This is a fascinating study of how our modern apples evolved. The study involved examining the genomes of the array of apple varieties, including related types of fruit.
From it we can learn that the fruit types we know today, may not have existed in ancient times
From its origins in what we now call Kazakhstan, it seems the original fruit changed as trees grew in many places along the great ancient network of trade routes we call the Silk Road, and as different varieties evolved in various ways.
A readable version of the story can be found in Popular Archaeology:
But an even more fascinating version (for the technically-minded) may be found in a British academic journal, Nature Communications.
Here's an extract from the Abstract:
"A comprehensive model of apple speciation and domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an “ancient” isolated ecotype not directly contributing to apple domestication. We have identified selective sweeps underlying quantitative trait loci/genes of important fruit quality traits including fruit texture and flavor, and provide evidences supporting a model of apple fruit size evolution comprising two major events with one occurring prior to domestication and the other during domestication. This study outlines the genetic basis of apple domestication and evolution, and provides valuable information for facilitating marker-assisted breeding and apple improvement."
The primary authors are: Naibin Duan, Yang Bai and Xuesen Chen.
The lead institution for the research appears to be (at least it's listed first in the journal's write-up),