Community ecology usually concerns itself with understanding the causes and consequences of diversity at a given taxonomic resolution, most classically at the species level. Yet there is no doubt that diversity exists at all scales, and phenotypic variability within a taxon can be comparable to differences between taxa, as observed from bacteria to fish and trees. The question that motivates an active and growing body of work (e.g. Raffard et al 2019) is not so much whether intraspecific variability matters, but what we get wrong by ignoring it and how to incorporate it into our understanding of communities. There is no established way to think about diversity at multiple nested taxonomic levels, and it is tempting to summarize intraspecific variability simply by measuring species mean and variance in any trait and metric.

In this study, Girard-Tercieux et al (2023a) propose that, to understand its impact on community-level outcomes and in particular on species coexistence, we should carefully distinguish between two ways of thinking about intraspecific variability:

-"unstructured" variation, where every individual's features are like an independent random draw from a species-specific distribution, for instance, due to genetic lottery and developmental accidents

-"structured" variation that is due to each individual encountering a different but enduring microenvironment.

The latter type of variability may still appear complex and random-like when the environment is high-dimensional (i.e. multifaceted, with many different factors contributing to each individual's performance and development). Thus, it is not necessarily "structured" in the sense of being easily understood -- we may need to measure more aspects of the environment than is practical if we want to fully predict these variations.

What distinguishes this "structured" variability is that it is, in a loose sense, inheritable: individuals from the same species that grow in the same microenvironment will have the same performance, in a repeatable fashion. Thus, if each species is best at exploiting at least a fraction of environmental conditions, it is likely to avoid extinction by competition, except in the unlucky case of no propagule reaching any of the favorable sites.
By contrast, drawing each individual's preferences and performance randomly at each generation (from its own species distribution, but independently from other and past individuals) leads to stochastic dynamics, so-called ecological drift, that easily induce a large number of species extinctions.

The core intuition, that the complex spatial structure and high-dimensional nature of the environment plays a key explanatory role in species coexistence, is a running thread through several of the authors' work (e.g. Clark et al 2010), clearly inspired by their focus on tropical forests. This study, by tackling the question of intraspecific determinants of interspecific outcomes, makes a compelling addition to this line of investigation, coming as a theoretical companion to a more data-oriented study (Girard-Tercieux et al 2023b). But I believe it raises a question that is even broader in scope.

This kind of intraspecific variability, due to different individuals growing in different microenvironments, is perhaps most relevant for trees and other sessile organisms, but the distinction made here between "unstructured" and "structured" variability can likely be extended to many other ecological settings.

In my understanding, what matters most in "structured" variability is not so much it stemming from a fixed environment, but rather it being maintained across generations, rather than possibly lost by drift. This difference between variability in the form of "frozen" randomness and in the form of stochastic drift over time is highly relevant in other theoretical fields (e.g. in physics, where it is the difference between a disordered solid and a liquid), and thus, I expect that it is a meaningful distinction to make throughout community ecology.

References

James S. Clark, David Bell, Chengjin Chu, Benoit Courbaud, Michael Dietze, Michelle Hersh, Janneke HilleRisLambers et al. (2010) "High‐dimensional coexistence based on individual variation: a synthesis of evidence." Ecological Monographs 80, no. 4 : 569-608. https://doi.org/10.1890/09-1541.1

Camille Girard-Tercieux, Ghislain Vieilledent, Adam Clark, James S. Clark, Benoît Courbaud, Claire Fortunel, Georges Kunstler, Raphaël Pélissier, Nadja Rüger, Isabelle Maréchaux (2023a) "Beyond variance: simple random distributions are not a good proxy for intraspecific variability in systems with environmental structure." bioRxiv, ver. 4 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2022.08.06.503032

Camille Girard‐Tercieux, Isabelle Maréchaux, Adam T. Clark, James S. Clark, Benoît Courbaud, Claire Fortunel, Joannès Guillemot et al. (2023b) "Rethinking the nature of intraspecific variability and its consequences on species coexistence." Ecology and Evolution 13, no. 3 : e9860. https://doi.org/10.1002/ece3.9860

Allan Raffard, Frédéric Santoul, Julien Cucherousset, and Simon Blanchet. (2019) "The community and ecosystem consequences of intraspecific diversity: A meta‐analysis." Biological Reviews 94, no. 2: 648-661. https://doi.org/10.1111/brv.12472

The ability to successfully sequence trace quantities of environmental DNA (eDNA) has provided unprecedented opportunities to use genetic analyses to elucidate animal ecology, behavior, and population structure without affecting the behavior, fitness, or welfare of the animal sampled. Hair associated with an animal track in the snow, the shed exoskeleton of an insect, or a swab of animal scat are all examples of non-invasive methods to collect eDNA. Despite the seemingly uncomplicated definition of "non-invasive" as proposed by Taberlet et al. [1], Lefort et al. [2] highlight that its appropriate application to sampling methods in practice is not so straightforward. For example, collecting scat left behind on the forest floor by a mammal could be invasive if feces is used by that species to mark territorial boundaries. Other collection strategies such as baited DNA traps to collect hair, capturing and handling an individual to swab or stimulate emission of a body fluid, or removal of a presumed non essential body part like a feather, fish scale, or even a leg from an insect are often described as "non-invasive" sampling methods. However, such methods cannot be considered truly non-invasive. At a minimum, attracting or capturing and handling an animal to obtain a DNA sample interrupts its normal behavioral routine, but additionally can cause both acute and long-lasting physiological and behavioral stress responses and other effects. Even invertebrates exhibit long-term hypersensitization after an injury, which manifests as heightened vigilance and enhanced escape responses [3-5].
Through an extensive analysis of 380 papers published from 2013-2018, Lefort et al. [2] document the widespread misapplication of the term "non-invasive" to methods used to sample DNA. An astonishing 58% of these papers employed the term incorrectly. A big part of the problem is that "non-invasive" is usually used by authors in the medical or veterinary sense of not breaking the skin or entering the body [6], rather than in the broader, ecological sense of Taberlet et al. [1]. The authors argue that correct use of the term matters, because it may lead naive readers – one can imagine students, policy makers, and the general public – to incorrectly assume a particular method is safe to use in a situation where disturbing the animal could affect experimental results or raise animal welfare concerns. Such assumptions can affect experimental design, as well as interpretations of one's own or others' data.
The importance of the Lefort et al. [2] paper lies in part on the authors' call for the research community to be much more careful when applying the term "non-invasive" to methods of DNA sampling. This call cannot be shrugged off as a minor problem in a few papers – as their literature review demonstrates, "non-invasive" is being applied incorrectly more often than not. The authors recognize that not all DNA sampling must be non-invasive to be useful or ethical. Examples include taking samples for DNA extraction from museum specimens, or opportunistically from carcasses of animals hunted either legally or seized by authorities from poachers. In many cases, there may be no viable non-invasive method to obtain DNA, but a researcher strives to collect samples using methods that, although they may involve taking a sample directly from the animal's body, do not disrupt, or only slightly disrupt behavior, fitness, or welfare of the animal. Thus, the other important contribution by Lefort et al. [2] is to propose the terms "non-disruptive" and "minimally-disruptive" to describe such sampling methods, which are not strictly non-invasive. While gray areas undoubtedly remain, as acknowledged by the authors, answering the call for correct use of "non-invasive" and applying the proposed new terms for certain types of invasive sampling with a focus on level of disruption, will go a long way in limiting misconceptions and misinterpretations caused by the current confusion in terminology.

References

[1] Taberlet P., Waits L. P. and Luikart G. 1999. Noninvasive genetic sampling: look before you leap. Trends Ecol. Evol. 14: 323-327. doi: 10.1016/S0169-5347(99)01637-7
[2] Lefort M.-C., Cruickshank R. H., Descovich K., Adams N. J., Barun A., Emami-Khoyi A., Ridden J., Smith V. R., Sprague R., Waterhouse B. R. and Boyer S. 2019. Blood, sweat and tears: a review of non-invasive DNA sampling. bioRxiv, 385120, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/385120
[3] Khuong T. M., Wang Q.-P., Manion J., Oyston L. J., Lau M.-T., Towler H., Lin Y. Q. and Neely G. G. 2019. Nerve injury drives a heightened state of vigilance and neuropathic sensitization in Drosophila. Science Advances 5: eaaw4099. doi: 10.1126/sciadv.aaw4099
[4] Crook, R. J., Hanlon, R. T. and Walters, E. T. 2013. Squid have nociceptors that display widespread long-term sensitization and spontaneous activity after bodily injury. Journal of Neuroscience, 33(24), 10021-10026. doi: 10.1523/JNEUROSCI.0646-13.2013
[5] Walters E. T. 2018. Nociceptive biology of molluscs and arthropods: evolutionary clues about functions and mechanisms potentially related to pain. Frontiers in Physiololgy 9: doi: 10.3389/fphys.2018.01049
[6] Garshelis, D. L. 2006. On the allure of noninvasive genetic sampling-putting a face to the name. Ursus 17: 109-123. doi: 10.2192/1537-6176(2006)17[109:OTAONG]2.0.CO;2

Mammals show a very low level of variation in vertebral count, both among and within species, in comparison to other vertebrates [1]. Jordan’s rule for fishes states that the vertebral number among species increases with latitude, due to ambient temperatures during development [2]. Temperature has also been shown to influence vertebral count within species in fish [3], amphibians [4], and birds [5]. However, in mammals the count appears to be constrained, on the one hand, by a possible relationship between the development of the skeleton and the proliferations of cell lines with associated costs (neural malformations, cancer etc., [6]), and on the other by the cervical origin of the diaphragm [7].
Knight et al. [8] investigate the effect of intrauterine temperature variation on skeletal morphology during development, and focus on a particular mammal, Dasypus novemcinctus, or nine-banded armadillo. Armadillos (Xenarthra) and are characterized by relatively low body temperatures and low basal rates of metabolism. Dasypus novemcinctus is the only xenarthran mammal to have naturally expanded its range into the middle latitudes of the U.S., and one of the few mammals that invaded North America from South America. It is one of few placentals that withstand considerable decrease of body temperature without torpor. It presents a resting body temperature that is low and variable for a placental mammal of its size [9] and is the only vertebrate that gives birth to monozygotic quadruplets. Among 42 monotreme, marsupial and placental genera, Dasypus novemcinctus shows the highest variation of thoracolumbar vertebral count [10].
The particularities of Dasypus novemcinctus regarding vertebral count variation and ability to withstand variable temperature qualify it as a target organism for study of the relationship between skeleton morphology and temperature in mammals.
Knight et al. [8] explored variability in vertebral count within Dasypus novemcinctus to understand whether temperature during development determines skeleton morphology. To this end they experimented with 22 armadillos (19 with data) and litters from 12 pregnant females, in two environments, for three years — an impressive effort and experimental setup. Moreover, they used a wide variety of advanced experimental and analytical techniques. For example, they implanted intra-abdominal, long-term temperature recorders, which recorded data every 6 to 120 minutes for up to several months. They analysed body temperature periodicity by approximation of the recordings with Fourier series, and they CT-scanned fetuses.
All 19 individuals (from which data could be gathered) exhibited substantial daily variation in body temperature. Several intriguing results emerged such as the counter-intuitive finding that the mammals’ body temperature fluctuates more indoors than outdoors. Furthermore, three females (out of 12) were found to have offspring with atypical skeletons, and two of these mothers presented an extremely low internal temperature early in pregnancy. Additionally, genetically identical quadruplets differed skeletally among themselves within two litters.
Results are not yet definitive about the relationship of temperature during development and vertebral count in Dasypus novemcinctus. However, Knight et al. [8] demonstrated that nine-banded armadillos survive with high daily internal temperature fluctuations and successfully bring to term offspring which vary in skeletal morphology among and within genetically identical litters despite major temperature extremes.

References

[1] Hautier L, Weisbecker V, Sánchez-Villagra MR, Goswami A, Asher RJ (2010) Skeletal development in sloths and the evolution of mammalian vertebral patterning. Proceedings of the National Academy of Sciences, 107, 18903–18908. doi: 10.1073/pnas.1010335107
[2] Jordan, D.S. (1892) Relations of temperature to vertebrae among fishes. Proceedings of the United States National Museum, 1891, 107-120. doi: 10.5479/si.00963801.14-845.107
[3] Tibblin P, Berggren H, Nordahl O, Larsson P, Forsman A (2016) Causes and consequences of intra-specific variation in vertebral number. Scientific Reports, 6, 1–12. doi: 10.1038/srep26372
[4] Peabody RB, Brodie ED (1975) Effect of temperature, salinity and photoperiod on the number of trunk vertebrae in Ambystoma maculatum. Copeia, 1975, 741–746. doi: 10.2307/1443326
[5] Lindsey CC, Moodie GEE (1967) The effect of incubation temperature on vertebral count in the chicken. Canadian Journal of Zoology, 45, 891–892. doi: 10.1139/z67-099
[6] Galis F, Dooren TJMV, Feuth JD, Metz JAJ, Witkam A, Ruinard S, Steigenga MJ, Wunaendts LCD (2006) Extreme selection in humans against homeotic transformations of cervical vertebrae. Evolution, 60, 2643–2654. doi: 10.1111/j.0014-3820.2006.tb01896.x
[7] Buchholtz EA, Stepien CC (2009) Anatomical transformation in mammals: developmental origin of aberrant cervical anatomy in tree sloths. Evolution and Development, 11, 69–79. doi: 10.1111/j.1525-142X.2008.00303.x
[8] Knight F, Connor C, Venkataramanan R, Asher RJ. (2020). Body temperatures, life history, and skeletal morphology in the nine-banded armadillo (Dasypus novemcinctus). PCI-Ecology. doi: 10.17863/CAM.50971
[9] McNab BK (1980) Energetics and the limits to a temperate distribution in armadillos. Journal of Mammalogy, 61, 606–627. doi: 10.2307/1380307
[10] Asher RJ, Lin KH, Kardjilov N, Hautier L (2011) Variability and constraint in the mammalian vertebral column. Journal of Evolutionary Biology, 24, 1080–1090. doi: 10.1111/j.1420-9101.2011.02240.x

Across the temporal expanse of history, the impact of human activities on global landscapes has manifested as a complex interplay of ecological alterations. From the advent of early agricultural practices to the successive waves of industrialization characterizing the 18th and 19th centuries, anthropogenic forces have exerted profound and enduring transformations upon Earth's ecosystems. Indeed, by 2017, more than 80% of the terrestrial biosphere was transformed by human populations and land use, and just 19% remains as wildlands (Ellis et al. 2021).
 
Urbanization engenders profound alterations in environmental conditions, exerting substantial impacts on biological communities. The expansion of built infrastructure, modification of land use patterns, and the introduction of impervious surfaces and habitat fragmentation are key facets of urbanization (Faeth et al. 2011). These alterations generate biodiversity loss, changes in the composition of biological communities, disruptions in access and availability of food and nutrients, and a loss of efficiency in the immune system's control of infections, etc. (Reyes et al. 2013).
 
In this study, Caizergues et al. (2023) investigated the prevalence and diversity of avian malaria parasites (Plasmodium/Haemoproteus sp. and Leucocytozoon sp.) in great tits (Parus major) living across an urbanization gradient. The study reveals nuanced patterns of avian malaria prevalence and lineage diversity in great tits across urban and non-urban environments. While overall parasite diversity remains consistent, there are marked differences in prevalence between life stages and habitats. They observed a high prevalence in adult birds (from 95% to 100%), yet lower prevalence in fledglings (from 0% to 38%). Notably, urban nestlings exhibit higher parasite prevalence than their non-urban counterparts, suggesting a potential link between early malaria infection and the urban heat island effect. This finding underscores the importance of considering both spatial and temporal aspects of urbanization in understanding disease dynamics. Parasite lineages were not habitat-specific. The results suggest a potential parasitic burden in more urbanized areas, with a marginal but notable effect of nest-level urbanization on Plasmodium prevalence. This challenges the common perception of lower parasitic prevalence in urban environments and highlights the need for further investigation into the factors influencing parasite prevalence at finer spatial scales.
 
The discussion emphasizes the significance of examining vector distributions, abundance, and diversity in urban areas, which may be influenced by ecological niches and the presence of suitable habitats such as marshes. The identification of habitat-specific Haemosporidian lineages, particularly those occurring more frequently in urban areas, raises intriguing questions about the factors influencing parasite diversity. The presence of rare lineages in urban environments, such as AFR065, DELURB4, and YWT4, suggests a potential connection between urban bird communities and specific parasite strains.
 
Future research should empirically demonstrate these relationships to enhance our understanding of urban parasitology. This finding has broader implications for wildlife epidemiology, especially when introducing or keeping exotic wildlife in contact with native species. The study highlights the importance of considering not only the prevalence but also the specific lineages of parasites in understanding the dynamics of avian malaria in urban and non-urban habitats. This preprint contributes valuable insights to the ongoing discourse on the intricate interplay between ecological repercussions of human-induced changes (urbanization), biological communities, and the prevalence of vector-borne diseases.
 
References

Caizergues AE, Robira B, Perrier C, Jeanneau M, Berthomieu A, Perret S, Gandon S, Charmantier A (2023) Cities as parasitic amplifiers? Malaria prevalence and diversity in great tits along an urbanization gradient. bioRxiv, 2023.05.03.539263, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/2023.05.03.539263

Ellis EC, Gauthier N, Klein Goldewijk K, Bliege Bird R, Boivin N, Díaz S, Fuller DQ, Gill JL, Kaplan JO, Kingston N, Locke H, McMichael CNH, Ranco D, Rick TC, Shaw MR, Stephens L, Svenning JC, Watson JEM. People have shaped most of terrestrial nature for at least 12,000 years. Proc Natl Acad Sci U S A. 2021 Apr 27;118(17):e2023483118. https://doi.org/10.1073/pnas.2023483118. 

Faeth  SH, Bang  C, Saari  S (2011) Urban biodiversity: Patterns and mechanisms. Ann N Y Acad Sci 1223:69–81. https://doi.org/10.1111/j.1749-6632.2010.05925.x

Faeth  SH, Bang  C, Saari  S (2011) Urban biodiversity: Patterns and mechanisms. Ann N Y Acad Sci 1223:69–81. https://doi.org/10.1111/j.1749-6632.2010.05925.x

Reyes  R, Ahn  R, Thurber  K, Burke  TF (2013) Urbanization and Infectious Diseases: General Principles, Historical Perspectives, and Contemporary Challenges. Challenges Infect Dis 123. https://doi.org/10.1007/978-1-4614-4496-1_4

Researchers do not live in a vacuum, and the social context we live in affects how we do science. On one hand, increased competition for scarce funding creates the wrong incentives to do fast analysis, leading sometimes to poorly checked results that accumulate errors (Fraser et al. 2018). On the other hand, the actual challenges the world faces require more than ever robust scientific evidence that can be used to tackle the current rapid human-induced environmental change. Moreover, scientists' credibility is at stake at this moment where the global flow of information can be politically manipulated, and accessing reliable sources of information is paramount for society. At the crossroads of these challenges is scientific reproducibility. Making our results transparent and reproducible ensures that no perverse incentives can compromise our findings, that results can be reliably applied to solve relevant problems, and that we regain societal credibility in the scientific process. Unfortunately, in ecology and evolution, we are still far from publishing open, transparent, and reproducible papers (Maitner et al. 2024). Understanding which factors promote increased use of good practices regarding reproducibility is hence very welcome.

Sanchez-Tojar and colleagues (2025) conducted a (reproducible) analysis of code and data-sharing practices (a cornerstone of scientific reproducibility) in journals with and without explicit policies regarding data and code deposition. The gist is that having policies in place increases data and code sharing. Doing science about how we do science (meta-science) is important to understand which actions drive our behavior as scientists. This paper highlights that in the absence of strong societal or personal incentives to share code and data, clear policies can catalyze this process. However, in my opinion, policies are a needed first step to consolidate a more permanent change in researchers' behavior regarding reproducible science, but policies alone will not be enough to fix the problem if we do not change also the cultural values around how we publish science. Appealing to inner values, and recognizing science needs to be reproducible to ensure potential errors are easily spotted and corrected requires a deep cultural change. 

References

Fraser, Hannah, Tim Parker, Shinichi Nakagawa, Ashley Barnett, and Fiona Fidler. "Questionable research practices in ecology and evolution." PloS one 13, no. 7 (2018): e0200303. https://doi.org/10.1371/journal.pone.0200303

Maitner, Brian, Paul Efren Santos Andrade, Luna Lei, Jamie Kass, Hannah L. Owens, George CG Barbosa, Brad Boyle et al. "Code sharing in ecology and evolution increases citation rates but remains uncommon." Ecology and Evolution 14, no. 8 (2024): e70030. https://doi.org/10.1002/ece3.70030

Alfredo Sánchez-Tójar, Aya Bezine, Marija Purgar, Antica Culina (2025) Code-sharing policies are associated with increased reproducibility potential of ecological findings. EcoEvoRxiv, ver.4 peer-reviewed and recommended by PCI Ecology. https://doi.org/10.32942/X21S7H