Submit a preprint

Latest recommendationsrsstwitter

IdTitleAuthorsAbstractPicture▲Thematic fieldsRecommenderReviewersSubmission date
16 Jun 2020
article picture

Environmental perturbations and transitions between ecological and evolutionary equilibria: an eco-evolutionary feedback framework

Stasis and the phenotypic gambit

Recommended by based on reviews by Jacob Johansson, Katja Räsänen and 1 anonymous reviewer

The preprint "Environmental perturbations and transitions between ecological and evolutionary equilibria: an eco-evolutionary feedback framework" by Coulson (2020) presents a general framework for evolutionary ecology, useful to interpret patterns of selection and evolutionary responses to environmental transitions. The paper is written in an accessible and intuitive manner. It reviews important concepts which are at the heart of evolutionary ecology. Together, they serve as a worldview which you can carry with you to interpret patterns in data or observations in nature. I very much appreciate it that Coulson (2020) presents his personal intuition laid bare, the framework he uses for his research and how several strong concepts from theoretical ecology fit in there. Overviews as presented in this paper are important to understand how we as researchers put the pieces together.
A main message of the paper is that resource detection and acquisition traits, broadly called "resource accrual traits" are at the core of evolutionary dynamics. These traits and the processes they are involved in often urge some degree of individual specialization. Not all traits are resource accrual traits all the time. Guppies are cited as an example, which have traits in high predation environments that make foraging easier for them, such as being less conspicuous to predators. In the absence of predators, these same traits might be neutral. Their colour pattern might then contribute much less to the odds of obtaining resources.
"Resource accrual" reminds me of discussions of resource holding potential (Parker 1974), which can be for example the capacity to remain on a bird feeder without being dislodged. However, the idea is much broader and aggression does not need to be important for the acquisition of resources. Evolutionary success is reserved for those steadily obtaining resources. This recalls the pessimization principle of Metz et al. (2008), which applies in a restricted set of situations and where the strategy which persists at the lowest resource levels systematically wins evolutionary contests. If this principle would apply universally, the world then inherently become the worst possible. Resources determine energy budgets and different life history strategies allocate these differently to maximize fitness. The fine grain of environments and the filtration by individual histories generate a lot of variation in outcomes. However, constraint-centered approaches (Kempes et al. 2019, Kooijman 2010) are mentioned but are not at the core of this preprint. Evolution is rather seen as dynamic programming optimization with interactions within and between species. Coulson thus extends life history studies such as for example Tonnabel et al. (2012) with eco-evolutionary feedbacks. Examples used are guppies, algae-rotifer interactions and others. Altogether, this makes for an optimistic paper pushing back the pessimization principle.
Populations are expected to spend most of the time in quasi-equilibrium states where the long run stochastic growth rate is close to zero for all genotypes, alleles or other chosen classes. In the preprint, attention is given to reproductive value calculus, another strong tool in evolutionary dynamics (Grafen 2006, Engen et al. 2009), which tells us how classes within a population contribute to population composition in the distant future. The expected asymptotic fitness of an individual is equated to its expected reproductive value, but this might require particular ways of calculating reproductive values (Coulson 2020). Life history strategies can also be described by per generation measures such as R0 (currently on everyone's radar due to the coronavirus pandemic), generation time etc. Here I might disagree because I believe that this focus in per generation measures can lead to an incomplete characterization of plastic and other strategies involved in strategies such as bet-hedging. A property at quasi-equilibrium states is precise enough to serve as a null hypothesis which can be falsified: all types must in the long run leave equal numbers of descendants. If there is any property in evolutionary ecology which is useful it is this one and it rightfully merits attention.
However, at quasi-equilibrium states, directional selection has been observed, often without the expected evolutionary response. The preprint aims to explain this and puts forward the presence of non-additive gene action as a mechanism. I don't believe that it is the absence of clonal inheritance which matters very much in itself (Van Dooren 2006) unless genes with major effect are present in protected polymorphisms. The preprint remains a bit unclear on how additive gene action is broken, and here I add from the sphere in which I operate. Non-additive gene action can be linked to non-linear genotype-phenotype maps (Van Dooren 2000, Gilchrist and Nijhout 2001) and if these maps are non-linear enough to create constraints on phenotype determination, by means of maximum or minimum phenotypes which cannot be surpassed for any combination of the underlying traits, then they create additional evolutionary quasi-equilibrium states, with directional selection on a phenotype such as body size. I believe Coulson hints at this option (Coulson et al. 2006), but also at a different one: if body size is mostly determined by variation in resource accrual traits, then the resource accrual traits can be under stabilizing selection while body size is not. This requires that all resource accrual traits affect other phenotypic or demographic properties next to body size. In both cases, microevolutionary outcomes cannot be inferred from inspecting body sizes alone, either resource accrual traits need to be included explicitly, or non-linearities, or both when the map between resource accrual and body size is non-linear (Van Dooren 2000).
The discussion of the phenotypic gambit (Grafen 1984) leads to another long-standing issue in evolutionary biology. Can predictions of adaptation be made by inspecting and modelling individual phenotypes alone? I agree that with strongly non-linear genotype-phenotype maps they cannot and for multivariate sets of traits, genetic and phenotypic correlations can be very different (Hadfield et al. 2007). However, has the phenotypic gambit ever claimed to be valid globally or should it rather be used locally for relatively small amounts of variation? Grafen (1984) already contained caveats which are repeated here. As a first approximation, additivity might produce quite correct predictions and thus make the gambit operational in many instances. When important individual traits are omitted, it may just be misspecified. I am interested to see cases where the framework Coulson (2020) proposes is used for very large numbers of phenotypic and genotypic attributes. In the end, these highly dimensional trait distributions might basically collapse to a few major axes of variation due to constraints on resource accrual.
I highly recommend reading this preprint and I am looking forward to the discussion it will generate.

References

[1] Coulson, T. (2020) Environmental perturbations and transitions between ecological and evolutionary equilibria: an eco-evolutionary feedback framework. bioRxiv, 509067, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/509067
[2] Coulson, T., Benton, T. G., Lundberg, P., Dall, S. R. X., and Kendall, B. E. (2006). Putting evolutionary biology back in the ecological theatre: a demographic framework mapping genes to communities. Evolutionary Ecology Research, 8(7), 1155-1171.
[3] Engen, S., Lande, R., Sæther, B. E. and Dobson, F. S. (2009) Reproductive value and the stochastic demography of age-structured populations. The American Naturalist 174: 795-804. doi: 10.1086/647930
[4] Gilchrist, M. A. and Nijhout, H. F. (2001). Nonlinear developmental processes as sources of dominance. Genetics, 159(1), 423-432.
[5] Grafen, A. (1984) Natural selection, kin selection and group selection. In: Behavioural Ecology: An Evolutionary Approach,2nd edn (JR Krebs & NB Davies eds), pp. 62–84. Blackwell Scientific, Oxford.
[6] Grafen, A. (2006). A theory of Fisher's reproductive value. Journal of mathematical biology, 53(1), 15-60. doi: 10.1007/s00285-006-0376-4
[7] Hadfield, J. D., Nutall, A., Osorio, D. and Owens, I. P. F. (2007). Testing the phenotypic gambit: phenotypic, genetic and environmental correlations of colour. Journal of evolutionary biology, 20(2), 549-557. doi: 10.1111/j.1420-9101.2006.01262.x
[8] Kempes, C. P., West, G. B., and Koehl, M. (2019). The scales that limit: the physical boundaries of evolution. Frontiers in Ecology and Evolution, 7, 242. doi: 10.3389/fevo.2019.00242
[9] Kooijman, S. A. L. M. (2010) Dynamic Energy Budget theory for metabolic organisation. University Press, third edition.
[10] Metz, J. A. J., Mylius, S.D. and Diekman, O. (2008) When does evolution optimize?. Evolutionary Ecology Research 10: 629-654.
[11] Parker, G. A. (1974). Assessment strategy and the evolution of fighting behaviour. Journal of theoretical Biology, 47(1), 223-243. doi: 10.1016/0022-5193(74)90111-8
[12] Tonnabel, J., Van Dooren, T. J. M., Midgley, J., Haccou, P., Mignot, A., Ronce, O., and Olivieri, I. (2012). Optimal resource allocation in a serotinous non‐resprouting plant species under different fire regimes. Journal of Ecology, 100(6), 1464-1474. doi: 10.1111/j.1365-2745.2012.02023.x
[13] Van Dooren, T. J. M. (2000). The evolutionary dynamics of direct phenotypic overdominance: emergence possible, loss probable. Evolution, 54(6), 1899-1914. doi: 10.1111/j.0014-3820.2000.tb01236.x
[14] Van Dooren, T. J. M. (2006). Protected polymorphism and evolutionary stability in pleiotropic models with trait‐specific dominance. Evolution, 60(10), 1991-2003. doi: 10.1111/j.0014-3820.2006.tb01837.x

Environmental perturbations and transitions between ecological and evolutionary equilibria: an eco-evolutionary feedback frameworkTim Coulson<p>I provide a general framework for linking ecology and evolution. I start from the fact that individuals require energy, trace molecules, water, and mates to survive and reproduce, and that phenotypic resource accrual traits determine an individ...Eco-evolutionary dynamics, Evolutionary ecologyTom Van Dooren2019-01-03 10:05:16 View
29 Jan 2020
article picture

Stoichiometric constraints modulate the effects of temperature and nutrients on biomass distribution and community stability

On the importance of stoichiometric constraints for understanding global change effects on food web dynamics

Recommended by based on reviews by 2 anonymous reviewers

The constraints associated with the mass balance of chemical elements (i.e. stoichiometric constraints) are critical to our understanding of ecological interactions, as outlined by the ecological stoichiometry theory [1]. Species in ecosystems differ in their elemental composition as well as in their level of elemental homeostasis [2], which can determine the outcome of interactions such as herbivory or decomposition on species coexistence and ecosystem functioning [3, 4].
Despite their importance, stoichiometric constraints are still often ignored in theoretical studies exploring the consequences of environmental perturbations on food web stability. Meanwhile, drivers of global change strongly alter biochemical cycles and the balance of chemical elements in ecosystems [5]. An important challenge is thus to understand how stoichiometric constraints affect food web responses to global changes.
The study of Sentis et al. [6] makes a step in that direction. This article investigates how stoichiometric constraints affect the response of consumer-resource dynamics to increasing temperature and nutrient inputs. It shows that the stoichiometric flexibility of the resource, coupled with lower consumer assimilation efficiency when stoichiometric unbalance between the resource and the consumer is higher, dampens the destabilizing effects of nutrient enrichment on species dynamics but reduces consumer persistence at extreme temperatures. Interestingly, these effects of stoichiometric constraints arise not only from changes in species assimilation efficiencies and carrying capacities but also from stoichiometric negative feedback loops on resource and consumer populations.
The results of this study are a call to further include stoichiometric constraints into food web models to better understand and predict the consequences of global changes on ecological communities. Many perspectives exist on that issue. For instance, it would be interesting to assess the effects of other stoichiometric mechanisms (e.g. changes in the element limiting growth [3]) on food web stability and its response to nutrient enrichment, as well as the effects of other global change drivers associated with altered biochemical cycles (e.g. carbon dioxide increase).

References

[1] Sterner, R. W. and Elser, J. J. (2017). Ecological Stoichiometry, The Biology of Elements from Molecules to the Biosphere. doi: 10.1515/9781400885695
[2] Elser, J. J., Sterner, R. W., Gorokhova, E., Fagan, W. F., Markow, T. A., Cotner, J. B., Harrison, J.F., Hobbie, S.E., Odell, G.M., Weider, L. W. (2000). Biological stoichiometry from genes to ecosystems. Ecology Letters, 3(6), 540–550. doi: 10.1111/j.1461-0248.2000.00185.x
[3] Daufresne, T., and Loreau, M. (2001). Plant–herbivore interactions and ecological stoichiometry: when do herbivores determine plant nutrient limitation? Ecology Letters, 4(3), 196–206. doi: 10.1046/j.1461-0248.2001.00210.x
[4] Zou, K., Thébault, E., Lacroix, G., and Barot, S. (2016). Interactions between the green and brown food web determine ecosystem functioning. Functional Ecology, 30(8), 1454–1465. doi: 10.1111/1365-2435.12626
[5] Peñuelas, J., Poulter, B., Sardans, J., Ciais, P., van der Velde, M., Bopp, L., Boucher, O., Godderis, Y., Hinsinger, P., Llusia, J., Nardin, E., Vicca, S., Obersteiner, M., Janssens, I. A. (2013). Human-induced nitrogen–phosphorus imbalances alter natural and managed ecosystems across the globe. Nature Communications, 4(1), 1–10. doi: 10.1038/ncomms3934
[6] Sentis, A., Haegeman, B. & Montoya, J.M. (2020). Stoichiometric constraints modulate the effects of temperature and nutrients on biomass distribution and community stability. bioRxiv, 589895, ver. 7 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/589895

Stoichiometric constraints modulate the effects of temperature and nutrients on biomass distribution and community stability Arnaud Sentis, Bart Haegeman, and José M. Montoya<p>Temperature and nutrients are two of the most important drivers of global change. Both can modify the elemental composition (i.e. stoichiometry) of primary producers and consumers. Yet their combined effect on the stoichiometry, dynamics, and s...Climate change, Community ecology, Food webs, Theoretical ecology, Thermal ecologyElisa Thebault2019-08-08 12:20:08 View
11 May 2020
article picture

Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa)

Urban past predicts contemporary genetic structure in city rats

Recommended by based on reviews by Torsti Schulz, ? and 1 anonymous reviewer

Urban areas are expanding worldwide, and have become a dominant part of the landscape for many species. Urbanization can fragment pre-existing populations of vulnerable species leading to population declines and the loss of connectivity. On the other hand, expansion of urban areas can also facilitate the spread of human commensals including pests. Knowledge of the features of cityscapes that facilitate gene flow and maintain diversity of pests is thus key to their management and eradication.
Cities are complex mosaics of natural and manmade surfaces, and habitat quality is not only influenced by physical aspects of the cityscape but also by socioeconomic factors and human behaviour. Constant development means that cities also change rapidly in time; contemporary urban life reflects only a snapshot of the environmental conditions faced by populations. It thus remains a challenge to identify the features that actually drive ecology and evolution of populations in cities [1]. While several studies have highlighted strong urban clines in genetic structure and adaption [2], few have considered the influence of factors beyond physical aspects of the cityscape or historical processes.
In this paper, Stragier et al. [3] sought to identify the current and past features of the cityscape and socioeconomic factors that shape genetic structure and diversity of the house mouse (Mus musculus domesticus) in Dakar, Senegal. The authors painstakingly digitized historical maps of Dakar from the time of European settlement in 1862 to present. The authors found that the main spatial genetic cline was best explained by historical cityscape features, with higher apparent gene flow and genetic diversity in areas that were connected earlier to initial European settlements. Beyond the main trend of spatial genetic structure, they found further evidence that current features of the cityscape were important. Specifically, areas with low vegetation and poor housing conditions were found to support large, genetically diverse populations. The authors demonstrate that their results are reproducible using several statistical approaches, including modeling that explicitly accounts for spatial autocorrelation.
The work of Stragier et al. [3] thus highlights that populations of city-dwelling species are the product of both past and present cityscapes. Going forward, urban evolutionary ecologists should consider that despite the potential for rapid evolution in urban landscapes, the signal of a species’ colonization can remain for generations.

References

[1] Rivkin, L. R., Santangelo, J. S., Alberti, M. et al. (2019). A roadmap for urban evolutionary ecology. Evolutionary Applications, 12(3), 384-398. doi: 10.1111/eva.12734
[2] Miles, L. S., Rivkin, L. R., Johnson, M. T., Munshi‐South, J. and Verrelli, B. C. (2019). Gene flow and genetic drift in urban environments. Molecular ecology, 28(18), 4138-4151. doi: 10.1111/mec.15221
[3] Stragier, C., Piry, S., Loiseau, A., Kane, M., Sow, A., Niang, Y., Diallo, M., Ndiaye, A., Gauthier, P., Borderon, M., Granjon, L., Brouat, C. and Berthier, K. (2020). Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa). bioRxiv, 557066, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/557066

Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa)Claire Stragier, Sylvain Piry, Anne Loiseau, Mamadou Kane, Aliou Sow, Youssoupha Niang, Mamoudou Diallo, Arame Ndiaye, Philippe Gauthier, Marion Borderon, Laurent Granjon, Carine Brouat, Karine Berthier<p>Population genetic approaches may be used to investigate dispersal patterns of species living in highly urbanized environment in order to improve management strategies for biodiversity conservation or pest control. However, in such environment,...Biological invasions, Landscape ecology, Molecular ecologyMichelle DiLeo2019-02-22 08:36:13 View
27 Jan 2023
article picture

Spatial heterogeneity of interaction strength has contrasting effects on synchrony and stability in trophic metacommunities

How does spatial heterogeneity affect stability of trophic metacommunities?

Recommended by based on reviews by Phillip P.A. Staniczenko, Ludek Berec and Diogo Provete

The temporal or spatial variability in species population sizes and interaction strength of animal and plant communities has a strong impact on aggregate community properties (for instance biomass), community composition, and species richness (Kokkoris et al. 2002). Early work on spatial and temporal variability strongly indicated that asynchronous population and environmental fluctuations tend to stabilise community structures and diversity (e.g. Holt 1984, Tilman and Pacala 1993, McCann et al. 1998, Amarasekare and Nisbet 2001). Similarly, trophic networks might be stabilised by spatial heterogeneity (Hastings 1977) and an asymmetry of energy flows along food chains (Rooney et al. 2006). The interplay between temporal, spatial, and trophic heterogeneity within the meta-community concept has got much less interest. In the recent preprint in PCI Ecology, Quévreux et al. (2023) report that Spatial heterogeneity of interaction strength has contrasting effects on synchrony and stability in trophic metacommunities. These authors rightly notice that the interplay between trophic and spatial heterogeneity might induce contrasting effects depending on the internal dynamics of the system. Their contribution builds on prior work (Quévreux et al. 2021a, b) on perturbed trophic cascades.

I found this paper particularly interesting because it is in the, now century-old, tradition to show that ecological things are not so easy. Since the 1930th, when Nicholson and Baily and others demonstrated that simple deterministic population models might generate stability and (pseudo-)chaos ecologists have realised that systems triggered by two or more independent processes might be intrinsically unpredictable and generate different outputs depending on the initial parameter settings. This resembles the three-body problem in physics. The present contribution of Quévreux et al. (2023) extends this knowledge to an example of a spatially explicit trophic model. Their main take-home message is that asymmetric energy flows in predator–prey relationships might have contrasting effects on the stability of metacommunities receiving localised perturbations. Stability is context dependent.

Of course, the work is merely a theoretical exercise using a simplistic trophic model. It demands verification with field data. Nevertheless, we might expect even stronger unpredictability in more realistic multitrophic situations. Therefore, it should be seen as a proof of concept. Remember that increasing trophic connectance tends to destabilise food webs (May 1972). In this respect, I found the final outlook to bioconservation ambitious but substantiated. Biodiversity management needs a holistic approach focusing on all aspects of ecological functioning. I would add the need to see stability and biodiversity within an evolutionary perspective.        

References

Amarasekare P, Nisbet RM (2001) Spatial Heterogeneity, Source‐Sink Dynamics, and the Local Coexistence of Competing Species. The American Naturalist, 158, 572–584. https://doi.org/10.1086/323586

Hastings A (1977) Spatial heterogeneity and the stability of predator-prey systems. Theoretical Population Biology, 12, 37–48. https://doi.org/10.1016/0040-5809(77)90034-X

Holt RD (1984) Spatial Heterogeneity, Indirect Interactions, and the Coexistence of Prey Species. The American Naturalist, 124, 377–406. https://doi.org/10.1086/284280

Kokkoris GD, Jansen VAA, Loreau M, Troumbis AY (2002) Variability in interaction strength and implications for biodiversity. Journal of Animal Ecology, 71, 362–371. https://doi.org/10.1046/j.1365-2656.2002.00604.x

May RM (1972) Will a Large Complex System be Stable? Nature, 238, 413–414. https://doi.org/10.1038/238413a0

McCann K, Hastings A, Huxel GR (1998) Weak trophic interactions and the balance of nature. Nature, 395, 794–798. https://doi.org/10.1038/27427

Quévreux P, Barbier M, Loreau M (2021) Synchrony and Perturbation Transmission in Trophic Metacommunities. The American Naturalist, 197, E188–E203. https://doi.org/10.1086/714131

Quévreux P, Pigeault R, Loreau M (2021) Predator avoidance and foraging for food shape synchrony and response to perturbations in trophic metacommunities. Journal of Theoretical Biology, 528, 110836. https://doi.org/10.1016/j.jtbi.2021.110836

Quévreux P, Haegeman B, Loreau M (2023) Spatial heterogeneity of interaction strength has contrasting effects on synchrony and stability in trophic metacommunities. hal-03829838, ver. 2 peer-reviewed and recommended by Peer Community in Ecology. https://hal.science/hal-03829838

Rooney N, McCann K, Gellner G, Moore JC (2006) Structural asymmetry and the stability of diverse food webs. Nature, 442, 265–269. https://doi.org/10.1038/nature04887

Tilman D, Pacala S (1993) The maintenance of species richness in plant communities. In: Ricklefs, R.E., Schluter, D. (eds) Species Diversity in Ecological Communities: Historical and Geographical Perspectives. University of Chicago Press, pp. 13–25.

Spatial heterogeneity of interaction strength has contrasting effects on synchrony and stability in trophic metacommunitiesPierre Quévreux, Bart Haegeman and Michel Loreau<p>&nbsp;Spatial heterogeneity is a fundamental feature of ecosystems, and ecologists have identified it as a factor promoting the stability of population dynamics. In particular, differences in interaction strengths and resource supply between pa...Dispersal & Migration, Food webs, Interaction networks, Spatial ecology, Metacommunities & Metapopulations, Theoretical ecologyWerner Ulrich2022-10-26 13:38:34 View
06 Oct 2020
article picture

Implementing a rapid geographic range expansion - the role of behavior and habitat changes

The role of behavior and habitat availability on species geographic expansion

Recommended by ORCID_LOGO based on reviews by Caroline Marie Jeanne Yvonne Nieberding, Pizza Ka Yee Chow, Tim Parker and 1 anonymous reviewer

Understanding the relative importance of species-specific traits and environmental factors in modulating species distributions is an intriguing question in ecology [1]. Both behavioral flexibility (i.e., the ability to change the behavior in changing circumstances) and habitat availability are known to influence the ability of a species to expand its geographic range [2,3]. However, the role of each factor is context and species dependent and more information is needed to understand how these two factors interact. In this pre-registration, Logan et al. [4] explain how they will use Great-tailed grackles (Quiscalus mexicanus), a species with a flexible behavior and a rapid geographic range expansion, to evaluate the relative role of habitat and behavior as drivers of the species’ expansion [4]. The authors present very clear hypotheses, predicted results and also include alternative predictions. The rationales for all the hypotheses are clearly stated, and the methodology (data and analyses plans) are described with detail. The large amount of information already collected by the authors for the studied species during previous projects warrants the success of this study. It is also remarkable that the authors will make all their data available in a public repository, and that the pre-registration in already stored in GitHub, supporting open access and reproducible science. I agree with the three reviewers of this pre-registration about its value and I think its quality has largely improved during the review process. Thus, I am happy to recommend it and I am looking forward to seeing the results.

References

[1] Gaston KJ. 2003. The structure and dynamics of geographic ranges. Oxford series in Ecology and Evolution. Oxford University Press, New York.

[2] Sol D, Lefebvre L. 2000. Behavioural flexibility predicts invasion success in birds introduced to new zealand. Oikos. 90(3): 599–605. https://doi.org/10.1034/j.1600-0706.2000.900317.x

[3] Hanski I, Gilpin M. 1991. Metapopulation dynamics: Brief history and conceptual domain. Biological journal of the Linnean Society. 42(1-2): 3–16. https://doi.org/10.1111/j.1095-8312.1991.tb00548.x

[4] Logan CJ, McCune KB, Chen N, Lukas D. 2020. Implementing a rapid geographic range expansion - the role of behavior and habitat changes (http://corinalogan.com/Preregistrations/gxpopbehaviorhabitat.html) In principle acceptance by PCI Ecology of the version on 16 Dec 2021 https://github.com/corinalogan/grackles/blob/0fb956040a34986902a384a1d8355de65010effd/Files/Preregistrations/gxpopbehaviorhabitat.Rmd.

Implementing a rapid geographic range expansion - the role of behavior and habitat changesLogan CJ, McCune KB, Chen N, Lukas D<p>It is generally thought that behavioral flexibility, the ability to change behavior when circumstances change, plays an important role in the ability of a species to rapidly expand their geographic range (e.g., Lefebvre et al. (1997), Griffin a...Behaviour & Ethology, Biological invasions, Dispersal & Migration, Foraging, Habitat selection, Human impact, Phenotypic plasticity, Preregistrations, ZoologyEsther Sebastián GonzálezAnonymous, Caroline Marie Jeanne Yvonne Nieberding, Tim Parker2020-05-14 11:18:57 View
14 May 2019
article picture

Field assessment of precocious maturation in salmon parr using ultrasound imaging

OB-GYN for salmon parrs

Recommended by based on reviews by Hervé CAPRA and 1 anonymous reviewer

Population dynamics and stock assessment models are only as good as the data used to parameterise them. For Atlantic salmon (Salmo salar) populations, a critical parameter may be frequency of precocious maturation. Indeed, the young males (parrs) that mature early, before leaving the river to reach the ocean, can contribute to reproduction but have much lower survival rates afterwards. The authors cite evidence of the potentially major consequences of this alternate reproductive strategy. So, to be parameterised correctly, it needs to be assessed correctly. Cue the ultrasound machine.

Through a thorough analysis of data collected on 850 individuals [1], over three years, the authors clearly show that the non-invasive examination of the internal cavity of young fishes to look for gonads, using a portable ultrasound machine, provides reliable and replicable evidence of precocious maturation. They turned into OB-GYN for salmons (albeit for male salmons!) and it worked. While using ultrasounds to detect fish gonads is not a new idea (early attempts for salmonids date back to the 80s [2]), the value here is in the comparison with the classic visual inspection technique (which turns out to be less reliable) and the fact that ultrasounds can now easily be carried out in the field.

Beyond the potentially important consequences of this new technique for the correct assessment of salmon population dynamics, the authors also make the case for the acquisition of more reliable individual-level data in ecological studies, which I applaud.

References.

[1] Nevoux M, Marchand F, Forget G, Huteau D, Tremblay J, and Destouches J-P. (2019). Field assessment of precocious maturation in salmon parr using ultrasound imaging. bioRxiv 425561, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/425561
[2] Reimers E, Landmark P, Sorsdal T, Bohmer E, Solum T. (1987). Determination of salmonids’ sex, maturation and size: an ultrasound and photocell approach. Aquaculture Magazine.13:41-44.

Field assessment of precocious maturation in salmon parr using ultrasound imagingMarie Nevoux, Frédéric Marchand, Guillaume Forget, Dominique Huteau, Julien Tremblay, Jean-Pierre Destouches<p>Salmonids are characterized by a large diversity of life histories, but their study is often limited by the imperfect observation of the true state of an individual in the wild. Challenged by the need to reduce uncertainty of empirical data, re...Conservation biology, Demography, Experimental ecology, Freshwater ecology, Life history, Phenotypic plasticity, Population ecologyJean-Olivier Irisson2018-09-25 17:24:59 View
19 Dec 2020
article picture

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
20 Feb 2019
article picture

Differential immune gene expression associated with contemporary range expansion of two invasive rodents in Senegal

Are all the roads leading to Rome?

Recommended by based on reviews by Nadia Aubin-Horth and 1 anonymous reviewer

Identifying the factors which favour the establishment and spread of non-native species in novel environments is one of the keys to predict - and hence prevent or control - biological invasions. This includes biological factors (i.e. factors associated with the invasive species themselves), and one of the prevailing hypotheses is that some species traits may explain their impressive success to establish and spread in novel environments [1]. In animals, most research studies have focused on traits associated with fecundity, age at maturity, level of affiliation to humans or dispersal ability for instance. The “composite picture” of the perfect (i.e. successful) invader that has gradually emerged is a small-bodied animal strongly affiliated to human activities with high fecundity, high dispersal ability and a super high level of plasticity. Of course, the story is not that simple, and actually a perfect invader sometimes – if not often- takes another form… Carrying on to identify what makes a species a successful invader or not is hence still an important research axis with major implications.
In this manuscript, Charbonnel and collaborators [2] provide an interesting opportunity to gain novel insights into our understanding of (the) traits underlying invasion success. They nicely combine the power of Next-Generation Sequencing (NGS) with a clever comparative approach of two closely-related invasive rodents (the house mouse Mus musculus and the black rat Rattus rattus) in a common environment. They use this experimental design to test the appealing hypothesis that pathogens may be actors of the story, and may indirectly explain why some non-native species are so successful in invading novel habitats.
It is generally assumed that the community of pathogens encountered by non-native species in novel environments is different from that of their native area. On the one hand (the enemy-release hypothesis), it can be hypothesized that non-native species, when they arrive into a novel environment, will be relaxed from the pressure imposed by their native pathogens because local pathogens are not adapted (and hence do not infect) to this novel host. Because immune defence against pathogens is highly costly, non-native species establishing into a novel environment could hence reallocate these costs to other functions such as fecundity or dispersal apparatus. This scenario has been termed the “evolution of increased competitive ability” (EICA) hypothesis [3]. On the other hand (the EICA-refined hypothesis [4]), one can assume that invaders will encounter new pathogens in newly established areas, and will allocate energy toward cost-effective immune pathways to permit allocating a non-negligible amount of energy toward other functions. Finally, a last hypothesis (the “immune protection” hypothesis) assumes major changes in pathogen composition between native and invaded areas, which should lead to an overall increase in immune investment by the native species to successfully invade novel environments [4]. This last hypothesis suggests that only non-native species being able to take up the associated costs of immunity will be successful invaders.
The role of immunity in invasion success has yet been poorly investigated, mainly because of the difficulty to simultaneously analyse multiple immune pathways [4]. Charbonnel and collaborators [2] overpass this difficulty by screening all genes expressed (using a whole RNA sequencing approach) in an immune tissue: the spleen. They do so along the invasion routes of two sympatric invasive rodents in Africa and compare anciently and newly invaded areas (respectively). For one of the two species (the house mouse), they found a high number of immune-related genes to be up-regulated in newly invaded areas compared to anciently invaded areas. All categories of immune pathways (costly and cost-effective) were up-regulated, suggesting an overall increase in immune investment in the mouse, which corroborates the “immune protection” hypothesis. For the black rat, patterns of gene expression were somewhat different, with much less pronounced differentiation in gene expression between newly and anciently invaded areas. Among the few differentiated genes, a few were associated to immune responses and some of theses genes were even down-regulated in the newly invaded areas. This pattern may actually corroborate the EICA hypothesis, although it could alternatively suggest that stochastic processes (drift) associated to recent decrease in population size (which is expected during a colonisation event) are more important than selection imposed by pathogens in shaping patterns of immune gene expression.
Overall, this study [2] suggests (i) that immune-related traits are important in predicting invasion success and (ii) that two successful species with a similar invasion history and living in similar environments can use different life-history strategies to reach the same success. This later finding is particularly relevant and intriguing as it suggests that the traits and strategies deployed by species to colonise new habitats might actually be idiosyncratic, and that, if general trends actually emerge in regards of traits predicting the success of invaders, the devil might actually be into the details. Comparative studies are extremely important to identify the general rules and the specificities sustaining actual patterns, but these approaches are yet poorly used in biological invasions (at least empirically). The work presented by Charbonnel and colleagues [2] calls for future comparative studies performed at multiple spatial scales (native vs. non-native areas, anciently vs. recently invaded areas), multiple taxonomic resolutions and across multiple traits (to search for trade-offs), so that the success of invasive species can be properly understood and predicted.

References

[1] Jeschke, J. M., & Strayer, D. L. (2006). Determinants of vertebrate invasion success in Europe and North America. Global Change Biology, 12(9), 1608-1619. doi: 10.1111/j.1365-2486.2006.01213.x
[2] Blossey, B., & Notzold, R. (1995). Evolution of increased competitive ability in invasive nonindigenous plants: a hypothesis. Journal of Ecology, 83(5), 887-889. doi: 10.2307/2261425
[3] Charbonnel, N., Galan, M., Tatard, C., Loiseau, A., Diagne, C. A., Dalecky, A., Parrinello, H., Rialle, S., Severac, D., & Brouat, C. (2019). Differential immune gene expression associated with contemporary range expansion of two invasive rodents in Senegal. bioRxiv, 442160, ver. 5 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/442160
[4] Lee, K. A., & Klasing, K. C. (2004). A role for immunology in invasion biology. Trends in Ecology & Evolution, 19(10), 523-529. doi: 10.1016/j.tree.2004.07.012

Differential immune gene expression associated with contemporary range expansion of two invasive rodents in SenegalNathalie Charbonnel, Maxime Galan, Caroline Tatard, Anne Loiseau, Christophe Diagne, Ambroise Dalecky, Hugues Parrinello, Stephanie Rialle, Dany Severac and Carine Brouat<p>Background: Biological invasions are major anthropogenic changes associated with threats to biodiversity and health. What determines the successful establishment of introduced populations still remains unsolved. Here we explore the appealing as...Biological invasions, Eco-immunology & Immunity, Population ecologySimon Blanchet2018-10-14 12:21:52 View
03 Jun 2022
article picture

Evolutionary emergence of alternative stable states in shallow lakes

How to evolve an alternative stable state

Recommended by ORCID_LOGO based on reviews by Jean-François Arnoldi and 1 anonymous reviewer

Alternative stable states describe ecosystems that can persist in more than one configuration. An ecosystem can shift between stable states following some form of perturbation. There has been much work on predicting when ecosystems will shift between stable states, but less work on why some ecosystems are able to exist in alternative stable states in the first place. The paper by Ardichvili, Loeuille, and Dakos (2022) addresses this question using a simple model of a shallow lake. Their model is based on a trade-off between access to light and nutrient availability in the water column, two essential resources for the macrophytes they model. They then identify conditions when the ancestral macrophyte will diversify resulting in macrophyte species living at new depths within the lake. The authors find a range of conditions where alternative stable states can evolve, but the range is narrow. Nonetheless, their model suggests that for alternative stable states to exist, one requirement is for there to be asymmetric competition between competing species, with one species being a better competitor on one limiting resource, with the other being a better competitor on a second limiting resource. 

These results are interesting and add to growing literature on how asymmetric competition can aid species coexistence. Asymmetric competition may be widespread in nature, with closely related species often being superior competitors on different resources. Incorporating asymmetric competition, and its evolution, into models does complicate theoretical investigations, but Ardichvili, Loeuille, and Dakos’ paper elegantly shows how substantial progress can be made with a model that is still (relatively) simple.

References 

Ardichvili A, Loeuille N, Dakos V (2022) Evolutionary emergence of alternative stable states in shallow lakes. bioRxiv, 2022.02.23.481597, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2022.02.23.481597

Evolutionary emergence of alternative stable states in shallow lakesAlice Ardichvili, Nicolas Loeuille, Vasilis Dakos<p style="text-align: justify;">Ecosystems under stress may respond abruptly and irreversibly through tipping points. Although much is explored on the mechanisms that affect tipping points and alternative stable states, little is known on how ecos...Community ecology, Competition, Eco-evolutionary dynamics, Theoretical ecologyTim Coulson2022-03-01 10:54:05 View
05 Feb 2020
article picture

A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding

A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding

Recommended by based on reviews by Tiago Pereira and 1 anonymous reviewer

High-throughput sequencing-based techniques such as DNA metabarcoding are increasingly advocated as providing numerous benefits over morphology‐based identifications for biodiversity inventories and ecosystem biomonitoring [1]. These benefits are particularly apparent for highly-diversified and/or hardly accessible aquatic and marine environments, where simple water or sediment samples could already produce acceptably accurate biodiversity estimates based on the environmental DNA present in the samples [2,3]. However, sequence-based characterization of biodiversity comes with its own challenges. A major one resides in the capacity to disentangle true biological diversity (be it taxonomic or genetic) from artefactual diversity generated by sequence-errors accumulation during PCR and sequencing processes, or from the amplification of non-target genes (i.e. pseudo-genes). On one hand, the stringent elimination of sequence variants might lead to biodiversity underestimation through the removal of true species, or the clustering of closely-related ones. On the other hand, a more permissive sequence filtering bears the risks of biodiversity inflation. Recent studies have outlined an excellent methodological framework for addressing this issue by proposing bioinformatic tools that allow the amplicon-specific error-correction as alternative or as complement to the more arbitrary approach of clustering into Molecular Taxonomic Units (MOTUs) based on sequence dissimilarity [4,5]. But to date, the relevance of amplicon-specific error-correction tools has been demonstrated only for a limited set of taxonomic groups and gene markers.
The study of Brandt et al. [6] successfully builds upon existing methodological frameworks for filling this gap in current literature. By proposing a bioinformatic pipeline combining Amplicon Sequence Variants (ASV) curation with MOTU clustering and additional post-clustering curation, the authors show that contrary to previous recommendations, ASV-based curation alone does not represent an adequate approach for DNA metabarcoding-based inventories of metazoans. Metazoans indeed, do exhibit inherently higher intra-specific and intra-individual genetic variability, necessarily leading to biased biodiversity estimates unbalanced in favor of species with higher intraspecific diversity in the absence of MOTU clustering. Interestingly, the positive effect of additional clustering showed to be dependent on the target gene region. Additional clustering had proportionally higher effect on the more polymorphic mitochondrial COI region (as compared to the 18S ribosomal gene). Thus, the major advantage of the study lies in the provision of optimal curation parameters that reflect the best possible balance between minimizing the impact of PCR/sequencing errors and the loss of true biodiversity across markers with contrasting levels of intragenomic variation. This is important as combining multiple markers is increasingly considered for improving the taxonomic coverage and resolution of data in DNA metabarcoding studies.
Another critical aspect of the study is the taxonomic assignation of curated OTUs (which is also the case for the majority of DNA metabarcoding-based biodiversity assessments). Facing the double challenge of focusing on taxonomic groups that are both highly diverse and poorly represented in public sequence reference databases, the authors failed to obtain high-resolution taxonomic assignments for several of the most closely-related species. As a result, taxa with low divergence levels were clustered as single taxonomic units, subsequently leading to underestimation of true biodiversity present. This finding adds to the argument that in order to be successful, sequence-based techniques still require the availability of comprehensive, high-quality reference databases.
Perhaps the only regret we might have with the study is the absence of mock community validation for the prokaryotes compartment. Even though the analyses of natural samples seem to suggest a positive effect of the curation pipeline, the concept of intra- versus inter-species variation in naturally occurring prokaryote communities remains at best ambiguous. Of course, constituting a representative sample of taxonomically-resolved prokaryote taxa from deep-sea habitats does not come without difficulties but has the benefit of opening opportunities for further studies on the matter.

References

[1] Porter, T. M., and Hajibabaei, M. (2018). Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis. Molecular Ecology, 27(2), 313–338. doi: 10.1111/mec.14478
[2] Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., … Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929–942. doi: 10.1111/mec.13428
[3] Leray, M., and Knowlton, N. (2015). DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proceedings of the National Academy of Sciences, 112(7), 2076–2081. doi: 10.1073/pnas.1424997112
[4] Callahan, B. J., McMurdie, P. J., and Holmes, S. P. (2017). Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. The ISME Journal, 11(12), 2639–2643. doi: 10.1038/ismej.2017.119
[5] Edgar, R. C. (2016). UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. BioRxiv, 081257. doi: 10.1101/081257
[6] Brandt, M. I., Trouche, B., Quintric, L., Wincker, P., Poulain, J., and Arnaud-Haond, S. (2020). A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding. BioRxiv, 717355, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/717355

A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding Miriam I Brandt, Blandine Trouche, Laure Quintric, Patrick Wincker, Julie Poulain, Sophie Arnaud-Haond<p>Environmental metabarcoding is an increasingly popular tool for studying biodiversity in marine and terrestrial biomes. With sequencing costs decreasing, multiple-marker metabarcoding, spanning several branches of the tree of life, is becoming ...Biodiversity, Community ecology, Marine ecology, Molecular ecologyStefaniya Kamenova2019-08-02 20:52:45 View