Holobiont Evolution: Model with Vertical vs. Horizontal Microbiome Transmission with Remarks on Lineal vs. Collective Inheritance
Joan Roughgarden, 2019.
A holobiont is a composite organism consisting of a
host together with its microbiome, such as a coral with its
zooxanthellae. Some investigators contend that selection operates on
entire holobionts and view the microbiome’s genes as extending the
host’s nuclear genome to jointly comprise a hologenome.
Holobiont
selection then operates on entire hologenomes by analogy to how
ordinary natural selection operates on genes in a Mendelian population.
Other investigators argue that vertical transmission of microbiomes is
uncommon. Therefore, holobiont selection cannot be evolutionarily
important because the microbiome is an acquired condition rather than
an inherited trait.
The conceptual
disagreement between these positions invites a simple mathematical model
to see how holobiont selection might operate and to assess the
plausibility of holobiont selection as an evolutionary force.
Here
I present two variants of such a model. In one variant, juvenile hosts
obtain microbiomes from their parents (vertical transmission). In the
other variant, microbiomes of juvenile hosts are assembled from source
pools containing the combined microbiomes of all parents (horizontal
transmission). According to both variants, holobiont selection indeed
causes evolutionary change in holobiont traits. Therefore, holobiont
selection is plausibly an important evolutionary force with either mode
of microbiome transmission.
Furthermore, a new concept of inheritance emerges from the modeling:
collective inheritance whereby juveniles inherit a sample of the
collected genomes from all parents as contrasted with traditional lineal
inheritance whereby juveniles inherit the genomes only from their own
parents. This new concept of collective inheritance may apply to the
evolution of soil and other microbes that feature large amounts of
horizontal gene transfer and may underlie cultural evolution wherein
each generation inherits a sample of knowledge from the collected
knowledge of the preceding generation.
Sequence of processes with vertical transmission of mutualistic microbiome.
Results with vertical transmission of mutualistic microbiome. Top left and middle graphs show log of total holobiont and microbe numbers through time and top right graph shows holobiont fitness as function of number of microbes in host. Histograms show distribution of hologenotype frequencies through time. The horizontal axis in the histograms is number of microbes per host and vertical axis is fraction of holobiont population.
Sequence of processes with horizontal transmission of mutualistic microbiome.
Results with horizontal transmission of mutualistic microbiome.Top
left and middle graphs show log of total holobiont and microbe numbers
through time and top right graph shows holobiont fitness as function of
number of microbes in host. Histograms show distribution of hologenotype
frequencies through time. The horizontal axis in the histograms is
number of microbes per host and vertical axis is fraction of holobiont
population.
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