The ofCATS Genomic prints in the DNA of the world’s wild have clarified the tree and uncovered several remarkable migrations in their past

By Stephen J. O’Brien and Warren E. Johnson

legant and enigmatic, cats tantalize not only those of us KEY CONCEPTS who share our sofas with the smaller versions but scien- tists who have tried to puzzle out the origin and evolution ■ The family history of the cat has been murky E because cat are sparse and difficult to of their larger cousins. Where did the modern cat family evolve? tell apart. But advances in the study of DNA Why and when did they leave their homes and migrate across have made it possible to construct the first continents? How many actually exist, and which ones clearly resolved family tree for cats. are closely related? Experts generally agree that there are 37 species in the family ■ The DNA evidence shows that all living cats trace back to a pantherlike predator that lived , but they have offered dozens of classification schemes, in Southeast 10.8 million ago. The ordering cat species in as few as two to as many as 23 genera. great roaring cats were the first to branch off; Who could argue? Under the , one cat species appears pretty seven other lineages followed. similar to another. They look like big cats, midsize cats and small cats. Distinguishing a ’s from a ’s can be a challenge ■ As sea levels rose and fell, cats migrated to new continents and developed new species. even for an expert, and genetic investigations that we have tried A diminutive in the was over the past two decades have failed to sort the cats into defini- domesticated 8,000 to 10,000 years ago. tive groupings. In recent years, however, a revolution in sequencing the ge- ■ Despite their evolutionary success, almost all wild cats are now threatened with nomes of various creatures, spearheaded by the Human . —The Editors Project and by powerful technologies to probe DNA, has provid- ed some extremely valuable new tools for inquiry. Drawing on

68 SCIENTIFIC AMERICAN July 20 07 © 2007 SCIENTIFIC AMERICAN, INC. ) ); these novel techniques, the two of us, aided by ed—and encouraged—to see that the eight ( domestic ( colleagues at other institutions, have now con- groups defined exclusively by molecular analy-

Asiangolden cat structed the first clearly resolved Felidae family sis agreed with other kinds of observations, GettyImages tree. By comparing the same DNA sequences of such as that species in one lineage often shared image100/Corbis 30 genes in each living cat species, we were able morphological, biological and physiological

); DAVE KING);DAVE to determine the branches of the tree. Then, to characteristics found only in their group. For ( arrive at the time each branch emerged, we used example, one lineage contains all the great -

Corbis securely dated fossils and “” ing cats (lion, tiger, , and );ZAINAL ZAHARI ZAINUDDIN ( );RUSSELLGLENISTER analyses (which, based on the extent of differ- leopard). An incompletely ossified hyoid, a ( ences in given genes, can estimate how long ago in the neck that supports the , is what );FOXDANIEL J. Corbis rusty-spottedcat (

tiger species diverged from one another). The result allows them to roar. Also in this group are the (

DLILLC provided the first definitive look at how cats of and the Bornean clouded leop- all sizes are related to one another and led us to ard, little-known midsize cat species with a GettyImages left to right:left to discern how and when these superb predators beautiful marbled coat; because they have a colonized five continents. somewhat different bone structure in the neck,

Frank Lane PictureLaneFrankAgency/Corbis they cannot roar. );DARRYLESTRINE A of The comparison of gene sequences identified We immediately noticed that the DNA studies the lineages, the order of their emergence and, seemed to group the 37 species into eight dis- with the help of calibrations, the time );WHITTAKERTERRY cat PHOTOILLUSTRATIONJAMESPORTO; BY GETTYIMAGES( tinct clusters, or “lineages.” We were fascinat- they appeared. Nevertheless, we needed two

www.SciAm.com SCIENTIFIC AMERICAN 69 © 2007 SCIENTIFIC AMERICAN, INC. THE CAT FAMILY TREE Scientists compared DNA sequences in all 37 species of cats to determine the tree’s branches. Fossils provided dates that indicate when major branching occurred. 37 SPECIES Lion leo Leopard Panthera pardus Jaguar Panthera onca Panthera ancestor Tiger Panthera tigris 6.4 MYA Panthera uncia Clouded leopard nebulosa Neofelis diardi

Felid ancestor ancestor temmincki 5.41 MYA 10.8 MYA Bornean bay cat Pardofelis badia Pardofelis marmorata

Caracal caracal Caracal ancestor Caracal aurata 5.6 MYA 9.4 MYA Serval Caracal serval Geoffroy’s cat geoffroyi Ocelot ancestor Leopardus guigna 2.9 MYA Tigrina Leopardus tigrinus Leopardus jacobita 8.5 MYA cat Leopardus colocolo Leopardus wiedii Ocelot Leopardus pardalis ancestor 8.0 MYA 3.2 MYA Lynx pardina Lynx lynx lynx Lynx canadensis Bobcat Lynx rufus

Puma ancestor Puma Puma concolor 7.2 MYA 4.9 MYA Puma yaguarondi jubatus

Asian bengalensis 6.7 MYA Leopard cat ancestor Prionailurus viverrina 5.9 MYA Flat-headed cat Prionailurus planiceps Rusty-spotted cat Prionailurus rubiginosus Pallas’s cat Otocolobus manul 6.2 MYA Domestic cat catus Wildcat Felis silvestris Felis margarita Domestic cat ancestor -footed cat Felis nigripes 3.4 MYA Felis chaus 10 5 4 3 2 1 Today Millions of Years Ago (MYA)

200 Middle Late Miocene Early Late Pliocene 100

0 –50 Sea Level (meters)LevelSea

additional pieces of information to fill out our new domains. When sea levels rose again, ani- scenario and discern where cats first arose and mals on the continents were isolated once more. how they came to have their current distribu- Studies of show that isolation on tion around the world. First, we determined the continents, or on islands, provides just what is present distribution of each cat species and required for a population to drift apart so much where their ancestors occur in paleontological genetically that eventually it can no longer remains. Then we looked at the cats’ world breed with contemporary descendants of its through the eyes of geologists who have inter- former relatives—a reproductive distancing preted the composition of sedimentary depos- that is the hallmark of speciation. Armed with its to infer the rise and fall of sea levels. When these pieces of the puzzle, we could construct a sea levels were low, land bridges connected plausible sequence of migrations throughout

continents, allowing to migrate to the history of Felidae. JANABRENNING

70 SCIENTIFIC AMERICAN July 20 07 © 2007 SCIENTIFIC AMERICAN, INC. 8 LINEAGES ●1 PANTHERA These medium- to large-size cats (15 to 350 kilograms) are found throughout the world. They are the dominant predators in the and on the continents that they inhabit, often specializing on large species. The lion, tiger, jaguar, leopard and snow leopard have an incompletely ossified hyoid, which allows them to roar. The two clouded leopard species do not roar. Tiger ●2 BAY CAT This poorly known group of small- to medium-size cats (two to 16 kilograms) is restricted to forested in tropical . Before the authors’ genetic analyses, taxonomists did not consistently group these species together. Asian golden cat ●3 CARACAL These medium-size cats (five to 25 kilograms), which are restricted to , are distinctive and recognizable but were not typically grouped together before the authors’ genetic work. Serval ●4 OCELOT These small- to medium-size cats (1.5 to 16 kilograms) live in a broad range of habitats throughout Central and . They have a different number of than other Felidae species do (36 instead of 38). Ocelot ●5 LYNX These medium-size cats (six to 20 kilograms) all have short and pointed ears. They live in temperate climates of and and tend to specialize on and . With the exception of the Iberian lynx, these species have been among the most widely exploited for their .

Bobcat ●6 PUMA These diverse cats, from the small jaguarundi (three to 10 kilograms) to the large African cheetah (21 to 65 kilograms), originated in North America but have spread widely across four continents and remain broadly distributed. Pumas can be locally common and are legally hunted in parts of their range.

Puma ●7 ASIAN LEOPARD CAT (mountain lion) These small cats (two to 12 kilograms) occupy a wide range of habitats in Asia, from to Mongolian . The Asian leopard cat is the most common small cat in Asia. Rusty-spotted cat ●8 DOMESTIC CAT These small cats (one to 10 kilograms), with the exception of the domestic cat, which is worldwide, have African and Eurasian distribution.

Based on the fossil record alone, most re- are not certain which exact species this ances- searchers have accepted a cat called Pseudaelu- tral cat was, we do believe that the ancient rus that lived in nine million to 20 mil- group included the and Eve of today’s 37 lion years ago as the last common ancestor of species of Felidae. modern felids. ( was not the first cat; large saber-toothed cats, called nimravids, On the Move reach back as far as 35 million years ago, but The first group branched off from this mysteri- Domestic cat nearly all their descendants went extinct.) Our ous Asian cat approximately 10.8 million years recent molecular investigations, however, sug- ago, producing the panthera lineage ●1 [see gest that all modern cats are descended from table above], which today includes the great one of several Pseudaelurus species that lived in roaring cats and the two species of clouded

PHOTOILLUSTRATIONJAMESPORTO BY Asia some 11 million years ago. Although we leopard. A second split about 1.4 million years

www.SciAm.com SCIENTIFIC AMERICAN 71 © 2007 SCIENTIFIC AMERICAN, INC. 72 Sometime around nine million years ago descendants of the pantherlike predator that is the ancestor of all modern cats began to began cats modern all of ancestor is the that predator pantherlike the of descendants ago years million nine around Sometime the Red Sea, facilitating the cats’ journeys. journeys. cats’ the facilitating Sea, Red the sea levels during this period meant that “bridges” of land stretched across the and the northern and southern ends of of ends southern and northern the and Strait Bering the across stretched land of “bridges” that meant period this during levels sea First Wave of Feline Migrations Wave Feline of First migrate from its home in Asia to Africa to Africa in Asia home its from migrate Second Wave Second Africa Many other migrations occurred between one million and four million years ago, when lowered sea levels con levels sea lowered when ago, years million four and million one between occurred migrations other Many nected the continents once again. The most recent puma migration migration puma recent most The again. once continents the nected Africa

Europe SC IE NTIFIC AME RIC AN AN RIC AME NTIFIC IE SC Europ e Sea Red Lion M8 M1 caracal lineage Precursor of M1 M5 0 Cheetah Black-footed ca M1 and North America America North and Asia t Asia © 2007 SCIENTIFIC AMERICAN, INC. AMERICAN, SCIENTIFIC 2007 © Australi M7 M2 a M11 (and very much later to South America America to South later much very (and J Ly leopard anddomesticcatlineages aguar nx, cheetah and precursors of occurred 8,000 to 10,000 years ago. years to 10,000 8,000 occurred lynx, Precursor ofpuma,

ocelotlineages Equator M2 Lion M9 M4 Bering Strai Equator

t - M3 ocelot lineage Precursor of ). Unusually low low Unusually ). Puma M6 America North America North M3 M7 Jaguar America South July M11 America South 2 07 20 Puma

JANACREDIT BRENNING later, also in Asia, led to the Bornean bay cat across Asia and traversed the Bering land bridge [THE AUTHORS] lineage ●2 , now composed of three small cats to . As cats now prowled Asia, Europe, that evolved and still reside in Southeast Asia. Africa and North America, sea levels rose, sep- The next split from the original group founded arating continents, and with the isolation and the caracal lineage ●3 , today represented by changing habitats, a score of new species three midsize species whose progenitors crossed evolved. In North America, the ocelot ●4 and into Africa eight million to 10 million years ago, lynx ●5 lineages separated from the original mi- embarking on the first intercontinental migra- grants eight million and 7.2 million years ago, tion [see upper map on opposite page]. During respectively, with the ocelot lineage ultimately this period, sea levels dropped to 60 meters dividing into two species there and the other After receiving a doctorate in below modern levels, connecting Africa and the group producing four species: three and genetics at Cornell University in by land bridges at either end the bobcat. The puma lineage ●6 diverged 6.7 1971, Stephen J. O’Brien joined of the Red Sea and facilitating the migration million years ago, giving rise to the puma (also the National Cancer Institute as a to Africa. called or mountain lion), jaguarundi postdoc. He is now chief of the NCI’s Laboratory of Genomic Cats migrate because their hardwired behav- and . Fossil remains of all Diversity, which he founded in the ior demands dispersal every generation. Once these species in American deposits nail down late 1980s. This is his fourth article they reach adolescence, young males, and occa- their origin in the Western Hemisphere. for Scientific American. His most sionally females, are forced to vacate their natal Two million to three million years ago a new recent book is Atlas of Mammalian area. So, over time, growing cat populations re- ice age caused the oceans to recede once again, Chromosomes (Wiley, 2006). Warren E. Johnson earned his quire greater and greater for expansion. enough, along with shifting landmasses, to con- Ph.D. in ecology from Iowa This behavior, together with the pressure to fol- nect the two American continents via the Isth- State University in 1992 and joined low migrating prey species, probably explains mus of . A few cats of this time grasped the Laboratory of Genomic why cats have been motivated to travel far and the opportunity to migrate, headed south and Diversity that same . wide. They are also extremely skillful predators encountered a continent with no placental car- and quickly explore new regions as opportuni- nivores (no , , cats, , and so on). ties arise, so it is not surprising that they can South America had been isolated from northern move into unexploited areas successfully. landmasses for tens of millions of years and was ) During the same interval in which Asian cats teeming with species, including sev- jaguar ( began to move into Africa, they also dispersed eral successful carnivorous varieties. But when

); WHERE THE CATS ARE TODAY Foto Natura/MindenFoto Pictures snow leopardsnow ( Corbis ); SA TEAM);SA fishingcat ); TOM BRAKEFIELD);TOM


Europeanwildcat European wildcat5 ( Iberian lynx Chinese mountain wildcat Snow leopard5 Canada lynx5 Africanlion

( Eurasian lynx Jaguar Puma

TROPICAL ASIA Asiatic golden cat Jungle cat Asian lion Leopard SOUTH AMERICA SUB-SAHARAN AFRICA Bornean bay cat Leopard cat Andean mountain cat Margay Geoffroy’s cat NationalGeographic ImageCollection African golden cat Caracal Bornean clouded leopard Marbled cat Ocelot African lion6 Cheetah Clouded leopard Rusty-spotted cat Jaguar6 NationalGeographic ImageCollection Leopard Fishing cat 6 Sand cat Jaguarundi Black-footed cat Serval Flat-headed cat Tiger Kodkod Puma );NORBERT ROSING );BEVERLYJOUBERT Brien,Johnson ’ O Canadalynx SHARONANGLIN ( JOE MCDONALDJOE (

www.SciAm.com SCIENTIFIC AMERICAN 73 © 2007 SCIENTIFIC AMERICAN, INC. FAST FACTS the cats arrived across Panama, they had already ing the late Pliocene, roughly three million to become the ultimate predators: large, fast, dex- four million years ago. Although the Pleistocene There are 600 million domestic terous, ferocious and . The more modest eliminated both species from North cats around the world. marsupial were no match for them. America, had escaped to South America, Cat fossils are so similar that Nearly all resident were quickly re- and , which had also dispersed to Africa, even experts struggle to tell a placed by migrant carnivores such as cats of the found a continent more hospitable than Europe, lion’s skull from a tiger’s. ocelot lineage, which diversified still further in Asia or the had been. The king of their new home, creating seven species that still beasts clings to survival today in Africa, num- survive in South America. bering fewer than 30,000 individuals. In Asia,

Lion As the last ice age wound down about 12,000 lions are virtually extinct; only a tiny relict pop- years ago, the thick ice sheets that covered all ulation of around 200 highly inbred Asiatic li- of Canada and the northern tier of the U.S. ons survives in the Gir Forest sanctuary in the gradually melted, transforming the barren land- Gujarat province of western . scapes into the forested terrain and Our genetic analyses have also revealed a prairies of North America. After the big thaw, close call with extinction for . Around a cataclysm abruptly extirpated 40 species of 73,000 years ago the massive Toba volcanic mammals from North America. The Pleisto- eruptions on annihilated scores of

Tiger cene extinctions, as they are called, eliminated species in , including a wide- 75 percent of the large living there. spread tiger population. A tiny group of tigers Mammoths, mastodons, dire , massive survived and repopulated a new race across the short-faced bears, giant ground , Ameri- region, but the lack of in their can lions, saber-toothed cats, pumas and chee- modern descendants indicates the survivors tahs would all disappear from North America. passed through a population bottleneck at the escaped extinction because several time of the Toba eruption—leaving only a small million years earlier, when seas were still low, a group of animals to carry on the species. Like number of their ancestors had made their way the cheetahs and pumas in North America, the Lions, tigers, jaguars, back to Asia [see lower map on page 72] and tiger slipped through by a whisker. and snow leopards are the only then Africa. Pumas avoided annihilation in a cats that can roar. An incomplete- South American refuge and restocked North Into Our Living Rooms ly ossified bone in the throat America many generations later. The other spe- The final act in the cats’ journey, from the jun- called the hyoid makes these unusual vocalizations possible. cies would never return. gle to our living rooms, began in the dense for- ests and vast around the Mediterranean The Journey Continues basin. There a handful of diminutive cat species At roughly the same time the cheetahs made (weighing less than 10 kilograms) had gradual- their way back across the Bering Strait from ly emerged—the East Asian jungle cat, Middle America to Asia, the precursors of the leopard Eastern sand cat, African black-footed cat and cat ●7 and the domestic cat ●8 lineages slipped a ubiquitous wildcat species with four well-rec- from their American roots and crossed the Ber- ognized (European, Central Asian, ing land bridge to Asia. Subsequently, the leop- Near Eastern and Chinese). From one of these ard cat lineage blossomed to produce the Asian wildcat subspecies, one of the most successful leopard cat and four small species that today are experiments in history began—that of cat Hyoid in found in India (rusty-spotted cat), . A wide-reaching molecular roaring cat (Pallas’s cat), (flat-headed cat) and genetics study of the world’s domestic cats and other scattered Asian locales (fishing cat). by graduate student Carlos Driscoll of Also in Asia during this period, the great the University of Oxford has brought this pro- roaring cats of the panthera lineage spread cess into clear focus. All domestic cats carry much more widely than before. Massive 320-ki- genetic signatures matching Asian wildcats )

logram tigers ranged throughout southern and from and the Near East. d

eastern Asia (India, Indochina, the Sunda Shelf We now believe that the cat was domesticat- hyoi and ), whereas in northern and western ed on several occasions, all within the Fertile , the snow leopards adapted to high Crescent 8,000 to 10,000 years ago, as nomad- elevations in the and Altai Moun- ic human populations began to gather in small tains. Leopards dispersed not only across Asia villages around the first agricultural settlements. but also into Africa, where they occur today. Li- These early cultivated wheat and barley.

ons and jaguars traveled to North America dur- Wildcats in the region, perhaps attracted by the SKULLSUNLIMITED; MELISSA THOMAS (


axonomists have historically to resolve the branching nodes, Tfound it difficult to classify the or “forks,” in the cat family cat family because the fossil tree, they turned to fossils to record is sparse and it is hard to estimate when the forks actual- distinguish one fossil species from ly happened. Paleontologists another. By analyzing the DNA of have determined the age of all 37 living species, the authors dozens of fossils of ancient cats were able to sort the cat family using radiocarbon-dating into eight lineages. They obtained methods. Certain cat fossils the DNA by collecting or tis- considered as missing links (the sue samples from each of the 37 most recent common ancestor species. Getting all the samples of a group such as the great was not easy, because some of cats, lynxes or ) provid- the species are rare and live in ed 16 firm fossil dates for spe- remote locations. They also ana- cific branch points on the tree. lyzed seven “outgroup” species, CINNAMON: Then, mathematical computer close relatives of cats in the - Her DNA was sequenced. scripts based on a steady cumu- family, . The lative molecular clock translat- outgroup species provide a baseline for estimating ed the genomic data into estimates of the time the divergence dates within the Felidae family. elapsed since each divergence node. (The molecular The scientists looked at DNA from the X and Y chro- clock idea assumes that some evolutionary changes mosomes and from the mitochondria (parts of the cell occur at a regular rate. , for example, may that generate energy and are passed along the mater- be incorporated in the DNA of genes at a steady rate nal line). They focused on the DNA sequence of 30 dif- over millions of years. Differences in the DNA, there- ferent genes—in all, 22,789 nucleotide letters for each fore, can act as a “clock” for measuring the date at cat species. Nearly half of these sequences were vari- which two lineages split from a common ancestor.) able across the range of species. The differences are The most recent addition to genome sequences is what allowed investigators to determine which groups the complete set of genetic information in the DNA of were most related and which were oldest. Genes accu- an named Cinnamon. Cinnamon’s full mulate changes over time. If these are not detrimental, genome sequence, along with the sequence of 32 other they persist. So a species that emerged earliest would species of mammals (including human, , , ➥ MORE TO have had the most time for its genes to change and cow, elephant and representatives of most mammalian EXPLORE would show the most variation within any given gene, orders), has given students of evolution an almost Wild Cats of the World. M. Sun- and one can safely assume that species whose genes unlimited assemblage of genetic information across the quist and F. Sunquist. University of share many of the same changes are most related. 100-million-year-old history of modern mammals. Chicago Press, 2002. Once the DNA analyses had allowed investigators — The Editors Tears of the Cheetah and Other Tales from the Genetic Frontier. S. J. O’Brien. St. Martin’s Press, 2003. plentiful in the grain stores, apparently tions. By the 19th century, cat owners were se- and Conserva- offered themselves as cautious companions, lectively their tabbies to produce tion Genetics of Tigers (Panthera earning their keep by dispatching the pesky ro- fancy breeds. The American Cat Fanciers Asso- tigris). S.-J. Luo et al. in PLoS Biolo- dents. The increasingly tame wildcats bred pro- ciation lists 41 official cat breeds, from gy, Vol. 2, pages 2277–2293; 2004. lifically and linked their fortunes to those of the Coon to Siamese to Persian to , all tracing humans. their roots to the birth of human and feline civ- Genomics. S. J. O’Brien and W. E. Johnson in Annual Review These animals ultimately undertook a new ilization in the . of Genomics and Human Genetics, migration. It began on foot, then progressed in The evolutionary story that emerges from Vol. 6, pages 407–429; 2005. wagons, and eventually on oceanic vessels, ulti- our studies of the cat family serves as a harbin- mately spreading the domesticated cat compan- ger for the fledgling field of “genomic prehisto- The Late Miocene Radiation of

M Modern Felidae: A Genetic Ö ions across the globe. Some 600 million domes- ry.” Just as for the cats, the patterns of genomic Assessment. W. E. Johnson, E. Eizirik, tic cats live worldwide today, almost the only variation carried by each species contain foot- J. Pecon-Slattery, W. J. Murphy, cat species not considered threatened or endan- prints of kinship, migrations, bottlenecks and A. Antunes, E. Teeling and S. J. O’Brien g KRISTINANARFSTR gered by the world’s conservation organiza- expansions across the planet. in Science, Vol. 311, pages 73–77; 2006.