Hi all -

Does anyone have ideas for how to detect whether a particular genome has undergone a whole genome duplication? I have an assembly file (scaffolds) from a de-novo genome assembly. I have identified some duplicated proteins, but after reassembling with an assembler for highly heterozygous genomes, most of these duplicated genes disappear. I'm not sure if this actually answers the question regarding whole genome duplication though. Any thoughts are appreciated!

Thank you.
One common and relatively simple method of looking for evidence of a whole genome duplication is to estimate the rate of synonymous substitutions (Ks) between duplicated gene copies and then plot the distribution of Ks and look for peaks in the distribution.  The logic of this is that if many genes are duplicated at once (which obviously occurs during a WGD), there should be a relatively large number of paralogous gene copies with similar Ks values, but if genes are simply being duplicated at some low underlying rate, you would not expect peaks in the distribution.

There are many papers that discuss this type of method (and its limitations).  Here is recent one:

https://academic.oup.com/gbe/article/10/11/2882/5100828