Ancient DNA Evidence from China Reveals the Expansion of Pacific Dogs

Zhang, Ming; Sun, Ge; Ren, Lele; Yuan, Haibing; Guo, Dong; Zhang, Lizhao; Liu, Feng; Ko, Albert Min-Shan; Yang, Melinda A.; Hu, Songmei; Wang, Guodong; Fu, Qiaomei

doi:10.1093/molbev/msz311

Cited by 24 publications

(58 citation statements)

References 41 publications

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“…In order to investigate haplogroup patterns and dynamics, ggplot2 [58], a data visualization package in R [59], was used to create a graphical representation of the proportions of haplogroup through time. The plot included the ancient Eurasian dogs from this study and those available in the literature [6,9,10,13,29,31,33,34,52,[60][61][62][63][64] (Table S1).…”

Section: Haplotype Identification and Phylogenetic Analysesmentioning

confidence: 99%

Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age

Koupadi

Fontani

Ciucani

et al. 2020

Genes

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Dog domestication is still largely unresolved due to time-gaps in the sampling of regions. Ancient Italian canids are particularly understudied, currently represented by only a few specimens. In the present study, we sampled 27 canid remains from Northern Italy dated between the Late Pleistocene and Bronze Age to assess their genetic variability, and thus add context to dog domestication dynamics. They were targeted at four DNA fragments of the hypervariable region 1 of mitochondrial DNA. A total of 11 samples had good DNA preservation and were used for phylogenetic analyses. The dog samples were assigned to dog haplogroups A, C and D, and a Late Pleistocene wolf was set into wolf haplogroup 2. We present our data in the landscape of ancient and modern dog genetic variability, with a particular focus on the ancient Italian samples published thus far. Our results suggest there is high genetic variability within ancient Italian canids, where close relationships were evident between both a ~24,700 years old Italian canid, and Iberian and Bulgarian ancient dogs. These findings emphasize that disentangling dog domestication dynamics benefits from the analysis of specimens from Southern European regions.

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Section: Haplotype Identification and Phylogenetic Analysesmentioning

confidence: 99%

Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age

Koupadi

Fontani

Ciucani

et al. 2020

Genes

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“…Shisanhang (Taiwan) is one of two samples from the region and is considered the root of the network [19].…”

Section: Comparison Of Dingo Mtdna Genomesmentioning

confidence: 99%

“…Australian mtDNA type of the canine A1b4 subhaplogroup. This southeastern type has been proposed to originate in southern China and includes dogs from Papua New Guinea [19,22].…”

Section: Phylogenetic and Network Analyses Show That Dingo Cooinda Ha...mentioning

confidence: 99%

“…Next, we conducted a network analysis in Popart [53] to determine whether the mtDNA of dingo Cooinda fell within the previously described dingo southeastern or northwest clade (Fig. 4) [19,22]. We included dingo mtDNA from four previous studies, a New Guinea Singing Dog, and an ancient Iron Age dog from Taiwan [6,22,[54][55][56].…”

Section: Comparison Of Dingo Mtdna Genomesmentioning

confidence: 99%

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The Australasian dingo archetype:De novochromosome-length genome assembly, DNA methylome, and cranial morphology

Ballard

Field

Edwards

et al. 2023

Preprint

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Background: One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. Findings: We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on Chromosomes 11, 16, 25 and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and nine previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mtDNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified two differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphological data, comprising geometric morphometric assessment of cranial morphology place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue show she had a larger cranial capacity than a similar-sized domestic dog. Conclusions: These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphological characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.

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“…This makes it difficult to harvest the target DNA of ancient remains through the conventional method of PCR amplification. One possible alternative to PCR amplification is target enrichment via DNA hybridization capture, a well‐tested method for obtaining DNA data from bones of ancient humans (Haak et al, 2015; Liu et al, 2021; Wang et al, 2019; Yang et al, 2020), ancient animals (Wen et al, 2022; Zhang, Sun, et al, 2020), and environmental sediments (Massilani et al, 2022; Schulte et al, 2021; Slon et al, 2017; Zhang, Xia, et al, 2020). However, to our knowledge, no studies on aDNA capture from wood remains have reported using this method so far (Orlando et al, 2021; Wagner et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Ancient plastid genomes solve the tree species mystery of the imperial wood “Nanmu” in the Forbidden City, the largest existing wooden palace complex in the world

Jiao

Zhang

et al. 2022

Plants People Planet

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Societal Impact Statement Combining natural and social science approaches to conduct archeological research on wooden cultural relics is important for exploring major aspects of ancient civilizations. The Forbidden City in Beijing, China, is the largest existing wooden palace complex in the world. We examined ancient DNA of imperial wood “Nanmu” specimens taken from representative structural components of the Forbidden City, in order to provide a new perspective on the long‐standing dispute about its species. This allowed us to accurately identify and properly restore these wooden artifacts and improved our understanding of the past interactions between plant distribution, forest resources, and human activities. Summary Exploring the life styles and production methods of past generations using plant resources can help us to improve our understanding of human civilization. Nanmu, known for its high wood quality, was exclusively used for imperial palace construction in the 15th–19th centuries in China, yet its species has been a subject of long‐standing debate. Here, we revisit this unresolved problem, using morphology and ancient DNA (aDNA) to analyze 21 centuries‐old Nanmu specimens sampled from representative palaces of the Forbidden City. Cytochemical staining demonstrated that endogenous aDNA sporadically occurs in the wood ray parenchyma cells of Nanmu specimens. High‐quality plastid genomes were retrieved from archeological woods for the first time via an aDNA capture method, with 90%–100% coverage (137,663–152,805 bp) and sequence depths of 27.05‐ to 1409.94‐fold. Utilizing these ancient genomes, our results demonstrate that Phoebe zhennan and Phoebe hui are most likely the main species of Nanmu in the Forbidden City. This finding diverges from the prevailing view that Nanmu encompasses woods from the whole genus Phoebe and even its close relative Machilus. It also shows that stringent criteria were used when selecting construction materials for the Forbidden City. By combining morphological traits with aDNA analyses, we provide a new solution for identifying the species of timber used for ancient architecture, and we increase our understanding of the way in which forest resources were recognized and utilized by our ancestors despite the lack of a plant taxonomic framework in ancient times.

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Ancient DNA Evidence from China Reveals the Expansion of Pacific Dogs

Cited by 24 publications

References 41 publications

Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age

Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age

The Australasian dingo archetype:De novochromosome-length genome assembly, DNA methylome, and cranial morphology

Ancient plastid genomes solve the tree species mystery of the imperial wood “Nanmu” in the Forbidden City, the largest existing wooden palace complex in the world

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