The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the

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1The distribution, antiquity and epidemiology of tuberculosis (TB) have previously been studied in 2 osteoarchaeological material in the eastern part of Hungary, mainly on the Great Plain. The 3 purpose of this study is to map the occurrence of skeletal TB in different centuries in the Western 4 part of Hungary, Transdanubia, and to present new cases we have found. Paleopathological 5 analysis was carried out using gross observation supported by radiographic and molecular 6 methods. A large human osteoarchaeological sample (n=5684) from Transdanubian 7 archaeological sites ranging from the 2nd to the 18th centuries served as a source of material. 8Spinal TB was observed in seven individuals (in three specimens with Pott's disease two of 9 which also had cold abscess) and hip TB was assumed in one case. The results of DNA for 10Mycobacterium tuberculosis were positive in seven of the eight cases identified by 11 paleopathology, and negative in the assumed case of hip TB. However, the molecular results are 12 consistent with highly fragmented DNA, which limited further analysis. Based on the present 13 study and previously published cases, osteotuberculosis was found in Transdanubia mainly 14 during the 9th-13th centuries. However, there are no signs of TB in many other 9th-13th 15 centuries, even in those that lie geographically close to those where osteotuberculous cases were 16found. This may be due to a true absence of TB caused by the different living conditions, way of 17 life, or origin of these populations An alternative explanation is that TB was present in some 18 individuals with no typical paleopathology, but that death occurred before skeletal morphological 19 features could develop. 20 21 3

1DNA recovery from ancient human remains has revolutionized our ability to 2 reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the 3 identification of skeletal elements, such as the cochlear part of the osseous inner ear, that 4 provide optimal contexts for DNA preservation; however, the rich genetic information obtained 5 from the cochlea must be counterbalanced against the loss of valuable morphological 6 information caused by its sampling. Motivated by similarities in developmental processes and 7 histological properties between the cochlea and auditory ossicles, we evaluated the efficacy 8 of ossicles as an alternative source of ancient DNA. We demonstrate that ossicles perform 9 comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data 10 quality, quantity, or authenticity across a range of preservation conditions. Ossicles can be 11 sampled from intact skulls or disarticulated petrous bones without damage to surrounding 12 bone, and we argue that, when available, they should be selected over the cochlea to reduce 13 damage to skeletal integrity. These results identify a second optimal skeletal element for 14 ancient DNA analysis and add to a growing toolkit of sampling methods that help to better 15 preserve skeletal remains for future research while maximizing the likelihood that ancient DNA 16 analysis will produce useable results. 17 18 24 Briggs et al. 2010; Ginolhac et al. 2011; Skoglund et al. 2014) small quantities of degraded 25 DNA. While these methodological advances have contributed to an improvement in the quality 26 and quantity of paleogenomic data obtained from ancient human remains, all ancient DNA 27 4 research fundamentally depends upon access to biological material that has sufficient 28 biomolecular preservation. 29Skeletal tissue (i.e., bone or teeth) is the preferred biological material for human 30 ancient DNA analysis due to its ability to resist post-mortem degradation better than other 31 types of tissues, including skin and hair (Lindahl 1993; Smith et al. 2001 Smith et al. , 2003 Collins et al. 32 2002). Recent research has shown that not all bone elements are equally effective in 33 preserving DNA, however, and has identified the bone encapsulating the cochlea within the 34 petrous pyramid of the temporal bone (referred to henceforth as the 'cochlea') (Gamba et al.35 2014; Pinhasi et al. 2015), as well as the cementum layer in teeth roots (Damgaard et al. 2015; 36 Hansen et al. 2017) as especially DNA-rich parts of the skeleton. The use of these skeletal 37 elements that act as repositories for the long-term survival of DNA has proven to be particularly 38 important for the analysis of biological samples recovered from regions where high 39 temperatures and/or humidity increase the rate of molecular degradation and result in low 40 concentrations of damaged DNA with reduced molecular complexity (e.g., Broushaki et al. 41 2016; Lazaridis et al. 2016; Schuenemann et al. 2017; Skoglund et al. 2017; Fregel e...