Siberian wolf, Canis lupus
These days, no serious scientist sets out to prove the Bible is wrong; discovering truth does that anyway - for anyone who can join the dots and do the simple logic. For example, humans could not have domesticated dogs some 23,000 years ago in Siberia by domesticating the local variety of grey wolf, if the Universe is just 10,000 years old.
And yet a paper published recently in the journal Molecular Biology & Evolution shows that they did exactly that.
In the context of mitochondrial DNA, what are haplotypes? In the context of mitochondrial DNA (mtDNA), haplotypes refer to specific combinations of genetic variants or polymorphisms within the mitochondrial genome. Unlike nuclear DNA, which is inherited from both parents, mtDNA is passed down exclusively from the mother to all of her offspring. This maternal inheritance pattern makes mtDNA useful for studying ancestry, population genetics, and evolutionary history.Refuting the Bible was almost certainly not the intention of the authors, jointly led by Songmei Hu, of Joint International Research Laboratory of Environmental and Social Archaeology, Shandong University, Qingdao, China, and Xijun Ni and Qiaomei Fu, both of the Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China, but the facts they discovered do just that. They had set out to resolve the question of where exactly dogs had been domesticated, based on an analysis of the mitochondrial DNA.
A haplotype represents a unique combination of nucleotide variations or mutations along the mtDNA sequence. By analyzing these haplotypes, researchers can track maternal lineages, study population migrations, and infer evolutionary relationships among different groups of individuals. Haplotypes are often used in studies of human populations, as well as in forensic genetics and medical research related to mitochondrial disorders.
Mitochondrial DNA (mDNA) is inherited through the maternal line, so an analysis of the geographical and temporal distribution of the various haplotypes of mDNA and how they relate to one another should give an indication of where and when the ancestral haplotype lived.
How the team did this is explained in their paper:
AbstractNot only is there very reliable evidence of the evolution of domestic dogs, Canis lupus familiaris from the grey wolf, Canis lupus, but this mitochondrial DNA analysis places the geographical and temporal divergence in Siberia, some 23,000 years ago around the Last Glacial Maximum. Of course, the simple Bronze Age pastoralists who wrote their origins myths in the Bible knew nothing of Siberia or glacial maxima, or what people living there and then were doing with their first domesticated animals. Now we have the tools to discover the truth, we can readily see where they got things so badly wrong and so see what creationists have failed to grasp - that ignorance really is not the quickest way to expertise in any subject.
Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.
Introduction
The gray wolf (Canis lupus) was the first species to be domesticated, eventually giving rise to dogs. Dogs have accompanied humans on every continent they have inhabited as demonstrated by archaeological records (Frantz et al. 2016; Bergström et al. 2020) and genetic studies (Pang et al. 2009; Thalmann et al. 2013; Peng et al. 2015; Song et al.2016; Ní-Leathlobhair et al. 2018; Ameen et al. 2019; Bergström et al. 2020; Zhang et al. 2020.1; Perri et al. 2021); thus, the genetic history of dogs also reflects human history (Frantz et al. 2016; Ní-Leathlobhair et al. 2018; Bergström et al. 2020; Zhang et al. 2020.1; Perri et al. 2021). Despite their importance in human history, the timing of their domestication and geographical origins are still unclear. Potential domestic centers have been proposed, including Europe (Thalmann et al. 2013), the Middle East (VonHoldt et al. 2010), and southern East Asia (Pang et al. 2009; Wang et al. 2016.2). Genomic data have shown that southern East Asian gray wolves (the likely ancestor of dogs based on modern genetic studies) originate from a single lineage and may form a distinct sub-population (Wang et al. 2019.1) suggested the dogs may not originate from southern East Asia. Ancient dog remains from the northern part of East Asia are older and more numerous than in the southern part (Wu 2014; Zhao 2014.1; Ren and Dong 2016.3), indicating that dogs at least appeared in northern East Asia before they are recorded in the south, contradicting the expectations of a southern East Asian origin hypothesis.
Recent studies based on ancient DNA (aDNA) have suggested that dogs may have originated in Siberia (Perri et al. 2021). Dogs are generally more closely related to ancient wolves from eastern Eurasia (northern East Asia and eastern Siberia) than to those from western Eurasia (Europe and the Middle East), and an eastern Eurasian-related source appears to have contributed approximately 100% of the ancestry of early dogs in Siberia, the Americas, East Asia, and northeastern Europe (Bergström et al. 2022). Perri et al. (2021) proposed that during the harsh environment of the last glacial maximum (LGM), the ancestor of dogs was domesticated due to coexistence with humans in Siberia, also suggesting a domestication process in eastern Eurasia. These studies have shown that aDNA can be used to understand dog evolution in a powerful way. More aDNA data from East Asia will improve our understanding of the genetic origins of dogs.
To establish a more precise geographic and temporal framework for dog genetic history in East Asia, we recently sequenced 102 complete mitochondrial genomes of ancient individuals (see supplementary table S1, Supplementary Material online). Published ancient and modern mitogenomes (see supplementary table S2, Supplementary Material online) were also selected to profile the maternal genetic history and migration waves of dogs in East Asia.
[…]
Probable Northeastern Eurasian Origin and Southwards Expansion of East Asian Dogs
Recently, Perri et al. (2021) proposed that during the harsh environment of the LGM, the ancestors of dogs were domesticated in Siberia by approximately 23 ka BP. Bergström et al. (2022) by demonstrating that dogs share a closer genetic affinity with ancient wolves from eastern Eurasia rather than those from western Eurasia. This also implies a domestication process centered in eastern Eurasia. After comprehensive examinations of zooarchaeological studies across East Asia, a notable disparity emerges in the distribution of dog remains. These findings indicate a significantly earlier and more abundant presence of dog remains in northern East Asia compared to southern East Asia. The absence of dog remains in southern East Asia before 8.3 ka BP is not likely to be attributable to biases in the archaeological record caused by poor preservation of remains due to the acidic soil or a humid climate of southern East Asia, since older, nondog remains are abundant at multiple southern East Asian archaeological sites (e.g. Wu 2014; Zhao 2014) (see supplementary fig. S1, Supplementary Material online). Moreover, the maternal lineages of ancient dogs from northern East Asia were deeper than the ancient and modern dogs from the south (see supplementary figs. S3, S4 and table S1, Supplementary Material online). The absence of archaeological evidence and the presence of younger maternal lineages suggest a lack of dogs in southern East Asia before 8.3 ka BP (see supplementary fig. S1, Supplementary Material online), further supporting a northeastern Eurasia origin for East Asian domesticated dogs (Perri et al. 2021; Bergström et al. 2022) after the LGM (Fig. 3).
[…]
Conclusions
East Asia has preserved most dog mitochondrial haplogroups from ancient to modern times, which may attest to its important role in dog domestication. East Asian dogs were likely derived from northeastern Eurasian populations after the LGM (Bergström et al. 2020, 2022; Perri et al. 2021). The dog population began to expand at the end of the LGM (Fig. 2a), coinciding with the warming climate. Two major dispersal directions of domesticated dogs into East Asia can be ascertained. One southward into eastern China and the other southwestward to western China, gradually forming the AEC and the AWC groups (Fig. 3a) during 8 to 5 ka BP. The emergence of haplogroups A1a, B, and C in East Asia indicated a maternal genetic contribution from western to eastern Eurasian dogs approximately 4 ka BP, with the western Eurasian influence increasing rapidly after 3 ka BP (Fig. 2c). Subsequently, it largely replaced most primary maternal lineages in northern East Asia during the ensuing periods. We identified at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) that represent two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times. Further aDNA studies, particularly those incorporating nuclear genome data, from less sampled regions will contribute to filling in the remaining details of the population history and origin of dogs.Fig. 1a) Geographic locations of different archaeological sites. The dots depict all 38 sites from East Asia, where the number of specimens is listed after the location. The samples are marked with colors ranging from red to green, indicating the range of their ages from older to younger. Two concentrated areas are enlarged for better viewing. Base map downloaded from Natural Earth (www.naturalearthdata.com). b) A map of China with pie charts showing the location of the specimens and associated sub-haplogroups belonging to haplogroup A. Data of modern Europe, Australian dingoes, precolonial Pacific Island, and ancient Siberia were cited from Zhang et al. (2020); and North America was cited from Ameen et al. (2019). c) A simplified tree was based on a Bayesian phylogenetic tree (see supplementary fig. S3, Supplementary Material online). Four main East Asian sub-haplogroups (A1b1, A1b2, A1b3, and A2c) are marked in different colors. d) Geographic distribution heatmaps of four main East Asian sub-haplogroups (A1b1, A1b2, A1b3, and A2c). The dots depict ancient individuals of each sub-haplogroups, and colors represent the age of the samples.a) Bayesian skyline plot based on 188 individuals for effective female population size (Nef) estimation. The plot shows three obvious expansions: the first one starts at approximately 20 to 19 ka BP, the second one starts at approximately 8 to 7.5 ka BP, and the third one starts at approximately 3 to 2.5 ka BP. b) Median-joining network of sub-haplogroup A1b, divided into four main lineages (A1b1, A1b2, A1b3, and A1b4). Haplotypes are represented by circles whose sizes are proportional to the number of individuals. c) Haplogroup proportion of different time periods (five time periods spanning the Neolithic to the Iron Age) in East Asia. Ancient individuals within sub-haplogroup A1a found in East Asia increased quickly after 3 ka BP. d) Median-joining network of sub-haplogroup A3. It showed clear connections among ancient dogs from northeastern Eurasia (New Siberian Islands, approximately 9 ka BP), northern China (Xinglong, approximately 8.5 to 8 ka BP), western China (Donglongshan, approximately 3.7 ka BP), and the Qinghai-Tibet Plateau (Talitaliha, approximately 2.9 ka BP; Meilongdapu, approximately 3 ka BP; and Sangdalongguo, approximately 1.7 ka BP).Fig. 2Fig. 3
Main migratory events associated with the maternal genetic history of dogs from the Neolithic to Iron Age (approximately 12.9 to 1 ka BP), derived from a synthesis of available evidence. The specific migratory events of dogs belonging to haplogroup A1b as in (a); A1a as in (b); A3 as in (c); A2 as in (d), and A2c as in (e).
Ming Zhang, Yanbo Song, Caihui Wang, et.al, (2024) Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs Molecular Biology and Evolution 41(4) msae062, https://doi.org/10.1093/molbev/msae062
Copyright: © 2024 The authors.
Published by Oxford University Press. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
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