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\begin{document}

\title{Opportunities to advance the synthesis of ecology and evolution}



\author[1]{Michel Loreau}%
\author[2]{Philippe Jarne}%
\author[3]{Jennifer Martiny}%
\affil[1]{Centre National de la Recherche Scientifique}%
\affil[2]{CEFE}%
\affil[3]{University of California Irvine}%


\vspace{-1em}



  
  \date{May 19, 2024}


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\selectlanguage{english}
\begin{abstract}
Despite growing interactions between ecology and evolution, there still
remain opportunities to further integrate the two disciplines,
especially when considering multispecies systems. Here, we discuss two
such opportunities. First, we suggest to relax the focus on the
distinction between evolutionary and ecological processes. This focus is
particularly unhelpful in the study of microbial communities, where the
very notion of species is hard to define. Second, we propose that key
processes of evolutionary theory such as adaptation should be exported
to hierarchical levels higher than populations to make sense of
biodiversity dynamics. Together, we argue that broadening our
perspective of eco-evolutionary dynamics to be more inclusive of all
biodiversity, both phylogenetically and hierarchically, will open up
fertile new research directions and help us to address one the major
scientific challenges of our time, i.e. to understand and predict
changes in biodiversity in the face of rapid environmental change.%
\end{abstract}%



\sloppy


\section*{Opportunities to advance the synthesis of ecology and
evolution}

{\label{opportunities-to-advance-the-synthesis-of-ecology-and-evolution}}

\textbf{Michel Loreau\textsuperscript{1}, Philippe
Jarne\textsuperscript{2} \& Jennifer B. H. Martiny\textsuperscript{3}}

\textsuperscript{1}Theoretical and Experimental Ecology Station, CNRS, 2
route du CNRS, 09200 Moulis, France. Email: michel.loreau@gmail.com
(author for correspondence)

\textsuperscript{2}CEFE, UMR 5175, CNRS - Universit\selectlanguage{ngerman}é de Montpellier \selectlanguage{english}-
Universite Paul-Valery Montpellier \selectlanguage{english}- IRD \selectlanguage{english}- EPHE, 1919 route de Mende,
34293 Montpellier Cedex 5, France. Email: philippe.jarne@cefe.cnrs.fr

\textsuperscript{3}Department of Ecology and Evolutionary Biology,
University of California, Irvine, CA 92697, USA. Email: jmartiny@uci.edu

\textbf{Type of article:} \emph{Viewpoint} in the special issue
``Exploring the border between ecology and evolution''

\textbf{Statement of authorship:} ML wrote the first draft of the
manuscript, and all authors contributed substantially to revisions.

\textbf{Keywords:} Ecology, Evolution, Synthesis, Concepts,
Eco-evolutionary dynamics, Rapid environmental change, Adaptation,
Levels of biological organisation, Abrupt ecological change, Microbes

\textbf{Number of words in the main text:} 2,043

\textbf{Abstract}

Despite growing interactions between ecology and evolution, there still
remain opportunities to further integrate the two disciplines,
especially when considering multispecies systems. Here, we discuss two
such opportunities. First, we suggest to relax the focus on the
distinction between evolutionary and ecological processes. This focus is
particularly unhelpful in the study of microbial communities, where the
very notion of species is hard to define. Second, we propose that key
processes of evolutionary theory such as adaptation should be exported
to hierarchical levels higher than populations to make sense of
biodiversity dynamics. Together, we argue that broadening our
perspective of eco-evolutionary dynamics to be more inclusive of all
biodiversity, both phylogenetically and hierarchically, will open up
fertile new research directions and help us to address one the major
scientific challenges of our time, i.e. to understand and predict
changes in biodiversity in the face of rapid environmental change.

Although Darwin, the father of modern evolutionary biology, had a strong
interest in ecological issues, ecology and evolution developed
historically as separate scientific disciplines, each with its own set
of concepts, methods and study objects (Futuyma 1986). While ecology is
broadly concerned with the interactions between living organisms and
their biotic and abiotic environment, evolutionary biology focuses on
changes in the intrinsic characteristics, or traits, of these organisms
through time under changing environments. As a result of this focus,
evolutionary biology built a coherent body of theory that gave rise to
the so-called ``modern synthesis''. This synthesis integrated knowledge
from genetics, palaeontology, systematics and morphology, but ecology
played a relatively small role, even though the influence of ecological
processes on evolution was recognised (Huneman 2019). By contrast,
ecology developed a wide range of perspectives, from the dynamics of a
single population to the functioning of the entire biosphere, but it is
arguably still searching for a general synthesis that includes
evolutionary thinking at all scales (Loreau 2010).

A number of attempts have been made to bring ecology and evolution
together over the past 70 years (e.g. Pimentel 1961; Antonovics 1976).
In particular, the recent emergence of the field of eco-evolutionary
dynamics has greatly contributed to this effort by revealing how ecology
affects evolution and, conversely, how evolution affects ecology
(Fussmann \emph{et al.} 2007; Schoener 2011; Hendry 2017;
Govaert\emph{et al.} 2019). We now know that emergent properties of
communities and ecosystems, such as material cycling, functional
complementarity between species and community stability, have the
potential to affect evolutionary processes, just as evolution can affect
ecosystem functioning (Loreau 2010; Borrelli \emph{et al.} 2015;
Calcagno \emph{et al.} 2017; Aubree \emph{et al.} 2020). Other advances
that strengthen the links between ecology and evolution include
consideration of concepts that could be relevant across the hierarchy of
life from genes to ecosystems, such as heritability above the individual
level (Shuster\emph{et al.} 2006) and the role of trait-based
intraspecific variability in community dynamics (Violle \emph{et al.}
2012). Despite growing recognition of the interactions between
ecological and evolutionary processes, however, there still remain
opportunities to further integrate ecology and evolution, especially
when considering multispecies ecological systems.

Here, we discuss two such opportunities. First, we suggest to relax the
focus on the distinction between evolutionary and ecological processes.
This focus is particularly unhelpful in the study of microbial
communities, where the very notion of species is much harder to define
than for macroorganisms. Second, we propose that key processes of
evolutionary theory such as adaptation should be exported to
hierarchical levels higher than populations to make sense of
biodiversity dynamics. Together, broadening our perspective of
eco-evolutionary dynamics to be more inclusive of all biodiversity, both
phylogenetically and hierarchically, will open up fertile new research
directions.

Microbes constitute a large part of the Earth's biodiversity, displaying
enormous abundance, phylogenetic diversity and functional importance
(Whitman \emph{et al.} 1998; Falkowski \emph{et al.} 2008). One
important aspect of their biology is that within-species evolutionary
processes cannot be neatly separated from between-species ecological
processes. While this distinction may generally make sense for large,
complex, sexually reproducing multicellular eukaryotes, they are far
less relevant for bacteria, archaea and other microbes, where asexual
reproduction and gene transfer are widespread (Doolittle 1999). Although
asexual reproduction and gene transfer do not preclude a taxonomic
classification of microbes as their traits are phylogenetically
conserved in a hierarchical fashion (Martiny \emph{et al.} 2015), the
species level in this hierarchy is ill-defined and differs from that
used for most macroorganisms (Rossello-Mora \& Amann 2001;
Fraser\emph{et al.} 2009). Therefore, there is no fundamental difference
between changes in the abundance of different microbial ``species''
through time --- the traditional focus of community ecology --- and
changes in the relative frequency of different microbial ``genotypes''
--- the traditional focus of evolutionary biology. Indeed, some classic
examples of eco-evolutionary dynamics, such as Yoshida et al.'s (2003)
predator\selectlanguage{english}-prey cycles driven by the ``rapid evolution'' of clonal algae,
could be easily reinterpreted as simple ecological dynamics in which the
abundance of different algal ``species'' changes. A similar issue arises
in clonal multicellular organisms (e.g. parthenogenetic freshwater
snails: Facon \emph{et al.} 2008). Changes in species abundances and
changes in phenotype frequencies generate the same type of effect, i.e.
changes in mean trait values. Whether these changes in mean trait values
take place at the population or community level is largely irrelevant in
the case of microbes, as the two hierarchical levels cannot be
distinguished unambiguously. Note that this also challenges the
distinction between intra- and interspecific competition, which is
widely regarded as a key factor explaining the maintenance of
biodiversity (Chesson 2000).

Many studies have considered microbial evolution in the laboratory,
where particular strains can be examined for new mutations and their
effects on fitness (Lenski 2017). Under natural conditions in diverse
communities, however, it is much more difficult to define what a
microbial species is, and almost impossible to distinguish between
standing genetic variation and new mutations. Recent advances in
sequencing have revealed that natural microbial communities are not
unstructured swarms of genotypes, but rather assemblages of coexisting,
genetically distinct lineages (Arevalo \emph{et al.} 2019; Chase\emph{et
al.} 2019). Further, the genetic differences between such lineages yield
hypotheses about the ecological distinctions between them (Arevalo
\emph{et al.} 2019). It is even possible now to detect evolution of
free-living microbes in the wild. For instance, a strain
of\emph{Curtobacterium} , dominant in the surface soil, was inoculated
into microbial ``cages'' and transplanted into five sites across a
temperature and precipitation gradient (Chase \emph{et al.} 2021). After
just six months in the field, the strain accumulated genomic mutations,
and some mutations occurred in parallel across sites, indicating that
some mutations were likely adaptive to the new conditions. Together,
these advances reveal a previously unknown structure of fine-scale
diversity in microbial communities, while clarifying the absence of a
distinct species boundary, which makes it difficult to apply classic
evolutionary principles.

To overcome this difficulty, we suggest that more attention should be
paid in both ecology and evolution to the general fact that evolutionary
and ecological dynamics can have similar effects, to the point of being
sometimes indistinguishable in microbes. This could contribute to the
development of a more integrative conceptual framework that crosses the
traditional disciplinary boundaries. Microbes invite us to rethink what
ecology is and what evolution is (see also West \emph{et al.} 2006), and
we feel this invitation should be seen as a great opportunity rather
than a problem.

The second aspect we wish to highlight is that, to achieve greater
integration of ecology and evolution, many concepts used in either
discipline could be profitably generalised to the other --- they would
serve as `boundary objects' (Star \& Griesemer 1989) in their conceptual
unification. Nosil et al. (2021) provided an example when applying the
concepts of stability and resilience, imported from ecology, to
evolutionary biology. Here we propose to go in the other direction by
extending the concept of adaptation from evolution to ecology. In
evolutionary biology, `adaptation' \emph{sensu stricto} is generally
considered as a process leading to higher fitness as a result of natural
selection (Williams 1966; Gardner 2017), while `adaptedness' denotes the
state of being adapted, but the distinction is not always so clear
(Lewens 2016). Moreover, adaptation is traditionally assumed to take
place at the individual or genotype level. Even such a strong proponent
of individual-level selection as Williams (1966), however, distinguished
between `organic adaptations' and `biotic adaptations', which help
perpetuate a group or population and open up the possibility of clade
selection, a very controversial issue (Eldakar \& Wilson 2011; Goodnight
2015; West \emph{et al.} 2021).

It would be particularly useful to extend and generalise the concept of
adaptation to wider ecological contexts. For example, soil microbial
ecologists use this concept at the community level to describe an
increase in overall microbial activity as temperature changes, an
approach that integrates across the mechanisms and timescales involved
(Bradford 2013; Nottingham \emph{et al.} 2021). This extension of the
adaptation concept is fully consistent with that formally proposed by
hierarchical adaptability theory (Conrad 1983; Lekevi\selectlanguage{polish}č\selectlanguage{english}ius \& Loreau
2012). Hierarchical adaptability theory generalises adaptation to any
process that results in improved performance in response to
environmental change in a multilevel hierarchical perspective, from
molecules to ecosystems. These responses range from differential gene
activity (molecular-level mechanism), through phenotypic plasticity
(individual-level mechanism) and differential reproduction of genotypes
(population-level mechanism), to changes in species abundance
(community- or ecosystem-level mechanism). This theory could be further
extended to include the evolutionary, ecological, and social changes
that reduce the vulnerability of social and ecological systems to
environmental change (Moore \& Schindler 2022).

These extensions, of course, raise the question of how to measure
performance below or above the hierarchical level of the individual
organism. In evolutionary theory, performance is encapsulated in the
concept of fitness, which is traditionally defined at the individual or
genotype level, although theory has long been proposed to apply it to
higher levels of organisation (Wilson 1980; Swenson \emph{et al.} 2000;
West \emph{et al.} 2006; Goodnight 2015). Defining and measuring fitness
is associated with several, though not insurmountable, difficulties.
First, fitness should be defined fitness as a propensity, not a realised
property, if it is to have any explanatory power (Mills \& Beatty 1979;
Orr 2009), a criterion that should apply to any performance indicator at
any biological level. Second, many ecosystem processes, such as resource
uptake, primary production, secondary production and material cycling
efficiency, are closely linked (Loreau 2010), so that different measures
of ecosystem performance may often provide broadly consistent results
when assessing the response of an ecosystem to abrupt environmental
changes. Third, current environmental changes are likely to shed new
empirical light on this issue in the near future by pushing ecosystems
beyond critical thresholds, leading to major, readily observable changes
in ecosystem structure and functioning. Interestingly, recent ecological
theory predicts that simple competitive communities with high variance
in species interaction strength produce coalitions of strong and weak
interactors that behave somewhat like superorganisms along environmental
gradients, with abrupt species turnover and sharp boundaries between
communities, despite the absence of strong functional integration
(Liautaud \emph{et al.} 2019). Furthermore, these communities can
exhibit directional dynamics in time, i.e., they are characterised by a
maturity function that systematically increases over time, as well as
community-level selection in space, i.e. they expand across space by
replacing other communities with copies of themselves (Bunin 2021).
Thus, we may soon have access to performance measures that will allow us
to rigorously define adaptation at the community and ecosystem levels in
changing environments.

Successful integration of ecology and evolution is likely to require a
great deal of theoretical and empirical effort to examine how the
various ecological and evolutionary processes operate, interact and
combine at multiple scales of time, space and biological levels. But
this effort is well worth it, as it would bring enormous benefits. In
particular, it would help us to address one the major scientific
challenges of our time, i.e. to understand and predict changes in
biodiversity in the face of rapid environmental change. The ongoing
anthropogenic environmental changes are so widespread, rapid and
profound that the historically inherited distinction between ecology and
evolution might soon become an obstacle to our understanding of the many
consequences of these changes. To meet this challenge, ecology and
evolution should join forces and build a broader synthesis adapted to
our time.

\textbf{Acknowledgements}

We thank Andrew Hendry, Philippe Huneman and two anonymous referees for
their critical but stimulating comments and discussions. ML was
supported by the TULIP Laboratory of Excellence (ANR-10-LABX-41), PJ by
the CNRS Institute for Ecology and Environment, and JM by the U.S.
Department of Energy, Office of Biological and Environmental Research
(DE-SC0020382).

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