DNA Extracted From Woolly Mammoth Hair

Stephan C. Schuster and Webb Miller of Penn State, working with Thomas Gilbert from Copenhagen and a large international consortium, discovered that hair shafts provide an ideal source of ancient DNA — a better source than bones and muscle for studying the genome sequences of extinct animals. Their research achievement, described in a paper to be published in the journal Science on Sept. 28, includes the sequencing of entire mitochondrial genomes from 10 individual woolly mammoths.

Schuster and Miller, working at Penn State’s Center for Comparative Genomics and Bioinformatics, and Gilbert, from the Center for Ancient Genetics at the University of Copenhagen, led a team of collaborators that includes a large group of researchers and museum curators from the United States, Russia, Belgium, Denmark, France, Italy, Sweden and the United Kingdom. The research team obtained hair from 10 woolly mammoths collected from a wide swathe of northern Siberia and with dates of death spanning approximately 38,000 years — from 50,000 years to 12,000 years ago. Before this study, only seven mitochondrial genomes from extinct animals had been published: four from ancient birds, two from mammoths and one from a mastodon.

“DNA in bones and muscle usually degrades and becomes contaminated with genetic material from other sources such as bacteria, limiting its usefulness in scientific studies,” Schuster explained. Because only a tiny proportion of ancient bones and muscle are preserved in such a way that uncontaminated DNA can be recovered, research with such materials has involved laborious efforts, sometimes spanning as long as six years for a single study. In contrast, Miller said, “Once I get the data from the genome sequencer, it takes only five minutes to assemble the entire mitochondrial genome.”

The discovery demonstrates that hair clippings can give researchers enormous power and efficiency for divining the genetic makeup of ancient species.

The methods the team members developed for efficiently generating and analyzing large amounts of ancient mitochondrial-genome sequences now position them to generate such data for other extinct species, as well as to sequence the huge nuclear genome of an extinct species. “The data already generated from this study set the stage for the sequencing of a complete mammoth genome,” said Schuster.

“We realized that the keratin in hair could protect the DNA it contains from outside influences and hence from the sorts of degradation that affect DNA in other parts of the body, such as bone,” Gilbert said. Hair also can more easily be cleaned of environmental contaminants, such as bacteria. The researchers discovered that, even if the hair is washed in a solution that kills and washes off external DNA, the genetic material within the hair is unaffected.

“When people thought of sequencing DNA from hair, the usual assumption was that the material must come from the hair root, which contains recognizable cells, because the hair shaft appears to be dead,” Miller explained; “however, we now know that a hair shaft consists essentially of DNA encased in a kind of biological plastic.” Protected in this way, the DNA resists damage and readily can be separated from any bacteria that may contaminate the sample. “We discovered, moreover, that the DNA in hair shafts is remarkably enriched for mitochondrial DNA, the special type of DNA frequently used to measure the genetic diversity of a population,” Gilbert added.

Several of the hair samples investigated were up to 50,000 years old. One of the samples came from the first specimen ever recorded: the so-called Adams mammoth, found in 1799 and dug out of the permafrost between1804 and 1806 by the botanist Michael Adams and members of the Tungus tribe. This mammoth died around 36,000 years ago. “Hair samples from this find were stored in a Russian museum for 200 years at room temperature, but still allowed for a complete analysis of its mitochondrial genome using only 0.2 grams of hair,” Schuster said. As a result, he uses the term “museumomics” for his dream of deriving molecular-genomic-analysis data from the specimens stored in the collections of Charles Darwin, Alexander von Humboldt and Carl von Linne.

The new route to the genetic material of extinct animals also will enable researchers to study the relatedness of individual animals from different populations at a much higher resolution than previously thought possible. “We plan to use hair and other keratin-containing body parts, such as nail and horn, to untangle the secrets of populations that lived long ago, so these populations can send a message from the past about what it might have taken for them to survive,” Schuster said. “This discovery is good news for anyone interested in learning more about how species of large mammals can go extinct.”

Source: Science Daily

Whale and dolphin sonar evolution

U.S. biologists have determined that, as bats developed sonar to chase flying insects, whales and dolphins developed sonar to chase squid at night. And because squid migrate to deeper, darker waters during the day, toothed whales eventually perfected an exquisite echolocation system that allows them to follow the squid down to that “refrigerator in the deep, where food is available day or night, 24/7,” said evolutionary biologist Professor David Lindberg of the University of California-Berkeley and coauthor of a new paper on the evolution of echolocation in toothed whales.

“When the early toothed whales began to cross the open ocean, they found this incredibly rich source of food surfacing around them every night, bumping into them,” said Lindberg, a curator at University of California-Berkeley’s Museum of Palaeontology. “This set the stage for the evolution of the more sophisticated biosonar system that their descendants use today to hunt squids at depth.”

Lindberg and graduate student Nick Pyenson reported their research in the July 23 online edition of the journal Lethaia in advance of its print publication.

Source: Science Daily

Blog Carnival – Tangled Bank

Today’s second blog carnival comes courtesy of Dr Martin Rundkvist at Aaradvarchaeology. The 89th edition of the Tangled Bank has submissions on everything from beasties to doctorin’, and from neurology to climate change. Particularly interesting to me was the clear review of the weird world of virus taxonomy in ‘What’s in a Name?‘ at A Mad Tea-Party, as well as Grrlscientist’s explanation of how ‘Salmon + Salmon = Trout‘.

Confused?

It’s all the result of a little embryo manipulation, apparently.

Blog Carnival – Four Stone Hearth

The 24th volume of the anthropology and archaeology blog carnival, Four Stone Hearth, can be read at Paddy K’s Swedish Extravangaza. There are a wide range of topics covered by the submissions, ranging from bonobos and farming to the illegal antiquities trade. Along the way, we also pass through discussions about morality and the intriguing story of Homo floriensis. Is this a whole new species or merely an example of microcephaly? There has been much discussion about the latter recently, and Eric Johnson’s view of ‘The Original Cast of Survivor‘ is an interesting addition to the debate.

Enamel Hypoplasia, Fluoride Toxicosis and Bison

An appreciation for the palaeoecology of prey species is a recognised necessity for modelling prehistoric human subsistence behaviours, such as the interaction between humans and bison on the North American Great Plains from the late Pleistocene into the Holocene. Previous investigations have emphasised the prominence of dental enamel hypoplasia (DEH) in such studies, where it has been valued both as a palaeoclimate proxy and an indicator of seasonally-variable stress. However, DEH is a common response to multiple pathological agents, making the isolation of specific aetiologies difficult. It is hypothesised, however, that DEH was related to common seasonal variables (birthing, weaning, and forage quality) and thus exacerbated by external stimuli such as human hunting pressure, drought and winter conditions. In this paper, fluoride toxicosis was examined as a potential contributor to this DEH formation.

Dental enamel hypoplasia

DEH is a deficency in enamel thickness stemming from the temporary cessation of amelogenesis. Among prehistoric bison, hypothesised causes include: foetal nutritional strain related to departure from umbilical input, juvenile nutritional upset caused by weaning, dietary stress stemming from seasonal changes and vitamin deficiencies reflecting photoperiodicity.

Fluoride toxicosis

Fluorides are beneficial in moderation, but overdose is hazardous. In the absence of industrial output and agricultural contamination, animals are typically introduced to excess fluoride via long-term ingestion of geothermal waters and by foraging in areas of volcanic soils. Prehistoric bison regularly utilising such environments may have invited toxicosis. With intoxication, new-forming hard tissues readily absorb excess fluoride, causing chronic diarrhoea, low milk yield, anaemia, cachexia, and marrow atrophy. As bones absorb fluorine, hydroxyls are replaced on the apatite lattice, resulting in a weakened structure prompting compensatory growth that can engender lameness-inducing hyperostosis, osteosclerosis, osteomalacia, and osteoporosis in long bones.

Enamel fluorosis is characterised by mottling and hypomineralisation of incisive and cheek dentition, and hypoplasia if toxicosis occurs during enamel formation. Enamel softened by fluorosis is prone to aberrant wear, which can result in reduced feed intake, premature senescence, diminished body condition and retarded milk production.

Results

The characteristic mottling and/or enamel chalkiness were absent on the teeth studied. No significant inter-site difference in cusp attrition were apparent. Pedal elements are likewise devoid of osteofluorosis and bear no pathologies beyond limited articular surface exostosis, common in larger and older-aged individuals. A single metacarpal displayed a small ossified haematoma on the anteromedial aspect of the proximal metaphysis, but lameness is not implied.

DEH was significantly abundant at one site (Frasca), but only generally more so at Lamb Spring when compared to Hudson-Meng and Jones-Miller. DEH was significantly more prevalent on the second molars and less so on the third molars. Seasonal estimates suggest fairly consistent timing among modern and archaeological populations, coinciding with late summer/early autumn of the first year and spring of the first and second years, assuming May calving.

Conclusions

• The over-abundance of molars with DEH and the significantly worn M1 occlusal surfaces at Frasca may indicate fluoride toxicosis. However, the lack of aberrant wear, combined with a dearth of supporting evidence, speaks against a chronic condition.
• The relative consistency of DEH frequencies across all examined sites supports the idea of common agents.

Reference:

Byerly, R.M. 2007. Palaeopathology in late Pleistocene and early Holocene Central Plains bison: dental enamel hypoplasia, fluoride toxicosis and the archaeological record. Journal of Archaeological Science 34: 1847-1858

The Origins of the Domestic Dog

The archaeological record indicates that man’s best friend – the domestic dog Canis familaris – was likely also its first domestic animal. What though are its origins? Was it domesticated once or did several events take place independent of one another?

Circumstantial evidence suggests that dogs have diverse origins. During most of the late Pleistocene, humans and wolves co-existed over a wide geographical area, providing ample opportunity for independent domestication events and continued genetic exchange between wolves and dogs. Indeed, the extreme phenotypic diversity of dogs, even during the early stages of domestication, is highly suggestive of a varied genetic heritage. Whilst this question cannot be resolved through archaeological evidence, it is possible that genetic evidence may, therefore, be able to help.

When portions of mitochondrial DNA from wolves and domestic dogs was sequenced, the control region of wolves and dogs was demonstrated to be highly polymorphic. The distribution of wolf haplotypes displayed geographic specificity, with most localities containing haplotypes unique to a particular region. Sequence diversity amongst dogs was similar. However, mitochondrial haplotype diversity in dogs could not be partitioned according to breed. Many breeds shared sequences with other breeds. No dog sequence differed from any wolf sequence by more than 12 substitutions, whereas dog differed from coyotes and jackals by at least 20 substitutions and 2 insertions. This supported a wolf ancestry for dogs.

However, because mitochondrial DNA is maternally inherited, interbreeding between female dogs and male coyotes or jackals would not be detected. Therefore, a more limited study of nuclear DNA was also carried out. This also supported the conclusion that the wolf was the ancestor of the domestic dog.

Various methods of phylogenetic analysis distinguised four distinct clades. Clade 1 included 19 of the dog haplotypes. This group included representatives of many common breeds, as well as ancient breeds such as the dingo, New Guinea singing dog, and African basenji. Clade II included dog haplotype D8, found in two Scandinavian breeds: the elkhound and jamthund. This was also closely related to two wolf haplotypes found in Italy, France, Romania and Greece. Clade III contained 3 dog haplotypes, which were found in a variety of breeds such as the German shepherd, Siberian husky, and Mexican hairless. Clade IV also contained 3 haplotypes that were identical or very similar to wolf haplotype W6 found in Romania and western Russia, which suggests recented hybridisation between dogs and wolves.

Dog haplotype clades II and IV are most closely related to wolf sequences from eastern Europe. The coyote and wolf sequences were estimated as diverging one million years ago based upon the fossil record. Consequently, this implies that the sequence divergence between the most different genotypes in clade I (the most diverse group) could have originated as much as 135,000 years ago. The sequence divergence within clade I implies an origin of greater than 14,000 years before present, which is what is indicated by the archaeological record. Nevertheless, bones of wolves have been found in association with those of hominids from as early as the middle Pleistocene, up to 400,000 years ago.

It is suggested that early domestic dogs may not have been morphologically distinct from their wild relatives. Conceivably, the change from nomadic hunter-gatherer societies to more sedentary agricultural population centres around 10,000 to 15,000 years ago may have imposed new selective regimes on dogs that resulted in marked phenotypic divergence from wild wolves. Although breeds show uniformity with respect to behaviour and morphology, most breeds show evidence of a genetically diverse heritage because they contain different haplotypes. Moreover, dog sequences cluster with different groups of wolf haplotypes. Therefore, after the origin of dogs from a wild ancestor, dogs and wolves have continued to exchange genes.

References:

Morey, D.F. 1994. The Early Evolution of the Domestic Dog. American Scientist 82: 336-347

Vila, C.V., Savolainen, P., Maldonado, J.E., Amorim, I.R., Rice, J.E., Honeycutt, R.L., Crandall, K.A., Lundeberg., Wayne, R.K. 1997. Multiple and Ancient Origins of the Domestic Dog. Science 276: 1687-1689

Hawking in medieval England – the archaeological evidence

“An eagle for an Emperor, a gyrfalcon for a King,
a peregrine for a prince, a saker for a knight,
a Merlin for a Lady, a goshawk for a yeoman,
a sparrowhawk for a priest, a musket for a holy water clerk,
a kestrel for a knave.”
(The Boke of St Albans, c. 1486)

Hawking or falconry is the pursuit and capture of birds and small mammals by trained birds of prey. The origins for the sport are unclear, but from its introduction into Europe from Asia in the 3rd and 4th centuries AD, it rose to become one of the great field sports of the medieval period. Unlike the pursuit of deer, hawking was not the sole preserve of the nobility, but was accessible to those lower down the social strata, provided they had sufficient resources, although this in effect prevented ownership of hunting birds by the poor. The ‘Boke of St Albans’ (c. 1486) demonstrates how the type of bird kept related to an individual place in the social hierarchy.

What evidence though exists for this sport in the archaeological record?

Finds of hawking equipment such as hawk rings have been recovered from sites such as Heddingham Castle and Bigglewade. Such items are obviously direct evidence for hawking, and as such have great value in tracing the history of the sport. However, the small size of many items of falconry equipment and the fact that a number are made of leather, which has often decayed in archaeological deposits, means that such survivals are rare.

Another potential source of data is the remains of the birds themselves. The recovery of hawk bones obviously confirms the existence of those species at the site. However, it is necessary to consider in what capacity the birds were present. Were they trained birds involved in field sports or were they wild? This question can perhaps never be resolved with absolute certainty, but certain sources of evidence do provide the means of resolving the question with some degree of confidence.

Firstly, it is necessary to investigate whether the birds would be expected to occur naturally in the environment in which they were found. Non-native species are far more likely to represent a bird imported for falconry than an accidental death of a wild bird. In addition, ecological requirements and patterns of behaviour can be informative. The two most common falconer’s birds, the Goshawk (Accipter gentilis) and the Sparrowhawk (Accipter nisus), are specialist hunters which require sufficient cover in the form of trees or scrub to be able to ambush their prey. This hunting behaviour, combined with a lack of predisposition towards carrion, makes them ill-suited to urban environments. The presence of either in an urban context is most likely, therefore, the result of human activity.

The situation with falcons is more complex. The Peregrine Falcon (Falco peregrinus) and the Kestrel (Falco tinnunculus) are both common sights in modern town centres, which is a testament to their adaptability. However, with regards to the Peregrine, this has only occurred in areas where there were suitable roosting and nesting sites, such as office blocks, which would have been less readily available in most medieval urban centres. This would suggest urban finds of this species in a medieval context represent trained birds. However, the presence of wild birds drawn in from nearby mountains or sea cliffs can never be entirely excluded. Rural sites are, of course, another matter entirely, and such criteria are of less use for distinguishing between wild and trained birds.

In a few cases, such as that at Faccombe Netherton, pathological changes were observed in two of the Goshawk skeletons that may provided additional osteological evidence for hawking. One had slight exostoses on the left tarsometatarsus, though to be the result of trauma due to the jesses. Another possessed a possible false joint on the dorsal end of the left coracoid, a type of injury that is generally the result of chasing prey in modern birds.

A final source of evidence lies in the remains of the game caught by trained birds. However, such an approach should be treated with caution given the many other possible sources of such game.

Reference:

Cherryson, A. K. 2002. The identification of archaeological evidence for hawking in medieval England. Acta zoologica cracoviensia 45 (special issue): 307-314

Current Hot Topics in Palaeoanthropology

One topic that seems to be causing quite a stir in the anthropological blogosphere is that of Zeresenay Alemseged and the Selam a.k.a. Dikika fossil. Selam is a 3.3 million year old Australopithecus afarensis child. Remote Central and Anthropology.net both provide interesting and thorough discussions of the video clip, as well as the context in which it is set.

In addition, you might also want to take a look at the review of ‘Dmanisi’s Paleoanthropological Importance‘ at Anthropology.net, which discusses the importance of the site, and the human fossils which have come from it, in light of an anticipated new study to be published in Nature in the next day or so.

Roast hedgehog and nettle pud – a Neolithic feast?

Everyone loves hedgehogs, with their snuffly little noses and punky hairdos. But research into Britain’s oldest recipes suggests our ancestors loved them in a rather different way – roasted.

A team from the food science department at the University of Wales Institute in Cardiff has discovered that, along with nettle pudding, roasted hedgehogs can be traced back thousands of years. Research suggests nettle pudding may be the oldest known recipe, dating from 6000BC, closely followed by smoky stew, meat pudding, barley bread and roast hedgehog.

Ruth Fairchild, who led the research, said that however off-putting the Neolithic dishes might sound, many were forerunners of the food we enjoy today. “The way our ancestors cooked hedgehog – wrapped in a casing of grass or leaves to stop the meat burning – is an early version of many modern recipes which involve meat being wrapped or coated, such as chicken kiev, beef wellington or cornish pasties,” she said.

Source: Pidd, H. 2007. Roast hedgehog and nettle pud – a slap-up feast for ancient Britons. The Guardian.

The Archaeozoology of Luxury

What is luxury?

This is not something that can be easily defined, particularly when dealing with food. Just having enough could be viewed as a luxury, particularly when dealing with the problem of acquiring it. Composing one’s menu according to the rules of gastronomy, fashion or the desire to show off could be called a luxury. What is luxurious for some can be perceived as a basic need for others. Luxury is a relative term.

The dictionary definition of luxury as a state or condition is: ‘a condition of abundance or great ease and comfort’. When referring to an item, it is ’something adding to pleasure or comfort but not absolutely necessary’. In terms of food or diet, this would therefore encompass all ingredients above the level of basic needs. However, such a definition is hardly useful within the context of archaeozoology. For a variety of reasons, significant numbers of people believe that all animal products can be viewed as non-essential. Whilst from a strictly medical point of view this may not be entirely correct, the fact remains that they believe it and behave accordingly. Others, however, view their daily portion of meat as a basic need.

Perceptions of basic needs and luxuries have also changed through time. Products once regarded as luxuries, e.g. chocolate, coffee or tea, are now treated as staple parts of the western diet.

Another relative term is affluence: ‘the abundance of property’. This could simply mean a general state of well-being. Luxury will, therefore, be treated here as something more than affluence, a state in which one can enjoy the consumption of special food products, accessible only to a very small part of society.

Food consumption can be divided into four categories:

Level 1: what is physiologically needed to survive, be active and grow
Level 2: what is considered to be a basic need by a person, a group or a society above the level of strictly physiological needs
Level 3: affluence: the consumption of goods beyond basic and considered needs
Level 4: luxury: the consumption, beyond the level of affluence, of goods that are special, limited in supply, difficult to procure or very expensive for other reasons

How, though, do we recognise luxuries in the archaeozooological record?

Rarities often represent the best examples of luxury foods, simply because they are generally more expensive. This can be caused by their low abundance, people having to spend a lot of time and energy to procure them, or simply their rarity. As with art, the price of a product is often determined by what one is prepared to pay for it. Moreover, a meal can impress simply because of the price paid for it, rather than because of its taste.

Imported goods can be luxuries in that, even when they are abundant at their place of origin, they are rare at the place of consumption. Transport costs and limited availability make these goods especially expensive. Obviously, however, imported goods that become available in large quantities become cheaper and thus lose their luxury status.

Luxury items can also consist of products subject to restrictive rights, e.g. sumptuary laws, that make them available only to a limited part of society.

In general, a diet with much variety can be called luxurious because it will contain items that are not strictly optimal in terms of the ratio of costs versus nutritional value. Another possible characteristic of a luxury diet is the selection of the prime quality parts of an animal, or derived from animals killed before their optimal slaughter age. Given the loss for the producer, this latter makes the product more expensive. The same is true for animals killed outside the optimal slaughtering season.

Luxury items are not always easy to detect, however. All archaeological information contains bias. Certain animal food products leave no remains that survive in most soil types e.g. meat or fish that has been filleted and de-boned before being brought onto site. Preservation can hide information about a species as a whole, e.g. the lamprey with its cartilaginous skeleton. Recovery techniques can have even more severe consequences, e.g. whether the site was sieved or not.

It will always be difficult to identify luxury items at a single site if the contextual data is insufficient. A safer approach is to compare the data from a number of sites, dating from the same period, belonging to the same economy. This is not a weak method of analysis. Luxury is, as previously stated, a relative concept. It cannot be studied on the basis of a single find collection or even a single class of sites.

Reference: Ervynck, A., Van Neer, W., Huster-Plogmann, H and Schibler, J. 2003. Beyond affluence: the zooarchaeology of luxury. World Archaeology 34 (3): 428-441