The Japanese wolf is most closely related to modern dogs and its ancestral genome has been widely inherited by dogs throughout East Eurasia

Gojobori, Jun; Arakawa, Nami; Xiayire, Xiaokaiti; Matsumoto, Yuki; Matsumura, Shuichi; Hongo, Hitomi; Ishiguro, Naotaka; Terai, Yohey

doi:10.1101/2021.10.10.463851

Cited by 6 publications

(21 citation statements)

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Section: Resultsmentioning

confidence: 99%

“…In Eurasia, the genomes of dogs of Eastern and Western Eurasian lineages have been admixed (Gojobori, et al 2021). However, dingo/NGSD and African dogs rarely admixed with Eurasian dogs, and they were reported as genetically the most distantly related pair of dogs (Gojobori, et al 2021). Therefore, if Jomon dogs belong to one of the oldest lineages of dogs in East Eurasian lineage, we expect that Jomon dogs are genetically the most distantly related to African dogs.…”

Section: Resultsmentioning

confidence: 99%

“…A recent study reported that the genomes of East Eurasian dogs contain the genome of the Japanese wolf ancestry resulted in high genetic affinity of these two groups (Gojobori, et al 2021). To further examine the relationship of the Jomon dogs to wolves, we analyzed the genetic affinity between Jomon dogs and gray wolves using f3 statistics.…”

Section: Resultsmentioning

confidence: 99%

“…Jomon dog lineage is one of the genomic sources of the modern dogs Dogs form a monophyletic group and are, therefore, genetically monophyletic origin (Freedman, et al 2014;Leathlobhair, et al 2018;Gojobori, et al 2021).…”

Section: Discussionmentioning

confidence: 99%

“…In addition, East Eurasian dogs contain the genome of the ancestor of the Japanese wolf (Gojobori, et al 2021). The most eastern Eurasian ancient dog genomes analyzed in previous studies were from the Lake Baikal area or Siberia, and no ancient dog genomes from East Asia have been reported to date.…”

Section: Introductionmentioning

confidence: 99%

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Genome analysis of the Jomon dogs reveals the oldest domestic dog lineage in Eastern Eurasia

Terai,

Xiaokaiti,

Gojobori

et al. 2023

Preprint

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Dog is the oldest domesticated animal that established close relationships with humans. Due to its ancient origin, when, where, and whether a single or dual domestication event occurred is still under debate. The dogs in the Jomon period (Jomon dogs) in the Japanese archipelago had little change in morphology from 10,000 to 3,000 years ago. Therefore, we expected that the ancient genome of the Jomon dogs would provide a clue to reveal the characteristics of the ancient East Asian dogs. Here, we have sequenced the genomes of three 6000-year-old Jomon dogs, one 3000-4000-year-old Jomon dog, and four late 8th century dogs excavated in Japan. Our analyses suggest that the Jomon dogs are a distinct lineage from the previously known ancient dogs and are one of the oldest among the dogs in East Eurasian lineages. In addition, the genome of the Jomon dogs contained 9.5% of the genome of Japanese wolf ancestry due to a single introgression event. We estimated the proportion of the Jomon dog lineage genome in the genomes of dogs, which indicates that the genomic composition derived from the Jomon dog lineage is one of the major sources of modern dog genomes. Furthermore, we estimated the early admixture events of dogs in East Eurasia by analyzing the ancient genomes of the Jomon dogs. Due to the admixture events, the Jomon dog-derived genome has been one of the genomic sources of a wide range of modern dogs.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome analysis of the Jomon dogs reveals the oldest domestic dog lineage in Eastern Eurasia

Terai,

Xiaokaiti,

Gojobori

et al. 2023

Preprint

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COL1A2 Barcoding: Bone Species Identification via Shotgun Proteomics

Taniguchi,

Miyaguchi

2023

J. Proteome Res.

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Species identification of fragmentary bones remains a challenging task in archeology and forensics. A species identification method for such fragmentary bones that has recently attracted interest is the use of bone collagen proteins. Here, we describe a method similar to DNA barcoding that reads collagen protein sequences in bone and automatically determines the species by performing sequence database searches. The method is almost identical to conventional shotgun proteomics analysis of bone samples, except that the database used by the SEQUEST search engine consisted only of entries for collagen type 1 alpha 2 (COL1A2) proteins from various vertebrates. Accordingly, the COL1A2 peptides that differ in sequence among species act as species marker peptides. In SEQUEST-based shotgun proteomics, the protein entries that contain more marker peptide sequences are assigned higher scores; therefore, the highest-scoring protein entry will be the COL1A2 entry for the species from which the analyzed bone was derived. We tested our method using bone samples from 30 vertebrate species and found that all species were correctly identified. In conclusion, COL1A2 can be used as a bone protein barcode and can be read through shotgun proteomics, allowing for automatic bone species identification. Data are available via ProteomeXchange with the identifier PXD045402.

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Genomes of the extinct Sicilian wolf reveal a complex history of isolation and admixture with ancient dogs

Ciucani

Ramos‐Madrigal

Hernández-Alonso

et al. 2022

Preprint

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The Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s). Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM), until human persecutions led them to extinction. There are only seven known Sicilian wolf specimens from the 19th and 20th century preserved in museums in Italy and recent morphometric analyses assigned them to the new subspecies Canis lupus cristaldii 10. To better understand the origins of the Sicilian wolf, and its relationship to other wolf populations, we sequenced four whole genomes (3.8x-11.6x) and five mitogenomes. We investigated the relationship between Sicilian wolves and other modern breeds to identify potential admixture. Furthermore, considering that the last land-bridge between Sicily and Italy disappeared after the LGM, around 17 kya, we explored the possibility that the Sicilian wolf retained ancestry from ancient wolf and dog lineages. Additionally, we explored whether the long-term isolation might have affected the genomic diversity, inbreeding levels and genetic load of the Sicilian wolf. Our findings show that the Sicilian wolves shared most ancestry with the modern Italian wolf population but are better modelled as admixed with European dog breeds, and shared traces of Eneolithic and Bronze age European dogs. We also find signatures of severe inbreeding and low genomic diversity at population and individual levels due to long-term isolation and drift, suggesting also low effective population size.

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The Japanese wolf is most closely related to modern dogs and its ancestral genome has been widely inherited by dogs throughout East Eurasia

Cited by 6 publications

References 50 publications

Genome analysis of the Jomon dogs reveals the oldest domestic dog lineage in Eastern Eurasia

Genome analysis of the Jomon dogs reveals the oldest domestic dog lineage in Eastern Eurasia

COL1A2 Barcoding: Bone Species Identification via Shotgun Proteomics

Genomes of the extinct Sicilian wolf reveal a complex history of isolation and admixture with ancient dogs

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