Guilhem Doulcier's research while affiliated with Macquarie University and other places
What is this page?
This page lists the scientific contributions of an author, who either does not have a ResearchGate profile, or has not yet added these contributions to their profile.
It was automatically created by ResearchGate to create a record of this author's body of work. We create such pages to advance our goal of creating and maintaining the most comprehensive scientific repository possible. In doing so, we process publicly available (personal) data relating to the author as a member of the scientific community.
If you're a ResearchGate member, you can follow this page to keep up with this author's work.
If you are this author, and you don't want us to display this page anymore, please let us know.
It was automatically created by ResearchGate to create a record of this author's body of work. We create such pages to advance our goal of creating and maintaining the most comprehensive scientific repository possible. In doing so, we process publicly available (personal) data relating to the author as a member of the scientific community.
If you're a ResearchGate member, you can follow this page to keep up with this author's work.
If you are this author, and you don't want us to display this page anymore, please let us know.
Publications (29)
The relationship between the number of cells colonizing a new environment and time for resumption of growth is a subject of long-standing interest. In microbiology this is known as the ‘inoculum effect’. Its mechanistic basis is unclear with possible explanations ranging from the independent actions of individual cells, to collective actions of pop...
Evolutionary transitions in individuality (ETIs) involve the formation of Darwinian collectives from Darwinian particles. The transition from cells to multicellular life is a prime example. During an ETI, collectives become units of selection in their own right. However, the underlying processes are poorly understood. One observation used to identi...
The relationship between the number of cells colonizing a new environment and time for resumption of growth is a subject of long-standing interest. In microbiology this is known as the "inoculum effect". Its mechanistic basis is unclear with possible explanations ranging from the independent actions of individual cells, to collective actions of pop...
Evolutionary transitions in individuality (ETIs) involve the formation of Darwinian collectives from Darwinian particles. The transition from cells to multicellular life is a prime example. During an ETI, collectives become units of selection in their own right. However, the underlying processes are poorly understood. One observation used to identi...
Fitness is a central but notoriously vexing concept in evolutionary biology. The propensity interpretation of fitness is often regarded as the least problematic account for fitness. It ties an individual's fitness to a probabilistic capacity to produce offspring. Fitness has a clear causal role in evolutionary dynamics under this account. Neverthel...
Reproductive division of labor has been proposed to play a key role for evolutionary transitions in individuality (ETIs). This chapter provides a guide to a theoretical model that addresses the role of a tradeoff between life-history traits in selecting for a reproductive division of labor during the transition from unicellular to multicellular org...
Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities....
Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities....
Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities....
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were...
Life has a nested structure where lower level entities are embedded in higher level collectives (genes in chromosomes, organelles in cells, cells in organisms, organisms in eusocial groups). All levels are subject to evolution by natural selection. This arises from the fact that at each level the focal entities are Darwinian, that is, they are disc...
Chance interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on commun...
We have little information on how and why soil microbial community assembly will respond to predicted increases in aridity by the end of this century. Here, we used correlation networks and structural equation modeling to assess the changes in the abundance of the ecological clusters including potential winner and loser microbial taxa associated wi...
Microbial communities underpin earth's biological and biogeochemical processes, but their complexity hampers understanding. Here we draw upon predictions from the theory of selfish genetic elements (SGEs), combined with approaches from experimental evolution, comparative metagenomics and biochemistry, and show how naturally occurring SGEs can be us...
Community Weighted Means (CWM) are valuable tools describing community composition with respect to one given trait. They have been widely used as indicators in global change studies to measure biodiversity responses to environmental perturbations. However, how individual species contribute to such community indicators has hardly been investigated....
Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approa...
The matrix of edge weight (Sig score) for network construction
Gene presence/absence profile of viruses within 21 heterogeneous VCs
In the matrix view, each row and column represent a virus and PC, respectively. In each VC, different colors indicate viral members belonging to the ICTV genus (upper left of the matrix) and dark boxes indicate the presence of PCs. Genomes are further partitioned by hierarchical c...
Detecting mycophages that highly link to other myco-/phages with the betweenness centrality
Each dot represents the betweenness centrality of an individual virus. The x-axis is the virus, and the y-axis is the value of betweenness centrality. A total of 393 mycophages and their relatives that link to mycophages are represented. Eight mycophages bel...
The list of member viruses of heterogeneous VCs
The list of member viruses of heterogeneous VCs having <20% intragenus similarities and separation of the genera from each VC after computational increase in the number of genomes by holding the number and weight of their connections. Copy number indicated the number of increase in the genome.
The fraction of PCs in common between genomes
The VC and genera each genome belongs to are in the columns (B) and (C) and (D) and (E), respectively (“n” in genus column indicates taxonomically-unassigned). The average shared PC percentage is calculated based on the Geometric formula (‘Materials and Methods’).
vConTACT family of tools on CyVerse
Gene presence/absence profile across five viral clusters (VCs) assigned to the Tevenvirinae and their potential relatives
Rows correspond to individual viral genomes, whereas columns are the PCs. Different colors indicate VCs (left in the matrix) and dark boxes indicate the presence of PCs. Genomes are further partitioned by hierarchical clustering...
Cluster connectivity of viral genomes
The cluster connectivity of each viral genome within the VC it belongs to and to other VCs. Each average weight value is generated as shown in Materials and Methods.
Gene presence/absence profile across eight viral clusters (VCs) assigned to the Autographivirinae and their potential relatives
Rows correspond to individual viral genomes, whereas columns are the PCs. Different colors indicate VCs (left in the matrix) and dark boxes indicate the presence of PCs. Genomes are further partitioned by hierarchical clus...
Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approa...
Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approa...
Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the...
Citations
... This phenomenon has previously been called ''fitness decoupling'', referring to the fact that fitness at the two levels might no longer be aligned (Michod, 1999;Okasha, 2008;Black et al., 2020;Bourrat, 2021). However, this interpretation has been called into question, and an alternative interpretation in terms of environment of reference has been provided by Bourrat et al. (2022). Following this interpretation, the reason why cell and collective fitness might appear decoupled is that they refer to different sets of events. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/272820873723920-1442056973870_Q64/Pierrick-Bourrat.jpg)
![[object Object]](https://i1.rgstatic.net/ii/profile.image/279179372318721-1443572957366_Q64/Caroline-Rose-3.jpg)
![[object Object]](https://i1.rgstatic.net/ii/profile.image/327137971195907-1455007178980_Q64/Katrin-Hammerschmidt-2.jpg)
... If the lower levels units have lost their autonomy, the individual on which Natural Selection acts is now the group of lower level units, who carries the fitness of the genotype. Bourrat et al. (2021) have recently made the case that no fitness decoupling occurs, provided fitness is considered at the relevant timescale (see Box 3 for more details). ...
... If a dependence of the environment on the type exists, this environment effectively becomes an extended phenotype (Lu and Bourrat, 2018). If the environmental changes are not deterministic, a weaker condition than the same temporal succession of environments is that the two organisms experience the same distribution of environments and transition probabilities between environments (steady-state) (see Doulcier et al., 2021). This type of scenario is not discussed in the main text (but see Box 3). ...
... Division (Koufopanou et al., 1993;Szathmáry et al., 1995;Michod et al., 1997;Michod, 2005;Gavrilets, 2010;Simpson, 2012;West et al., 2015;Szathmáry, 2015;Cooper et al., 2018;Doulcier et al., 2020;Hammerschmidt et al., 2021), where lower level units specialise at one task. ...
... For natural selection to take place, three conditions need to be met [162,84]: ...
... Here, scientists are interested in examining how particular types of changes in the environment can result in otherwise unlikely evolutionary changes in populations (whether of conspecifics or of multispecies communities). For instance, while the evolution of cooperation might be hard to obtain from standard conditions of individual-level selection, the imposition of particular environmental structures, specifically configured as ecological scaffolds, render such transitions considerably more likely (Black et al. 2020;Doulcier et al. 2020). ...
... In section 2, we describe how developmental psychologists employ the term "scaffold." In section 3, we introduce the work of Paul Rainey and collaborators (Black et al. 2020;Doulcier et al. 2020) as examples of recent discussions of scaffolding in evolutionary biology. In section 4, we draw from some philosophical analyses of causal explanation to articulate the common features of scaffolding explanations in developmental psychology and evolutionary biology (4.1 and 4.2). ...
... Experimental and numerical studies have tested artificial selection of collectives (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26). While some of the selection efforts seem successful to improve collective functions, others highlight challenges in selecting collectives (9, 10, 12-16, 18, 20). ...
... Recently, Quistad et al. reported an experimental approach to investigate the impact of MGEs on the ecology and functioning of complex microbial communities [50]. In the experiment, MGE cocktails were routinely collected from independent compost communities, pooled, and then redistributed across mesocosms (see Figure 1a). ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/278466307084292-1443402949300_Q64/Steven-Quistad.jpg)
... In the laboratory environment, and aided particularly by advances in micro/millifluidic technologies, it is a relatively trivial matter to confine populations and/or communities to thousands of discretized droplets that can then be subject to a death-birth process 21,84 . In a forthcoming paper, we detail this process and its outcome for the evolution of interactions that build integrated communities 85 . ...
