The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics


Cute baby lion kittens. When they grow up, they will want to eat you.
I'll never forget the first wild lion I ever saw. It was a pitch black night, on the savanna in the Western Rift Valley. I had climbed on top of the hood of the Land Rover, engine off, but headlights on. My plan was to search the horizon for lights indicating the presence of the research camp I was trying to find. Once I was on the hood, I was about to tell my colleague, still in the vehicle, to cut the headlights so I could see better. That's when she walked into view.

She was a fully adult lioness. Eventually, I would see this animal countless times while studying the interrelationship between lions and their prey, but at this moment, I thought briefly that this might be the last time I would ever see anything. She walked casually and fully into the headlight beams, perpendicular to the direction of the truck, and stopped for a moment like a diva on stage, with her head just above the shining lights so she could get a very good look at me. If she was pointing the other way, she could have easily brushed me with her tail. She probably could have kept three paws on the ground and easily hooked my ankle with the fourth. But if her main interest was to teach me that it was a good idea to be afraid of lions, she did exactly the right thing.

ResearchBlogging.orgShe just looked straight into my eyes for about two seconds, then slipped into the darkness. This meant that I had two choices: Remain standing, like some kind of idiot, on the hood of the car, or follow the lioness into the darkness on the way back inside the vehicle.

This was the first of several instances in which the same exact thing happened in one form or another: There I was, inside the Land Rover with the door closed and the windows secured. I have no idea how I got there. I just got there.

So, why are we talking about this lioness? As an introduction to an interesting study just out in PLoS. Lions are found today throughout much of Sub Saharan Africa, and there is a tiny population in India. In recorded history, Lions existed in a continuous distribution from southern Asia westward across much of southern Europe, across North and West Africa, and, of course, sub Saharan Africa. The West African and North African lions are represented primarily in zoo populations today.

People have argued over the years as to whether or not the Asian and African lions are different species, subspecies, or whatever ... and this argument has been made at a finer level regarding the different populations of sub Saharan lions. This recent research, which looks at lion and viral DNA, suggests that different groups of lions are best seen as quite separate and with very little recent interbreeding.

This makes sense to me, as lions in different areas of Africa look internally similar but very different between regions, and even behave differently in some cases. Many of the different groups of lions are today separated by vast regions with few or no lions. In the past, with fewer humans and human-made barriers, this may still have been somewhat true because lions do best with large game. If you look, for instance, at wildebeest populations, you will find that there are distinct regions with distinct subspecies. If the large game are divvied up across the content in this manner, some of the predators may be as well.

Here is the abstract from the paper:

The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIVPle), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA ΦST = 0.92; nDNA FST = 0.18), and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIVPle subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa (~324,000-169,000 years ago), which expanded during the Late Pleistocene (~100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition (~14,000-7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIVPle variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently.

That is pretty much the study in a nutshell. Here are some graphics that make the key points clear:
Top: Three-dimensional factorial correspondence analysis [23] (FCA) based on the 24 nDNA loci genotypes in the 357 lions. Axe 1, 2, and 3 represent 49.90% of the genetic variation observed. Middle: FCA representation excluding the GIR (Asian) lions. Axe 1, 2, and 3 represent 51.35% of the genetic variation observed. Bottom: FCA representation considering only the SER (Serengeti) lions supportive of a three distinct population clusters subdivision (SER-I, SER-II, and SER-III).

And here is one of the phylogenies derived from this study:
Unrooted neighbour-joining (NJ) tree from nDNA genotypes of 24 loci (ADA, TF, and 22 microsatellites) in the 11 lion populations (left), and rooted NJ tree for the distinct mtDNA (12S-16S, 1,882 bp) haplotypes in lion (right). The distinct mtDNA lineages were labelled I to IV. Bootstrap support (BPS) values >50 are indicated.

You get the idea.

Agostinho Antunes, Jennifer L. Troyer, Melody E. Roelke, Jill Pecon-Slattery, Craig Packer, Christiaan Winterbach, Hanlie Winterbach, Graham Hemson, Laurence Frank, Philip Stander, Ludwig Siefert, Margaret Driciru, Paul J. Funston, Kathy A. Alexander, Katherine C. Prager, Gus Mills, David Wildt, Mitch Bush, Stephen J. O'Brien, Warren E. Johnson (2008). The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics PLoS Genetics, 4 (11) DOI: 10.1371/journal.pgen.1000251

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"This was the first of several instances in which the same exact thing happened in one form or another: There I was, inside the Land Rover with the door closed and the windows secured. I have no idea how I got there. I just got there."

AHAH! Teleportation is possible!

By Tsu Dho Nimh (not verified) on 11 Nov 2008 #permalink

And here is one of the phylogenies derived from this study:

No, that's not a phylogeny. That's a neighbor-joining tree. A measurement of overall similarity, not a count of shared derived character states. A phenogram, not a cladogram.

If there is little enough convergence or other trouble in the data, then the phenogram is identical in shape to the phylogeny, but one cannot simply make these assumptions, one has to test them by doing an actually phylogenetic analysis. Doing a phenetic analysis and presenting the results as a phylogenetic hypothesis is a category error.

By David Marjanović (not verified) on 11 Nov 2008 #permalink


We've had this argument before. You are an unmitigated Cladist and as such believe that the quirky way in which Cladists view the world is correct and immutable. I would have thought Cladism would be beyond this by now (as a formerly new approach) but it seems to only get worse.

A phylogeny is an evolutionary tree, not a particular kind of evolutionary tree. All the different methods out there .... including thumbsuck guessing ... that produce putative evolutionary relationships produce phylogenies, and all are approximations with their positives and negatives.


I'm afraid David is correct here. It is a phenogram, since it only looks at bulk similarity. There is no polarity of characters in the analysis. Cladistics is commonly accepted by scientists, not as "correct and immutable" but as the best hypothesis of common ancestry. When you don't know which characters are ancestral, its difficult to infer a phylogeny (evolutionary relationships) from it.

I chose, and I can do this, to retain the use of the word "phylogeny" to mean "evolutionary tree" regardless of it's accuracy or the method of creating it, or the method of displaying it. That is the policy of this blog.

This is not unusual to me, but rather, widespread practice. This is how the word has been used for decades, and it is how it is used at this time across the world.

I am interested in discussion of the details of how we approach reconstructing evolutionary relationships. Please read the paper and tell us what you think about it! You can even use quirky cladism-speak, but use phrases like "I like to use the word 'phylogeny' to mean .... xyz ..." ... but we are not going to set terminological rules based on cladistics. Cladistics is a method, not a way of rethinking evolution. I appreciate cladistics, I am not a cladistics. Cladists are welcome on this blog, but this is not a cladistic blog.

So this is what a cat fight between science guys arguing dogma looks like. Greg wins. It's his blog and he showed great perception and sound thinking upon meeting that lioness, teleportation or not.

This study actually backs up some of the arlier ones that show very little diversity within the lions species as a whole. In fact, one of the paragraphs in this study points this out. So again, only the Asian lions seem to warrant being called a sub-species, with all of the sub-Saharan lions being correctly lumped under one classification these days.

Of course, this doesn't mean there is no genetic sub-structure within African lions. Clearly there is, and ideally each of these relative genetic isolates should be managed captivity too. Or at the very least, we should try and preserve most of the genetic diversity, even if in the end it means mixing in captivity if we don't have "pure" representatives.

Tigers show even less genetic diversty than lions, so classifying them into several sub-species is even more absurd. However, like lions, they do show substructure. In fact, various Indian tiger populations exhibit unique markers and ideally should also be treated as seperate conservation units.

I recall my dad telling me that when he was being chased by a bull he could jump a field fence without even touching it. And he was never taller than 5'4" (162 cm).