You are collaborating with a group of archeologists to reconstruct the history of cattle domestication. Your archeologist colleagues tell you that cattle were already domesticated by 9000 years ago, as evidenced by the appearance of pottery fragments containing traces of milk. However, it is not clear from archeological records when the domestication began, or how large the cattle herds were in the first few millennia after domestication. As a biologist, you are familiar with genetic drift and coalescence so you know that effective population size and the time to last common ancestor can be estimated from the patterns of contemporary genetic diversity. You sequence the coding sequence of a milk protein gene from many cows belonging to different breeds on several continents. From these sequences, you estimate that the effective population size of cattle is 100,000, and all present-day alleles coalesce 600,000 years ago. You realize that this is inconsistent with archeological data (no milk pottery is observed until 9,000 years ago) as well as with our knowledge of human evolution (modern humans evolved only 100,000 years ago). To get more genetic data, you sequence the upstream non-coding sequence of the same gene. When you analyze these sequences, they indicate an effective population size of 5,000 and coalescence time of 3,000 years ago. Given this obvious contradiction between two parts of the same gene, you decide to get more independent data by sequencing the mitochondrial genome and several neutrally evolving nuclear genes. The mtDNA produces the same estimate of population size and coalescence time as the upstream non-coding region of the milk protein gene, while the nuclear genes give you the same estimate as the protein-coding portion of the milk gene. You must now propose evolutionary scenarios that could explain your observations. 
The current number of cattle on the planet is approximately 1.3 billion, yet all estimates of the effective population size are much lower. List several factors that could contribute to this mismatch.