Post by Admin on Jul 18, 2022 19:47:32 GMT
Discussion
Southern East Asia harbors rich archaeo-anthropological sites with rich morphological diversities, including the ∼100 kya Zhiren Cave72 and ∼120–80 kya Fuyan Cave73 in southern China (although a recent study suggested much younger dates for these two sites74), the ∼190–50 kya H. floresiensis,28 and the 67 kya H. luzonensis in Southeast Asia.75 Indeed, based on the published mitochondrial genome data, the matrilineal lineage diversity of the Late Pleistocene hominins in eastern Eurasia is quite high, including the reported Ust’-Ishim (45.0 kya, novel N∗),76 Salkhit (34.0 kya, independent novel N∗),77,78 Tianyuan (40.0 kya, basal B∗),79 Yana-old (32.0 kya, U),80 MA-1 (24.3 kya, novel U∗),81 LLR (11.0 kya, M27d), and MZR (14.0 kya, basal M9∗) in this study, many of which were lost during the post Pleistocene (<11.7 kya) human evolutionary histories. In addition, the hominin fossils from these archaeological sites, such as MZR and LLR, all exhibit rich physical anthropological diversities, some of which were thought to overlap with the morphological characteristics of archaic hominins and triggered proposals of different scenarios of human evolution in this area.12,20, 21, 22,29,82
In this study, we provide compelling evidence that the Late Pleistocene MZR from Malu Dong in Southwest China is an AMH. The nuclear genome data indicate that MZR represents an early diversified AMH lineage in East Asia. The mtDNA of MZR belongs to one of the root matrilineal lineages of AMHs in southern East Asia. Identified as a novel basal M9 lineage, MZR may represent one of the extinct pioneer hunter-gatherers ancestral to millet and rice farmers in China who emerged in the Yellow River and Yangtze River valley during the Early Neolithic period.83,84 Additionally, we observe obvious stratification and substructure of ancient human populations between southern China and mainland Southeast Asia, an indication of already diversified genetic backgrounds of the Late Pleistocene populations in southern East Asia.
Importantly, we observed similar levels of introgression of Denisovan and Neanderthal ancestries in the MZR compared with current East Asians, consistent with the reported introgression levels in the LLR.19 Thus, these observations are against the proposal of hybridization between AMHs and archaic hominins in explaining the unusual morphologies of MZR. However, due to the low coverage of the reported MZR nuclear genome, we cannot completely rule out the possibility that MZR may carry individual archaic alleles in key genomic regions that contribute to her unusual morphological features, and this possibility can be tested in the future when high-coverage genome data are available.
It should be noted that the MZR morphological data are indeed informative in reconstructing human morphological diversity during the Late Pleistocene in southern East Asia.20,21 However, due to the limited human remains as well as the limited number of morphological traits, it would be hard to confidently reveal the identity of the studied subject. To this end, genome sequence data are critical for unequivocal species identification, quantification of genetic introgression, and reconstruction of population history.
Spatiotemporal tracing of mutations related to phenotypic changes in human populations can help reconstruct the prehistoric patterns of how natural selection has shaped these adaptive events. We observed that the OCA2-HiS615Arg (rs1800414) variant, a key adaptive mutation causing skin lightening in East Asians, initially emerged in the southern coastal region of China during the early Neolithic (Liangdao2-7.5kya). The rapid dispersal of this variant during the past 4,000 years in East Asia is consistent with the proposed Darwinian positive selection on the adaptive allele (OCA2-615Arg), leading to skin lightening in East Asians to cope with the relatively low UV radiation in high-latitude areas. Interestingly, the rapid explosion of OCA2-615Arg coincides with the known major population expansion in China during the Late Holocene epoch.64, 65, 66, 67 It should be noted that due to the limited aDNA data in East Asia, the inferred time of selection onset for OCA2-HiS615Arg is a rough estimation. With more aDNA data available in the future, we expect more accurate time estimation and high-resolution spatial-temporal tracking of adaptive genetic variants in East Asia.
Consistent with the dating of MZR (14.0 kya), following the end of the LGM (26.5–19.0 kya)85 and the earliest securely dated sites in Beringia (15–14 kya),86 we demonstrate that MZR has a higher affinity to First Americans than to Tianyuan (40 kya) and all the pre-LGM Late Pleistocene Siberians. MZR, Amur-19K, and UKY are cladal with respect to First Americans, while Amur-14kya and UKY exhibit a higher affinity to the Americans compared to MZR. Thus, MZR is linked deeply and indirectly to the ancestry that contributed to First Americans. We speculate that during the Late Pleistocene, there was an express northward expansion of AMHs starting in southern East Asia through the coastal line of China, possibly by way of the Japanese Islands, and eventually crossing the Bering Strait and reaching the Americas. However, the scenario that MZR shows a higher affinity to Americans compared to Jomon likely reflects that the 2.6 kya Jomon population does not represent the early post-LGM humans who settled in the Japanese archipelago. The proposed migratory route along the east coast of East Asia by way of the Japanese Islands is supported by a recent finding of a Paleolithic site (∼16 kya) at Cooper’s Ferry of western Idaho, USA, where they found the use of unfluted stemmed projectile point technologies before the appearance of the Clovis Paleoindian tradition.87 Notably, it exhibits early cultural connections with Paleolithic nonfluted projectile point traditions in Japan.87 The bifacial point and backed blade technologies (∼22–16 kya) in Honshu, Japan, lend technological correlates to the shared ecological and geographical factors with the Americas.88
This scenario is also supported by the current distribution pattern of the ancient Y-chromosome lineage Hg C in coastal East Asia, Siberia, and North America.59 Approximately 40 kya, stemming from southern East Asia, the Hg C carriers started a northward expansion along the coastal regions of mainland China, the Korean Peninsula, and the Japanese archipelago, reaching Siberia ∼15 kya, and finally made their way to the Americas.59 In addition, unlike all other East Asian populations, the indigenous Ainu people in northern Japan and Sakhalin Island, Russia, show a closer genetic affinity with northeastern Siberians than with central Siberians.89 Hence, the Japanese Islands may serve as the midway station along the proposed migratory route, and aDNA data of Late Pleistocene human remains from Japan will be highly informative in testing the proposed coastal route. Finally, the spatial-temporal distribution of the East Asian-specific EDAR-V370A variant, as well as its early presence in the LosRieles-12.0kya sample from coastal Chile of South America, supported a clear contribution of the Late Pleistocene East Asians to the first Americans.
In summary, we generated ancient genome sequences of MZR, a Late Pleistocene female who lived in Southwest China, one of the global biodiversity hotspots and the ice age refuge region. The aDNA data confirm that she possesses diverse genetic components and represents an early diversified population, suggesting the scenario of more diverse AMH lineages than previously thought during the Late Pleistocene in southern East Asia.58,72,73 Our study paves the way to explore genetic explanations of morphological complexities of early hominins. MZR also shows a deep and indirect link to the ancestry that contributed to First Americans, which may help reconstruct the earliest migratory route from East Asia to the Americas.
It should be noted that the presented sequencing data of MZR have a relatively low coverage of the genome, leading to limited numbers of shared informative SNPs for cross-population analyses, which may cause bias, e.g., in the f3 and D-stat statistics. Thus, more aDNA studies of Late Pleistocene hominins from East Asia are needed to delineate a clear picture of the earliest peopling of AMHs in this region.
Supplemental information
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Southern East Asia harbors rich archaeo-anthropological sites with rich morphological diversities, including the ∼100 kya Zhiren Cave72 and ∼120–80 kya Fuyan Cave73 in southern China (although a recent study suggested much younger dates for these two sites74), the ∼190–50 kya H. floresiensis,28 and the 67 kya H. luzonensis in Southeast Asia.75 Indeed, based on the published mitochondrial genome data, the matrilineal lineage diversity of the Late Pleistocene hominins in eastern Eurasia is quite high, including the reported Ust’-Ishim (45.0 kya, novel N∗),76 Salkhit (34.0 kya, independent novel N∗),77,78 Tianyuan (40.0 kya, basal B∗),79 Yana-old (32.0 kya, U),80 MA-1 (24.3 kya, novel U∗),81 LLR (11.0 kya, M27d), and MZR (14.0 kya, basal M9∗) in this study, many of which were lost during the post Pleistocene (<11.7 kya) human evolutionary histories. In addition, the hominin fossils from these archaeological sites, such as MZR and LLR, all exhibit rich physical anthropological diversities, some of which were thought to overlap with the morphological characteristics of archaic hominins and triggered proposals of different scenarios of human evolution in this area.12,20, 21, 22,29,82
In this study, we provide compelling evidence that the Late Pleistocene MZR from Malu Dong in Southwest China is an AMH. The nuclear genome data indicate that MZR represents an early diversified AMH lineage in East Asia. The mtDNA of MZR belongs to one of the root matrilineal lineages of AMHs in southern East Asia. Identified as a novel basal M9 lineage, MZR may represent one of the extinct pioneer hunter-gatherers ancestral to millet and rice farmers in China who emerged in the Yellow River and Yangtze River valley during the Early Neolithic period.83,84 Additionally, we observe obvious stratification and substructure of ancient human populations between southern China and mainland Southeast Asia, an indication of already diversified genetic backgrounds of the Late Pleistocene populations in southern East Asia.
Importantly, we observed similar levels of introgression of Denisovan and Neanderthal ancestries in the MZR compared with current East Asians, consistent with the reported introgression levels in the LLR.19 Thus, these observations are against the proposal of hybridization between AMHs and archaic hominins in explaining the unusual morphologies of MZR. However, due to the low coverage of the reported MZR nuclear genome, we cannot completely rule out the possibility that MZR may carry individual archaic alleles in key genomic regions that contribute to her unusual morphological features, and this possibility can be tested in the future when high-coverage genome data are available.
It should be noted that the MZR morphological data are indeed informative in reconstructing human morphological diversity during the Late Pleistocene in southern East Asia.20,21 However, due to the limited human remains as well as the limited number of morphological traits, it would be hard to confidently reveal the identity of the studied subject. To this end, genome sequence data are critical for unequivocal species identification, quantification of genetic introgression, and reconstruction of population history.
Spatiotemporal tracing of mutations related to phenotypic changes in human populations can help reconstruct the prehistoric patterns of how natural selection has shaped these adaptive events. We observed that the OCA2-HiS615Arg (rs1800414) variant, a key adaptive mutation causing skin lightening in East Asians, initially emerged in the southern coastal region of China during the early Neolithic (Liangdao2-7.5kya). The rapid dispersal of this variant during the past 4,000 years in East Asia is consistent with the proposed Darwinian positive selection on the adaptive allele (OCA2-615Arg), leading to skin lightening in East Asians to cope with the relatively low UV radiation in high-latitude areas. Interestingly, the rapid explosion of OCA2-615Arg coincides with the known major population expansion in China during the Late Holocene epoch.64, 65, 66, 67 It should be noted that due to the limited aDNA data in East Asia, the inferred time of selection onset for OCA2-HiS615Arg is a rough estimation. With more aDNA data available in the future, we expect more accurate time estimation and high-resolution spatial-temporal tracking of adaptive genetic variants in East Asia.
Consistent with the dating of MZR (14.0 kya), following the end of the LGM (26.5–19.0 kya)85 and the earliest securely dated sites in Beringia (15–14 kya),86 we demonstrate that MZR has a higher affinity to First Americans than to Tianyuan (40 kya) and all the pre-LGM Late Pleistocene Siberians. MZR, Amur-19K, and UKY are cladal with respect to First Americans, while Amur-14kya and UKY exhibit a higher affinity to the Americans compared to MZR. Thus, MZR is linked deeply and indirectly to the ancestry that contributed to First Americans. We speculate that during the Late Pleistocene, there was an express northward expansion of AMHs starting in southern East Asia through the coastal line of China, possibly by way of the Japanese Islands, and eventually crossing the Bering Strait and reaching the Americas. However, the scenario that MZR shows a higher affinity to Americans compared to Jomon likely reflects that the 2.6 kya Jomon population does not represent the early post-LGM humans who settled in the Japanese archipelago. The proposed migratory route along the east coast of East Asia by way of the Japanese Islands is supported by a recent finding of a Paleolithic site (∼16 kya) at Cooper’s Ferry of western Idaho, USA, where they found the use of unfluted stemmed projectile point technologies before the appearance of the Clovis Paleoindian tradition.87 Notably, it exhibits early cultural connections with Paleolithic nonfluted projectile point traditions in Japan.87 The bifacial point and backed blade technologies (∼22–16 kya) in Honshu, Japan, lend technological correlates to the shared ecological and geographical factors with the Americas.88
This scenario is also supported by the current distribution pattern of the ancient Y-chromosome lineage Hg C in coastal East Asia, Siberia, and North America.59 Approximately 40 kya, stemming from southern East Asia, the Hg C carriers started a northward expansion along the coastal regions of mainland China, the Korean Peninsula, and the Japanese archipelago, reaching Siberia ∼15 kya, and finally made their way to the Americas.59 In addition, unlike all other East Asian populations, the indigenous Ainu people in northern Japan and Sakhalin Island, Russia, show a closer genetic affinity with northeastern Siberians than with central Siberians.89 Hence, the Japanese Islands may serve as the midway station along the proposed migratory route, and aDNA data of Late Pleistocene human remains from Japan will be highly informative in testing the proposed coastal route. Finally, the spatial-temporal distribution of the East Asian-specific EDAR-V370A variant, as well as its early presence in the LosRieles-12.0kya sample from coastal Chile of South America, supported a clear contribution of the Late Pleistocene East Asians to the first Americans.
In summary, we generated ancient genome sequences of MZR, a Late Pleistocene female who lived in Southwest China, one of the global biodiversity hotspots and the ice age refuge region. The aDNA data confirm that she possesses diverse genetic components and represents an early diversified population, suggesting the scenario of more diverse AMH lineages than previously thought during the Late Pleistocene in southern East Asia.58,72,73 Our study paves the way to explore genetic explanations of morphological complexities of early hominins. MZR also shows a deep and indirect link to the ancestry that contributed to First Americans, which may help reconstruct the earliest migratory route from East Asia to the Americas.
It should be noted that the presented sequencing data of MZR have a relatively low coverage of the genome, leading to limited numbers of shared informative SNPs for cross-population analyses, which may cause bias, e.g., in the f3 and D-stat statistics. Thus, more aDNA studies of Late Pleistocene hominins from East Asia are needed to delineate a clear picture of the earliest peopling of AMHs in this region.
Supplemental information
Download .pdf (5.29 MB)