Many Mesolithic and Neolithic lineages disappeared (or significantly reduced) after the arrival of PIE speakers, C1a2-V20 and H2 almost don't exist in Europe anymore, the majority of G2a branches that were not assimilated by Indo-Europeans are confined to mountainous regions and Mediterranean Islands in low numbers, the two most numerous I2 subclades (I2a1b-CTS10228 and I2a2a-L801) are young and are associated with the Slavic and Germanic expansions in the Migration Period of the early middle ages, if you remove these two subclades the frequency of I2 in mainland Europe would significantly drop.
Haplogroup A1a* (M31) has been found in Finland, Norway and eastern England. This subclade is normally found along the west coast of Africa (Guinea-Bissau, Cape Verde, Mali, Morocco) and could have come to Europe during the Paleolithic. Indeed a few percent of sub-Saharan admixture was found among ancient DNA samples from Mesolithic Scandinavia tested by Skoglund et al. (2012). If this lineage survived in low numbers since the Paleolithic, then why couldn't a branch of Haplogroup I that would give rise to I1 later ?
I1 expanded during the Bronze age, my personal opinion is that I1 was assimilated early by the Corded Ware IE advance, but that alone isn't enough to give it this frequency,
most I1 men today probably descend from a a lucky man that rose to prominence in the early Bronze Age and that allowed him and his progeny to increase their numbers and become a founding lineage in proto-Germanic society. a romantic story of survival and rise to power.
R.I.P Old Europe ... their only sin was fighting against a horde of horse riding screamers with bronze weapons .. a deadly mistake.
Something I noticed, the ancient Iberians (who were not Indo-European) worshipped a Horse taming god (
https://en.wikipedia.org/wiki/Iberians#Art_and_religion), they must have realised that taming horses was the only way to resist Celtic incursions, maybe that was the reason they survived while others didn't.