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X
S F
¼
; m F ;
;
N ðÞ
o
N S ðÞ
o
q min
F
log PN ðÞ
o
N ðÞ
q min
F
'
; ... ;
jm F ;
j
ð
32
Þ
i ¼ 1
X
S M
¼
; m M ;
;
N ðÞ
o
N S ðÞ
o
q min
M
log PN ðÞ
o
N ðÞ
q min
M
'
; ... ;
jm M ;
j
ð
33
Þ
i ¼ 1
where S F and S M are the number of species in the fish and mysid community,
respectively, N ð o and N (i) are the observed and the model prediction of the
number of individuals of species i, and
m M , q mi F and q mi M are the mutation
rate and the minimum genetic similarity value for the fish and mysid com-
munity, respectively.
Simulations were carried out using Eq. (26)-(28) with a system size,
J P ¼
m F ,
10 3 individuals (J P and J R represent the number of individual fish
and mysids, respectively). This size was sufficient to recover the rank species
in abundance for the 10 and 3 most common sampled fish and mysid species,
respectively (see Section III ). Results were obtained after 2
J R ¼
10 3 generations
of a single model run, where a generation is an update of J P and J R time steps.
At this stage, species diversity had reached a steady state confirmed by
studying the equilibrium between speciation and extinction rate. Metacom-
munity size was kept constant by assuming zero-sum dynamics. A practical
advantage of assuming zero-sum dynamics is that it is computationally more
efficient, resulting in a substantial decrease in computing time for the simula-
tions. Zero-sum models are equivalent to their non zero-sum counterparts at
stationarity ( Etienne et al., 2007 ).
For the fish and mysid communities, we tested 800 combinations of the key
parameters:
[10 4 ,10 2 ] and q min
R
q min
P
[0.75, 0.98]. The values
of the minimum genetic similarity required to complete reproductive isola-
tion were chosen to satisfy the speciation condition, q min
m R ¼m P 2
¼
2
Q * . The values of
the parameters are within the range of the observed values of mutation rate
for eukaryotes,
>
[10 6 ,10 4 ]( Drake et al., 1998 ) and genetic divergence
values between species in the range of [5, 10] times greater than genetic
divergence within species to have complete reproductive isolation in the
context of large genomes ( Hickerson et al., 2006 ). At each parameter combi-
nation, 100 replicate simulations were completed.
m2
5. Sampling Effort and Species Level Food Web Connectance
A significant body of literature on food webs has explored the sensitivity of
species-level connectance and other species-level food web properties to the
effect of aggregation of different species to the same 'node'. Different meth-
ods of aggregation exist, using different measures of qualitative and quanti-
tative trophic similarity ( Bersier et al., 1999; Goldwasser and Roughgarden,
1997; Martinez, 1991 ).
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