Very interesting. The genetic landscape of Mongolia changed more often and more radically from the Copper Age to the Iron Age than anywhere in western Eurasia.
Here is the Y-DNA and mtDNA summary from the paper.
What struck me at first is that Y-haplogroup J1a was present from the Copper Age to the Early Medieval period (and probably still today). There are only 5 pre-EBA samples and we can see that G2a was already there too by the MLBA, so I would think that J1a and G2a came together, probably arriving with domesticated animals from the Middle East during the Neolithic period. R1b came from the eastward expansion of Proto-Indo-Europeans through the Botai culture in the Altai (that was already confirmed before). Haplogroup N presumably expanded from northern China to Mongolia and Siberia during the Neolithic. Q1a would be the Mesolithic Siberia hunter-gatherers already living in the region.
From the Early Iron Age we see the arrival and R1a and Q1b, surely from Central Asia (Kazakhstan).
In the Late Iron Age, the Xiongnu/Huns emerged as a mix of the Bronze Age Mongolian population with two sets of newcomers:
1) Chinese and/or Manchus bring haplogroups O2a and C2b.
2) Middle Eastern E1b1b and J2a who almost certainly came along more R1a(-Z93) and Q1b with Scythian-related tribes.
By the
Late Medieval period, after the Mongols conquered China under Kubilai Khan, we see a sharp rise in the percentage of Manchu and Chinese haplogroups. If C2b was the lineage of Genghis Khan, as was previously suggested, then that may also explain the doubling of that haplogroup's frequency from 15 to 30% from the Iron Age and Early Medieval to the Late Medieval period.
On the maternal side, it looks like the original North Chinese farmers (Y-DNA N) who settled in Mongolia only carried haplogroups A, C and F. The other main East Asian maternal haplogroups (B, D, F and G) only appear from the MLBA, after they mixed with the Q1a tribes.
The Manchus and Han Chinese seem to have added C5, M1, Z1, Z4 and considerably more B. If we subtract the western Eurasian haplogroups, the proportion of D4 and G also increased in the late Iron Age (Xiongnu).
The merger between China and Mongolia under the Yuan dynasty increased the percentage of East Asian maternal lineages from about 65% to 85%. We see a further appearance of new lineages like M7, M8, M9.