modify msprime engine to do appropriate things for bacterial species

[petrelharp]

As discussed with @jeanrjc, for bacteria we need to use information in #848 to

• have individuals be haploid
• do gene conversion (for HGT)

(and circular chromosomes, but this isn't implemented in msprime).

Also ping @fbaumdicker.

[jeromekelleher]

Should we add a ploidy value to the Species class @petrelharp?

[petrelharp]

Yes!