5. Create a tree of relationships for each remaining character and
construct an overall consensus tree from these based on combinable components [181].
6.4 Evaluation
of Tree Topology
1. Make phylogenetic calculations according to a neighbor joining algorithm implemented in MEGA 4.0 software [182] by
applying an “evolutionary model”, which infers different evolutionary rates at different sites.
2. Perform bootstrap analyses with 1000 resamplings to obtain
estimates of phylogenetic tree topologies for all methods.
3. Concerning the importance of the DNA sequence alignment,
perform RNA secondary structure and minimum energy calculations perform by GeneBee-NET program [183, 184] using a
greedy algorithm.
4. Set the parameters as: energy threshold ¼ À4.0; cluster factor ¼ 2; conserved factor ¼ 2; compensated factor ¼ 4; and
conservativity ¼ 0.8.
5. Analyze the resulting genetic distance table using the Fitch
package of PHYLIP [185] which does not assume a molecular
clock. Use this program to select the best tree from 100 runs.
7 Ecological Characterization
The entomopathogens (steinernematid and heterorhabditid nematodes) perform differently under a range of environmental conditions, and this is reliant on their biological characteristics. Fruitful
biological control with entomopathogens can rely on the control of
certain beneficial traits. Various beneficial traits have been reported
in entomopathogenic nematodes to vary between strains within a
species. Environmental tolerance can be studied for tolerance to
heat, cold, pH, moisture, desiccation, and hypoxia.
All nematode strains are reared at 25
C in final instar larvae of
the greater wax moth, G. mellonella, according to Woodring and
Kaya [164]. IJs that appeared from cadavers are recuperated using
modified White traps [163] and stored at 7
C for 7–14 days prior
to use. Allow the nematodes in water suspensions to acclimatize at
room temperature (23
C) for 12 h prior to use.
The concentration is adjusted by volumetric dilutions, as
required in each bioassay.
7.1 Volumetric
Counts
Great numbers of nematodes can be assessed on the settled volume.
This method is helpful as the IJs of entomopathogenic nematodes
are similar in size.
1. Dispense 10 ml of a known (high) concentration of nematodes
to a graduated centrifuge tube.
Ecological Characterization
95
construct an overall consensus tree from these based on combinable components [181].
6.4 Evaluation
of Tree Topology
1. Make phylogenetic calculations according to a neighbor joining algorithm implemented in MEGA 4.0 software [182] by
applying an “evolutionary model”, which infers different evolutionary rates at different sites.
2. Perform bootstrap analyses with 1000 resamplings to obtain
estimates of phylogenetic tree topologies for all methods.
3. Concerning the importance of the DNA sequence alignment,
perform RNA secondary structure and minimum energy calculations perform by GeneBee-NET program [183, 184] using a
greedy algorithm.
4. Set the parameters as: energy threshold ¼ À4.0; cluster factor ¼ 2; conserved factor ¼ 2; compensated factor ¼ 4; and
conservativity ¼ 0.8.
5. Analyze the resulting genetic distance table using the Fitch
package of PHYLIP [185] which does not assume a molecular
clock. Use this program to select the best tree from 100 runs.
7 Ecological Characterization
The entomopathogens (steinernematid and heterorhabditid nematodes) perform differently under a range of environmental conditions, and this is reliant on their biological characteristics. Fruitful
biological control with entomopathogens can rely on the control of
certain beneficial traits. Various beneficial traits have been reported
in entomopathogenic nematodes to vary between strains within a
species. Environmental tolerance can be studied for tolerance to
heat, cold, pH, moisture, desiccation, and hypoxia.
All nematode strains are reared at 25
C in final instar larvae of
the greater wax moth, G. mellonella, according to Woodring and
Kaya [164]. IJs that appeared from cadavers are recuperated using
modified White traps [163] and stored at 7
C for 7–14 days prior
to use. Allow the nematodes in water suspensions to acclimatize at
room temperature (23
C) for 12 h prior to use.
The concentration is adjusted by volumetric dilutions, as
required in each bioassay.
7.1 Volumetric
Counts
Great numbers of nematodes can be assessed on the settled volume.
This method is helpful as the IJs of entomopathogenic nematodes
are similar in size.
1. Dispense 10 ml of a known (high) concentration of nematodes
to a graduated centrifuge tube.
Ecological Characterization
95