New Study on the Evolutionary History of Extinct and Living Lions

The “king of the jungle” is in peril.

Over the past 200 years the lion has lost 90% of its former numbers – today they are found in small, isolated populations, principally in southern and eastern Africa. Tiny relict populations persist in central Africa, West Africa and in the Gir Forest Reserve within the Kathiawar peninsula of India.

North African subspecies, the Barbary lion and the Cape Province lion, disappeared within the last century and a half, and they have all but disappeared from Eurasia since their apex during the late Pleistocene ice age when cave lions were dispersed from Iberia to Alaska. Lions are listed as vulnerable by Red List, IUCN, and US Endangered Species Act.

The details of lion natural history are murky.

• When did Pleistocene cave lion split from modern lions?
• What was their ancestral hierarchy?
• Did the lost lion subspecies hybridize with ancestors of modern African or Asian lions?
• Was their extinction preceded by genetic impoverishment, reminiscent of other lost mammal groups?

To help answer some of these questions, a new study “The Evolutionary History of Extinct and Living Lions” published in Proceedings of The National Academy of Sciences, uses the power of ancient DNA and whole genome analyses to resolve these issues. Stephen J. O’Brien, Ph.D., a research scientist and professor in Nova Southeastern University’s (NSU) Halmos College of Natural Sciences and Oceanography, was part of the research team.

“The new results illustrate the power of the genomics era in revealing lost secrets of pre-history by reading DNA footprint codes in the ancestors of modern species,” O’Brien said. “And the ‘Indian Lion’s’ alarming genetic impoverishment is clearly affirmed.”

O’Brien’s career spans several decades, going back to a 25-year tenure as the Chief of the Laboratory of Genomic Diversity at the National Cancer Institute (NCI), National Institutes of Health (NIH) from 1986-2011. He joined the Theodosius Dobzhansky Center for Genome Bioinformatics in St. Petersburg State University (Russia) in December 2011, where he serves as its Chief Scientific Officer.

Lead authors Marc de Manuel and Ross Barnett sequenced museum and permafrost paleontological samples of lions (up to 30,000 years old) from outside their current range, alongside modern samples from living lions to look at how historic lions evolved and spread.

“It was amazing to work with samples from 30,000 year-old cave lions and get the whole genome of the animal,” said Barnett. “It shows just how much the technology for ancient DNA has advanced in the past decade and how genomics of the past can inform the conservation of the future.”

Along with NSU’s Halmos College, the research team included members from the Globe Institute – University of Copenhagen and the Barcelona Institute of Science and Technology. They concluded that the ancestors of living modern lions and extinct cave lions diverged into distinct lineages approximately 500,000 years ago. Computer modelled simulations indicated little gene flow or detectable hybridization after the split despite potential areas of range overlap in western Asia and prior strong evidence for widespread hybridization among other Panthera (great cat) species.

This tentatively suggests that as yet unidentified factors conspired to prevent effective breeding between the two lion types during the Pleistocene. The authors also find no clear evidence of a decline in genetic diversity in Cave lions, Barbary lions or Cape lions prior to extinction.

Around 70,000 years ago, modern lions clearly split into two distinct lineages: (1) Lions found in central, eastern and southern Africa today; and (2) Indian, West African, and extinct North African lions.

This has strong conservation implications.

Knowing the closest relative of the extinct Barbary lion will inform any potential reintroduction attempts. Similarly, the precarity of the Indian population (less than 500 individuals) is a politically sensitive topic, but resolving their closest living relatives could inform future restoration and outbreeding initiatives.

Modern Indian lions were found to be near genetically uniform consequent of centuries of persecution and historic genetic bottlenecks. These lions show multiple physiological correlates of inbreeding (e.g. depleted sperm counts, skeletal defects, testosterone reduction and derivative reduced mane size.) Also, the new study demonstrated firmly the Indian lions of today are, in fact, native to the region and were not brought over from Africa during pre- colonial times as has been floated in the popular media.

This new study provides unparalleled detail of the evolutionary history of the lion, showing relationships between different modern geographic populations and even extinct populations. The results have wide implications for future conservation work in what is now a vulnerable species.