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Through DNA, breathing new life into old museum pieces

Jan. 13, 2009
World Science staff

In 1902, the Na­tional Zoo in Wash­ing­ton D.C. brought in a un­ique and en­dan­gered an­i­mal called the thy­la­cine, or Tas­ma­ni­an Tiger—a fe­male and her three cubs. 

But by the mid-1930s, the thy­la­cine was ex­tinct, leav­ing be­hind only pre­served mu­se­um spec­i­mens. 

The two sur­viv­ing thy­la­cine cubs brought to the Na­tion­al Zoo in 1902, pho­to­graphed two to three years af­ter their ar­ri­val. One of these an­i­mals, most like­ly the one in front, is a spec­i­men se­quenced for the new stu­dy. (Pho­to cour­te­sy of the Smith­so­nian Ar­chives)

Now, re­search­ers are us­ing DNA se­quenc­ing tech­nol­o­gy to an­a­lyze pre­served thy­la­cines, in­clud­ing one of those brought to the Na­tional Zoo. In the pro­cess they’re mak­ing new dis­cov­er­ies in thy­la­cine ge­nom­ics and a bur­geon­ing field called “mu­seo­mics,” the ge­net­ic study of mu­se­um spec­i­mens.

Broadly speak­ing, such re­search is­n’t lim­it­ed to bi­ol­o­gy alone. A re­searcher from North Car­o­li­na State Uni­ver­s­ity is us­ing DNA anal­y­sis to pin­point the or­i­gin of me­di­e­val man­u­scripts, many of which were writ­ten on an­i­mal skin parch­ments.

The thy­la­cine study is pub­lished in the Jan. 12 on­line edi­tion of the jour­nal Ge­nome Re­search. The thy­la­cine was­n’t really a ti­ger, but a mar­su­pi­al with many dog-like fea­tures—a strik­ing ex­am­ple of “con­ver­gent evo­lu­tion,” sci­en­tists say, a pro­cess in which two un­re­lat­ed crea­tures evolve si­m­i­lar char­ac­ter­is­tics.

Ex­ten­sively hunt­ed by farm­ers, the thy­la­cine was be­com­ing in­creas­ingly rare in the wild when the Na­tional Zoo ac­quired the fe­male and cubs. Ge­net­ic se­quences sam­pled from the pre­served spec­i­mens of the Na­tional Zoo thy­la­cine family have been stud­ied in re­cent years, but these in­ves­ti­ga­t­ions were lim­it­ed by DNA con­tamina­t­ion and de­grada­t­ion.

Now, re­search­ers say they’re us­ing im­proved meth­ods for sam­pling and se­quenc­ing, or de­cod­ing, DNA from old hair to an­a­lyze the sam­ples. 

In ad­di­tion to re­fin­ing the place of this un­usu­al an­i­mal in ev­o­lu­tion­ary his­to­ry, ge­net­ic clues to the im­pend­ing ex­tinction of the thy­la­cine be­came ap­par­ent, said An­ders Gö­ther­ström of Upp­sa­la Uni­ver­s­ity in Swe­den, one of the au­thors of the stu­dy.

“What I find amaz­ing is that the two spec­i­mens are so sim­i­lar,” said Gö­ther­ström. “There is very lit­tle ge­net­ic varia­t­ion be­tween them.” Göther­strön said a lack of ge­net­ic di­vers­ity is in­dic­a­tive of a spe­cies dy­ing out, as the an­i­mal in­deed was. 

The work has paved the way for more de­tailed ge­net­ic anal­y­sis of the thy­la­cine, opened the door to more museomic stud­ies us­ing the treas­ure trove of mu­se­um spec­i­mens world­wide, and will raise di­a­logue about even big­ger pro­jects, the re­search­ers said. The large amount of DNA ob­tained in the study “demon­strates the fea­si­bil­ity of a thy­la­cine ge­nome pro­jec­t,” said Stephan Schus­ter of Penn State Uni­ver­s­ity, al­so an au­thor of the re­port.. “It will al­so re­vive dis­cus­sions on the pos­si­ble res­ur­rec­tion of the an­i­mal.”

The use of DNA as a tool to shed light on mu­se­um spec­i­mens can ex­tend well be­yond the study of or­gan­isms them­selves.

Thou­sands of pains­tak­ingly handwrit­ten books pro­duced in me­di­e­val Eu­rope still ex­ist, but schol­ars have long strug­gled with ques­tions about when and where the ma­jor­ity of these works or­i­ginated. Now a re­searcher from North Car­o­li­na State Uni­ver­s­ity is us­ing mod­ern ad­vanc­es in ge­net­ics to de­vel­op tech­niques that will shed light on the or­i­gins of these cul­tur­al ar­ti­facts.

Many me­di­e­val man­u­scripts were writ­ten on parch­ment made from an­i­mal skin. Eng­lish pro­fes­sor Tim­o­thy Stin­son of the uni­ver­s­ity is work­ing to per­fect tech­niques for ex­tract­ing and an­a­lyz­ing the DNA con­tained in these skins in hopes of cre­at­ing a ge­net­ic da­tabase that can be used to de­ter­mine when and where a man­u­script was writ­ten. Pre­vi­ous de­ter­mina­t­ions of man­u­script or­i­gins were largely “based on the hand­writ­ing and di­a­lect of the scribes who cre­at­ed the man­u­scripts – tech­niques that have prov­en un­re­li­a­ble for a num­ber of rea­sons,” Stin­son said.

Stin­son said ge­net­ic test­ing could re­solve these is­sues. The stra­tegy would be to com­pare the DNA in mys­te­ri­ous man­u­scripts to the DNA in man­u­scripts whose or­i­gins are al­ready re­liably de­ter­mined. Each man­u­script can pro­vide a wealth of ge­net­ic da­ta, Stin­son ex­plains, be­cause a typ­i­cal me­di­e­val parch­ment book in­cludes the skins of more than 100 an­i­mals. Stin­son is to pre­s­ent find­ings of his early re­search at the an­nu­al meet­ing of the Bib­lio­graph­i­cal So­ci­e­ty of Amer­i­ca in New York City on Jan. 23.

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In 1902, the National Zoo in Washington D.C. brought in a unique and endangered animal called the thylacine, or Tasmanian Tiger—a female and her three cubs. But by the mid-1930s, the thylacine was extinct, leaving behind only preserved museum specimens. Now, researchers are using DNA sequencing technology to analyze preserved thylacines, including one of those brought to the National Zoo. In the process they’re making new discoveries in thylacine genomics and a burgeoning field called “museomics,” the genetic study of museum specimens. Broadly speaking, such research isn’t limited to biology alone. A researcher from North Carolina State University is using DNA analysis to pinpoint the origin of medieval manuscripts, which were written on animal skin parchments. The thylacine study is published in the Jan. 12 online edition of the journal Genome Research. The thylacine wasn’t actually not a tiger, but a marsupial with many dog-like features—a striking example of “convergent evolution,” scientists say, a process in which two unrelated creatures evolve similar characteristics. Extensively hunted by farmers, the thylacine was becoming increasingly rare in the wild when the National Zoo acquired the female and cubs. Genetic sequences sampled from the preserved specimens of the National Zoo thyalcine family have been studied in recent years, but these investigations were limited by DNA contamination and degradation. Now, researchers say they’re using improved methods for sampling and sequencing, or decoding, DNA to analyze the samples. In addition to refining the place of this unusual animal in evolutionary history, genetic clues to the impending extinction of the thylacine became apparent, said Anders Götherström of Uppsala University in Sweden, one of the authors of the study. “What I find amazing is that the two specimens are so similar,” said Götherström. “There is very little genetic variation between them.” Götherströn said a lack of genetic diversity is indicative of a species dying out, as the animal indeed was. The work has paved the way for more detailed genetic analysis of the thylacine, opened the door to more museomic studies using the treasure trove of museum specimens worldwide, and will raise dialogue about even bigger projects, the researchers said. The large amount of DNA obtained in the study “demonstrates the feasibility of a thylacine genome project,” said Stephan Schuster of Penn State University, also an author of the report.. “It will also revive discussions on the possible resurrection of the animal.” The use of DNA as a tool to shed light on museum specimens can extend well beyond the study of organisms themselves. Thousands of painstakingly handwritten books produced in medieval Europe still exist today, but scholars have long struggled with questions about when and where the majority of these works originated. Now a researcher from North Carolina State University is using modern advances in genetics to develop techniques that will shed light on the origins of these cultural artifacts. Many medieval manuscripts were written on parchment made from animal skin. English professor Timothy Stinson of the university is working to perfect techniques for extracting and analyzing the DNA contained in these skins with the long-term goal of creating a genetic database that can be used to determine when and where a manuscript was written. Previous determinations of manuscript origins were largely “based on the handwriting and dialect of the scribes who created the manuscripts – techniques that have proven unreliable for a number of reasons,” Stinson said. Stinson said genetic testing could resolve these issues by comparing the DNA in mysterious manuscripts to the DNA in manuscripts whose origins are already reliably determined. Each manuscript can provide a wealth of genetic data, Stinson explains, because a typical medieval parchment book includes the skins of more than 100 animals. Stinson is to present findings of his early research at the annual meeting of the Bibliographical Society of America in New York City on Jan. 23.