Homo Sapiens: Anatomically Modern Humans (AMH)

Humans are nothing if not an arrogant species. It’s understandable: out of all the various hominid species, we’re the only ones that managed to make it – we fought, foraged, fluked, flu-ed, and fornicated everybody else straight out of the gene pool.

But just because we won the war, that doesn’t mean there aren’t some battles out there that our ancient cousins would have bested us at. Neanderthals, for instance, had better vision than your average human, and could probably take you in a fist fight, honestly.

And another one of our hominid relatives may have had an even more peculiar advantage over us. According to a new study out of the University of Alaska Fairbanks, the Denisovans – the elusive human lineage first identified in 2010 – were particularly good at sniffing out sweet treats.

“This is the most exciting research I have ever been involved in,” Matthew Cobb, a professor of zoology at the University of Manchester and co-author on the study, said in a statement. “It shows how we can use genetics to peer back into the sensory world of our long-lost relatives, giving us insight into how they will have perceived their environment and, perhaps, how they were able to survive.”

You may wonder how, exactly, one measures the smelling ability of a species that died out at least 30,000 years ago and is only known via a handful of tiny fossil fragments, and it’s a fair question. The answer, though, is as impressive as the discovery itself: the researchers used publicly available genome sequences harvested from multiple Neanderthals, one Denisovan, and one ancient human – as well as genomic data on modern humans from the 1000 Genomes project – to recreate these ancient noses in the lab and test them directly.

To be more accurate, the team isolated the olfactory receptor genes in each of the samples, discovering that 11 of the receptors had some novel mutations present only in extinct lineages. Those 11 were created in vitro by the team, who then exposed the lab-grown receptors to hundreds of different smells in various concentrations.

And just like when somebody wafts an aroma towards your own nasal passages, the olfactory receptors reacted to the smells. “We literally reproduced an event that hadn’t happened since the extinction of Denisova and Neanderthal 30,000 years ago: an extinct odorant receptor responding to an odor in cells on a lab bench,” said Universite Paris-Saclay biochemist and study co-lead Claire de March. “This took us closer to understanding how Neanderthal and Denisova perceived and interacted with their olfactory environment.”

And without a doubt, the Denisovans were the olfactory winners in the ancient human smelling Olympics: their noses were more sensitive than both humans’ and Neanderthals’. They were most responsive to sweet and spicy smells like honey, vanilla, cloves, and herbs – a trait which could have helped them find high-calorie food, the researchers believe, or at the very least to whip up delicious baklava.

Neanderthals, by contrast, fared pretty poorly. One sample from the species was found to be completely unresponsive to the sex steroid androstadienone, for example – though that may not have actually been too much of a disadvantage in the era before regular showers, since it smells a bit like sweat and urine.

Present-day humans fell somewhere in the middle, which makes some sense, since we’re nothing if not generalists. “Each species must evolve olfactory receptors to maximize their fitness for finding food,” explained Duke University Professor of Molecular Genetics and Microbiology and study co-author Hiroaki Matsunami. “In humans, it's more complicated because we eat a lot of things. We're not really specialized.”

In fact, our middling sense of smell might point to precisely the reason our species was so successful – even where our ancient cousins died out.

"This research has allowed us to draw some larger conclusions about the sense of smell in our closest genetic relatives and understand the role that smell played in adapting to new environments and foods during our migrations out of Africa,” said Kara C. Hoover, a professor in the Department of Anthropology at UAF and study lead.

“Such a strongly overlapping olfactory repertoire suggests that our generalist approach to smelling has enabled us to find new foods when migrating to new places,” she concluded. “Not just us but our cousins who left Africa much earlier than us!”

The results have been published in the journal iScience.

Introduction
Terrestrial animals probe the environment for information about food, mates, and danger1,2 by binding odor molecules to odorant receptors (ORs). Variation in mammalian ORs is linked to dietary niche, habitat, and sociability.3 In comparison, human ORs are strongly biased toward food odors,4 which reflects the evolutionary importance of dietary niche to our species. Although evolutionarily recent changes in human OR protein function have been linked to major dietary shifts, such as scavenging, hunting, animal milk consumption, cooking, domestication,3,5,6,7,8,9 what about deeper evolutionary changes?

The human genus Homo underwent the most radical ecological niche expansion of all primates when migrating out of Africa and adapting to diverse global environments.10 Denisovans and Neanderthals ancestors dispersed from Africa earlier than contemporary humans (∼750,000 versus 65,000 years ago)11 and separated from each other ∼300,000 years ago12 (Figure S1). Neanderthals were geographically wide-ranging from Western Europe to the Middle East and Asia. Although Denisovans have been primarily found in Siberia,13,14 the Tibetan plateau,15 and possibly beyond Wallace’s Line,16 their genetic signature is found in Asian, Papua New Guinea, Australian, and indigenous American groups.16,17,18,19,20,21 Olfactory stimuli from divergent environments following independent dispersals from Africa may have left traces of variation in Homo OR genes. Whether there is a shared genetic and/or functional olfactory repertoire across the genus Homo or not may provide clues to evolutionary adaptive trends.
Two prior studies examined genetic variation in contemporary humans, Altai Neanderthal, and Denisovan for OR7D422 and OR2M3.23

Both studies identified novel Denisovan variants and subjected them to functional testing. Our work exponentially increases knowledge on functional differences in two novel OR variants to 29 additional open reading frames (Table S1) for ORs with known human receptor-odor relationships and well-established agonist responses.24,25 We also more than double the number of ancient samples by including two additional Neanderthal genomes (Chagyrskaya, Vindija) and one ancient human (Ust’-Ishim) who lived in the same Altai montane locality (Table S2). The contemporary human sample used is 1000 Genomes (Table S3).13 There is more variation in the contemporary human ORs studied compared to extinct lineages. Functional testing indicates that novel variants found in extinct lineages alter sensitivity more than specificity. Our wide survey of the OR family suggests that the genetic and functional olfactory repertoires of extinct lineages were highly over-lapping and that increased genetic variation in the human repertoire occurred after our split with other migratory members of our genus.