<p>Red heat map displays the geographic distribution of closest East Eurasian sequence matc... more <p>Red heat map displays the geographic distribution of closest East Eurasian sequence matches to individual Conqueror samples. Stars denote geolocations of East Eurasian ethnic groups listed on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0205920#pone.0205920.s002" target="_blank">S1 Fig</a> (summarized on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0205920#pone.0205920.s003" target="_blank">S1A Table</a>), map was drawn from their frequency of occurence. Heat map designate the area from which the East Eurasian lineages most likely originated, well corresponding to the range of the ancient Xiongnu Empire outlined by dashed line. Areas where Asian and European Scythian remains were found are labeled green. Asian Scythians around Tuva correspond to the most probable sources of Eurasian lineages. Pink label shows the presumptive range of the Srubnaya culture, from where European lineages were most likely derived. Bluish line frames the Eurasian steppe zone, within which all presumptive ancestors of the Conquerors were found. The map was created using QGIS 2.18.4[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0205920#pone.0205920.ref051" target="_blank">51</a>].</p
<p>Data are summarized from <a href="http://www.plosone.org/article/info:doi/10.137... more <p>Data are summarized from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0205920#pone.0205920.s002" target="_blank">S1 Fig</a>. Origin of modern individuals with closest matches to Conqueror sequences are listed next to the indicated regions, ordered according to the frequency of appearances.</p
Background Current state of art kinship analysis is capable to infer relatedness up to the 5-6th ... more Background Current state of art kinship analysis is capable to infer relatedness up to the 5-6th degree from deeply sequenced DNA if the proper reference population is known. Low coverage, partially genotyped, degraded archaic (or forensic) DNA and often unavailable or unknown reference population poses additional challenges, hence kinship analysis from low coverage archaic sequences so far has been possible up to the second degree with large uncertainties. Results We performed extensive simulations to identify and correct the main factors of bias in kinship analysis from low coverage data. As a result, we introduce a new metric for correction and offer a guideline, which overcomes the difficulties associated with low coverage samples. We validated our methodology on experimental modern and archaic data with widely different genome coverages (0.12x-11.9x) using samples with known family relations and known or unknown population structure. Out of 2526 ancient individuals from the REI...
According to the written historical sources, the Gepids were a Germanic tribe that settled in the... more According to the written historical sources, the Gepids were a Germanic tribe that settled in the Carpathian Basin during the Migration Period. They were allies of the Huns, and an independent Gepid Kingdom arose after the collapse of the Hun Empire. In this period, the Carpathian Basin was characterized by so-called row-grave cemeteries. Due to the scarcity of historical and archaeological data, we have a poor knowledge of the origin and composition of these barbarian populations, and this is still a subject of debate. To better understand the genetic legacy of migration period societies, we obtained 46 full mitogenome sequences from three Gepid cemeteries located in Transylvania, Romania. The studied samples represent the Classical Gepidic period and illustrate the genetic make-up of this group from the late 5th and early 6th centuries AD, which is characterized by cultural markers associated with the Gepid culture in Transylvania. The genetic structure of the Gepid people is expl...
According to the written historical sources, the Gepids were a Germanic tribe that settled in the... more According to the written historical sources, the Gepids were a Germanic tribe that settled in the Carpathian Basin during the Migration Period. They were allies of the Huns, and an independent Gepid Kingdom arose after the collapse of the Hun Empire. In this period, the Carpathian Basin was characterized by so-called row-grave cemeteries. Due to the scarcity of historical and archaeological data, we have a poor knowledge of the origin and composition of these barbarian populations, and this is still a subject of debate. To better understand the genetic legacy of migration period societies, we obtained 46 full mitogenome sequences from three Gepid cemeteries located in Transylvania, Romania. The studied samples represent the Classical Gepidic period and illustrate the genetic make-up of this group from the late 5th and early 6th centuries AD, which is characterized by cultural markers associated with the Gepid culture in Transylvania. The genetic structure of the Gepid people is expl...
We applied ancient DNA methods to shed light on the origin of ancient Hungarians and their relati... more We applied ancient DNA methods to shed light on the origin of ancient Hungarians and their relation to modern populations. Hungarians moved into the Carpathian Basin from the Eurasian Pontic steppes in the year 895 AD as a confederation of seven tribes, but their further origin remains obscure. Here, we present 17 mtDNA haplotypes and four Y-chromosome haplogroups, which portray the genetic composition of an entire small cemetery of the first generation Hungarians. Using novel algorithms to compare these mitochondrial DNA haplogroups with other ancient and modern Eurasian data, we revealed that a significant portion of the Hungarians probably originated from a long ago consolidated gene pool in Central Asia-South Siberia, which still persists in modern Hungarians. Another genetic layer of the early Hungarians was obtained during their westward migrations by admixing with various populations of European origin, and an important component of these was derived from the Caucasus region....
Fontosabb eredmenyek Kimutattuk, hogy a bithorax komplexben (Bx-C) a Polycomb Response Elementek ... more Fontosabb eredmenyek Kimutattuk, hogy a bithorax komplexben (Bx-C) a Polycomb Response Elementek (PRE-k), es a hozzajuk kapcsolodo Polycomb feherjek nemcsak a cisz-regulator regiok inaktiv/zart allapotanak fenntartasaban jatszanak fontos szerepet, hanem az aktiv/nyilt allapotu cisz-regulatorokban talalhato enhanszerek hatasanak modulalasaban is. Ezt a hatas ugy fejti ki, hogy fizikailag a celgen promoterehez kotődik. Ezzel osszefuggesben kimutattuk egy, a bxd PRE-vel reszben atfedő Targetalo Elem (TE) jelenletet. A TE a PRE-hez hasonloan modularis szerkezetű. Igazoltuk, hogy ez az elem nemcsak a PRE promoterhez valo kőtődeseben jatszik szerepet, hanem reszt vesz a bxd regioban talalhato enhanszereknek az Ubx promotere kore valo szervezeseben, azaz az „acticve chromatin hub” kialakitasaban. A TE ezt a funkciojat ektopikus kornyezetben, az iab-7 cisz regulatorban is megőrzi. A PRE-től hatarolo elemmel elvalasztott bxd enhanszerek ektopikus aktivitast mutatnak, amely mind fenotipus analizissel, mind markergen expressziojanak kovetesevel kimutathato. Kinutattuk, hogy az ebi gen a Polycomb csoport genjei koze sorolando, es a polyhomeotic gennel egyutt az aktiv allapotu cisz-regulatorokban fejti ki modulalo hatasat. Kvantitativ RTPCR segitsegevel kimutattuk, hogy az Abd-B RNS mennyisege korulbelul duplajara nő polyhomeotic mutans hatteren. | We showed that Polycomb Response Elements (PREs) and Polycomb proteins bound to them play an important role not only in maintaining inactive/closed conformation of cis-regulatory elements in the bithorax complex, but they are also involved in modulating the regulatory output of enhancers in the active/open domains. This latter effect is mediated by direct physical contact between the PRE and the promoter – enhancer complex. In connection with this we demonstrated the presence of a Targeting Element (TE) that partially overlaps with the bxd PRE. TE is, similarly to the PRE, modularly organized. We showed that this element is involved not only in targeting the PRE to the Ubx promoter, but also part of the machinery organizing the active chromatin hub around cognate promoter. We also demonstrated that the TE maintains its activity in ectopic context, in the iab-7 cis-regulatory region. Enhancers separated from the bxd PRE by a boundary region exhibit ectopic activity, as revealed by both phenotypic analysis and by monitoring the expression pattern of a marker gene. We identified the ebi gene as an unusual Polycomb group member, which, similarly to the polyhometic gene, participates in the modulation of enhancer output of active cis-regulatory regions. Using quantitative RTPCR we showed that the amount of the Abd-B RNA is doubled in polyhomeotic mutant background.
SummaryHuns, Avars and conquering Hungarians were Migration Period nomadic groups which arrived i... more SummaryHuns, Avars and conquering Hungarians were Migration Period nomadic groups which arrived in three successive waves in the Carpathian Basin between the 5th and 9th centuries. Based on historical data each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations has been debated. In this study we have sequenced 9 Hun, 143 Avar and 113 Hungarian conquest period samples, and identified three core populations, representing immigrants from each period, with no recent European ancestry. Our results suggest that this “immigrant core” of both Huns and Avars originated in present day Mongolia, and their origin can be traced back to Xiongnus. On the other hand, the “immigrant core” of the conquering Hungarians derived from an earlier admixture of Mansis, early Sarmatians and descendants of late Xiongnus. In addition, we detected shared Hun-related ancestry in numerous Avar and Hungarian conquest period geneti...
Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but ge... more Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10–11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the immigrant elite have been widely debated. Mitogenome sequences were obtained from 202 individuals with next generation sequencing combined with hybridization capture. Median joining networks were used for phylogenetic analysis. The commoner population was compared to 87 ancient Eurasian populations with sequence-based (Fst) and haplogroup-based population genetic methods. The haplogroup composition of the commoner population markedly differs from that of the elite, and, in contrast to the elite, commoners cluster with European populations. Alongside this, detectable sub-haplogroup sharing indicates admixture between the elite and the commoners. The majority of the 10–11th century commoners most likely represen...
<p>Red heat map displays the geographic distribution of closest East Eurasian sequence matc... more <p>Red heat map displays the geographic distribution of closest East Eurasian sequence matches to individual Conqueror samples. Stars denote geolocations of East Eurasian ethnic groups listed on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0205920#pone.0205920.s002" target="_blank">S1 Fig</a> (summarized on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0205920#pone.0205920.s003" target="_blank">S1A Table</a>), map was drawn from their frequency of occurence. Heat map designate the area from which the East Eurasian lineages most likely originated, well corresponding to the range of the ancient Xiongnu Empire outlined by dashed line. Areas where Asian and European Scythian remains were found are labeled green. Asian Scythians around Tuva correspond to the most probable sources of Eurasian lineages. Pink label shows the presumptive range of the Srubnaya culture, from where European lineages were most likely derived. Bluish line frames the Eurasian steppe zone, within which all presumptive ancestors of the Conquerors were found. The map was created using QGIS 2.18.4[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0205920#pone.0205920.ref051" target="_blank">51</a>].</p
<p>Data are summarized from <a href="http://www.plosone.org/article/info:doi/10.137... more <p>Data are summarized from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0205920#pone.0205920.s002" target="_blank">S1 Fig</a>. Origin of modern individuals with closest matches to Conqueror sequences are listed next to the indicated regions, ordered according to the frequency of appearances.</p
Background Current state of art kinship analysis is capable to infer relatedness up to the 5-6th ... more Background Current state of art kinship analysis is capable to infer relatedness up to the 5-6th degree from deeply sequenced DNA if the proper reference population is known. Low coverage, partially genotyped, degraded archaic (or forensic) DNA and often unavailable or unknown reference population poses additional challenges, hence kinship analysis from low coverage archaic sequences so far has been possible up to the second degree with large uncertainties. Results We performed extensive simulations to identify and correct the main factors of bias in kinship analysis from low coverage data. As a result, we introduce a new metric for correction and offer a guideline, which overcomes the difficulties associated with low coverage samples. We validated our methodology on experimental modern and archaic data with widely different genome coverages (0.12x-11.9x) using samples with known family relations and known or unknown population structure. Out of 2526 ancient individuals from the REI...
According to the written historical sources, the Gepids were a Germanic tribe that settled in the... more According to the written historical sources, the Gepids were a Germanic tribe that settled in the Carpathian Basin during the Migration Period. They were allies of the Huns, and an independent Gepid Kingdom arose after the collapse of the Hun Empire. In this period, the Carpathian Basin was characterized by so-called row-grave cemeteries. Due to the scarcity of historical and archaeological data, we have a poor knowledge of the origin and composition of these barbarian populations, and this is still a subject of debate. To better understand the genetic legacy of migration period societies, we obtained 46 full mitogenome sequences from three Gepid cemeteries located in Transylvania, Romania. The studied samples represent the Classical Gepidic period and illustrate the genetic make-up of this group from the late 5th and early 6th centuries AD, which is characterized by cultural markers associated with the Gepid culture in Transylvania. The genetic structure of the Gepid people is expl...
According to the written historical sources, the Gepids were a Germanic tribe that settled in the... more According to the written historical sources, the Gepids were a Germanic tribe that settled in the Carpathian Basin during the Migration Period. They were allies of the Huns, and an independent Gepid Kingdom arose after the collapse of the Hun Empire. In this period, the Carpathian Basin was characterized by so-called row-grave cemeteries. Due to the scarcity of historical and archaeological data, we have a poor knowledge of the origin and composition of these barbarian populations, and this is still a subject of debate. To better understand the genetic legacy of migration period societies, we obtained 46 full mitogenome sequences from three Gepid cemeteries located in Transylvania, Romania. The studied samples represent the Classical Gepidic period and illustrate the genetic make-up of this group from the late 5th and early 6th centuries AD, which is characterized by cultural markers associated with the Gepid culture in Transylvania. The genetic structure of the Gepid people is expl...
We applied ancient DNA methods to shed light on the origin of ancient Hungarians and their relati... more We applied ancient DNA methods to shed light on the origin of ancient Hungarians and their relation to modern populations. Hungarians moved into the Carpathian Basin from the Eurasian Pontic steppes in the year 895 AD as a confederation of seven tribes, but their further origin remains obscure. Here, we present 17 mtDNA haplotypes and four Y-chromosome haplogroups, which portray the genetic composition of an entire small cemetery of the first generation Hungarians. Using novel algorithms to compare these mitochondrial DNA haplogroups with other ancient and modern Eurasian data, we revealed that a significant portion of the Hungarians probably originated from a long ago consolidated gene pool in Central Asia-South Siberia, which still persists in modern Hungarians. Another genetic layer of the early Hungarians was obtained during their westward migrations by admixing with various populations of European origin, and an important component of these was derived from the Caucasus region....
Fontosabb eredmenyek Kimutattuk, hogy a bithorax komplexben (Bx-C) a Polycomb Response Elementek ... more Fontosabb eredmenyek Kimutattuk, hogy a bithorax komplexben (Bx-C) a Polycomb Response Elementek (PRE-k), es a hozzajuk kapcsolodo Polycomb feherjek nemcsak a cisz-regulator regiok inaktiv/zart allapotanak fenntartasaban jatszanak fontos szerepet, hanem az aktiv/nyilt allapotu cisz-regulatorokban talalhato enhanszerek hatasanak modulalasaban is. Ezt a hatas ugy fejti ki, hogy fizikailag a celgen promoterehez kotődik. Ezzel osszefuggesben kimutattuk egy, a bxd PRE-vel reszben atfedő Targetalo Elem (TE) jelenletet. A TE a PRE-hez hasonloan modularis szerkezetű. Igazoltuk, hogy ez az elem nemcsak a PRE promoterhez valo kőtődeseben jatszik szerepet, hanem reszt vesz a bxd regioban talalhato enhanszereknek az Ubx promotere kore valo szervezeseben, azaz az „acticve chromatin hub” kialakitasaban. A TE ezt a funkciojat ektopikus kornyezetben, az iab-7 cisz regulatorban is megőrzi. A PRE-től hatarolo elemmel elvalasztott bxd enhanszerek ektopikus aktivitast mutatnak, amely mind fenotipus analizissel, mind markergen expressziojanak kovetesevel kimutathato. Kinutattuk, hogy az ebi gen a Polycomb csoport genjei koze sorolando, es a polyhomeotic gennel egyutt az aktiv allapotu cisz-regulatorokban fejti ki modulalo hatasat. Kvantitativ RTPCR segitsegevel kimutattuk, hogy az Abd-B RNS mennyisege korulbelul duplajara nő polyhomeotic mutans hatteren. | We showed that Polycomb Response Elements (PREs) and Polycomb proteins bound to them play an important role not only in maintaining inactive/closed conformation of cis-regulatory elements in the bithorax complex, but they are also involved in modulating the regulatory output of enhancers in the active/open domains. This latter effect is mediated by direct physical contact between the PRE and the promoter – enhancer complex. In connection with this we demonstrated the presence of a Targeting Element (TE) that partially overlaps with the bxd PRE. TE is, similarly to the PRE, modularly organized. We showed that this element is involved not only in targeting the PRE to the Ubx promoter, but also part of the machinery organizing the active chromatin hub around cognate promoter. We also demonstrated that the TE maintains its activity in ectopic context, in the iab-7 cis-regulatory region. Enhancers separated from the bxd PRE by a boundary region exhibit ectopic activity, as revealed by both phenotypic analysis and by monitoring the expression pattern of a marker gene. We identified the ebi gene as an unusual Polycomb group member, which, similarly to the polyhometic gene, participates in the modulation of enhancer output of active cis-regulatory regions. Using quantitative RTPCR we showed that the amount of the Abd-B RNA is doubled in polyhomeotic mutant background.
SummaryHuns, Avars and conquering Hungarians were Migration Period nomadic groups which arrived i... more SummaryHuns, Avars and conquering Hungarians were Migration Period nomadic groups which arrived in three successive waves in the Carpathian Basin between the 5th and 9th centuries. Based on historical data each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations has been debated. In this study we have sequenced 9 Hun, 143 Avar and 113 Hungarian conquest period samples, and identified three core populations, representing immigrants from each period, with no recent European ancestry. Our results suggest that this “immigrant core” of both Huns and Avars originated in present day Mongolia, and their origin can be traced back to Xiongnus. On the other hand, the “immigrant core” of the conquering Hungarians derived from an earlier admixture of Mansis, early Sarmatians and descendants of late Xiongnus. In addition, we detected shared Hun-related ancestry in numerous Avar and Hungarian conquest period geneti...
Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but ge... more Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10–11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the immigrant elite have been widely debated. Mitogenome sequences were obtained from 202 individuals with next generation sequencing combined with hybridization capture. Median joining networks were used for phylogenetic analysis. The commoner population was compared to 87 ancient Eurasian populations with sequence-based (Fst) and haplogroup-based population genetic methods. The haplogroup composition of the commoner population markedly differs from that of the elite, and, in contrast to the elite, commoners cluster with European populations. Alongside this, detectable sub-haplogroup sharing indicates admixture between the elite and the commoners. The majority of the 10–11th century commoners most likely represen...
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