step1.md

Theoretical definition of Biological Interactions

The main goal on this step is to collaborative create a robust definition of biological interactions which can handle different cases, like food webs, ecologial networks, microorganism interactions.

Definitions

• United Nations, 1997, page 43:

  • Interaction (between species): positive and negative associations between species that favour or inhibit mutual growth and evolution of populations. It may take the form of competition, predation, parasitism, commensalism or mutualism.

  • Ecological definiton of species interaction.
  • Species-level.
  • Interspecific interactions.
  • Association: population dynamics and evolution of populations (positive and negative impacts on an individual's fitness).
• Nakazawa, 2020:

  • As the second benefit, the simplified view of the ecological community makes ecological research more accessible to, and facilitates collaboration with, other research fields (consolidation). For example, analyses of chemical compounds and stable isotopes have already become a common approach for assessing material flows via "species interactions" (Dyer et al., 2018; Layman et al., 2012). More recently, DNA metabarcoding has been proven to detect the presence of "species interactions” (Evans, Kitson, Lunt, Straw, & Pocock, 2016; Pompanon et al., 2012; Ushio et al., 2015). Theoretical approaches (e.g., mathematics, statistics and computer science) are powerful tools for predicting community dynamics mediated by "species interactions” (King, 2014; May & Mclean, 2007; Petrovskii & Petrovskaya, 2012). In addition, the concept of "species interaction” is currently of great public interest for its applications in ecosystem management for various issues such as agriculture (Tittonell, 2014), climate change (Post, 2013), environmental engineering (Peralta‐Maraver, Reiss, & Robertson, 2018), epidemiology (Johnson, de Roode, & Fenton, 2015), landscape design (Wainwright et al., 2018) and so on. This would be because the concept of "species interaction” provides a mechanical basis of biodiversity maintenance and ecosystem functioning. Ecology has become truly interdisciplinary probably due to the simplified view of ecological community, which would be ultimately due to the concept of "species interaction."

  • The term "species interaction” is apparently intelligible (see above) but its definition is somewhat ambiguous and controversial (vagueness). Specifically, it can often be replaced by other similar terms such as "biotic interaction” and "inter(‐)specific interaction” (Figure 1).

  • In addition, "species interactions” can be quantified using various metrics that reflect different mathematical definitions. According to Berlow et al. (2004), there are at least 15 interaction strength metrics (e.g., interaction matrix, community matrix, nonlinear functional response and relative prey preference). This polysemy has sometimes caused miscommunication even among expert ecologists. These problems can prevent the successful conduct of ecological research.

  • More conceptually, the term "species interaction” is misleading, because interactions occur between individuals but not between species in real nature.

  • More conceptually, the term "species interaction” is misleading, because interactions occur between individuals but not between species in real nature. This contradicts the species‐based concept of "species interaction” that has promoted traditional ecology (see above). In other words, the term can mask and distract our attention from the fact that interactions occur at the individual level. This inconsistency between the species‐based (Figure 2a) and individual‐based views (Figure 2b) can be resolved by the assumption that "all conspecific individuals are effectively interchangeable” (Bolnick et al., 2011), but that is also not true because intraspecific variations are ubiquitous due to factors such as ontogeny, sex and genotype (see reviews cited below). This argument can be applied to a wide range of taxonomic groups (e.g., animals, plants and microbes) and their interactions, except for the case that both species are completely homogeneous in an interaction; even if one side of species is completely homogeneous in an interaction, the other side of species may have individual heterogeneity. Consequently, the term leads us to distort and obscure the true nature of ecological communities mediated by individual heterogeneity (concealment).

  • Notably, individual heterogeneity does matter for community dynamics. As an example of this in action, Bolnick et al. (2011) showed that the consumption rate expected from the species‐averaged attack rate is always higher than the species‐averaged consumption rate expected from attack rates of individual consumers in the case of Holling Type II functional response. This is known as an example of Jensen's inequality. Likewise, Nakazawa, Ushio, and Kondoh (2011) showed that the estimation of predator–prey mass ratio, a key parameter in size‐structured food‐web modeling, can vary substantially depending on whether species‐averaged or individual body masses are used (reviewed by Nakazawa, 2017). This problem arises from the difference between the average of ratios and the ratio of averages. These examples illustrate that community dynamics predicted by species‐averaged parameters can be inaccurate. Indeed, numerous studies have recently shown that individual heterogeneity caused by ontogeny, sex, genotype, plasticity and personality are all crucial for community dynamics (reviewed by de Roos & Persson, 2013; Hairston, Ellner, Geber, Yoshida, & Fox, 2005; Hendry, 2016; Giery & Layman, 2019; Kobayashi, 2019; Miller & Rudolf, 2011; Miner, Sultan, Morgan, Padilla, & Relyea, 2005; Nakazawa, 2015; Raffard, Santoul, Cucherousset, & Blanchet, 2019; Turcotte & Levine, 2016; Werner & Peacor, 2003 Wolf & Weissing, 2012). Nevertheless, most ecologists have not yet fully considered those individual‐based community perspectives in their research, as the mainstream of ecology remains species‐based. Almost all textbooks of ecology introduce the concept of food webs or ecological communities as a network of interactions between homogeneous species (e.g., Begon et al., 2006; Molles Jr & Sher, 2019; Smith & Smith, 2015; Stiling, 2015). Furthermore, internet image searching can easily find thousands of similar topological views of interspecific links, in which individual heterogeneity of interactions is rarely depicted. Hence, the term can reinforce the prejudice that interactions occur between homogeneous species (reification).

  • The main concern on this side of the argument would be how we can reach a practical consensus that interactions occur between individuals, despite the majority of ecologists assuming that "species interactions” are species‐level phenomena in their research (Figure 2a). Intriguingly, this concern is reminiscent of the time when evolutionary biologists were believing that evolution occurs for the good of the species. In the 1930s, only a small part of population genetics researchers casted doubt on this view (Fisher, 1930; Haldane, 1932). A breakthrough was made in the 1960s, when some evolutionary biologists claimed that natural selection acts on individuals or genes (e.g., Maynard Smith, 1964; Williams, 1966), and when Hamilton (1964) formulated inclusive fitness theory. Their views were thereafter established and incorporated into modern evolutionary theory. As a consequence, the primary unit of selection was changed from species to individuals (or genes) in evolutionary biology (Brandon & Burian, 1984; Sober & Wilson, 1994). Ecology may require a similar paradigm shift in the unit of interaction from species to individuals, since interactions between organisms occur at the individual level (Figure 2b). This scenario, if it takes place, can mitigate the demerits of concealment and reification (see above).

Figures

Figure 1 Nakazawa, 2020

Number of publications including the term "species interaction” and other similar terms throughout the years. Web of Science was used (April 2020) to search for Research articles including those words in Topic and published between 1970 and 2019 in the field of Ecology. Both singular and plural forms were counted. Different line colors indicate different terms: species interaction (red), biotic interaction (blue), ecological interaction (green), inter(‐)specific interaction (orange), biological interaction (light blue) and community interaction (light green). The most frequently used term is "species interaction.” The relative frequency of "biotic interaction” is rapidly increasing since the late 2000s probably due to growing interest in environmental sciences

Figure 2 Nakazawa, 2020

*Species‐based and individual‐based views of "species interaction.” (a) The species interaction is a species‐level phenomenon in which species are assumed to consist of identical individuals with invariant traits. The unit of interaction is species under the assumption of species homogeneity. (b) The species interaction is a set of individual‐level phenomena in which intraspecific trait variation (individual heterogeneity) mediates interactions between heterospecific individuals. Solid and dashed lines indicate that interaction strength varies between individual pairs. In both panels, large and small circles indicate species and individual identities, respectively

References

Nakazawa, T. Species interaction: Revisiting its terminology and concept. Ecological Research. 2020; 35: 1106– 1113. [doi.org/10.1111/1440-1703.12164](https://doi.org/10.1111/1440-1703.12164)

United Nations, Glossary of Environment Statistics, Studies in Methods, Series F, No. 67, United Nations, New York, 1997.Url: [unstats.un.org/unsd/environmentgl/](https://unstats.un.org/unsd/environmentgl/)