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Captive tigers in the United States outnumber those living in the wild. The World Wildlife Federation estimates around 5,000 of the big cats reside in the U.S., mostly owned by private citizens.

The health of this population is a genetic mystery for conservation groups and researchers interested in how captive tigers could help stabilize or restore wild tiger populations. Are the privately owned animals just like tigers in the wild, or do they reflect characteristics popular in the illegal trade? Are they a hodgepodge of wild tiger ancestry, or are they detrimentally inbred?

New research from Stanford University, published Sept. 19 in Proceedings of the National Academy of Sciences, digs into these questions and offers a new tool that conservationists and law enforcement can use to protect the animals and prosecute those responsible for their abuse.

“We’re trying to leverage genomic technology to be useful in a conservation context – there are so few tigers. We won’t get a second chance if they go extinct,” said Ellie Armstrong, PhD ’21, who is lead author of the paper.

The study was led by Armstrong, who conducted the research as part of her doctoral studies in biology, with her co-advisors and co-authors Elizabeth Hadly, the Paul S. and Billie Achilles Professor in Environmental Biology, Emerita, and Dmitri Petrov, the Michelle and Kevin Douglas Professor, both in the School of Humanities and Sciences.

The researchers became interested in studying the genetic diversity of privately held tigers – called “generic” because their sources are unknown – after conducting a study on the genetic impact of isolation on wild tiger populations.

“We were conducting a large study on wild tiger populations and leveraged these data to address the issue of captive tigers in the United States. It was a bit unbelievable at first that you could have a tiger living right next door and not know it,” said Armstrong, who is now an assistant professor of evolution, ecology, and organismal biology at the University of California, Riverside. “We got connected with Tigers in America, and that’s when we realized that there’s an enormous number of these cats outside accredited facilities that were bred for animal encounters, performed as circus animals or were trafficked as exotic pets. But we didn’t have any idea what kind of tiger they were or where they came from.”

A hurdle for the research team was the absence of official data on generic tigers. Shows like Netflix’s 2020 Tiger King and the 2009 documentary The Tiger Next Door helped grow public knowledge about privately owned tigers but accessing them for research purposes remained challenging.

“There was so much hearsay associated with this captive population and a lot of it contradicts itself. People said ‘All of the cats are really inbred,’ or ‘All of the cats are genetically diverse,’” said Armstrong. “We had no idea what to expect and thought that genomic technology could help us answer some of these questions.”

Through relationships with sanctuaries that had rescued generic tigers, the team obtained samples and learned about many animals' rescue locations.

The researchers collected samples from 154 generic tigers and used another 100 available wild tiger samples existing in the National Center for Biotechnology Information (NCBI) database. From their previous work, they knew there are six wild subspecies of tigers. With these data, they developed a reference panel for tigers used to accurately distinguish individual animals and assign their genetic ancestry. Armstrong compares it to popular genetic ancestry tests for humans.

“When we do 23andMe, we’re not sequencing the whole genome – we’re sequencing a portion that informs us about your health and ancestry,” she said. “That’s what we want to be able to do but for tigers. It’s difficult and expensive to sequence and analyze a whole genome, especially in a conservation context. The workflow we built allows you to sequence a portion of the genome and get answers about an individual tiger's ancestry.”

Knowing a tiger’s ancestry has uses beyond conservation and breeding programs – law enforcement can use it to prosecute.

The Big Cat Public Safety Act went into effect Dec. 20, 2022 ending private ownership of big cats as pets while placing restrictions on breeding commerce possession usage certain species including tigers Individuals who owned cats prior must register Still U.S Fish Wildlife Service storerooms full confiscated pelts bones teeth cases unable prosecute positively identify origin agency requested work researchers

“We’ll be working with law enforcement to try applying forensic context prosecute wildlife crimes seen Tiger King monitor populations track illegal trade,” Armstrong said “Materials like teeth pelts limited DNA reference panel allow wildlife agencies determine ancestry identity confiscated samples even only sequencing small portion genome That’s been most rewarding part this research know mattered immediate future applications”

As for those wondering “What are these animals?” researchers feel can put question rest U.S captive population did not show widespread relative populations Nor did show maintain single subspecies true zoo-bred wild mix different subspecies Armstrong colleagues also show non-zoo harbor more diversity found

“This absence unique diversity means will no ‘genetic rescue’ individuals now captivity,” Hadly said “In other words diversity all evolution work going future”

DNA only way identify subspecies distinguishable physical differences six recognized remain priority management overcome enormous hurdles releasing back reference used identify mixed

Said Armstrong “This technology usually ‘for fun’ thing humans find more about ancestry use genomics serious way help wildlife thrive keep exploited”

Additional Stanford co-authors former CEHG/NSF postdoctoral fellow Jazlyn A Mooney now Gabilan Assistant Professor University Southern California Department Quantitative Computational Biology postdoctoral scholar Katie Solari professor emeritus genetics Gregory Barsh researcher Christopher B Kaelin Bernard Y Kim doctoral student Victoria Grant Noah Rosenberg Stanford Population Genetics Society Tsuya Yokoyama member Bio-X senior fellow Woods Institute Environment Howard Hughes Medical Institute Petrov Maternal Child Health Research Institute Cancer Institute Other HudsonAlpha Institute Hebrew Jerusalem Gencove Inc San Diego Zoo Alliance National Centre Biological Sciences India funded National Science Foundation Graduate Fellowship Program Media contact mediarelations@stanford.edu News insights events delivered inbox each weekday morning ©CopyrightStanford University Stanford California

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