The evidence pointing towards monophyly for the nervous system comes from comparing the development of the nervous system of the fruit fly (you'd be surprised how much neuroscience comes from those little guys) to the development of chordate nervous systems. What we know is that the gene transcription factors for the ventral (i.e. front side) nervous system in the fruit fly are the same as the dorsal (i.e. back side) gene transcription factors in mammals. Also, we see the same gene expression pattern in the front, middle and back of the developing nervous system for mice, fruit flies and sea squirts. The fact that there are common gene transcription factors between insects and mammals points to a common ancestor way back in the evolutionary framework. The monophyletic hypothesis suggests that there is a 'common ancestor' of all animals that has a compact nervous system and that this compact nervous system (that came from one cell type) diversified into the complex nervous systems that we see today. This is all well and good, the evolutionary tree has some animals who have a dorsal and a ventral nervous system, and some that have a diffuse neural net, and these animals appear AFTER (evolutionarily speaking) the 'common ancestor' who had a compact nervous system. You might be thinking "what's the problem with that?" (I thought that too). Here it is- in order for the monophyletic theory to explain how simplification and reduction of the compact nervous system into different cords or neural nets the animal would either have to be a parasite or live in an environment that allows for no sensory input. Unfortunately (for the monophyletic hypothesis), these systems are seen in animals that are free roaming and preditory.
So, we need a new hypothesis...polygenesis. Here we start with a 'common ancestor' who has a diffuse neural net consisting of many different cell types. The neural net then evolves in parallel across many different lineages to create the complex nervous systems that we see today. The 'common ancestor' would still have the same gene experession that we see in fruit flies and mammals, but since the fruit fly and mammal nervous systems developed in separate but parallel lineages, these transcription factors became switched to their current locations.
Alright, really, so what. A neuron is a neuron, right? When we think in broad terms of what a neuron is (a polarized cell that quickly transmits messages from one place to another), sure a neuron is a neuron. But, the HOW of the neuron is where complexity comes in. If a neuron was "just" a neuron and all neurons were the same, then we wouldn't be able to see, smell, taste, touch, run, type, feel emotions, and think- we would only be able to do ONE of these things which would be to feel pain(most likely based on the nervous systems of the simplest animals out there). With a nervous system that developed from many different types of secretory cells, we can have nervous system cells that become specialized as sense receptors, specialized at carrying signals, and those that specialize in transimitting signals. We can have neurons that increase the sensitivity of other neurons and those that inhibit other neurons. With a polygenetic viewpoint, the specialization of the neurons can develop simultaneously rather than having to develop linearly and, therefore, we can develop the vast amount of biodiversity that we see both in the fossil record and in the environment today.
Where does this lead us? The information here sets the stage for understanding how the nervous system manages all its jobs. From sensation to output, we need complexity to function in the world. In addition, understanding how cells evolved in parallel (from a molecular and genetic standpoint) may allow us to develop methods for reparing damaged neurons. 
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