Graham M. Hughes, Emma C. Teeling, Desmond G. Higgins, Loss of Olfactory Receptor Function in Hominin Evolution, PLoS ONE 9(1): e84714, 2 January 2014

The mammalian sense of smell is governed by the largest gene family, which encodes the olfactory receptors (ORs). The gain and loss of OR genes is typically correlated with adaptations to various ecological niches. Modern humans have 853 OR genes but 55% of these have lost their function. Here we show evidence of additional OR loss of function in the Neanderthal and Denisovan hominin genomes using comparative genomic methodologies. Ten Neanderthal and 8 Denisovan ORs show evidence of loss of function that differ from the reference modern human OR genome. Some of these losses are also present in a subset of modern humans, while some are unique to each lineage. Morphological changes in the cranium of Neanderthals suggest different sensory arrangements to that of modern humans. We identify differences in functional olfactory receptor genes among modern humans, Neanderthals and Denisovans, suggesting varied loss of function across all three taxa and we highlight the utility of using genomic information to elucidate the sensory niches of extinct species.
All very complex, clearly. Extracts:

The mutation leading to non-functionality for OR2L8, OR8I2 and OR5M11 are shared between the Denisovan and Neanderthal, with the same mutation existing in some modern humans. This may indicate that the ancestral state for these ORs in the Neanderthal-Denisovan-modern human most recent common ancestor is non-functional, with modern humans regaining function post-divergence.
The mutation that retains function for OR1P1P, OR2J1P and OR9H1P is shared between Neanderthals, Denisovans and some modern humans. This may indicate an ancestral functional state, with a loss of function happening along the modern human lineage. However, without a larger population sampling of extinct genomes for each hominin species, it is difficult to discriminate among alternative evolutionary trajectories.