I know this is too late, but since this is something I'm struggling with too I thought I'd post here in case others also find there way here. I don't have an answer but, here are some quotes that might help (I found them at least partially helpful).
Yang (2004): "Marginal reconstruction is more suitable when one wants the sequence at a particular node, as ...
Volterra’s Variations and Fluctuations of the Number of Individuals in Animal Species living together features what is nowadays often called the generalised Lotka–Volterra model.
Thus it captures competition between and with populations.
In particular, Section 2 is titled:
Biological Association of two Species which contend for the same Food.
I imagine that for case 1 you have data of the type:
Plant1, $t_f$, $t_l$;
Plant2, $t_f$, $t_l$;
If you are interested in comparing the mean temperatures between flowers and leaves, your data would consist of n measurements coming from flowers and n measurements from leaves. You may surely try a t-test for independent samples, especially if you have ...