..

"Long before it's in the papers"
January 28, 2015

RETURN TO THE WORLD SCIENCE HOME PAGE


Woolly-mammoth genome decoded

Nov. 19, 2008
Courtesy Penn State University
and World Science staff

Bi­ol­o­gists re­port that they have for the first time un­rav­eled nearly the whole ge­net­ic code of an ex­tinct an­i­mal: the woolly mam­moth, the icon­ic gi­ant el­e­phant that roamed the cold north­ern hem­i­sphere. 

Past pro­jects have de­cod­ed chunks of the DNA of an­cient spe­cies, such as cave bears, but not most of the ge­nome, as the re­search­ers in the new study claim to have done.

Woolly mam­moth in an artist's im­age. (Cour­tesy Ex­hi­bit­Ease LLC - Steven W. Mar­cus)


They charted four bil­lion bas­es, or “let­ters,” of code us­ing cutting-edge DNA-se­quenc­ing tools and a new high-efficiency ap­proach, said Webb Mill­er of Penn State Uni­ver­s­ity, one of the pro­jec­t’s two lead­ers. 

“Our da­ta set is 100 times more ex­ten­sive than any oth­er pub­lished da­ta set for an ex­tinct spe­cies, dem­on­strat­ing that an­cient DNA stud­ies can be brought up to the same lev­el as mod­ern ge­nome pro­jects,” said Stephan C. Schus­ter, the pro­jec­t’s oth­er lead­er, al­so at Penn State. 

The re­search­ers said the full woolly-mam­moth ge­nome probably con­sists of over four bil­lion DNA bas­es, about the size of the mod­ern-day Af­ri­can el­e­phant’s ge­nome. Al­though the study com­prised more than four bil­lion DNA bas­es, only 3.3 bil­lion of them—a lit­tle over the size of the hu­man ge­nome—currently can be as­signed to the mam­moth ge­nome, the in­ves­ti­ga­tors added.

Some of the re­main­ing DNA bas­es may be­long to the mam­moth, they ex­plained; oth­ers could be­long to oth­er or­gan­isms, like bac­te­ria and fun­gi, from the sur­round­ing en­vi­ron­ment that had con­tam­i­nated the sam­ple. The team used a draft ver­sion of the Af­ri­can el­e­phant’s ge­nome, which oth­er sci­en­tists are work­ing on, to dis­tin­guish code that truly be­long to the mam­moth from pos­si­ble con­tam­i­nants.

The findings are de­scribed in the Nov. 20 issue of the re­search jour­nal Na­ture.

“Only af­ter the ge­nome of the Af­ri­can el­e­phant has been com­plet­ed will we be able to make a fi­nal as­sess­ment about how much of the full woolly-mam­moth ge­nome we have se­quenced,” said Mill­er. The team used DNA ex­tracted from the hairs of a mam­moth mum­my bur­ied in fro­zen Si­be­ri­an ground for 20,000 years, and a sec­ond mam­moth mum­my es­ti­mat­ed to be at least 60,000 years old. 

By us­ing hair, the sci­en­tists said they avoided some past prob­lems that have be­dev­iled the se­quenc­ing, or de­cod­ing, of an­cient genes. That’s be­cause DNA in the hair is easier to sep­a­rate from con­tam­i­nat­ing DNA of bac­te­ria and fun­gi, compared to us­ing DNA from bone. Al­so, hair com­po­nents act as a bi­o­log­i­cal plas­tic that en­cases and pro­tects ge­net­ic ma­te­ri­al.

Ge­net­ic ev­i­dence in­di­cates woolly mam­moths evolved in­to two ge­net­ic­ally dis­tinct sub-popula­t­ions start­ing around two mil­lion years ago, ac­cord­ing to Schus­ter and Mill­er. One of these groups died out some 45,000 years ago; anoth­er lived on un­til af­ter the last ice age, about 10,000 years ago. 

The new re­search al­so shows woolly mam­moths are more closely re­lat­ed to mod­ern-day el­e­phants than pre­vi­ously was be­lieved, said Schus­ter and Mill­er.

“Our da­ta sug­gest that mam­moths and mod­ern-day el­e­phants sep­a­rat­ed around six mil­lion years ago, about the same time that hu­mans and chim­panzees sep­a­rat­ed,” said Mill­er. “How­ever, un­like hu­mans and chim­panzees, which rel­a­tively rap­idly evolved in­to two dis­tinct spe­cies, mam­moths and el­e­phants evolved at a more grad­u­al pace.”

To gauge how long it has been since spec­ies branched apart in evo­lu­tion, researchers gen­er­ally assess the ex­tent of the ge­ne­tic dif­fer­ences be­tween them, and other evi­dence.

The research team also “disco­vered that in­di­vid­ual woolly mam­moths were so ge­net­ic­ally si­m­i­lar to one anoth­er that they may have been es­pe­cially sus­cep­ti­ble to be­ing wiped out by a dis­ease, by a change in the cli­mate, or by hu­mans,” said Schus­ter. Populations with high genetic di­v­er­sity are con­sid­ered more re­sis­tant to sud­den dif­fi­cul­ties, because it’s more like­ly that at least some members of the pop­u­lation will be gene­ti­cally equip­ped to sur­vive. 

Mem­bers of Schus­ter and Mill­er’s research team pre­vi­ously exon­er­ated hu­mans in the die­off of one of the Si­be­ri­an mam­moth sub-popula­t­ions. No hu­mans seem to have lived in Si­be­ria when this group van­ished. But de­bate con­tin­ues over the causes of ex­tinction for mam­moths that lived else­where, in­clud­ing North Amer­i­ca.


* * *

Send us a comment on this story, or send it to a friend









 

Sign up for
e-newsletter
   
 
subscribe
 
cancel

On Home Page         

LATEST

  • St­ar found to have lit­tle plan­ets over twice as old as our own

  • “Kind­ness curricu­lum” may bo­ost suc­cess in pre­schoolers

EXCLUSIVES

  • Smart­er mice with a “hum­anized” gene?

  • Was black­mail essen­tial for marr­iage to evolve?

  • Plu­to has even cold­er “twin” of sim­ilar size, studies find

  • Could simple an­ger have taught people to coop­erate?

MORE NEWS

  • F­rog said to de­scribe its home through song

  • Even r­ats will lend a help­ing paw: study

  • D­rug may undo aging-assoc­iated brain changes in ani­mals

Biologists report that they have for the first time unraveled nearly the whole genetic code of an extinct animal: the woolly mammoth, the iconic giant elephant that roamed the cold northern hemisphere. Past projects have decoded chunks of the DNA of ancient species, such as the cave bears, but not most of the genome, as the researchers in the new study claim to have done. The researchers charted four billion bases, or “letters,” of code using cutting-edge DNA-sequencing instruments and a new high-efficiency approach, said Webb Miller of Penn State University, one of the project’s two leaders. “Our data set is 100 times more extensive than any other published dataset for an extinct species, demonstrating that ancient DNA studies can be brought up to the same level as modern genome projects,” said Stephan C. Schuster, the project’s other leader and also at Penn State. The researchers said the full woolly-mammoth genome probably consists of over four billion DNA bases, about the size of the modern-day African elephant’s genome. Although the study comprised more than four billion DNA bases, only 3.3 billion of them—a little over the size of the human genome—currently can be assigned to the mammoth genome, the investigators added. Some of the remaining DNA bases may belong to the mammoth, they explained; others could belong to other organisms, like bacteria and fungi, from the surrounding environment that had contaminated the sample. The team used a draft version of the African elephant’s genome, which other scientists are working on, to distinguish those sequences of code that truly belong to the mammoth from possible contaminants. “Only after the genome of the African elephant has been completed will we be able to make a final assessment about how much of the full woolly-mammoth genome we have sequenced,” said Miller. The team used DNA extracted from the hairs of a mammoth mummy buried in frozen Siberian ground for 20,000 years, and a second mammoth mummy estimated to be at least 60,000 years old. By using hair, the scientists said they avoided problems that have bedeviled the sequencing, or decoding, of ancient genes from bones. That’s because DNA in the hair is more easily separated from contaminating DNA of bacteria and fungi. Also, hair components act as a biological plastic that encases and protects genetic material. Genetic evidence indicates woolly mammoths evolved into two genetically distinct sub-populations starting around two million years ago, according to Schuster and Miller. One of these died out some 45,000 years ago; another lived on until after the last ice age, about 10,000 years ago. The new research also shows woolly mammoths are more closely related to modern-day elephants than previously was believed, said Schuster and Miller. “Our data suggest that mammoths and modern-day elephants separated around six-million years ago, about the same time that humans and chimpanzees separated,” said Miller. “However, unlike humans and chimpanzees, which relatively rapidly evolved into two distinct species, mammoths and elephants evolved at a more gradual pace.” Also, “we discovered that individual woolly mammoths were so genetically similar to one another that they may have been especially susceptible to being wiped out by a disease, by a change in the climate, or by humans,” said Schuster. Members of his group previously ruled out that humans might have killed off at least one of the Siberian sub-populations, which appears to have gone extinct when no humans lived in Siberia. But debate continues over the causes of extinction for mammoths that lived elsewhere, including North America.