Woolly Mammoth Genomes Provide New Clues to Their Extinction

In a manner somewhat reminiscent of Jurassic Park, scientists have cloned the full genomes of two woolly mammoths. The actual resemblance to Jurassic Park is scant to none however, because the DNA was obtained from actual preserved mammoth tissue as opposed to extraction from amber, and the researchers had a different goal in mind than recreation of the extinct creature. They sought to better understand why the mammoths went extinct in the first place.

Woolly mammoths (Mammuthus primigenius) were one of the most abundant mammals of the Pleistocene epoch (part of the Quaternary period) which lasted from 2.588 million years ago to 11,700 years ago. Following the Pleistocene epoch is the Holocene, which represents the current geological age in which we reside. The Pleistocene was marked by repeated glaciations commonly known as the “Ice Age,” and the woolly mammoth along with many other large prehistoric animals collectively referred to as “megafauna” became extinct along the Pleistocene to Holocene transition. A handful of remote mammoth populations survived into the Holocene, with the last known population to have existed on Wrangel Island about 4,000 years ago.

Our knowledge about most prehistoric beasts is derived from scientific interpretations of fossilized remains. Information available on the woolly mammoth is much more tactile however, as the discovery of multiple frozen woolly mammoth carcasses has led to what is perhaps the most thorough understanding of any prehistoric animal’s physiology and ecological significance. The remarkable preservation of the frozen mammoths allows researchers to study the mammoth from a certain molecular perspective that is often outside the realm of paleontology. Namely, the mammoth’s genetics.

In a study recently published in the journal Current Biology by twelve scientists from several institutions including the Swedish Museum of Natural History, Stockholm University, and Harvard Medical School, Palkopoulou et al. extracted DNA from the molar tooth of a preserved woolly mammoth found on Wrangel Island. Situated in the frigid Artic Ocean waters east of Alaska and north of Siberia, Wrangel Island is a Russian national wildlife preserve in the strictest sense, with only a handful of rangers who live there year round and a dozen or so scientists that are permitted to visit in the summer. Utilizing 14C radiocarbon dating, they determined that the Wrangel Island mammoth was approximately 4,300 years old. A second mammoth was dated to about 44,800 years old using a soft tissue sample from a specimen discovered in the Oimyakon District in northeastern Siberia.

Wrangel Island is thought to be one of the last places woolly mammoths were alive, around 4,000 years ago. It's location in the Artic Sea would have been reachable in the ice age in the Pleistocene. From Wikipedia
Wrangel Island is thought to be one of the last places woolly mammoths were alive, around 4,000 years ago. It’s location in the Artic Sea would have been reachable in the ice age in the Pleistocene.
From Wikipedia

The scientists hoped that the two mammoth specimens would allow them to paint a picture of the species’ genomic diversity across time. The Oimyakon individual is from the Late Pleistocene when mammoths were still relatively abundant in mainland Russia. The Wrangel Island mammoth on the other hand is thought to represent one of the last surviving individuals isolated on the island after the mainland population died out, probably due to a combination of hunting by humans and climate change at the end of the ice age. These influences, the warming climate and human hunters, are often given sole credit for the demise of the mammoths, but some scientists wonder if the smaller populations created by these factors were ultimately driven to extinction by a third factor: loss of genetic diversity.

Genetic diversity is a term used to describe the variability of a population. Species that have greater genetic diversity have an evolutionary advantage, because if the genetic makeup of one individual proves to be weak in response to an external influence, the genetic composition of another individual may be able to withstand environmental or predatory pressures. In other words, a population that is very similar, or homogenous, is more susceptible to dying out in response to the same pressure, whereas a more diverse, or heterogeneous population is likely to contain individuals that will survive whatever nature throws at them and enable them to pass their genes onto the next generation.

Using a model known as the pairwise sequentially Markovian coalescent (PSMC) method, the researchers were able to infer that the effective population size (Ne) of the mammoths plummeted around 12,000 years ago. This genetic data corresponds well to the Pleistocene to Holocene transition, a time of rising sea levels at the end of the ice age. This is also the estimated time for the disappearance of mammoths in mainland Eurasia and the establishment of an isolated population on Wrangel Island. Studies such as these reaffirm scientists’ confidence in the models they use, where similar conclusions are reached from fields as different as genetics and geology.

To better understand the genetic diversity of the mammoth populations, that is a measure of diversity between individuals, the researchers first studied the genomic diversity of the two individuals themselves. Woolly mammoths, just like people, have two copies of every chromosome, and thus every gene in their genome. Sometimes the two copies of a gene are identical, and are therefore referred to as homozygous. In the event that the two copies of a gene are different, they are considered heterozygous. Individuals with many heterozygous genes have the ability to contribute to a greater genetic diversity.

The average autosomal (the non-sex, or non-X and -Y chromosomes) heterozygosity was compared between the Wrangel and Oimyakon mammoths to uncover the change in genomic diversity across the 40,000 years separating the populations. While the Wrangel mammoth’s genome contained an average of 1.00 heterozygous sites per 1,000 base pairs, the Oimyakon individual was estimated to contain 1.23-1.27 heterozygous sites per 1,000 base pairs. In other words, the 4,300 year old Wrangel Island mammoth exhibited approximately 20% lower heterozygosity when compared to its 44,800 year old Oimyakon relative. The isolated Wrangel Island mammoths had lost a significant chunk of genomic diversity over time.

Restoration of a group in late Pleistocene northern Spain, by Mauricio Antón From Wikipedia
Restoration of a group in late Pleistocene northern Spain, by Mauricio Antón
From Wikipedia

When comparing the heterozygosity of the mammoth’s genomes to extant mammals however, their values were not quite as low as expected. The Wrangel mammoth’s heterozygosity was similar to that of the Eastern lowland gorilla, Western chimpanzee and bonobo, while the Oimyakon mammoth’s heterozygosity was similar to the Cross River gorilla, giant panda, and Cameroon chimpanzee. The Wrangel mammoth’s heterozygosity was actually greater than several currently endangered animals including lions, tigers, polar bears, Tasmanian devils and the snow leopard. Given that these species are all carnivores and typically occur in significantly lower population densities than herbivores, it is not surprising that the mammoth’s heterozygosity never reached the low levels of these present-day carnivores.

Another method for comparing the internal diversity of a genome is measuring the “runs of homozygosity” (ROH). When the chromosomes of two parents are combined, they will contribute the same copies of some genes and different copies of others. When both mom and dad have the same sequence of a gene, called an allele, their offspring will be homozygous for that gene. In other instances when the paternal and maternal alleles for a given gene are different, a heterozygous region is created.  A greater number of homozygous stretches in the genome of the offspring indicates that the mother and father are more closely related. When cousins or other close family members marry and have children, the resulting genomes will contain long runs of homozygosity, but shorter runs of homozygosity are present even in more distantly related individuals. After all, assuming humans all have one common ancestor it comes to reason that a certain degree of homozygosity will be expected for all individuals. The runs of homozygosity (ROH) are simply increased with relatedness.

Applying the ROH principle to the mammoth DNA, the investigators found a stark difference between the Oimyakon and Wrangel genomes. Whereas ROHs comprised 0.83% of the Oimyakon genome, ROH’s contributed to 23.3% of the Wrangel mammoth’s genome, a drastic 28-fold increase. It is thus quite likely that this jump in ROHs led to a decline in the fitness of the woolly mammoths as a species and accelerated their demise on Wrangel Island.

An obvious explanation for such a significant increase in ROHs would come from inbreeding on the island, but the genomic data indicates otherwise. The ROHs were found in segments spanning few million base pairs, and were furthermore scattered across all autosomes. The increase in ROHs is thus likely the result of several dozen or hundreds of generations of breeding between moderately distant relatives. If close relative inbreeding was the cause, the ROHs would be expected to form much longer stretches of homozygous regions rather than the many dispersed ROHs the researchers observed.

While it is clear that the woolly mammoth genetic diversity declined over time, at least from the period of the Oimyakon mammoth 44,800 years ago to the Wrangel Island mammoth 4,300 years ago, it is more difficult to say exactly how important this was in the course of the mammoths’ demise. The final cause of extinction in mammoths was likely multifactorial, resulting from a combination of warming climates, melting ice, and hunting, all of which probably contributed to decreased genetic diversity among the surviving populations. In the end, the last surviving mammoths may have been too genetically homogenous to fare well.  While the results of this study may not be as attention-grabbing as an attempt to clone a woolly mammoth, the ability of scientists to sequence these creature’s ancient genomes and reconstruct a more accurate history of their past is a wonderful example of the detective work that enables geneticists to investigate the past.

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