A core challenge facing ecologists is to work through an ever-increasing amount of data. The accelerating decline in biodiversity worldwide, mounting pressure of anthropogenic impacts, and increasing demand for actionable indicators to guide effective policy means that monitoring will only intensify, and rely on tools that can generate even more information (Gonzalez et al., 2023). How, then, do we handle this new volume and diversity of data?

This is the question Royaux et al. (2024) are tackling with their contribution. By introducing both a conceptual ("How should we think about our work?") and an operational ("Here is a tool to do our work with") framework, they establish a series of best practices for the analysis of ecological data.

It is easy to think about best practices in ecological data analysis in its most proximal form: is it good statistical practice? Is the experimental design correct? These have formed the basis of many recommendations over the years (see e.g. Popovic et al., 2024, for a recent example). But the contribution of Royaux et al. focuses on a different part of the analysis pipeline: the computer science (and software engineering) aspect of it.

As data grows in volume and complexity, the code needed to handle it follows the same trend. It is not a surprise, therefore, to see that the demand for programming skills in ecologists has doubled recently (Feng et al., 2020), prompting calls to make computational literacy a core component of undergraduate education (Farrell & Carrey, 2018). But beyond training, an obvious way to make computational analysis ecological data more reliable and effective is to build better tools. This is precisely what Royaux et al. have achieved.

They illustrate their approach through their experience building Galaxy-Ecology, a computing environment for ecological analysis: by introducing a clear taxonomy of computing concepts (data exploration, pre-processing, analysis, representation), with a hierarchy between them (formatting, data correction, anonymization), they show that we can think about the pipeline going from data to results in a way that is more systematized, and therefore more prone to generalization.

We may buckle at the idea of yet another ontology, or yet another framework, for our work, but I am convinced that the work of Royaux et al. is precisely what our field needs. Because their levels of atomization (their term for the splitting of complex pipelines into small, single-purpose tasks) are easy to understand, and map naturally onto tasks that we already perform, it is likely to see wide adoption. Solving the big, existential challenges of monitoring and managing biodiversity at the global scale requires the adoption of good practices, and a tool like Galaxy-Ecology goes a long way towards this goal.

References

Farrell, K.J., and Carey, C.C. (2018). Power, pitfalls, and potential for integrating computational literacy into undergraduate ecology courses. Ecol. Evol. 8, 7744-7751.
https://doi.org/10.1002/ece3.4363

Feng, X., Qiao, H., and Enquist, B. (2020). Doubling demands in programming skills call for ecoinformatics education. Frontiers in Ecology and the Environment 18, 123-124.
https://doi.org/10.1002/fee.2179
 
Gonzalez, A., Vihervaara, P., Balvanera, P., Bates, A.E., Bayraktarov, E., Bellingham, P.J., Bruder, A., Campbell, J., Catchen, M.D., Cavender-Bares, J., et al. (2023). A global biodiversity observing system to unite monitoring and guide action. Nat. Ecol. Evol., 1-5. 
https://doi.org/10.1038/s41559-023-02171-0
 
Popovic, G., Mason, T.J., Drobniak, S.M., Marques, T.A., Potts, J., Joo, R., Altwegg, R., Burns, C.C.I., McCarthy, M.A., Johnston, A., et al. (2024). Four principles for improved statistical ecology. Methods Ecol. Evol. 15, 266-281.
https://doi.org/10.1111/2041-210X.14270
 
Coline Royaux, Jean-Baptiste Mihoub, Marie Jossé, Dominique Pelletier, Olivier Norvez, Yves Reecht, Anne Fouilloux, Helena Rasche, Saskia Hiltemann, Bérénice Batut, Marc Eléaume, Pauline Seguineau, Guillaume Massé, Alan Amossé, Claire Bissery, Romain Lorrilliere, Alexis Martin, Yves Bas, Thimothée Virgoulay, Valentin Chambon, Elie Arnaud, Elisa Michon, Clara Urfer, Eloïse Trigodet, Marie Delannoy, Gregoire Loïs, Romain Julliard, Björn Grüning, Yvan Le Bras (2024) Guidance framework to apply best practices in ecological data analysis: Lessons learned from building Galaxy-Ecology. EcoEvoRxiv, ver.3 peer-reviewed and recommended by PCI Ecology. 
https://doi.org/10.32942/X2G033

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

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

References

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

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

References

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

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

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

References

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