"Evolution does not necessarily reward intelligence. With no natural predators to thin the herd it began to reward those who reproduced the most and left the intelligent to become an endangered species."
"No, I am not speaking of layoffs, plant closures and terminations, but rather thinning your “herd” of out-dated projects, failed initiatives, worthless bureaucracy and old hardware and software."
The first one is clear - if there are no natural predators to control the breeding herds, then even the weakest specimens will survive to the overall disadvantage of the species.
The second one seems to be that someone is cleaning up an outdated office of redundant projects and equipment in order to make it faster and more efficient.
Both examples imply that weak elements must be got rid of in order for good survival.
I forgot to mention that the first quotation was taken from the film 'Idiocracy' so it is talking about people, not animals. That's why I was a bit confused with the idiom. So I guess this idiom is another way of talking about Darwin's natural selection, but couldn't find any online dictionaries which give the meaning.