Farmers Almost Completely Superseded Central Hunters (Silva et al, 2016)

This is a model for population continuity testing. I won't address the math since I basically skip numbers, but interested to see numbers that make sense.  Silva, Kreutzer, Papageorgopoulou and Currat estimate a potentially severe population replacement in the Neolithic, something up to 91% in Central Europe, although they have other scenarios as well.

The conclusions of Silva aren't new or strange, but as an interesting side note, there is a new study from last week that looks at the ancient genomic and population movement tendencies of these very people. See Maju's comments [here].

Here's an interesting excerpt:

"We estimated an admixture rate γ between PHG and NFA in central Europe of 0.01 with a high density interval (HDI) varying from 0.001 to 0.066 (Figure 5 and Table 2). This result means that around 1% of the contacts between PHG and NFA resulted in the adoption of farming by PHG or to the birth of a child in the farming community." 

If you look at population continuity in the Americas since the 16th century, you'll find that indigenous farmers with high population densities like the Aztecs contributed significantly to modern populations, whereas low density hunter-gatherer-mixed-agriculture populations like the Comanches were effectively superseded.

I've mentioned this point before regarding farmer density; the farm economy is an economy of scale. The more babies that are born, the more food and water that can be generated with less overall manpower, which enables greater specialty diversification, looping around and reducing elapsed maintenance manhours through higher productivity.  It sort of feeds on itself.  It has.

There is no upper limit to the size of a farm population structure (it keeps expanding) and the density can sometimes be very dense. (The entire landmass of China might support less than 2 million Hunter-Gatherers considering deserts and swamps)

Farmers aren't subject to native ecology restraints either. They basically transplant their own ecology, slashing and burning jungles, forests, draining swamps or terracing mountains. Farmers make babies and sprawl by necessity, and they change the landscape while pushing thinly populated hunters into the margins.

Importantly, there is little evidence of aboriginal hunters quickly adapting to the advance of the farmer baby-factory. On every continent and in every island the hunters are quickly marginalized and confused, often abused.  There is so much more than just food, it is ideas about conquering the material world, property rights and economic worth in a society that values material wealth over more ancient virtues. 

The farmer advance must have been a neutron bomb on Europe, so I'll buy 91% and then some.  Totally believable.

Here's what Silva et al wrote:

"Ancient mitochondrial population samples have been studied independently for different regions in Europe, and most of them revealed regional genetic discontinuity through time, from prehistoric times until today, meaning that the observed shifts in allele frequencies cannot be explained by genetic drift alone."

Effect of population structure and migration when investigating genetic continuity using ancient DNA [link]
Silva NM1, Kreutzer S2, Papageorgopoulou C3, Currat M1,4*
bioRxiv preprint first posted online May. 10, 2016; doi: http://dx.doi.org/10.1101/052548 

Abstract
Recent advances in sequencing techniques provide means to access direct genetic snapshots from the past with ancient DNA data (aDNA) from diverse periods of human prehistory. Comparing samples taken in the same region but at different time periods may indicate if there is continuity in the peopling history of that area or if a large genetic input, such as an immigration wave, has occurred. Here we propose a new modeling approach for investigating population continuity using aDNA, including two fundamental elements in human evolution that were absent from previous methods: population structure and migration. The method also considers the extensive temporal and geographic heterogeneity commonly found in aDNA datasets. We compare our spatially‐explicit approach to the previous non‐spatial method and show that it is more conservative and thus suitable for testing population continuity, especially when small, isolated populations, such as prehistoric ones, are considered. Moreover, our approach also allows investigating partial population continuity and we apply it to a real dataset of ancient mitochondrial DNA. We estimate that 91% of the current genetic pool in central Europe entered the area with immigrant Neolithic farmers, but a genetic contribution of local hunter‐gatherers as large as 83% cannot be entirely ruled out.