63 Matching Annotations
  1. Jan 2019
    1. 18. G. D. Wang et al., Nat. Commun. 4, 1860 (2013).

      In 2013, scientists traced the ancestry of Chinese native dogs using whole genome sequencing. They compared the DNA of four gray wolves (three from different parts of Russia, one Chinese), three native Chinese dogs (dogs present in China for a very long time), and three dogs considered very diverse from each other—a German Shepard, Belgian Malinois, and Tibetan Mastiff.

      They suggest a Southeastern Asia origin for dogs, and domestication of Chinese indigenous dogs occurred 32,000 years ago.

    2. 16. M. Pilot et al., Proc. R. Soc. B Biol. Sci. 282, 20152189 (2015).

      Scientists studied the evolutionary history of free breeding dogs—that is, dogs without restricted, human-controlled breeding. They compared the genetic information of 200 free-breeding dogs from across Eurasia, with 51 ancient and modern breeds. They concluded that the origin for these dogs was East Asia and that they gradually moved West.

    3. 11. W. Haak et al., Nature 522, 207–211 (2015).

      A large team of scientists from around the world sought to trace the origins of one of the world's primary language families, Indo-European languages. Through tracing language, in a way the scientists also trace the origins of European people. They studied DNA from 94 Europeans who lived 8000-3000 years ago. They found that many modern day Europeans can be traced back to the Yamnaya population, nomadic herders from Steppe, a region now know as Ukraine and Russia.

    4. 9. G.-D. Wang et al., Cell Res. 26, 21–33 (2016).

      The authors suggest that dogs were domesticated 33,000 years ago in Southeast Asia.

    5. 4. T. Dayan, J. Archaeol. Sci. 21, 633–640 (1994).

      Studying teeth and facial bones from wolf/doglike animals found buried in Israel (alongside human skeletons), it was estimated that these animals were 12,000-year-old dogs that had recently been domesticated.

      A shorter face and smaller teeth are some of the most recognizable features of domestication. The author, Tamar Dayan, remains open to the possibility that there were several geographic origins of domestication and that small and large-sized wolves—from different populations—were domesticated separately, explaining why there were both large and small early dogs.

    6. 3. M. Pionnier-Capitan et al., J. Archaeol. Sci. 38, 2123–2140 (2011).

      Scientists carried out detailed archaeological studies on bones from 49 small doglike animals from three separate sites in France. The fossils were, in fact, from dogs 11,500-15,00 years old, the same time-frame that much larger dogs existed in Russia, suggesting that there may have been two origins of domestication.

    7. 2. M. Germonpré, M. Lázničková-Galetová, M. V. Sablin, J. Archaeol. Sci. 39, 184–202 (2012).

      Archaeologists discovered seven dog/wolflike skulls at a site in the Czech Republic. By measuring and comparing the skulls and skulls fragments to those of wolves and recent dogs, scientists estimated that wolves were domesticated in the early upper Paleolithic era (~30,000 years ago)

    8. Two genetically differentiated and potentially extinct wolf populations in Eastern (8, 9) and Western (7) Eurasia may have been independently domesticated before the advent of settled agriculture

      Scientists don't always agree. A paper published in 2017 disagrees with the dual origins theory presented here. To learn more about the disagreement, check out this article in the Washington Post: https://www.washingtonpost.com/news/speaking-of-science/wp/2017/07/18/your-dogs-ancestor-came-from-a-group-of-wolves-40000-years-ago-study-says/

    9. A genome-wide PCA analysis

      Analyzing multiple whole genomes at the same time is so complex that scientists needed to simplify the data to make it easier to see patterns and differences between the genomes. The mathematical tool that they used was PCA analysis, which reduces the complexity of the data and retains its variance.

      PCA analysis works by setting principal components (e.g. PC1, PC2, PC3), which are essentially directions in which the data has the largest spread.

      In this case, PC1 and PC2 are studied.

    10. Instead, this pattern arose from clear turnover in the mitochondrial ancestry of European dogs, most likely as a result of the arrival of East Asian dogs

      If ancient European dogs were the ancestors of modern European dogs, we expect that they would mostly belong to the same haplogroups. This is not the case, however, which tells us that these ancient dogs were replaced by another population of dogs.

    11. sequenced and analyzed 59 hypervariable mtDNA fragments from ancient dogs spread across Europe, and we combined those with 167 modern sequences

      The d-loop sequences of mitochondrial DNA are considered to be mutational hotspots (places where mutations appear to happen more frequently than others), and therefore looking at this region can provide important information about how evolution occurred.

      Modern dog sequences and seven of the 59 ancient d-loop sequences were already available on a public database. The rest of the sequences were generated from ancient DNA samples by polymerase chain reaction (PCR). The sequences were then compared to each other using DomeTree, a program that creates haplogroup phylogenetic trees based on mitochondrial DNA.

    12. this early indigenous dog population in Europe was replaced (at least partially) by the arrival of East Eurasian dogs

      We know that there were indigenous dogs in Europe 15,000 years ago. It's estimated that East Asian and Western Eurasian dogs had common ancestors 14,000-6400 years ago, and probably sooner than that (Western Eurasian dogs kept some of their ancestral wolf DNA, which is throwing off the estimated divergence time). The authors suggest that the dogs present 15,000 years ago were replaced by dogs that arrived from East Eurasia.

    13. Russian wolves (18)

      A 2013 study used whole genome sequencing to trace the ancestry of Chinese native dogs. They compared the DNA of four gray wolves—three from different parts of Russia, one Chinese—three native Chinese dogs (dogs present in China for a very long time), and three dogs considered very diverse from each other; a German Shepard, Belgian Malinois, and Tibetan Mastiff.

      They suggest a Southeastern Asia origin for dogs, and domestication of Chinese indigenous dogs occurred 32,000 years ago.

    14. we used the radiocarbon age of the Newgrange dog to calibrate the mutation rate for dogs

      The team of scientists used radiocarbon dating techniques to calculate the dog as 4700-4900 years old.

      Since they knew how old the Newgrange dog was, they were able to estimate the time at which the Newgrange dog and the Portuguese village dogs last had a common ancestor, and figure out when they diverged from each other.

      Based on the assumption that a new generation of dogs were born every 3 years, the scientists were able to calculate the mutation rate.

    15. transportation of dogs from east to west

      It was already known that American dogs came from Europe, but in 2017 scientists found evidence that dogs also came with humans across the Bering land bridge—a small piece of land that once connected North America and Russia.

      Read more in Forbes: https://www.forbes.com/sites/grrlscientist/2017/04/25/old-dog-new-dog-genetic-map-tracks-the-evolution-of-mans-best-friend/

    16. bottleneck

      An event that drastically reduces the size of the population. Loss of genetic variation is a knock-on effect. Causes can be disease, intense animal hunting, and mass migration.

    17. we defined Western Eurasian and East Asian “core” groups (Fig. 1A), supported by the strength of the node leading to each cluster (12).

      The information represented in Figure 1A was used to define the two core groups. The dogs needed to have very high bootstrap values (>90)—high-quality genetic data—to support their placement in the groups.

      The Western Eurasian core group consisted of all modern breeds and Portugal village dogs. The East Asian core group consisted of Sharpei, Village dogs from China, Tibet, and Vietnam, and Tibetan Mastiffs.

    18. admixed lineages

      New populations that arise when two genetically distinct breeds begin interbreeding. One reason for this is the coming together of breeds that were previously geographically separated.

    19. bootstrap values

      These indicate the reliability of the data for a specific branch of the tree. Out of 100, this number estimates how closely a subset of the samples match the original result. One-hundred out of 100 suggests a high degree of certainty, whereas a value of 40 suggests uncertainty—it could be wrong. Bootstrap values are written on the nodes of the tree.

      The term bootstrapping is associated with the expression, "Pull yourself up by your bootstraps." In statistics, one often does not have access to replicates for an experiment. Bootstrapping means randomly re-sampling your data as a mean to create replicates. Hence the analogy with bootstrapping, a self-sustaining process that allows for evaluating confidence without obtaining new data.

    20. neighbor-joining tree

      A type of graph used to map ancestry that is known as a phylogenetic tree. A neighbor-joining tree uses either the DNA or protein sequence of organisms to find differences between them. The two nearest nodes are defined as neighbors, based on how similar their DNA sequences are. This is done until all of the nodes have been paired together. The tree is directional, with older ancestors on the left and newer members on the right.

    21. radiocarbon dated

      This technique allows scientists to estimate the age of a plant or animal based on the amount of carbon-14 that is present at the time of measurement. Carbon-14, also known as radiocarbon, is a weakly radioactive type of carbon molecule that decays over time. The age of samples up to 60,000 years old can be estimated.

      To learn more about radiocarbon dating, check out this video from Scientific American.

    22. unequivocally placed the Newgrange dog with modern European dogs

      According to radiocarbon dating, the Newgrange dog is 4800 years old. By using three different ancestry analysis tools, there was no doubt that the Newgrange dog is most similar to the modern European dogs, which tells us that the East Asian dogs and Western Eurasian dogs had evolved from each other before 4800 years ago.

    23. This breed, created in the 1930s in the Netherlands, involved breeding German Shepherds with captive wolves

      The Sarloos breed was created by Leendert Saarloos, in an attempt to create a superior police dog. He bred a male German Shepard and a female wolf. Despite the efforts of Mr. Saarloos, the dog was never a successful police dog and was not formally recognized as a new breed.

    24. single-nucleotide polymorphism (SNP)

      Single-base variations that exist at specific positions in the genome. For example, dog 1 has a T nucleotide at a specific position, whereas dog 2 has a C at the same position in the genome; that means that there's an SNP at this position.

    25. CanineHD 170,000 (170 K)

      A type of genetic test that covers 170,000 single-position variations in the genome of a dog. It is essentially a chip, upon which the genetic material of the dog of interest is placed. It contains thousands (170,000 in this case) of probes—short DNA sequences that can stick to the complementary sequence in the sample, if that matching DNA variant is present. Each interaction can be recorded to easily measure the presence of a large number of genes at the same time.

    26. (28x) of an ancient dog dated to ~4800 calendar years before the present (12) from the Neolithic passage grave complex of Newgrange (Sí an Bhrú) in Ireland.

      The scientists isolated DNA from a portion of the temporal bone in the dog's skull.

      They made a library of single-stranded DNA sequences; smaller pieces of DNA that together represent the entire genome of the dog. The DNA library is sequenced on a machine that can read the order of the bases (As, Ts, Gs, and Cs) that make up the genome of the particular dog being studied.

      Check out this video from TED-Ed on how to sequence the human genome (it also applies to the dog genome).

    27. sequences from European dogs (from 14,000 to 3000 years ago)

      They sequenced the d-loop of mitochondrial DNA, an area where mutations happen more often than other parts of mitochondrial DNA.

      Seven of the d-loop sequences were already available on a public database, and the others were generated from DNA in bone samples. A very small amount of bone was ground to a fine powder. The scientists were very careful to make sure contamination of the samples did not occur. Once the cells in the bone sample were broken open, and the DNA was isolated from other parts of the cell, the DNA could be sequenced by polymerase chain reaction (PCR).

      Check out this video from Khan Academy to learn how DNA is sequenced by PCR.

    28. evolutionary history of dogs

      After their domestication, dogs were selected to perform specific tasks. Some were used for hunting, some for sledding.

      The domestication of cats doesn't appear to have been as deliberate as dog domestication. As a result, dog breeds are very different from each other, whereas cats didn't change very much from their wild ancestors when they were domesticated.

      Read more at National Geographic: https://news.nationalgeographic.com/2017/06/domesticated-cats-dna-genetics-pets-science

    29. most genetic studies have concluded that dogs were probably domesticated just once

      Scientists studied DNA from wolves (one each from East Asia, the Middle East, and Europe—all regions where domestication had potentially occurred) and two ancient dog breeds. A third group, the golden jackal, was included as a comparison. The scientists found that none of the wolves were more closely related to dogs than the other, which suggested that dogs were not domesticated separately in the three different areas. The scientists thus concluded that domestication must have happened just once.

    30. Dogs were the first domestic animal and the only animal domesticated before the advent of settled agriculture

      Dogs were tamed from wild animals (wolves) long before—several thousand years before—any other domestic animal (e.g. pigs), and before farming practices began, according to the archaeological record. Some studies estimate that farming practices and farm animal domestication started place 9000-12,000 years ago, and dog domestication took place at least 15,000 years ago.

      Check out this 2018 paper on the spread of dogs alongside farming in Europe. Find the full PDF in the "Related content" tab.

    31. ancient

      In this case, the DNA specimens are ~14,000 to 3000 years old.

  2. Dec 2018
    1. basal breeds

      A group of 16 dogs breeds, which are distinct from modern dogs because their DNA is less mixed. Basal breeds include: Afghan hound, Akita, Alaskan Malamute, American Eskimo, Basenji, Canaan, Chow Chow, Dingo, Eurasier, Finnish Spitz, New Guinea singing dog, Saluki, Samoyed, Shar-Pei, Shiba Inu, and the Siberian Husky.

    2. similar to that obtained with an ancient grey wolf genome

      Scientists studied the DNA of a Siberian wolf thought to have lived 35,000 years ago (based on radiocarbon dating). The Siberian wolf's DNA mutated at a rate of 0.45 × 10^−8 per generation, much slower than the previously assumed mutation rate of 1.0 × 10^−8. This meant that wolf-dog divergence must have occurred much longer ago (27,000-40,000 years ago) than previous estimates suggested (11,000-16,000 years ago).

  3. Nov 2018
    1. he null hypothesis should be that individual animal species were domesticated just once

      The majority of research findings up until this point suggested that domestication occurred just once, so this became the most acceptable theory for how domestication occurred. Based on their findings, the authors disagree with the null hypothesis (reject the null hypothesis), and because of this, they go to great lengths to prove their alternative hypothesis.

    2. secondary gene flow

      Genetic variation is transferred from one population to another, two times over. That is, after the first transfer, there is a period of separation between the two populations and then genetic variation is transferred again.

    3. divergence times

      The date in evolutionary history when different populations of dogs split from each other.

    4. genotyped

      A type of technology that detects small genetic differences that occur in the DNA of a population.

    5. haplotype

      A set of single DNA bases that tend to be inherited together from a single parent, and often vary between individuals. Variation in single bases gives us information about evolution.

      Check out this video from the University of Utah to learn more about how halotypes can be used to understand genetic relationships between humans, and dogs too!

    6. 14. S. Schiffels, R. Durbin, Nat. Genet. 46, 919–925 (2014)

      A new technique—multiple sequentially Markovian coalescent (MSMC)—was developed. Eight haplotypes from four individuals can be analysed at the same time to trace lineages until the most recent common ancestor is identified. It is a powerful technique that provides information about population sizes, population splits, and migration patterns. In this study, they analyzed the genomes of nine different human populations and discovered that humans began to migrate out of Africa over 50,000 years ago.

    7. 6. A. H. Freedman et al., PLOS Genet. 10, e1004016 (2014).

      Dogs and wolves diverged 11,000-16,000 years ago, the authors conclude. A severe reduction in the population (a bottleneck) of wolves occurred shorly thereafter. They traced the ancestry of the amylase gene, a gene that allows dogs to eat starchy foods. Their data showed that dogs were mostly carnivores when they were first domesticated, which supports the theory that dogs were domesticated by hunter-gatherers, rather than starch-loving farmers.

    8. incomplete nature of the archaeological record

      A recent study (2017) on fossils found in Siberia provides evidence for the earliest dog breeding program, but it doesn't necessarily contradict the research presented here. Read more in Science News: https://www.sciencemag.org/news/2017/05/earliest-evidence-dog-breeding-found-remote-siberian-island

    9. consilience

      Agreement between two different approaches.

    10. cross coalescence rate (CCR)

      A method of estimating the time at which populations had a common ancestor, based on their genetic differences and similarities.

    11. drift

      This is one way that evolution can occur. It is an entirely random process, in which some individuals, by chance, contribute more of their genes to the future population that other individuals.

    12. admixture signatures from wolves into Western Eurasian dogs

      In this 2016 study, we see that there's evidence of wolf DNA in dogs, but a study published in 2018 showed the first evidence for dog DNA in wild wolf populations. Read more: https://phys.org/news/2018-03-extent-cross-breeding-wild-wolves-domestic.html

    13. wolves we examined may not have been closely related to the population(s)/s that gave rise to dogs

      Wolves went through a sudden bottleneck—a big, sudden drop in population—right after dogs were domesticated. Three wolves were studied, and considering how different they were from each other and that none of them were more closely related to dogs than the others, it's a possibility that the wolf ancestor of dogs died off in the bottleneck.

    14. 60,000 to 20,000 years ago (fig. S17 and Fig. 2B). This date should not be interpreted as a time frame for domestication

      The wolves used in this study were modern wolves. We know that there was a bottleneck in the wolf population shortly after dogs were domesticated (see Freedman et al. in reference 6), so the wolves studied here may not be a close ancestor of the wolves that dogs came from. For this reason, 60,000-20,000 years is not an estimate of when dogs and wolves evolved from each other.

    15. mitochondrial DNA

      Genetic material that exists in the cell's mitochondrion. It is very important for studying ancestry since it is inherited from the mother only, and it allows researchers to trace the maternal lineage.

    16. complete (28x) genome

      Certain bases that are always present in dogs were covered by sequencing 28 times, so the whole genome is said to have been covered 28 times.

    17. Despite their importance in human history

      Humans have had an emotional bond with dogs for a very long time—14,000 years, according to new archaeological evidence.

      Read more: https://phys.org/news/2018-02-emotional-bond-humans-dogs-dates.html

    18. frequencies

      In this case, refers to how often a set of DNA bases that are always inherited together are found in the population.

    19. 19. P. Savolainen, Y. P. Zhang, J. Luo, J. Lundeberg, T. Leitner, Science 298, 1610–1613 (2002).

      The authors investigate the specific time and place of domestication by using the mitochondrial DNA of over 600 dogs and 38 wolves to trace the maternal lineage.They determine that dogs were domesticated about 15,000 years ago in East Asia, and that dogs were isolated to East Asia for a long time thereafter.

    20. 5. M. Ollivier et al., PLOS One 8, e75110 (2013)

      Scientists traced the ancestry of two genes associated with coat color. They examined DNA from teeth and bones from 28 different sites across Europe and Asia and determined that coat color was lost when dogs were domesticated. Variants in one coat color gene was detected in the early "ancient" breeds, which suggested that a pool of early dogs may have been geographically isolated 14,000-12,000 years ago, maybe as a result of rising sea levels.

    21. generation times

      The average time between one generation and the next in the lineage of a population; in other words, the average age between a parent and its offspring.

    22. mutation rates

      The speed of change in genetic material over time.

    23. Given the current lack of dog remains prior to 8000 years ago in Central Eurasia, a scenario involving a single origin followed by an early dispersal seems less likely.

      The lack of evidence for dogs in Central Eurasia over 12,500 years ago, and the presence of dogs on either side of the region suggests that dogs were domesticated twice.

      If dogs were domesticated just once in East Eurasia and transported west, there should be evidence for dogs in Central Eurasia and/or a gradual change in the dog genome as dogs moved East to West.

    24. temporal cline

      A gradual change in genetic material, and the characteristics it codes for, over time.

    25. founder effects

      A few members of a population starts a new population. This new population has less genetic variation.

    26. Newgrange dog retained a degree of ancestry from an ancient canid population that falls outside of the variation of modern dogs, but that is also different from modern wolves.

      The Newgrange dog and East Asian dogs diverged earlier than East Asian and West Eurasian dogs. The best explanation for this, according to the data, is that the Newgrange dog retained some DNA from ancient wolves, wolves that are not closely related to modern wolves.

    27. mtDNA turnover

      Mitochondria have their own genetic material, and DNA mutations may accumulate over time.

    28. This migration led to a partial replacement of ancient dog lineages in Europe that were present by at least 15,000 years ago

      Through archaeological evidence, we know that dogs were present in Europe about 15,000 years ago. The fact that the Finnish Spitz is the only European dog breed that kept its basal genetic signature suggests that the original European dogs were mostly replaced.

    29. node

      A point on a graph of ancestry that is used to represent a split of one lineage to form two or more lineages.

    30. nuclear genome

      Genetic material that exists in the nucleus of the cell.