Petrous bone is the new black

I was just reading an article about skeletal reconstruction of another fascinating extinct species when my supervisor came to my office. I asked: “How about we sequence this creature’s genome?” He replied by asking where the animal had lived. As I answered “Africa”, I already knew that it would end the discussion. With “Then get a petrous bone” he left the office.

Where to drill, that is the question

With the improved sequencing technologies, the field of ancient DNA (aDNA) is advancing rapidly. Things that we had once considered impossible have already happened. For now, the border or what is technically possible with aDNA has been set by sequencing the genome of a 700,000-year-old horse.

Recently, some of the aDNA research has focused on answering the basic question ‘Which bones or which part of a bone should we sample to maximize the yield of endogenous DNA?’.

Several factors have been suggested to influence the DNA yield including differences in the bone’s morphology, microscopic preservation, and environmental factors such as temperature and moisture levels.

However, a forensic study by Misner et al. showed that the only factor with a significant influence on the quality and quantity of extracted DNA is the type of bone.

“The general notion in both forensic genetics and aDNA is that the density of a bone is positively correlated with DNA preservation and that sampling should be carried out whenever possible on dense, weight bearing bones, with a preference for the femur and tibia.” (Pinhasi et al. 2015, PLOS ONE)

But neither femur nor tibia is the densest and hardest bone of a mammal’s body. It’s a well-hidden piece of skull, known as petrous bone.

What is this miraculous thing called petrous bone?

Petrous bone actually isn’t a bone but a petrous portion of the skull’s temporal bone, where the inner ear is located. The inner ear consists of bony cavities (the bony labyrinth) inside the petrous bone, which house the organs of hearing and balance.

The madness broke out application to ancient DNA started in 2014 when Cristina Gamba and colleagues showed that the rates of endogenous DNA extracted from the petrous bones are 4- to 16-fold higher than those from the teeth, and up to 183-fold higher than those from other bones.

A comparison of the proportion of endogenous DNA extracted from the petrous versus other bones. Gamba et al. 2014, Nature

A comparison of the proportion of endogenous DNA extracted from the petrous (right) versus other (left) bones. Gamba et al. 2014, Nature

Gamba et al. suggested that the high proportion of endogenous DNA is caused by the “reduced bacterial and chemical-mediated post-mortem DNA decay” in the petrous bones. In other words, compact bones like the femur, tibia, and especially petrous bone protect the DNA better from being degraded by chemicals and microorganisms that affect bones after death.

Getting to the core (of the inner ear)

In 2015, Pinhasi and colleagues examined differences in the endogenous DNA yield within the petrous bone. They sampled three parts of the bone: A) a spongy part, B) dense white bone surrounding the inner ear, and C) dense bone of the inner ear.

They compared the yields in 10 ancient human samples spanning in age between 10,000 and 1,800 calibrated years before present (cal BP). Out of these, 5 samples were from hot and tropical climates and the other 5 samples were from temperate regions of Europe.

Location of the three compared parts of the petrous bone. Pinhasi et al. 2015, PLOS ONE

Location of the three compared parts of the petrous bone. Pinhasi et al. 2015, PLOS ONE

It’s not a huge surprise that the denser the bone (A < B < C), the higher the proportion of endogenous DNA that Pinhasi et al. obtained from the bones. In the five temperate European samples, the endogenous DNA content is the lowest in part A, intermediate in part B and the highest in part C. The dense bone of the inner ear (part C) yielded 35 – 70 % of endogenous DNA.

On the other hand, the results of the hot-climate samples were less positive:

“…our results show that endogenous yields from the five samples which originated from hot (either arid or humid) regions were always lower than 1% including extractions from part C of the petrous bone.”

If you think that this result is the end of our hopes of sequencing aDNA from the tropical regions, you are overly pessimistic. Even though the endogenous content of these samples was extremely low, it wasn’t zero, which means that if your name is Svante or Eske you probably have enough money to sequence it as much as you want.

Proportions of the endogenous DNA content in 10 ancient human samples, extracted from three different parts of the petrous bone. Pilhasi et al. 2015, PLOS ONE

Proportions of the endogenous DNA content in 10 ancient human samples, extracted from three different parts of the petrous bone. Pilhasi et al. 2015, PLOS ONE

And maybe you just need to be lucky and find the right sample

To confirm that people are serious about sequencing aDNA genomes of our more distant ancestors, the first ancient African genome was recently published by Gallego Llorente et al. in Nature. The 4,500-year-old Ethiopian ancient human was sequenced to 12.5x average coverage. And guess what, they managed to do that by extracting DNA from the petrous bone, which yielded about 47% of endogenous DNA.

To sum this up and get back to the title, using the petrous bone has become incredibly trendy. If you also want your double-digit IF publication, follow the example of Cassidy et al. (2015), Jones et al. (2015), Mathieson et al. (2015), and Martiniano et al. (2015), and start looking for petrous bones.

References:

Cassidy et al. (2016) Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome. PNAS 113: 2, 368-373. DOI:10.1073/pnas.1518445113

Gallego Llorente et al. (2015) Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 350: 6262, 820-822. DOI: 10.1126/science.aad2879

Gamba et al. (2014) Genome flux and stasis in a five millennium transect of European prehistory. Nature Communications 5: 5257. DOI:10.1038/ncomms6257

Jones et al. (2015) Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nature Communications 6: 8912. DOI:10.1038/ncomms9912

Martiniano et al. (2016) Genomic signals of migration and continuity in Britain before the Anglo-Saxons. Nature Communications 7: 10326. DOI:10.1038/ncomms10326

Mathieson et al. (2015) Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499-503. DOI:10.1038/nature16152

Pinhasi et al. (2015) Optimal ancient DNA yields from the inner ear part of the human petrous bone. PLoS ONE 10(6): e0129102. doi:10.1371/journal.pone.0129102

 

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About Patrícia Pečnerová

I'm currently a postdoctoral researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. My research interests focus on evolutionary processes in extinct and endangered species. For my PhD, I studied genetic extinction factors in the last population of the woolly mammoth. Now I'm working on genomics of wild mountain gorillas
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