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The figures represent a host (bat) plus the set of microbial taxa it interacts with. (A) Represents each taxa, and assumes that the individuality of the holobiont consists in the collection of organisms, including the host and the bacterial taxa that reside on its microbiome (represented by a dashed blue circle). (B) Represents our emergentist account, according to which the holobiont is the entity composed by the host plus the etiological adaptations that allowed the evolution of sanguivory that are borne by the taxa that compose its microbiome (the adaptive traits are represented by the red circles, and the boundaries of the emergent holobiont are represented by the dashed red circle). These adaptive traits that belong to the emergent holobiont (despite being borne by the bacterial taxa) include the set of genetic components that Mendoza et al. (2018) proved to have been selected to cope with the challenges of sanguivory.
Source publication
Contemporary biological research has suggested that some host–microbiome multispecies systems (referred to as “holobionts”) can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the mu...
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... The holobiont functional traits resulting from the assembly of microbiota and host can encompass various aspects, all of which contribute to the holobiont's adaptation in a changing environment [28,29]. Microbiota associated with the host can facilitate nutrient uptake and metabolism, including the acquisition of essential nutrients from the environment and the breakdown of complex organic compounds [30]. ...
Forests have a key role in mitigating both non-biological and biological ecological disturbances. However, major disturbances (soil pollution, shift from native forest species to exoticones, forested watersheds and climate changes) can have different impacts on a forest’s soil microbiome. Because the soil microbial community of forests has a key role in a variety of ecosystem services that promote the forest’s health, this review tries to answer the following questions: (i) Which are the main ecological disturbances that drive the responses of the forest soil microbiome? (ii) How can we measure these changes? For this aim, the review summarizes details on the tree vegetation type, the microbial communities in forest ecosystems, and the mutual influence between plants, soil, and microbiomes. Microbial communities are shaped by factors such as soil type and composition, plant and vegetation types, nutrient levels and soil fertility, disturbance patterns, symbiotic associations, biotic interactions, and the progression of forest succession. Anthropogenic activities produce a rapid response in the microbial communities, leading to both short- and long-term alterations. Harvesting processes reduce drastically the microbiome diversity, forcing a shift from specialized to more generalist microorganisms. Restoration scenarios indicate a re-establishment of microbial communities to a level similar to the native forest, but with a high percentage of replaced native microorganisms. This review emphasizes that the forest soil microbiome is shaped by a range of environmental, ecological, and biotic factors. The primary drivers of the soil microbiome in forest ecosystems discussed in this review include soil composition and nutrient availability, plant community structure, microbial interactions within the soil, disturbances, succession, and temporal dynamics. When considered together, these factors interact in complex ways, influencing the diversity, function, and resilience of the soil microbiome in forest ecosystems.
... Concretamente, la simbiosis se ha usado como "cabeza de turco" para repensar problemas que se creían "resueltos". Estos incluyen el problema de la individualidad biológica (Booth, 2014a;Pradeu, 2016;Suárez, 2020), problemas en torno a la aplicación excesiva del programa adaptacionista (Lloyd & Wade, 2019), o problemas en torno al nivel en que sucede la selección natural o en que ocurre la adaptación (Suárez & Triviño, 2020). ...
Muchos conceptos en ecología y evolución se han construido en base a observaciones zoológicas y, en menor medida, botánicas, mientras que una visión fúngica en estas áreas es prácticamente inexistente. Mucho menos se han indagado aspectos de la filo-sofía de la biología en base a los hongos. Sin embargo, en este artículo mostramos que dadas sus características particulares, el reino Fungi constituye un sistema de estudio ideal para examinar teórica y empíricamente diferentes aspectos de la filosofía de la biología. Los hongos presentan características de las plantas (como su carácter sésil) y de los animales (como su carácter heterotrófo), pero tienen una plétora de atributos particulares que requieren su propia filosofía, una filosofía Fungi. En esta revisión se aborda cómo entender la individualidad y las unidades de selección natural en los hon-gos, los diferentes conceptos de adaptación (y sesgos adaptacionistas) en su estudio, y cómo entender los hongos como agentes que construyen su nicho. Estas temáticas se abordan de forma introductoria, presentando las definiciones de estos diferentes con-ceptos, y cómo los mismos pueden aplicarse en la micología. Se hace una invitación a profundizar en cada tema y, sobre todo, a incentivar un diálogo entre micólogos y filósofos de la biología.
... Concretamente, la simbiosis se ha usado como "cabeza de turco" para repensar problemas que se creían "resueltos". Estos incluyen el problema de la individualidad biológica (Booth, 2014a;Pradeu, 2016;Suárez, 2020), problemas en torno a la aplicación excesiva del programa adaptacionista (Lloyd & Wade, 2019), o problemas en torno al nivel en que sucede la selección natural o en que ocurre la adaptación (Suárez & Triviño, 2020 En lo que sigue, revisamos el modo en que el estudio de los hongos y la filosofía actual de la biología se pueden nutrir mutuamente. Para ello, revisamos el modo en que algunos debates en ambos campos se iluminan mutuamente. ...
... Cuando esto ocurre, se pueden generar dos situaciones: o bien un secuestro reproductivo del simbionte y una transferencia del fitness de los componentes al nivel jerárquico superior; o bien una situación intermedia en que solo algunos caracteres de los simbiontes estarían alineados con el nivel superior. Esta última situación generaría la evolución del conjunto mediante el mecanismo de "estabilidad de rasgos" (Suárez, 2020(Suárez, , 2021) el cual podría incluso llevar a la evolución de una organización funcional adaptativa a nivel superior ("adaptación hologenómica"; Suárez & Triviño, 2020), si las circunstancias ecológicas son las correctas. En esta línea, algunos autores (Johnson & Marín, 2023) proponen que el microbioma presente en las hifas de los HMA (la hifósfera), que es el que de hecho mineraliza nutrientes fundamentales en esta simbiosis, como el fósforo (Wang et al., 2023;Zhang et al., 2024), sean a su vez considerados como extensiones o parte de las hifas, pues como Zhang et al. (2024, p. 1) concluyen: los HMA "no funcionan de forma aislada [a las bacterias de la hifósfera] y el simbionte planta-micorriza puede reclutar bacterias beneficiosas que apoyan la simbiosis". ...
Muchos conceptos en ecología y evolución se han construido en base a observaciones zoológicas y, en menor medida, botánicas, mientras que una visión fúngica en estas áreas es prácticamente inexistente. Mucho menos se han indagado aspectos de la filosofía de la biología en base a los hongos. Sin embargo, en este artículo mostramos que dadas sus características particulares, el Reino Fungi constituye un sistema de estudio ideal para examinar teórica y empíricamente diferentes aspectos de la filosofía de la biología. Los hongos presentan características de las plantas (como su carácter sésil) y de los animales (como su carácter heterotrófo), pero tienen una plétora de atributos particulares que requieren su propia filosofía, una filosofía Fungi. En esta revisión se aborda cómo entender la individualidad y las unidades de selección natural en los hongos, los diferentes conceptos de adaptación (y sesgos adaptacionistas) en su estudio, y cómo entender los hongos como agentes que construyen su nicho. Estas temáticas se abordan de forma introductoria, presentando las definiciones de estos diferentes conceptos, y cómo los mismos pueden aplicarse en la micología. Se hace una invitación a profundizar en cada tema y, sobre todo, a incentivar un diálogo entre micólogos y filósofos de la biología.
... Furthermore, the concept of interorganismal character does not need to be restricted to reproduction. Interorganismal characters can be found in other domains of life and also in phenomena unrelated to reproduction, such symbiotic assemblies (Chiu and Gilbert 2020;Suárez and Triviño 2020). Hence, although in this article we focus on interorganismal traits in sexually reproducing animals, they can be seen as an instantiation of a more general category encompassing different kinds of interorganismal characters. ...
This paper delves into the character concept as applied to reproduction. Our argument is that the prevailing functional-adaptationist perspective falls short in explaining the evolution of reproductive traits, and we propose an alternative organismal-relational approach that incorporates the developmental and interactive aspects of reproduction. To begin, we define the functional individuation of reproductive traits as evolutionary strategies aimed at enhancing fitness, and we demonstrate how this perspective influences the classification of reproductive characters and modes, the comprehension of shared traits as resulting from conflicts of evolutionary interest between individuals, and the explanation of reproductive diversity. After outlining the shortcomings of this framework, we introduce an organismal-relational approach grounded in evolutionary developmental studies of reproduction. This view provides a revised classification for reproductive characters and modes and offers a new understanding of interorganismal traits that takes into account their inherently relational nature. Lastly, we present the research agenda that emerges from this approach, which addresses the core explanatory gaps left by the adaptationist perspective, including the explanation of reproductive homologies and homoplasies, the developmental constraints associated with the evolution of reproductive modes, and the evolvability of reproductive characters.
... Although the metaphysical notion of emergence is highly controversial (Kim 2006), it has been widely recognized in different disciplines (Goldstein 1999;Witherington 2011). In philosophy of biology, the notion of emergence is widely used to characterize some biological features, such as the features of biochemical networks (Boogerd et al. 2005), the amount of nectar stored in a hive (Mitchell 2012), or holobionts (Suárez and Triviño 2020). The recourse to the notion of emergence in the particular case of fitness, therefore, can serve to shed light on its ontological status. ...
In this paper, I aim to explore whether fitness, understood as a causal disposition, can be characterized as an emergent property of organisms, or if it is reducible to the anatomical, physiological, and environmentally relative properties that characterize them. In doing so, I refer to Jessica Wilson’s characterization of ontological emergence and examine if fitness meets her criteria for ontological emergent properties (dependence and autonomy); and, if so, to what degree (weak or strong).
... This paper alleviates these tensions by relying on the tools provided by philosophical theorizing. Particularly, I follow the recent way of doing philosophy of biology called "metaphysics in biology," a branch of metaphysics of biology (Guay and Pradeu 2017) which consists in analysing scientific practices (phenomena or theories) to uncover the metaphysical assumptions and commitments underlying them (Triviño 2022; for some previous applications, see Reydon 2008;Waters 2017;Triviño and Suárez 2020;Suárez and Stencel 2020). 3 Drawing on this method, I offer a dispositional view of stemness and stem cells. ...
... The way in which topological explanations work immediately suggest some ways of thinking of potential interventions on these systems. In the case of systems realizing a topological structure, interventions are systematically conceived in terms of the network or emergent properties of the system, as these would condition its dynamics and therefore the final outcomes (Wilson 2016;Huneman 2018;Suárez and Triviño 2020;Green 2021). Empirically intervening on these properties requires knowledge of the specific population or system properties that induce the dynamics, as well as how these could be modified to avoid the dynamics or its outcome. ...
This paper presents an account of the nature of stem cells based on the philosophical concept of disposition. It is argued that stem cells can be conceived as dispositional objects, and adopting this attitude allows overcoming some of the controversies surrounding the nature of stemness (most notably, the state vs. entity debate) because it offers a framework that accommodates the lessons from different theories. Additionally, the account is simultaneously useful for interpreting stem cell experiments and guiding potential interventions. The account shows how different levels, both molecular and emergent network-level, play the primary causal role in explaining some empirical results, and hence they suggest that the explanations can be mechanistic or topological, respectively. The realization that any of these levels may play a more prominent causal role than another allows suggesting interventions at the genetic, molecular and population levels.
... The fundamental difference between symbiogenesis and the use of the term symbiosis in ecology is that while the latter is a relation between separate individuals, often understood in game theoretical terms, in the former a partnership is established at the organizational level, which alters both the topological configuration and the functional dimension of the new system, from which arises an entangled inter-being between the two parties that are associated. The distinction between the strongest cases (i.e., endosymbiosis) and the weakest (i.e., temporal association) is not sharp, as nicely shown by Javier Suárez and Vanesa Triviño, who argue that cases of symbiosis apart from endosymbiosis, such as holobionts, also entail a fundamental reorganization of the interacting individuals to the point of altering their individuality and identity (Suárez & Triviño, 2020). ...
We examine some implications of Kropotkin’s seminal work on mutual aid as a factor of evolution to analyze how non-competitive life relations are understood in current biological theories. We distinguish two research lines deriving from his work: one of them studies intraspecific relations of altruism and selfishness, and the other one is focused on interspecific symbiotic relations. Furthermore, we use the example of pregnancy and viviparity to extend the analysis to the evolution of novel interorganismic characters. We conclude with a conceptual review of how collaborations and inter-dependencies among organisms shape individual autonomy and sociability in organismal evolutionary biology.
... In doing so, the biological concept itself is clarified. The characterization of fitness by means of the dispositional theory of causation (Triviño and Nuño de la Rosa 2016), or that of holobionts using of the metaphysical notion of emergence (Suárez and Triviño 2020) are some examples of this interaction. ...
The debate in Metaphysics of Science concerning the interaction between metaphysics and science has been mainly approached from the perspective of the scientificdiscipline of physics. In this paper, I address this debate from a different framework, namely that of biology. I pay attention to the recent characterization of Metaphysics of Biology and the different forms in which philosophers use metaphysics when addressing conceptual biological problems. In doing so, I argue that two main lessons can be obtained that can serve to enrich the debate in Metaphysics of Science: i) that the interaction between metaphysics and science seems to be more complex than generally considered; and ii) that the type of metaphysics that is interacting with science when characterizing the ontological status of the world is neither the a priori nor the naturalized one, but a different form of metaphysics that will be labelled here as applied metaphysics.
... According to Suarez and Triviño's proposal, holobionts manifest some properties that meet the criteria for being emergent, namely dependence and autonomy. Suárez and Triviño (2020) use the property of having a sanguivory diet (present in vampire bats (Desmodus rotundus)) as an example of emergent property, but there are others (see Doolittle & Booth, 2017). ...
Since the last decades of the twentieth and the beginning of the twenty-first century, the use of metaphysics by philosophers when approaching conceptual problems in biology has increased. Some philosophers call this tendency in philosophy of biology ‘Metaphysics of Biology’ (Guay and Pradeu in Synthese 1–20, 2017). In this paper, I aim at characterizing Metaphysics of Biology by paying attention to the diverse ways philosophers use metaphysics when addressing conceptual problems in biology. I will claim that there are two different modes of doing Metaphysics of Biology, namely Metaphysics for Biology and Metaphysics in Biology.
... This suggests a convergent evolution that has generated complementarity such that several phenotypic effects on cicadas may result from the joint action of these three endosymbionts. A theoretical example comes from Huitzil et al.'s (2018) modeling of holobiont evolution in terms of genetic networks, which could be used to interpret the evolution of sanguivory in bats (Suárez & Triviño, 2020). In the Huitzil et al. (2018) model, genetic regulation is not transmitted: instead, it is recreated in every new generation. ...
... In this case, the epistatic effects between the host and the microbes would increase the frequency of transgenerational recurrence of host and microbial association, which would guarantee the transgenerational production of trait variants at the holobiont level. This is the case in squid-Vibrio symbiosis, but also in other symbioses in which the host/microbe serve as genetic environments for each other (Drown & Wade, 2014;Drown et al., 2013) (2) specific joint effects that will tend to drive the host-microbiome system towards specific points of equilibria where the phenotypic effects will be channelled and maintained despite perturbations (Suárez, 2020;Suárez & Triviño, 2020). An example would be the case of vampire bats, in which the host environment creates the conditions in which genetic amplification of specific variants, triggered by selection between microorganisms within the microbiome, and horizontal gene transfer generate a microbiome that is apt to cope with the challenges of sanguivory that the bat genome cannot cope with without its microbiome (Zepeda Mendoza et al., 2018). ...
... Several explanatory avenues can be opened: the phenotype may reappear because a functionally equivalent small RNA state can be reconstituted in the next generation (Veigl, 2017). Or, in the holobiont case, it may reappear because the traits are hologenomic adaptations, and thus they are motile, engaged in abundant horizontal gene transfer within the microbiome, and functionally redundant (Suárez & Triviño, 2020;Suárez, 2020). Presupposing SOL instead of SOT limits the possible research avenues and phenomena amenable for scientific investigation. ...
This paper introduces the reconstitutor as a comprehensive unit of heredity within the context of evolutionary research. A reconstitutor is the structure resulting from a set of relationships between different elements or processes that are actively involved in the recreation of a specific phenotypic variant in each generation regardless of the biomolecular basis of the elements or whether they stand in a continuous line of ancestry. Firstly, we justify the necessity of introducing the reconstitutor by showing the limitations of other evolutionary conceptions of the unit of heredity, such as the replicator, the reproducer, and the Darwinian individual. We argue that these conceptions are based on the requirement of lineage formation (Stability of Lineages), which we argue to be unnecessary for the existence of evolutionary heredity. In the second part, we introduce the reconstitutor, which we base on the concept of Stability of Traits, and illustrate how it covers cases of hereditary phenomena (small RNAs, microbiota) not covered by the previous accounts. Secondly, we illustrate how the reconstitutor could serve as a platform to rethink ecological inheritance and other forms of inheritance that have been recently introduced under the song/singer model of evolution.
