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22 Apr 2021
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The hidden side of the Allee effect: correlated demographic traits and extinction risk in experimental populations

Allee effects under the magnifying glass

Recommended by ORCID_LOGO based on reviews by Tom Van Dooren, Dani Oro and 1 anonymous reviewer

For decades, the effect of population density on individual performance has been studied by ecologists using both theoretical, observational, and experimental approaches. The generally accepted definition of the Allee effect is a positive correlation between population density and average individual fitness that occurs at low population densities, while individual fitness is typically decreased through intraspecific competition for resources at high population densities.  Allee effects are very relevant in conservation biology because species at low population densities would then be subjected to much higher extinction risks. 

However, due to all kinds of stochasticity, low population numbers are always more vulnerable to extinction than larger population sizes. This effect by itself cannot be necessarily ascribed to lower individual performance at low densities, i.e, Allee effects. Vercken and colleagues (2021) address this challenging question and measure the extent to which average individual fitness is affected by population density analyzing 30 experimental populations. As a model system, they use populations of parasitoid wasps of the genus Trichogramma. They report Allee effect in 8 out 30 experimental populations. Vercken and colleagues's work has several strengths. 

First of all, it is nice to see that they put theory at work. This is a very productive way of using theory in ecology. As a starting point, they look at what simple theoretical population models say about Allee effects (Lewis and Kareiva 1993; Amarasekare 1998; Boukal and Berec 2002). These models invariably predict a one-humped relation between population-density and per-capita growth rate. It is important to remark that pure logistic growth, the paradigm of density-dependence, would never predict such qualitative behavior. It is only when there is a depression of per-capita growth rates at low densities that true Allee effects arise. Second, these authors manage to not only experimentally test this main prediction but also report additional demographic traits that are consistently affected by population density. 

In these wasps, individual performance can be measured in terms of the average number of individuals every adult is able to put into the next generation ---the lambda parameter in their analysis. The first panel in figure 3 shows that the per-capita growth rates are lower in populations presenting Allee effects, the ones showing a one-humped behavior in the relation between per-capita growth rates and population densities (see figure 2). Also other population traits, such maximum population size and exitinction probability, change in a correlated and consistent manner. 

In sum, Vercken and colleagues's results are experimentally solid and based on theory expectations. However, they are very intriguing. They find the signature of Allee effects in only 8 out 30 populations, all from the same genus Trichogramma, and some populations belonging to the same species (from different sampling sites) do not show consistently Allee effects. Where does this population variability comes from? What are the reasons underlying this within- and between-species variability? What are the individual mechanisms driving Allee effects in these populations? Good enough, this piece of work generates more intriguing questions than the question is able to clearly answer. Science is not a collection of final answers but instead good questions are the ones that make science progress. 

References

Amarasekare P (1998) Allee Effects in Metapopulation Dynamics. The American Naturalist, 152, 298–302. https://doi.org/10.1086/286169

Boukal DS, Berec L (2002) Single-species Models of the Allee Effect: Extinction Boundaries, Sex Ratios and Mate Encounters. Journal of Theoretical Biology, 218, 375–394. https://doi.org/10.1006/jtbi.2002.3084

Lewis MA, Kareiva P (1993) Allee Dynamics and the Spread of Invading Organisms. Theoretical Population Biology, 43, 141–158. https://doi.org/10.1006/tpbi.1993.1007

Vercken E, Groussier G, Lamy L, Mailleret L (2021) The hidden side of the Allee effect: correlated demographic traits and extinction risk in experimental populations. HAL, hal-02570868, ver. 4 peer-reviewed and recommended by Peer community in Ecology. https://hal.archives-ouvertes.fr/hal-02570868

The hidden side of the Allee effect: correlated demographic traits and extinction risk in experimental populationsVercken Elodie, Groussier Géraldine, Lamy Laurent, Mailleret Ludovic<p style="text-align: justify;">Because Allee effects (i.e., the presence of positive density-dependence at low population size or density) have major impacts on the dynamics of small populations, they are routinely included in demographic models ...Demography, Experimental ecology, Population ecologyDavid Alonso2020-09-30 16:38:29 View
02 Dec 2021
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Metabarcoding faecal samples to investigate spatiotemporal variation in the diet of the endangered Westland petrel (Procellaria westlandica)

The promise and limits of DNA based approach to infer diet flexibility in endangered top predators

Recommended by based on reviews by Francis John Burdon and Babett Günther

There is growing evidence of worldwide decline of populations of top predators, including marine ones (Heithaus et al, 2008, Mc Cauley et al., 2015), with cascading effects expected at the ecosystem level, due to global change and human activities, including habitat loss or fragmentation, the collapse or the range shifts of their preys. On a global scale, seabirds are among the most threatened group of birds, about one-third of them being considered as threatened or endangered (Votier& Sherley, 2017). The large consequences of the decrease of the populations of preys they feed on (Cury et al, 2011) points diet flexibility as one important element to understand for effective management (McInnes et al, 2017).  Nevertheless, morphological inventory of preys requires intrusive protocols, and the differential digestion rate of distinct taxa may lead to a large bias in morphological-based diet assessments. The use of DNA metabarcoding on feces (or diet DNA, dDNA) now allows non-invasive approaches facilitating the recollection of samples and the detection of multiple preys independently of their digestion rates (Deagle et al., 2019). Although no gold standard exists yet to avoid bias associated with metabarcoding (primer bias, gaps in reference databases, inability to differentiate primary from secondary predation…), the use of these recent techniques has already improved the knowledge of the foraging behaviour and diet of many animals (Ando et al., 2020).

Both promise and shortcomings of this approach are illustrated in the article “Metabarcoding faecal samples to investigate spatiotemporal variation in the diet of the endangered Westland petrel (Procellaria westlandica)” by Quereteja et al. (2021). In this work, the authors assessed the nature and spatio-temporal flexibility of the foraging behaviour and consequent diet of the endangered petrel Procellaria westlandica from New-Zealand through metabarcoding of faeces samples.

The results of this dDNA, non-invasive approach, identify some expected and also unexpected prey items, some of which require further investigation likely due to large gaps in the reference databases. They also reveal the temporal (before and after hatching) and spatial (across colonies only 1.5km apart) flexibility of the foraging behaviour, additionally suggesting a possible influence of fisheries activities in the surroundings of the colonies. This study thus both underlines the power of the non-invasive metabarcoding approach on faeces, and the important results such analysis can deliver for conservation, pointing a potential for diet flexibility that may be essential for the resilience of this iconic yet endangered species.

References

Ando H, Mukai H, Komura T, Dewi T, Ando M, Isagi Y (2020) Methodological trends and perspectives of animal dietary studies by noninvasive fecal DNA metabarcoding. Environmental DNA, 2, 391–406. https://doi.org/10.1002/edn3.117

Cury PM, Boyd IL, Bonhommeau S, Anker-Nilssen T, Crawford RJM, Furness RW, Mills JA, Murphy EJ, Österblom H, Paleczny M, Piatt JF, Roux J-P, Shannon L, Sydeman WJ (2011) Global Seabird Response to Forage Fish Depletion—One-Third for the Birds. Science, 334, 1703–1706. https://doi.org/10.1126/science.1212928

Deagle BE, Thomas AC, McInnes JC, Clarke LJ, Vesterinen EJ, Clare EL, Kartzinel TR, Eveson JP (2019) Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data? Molecular Ecology, 28, 391–406. https://doi.org/10.1111/mec.14734

Heithaus MR, Frid A, Wirsing AJ, Worm B (2008) Predicting ecological consequences of marine top predator declines. Trends in Ecology & Evolution, 23, 202–210. https://doi.org/10.1016/j.tree.2008.01.003

McCauley DJ, Pinsky ML, Palumbi SR, Estes JA, Joyce FH, Warner RR (2015) Marine defaunation: Animal loss in the global ocean. Science, 347, 1255641. https://doi.org/10.1126/science.1255641

McInnes JC, Jarman SN, Lea M-A, Raymond B, Deagle BE, Phillips RA, Catry P, Stanworth A, Weimerskirch H, Kusch A, Gras M, Cherel Y, Maschette D, Alderman R (2017) DNA Metabarcoding as a Marine Conservation and Management Tool: A Circumpolar Examination of Fishery Discards in the Diet of Threatened Albatrosses. Frontiers in Marine Science, 4, 277. https://doi.org/10.3389/fmars.2017.00277

Querejeta M, Lefort M-C, Bretagnolle V, Boyer S (2021) Metabarcoding faecal samples to investigate spatiotemporal variation in the diet of the endangered Westland petrel (Procellaria westlandica). bioRxiv, 2020.10.30.360289, ver. 4 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2020.10.30.360289

Votier SC, Sherley RB (2017) Seabirds. Current Biology, 27, R448–R450. https://doi.org/10.1016/j.cub.2017.01.042

Metabarcoding faecal samples to investigate spatiotemporal variation in the diet of the endangered Westland petrel (Procellaria westlandica)Marina Querejeta, Marie-Caroline Lefort, Vincent Bretagnolle, Stéphane Boyer<p style="text-align: justify;">As top predators, seabirds can be indirectly impacted by climate variability and commercial fishing activities through changes in marine communities. However, high mobility and foraging behaviour enables seabirds to...Conservation biology, Food webs, Marine ecology, Molecular ecologySophie Arnaud-Haond2020-10-30 20:14:50 View
30 Mar 2021
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Do the more flexible individuals rely more on causal cognition? Observation versus intervention in causal inference in great-tailed grackles

From cognition to range dynamics – and from preregistration to peer-reviewed preprint

Recommended by based on reviews by Laure Cauchard and 1 anonymous reviewer

In 2018 Blaisdell and colleagues set out to study how causal cognition may impact large scale macroecological patterns, more specifically range dynamics, in the great-tailed grackle (Fronhofer 2019). This line of research is at the forefront of current thought in macroecology, a field that has started to recognize the importance of animal behaviour more generally (see e.g. Keith and Bull (2017)). Importantly, the authors were pioneering the use of preregistrations in ecology and evolution with the aim of improving the quality of academic research.

Now, nearly 3 years later, it is thanks to their endeavour of making research better that we learn that the authors are “[...] unable to speculate about the potential role of causal cognition in a species that is rapidly expanding its geographic range.” (Blaisdell et al. 2021; page 2). Is this a success or a failure? Every reader will have to find an answer to this question individually and there will certainly be variation in these answers as becomes clear from the referees’ comments. In my opinion, this is a success story of a more stringent and transparent approach to doing research which will help us move forward, both methodologically and conceptually.

References

Fronhofer (2019) From cognition to range dynamics: advancing our understanding of macroe-
cological patterns. Peer Community in Ecology, 100014. doi: https://doi.org/10.24072/pci.ecology.100014

Keith, S. A. and Bull, J. W. (2017) Animal culture impacts species' capacity to realise climate-driven range shifts. Ecography, 40: 296-304. doi: https://doi.org/10.1111/ecog.02481

Blaisdell, A., Seitz, B., Rowney, C., Folsom, M., MacPherson, M., Deffner, D., and Logan, C. J. (2021) Do the more flexible individuals rely more on causal cognition? Observation versus intervention in causal inference in great-tailed grackles. PsyArXiv, ver. 5 peer-reviewed and recommended by Peer community in Ecology. doi: https://doi.org/10.31234/osf.io/z4p6s

Do the more flexible individuals rely more on causal cognition? Observation versus intervention in causal inference in great-tailed gracklesBlaisdell A, Seitz B, Rowney C, Folsom M, MacPherson M, Deffner D, Logan CJ<p>Behavioral flexibility, the ability to change behavior when circumstances change based on learning from previous experience, is thought to play an important role in a species’ ability to successfully adapt to new environments and expand its geo...PreregistrationsEmanuel A. Fronhofer2020-11-27 09:49:55 View
12 Aug 2021
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A study on the role of social information sharing leading to range expansion in songbirds with large vocal repertoires: Enhancing our understanding of the Great-Tailed Grackle (Quiscalus mexicanus) alarm call

Does the active vocabulary in Great-tailed Grackles supports their range expansion? New study will find out

Recommended by Jan Oliver Engler based on reviews by Guillermo Fandos and 2 anonymous reviewers

Alarm calls are an important acoustic signal that can decide the life or death of an individual. Many birds are able to vary their alarm calls to provide more accurate information on e.g. urgency or even the type of a threatening predator. According to the acoustic adaptation hypothesis, the habitat plays an important role too in how acoustic patterns get transmitted. This is of particular interest for range-expanding species that will face new environmental conditions along the leading edge. One could hypothesize that the alarm call repertoire of a species could increase in newly founded ranges to incorporate new habitats and threats individuals might face. Hence selection for a larger active vocabulary might be beneficial for new colonizers. Using the Great-Tailed Grackle (Quiscalus mexicanus) as a model species, Samantha Bowser from Arizona State University and Maggie MacPherson from Louisiana State University want to find out exactly that. 

The Great-Tailed Grackle is an appropriate species given its high vocal diversity. Also, the species consists of different subspecies that show range expansions along the northern range edge yet to a varying degree. Using vocal experiments and field recordings the researchers have a high potential to understand more about the acoustic adaptation hypothesis within a range dynamic process. 

Over the course of this assessment, the authors incorporated the comments made by two reviewers into a strong revision of their research plans. With that being said, the few additional comments made by one of the initial reviewers round up the current stage this interesting research project is in. 

To this end, I can only fully recommend the revised research plan and am much looking forward to the outcomes from the author’s experiments, modeling, and field data. With the suggestions being made at such an early stage I firmly believe that the final outcome will be highly interesting not only to an ornithological readership but to every ecologist and biogeographer interested in drivers of range dynamic processes.

References

Bowser, S., MacPherson, M. (2021). A study on the role of social information sharing leading to range expansion in songbirds with large vocal repertoires: Enhancing our understanding of the Great-Tailed Grackle (Quiscalus mexicanus) alarm call. In principle recommendation by PCI Ecology. https://doi.org/10.17605/OSF.IO/2UFJ5. Version 3

A study on the role of social information sharing leading to range expansion in songbirds with large vocal repertoires: Enhancing our understanding of the Great-Tailed Grackle (Quiscalus mexicanus) alarm call Samantha Bowser, Maggie MacPherson<p>The acoustic adaptation hypothesis posits that animal sounds are influenced by the habitat properties that shape acoustic constraints (Ey and Fischer 2009, Morton 2015, Sueur and Farina 2015).Alarm calls are expected to signal important habitat...Biogeography, Biological invasions, Coexistence, Dispersal & Migration, Habitat selection, Landscape ecologyNone Darius Stiels, Anonymous2020-12-01 18:11:02 View
04 May 2021
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Are the more flexible great-tailed grackles also better at behavioral inhibition?

Great-tailed grackle research reveals need for researchers to consider their own flexibility and test limitations in cognitive test batteries.

Recommended by based on reviews by Pizza Ka Yee Chow and Alex DeCasian

In the article, "Are the more flexible great-tailed grackles also better at behavioral inhibition?", Logan and colleagues (2021) are setting an excellent standard for cognitive research on wild-caught animals. Using a decent sample (N=18) of wild-caught birds, they set out to test the ambiguous link between behavioral flexibility and behavioral inhibition, which is supported by some studies but rejected by others. Where this study is more thorough and therefore also more revealing than most extant research, the authors ran a battery of tests, examining both flexibility (reversal learning and solution switching) and inhibition (go/no go task; detour task; delay of gratification) through multiple different test series. They also -- somewhat accidentally -- performed their experiments and analyses with and without different criteria for correctness (85%, 100%). Their mistakes, assumptions and amendments of plans made during preregistration are clearly stated and this demonstrates the thought-process of the researchers very clearly.

Logan et al. (2021) show that inhibition in great-tailed grackles is a multi-faceted construct, and demonstrate that the traditional go/no go task likely tests a very different aspect of inhibition than the detour task, which was never linked to any of their flexibility measures. Their comprehensive Bayesian analyses held up the results of some of the frequentist statistics, indicating a consistent relationship between flexibility and inhibition, with more flexible individuals also showing better inhibition (in the go/no go task). This same model, combined with inconsistencies in the GLM analyses (depending on the inclusion or exclusion of an outlier), led them to recommend caution in the creation of arbitrary thresholds for "success" in any cognitive tasks. Their accidental longer-term data collection also hinted at patterns of behaviour that shorter-term data collection did not. Of course, researchers have to decide on success criteria in order to conduct experiments, but in the same way that frequentist statistics are acknowledged to have flaws, the setting of success criteria must be acknowledged as inherently arbitrary. Where possible, researchers could reveal novel, biologically salient patterns by continuing beyond the point where a convenient success criterion has been reached. This research also underscores that tests may not be examining the features we expected them to measure, and are highly sensitive to biological and ecological variation between species as well as individual variation within populations.

To me, this study is an excellent argument for pre-registration of research (registered as Logan et al. 2019 and accepted by Vogel 2019), as the authors did not end up cherry-picking only those results or methods that worked. The fact that some of the tests did not "work", but was still examined, added much value to the study. The current paper is a bit densely written because of the comprehensiveness of the research. Some editorial polishing would likely make for more elegant writing. However, the arguments are clear, the results novel, and the questions thoroughly examined. The results are important not only for cognitive research on birds, but are potentially valuable to any cognitive scientist. I recommend this article as excellent food for thought.

References

Logan CJ, McCune K, Johnson-Ulrich Z, Bergeron L, Seitz B, Blaisdell AP, Wascher CAF. (2019) Are the more flexible individuals also better at inhibition? http://corinalogan.com/Preregistrations/g_inhibition.html  In principle acceptance by PCI Ecology of the version on 6 Mar 2019

Logan CJ, McCune KB, MacPherson M, Johnson-Ulrich Z, Rowney C, Seitz B, Blaisdell AP, Deffner D, Wascher CAF (2021) Are the more flexible great-tailed grackles also better at behavioral inhibition? PsyArXiv, ver. 7 peer-reviewed and recommended by Peer community in Ecology. https://doi.org/10.31234/osf.io/vpc39

Vogel E (2019) Adapting to a changing environment: advancing our understanding of the mechanisms that lead to behavioral flexibility. Peer Community in Ecology, 100016. https://doi.org/10.24072/pci.ecology.100016 

Are the more flexible great-tailed grackles also better at behavioral inhibition?Logan CJ, McCune KB, MacPherson M, Johnson-Ulrich Z, Rowney C, Seitz B, Blaisdell AP, Deffner D, Wascher CAF<p style="text-align: justify;">Behavioral flexibility (hereafter, flexibility) should theoretically be positively related to behavioral inhibition (hereafter, inhibition) because one should need to inhibit a previously learned behavior to change ...PreregistrationsAliza le Roux2020-12-04 13:57:07 View
27 Apr 2021
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Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of species abundances in fruit flies

Understanding the interplay between host-specificity, environmental conditions and competition through the sound application of Joint Species Distribution Models

Recommended by based on reviews by Joaquín Calatayud and Carsten Dormann

Understanding why and how species coexist in local communities is one of the central questions in ecology. There is general agreement that species distribution and coexistence are determined by a number of key mechanisms, including the environmental requirements of species, dispersal, evolutionary constraints, resource availability and selection, metapopulation dynamics, and biotic interactions (e.g. Soberón & Nakamura 2009; Colwell & Rangel 2009; Ricklefs 2015). These factors are however intricately intertwined in a scale-structured fashion (Hortal et al. 2010; D’Amen et al. 2017), making it particularly difficult to tease apart the effects of each one of them. This could be addressed by the novel field of Joint Species Distribution Modelling (JSDM; Okasvainen & Abrego 2020), as it allows assessing the effects of several sets of factors and the co-occurrence and/or covariation in abundances of potentially interacting species at the same time (Pollock et al. 2014; Ovaskainen et al. 2016; Dormann et al. 2018). However, the development of JSDM has been hampered by the general lack of good-quality detailed data on species co-occurrences and abundances (see Hortal et al. 2015).

Facon et al. (2021) use a particularly large compilation of field surveys to study the abundance and co-occurrence of Tephritidae fruit flies in c. 400 orchards, gardens and natural areas throughout the island of Réunion. Further, they combine such information with lab data on their host-selection fundamental niche (i.e. in the absence of competitors), codifying traits of female choice and larval performances in 21 host species. They use Poisson Log-Normal models, a type of mixed model that allows one to jointly model the random effects associated with all species, and retrieve the covariations in abundance that are not explained by environmental conditions or differences in sampling effort. Then, they use a series of models to evaluate the effects on these matrices of ecological covariates (date, elevation, habitat, climate and host plant), species interactions (by comparing with a constrained residual variance-covariance matrix) and the species’ host-selection fundamental niches (through separate models for each fly species).

The eight Tephritidae species inhabiting Réunion include both generalists and specialists in Solanaceae and Cucurbitaceae with a known history of interspecific competition. Facon et al. (2021) use a comprehensive JSDM approach to assess the effects of different factors separately and altogether. This allows them to identify large effects of plant hosts and the fundamental host-selection niche on species co-occurrence, but also to show that ecological covariates and weak –though not negligible– species interactions are necessary to account for all residual variance in the matrix of joint species abundances per site. Further, they also find evidence that the fitness per host measured in the lab has a strong influence on the abundances in each host plant in the field for specialist species, but not for generalists. Indeed, the stronger effects of competitive exclusion were found in pairs of Cucurbitaceae specialist species. However, these analyses fail to provide solid grounds to assess why generalists are rarely found in Cucurbitaceae and Solanaceae. Although they argue that this may be due to Connell’s (1980) ghost of competition past (past competition that led to current niche differentiation), further data on the evolutionary history of these fruit flies is needed to assess this hypothesis.

Finding evidence for the effects of competitive interactions on species’ occurrences and spatial distributions is often difficult, perhaps because these effects occur over longer time scales than the ones usually studied by ecologists (Yackulic 2017). The work by Facon and colleagues shows that weak effects of competition can be detected also at the short ecological timescales that determine coexistence in local communities, under the virtuous combination of good-quality data and sound analytical designs that account for several aspects of species’ niches, their biotopes and their joint population responses. This adds a new dimension to the application of Hutchinson’s (1978) niche framework to understand the spatial dynamics of species and communities (see also Colwell & Rangel 2009), although further advances to incorporate dispersal-driven metacommunity dynamics (see, e.g., Ovaskainen et al. 2016; Leibold et al. 2017) are certainly needed. Nonetheless, this work shows the potential value of in-depth analyses of species coexistence based on combining good-quality field data with well-thought out JSDM applications. If many studies like this are conducted, it is likely that the uprising field of Joint Species Distribution Modelling will improve our understanding of the hierarchical relationships between the different factors affecting species coexistence in ecological communities in the near future.

 

References

Colwell RK, Rangel TF (2009) Hutchinson’s duality: The once and future niche. Proceedings of the National Academy of Sciences, 106, 19651–19658. https://doi.org/10.1073/pnas.0901650106

Connell JH (1980) Diversity and the Coevolution of Competitors, or the Ghost of Competition Past. Oikos, 35, 131–138. https://doi.org/10.2307/3544421

D’Amen M, Rahbek C, Zimmermann NE, Guisan A (2017) Spatial predictions at the community level: from current approaches to future frameworks. Biological Reviews, 92, 169–187. https://doi.org/10.1111/brv.12222

Dormann CF, Bobrowski M, Dehling DM, Harris DJ, Hartig F, Lischke H, Moretti MD, Pagel J, Pinkert S, Schleuning M, Schmidt SI, Sheppard CS, Steinbauer MJ, Zeuss D, Kraan C (2018) Biotic interactions in species distribution modelling: 10 questions to guide interpretation and avoid false conclusions. Global Ecology and Biogeography, 27, 1004–1016. https://doi.org/10.1111/geb.12759

Facon B, Hafsi A, Masselière MC de la, Robin S, Massol F, Dubart M, Chiquet J, Frago E, Chiroleu F, Duyck P-F, Ravigné V (2021) Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of community structure in fruit flies. bioRxiv, 2020.12.07.414326. ver. 4 peer-reviewed and recommended by Peer community in Ecology. https://doi.org/10.1101/2020.12.07.414326

Hortal J, de Bello F, Diniz-Filho JAF, Lewinsohn TM, Lobo JM, Ladle RJ (2015) Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity. Annual Review of Ecology, Evolution, and Systematics, 46, 523–549. https://doi.org/10.1146/annurev-ecolsys-112414-054400

Hortal J, Roura‐Pascual N, Sanders NJ, Rahbek C (2010) Understanding (insect) species distributions across spatial scales. Ecography, 33, 51–53. https://doi.org/10.1111/j.1600-0587.2009.06428.x

Hutchinson, G.E. (1978) An introduction to population biology. Yale University Press, New Haven, CT.

Leibold MA, Chase JM, Ernest SKM (2017) Community assembly and the functioning of ecosystems: how metacommunity processes alter ecosystems attributes. Ecology, 98, 909–919. https://doi.org/10.1002/ecy.1697

Ovaskainen O, Abrego N (2020) Joint Species Distribution Modelling: With Applications in R. Cambridge University Press, Cambridge. https://doi.org/10.1017/9781108591720

Ovaskainen O, Roy DB, Fox R, Anderson BJ (2016) Uncovering hidden spatial structure in species communities with spatially explicit joint species distribution models. Methods in Ecology and Evolution, 7, 428–436. https://doi.org/10.1111/2041-210X.12502

Pollock LJ, Tingley R, Morris WK, Golding N, O’Hara RB, Parris KM, Vesk PA, McCarthy MA (2014) Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM). Methods in Ecology and Evolution, 5, 397–406. https://doi.org/10.1111/2041-210X.12180

Ricklefs RE (2015) Intrinsic dynamics of the regional community. Ecology Letters, 18, 497–503. https://doi.org/10.1111/ele.12431

Soberón J, Nakamura M (2009) Niches and distributional areas: Concepts, methods, and assumptions. Proceedings of the National Academy of Sciences, 106, 19644–19650. https://doi.org/10.1073/pnas.0901637106

Yackulic CB (2017) Competitive exclusion over broad spatial extents is a slow process: evidence and implications for species distribution modeling. Ecography, 40, 305–313. https://doi.org/10.1111/ecog.02836

Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of species abundances in fruit fliesBenoit Facon, Abir Hafsi, Maud Charlery de la Masselière, Stéphane Robin, François Massol, Maxime Dubart, Julien Chiquet, Enric Frago, Frédéric Chiroleu, Pierre-François Duyck & Virginie Ravigné<p style="text-align: justify;">The relative importance of ecological factors and species interactions for phytophagous insect species distributions has long been a controversial issue. Using field abundances of eight sympatric Tephritid fruit fli...Biodiversity, Coexistence, Community ecology, Competition, Herbivory, Interaction networks, Species distributionsJoaquín Hortal Carsten Dormann, Joaquín Calatayud2020-12-08 06:44:25 View
26 May 2021
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Spatial distribution of local patch extinctions drives recovery dynamics in metacommunities

Unity makes strength: clustered extinctions have stronger, longer-lasting effects on metacommunities dynamics

Recommended by based on reviews by David Murray-Stoker and Frederik De Laender

In this article, Saade et al. (2021) investigate how the rate of local extinctions and their spatial distribution affect recolonization dynamics in metacommunities. They use an elegant combination of microcosm experiments with metacommunities of freshwater ciliates and mathematical modelling mirroring their experimental system. Their main findings are (i) that local patch extinctions increase both local (α-) and inter-patch (β-) diversity in a transient way during the recolonization process, (ii) that these effects depend more on the spatial distribution of extinctions (dispersed or clustered) than on their amount, and (iii) that they may spread regionally.
Microcosm experiments are already quite cool just by themselves and have contributed largely to conceptual advances in community ecology (see Fraser and Keddy 1997, or Jessup et al. 2004 for reviews on this topic), but they are here exploited to a whole further level by the fitting of a metapopulation dynamics model. The model allows both to identify the underlying mechanisms most likely to generate the patterns observed (here, competitive interactions) and to assess the robustness of these patterns when considering larger spatial or temporal scales. This release of experimental limitations allows here for the analysis of quantitative metrics of spatial structure, like the distance to the closest patch, which gives an interesting insight into the functional basis of the effect of the spatial distribution of extinctions.

A major strength of this study is that it highlights the importance of considering the spatial structure explicitly. Recent work on ecological networks has shown repeatedly that network structure affects the propagation of pathogens (Badham and Stocker 2010), invaders (Morel-Journel et al. 2019), or perturbation events (Gilarranz et al. 2017). Here, the spatial structure of the metacommunity is a regular grid of patches, but the distribution of extinction events may be either regularly dispersed (i.e., extinct patches are distributed evenly over the grid and are all surrounded by non-extinct patches only) or clustered (all extinct patches are neighbours). This has a direct effect on the neighbourhood of perturbed patches, and because perturbations have mostly local effects, their recovery dynamics are dominated by the composition of this immediate neighbourhood. In landscapes with dispersed extinctions, the neighbourhood of a perturbed patch is not affected by the amount of extinctions, and neither is its recovery time. In contrast, in landscapes with clustered extinctions, the amount of extinctions affects the depth of the perturbed area, which takes longer to recover when it is larger. Interestingly, the spatial distribution of extinctions here is functionally equivalent to differences in connectivity between perturbed and unperturbed patches, which results in contrasted “rescue recovery” and “mixing recovery” regimes as described by Zelnick et al. (2019).
 
Furthermore, this study focuses on local dynamics of competition and short-term, transient patterns that may have been overlooked by more classical, equilibrium-based approaches of dynamical systems of metacommunities. Indeed, in a metacommunity composed of several competitors, early theoretical work demonstrated that species coexistence is possible at the regional scale only, provided that spatial heterogeneity creates spatial variance in fitness or precludes the superior competitor from accessing certain habitat patches (Skellam 1951, Levins 1969). In the spatially homogeneous experimental system of Saade et al., one of the three ciliate species ends up dominating the community at equilibrium. However, following local, one-time extinction events, the community endures a recolonization process in which differences in dispersal may provide temporary spatial niches for inferior competitors. These transient patterns might prove essential to understand and anticipate the resilience of natural systems that are under increasing pressure, and enduring ever more frequent and intense perturbations (IPBES 2019). Spatial autocorrelation in extinction events was previously identified as a risk for stability and persistence of metacommunities (Ruokolainen 2013, Kahilainen et al. 2018). These new results show that autocorrelated perturbations also have longer-lasting effects, which is likely to increase their overall impact on metacommunity dynamics. As spatial and temporal autocorrelation of temperature and extreme climatic events are expected to increase (Di Cecco and Gouthier 2018), studies that investigate how metacommunities respond to the structure of the distribution of perturbations are more necessary than ever.
 
References


Badham J, Stocker R (2010) The impact of network clustering and assortativity on epidemic behaviour. Theoretical Population Biology, 77, 71–75. https://doi.org/10.1016/j.tpb.2009.11.003
 
Di Cecco GJ, Gouhier TC (2018) Increased spatial and temporal autocorrelation of temperature under climate change. Scientific Reports, 8, 14850. https://doi.org/10.1038/s41598-018-33217-0
 
Fraser LH, Keddy P (1997) The role of experimental microcosms in ecological research. Trends in Ecology & Evolution, 12, 478–481. https://doi.org/10.1016/S0169-5347(97)01220-2
 
Gilarranz LJ, Rayfield B, Liñán-Cembrano G, Bascompte J, Gonzalez A (2017) Effects of network modularity on the spread of perturbation impact in experimental metapopulations. Science, 357, 199–201. https://doi.org/10.1126/science.aal4122
 
IPBES (2019) Summary for policymakers of the global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. S. Díaz, J. Settele, E. S. Brondízio E.S., H. T. Ngo, M. Guèze, J. Agard, A. Arneth, P. Balvanera, K. A. Brauman, S. H. M. Butchart, K. M. A. Chan, L. A. Garibaldi, K. Ichii, J. Liu, S. M. Subramanian, G. F. Midgley, P. Miloslavich, Z. Molnár, D. Obura, A. Pfaff, S. Polasky, A. Purvis, J. Razzaque, B. Reyers, R. Roy Chowdhury, Y. J. Shin, I. J. Visseren-Hamakers, K. J. Willis, and C. N. Zayas (eds.). IPBES secretariat, Bonn, Germany. 56 pages. https://doi.org/10.5281/zenodo.3553579 
 
Jessup CM, Kassen R, Forde SE, Kerr B, Buckling A, Rainey PB, Bohannan BJM (2004) Big questions, small worlds: microbial model systems in ecology. Trends in Ecology & Evolution, 19, 189–197. https://doi.org/10.1016/j.tree.2004.01.008
 
Kahilainen A, van Nouhuys S, Schulz T, Saastamoinen M (2018) Metapopulation dynamics in a changing climate: Increasing spatial synchrony in weather conditions drives metapopulation synchrony of a butterfly inhabiting a fragmented landscape. Global Change Biology, 24, 4316–4329. https://doi.org/10.1111/gcb.14280

Levins R (1969) Some Demographic and Genetic Consequences of Environmental Heterogeneity for Biological Control1. Bulletin of the Entomological Society of America, 15, 237–240. https://doi.org/10.1093/besa/15.3.237
 
Morel-Journel T, Assa CR, Mailleret L, Vercken E (2019) Its all about connections: hubs and invasion in habitat networks. Ecology Letters, 22, 313–321. https://doi.org/10.1111/ele.13192

Ruokolainen L (2013) Spatio-Temporal Environmental Correlation and Population Variability in Simple Metacommunities. PLOS ONE, 8, e72325. https://doi.org/10.1371/journal.pone.0072325

Saade C, Kefi S, Gougat-Barbera C, Rosenbaum B, Fronhofer EA (2021) Spatial distribution of local patch extinctions drives recovery dynamics in metacommunities. bioRxiv, 2020.12.03.409524, ver. 4 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2020.12.03.409524
 
Skellam JG (1951) Random Dispersal in Theoretical Populations. Biometrika, 38, 196–218. https://doi.org/10.2307/2332328
 
Zelnik YR, Arnoldi J-F, Loreau M (2019) The three regimes of spatial recovery. Ecology, 100, e02586. https://doi.org/10.1002/ecy.2586

Spatial distribution of local patch extinctions drives recovery dynamics in metacommunitiesCamille Saade, Sonia Kéfi, Claire Gougat-Barbera, Benjamin Rosenbaum, and Emanuel A. Fronhofer<p style="text-align: justify;">Human activities lead more and more to the disturbance of plant and animal communities with local extinctions as a consequence. While these negative effects are clearly visible at a local scale, it is less clear how...Biodiversity, Coexistence, Colonization, Community ecology, Competition, Dispersal & Migration, Experimental ecology, Landscape ecology, Spatial ecology, Metacommunities & MetapopulationsElodie Vercken2020-12-08 15:55:20 View
22 Nov 2021
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Beating your neighbor to the berry patch

When more competitors means less harvested resource

Recommended by ORCID_LOGO based on reviews by Francois Massol, Jeremy Van Cleve and 1 anonymous reviewer

In this paper, Alan R. Rogers (2021) examines the dynamics of foraging strategies for a resource that gains value over time (e.g., ripening fruits), while there is a fixed cost of attempting to forage the resource, and once the resource is harvested nothing is left for other harvesters. For this model, not any pure foraging strategy is evolutionary stable. A mixed equilibrium exists, i.e., with a mixture of foraging strategies within the population, which is still evolutionarily unstable. Nonetheless, Alan R. Rogers shows that for a large number of competitors and/or high harvesting cost, the mixture of strategies remains close to the mixed equilibrium when simulating the dynamics. Surprisingly, in a large population individuals will less often attempt to forage the resource and will instead “go fishing”. The paper also exposes an experiment of the game with students, which resulted in a strategy distribution somehow close to the theoretical mixture of strategies.

The economist John F. Nash Jr. (1950) gained the Nobel Prize of economy in 1994 for his game theoretical contributions. He gave his name to the “Nash equilibrium”, which represents a set of individual strategies that is reached whenever all the players have nothing to gain by changing their strategy while the strategies of others are unchanged. Alan R. Rogers shows that the mixed equilibrium in the foraging game is such a Nash equilibrium. Yet it is evolutionarily unstable insofar as a distribution close to the equilibrium can invade.

The insights of the study are twofold. First, it sheds light on the significance of Nash equilibrium in an ecological context of foraging strategies. Second, it shows that an evolutionarily unstable state can rule the composition of the ecological system. Therefore, the contribution made by the paper should be most significant to better understand the dynamics of competitive communities and their eco-evolutionary trajectories. 

References

Nash JF (1950) Equilibrium points in n-person games. Proceedings of the National Academy of Sciences, 36, 48–49. https://doi.org/10.1073/pnas.36.1.48

Rogers AR (2021) Beating your Neighbor to the Berry Patch. bioRxiv, 2020.11.12.380311, ver. 8 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2020.11.12.380311

 

Beating your neighbor to the berry patchAlan R. Rogers<p style="text-align: justify;">Foragers often compete for resources that ripen (or otherwise improve) gradually. What strategy is optimal in this situation? It turns out that there is no optimal strategy. There is no evolutionarily stable strateg...Behaviour & Ethology, Evolutionary ecology, ForagingFrançois Munoz, , Erol Akçay, , Jorge Peña, Sébastien Lion, , , , François Rousset, 2020-12-10 18:38:49 View
02 Aug 2021
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Dynamics of Fucus serratus thallus photosynthesis and community primary production during emersion across seasons: canopy dampening and biochemical acclimation

Towards a better understanding of the effects of self-shading on Fucus serratus populations

Recommended by ORCID_LOGO based on reviews by Gwenael Abril, Francesca Rossi and 1 anonymous reviewer

The importance of the vertical structure of vegetation cover for the functioning, management and conservation of ecosystems has received particular attention from ecologists in the last decades. Canopy architecture has many implications for light extinction coefficient, temperature variation reduction, self-shading which are all key parameters for the structuring and functioning of different ecosystems such as grasslands [1,2], forests [3,4], phytoplankton communities [5, 6], macroalgal populations [7] and even underwater animal forests such as octocoral communities [8].

This research topic, therefore, benefits from a large body of literature and the facilitative role of self-shadowing is no longer in question. However, it is always puzzling to note that some of the most common ecosystems turn out to be amongst the least known. This is precisely the case of the Fucus serratus communities which are widespread in Northeast Atlantic along the Atlantic coast of Europe from Svalbard to Portugal, as well as Northwest Atlantic & Gulf of St. Lawrence, easily accessible at low tide, but which have comparatively received less attention than more emblematic macro-algal communities such as Laminariales.

The lack of attention paid to these most common Fucales is particularly critical as some species such as F. serratus are proving to be particularly vulnerable to environmental change, leading to a predicted northward retreat from its current southern boundary [9].

In the present study [10], the authors showed the importance of the vegetation cover in resisting tide-induced environmental stresses. The canopy of F. serratus mitigates stress levels experienced in the lower layers during emersion, while various acclimation strategies take over to maintain the photosynthetic apparatus in optimal conditions.

They hereby highlight adaptation mechanisms to the extreme environment represented by the intertidal zone. These adaptation strategies were expected and similar mechanisms had been shown at the cellular level previously [11]. The earliest studies on the subject have shown that the structure of the bottom, the movement of water, and light availability all "influence the distribution of Fucaceae and disturb the regularity of their fine zonation, which itself is caused by the most important factor, desiccation", as Zaneveld states in his review [12]. He observed that the causes of the zonal distribution of marine algae are numerous, and identified several points of interest such as the relative period of emersion, the rapidity of desiccation, the loss of water, and the thickness of the cell walls.

The present study thus highlights the existence of facilitative mechanisms associated with F. serratus canopy and nicely confirms previous work with in situ observations. It also highlights the importance of the vegetative cover in combating desiccation and introduces the dampening effect as a facilitating mechanism.

The effect of the vegetation cover can sometimes even be felt beyond its immediate area of influence. A recent study shows that ground-level ozone is significantly reduced by the combined effects of canopy shading and turbulence [4]. Below the canopy, the light intensity becomes sufficiently low which inhibits ozone formation due to the decrease in the rates of hydroxyl radical formation and the rates of conversion of nitrogen dioxide to nitrogen oxide by photolysis. In addition, reductions in light levels associated with foliage promote ozone-destroying reactions between plant-emitted species, such as nitric oxide and/or alkenes, and ozone itself. The reduction in diffusivity slows the upward transport of surface emitted species, partially decoupling the area under the canopy from the rest of the atmosphere.

By analogy with the work of Makar et al [4], and in the light of the results provided by the authors of this study, one may wonder whether the canopy dampening of F. serratus communities (and other common fucoids widely distributed on our coasts) might not also influence atmospheric chemistry, both at the Earth's surface and in the atmospheric boundary layer. The lack of accumulation of reactive oxygen species under the canopy found by the authors is consistent with this hypothesis and suggests that the damping effect of F. serratus may well have much wider consequences than expected.

References

[1] Jurik TW, Kliebenstein H (2000) Canopy Architecture, Light Extinction and Self-Shading of a Prairie Grass, Andropogon Gerardii. The American Midland Naturalist, 144, 51–65. http://www.jstor.org/stable/3083010

[2] Mitchley J, Willems JH (1995) Vertical canopy structure of Dutch chalk grasslands in relation to their management. Vegetatio, 117, 17–27. https://doi.org/10.1007/BF00033256

[3] Kane VR, Gillespie AR, McGaughey R, Lutz JA, Ceder K, Franklin JF (2008) Interpretation and topographic compensation of conifer canopy self-shadowing. Remote Sensing of Environment, 112, 3820–3832. https://doi.org/10.1016/j.rse.2008.06.001

[4] Makar PA, Staebler RM, Akingunola A, Zhang J, McLinden C, Kharol SK, Pabla B, Cheung P, Zheng Q (2017) The effects of forest canopy shading and turbulence on boundary layer ozone. Nature Communications, 8, 15243. https://doi.org/10.1038/ncomms15243

[5] Shigesada N, Okubo A (1981) Analysis of the self-shading effect on algal vertical distribution in natural waters. Journal of Mathematical Biology, 12, 311–326. https://doi.org/10.1007/BF00276919

[6] Barros MP, Pedersén M, Colepicolo P, Snoeijs P (2003) Self-shading protects phytoplankton communities against H2O2-induced oxidative damage. Aquatic Microbial Ecology, 30, 275–282. https://doi.org/10.3354/ame030275

[7] Ørberg SB, Krause-Jensen D, Mouritsen KN, Olesen B, Marbà N, Larsen MH, Blicher ME, Sejr MK (2018) Canopy-Forming Macroalgae Facilitate Recolonization of Sub-Arctic Intertidal Fauna and Reduce Temperature Extremes. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00332

[8] Nelson H, Bramanti L (2020) From Trees to Octocorals: The Role of Self-Thinning and Shading in Underwater Animal Forests. In: Perspectives on the Marine Animal Forests of the World (eds Rossi S, Bramanti L), pp. 401–417. Springer International Publishing, Cham. https://doi.org/10.1007/978-3-030-57054-5_12

[9] Jueterbock A, Kollias S, Smolina I, Fernandes JMO, Coyer JA, Olsen JL, Hoarau G (2014) Thermal stress resistance of the brown alga Fucus serratus along the North-Atlantic coast: Acclimatization potential to climate change. Marine Genomics, 13, 27–36. https://doi.org/10.1016/j.margen.2013.12.008

[10] Migné A, Duong G, Menu D, Davoult D, Gévaert F (2021) Dynamics of Fucus serratus thallus photosynthesis and community primary production during emersion across seasons: canopy dampening and biochemical acclimation. HAL, hal-03079617, ver. 4 peer-reviewed and recommended by Peer community in Ecology. https://hal.archives-ouvertes.fr/hal-03079617

[11] Lichtenberg M, Kühl M (2015) Pronounced gradients of light, photosynthesis and O2 consumption in the tissue of the brown alga Fucus serratus. New Phytologist, 207, 559–569. https://doi.org/10.1111/nph.13396

[12] Zaneveld JS (1937) The Littoral Zonation of Some Fucaceae in Relation to Desiccation. Journal of Ecology, 25, 431–468. https://doi.org/10.2307/2256204

Dynamics of Fucus serratus thallus photosynthesis and community primary production during emersion across seasons: canopy dampening and biochemical acclimationAline Migné, Gwendoline Duong, Dominique Menu, Dominique Davoult & François Gévaert<p style="text-align: justify;">The brown alga <em>Fucus serratus</em> forms dense stands on the sheltered low intertidal rocky shores of the Northeast Atlantic coast. In the southern English Channel, these stands have proved to be highly producti...Marine ecologyCédric Hubas2021-01-05 16:24:02 View
02 Jun 2021
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Identifying drivers of spatio-temporal variation in survival in four blue tit populations

Blue tits surviving in an ever-changing world

Recommended by ORCID_LOGO based on reviews by Ana Sanz-Aguilar and Vicente García-Navas

How long individuals live has a large influence on a number of biological processes, both for the individuals themselves as well as for the populations they live in. For a given species, survival is often summarized in curves showing the probability to survive from one age to the next. However, these curves often hide a large amount of variation in survival. Variation can occur from chance, or if individuals have different genotypes or phenotypes that can influence how long they might live, or if environmental conditions are not the same across time or space. Such spatiotemporal variations in the conditions that individuals experience can lead to complex patterns of evolution (Kokko et al. 2017) but because of the difficulties to obtain the relevant data they have not been studied much in natural populations.
 
In this manuscript, Bastianelli and colleagues (2021) identify which environmental and population conditions are associated with variation in annual survival of blue tits. The analyses are based on an impressive dataset, tracking a total of almost 5500 adults in four populations studied for at least 19 years. The authors describe two core results. First, average annual survival is lower in deciduous forests compared to evergreen forests. The differences in average annual survival between the forest types link with previously described differences, with individuals having larger clutches (Charmantier et al. 2016) and higher aggression (Dubuc-Messier et al. 2017) in the populations where adult survival is lower. Second, there are huge fluctuations from one year to the next in the percentage of individuals surviving which occur similarly in all populations. Even though survival covaried across the four populations, this variation was not associated with any of the local or global climate indices the authors investigated.
 
Studies like these are fundamental to our understanding of population change. They are important from an applied side as they can reveal the sustainability of populations and inform potential management options. On a basic research side, they reveal how evolution operates in populations. Theoretical studies predict that individuals are often not adapted to average conditions they experience, but either selected to balance the extremes they encounter  or to make the best during harsh conditions when it really matters (Lewontin & Cohen 1969).
 
This study also opens the door to new research, highlighting that demographic studies should pay attention to variation in survival and other life history traits. For blue tits specifically, the study shows that in order to understand the demography of populations we need a better mechanistic understanding of the environmental and physiological pressures influencing whether individuals die or not to make predictions whether and how climate or other ecological effects shape variation in survival.
 
References
 
Bastianelli O, Robert A, Doutrelant C, Franceschi C de, Giovannini P, Charmantier A (2021) Identifying drivers of spatio-temporal variation in survival in four blue tit populations. bioRxiv, 2021.01.28.428563, ver. 4 peer-reviewed and recommended by Peer community in Ecology. https://doi.org/10.1101/2021.01.28.428563

Charmantier A, Doutrelant C, Dubuc-Messier G, Fargevieille A, Szulkin M (2016) Mediterranean blue tits as a case study of local adaptation. Evolutionary Applications, 9, 135–152. https://doi.org/10.1111/eva.12282

Dubuc-Messier G, Réale D, Perret P, Charmantier A (2017) Environmental heterogeneity and population differences in blue tits personality traits. Behavioral Ecology, 28, 448–459. https://doi.org/10.1093/beheco/arw148

Kokko H, Chaturvedi A, Croll D, Fischer MC, Guillaume F, Karrenberg S, Kerr B, Rolshausen G, Stapley J (2017) Can Evolution Supply What Ecology Demands? Trends in Ecology & Evolution, 32, 187–197. https://doi.org/10.1016/j.tree.2016.12.005

Lewontin RC, Cohen D (1969) On Population Growth in a Randomly Varying Environment. Proceedings of the National Academy of Sciences, 62, 1056–1060. https://doi.org/10.1073/pnas.62.4.1056

Identifying drivers of spatio-temporal variation in survival in four blue tit populationsOlivier Bastianelli, Alexandre Robert, Claire Doutrelant, Christophe de Franceschi, Pablo Giovannini, Anne Charmantier<p style="text-align: justify;">In a context of rapid climate change, the influence of large-scale and local climate on population demography is increasingly scrutinized, yet studies are usually focused on one population. Demographic parameters, i...Climate change, Demography, Evolutionary ecology, Life history, Population ecologyDieter Lukas2021-01-29 15:24:23 View