The fundamental problem with RAD is that if you hit paralogue - you're done.

Identifying a paraologue isn't necessarily easy depends on the species. Essentially if you're doing pop gen you need homologues and RAD has too many situations where it can fall over without you knowing.

What happens if you've a paralogue is that you start confusing concerted evolution (pop gen of a genome) with population structure between individuals. I do agree that without barcodes identifying individuals - thats a bit tricky ;-) , however RAD an approach loaded with pitfalls.

Pop gen means being able to identify populations and on face value that will not be trivial without barcodes (I suspect they are still there), but RAD is far from an ideal tool and can give weird and wonderful metrics which have little to do with the population structure.

The fundamental problem with RAD is that if you hit paralogue - you're done.

Identifying a paraologue isn't necessarily easy depends on the species. Essentially if you're doing pop gen you need homologues and RAD has too many situations where it can fall over without you knowing.

What happens if you've a paralogue is that you start confusing concerted evolution (pop gen of a genome) with population structure between individuals. I do agree that without barcodes identifying individuals - thats a bit tricky ;-) , however RAD an approach loaded with pitfalls.

Pop gen means being able to identify populations and on face value that will not be trivial without barcodes (I suspect they are still there), but RAD is far from an ideal tool and can give weird and wonderful metrics which have little to do with the population structure.

Its not the only problem with RAD for the purpose you are using it.

The fundamental problem with RAD is that if you hit paralogue - you're done.

Identifying a paraologue isn't necessarily easy depends on the species. Essentially if you're doing pop gen you need homologues and RAD has too many situations where it can fall over without you knowing.

What happens if you've a paralogue is that you start confusing concerted evolution (pop gen of a genome) with population structure between individuals. I do agree that without barcodes identifying individuals - thats a bit tricky ;-) , however RAD an approach loaded with pitfalls.

The fundamental problem with RAD is that if you hit paralogue - you're done.

Identifying a paraologue isn't necessarily easy depends on the species. Essentially if you're doing pop gen you need homologues and RAD has too many situations where it can fall over without you knowing.

What happens if you've a paralogue is that you start confusing concerted evolution (pop gen of a genome) with population structure between individuals. I do agree that without barcodes identifying individuals - thats a bit tricky ;-) , however RAD an approach loaded with pitfalls.

Pop gen means being able to identify populations and on face value that will not be trivial without barcodes (I suspect they are still there), but RAD is far from an ideal tool and can give weird and wonderful metrics which have little to do with the population structure.