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pmokeefe
10-29-2020, 06:43 PM
Origins and genetic legacy of prehistoric dogs (https://science.sciencemag.org/content/370/6516/557)
Bergström et al.

Dog domestication was multifaceted
Dogs were the first domesticated animal, likely originating from human-associated wolves, but their origin remains unclear. Bergstrom et al. sequenced 27 ancient dog genomes from multiple locations near to and corresponding in time to comparable human ancient DNA sites (see the Perspective by Pavlidis and Somel). By analyzing these genomes, along with other ancient and modern dog genomes, the authors found that dogs likely arose once from a now-extinct wolf population. They also found that at least five different dog populations ∼10,000 years before the present show replacement in Europe at later dates. Furthermore, some dog population genetics are similar to those of humans, whereas others differ, inferring a complex ancestral history for humanity's best friend.


Abstract
Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

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Fig. 1 Genomic structure of dogs dates to the Pleistocene.(A) Sampling locations of ancient dogs. k, 1000 years. (B ) PCA results for all possible f4-statistics among ancient dogs (gray) and a selection of worldwide modern dogs. (C) Outgroup f3-statistics reveal a cline of Levant-related versus Baikal-related (horizontal and vertical axes, respectively) ancestry across ancient West Eurasian dogs, but not among modern European dogs. (D) Coalescent simulations demonstrating that a diagonal f3 cline as in (C) is consistent with an admixture event, but less so with continuous gene flow and not with phylogenetic structure alone. (E) An admixture graph that fits all f4-statistics between major dog lineages. The European dog was grafted onto the graph identified through exhaustive testing. kya, 1000 years ago



Of dogs and men (https://science.sciencemag.org/content/370/6516/522)
Pavlos Pavlidis, Mehmet Somel
--- overview of the paper

pmokeefe
10-29-2020, 08:02 PM
Ancient dog DNA reveals 11,000 years of canine evolution
(https://www.nature.com/articles/d41586-020-03053-2)Genomes trace how the animals moved around the world — often with humans by their side.
Ewen Callaway
--- news article in Nature

Twitter thread about the article by Pontus Skoglund, one of the coauthors:
https://twitter.com/pontus_skoglund/status/1321875099348324358

davit
10-29-2020, 09:42 PM
Interesting. I'm more curious about the original domestication events though.

pmokeefe
10-30-2020, 02:19 AM
Interesting. I'm more curious about the original domestication events though.
"We find that the modern and ancient genomic data are consistent with a single origin for dogs, though a scenario involving multiple closely related wolf populations remains possible. However, in our view, the geographical origin of dogs remains unknown."
--- Discussion section of the paper (https://science.sciencemag.org/content/370/6516/557)

Kristiina
10-30-2020, 04:14 PM
The order of separation in the paper is this: New Guinea dogs, American dogs, Baikal dogs, Karelia dogs and Levant dogs. In the admixture analysis African Basenji dogs are descendants of Levant dogs. Karelian dogs are mixed between western (European) and Asian dogs. Modern European dogs are mixed between ancient European and Levant dogs. Ancient Iranian dogs are mixed between Levant and Siberian dogs with a little bit of European ancestry.

If we compare this order of separation to humans, e.g. to human yDNA or mtDNA trees, we should conclude that dogs were domesticated in northern Eurasia, as the deepest splits are in Asia.

According to the paper, "the >40-ka-ago divergence of human East and West Eurasian ancestries (47) is markedly older than the earliest appearance of dog morphology in the fossil record, conservatively dated to 14.5 ka ago (48), although older (3, 31), disputed (49, 50) specimens have been claimed."

If I try to fit the 14,5 kya separation time to human migration patterns, the following picture emerges. (A part of) Native Americans go to America together with dogs only after 14,5 kya. Before and after that there are two migrations to East Asia, the first ca 14,5 kya and the second from Baikal ca 10 kya. As for the western dogs, this model predicts that there is a migration of humans from Siberia to Europe after 14,5 kya and this migration would take the dogs to the Levant at the latest 7 kya.

I find this scheme quite tight and I doubt that the differences between dog breeds in different continents could have been so well established in only 5 000 years.

I hope that older dog samples can be obtained in order to clarify the issue.

pmokeefe
10-30-2020, 06:36 PM
Dog domestication and various megafauna extinction events seem to have occurred in roughly the same timeframe.
Could that have been a significant factor in the extinctions?

How do you kill 86 mammoths? Taphonomic investigations of mammoth megasites (https://pennstate.pure.elsevier.com/en/publications/how-do-you-kill-86-mammoths-taphonomic-investigations-of-mammoth-)
by Pat Shipman

Did Dogs Help Drive Mammoths to Their Graves? (https://www.sciencemag.org/news/2014/05/did-dogs-help-drive-mammoths-their-graves)
Report about the Shipman article in Science.

However, this critique:
Comment on “How do you kill 86 mammoths? Taphonomic investigations of mammoth megasites” by Pat Shipman (https://d1wqtxts1xzle7.cloudfront.net/37745863/Perri_et_al_2015_-_Shipman_reply.pdf?1432675625=&response-content-disposition=inline%3B+filename%3DPerri_Smith_and_B osch_2015_Comment_on_Ho.pdf&Expires=1604086276&Signature=YHCY5083R~rGitBSOTNnidSMqHcXnqMNSnsRNB76 cT1rifu1gd9K8M-OAVp64SIOuCsZKok5tSjB~MA-JYmB1RWQ~vymjRZWqe-mJyu6FlrFj111MO-9vb~5hClUqui1ocXW2u4Qr51EGsDyI2STog4~1BLS28TD0BUag FmMG9NuPzqfAVHMeyRDYdVnuqF3ZTjX8xcp6qCE65jHc75Nnkc yAFt~x-10BGPmV2z7WXSnTelSRtgUqd3Usm3HyW86aWSYur3z7VYOQUTd ThTzKSpTmRe9Qvd~SuILYowwSwj6IhlO69SJfi1WblGMXGiRjD LSfIKAkqpRA65JsDgodQ__&Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA)

Any other scientific articles about dogs and the extinctions of mammoths or other species?

Kristiina
10-30-2020, 06:50 PM
I took a look at the results of the mitochondrial DNA paper published earlier this year (Ancient DNA Evidence from China Reveals the Expansion of Pacific Dogs).

40816

There seems to be a lot of mtDNA variation in China compared to other continents. An ancient dog in New Siberian Islands (9,5-8,5 kya) carries the same haplotype as dogs in America. This haplotype reached also China in ancient times. An ancient dog in Zhejiang (7 kya) carries the same haplotype as dogs in Australia and in Pacific Islands. This oldest mtDNA haplotype in Asia, A1b, is a parallel branch of the European A1a.

This paper also supports the origin of dogs in Asia.

davit
10-30-2020, 06:58 PM
The order of separation in the paper is this: New Guinea dogs, American dogs, Baikal dogs, Karelia dogs and Levant dogs. In the admixture analysis African Basenji dogs are descendants of Levant dogs. Karelian dogs are mixed between western (European) and Asian dogs. Modern European dogs are mixed between ancient European and Levant dogs. Ancient Iranian dogs are mixed between Levant and Siberian dogs with a little bit of European ancestry.

If we compare this order of separation to humans, e.g. to human yDNA or mtDNA trees, we should conclude that dogs were domesticated in northern Eurasia, as the deepest splits are in Asia.

According to the paper, "the >40-ka-ago divergence of human East and West Eurasian ancestries (47) is markedly older than the earliest appearance of dog morphology in the fossil record, conservatively dated to 14.5 ka ago (48), although older (3, 31), disputed (49, 50) specimens have been claimed."

If I try to fit the 14,5 kya separation time to human migration patterns, the following picture emerges. (A part of) Native Americans go to America together with dogs only after 14,5 kya. Before and after that there are two migrations to East Asia, the first ca 14,5 kya and the second from Baikal ca 10 kya. As for the western dogs, this model predicts that there is a migration of humans from Siberia to Europe after 14,5 kya and this migration would take the dogs to the Levant at the latest 7 kya.

I find this scheme quite tight and I doubt that the differences between dog breeds in different continents could have been so well established in only 5 000 years.

I hope that older dog samples can be obtained in order to clarify the issue.


That's interesting. I think the consensus was that European dogs were largely replaced by East Asian dogs really recently. Cool to see that European dogs do descend from ancient European dogs in part.

Is this model suggesting a migration from Siberia to the Levant too?

pegasus
10-30-2020, 07:00 PM
Nice map, much of this indeed mirrors human population movements lol

Interestingly, Chihuahuas are almost entirely European descended contrary to the belief they were Meso-American dogs.

https://i.imgur.com/IhCfITw.jpg

Ryukendo
10-30-2020, 07:15 PM
I took a look at the results of the mitochondrial DNA paper published earlier this year (Ancient DNA Evidence from China Reveals the Expansion of Pacific Dogs).

40816

There seems to be a lot of mtDNA variation in China compared to other continents. An ancient dog in New Siberian Islands (9,5-8,5 kya) carries the same haplotype as dogs in America. This haplotype reached also China in ancient times. An ancient dog in Zhejiang (7 kya) carries the same haplotype as dogs in Australia and in Pacific Islands. This oldest mtDNA haplotype in Asia, A1b, is a parallel branch of the European A1a.

This paper also supports the origin of dogs in Asia.
Nice point Kristiina!
Another evidence of this is in the admixture graph, which shows New Guinean singing dogs as the most deeply diverging among all dogs--the phylogeography suggests that the "Pacific dog" (Neu Guinean dogs and Australian Dingoes) population originated in China and European, Baikal and Steppe clade ancestries subsequently entered China and displaced much of the "Pacific dog" ancestry there. This "Pacific ancestry" seems to exceed 50% only in Korean Jindo, Japanese Inus and Chinese village dogs...

Of course it could be the case that the domestication took place elsewhere, but every other population other than those that root in China died out.

Interestingly the most "Steppe"-related dog is actually the Tibetan Mastiff, one of the so-called "ancient breeds" from China--this forms not a clade with other ancient breeds such as Pekingnese, Shar Pei etc. but is more related to the Srubnaya dog, interesting.

Kristiina
10-30-2020, 07:29 PM
Of course it could be the case that the domestication took place elsewhere, but every other population other than those that root in China died out.


We could also apply that to human mtDNA and yDNA trees, and argue that humans originated in Asia, but all earlier haplogroups than those that root in Africa died out. Of course, this can indeed be true if we widen the perspective to Neanderthals and Denisovans.

Ryukendo
10-30-2020, 07:33 PM
Anyone see an estimate of population split times in the main text or supp? Theoretically the divergence between e.g. American or Levantine and New Guinean Singing Dogs should give us a terminus ante quem for dog domestication.

pmokeefe
10-30-2020, 08:25 PM
The first evidence for Late Pleistocene dogs in Italy (https://www.nature.com/articles/s41598-020-69940-w)
Francesco Boschin et al

Abstract
The identification of the earliest dogs is challenging because of the absence and/or mosaic pattern of morphological diagnostic features in the initial phases of the domestication process. Furthermore, the natural occurrence of some of these characters in Late Pleistocene wolf populations and the time it took from the onset of traits related to domestication to their prevalence remain indefinite. For these reasons, the spatiotemporal context of the early domestication of dogs is hotly debated. Our combined molecular and morphological analyses of fossil canid remains from the sites of Grotta Paglicci and Grotta Romanelli, in southern Italy, attest of the presence of dogs at least 14,000 calibrated years before present. This unambiguously documents one of the earliest occurrence of domesticates in the Upper Palaeolithic of Europe and in the Mediterranean. The genetic affinity between the Palaeolithic dogs from southern Italy and contemporaneous ones found in Germany also suggest that these animals were an important common adjunct during the Late Glacial, when strong cultural diversification occurred between the Mediterranean world and European areas north of the Alps. Additionally, aDNA analyses indicate that this Upper Palaeolithic dog lineage from Italy may have contributed to the genetic diversity of living dogs.

--- August 2020 paper that didn't make it into the references for Bergström et al

pmokeefe
10-30-2020, 08:45 PM
The curious case of the Mesolithic Iberian dogs: An archaeogenetic stud (https://www.sciencedirect.com/science/article/abs/pii/S0305440319300251)
Pires et al
Highlights
•We studied the oldest Portuguese dog remains (n = 6), dated to the Mesolithic .

•High frequency of dog haplogroup A is reported for pre-Neolithic Iberia.

•Dog haplogroup A did not necessarily arrive in Europe from the East.

• Pre-Neolithic local processes for an Iberian wolf domestication is suggested.


Abstract
We investigated the genetic composition of six Canis remains from western Iberia, directly radiocarbon dated to 7,903–7,570 years (cal BP). They were identified as dogs via their archaeological and depositional context, osteometry, and a high percentage of aquatic diet shared with humans. For comparison, genetic data were obtained from an additional 37 Iberian dog remains from the Neolithic to Late Antiquity, as well as two Palaeolithic and a Chalcolithic Canis identified as wolves. Previous data indicated that dog mtDNA haplogroup A (HgA) is prevalent in extant European dogs (>50%), in the Near East and Asia, but rare or absent (<10%) in European Canis older than 3,000 years (cal BP). We found a high frequency (83%) of dog HgA in Mesolithic Iberian dog remains. This is the first report of a high frequency of dog HgA in pre-Neolithic Europe. We show that, contrary to the current view, Canis with HgA did not necessarily arrive in Europe from East-Asia. This phylogeographical difference in HgA frequency demonstrates that genetic differentiation was high prior to, or as a consequence of, domestication which may be linked with pre-Neolithic local processes for Iberian wolf domestication. Our results emphasize that knowledge of both ancient wolves' and early dogs’ genetic profiles from the European periphery should improve our understanding of the evolution of the European dog.

-- May 2019 paper not in the references of Bergström et al

pmokeefe
10-30-2020, 09:19 PM
Anyone see an estimate of population split times in the main text or supp? Theoretically the divergence between e.g. American or Levantine and New Guinean Singing Dogs should give us a terminus ante quem for dog domestication.40822
Fig S11. Time-scaled mitochondrial genome phylogeny. Bayesian phylogeny of both novel (bolded) and publically available dog and wolf mitochondrial genomes (n=381). Posterior support values are indicated on the nodes. All monophyletic clades extant to the novel sequences are collapsed, and all dog haplogroup and subclades of haplogroups are marked as such with sample numbers indicated in parentheses. The MRCA of haplogroup C dates to ~17.5 KYA, D to ~10KYA, B to ~2.5KYA, X to ~5KYA, and subclades A1a to at least ~8KYA, A1b to between ~17.5-10KYA, A2b to ~17KYA, and A2a to ~16KYA.

Supplementary Materials (https://science.sciencemag.org/content/sci/suppl/2020/10/28/370.6516.557.DC1/aba9572_Bergstrom_SM.pdf)

Dieu
10-30-2020, 09:30 PM
what exactly is modern european cluster ?

CopperAxe
10-30-2020, 09:45 PM
Any theories as to why European dogs seemed more or less replaced by a single breed around 2000 bc?

Because the scant genetic evidence they have here does show that the Indo-Europeans did bring their dogs with them. But around 4k years ago a dog lineage best represented by a late Neolithic TRB sample becomes the base for the modern european dog genomes.

Maybe a breed from Southern Europe became really popular?

Also does anyone else think it is somewhat poor selection to use a 1800-1000 bc Srubnaya dog if you want to infer what happened to the dogs that spread with Indo-Europeans around 3000 bc?

pmokeefe
10-30-2020, 09:49 PM
what exactly is modern european cluster ?
In the Supplement:

A uniform ancestry of modern European dogs is largely approximated by the
ancient dog C88 from Sweden. For the 108 analyzed modern European dogs, the horizontal
axis displays the amount of their ancestry that is assigned to the German Shepherd, arbitrarily
chosen to represent the modern European dog ancestry, in qpAdm analyses. The fact that most of
them are assigned 100% German Shepherd ancestry, to the exclusion of all the ancient dogs in
the dataset, suggests that most modern European dogs are a clade that does not retain any
structure visible among the ancient dogs.

Dieu
10-30-2020, 11:32 PM
the exact phrase "modern european cluster" does not appear in the main paper or supplement, as far as I can tell.
Though "modern european dog" does, many times.
The Supplement text does have this:
"the tight cluster of modern European dogs appear slightly shifted down on both axes relative to the ancient cline"

Was that what you were referring to?

Also in the Supplement:

A uniform ancestry of modern European dogs is largely approximated by the
ancient dog C88 from Sweden. For the 108 analyzed modern European dogs, the horizontal
axis displays the amount of their ancestry that is assigned to the German Shepherd, arbitrarily
chosen to represent the modern European dog ancestry, in qpAdm analyses. The fact that most of
them are assigned 100% German Shepherd ancestry, to the exclusion of all the ancient dogs in
the dataset, suggests that most modern European dogs are a clade that does not retain any
structure visible among the ancient dogs.

Thanks but my question was more from which ancient dog breed, modern european dogs are coming from but I have my answer thanks to CopperAxes

Kristiina
10-31-2020, 08:52 AM
I quickly skimmed through "The first evidence for Late Pleistocene dogs in Italy", published in August 2020.
There seems to be a difference of interpretation in dating dogs and their domestication. This paper also provides a phylogenetic tree of dog MtDNA: https://www.nature.com/articles/s41598-020-69940-w/figures/5
According to the legend, "Tip dates for ancient samples were set according to their radiocarbon calibrated bp ages and used for calibrating and estimating the substitution rate."
This latter tree contains samples that are very old: the oldest date from Siberia is 52 500 BP and the oldest date from Belgium is 46 300 BP.

The new paper, Bergström et al, argues that "this result is consistent with a scenario in which all dogs derive from a single ancient, now-extinct wolf population, or possibly multiple closely related wolf populations." They also argue that "the gene flow was likely largely unidirectional from dogs into wolves, as we also identified some gray wolves that are symmetrically related to all modern and ancient dogs (Fig. 2C)."

To me the question is if the oldest samples in the phylogeny of Boschin et al represent this extinct wolf population. These 'extinct wolfs' covered an area from Europe to Siberia. Ancient dogs in Boschin et al cluster in a subclade in which all 'outgroups' are in Asia: Siberia 41 700, Alaska 28 000 and Japan. The oldest samples that are clustered in the branches that contain specifically dog specimens are even 35 000 kya old.

Domestication was probably a long process that can be dated between 35-15 kya. By 15 kya dogs were probably already fully-fledged dogs.

Saetro
11-01-2020, 02:05 AM
Domestication was probably a long process that can be dated between 35-15 kya. By 15 kya dogs were probably already fully-fledged dogs.

True dingoes are still considered wild - not yet domesticated -
Geographic hot spots of dingo genetic ancestry in southeastern Australia despite hybridisation with domestic dogs
Kylie M. Cairns, Bradley J. Nesbitt, Shawn W. Laffan, Mike Letnic & Mathew S. Crowther
Conservation Genetics volume 21, pages77–90(2020)
https://link.springer.com/article/10.1007/s10592-019-01230-z

The Bergstrom paper compares dingo amylase copy number with wolves, showing they are almost the same.
Which supports this.

Ryukendo
11-02-2020, 12:50 AM
True dingoes are still considered wild - not yet domesticated -
Geographic hot spots of dingo genetic ancestry in southeastern Australia despite hybridisation with domestic dogs
Kylie M. Cairns, Bradley J. Nesbitt, Shawn W. Laffan, Mike Letnic & Mathew S. Crowther
Conservation Genetics volume 21, pages77–90(2020)
https://link.springer.com/article/10.1007/s10592-019-01230-z

The Bergstrom paper compares dingo amylase copy number with wolves, showing they are almost the same.
Which supports this.

Dingoes are feralized wild dogs (as are New Guinean singing dogs), so domesticated then secondarily wild.

JoeyP37
11-02-2020, 02:00 AM
40921In the United States there is the Carolina Dog, which is similar to the dingo/New Guinea Singing type, descended from the domesticated dogs brought by the ancestors of the Native Americans over the Bering land bridge. You can see its primitive, yet still smart-looking type, in comparison to the modern dog breed, an OVERFED specimen of the English springer spaniel breed. 40922

pmokeefe
11-02-2020, 03:39 AM
The evolutionary history of dogs in the Americas (https://science.sciencemag.org/content/361/6397/81)
Leathlobhair et al
in Science 2018.

Our admixture analysis detected varying degrees (0 to 33%) of PCD/Arctic ancestry in three individual Carolina dogs (fig. S20). This analysis, however, could not distinguish between PCD and Arctic ancestry, and we cannot rule out that this signal was a result of admixture from modern Arctic dogs and not from PCDs (3). The majority of modern American dog populations, including 138 village dogs from South America and multiple “native” breeds (e.g., hairless dogs and Catahoulas), possess no detectable traces of PCD ancestry (Fig. 2A, fig. S20, and table S10), though this analysis may suffer from ascertainment bias.
where PCDs are precontact dogs.

America's lost dogs (https://science.sciencemag.org/content/361/6397/27.summary)
Linda Goodman, Elinor K. Karlsson
Perspective in the same issue of Science

However, as with earlier work (8, 9), Ní Leathlobhair et al. find almost no genetic traces of precontact dog ancestry in modern dogs, whether purebred or American village dog. Modern Arctic dogs are not descended from precontact dogs, but instead are part of a sister clade brought into the Americas within the last 1000 years (see the figure). None of the village dogs, Carolina dogs, or Chihuahuas could be confidently shown to have precontact dog ancestry of more than 2 to 4%.

RP48
11-02-2020, 05:52 PM
Facts are amazing and disappointing sometimes.

davit
11-07-2020, 03:07 PM
Does anyone know if the steppe dogs included something similar to the husky described by Kuzmina as having been used by Into-Iranians?