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natural populations. The addition of genetic drift and explicit mechanisms of
speciation to the neutral biodiversity theory allows us to test the effect
of genetic and ecological drift simultaneously.
Figure 1
B shows the link
between predator and preys under the assumption of equal feeding rate
among individuals by considering that each death event is a consequence of
predation. Finally, we run the model to steady state (
Figure 1
C) and compute
the number of individual prey per predator, the species abundance for two
communities and the species-level connectance in the food web.
1. The Population Genetics Model with Sexual Reproduction
Models of DNA evolution based on simple base-pair substitution have a long
history (i.e. the infinite sites model;
Jukes and Cantor, 1969; Kimura, 1983
),
and several variants have been proposed (
Durrett, 2008
). More realistic
extensions of those models include deletion, insertion, duplication and rear-
rangements of segments bases (
Ma et al., 2008
). Recent models also take into
account, as in the neutral theory of biodiversity, instantaneous speciation but
with an explicit genome evolving (i.e. an identical copy of one root genome is
made, each of the two genomes gets a new successor species name and they
each evolve independently thereafter; see
Ma et al., 2008
).
Our model incorporates a population with evolving genomes and explicit
speciation following previous studies in population genetics (
Higgs and
Derrida, 1992
). The model deals with haploid individuals and each individual
has an infinite genome and each site represents a nucleotide which has two
(B) The food web model starts with two initial populations with identical genomes for
all the individual predators (top left) and prey (bottom left). Each individual is
represented as a circle with the smaller dots within each circle representing the
genome. The graph is fully connected at the starting point because all the individuals
have an identical genome (left). First, at each time step, a randomly chosen individual
prey dies as a consequence of a randomly chosen individual predator (bottom, black
circle and the line connecting the predator and the prey) and a randomly chosen
predator also dies in this step (top, black circle). Second, parents are selected for
reproduction (dark circles (red in colour figure) ). Third, the dead individual is
replaced by an offspring (dark circles and orange in colour) and we track each
predator-prey interaction (two lines, right). The offspring has a new DNA-sequence
given by free recombination and mutation. Lastly, we repeat the cycle. (C) Represents
a cartoon at the steady state for the predator-prey interactions and species abun-
dance. Mating links within populations and trophic links between populations. The
loop in each predator species represents cannibalism. In this example, each metacom-
munity (predator, top and prey, bottom) has five isolated groups with different number
of individuals. Individuals within the most abundant groups are interacting frequently,
while individuals in the rare groups do not interact among them. Trophic interactions
are grouped to species level for clarity.
