of quolls represent phenotypically plastic changes or rapid evolutionary changes caused by novel selection pressures? Classically, TMII are assumed to be mostly caused by phenotypic plasticity (Werner and Peacor 2003), and this might be the case when the presence of the predator is historical. Phenotypic plasticity allows quick and reversible adjustments of the prey population to changes in the predator density. When the predator population declines, such rapid phenotypic changes can be reversed, reducing the cost associated with anti-predator behaviour (e.g., lower foraging efficiency) in the absence of predators. In the case of a novel predator, however, short-term evolutionary responses by the prey may play role in the TMII, as they would allow a phenotypic shift in prey’s traits along the trade-off between foraging efficiency and anti-predator response that will probably more advantageous over the longer term, if the predator does not disappear. The authors state that they could not rule out one or the other of these hypotheses. However, future work estimating the relative importance of phenotypic plasticity and evolutionary changes in the quoll-melomys system would be valuable. Phenotypic selection analysis, for example, by estimating the link between survival and the traits measured, might help test for a fitness advantage to altered behaviour in the presence of a predator. Common garden experiments, comparing the quoll-invaded and the quoll-free melomys populations, might also provide information on any potential evolutionary changes caused by predation. More work could also analyse the potential effects on the seed populations. Not only might the reduction in seed predation have consequences on the landscape in the future, as the authors mention, but it may also mean that the seeds themselves could be subject to novel selection pressures, which may affect their phenology, physiology or life history. Off course, the authors will have to switch from wheat to a more natural situation, and evaluate the effects of changes in the melomys population on the feature of the local vegetation and the ecosystem.
Finally, the authors have not yet found that the observed changes in the traits have translated into a demographic rebound for melomys. Here again, I can see an interesting potential for further studies. Should we really expect an evolutionary rescue (Bell and Gonzalez 2009) in this system? Alternatively, should the changes in behaviour be accompanied by permanent changes in life history, such as a slower pace-of-life (Réale et al. 2010) that could possibly lead to lower melomys density?
This paper provides nice in natura evidence for density- and trait-mediated indirect interactions hypotheses. I hope it will be the first of a long series of work on this interesting quoll-melomys system, and that the authors will be able to provide more information on the eco-evolutionary consequences of a novel predator on a trophic network.

References

-Bell G, Gonzalez A (2009) Evolutionary rescue can prevent extinction following environmental change. Ecology letters, 12(9), 942-948. https://doi.org/10.1111/j.1461-0248.2009.01350.x
-Jolly CJ, Smart AS, Moreen J, Webb JK, Gillespie GR, Phillips BL (2020) Trophic cascade driven by behavioural fine-tuning as naïve prey rapidly adjust to a novel predator. bioRxiv, 856997, ver. 6 peer-reviewed and recommended by PCI Ecology. https://doi.org/ 10.1101/856997
-Matassa C, Ewanchuk P, Trussell G (2018) Cascading effects of a top predator on intraspecific competition at intermediate and basal trophic levels. Functional Ecology, 32(9), 2241-2252. https://doi.org/10.1111/1365-2435.13131
-Réale D, Garant D, Humphries MM, Bergeron P, Careau V, Montiglio PO (2010) Personality and the emergence of the pace-of-life syndrome concept at the population level. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1560), 4051-4063. https://doi.org/10.1098/rstb.2010.0208
-Schmitz O, Krivan V, Ovadia O (2004) Trophic cascades: the primacy of trait‐mediated indirect interactions. Ecology Letters 7(2), 153-163. https://doi.org/10.1111/j.1461-0248.2003.00560.x
-Trussell G, Ewanchuk P, Matassa C (2006). Habitat effects on the relative importance of trait‐ and density‐mediated indirect interactions. Ecology Letters, 9(11), 1245-1252. https://doi.org/10.1111/j.1461-0248.2006.00981.x
-Werner EE, Peacor SD (2003) A review of trait‐mediated indirect interactions in ecological communities. Ecology, 84(5), 1083-1100. https://doi.org/10.1890/0012-9658(2003)084[1083:AROTII]2.0.CO;2

Trophic cascade driven by behavioural fine-tuning as naïve prey rapidly adjust to a novel predatorChris J Jolly, Adam S Smart, John Moreen, Jonathan K Webb, Graeme R Gillespie and Ben L Phillips<p>The arrival of novel predators can trigger trophic cascades driven by shifts in prey numbers. Predators also elicit behavioural change in prey populations, via phenotypic plasticity and/or rapid evolution, and such changes may also contribute t...Behaviour & Ethology, Biological invasions, Evolutionary ecology, Experimental ecology, Foraging, Herbivory, Population ecology, Terrestrial ecology, Tropical ecologyDenis Réale2019-11-27 21:39:44 View
10 Oct 2024
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Large-scale spatio-temporal variation in vital rates and population dynamics of an alpine bird

Do look up: building a comprehensive view of population dynamics from small scale observation through citizen science

Recommended by based on reviews by Todd Arnold and 1 anonymous reviewer

Population ecologists are in the business of decrypting the drivers of variation in the abundance of organisms across space and time (Begon et al. 1986). Comprehensive studies of wild vertebrate populations which provide the necessary information on variations in vital rates in relation to environmental conditions to construct informative models of large-scale population dynamics are rare, ostensibly because of the huge effort required to monitor individuals across ecological contexts and over generations. In this current aim, Nater et al. (2024) are leading the way forward by combining distance sampling data collected through a large-scale citizen science (Fraisl et al. 2022) programme in Norway with state-of-the-art modelling approaches to build a comprehensive overview of the population dynamics of willow ptarmigan. Their work enhances our fundamental understanding of this system and provides evidence-based tools to improve its management (Williams et al. 2002). Even better, they are working for the common good, by providing an open-source workflow that should enable ecologists and managers together to predict what will happen to their favourite model organism when the planet throws its next curve ball. In the case of the ptarmigan, for example, it seems that the impact of climate change on their population dynamics will differ across the species’ distributional range, with a slower pace of life (sensu Stearns 1983) at higher latitudes and altitudes. 

On a personal note, I have often mused whether citizen science, with its inherent limits and biases, was just another sticking plaster over the ever-deeper cuts in the research budgets to finance long-term ecological research. Here, Nater et al. are doing well to convince me that we would be foolish to ignore such opportunities, particularly when citizens are engaged, motivated, with an inherent capacity for the necessary discipline to employ common protocols in a standardised fashion. A key challenge for us professional ecologists is to inculcate the next generation of citizens with a sense of their opportunity to contribute to a better understanding of the natural world.

References

Begon, Michael, John L Harper, and Colin R Townsend. 1986. Ecology: individuals, populations and communities. Blackwell Science.

Fraisl, Dilek, Gerid Hager, Baptiste Bedessem, Margaret Gold, Pen-Yuan Hsing, Finn Danielsen, Colleen B Hitchcock, et al. 2022. Citizen Science in Environmental and Ecological Sciences. Nature Reviews Methods Primers 2 (1): 64. https://doi.org/10.1038/s43586-022-00144-4

Chloé R. Nater, Francesco Frassinelli, James A. Martin, Erlend B. Nilsen (2024) Large-scale spatio-temporal variation in vital rates and population dynamics of an alpine bird. EcoEvoRxiv, ver.4 peer-reviewed and recommended by PCI Ecology https://doi.org/10.32942/X2VP6J

Stearns, S.C. 1983. The influence of size and phylogeny of covariation among life-history traits in the mammals. Oikos, 41, 173–187. https://doi.org/10.2307/3544261

Williams, Byron K, James D Nichols, and Michael J Conroy. 2002. Analysis and Management of Animal Populations. Academic Press.

Large-scale spatio-temporal variation in vital rates and population dynamics of an alpine birdChloé R. Nater, Francesco Frassinelli, James A. Martin, Erlend B. Nilsen<p>Quantifying temporal and spatial variation in animal population size and demography is a central theme in ecological research and important for directing management and policy. However, this requires field sampling at large spatial extents and ...Biodiversity, Biogeography, Conservation biology, Demography, Euring Conference, Landscape ecology, Life history, Population ecology, Spatial ecology, Metacommunities & Metapopulations, Statistical ecology, Terrestrial ecologyAidan Jonathan Mark Hewison2024-02-02 08:54:06 View
10 Jun 2018
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A reply to “Ranging Behavior Drives Parasite Richness: A More Parsimonious Hypothesis”

Does elevated parasite richness in the environment affect daily path length of animals or is it the converse? An answer bringing some new elements of discussion

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

In 2015, Brockmeyer et al. [1] suggested that mandrills (Mandrillus sphinx) may accept additional ranging costs to avoid heavily parasitized areas. Following this paper, Bicca-Marques and Calegaro-Marques [2] questioned this interpretation and presented other hypotheses. To summarize, whilst Brockmeyer et al. [1] proposed that elevated daily path length may be a consequence of elevated parasite richness, Bicca-Marques and Calegaro-Marques [2] viewed it as a cause. In this current paper, Charpentier and Kappeler [3] respond to some of the criticisms by Bicca-Marques and Calegaro-Marques and discuss the putative parsimony of the two competing scenarios. The manuscript is interesting and focuses on an important question concerning the discussion about the social organization and home range use in wild mandrills. This answer helps to move this debate forward and should stimulate more empirical studies of the role of environmentally-transmitted parasites in shaping ranging and movement patterns of wild vertebrates. Given the elements this paper brings to the topics, it should have been published in American Journal of Primatology, the journal that published the two previous articles.

References

[1] Brockmeyer, T., Kappeler, P. M., Willaume, E., Benoit, L., Mboumba, S., & Charpentier, M. J. E. (2015). Social organization and space use of a wild mandrill (Mandrillus sphinx) group. American Journal of Primatology, 77(10), 1036–1048. doi: 10.1002/ajp.22439
[2] Bicca-Marques, J. C., & Calegaro-Marques, C. (2016). Ranging behavior drives parasite richness: A more parsimonious hypothesis. American Journal of Primatology, 78(9), 923–927. doi: 10.1002/ajp.22561
[3] Charpentier, M. J., & Kappeler, P. M. (2018). A reply to “Ranging Behavior Drives Parasite Richness: A More Parsimonious Hypothesis.” ArXiv:1805.08151v2 [q-Bio]. Retrieved from http://arxiv.org/abs/1805.08151

A reply to “Ranging Behavior Drives Parasite Richness: A More Parsimonious Hypothesis”Charpentier MJE, Kappeler PM<p>In a recent article, Bicca-Marques and Calegaro-Marques [2016] discussed the putative assumptions related to an interpretation we provided regarding an observed positive relationship between weekly averaged parasite richness of a group of mandr...Behaviour & Ethology, Evolutionary ecology, Foraging, Host-parasite interactions, Spatial ecology, Metacommunities & Metapopulations, ZoologyCédric Sueur2018-05-22 10:59:33 View
21 Dec 2020
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Influence of local landscape and time of year on bat-road collision risks

Assessing bat-vehicle collision risks using acoustic 3D tracking

Recommended by ORCID_LOGO based on reviews by Mark Brigham and ?

The loss of biodiversity is an issue of great concern, especially if the extinction of species or the loss of a large number of individuals within populations results in a loss of critical ecosystem services. We know that the most important threat to most species is habitat loss and degradation (Keil et al., 2015; Pimm et al., 2014); the latter can be caused by multiple anthropogenic activities, including pollution, introduction of invasive species and fragmentation (Brook et al., 2008; Scanes, 2018). Roads are a major cause of habitat fragmentation, isolating previously connected populations and being a direct source of mortality for animals that attempt to cross them (Spellberg, 1998).
While most studies have focused on the effect of roads on larger mammals (Bartonička et al., 2018; Litvaitis and Tash, 2008), in recent years many researchers have grown increasingly concerned about the risk of collision between bats and vehicles (Fensome and Mathews, 2016). For example, a recent publication by Medinas et al. (2021) found 509 bat casualties along a 51-km-long transect during a period of 3 years. Their study provides extremely valuable information to asses which factors primarily drive bat mortality on roads, yet it required a substantial investment of time coupled with the difficulty of detecting bat carcasses. Other studies have used acoustic monitoring as a proxy to gauge risk of collision based on estimates of bat density along roads (reviewed in Fensome and Mathews 2016); while the results of such studies are valuable, the number of passes recorded does not necessarily equal collision risk, as many species may simply avoid crossing the roads. Understanding the risk of collisions is of vital importance for adequate planning of road construction, particularly for key sites that harbor threatened bat species or unusually large populations, especially if these are already greatly impacted by other anthropogenic activities (e.g. wind turbines; Kunz et al. 2007) or unusually deadly pathogens (e.g. white-nose syndrome; Blehert et al. 2009).
The study by Roemer et al. (2020) titled “Influence of local landscape and time of year on bat-road collision risks”, is a welcome addition to our understanding of bat collision risk as it employs a more accurate assessment of bat collision risk based on acoustic monitoring and tracking of flight paths. The goal of the study of Roemer and collaborators, which was conducted at 66 study sites in the Mediterranean region, is to provide an assessment of collision risk based on bat activity near roads. They collected a substantial amount of information for several species: more than 30,000 estimated flight trajectories for 21+ species, including Barbastella barbastellus, Myotis spp., Plecotus sp., Rhinolophus ferrumequinum, Miniopterus schreibersii, Pipistrellus spp., Nyctalus leisleri, and others. They assess risk based on estimates of 1) species abundance from acoustic monitoring, 2) direction of flight paths along roads, and 3) bat-vehicle co-occurrence.
Their findings suggest that risk is habitat, species, guild, and season-specific. Roads within forested habitats posed the largest threats for most species, particularly since most flights within these habitats occurred at the zone of collision risk. They also found that bats typically fly parallel to the road axis regardless of habitat type, which they argue supports the idea that bats may use roads as corridors. The results of their study, as expected, also show that the majority of bat passes were detected during summer or autumn, depending on species, yet they provide novel findings of an increase in risky behaviors during autumn, when the number of passes at the zone of collision risk increased significantly. Their results also suggest that mid-range echolocators, a classification that is based on call design and parameters (Frey-Ehrenbold et al., 2013), had a larger portion of flights in the zone at risk, thus potentially making them more susceptible than short and long-range echolocators to collisions with vehicles.
The methods employed by Roemer et al. (2020) could further help us determine how roads pose species and site-specific threats in a diversity of places without the need to invest a significant amount of time locating bat carcasses. Their findings are also important as they could provide valuable information for deciding where new roads should be constructed, particularly if the most vulnerable species are abundant, perhaps due to the presence of important roost sites. They also show how habitats near larger roads could increase threats, providing an important first step for recommendations regarding road construction and maintenance. As pointed out by one reviewer, one possible limitation of the study is that the results are not supported by the identification of carcasses. For example, does an increase in the number of identified flights at the zone of risk really translate into an increase in the number of collisions? Regardless of the latter, the paper’s methods and results are very valuable and provide an important step towards developing additional tools to assess bat-vehicle collision risks.

References

[1] Bartonička T, Andrášik R, Duľa M, Sedoník J, Bíl M (2018) Identification of local factors causing clustering of animal-vehicle collisions. The Journal of Wildlife Management, 82, 940–947. https://doi.org/10.1002/jwmg.21467
[2] Blehert DS, Hicks AC, Behr M, Meteyer CU, Berlowski-Zier BM, Buckles EL, Coleman JTH, Darling SR, Gargas A, Niver R, Okoniewski JC, Rudd RJ, Stone WB (2009) Bat White-Nose Syndrome: An Emerging Fungal Pathogen? Science, 323, 227–227. https://doi.org/10.1126/science.1163874
[3] Brook BW, Sodhi NS, Bradshaw CJA (2008) Synergies among extinction drivers under global change. Trends in Ecology & Evolution, 23, 453–460. https://doi.org/10.1016/j.tree.2008.03.011
[4] Fensome AG, Mathews F (2016) Roads and bats: a meta-analysis and review of the evidence on vehicle collisions and barrier effects. Mammal Review, 46, 311–323. https://doi.org/10.1111/mam.12072
[5] Frey‐Ehrenbold A, Bontadina F, Arlettaz R, Obrist MK (2013) Landscape connectivity, habitat structure and activity of bat guilds in farmland-dominated matrices. Journal of Applied Ecology, 50, 252–261. https://doi.org/10.1111/1365-2664.12034
[6] Keil P, Storch D, Jetz W (2015) On the decline of biodiversity due to area loss. Nature Communications, 6, 8837. https://doi.org/10.1038/ncomms9837
[7] Kunz TH, Arnett EB, Erickson WP, Hoar AR, Johnson GD, Larkin RP, Strickland MD, Thresher RW, Tuttle MD (2007) Ecological impacts of wind energy development on bats: questions, research needs, and hypotheses. Frontiers in Ecology and the Environment, 5, 315–324. https://doi.org/10.1890/1540-9295(2007)5[315:EIOWED]2.0.CO;2
[8] Litvaitis JA, Tash JP (2008) An Approach Toward Understanding Wildlife-Vehicle Collisions. Environmental Management, 42, 688–697. https://doi.org/10.1007/s00267-008-9108-4
[9] Medinas D, Marques JT, Costa P, Santos S, Rebelo H, Barbosa AM, Mira A (2021) Spatiotemporal persistence of bat roadkill hotspots in response to dynamics of habitat suitability and activity patterns. Journal of Environmental Management, 277, 111412. https://doi.org/10.1016/j.jenvman.2020.111412
[10] Pimm SL, Jenkins CN, Abell R, Brooks TM, Gittleman JL, Joppa LN, Raven PH, Roberts CM, Sexton JO (2014) The biodiversity of species and their rates of extinction, distribution, and protection. Science, 344. https://doi.org/10.1126/science.1246752
[11] Roemer C, Coulon A, Disca T, Bas Y (2020) Influence of local landscape and time of year on bat-road collision risks. bioRxiv, 2020.07.15.204115, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2020.07.15.204115
[12] Scanes CG (2018) Chapter 19 - Human Activity and Habitat Loss: Destruction, Fragmentation, and Degradation. In: Animals and Human Society (eds Scanes CG, Toukhsati SR), pp. 451–482. Academic Press. https://doi.org/10.1016/B978-0-12-805247-1.00026-5
[13] Spellerberg I (1998) Ecological effects of roads and traffic: a literature review. Global Ecology & Biogeography Letters, 7, 317–333. https://doi.org/10.1046/j.1466-822x.1998.00308.x

Influence of local landscape and time of year on bat-road collision risksCharlotte Roemer, Aurélie Coulon, Thierry Disca, and Yves Bas<p>Roads impact bat populations through habitat loss and collisions. High quality habitats particularly increase bat mortalities on roads, yet many questions remain concerning how local landscape features may influence bat behaviour and lead to hi...Behaviour & Ethology, Biodiversity, Conservation biology, Human impact, Landscape ecologyGloriana Chaverri2020-07-20 10:56:29 View
23 Jan 2024
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Use of linear features by red-legged partridges in an intensive agricultural landscape: implications for landscape management in farmland

The importance of managing linear features in agricultural landscapes for farmland birds

Recommended by based on reviews by Matthew Grainger and 1 anonymous reviewer

European farmland bird populations continue declining at an alarming rate, and some species require urgent action to avoid their demise (Silva et al. 2024). While factors such as climate change and urbanization also play an important role in driving the decline of farmland bird populations, its main driver seems to be linked with agricultural intensification (Rigal et al. 2023). Besides increased pesticide and fertilizer use, agricultural intensification often results in the homogenization of agricultural landscapes through the removal of seminatural linear features such as hedgerows, field margins, and grassy strips that can be beneficial for biodiversity. These features may be particularly important during the breeding season, when breeding farmland birds can benefit from patches of denser vegetation to conceal nests and improve breeding success. It is both important and timely to understand how landscape management can help to address the ongoing decline of farmland birds by identifying specific actions that can boost breeding success.

Perrot et al. 2023 contribute to this effort by exploring how red-legged partridges use linear features in an intensive agricultural landscape during the breeding season. Through a combination of targeted fieldwork and GPS tracking, the authors highlight patterns in home range size and habitat selection that provide insights for landscape management. Specifically, their results suggest that birds have smaller range sizes in the vicinity of traffic routes and seminatural features structured by both herbaceous and woody cover. Furthermore, they show that breeding birds tend to choose linear elements with herbaceous cover whereas non-breeders prefer linear elements with woody cover, underlining the importance of accounting for the needs of both breeding and non-breeding birds. In particular, the authors stress the importance of providing additional vegetation elements such as hedges, grassy strips or embankments in order to increase landscape heterogeneity. These landscape elements are usually found in the vicinity of linear infrastructures such as roads and tracks, but it is important they are available also in separate areas to avoid the risk of bird collision and the authors provide specific recommendations towards this end. Overall, this is an important study with clear recommendations on how to improve landscape management for these farmland birds.

References

Perrot, C., Séranne, L., Berceaux, A., Noel, M., Arroyo, B., & Bacon, L. (2023) "Use of linear features by red-legged partridges in an intensive agricultural landscape: implications for landscape management in farmland." bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Ecology.
https://doi.org/10.1101/2023.07.27.550774
 
Rigal, S., Dakos, V., Alonso, H., Auniņš, A., Benkő, Z., Brotons, L., ... & Devictor, V. (2023) "Farmland practices are driving bird population decline across Europe." Proceedings of the National Academy of Sciences 120.21: e2216573120.
https://doi.org/10.1073/pnas.2216573120
 
Silva, J. P., Gameiro, J., Valerio, F., & Marques, A. T. (2024) "Portugal's farmland bird crisis requires action." Science 383.6679: 157-157.
https://doi.org/10.1126/science.adn1390

Use of linear features by red-legged partridges in an intensive agricultural landscape: implications for landscape management in farmlandCharlotte Perrot, Antoine Berceaux, Mathias Noel, Beatriz Arroyo, Leo Bacon<p>Current agricultural practices and change are the major cause of biodiversity loss. An important change associated with the intensification of agriculture in the last 50 years is the spatial homogenization of the landscape with substantial loss...Agroecology, Behaviour & Ethology, Biodiversity, Conservation biology, Habitat selectionRicardo Correia2023-08-01 10:27:33 View
06 Mar 2020
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The persistence in time of distributional patterns in marine megafauna impacts zonal conservation strategies

The importance of spatio-temporal dynamics on MPA's design

Recommended by based on reviews by Ana S. L. Rodrigues and 1 anonymous reviewer

Marine protected areas (MPA) have arisen as the main approach for conservation of marine species. Fishes, marine mammals and birds can be conservation targets that justify the implementation of these areas. However, MPAs undergo many of the problems faced by their terrestrial equivalent. One of the major concerns is that these conservation areas are spatially constrained, by logistic reasons, and many times these constraints caused that key areas for the species (reproductive sites, refugees, migration) fall outside the limits, making conservation efforts even more difficult. Lambert et al. [1] evaluate at what point the Bay of Biscay MPA contains key ecological areas for several emblematic species. The evaluation incorporated a spatio-temporal dimension. To evaluate these ideas, authors evaluate two population descriptors: aggregation and persistence of several species of cetaceans and seabirds.
The authors determined that despite the MPA contains key areas for some species, for many others the key areas fall outside the MPA (aggregation sites) or observed aggregation sites are poorly persistent in time. They found that aggregation and persistence behave as two uncorrelated descriptors of the spatio-temporal distribution of populations. Variability of both characteristics was species-specific, but in all cases the message is clear: both features must be taken into account to evaluate the effectiveness of MPAs. Both conclusions pointed out to the difficulties that a strategy based on MPAs could face when the target are those species with low aggregation or those where key sites show low persistence in time.
Conceptually, the manuscript and its conclusions are very interesting, specially its recommendation of including temporal variability of species abundances and aggregation in the design of MPAs. However, despite the clear biological importance of persistence and aggregation of the conservation targets for the design of a MPA, its implementation will still be an extremely complex task. A first constraint is that important areas for one species could not be relevant for others, making the design of the MPA difficult because the more target species we include the larger the area needed for the MPA. As a consequence, the management of the MPA turns difficult and expensive as the area increases. These increased costs could be a key point for accepting/rejecting the implementation of these MPAs for governments. Also larger areas could imply highest level of conflict with local communities or stakeholders. In many the inclusion inside MPAs of areas with traditional social or economic use will be a major source of conflict with the people.
Despite these difficulties, the results of Lambert et al. [1] give us a key message for improving MPA’s design. The best strategy for including their conclusions in the effective implementation of these areas will be the next target in conservation research.

References

[1] Lambert, C., Dorémus, G. and V. Ridoux (2020) The persistence in time of distributional patterns in marine megafauna impacts zonal conservation strategies. bioRxiv, 790634, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/790634

The persistence in time of distributional patterns in marine megafauna impacts zonal conservation strategiesCharlotte Lambert, Ghislain Dorémus, Vincent Ridoux<p>The main type of zonal conservation approaches corresponds to Marine Protected Areas (MPAs), which are spatially defined and generally static entities aiming at the protection of some target populations by the implementation of a management pla...Conservation biology, Habitat selection, Species distributionsSergio Estay2019-10-03 08:47:17 View
04 Apr 2023
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Data stochasticity and model parametrisation impact the performance of species distribution models: insights from a simulation study

Species Distribution Models: the delicate balance between signal and noise

Recommended by ORCID_LOGO based on reviews by Alejandra Zarzo Arias and 1 anonymous reviewer

Species Distribution Models (SDMs) are one of the most commonly used tools to predict where species are, where they may be in the future, and, at times, what are the variables driving this prediction. As such, applying an SDM to a dataset is akin to making a bet: that the known occurrence data are informative, that the resolution of predictors is adequate vis-à-vis the scale at which their impact is expressed, and that the model will adequately capture the shape of the relationships between predictors and predicted occurrence.

In this contribution, Lambert & Virgili (2023) perform a comprehensive assessment of different sources of complications to this process, using replicated simulations of two synthetic species. Their experimental process is interesting, in that both the data generation and the data analysis stick very close to what would happen in "real life". The use of synthetic species is particularly relevant to the assessment of SDM robustness, as they enable the design of species for which the shape of the relationship is given: in short, we know what the model should capture, and can evaluate the model performance against a ground truth that lacks uncertainty.

Any simulation study is limited by the assumptions established by the investigators; when it comes to spatial data, the "shape" of the landscape, both in terms of auto-correlation and in where the predictors are available. Lambert & Virgili (2023) nicely circumvent these issues by simulating synthetic species against the empirical distribution of predictors; in other words, the species are synthetic, but the environment for which the prediction is made is real. This is an important step forward when compared to the use of e.g. neutral landscapes (With 1997), which can have statistical properties that are not representative of natural landscapes (see e.g. Halley et al., 2004).

A striking point in the study by Lambert & Virgili (2023) is that they reveal a deep, indeed deeper than expected, stochasticity in SDMs; whether this is true in all models remains an open question, but does not invalidate their recommendation to the community: the interpretation of outcomes is a delicate exercise, especially because measures that inform on the goodness of the model fit do not capture the predictive quality of the model outputs. This preprint is both a call to more caution, and a call to more curiosity about the complex behavior of SDMs, while also providing a sensible template to perform future analyses of the potential issues with predictive models.


References

Halley, J. M., et al. (2004) “Uses and Abuses of Fractal Methodology in Ecology: Fractal Methodology in Ecology.” Ecology Letters, vol. 7, no. 3, pp. 254–71. https://doi.org/10.1111/j.1461-0248.2004.00568.x.

Lambert, Charlotte, and Auriane Virgili (2023). Data Stochasticity and Model Parametrisation Impact the Performance of Species Distribution Models: Insights from a Simulation Study. bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2023.01.17.524386

With, Kimberly A. (1997) “The Application of Neutral Landscape Models in Conservation Biology. Aplicacion de Modelos de Paisaje Neutros En La Biologia de La Conservacion.” Conservation Biology, vol. 11, no. 5, pp. 1069–80. https://doi.org/10.1046/j.1523-1739.1997.96210.x.

Data stochasticity and model parametrisation impact the performance of species distribution models: insights from a simulation studyCharlotte Lambert, Auriane Virgili<p>Species distribution models (SDM) are widely used to describe and explain how species relate to their environment, and predict their spatial distributions. As such, they are the cornerstone of most of spatial planning efforts worldwide. SDM can...Biogeography, Habitat selection, Macroecology, Marine ecology, Spatial ecology, Metacommunities & Metapopulations, Species distributions, Statistical ecologyTimothée Poisot2023-01-20 09:43:51 View
28 Dec 2022
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Deleterious effects of thermal and water stresses on life history and physiology: a case study on woodlouse

An experimental approach for understanding how terrestrial isopods respond to environmental stressors

Recommended by ORCID_LOGO based on reviews by Aaron Yilmaz and Michael Morris

​​In this article, the authors discuss the results of their study investigating the effects of heat stress and moisture stress on a terrestrial isopod Armadilldium vulgare, the common woodlouse [1]. Specifically, the authors have assessed how increased temperature or decreased moisture affects life history traits (such as growth, survival, and reproduction) as well as physiological traits (immune cell parameters and \( beta \)-galactosidase activity). This article quantitatively evaluates the effects of the two stressors on woodlouse. Terrestrial isopods like woodlouse are sensitive to thermal and moisture stress [2; 3] and are therefore good models to test hypotheses in global change biology and for monitoring ecosystem health.

​An important feature of this study is the combination of experimental, laboratory, and analytical techniques. Experiments were conducted under controlled conditions in the laboratory by modulating temperature and moisture, life history and physiological traits were measured/analyzed and then tested using models. Both stressors had negative impacts on survival and reproduction of woodlouse, and result in premature ageing. Although thermal stress did not affect survival, it slowed woodlouse growth. Moisture stress did not have a detectable effect on woodlouse growth but decreased survival and reproductive success. An important insight from this study is that effects of heat and moisture stressors on woodlouse are not necessarily linear, and experimental approaches can be used to better elucidate the mechanisms and understand how these organisms respond to environmental stress.

​This article is timely given the increasing attention on biological monitoring and ecosystem health.​

References:

[1] Depeux C, Branger A, Moulignier T, Moreau J, Lemaître J-F, Dechaume-Moncharmont F-X, Laverre T, Pauhlac H, Gaillard J-M, Beltran-Bech S (2022) Deleterious effects of thermal and water stresses on life history and physiology: a case study on woodlouse. bioRxiv, 2022.09.26.509512., ver. 3 peer-reviewd and recommended by PCI Ecology. https://doi.org/10.1101/2022.09.26.509512

[2] ​Warburg MR, Linsenmair KE, Bercovitz K (1984) The effect of climate on the distribution and abundance of isopods. In: Sutton SL, Holdich DM, editors. The Biology of Terrestrial Isopods. Oxford: Clarendon Press. pp. 339–367.​

[3] Hassall M, Helden A, Goldson A, Grant A (2005) Ecotypic differentiation and phenotypic plasticity in reproductive traits of Armadillidium vulgare (Isopoda: Oniscidea). Oecologia 143: 51–60.​ https://doi.org/10.1007/s00442-004-1772-3

Deleterious effects of thermal and water stresses on life history and physiology: a case study on woodlouseCharlotte Depeux, Angele Branger, Theo Moulignier, Jérôme Moreau, Jean-Francois Lemaitre, Francois-Xavier Dechaume-Moncharmont, Tiffany Laverre, Hélène Paulhac, Jean-Michel Gaillard, Sophie Beltran-Bech<p>We tested independently the influences of increasing temperature and decreasing moisture on life history and physiological traits in the arthropod <em>Armadillidium vulgare</em>. Both increasing temperature and decreasing moisture led individua...Biodiversity, Evolutionary ecology, Experimental ecology, Life history, Physiology, Terrestrial ecology, ZoologyAniruddha Belsare2022-09-28 13:13:47 View
19 Dec 2020
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Hough transform implementation to evaluate the morphological variability of the moon jellyfish (Aurelia spp.)

A new member of the morphometrics jungle to better monitor vulnerable lagoons

Recommended by based on reviews by Julien Claude and 1 anonymous reviewer

In the recent years, morphometrics, the quantitative description of shape and its covariation [1] gained considerable momentum in evolutionary ecology. Using the form of organisms to describe, classify and try to understand their diversity can be traced back at least to Aristotle. More recently, two successive revolutions rejuvenated this idea [1–3]: first, a proper mathematical refoundation of the theory of shape, then a technical revolution in the apparatus able to acquire raw data. By using a feature extraction method and planning its massive use on data acquired by aerial drones, the study by Lacaux and colleagues [4] retraces this curse of events.
The radial symmetry of Aurelia spp. jelly fish, a common species complex, is affected by stress and more largely by environmental variations, such as pollution exposition. Aurelia spp. normally present four gonads so that the proportion of non-tetramerous individuals in a population has been proposed as a biomarker [5,6].
In this study, the authors implemented the Hough transform to largely automate the detection of the gonads in Aurelia spp. Such use of the Hough transform, a long-used approach to identify shapes through edge detection, is new to morphometrics. Here, the Aurelia spp. gonads are identified as ellipses from which aspect descriptors can be derived, and primarily counted and thus can be used to quantify the proportion of individuals presenting body plans disorders.

The sample sizes studied here were too low to allow finer-grained ecophysiological investigations. That being said, the proof-of-concept is convincing and this paper paths the way for an operational and innovative approach to the ecological monitoring of sensible aquatic ecosystems.

References

[1] Kendall, D. G. (1989). A survey of the statistical theory of shape. Statistical Science, 87-99. doi: https://doi.org/10.1214/ss/1177012589
[2] Rohlf, F. J., and Marcus, L. F. (1993). A revolution morphometrics. Trends in ecology & evolution, 8(4), 129-132. doi: https://doi.org/10.1016/0169-5347(93)90024-J
[3] Adams, D. C., Rohlf, F. J., and Slice, D. E. (2004). Geometric morphometrics: ten years of progress following the ‘revolution’. Italian Journal of Zoology, 71(1), 5-16. doi: https://doi.org/10.1080/11250000409356545
[4] Lacaux, C., Desolneux, A., Gadreaud, J., Martin-Garin, B. and Thiéry, A. (2020) Hough transform implementation to evaluate the morphological variability of the moon jellyfish (Aurelia spp.). bioRxiv, 2020.03.11.986984, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. doi: https://doi.org/10.1101/2020.03.11.986984
[5] Gershwin, L. A. (1999). Clonal and population variation in jellyfish symmetry. Journal of the Marine Biological Association of the United Kingdom, 79(6), 993-1000. doi: https://doi.org/10.1017/S0025315499001228
[6] Gadreaud, J., Martin-Garin, B., Artells, E., Levard, C., Auffan, M., Barkate, A.-L. and Thiéry, A. (2017) The moon jellyfish as a new bioindicator: impact of silver nanoparticles on the morphogenesis. In: Mariottini GL, editor. Jellyfish: ecology, distribution patterns and human interactions. Nova Science Publishers; 2017. pp. 277–292.

Hough transform implementation to evaluate the morphological variability of the moon jellyfish (Aurelia spp.)Céline Lacaux, Agnès Desolneux, Justine Gadreaud, Bertrand Martin-Garin and Alain Thiéry<p>Variations of the animal body plan morphology and morphometry can be used as prognostic tools of their habitat quality. The potential of the moon jellyfish (Aurelia spp.) as a new model organism has been poorly tested. However, as a tetramerous...MorphometricsVincent Bonhomme2020-03-18 17:40:51 View
06 Jan 2025
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Using informative priors to account for identifiability issues in occupancy models with identification errors

Accounting for false positives and negatives in monitoring data from sensor networks and eDNA

Recommended by based on reviews by Saoirse Kelleher, Jonathan Rose and 2 anonymous reviewers

Biodiversity monitoring increasingly relies on modern technologies such as sensor networks and environmental DNA. These high-throughput methods allow biodiversity assessments with unprecedented detail and are especially useful to detect rare and secretive species that are otherwise difficult to observe with traditional survey-based methods. False negatives through imperfect detection are a typical problem in survey data and depend on intrinsic characteristics of the species, site characteristics of the survey site as well as survey characteristics (Guillera 2017). While imperfect detection might be reduced in modern sensor data and eDNA data, also these types of data are by no means error-free and may bare other challenges. In particular, the bioinformatics and image classification approaches used for species identification from these data can induce a higher rate of false positives than would be expected in expert-based survey data (Hartig et al. 2024).

Occupancy models (or occupancy-detection models) have been widely used to map species distributions by fitting a hierarchical model that estimates the paramaters of both the species-environment relationship and an observation submodel. They account for false negatives by inferring detectability from the detection history of a survey location, for example from replicate visits or multiple observers (Guillera 2017). These basic occupancy-detection models assume no false positive errors in the data. Other authors have proposed extensions for false positives that typically rely on unambiguous (known truth) information for some sites or observations (Chambert et al. 2015).

In their preprint, Monchy et al. (2024) propose an extension of classic occupancy models that considers a two-step observation process modelling the detection probability at occupied sites and the associated identification probability, separated into the true positive identification rate and the true negative identification rate. Using a simulation approach, the authors compare the effectiveness of a frequentist (maximum likelihood-based) and Bayesian approach for parameter estimation and identifiability, and additionally test the effectiveness of different priors (from non-informative to highly informative). Results of the maximum-likelihood approach indicated biased parameter estimates and identifiability problems. In the Bayesian approach, inclusion of prior information greatly reduces biases in parameter estimates, especially in detection and positive identification rate.

Importantly, informative priors for the identification process are a by-product of the classifiers that are developed for processing the eDNA data or sensor data. For example, species identification from acoustic sensors is based on image classifiers trained on labelled bird song spectrograms (Kahl et al. 2021) and as part of the evaluation of the classifier, the true positive rate (sensitivity) is routinely being estimated and could thus be readily used in occupancy models accounting for false positives. Thus, the approach proposed by Monchy et al. (2024) is not only highly relevant for biodiversity assessments based on novel sensor and eDNA data but also provides very practical solutions that do not require additional unambiguous data but recycle data that are already available in the processing pipeline. Applying their framework to real-world data will help reducing biases in biodiversity assessments and through improved understanding of the detection process it could also help optimising the design of sensor networks.

References

Thierry Chambert,  David A. W. Miller,  James D. Nichols (2015), Modeling false positive detections in species occurrence data under different study designs. Ecology, 96: 332-339. https://doi.org/10.1890/14-1507.1

Gurutzeta Guillera-Arroita (2017) Modelling of species distributions, range dynamics and communities under imperfect detection: advances, challenges and opportunities. Ecography, 40: 281-295. https://doi.org/10.1111/ecog.02445

Florian Hartig, Nerea Abrego, Alex Bush, Jonathan M. Chase, Gurutzeta Guillera-Arroita, Mathew A. Leibold,  Otso Ovaskainen, Loïc Pellissier, Maximilian Pichler, Giovanni Poggiato, Laura Pollock, Sara Si-Moussi, Wilfried Thuiller, Duarte S. Viana, David I. Warton, Damaris Zurell D, Douglas W. Yu (2024) Novel community data in ecology - properties and prospects. Trends in Ecology & Evolution, 39: 280-293. https://doi.org/10.1016/j.tree.2023.09.017

Stefan Kahl, Connor M. Wood, Maximilian Eibl, Holger Klinck (2021) BirdNET: A deep learning solution for avian diversity monitoring. Ecological Informatics, 61: 101236. https://doi.org/10.1016/j.ecoinf.2021.101236

Célian Monchy, Marie-Pierre Etienne, Olivier Gimenez (2024) Using informative priors to account for identifiability issues in occupancy models with identification errors. bioRxiv, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.1101/2024.05.07.592917

Using informative priors to account for identifiability issues in occupancy models with identification errorsCélian Monchy, Marie-Pierre Etienne, Olivier Gimenez<p>&nbsp;Non-invasive monitoring techniques like camera traps, autonomous recording units and environmental DNA are increasingly used to collect data for understanding species distribution. These methods have prompted the development of statistica...Statistical ecologyDamaris Zurell2024-05-11 12:04:10 View