Australia: The Land Where Time Began

A biography of the Australian continent 

WLH 50 Ancestry nDNA

The Denisovan mtDNA clade is a sister group to the mtDNA clades of Neanderthals and recent/living humans (Meyer et al., 2014). Though on its own mtDNA is not necessarily sufficient to examine hypotheses of relationship above the population level (Ballard & Whitlock, 2004; Eyre-Walker, 2006). It has seemed inexplicable that the Sima de los Huesos mtDNA is on the Denisovan mtDNA clade and not the Neanderthal mtDNA clade as the abundant Sima de los Huesos skeletal remains share features with later European Neanderthals that are uniquely common in the Neanderthal sample (Arsuaga et al., 1997; Martinón-Torres et al., 2012). One of the ancestors of the later Neanderthals is unquestionably the Sima de los Huesos hominids. Different phylogenies are given by nDNA and mtDNA for the same specimens because of their different patterns of evolution; mtDNA evolves with branching and extinction of lineages as the entire mtDNA genome is inherited as a whole, while nDNA both branches and reticulates with the result that gene flow is a powerful mechanism that alters the structure of the relationships of populations. Besides, mtDNA of Denisovans, like the Neanderthal anatomical form, can no longer be found.

When the analysis of the nDNA from the Denison Cave Sample was compared with the analysis of the mtDNA of Neanderthals it showed that the Denisovans and Neanderthals together are a sister group to recent and living humans (Prüfer et al., 2014). The implications of nDNA studies to date were summarised by Hawks (2013):  

“The pattern of variation outside Africa appears to reflect interbreeding among populations that were much more separate during the period before 100,000 years ago, including the Neanderthals and Denisovans. This historical pattern is not uncommon among mammals (Hawks & Cochran, 2006), for which incompatibility has rarely evolved in a period shorter than 1million years (Holliday, 2006). … the recurrence of the pattern within and outside Africa and the geographic specificity of Denisovan and Neanderthal descendants both show that interbreeding among these ancient people occurred within  their habitats. Neanderthals and Denisovans were part of the biological species Homo sapiens. Today’s people around the world are a relict mixture of populations from an ancient species much more genetically and morphologically diverse than now.”

Wolpoff & Lee agree with this appraisal (Wolpoff et al., 1994. A fundamental difference remains between Denisovans and Neanderthals, when it is accepted that Denisovans and Neanderthals are sister groups within the species Homo sapiens. It has not been identified within the fossil record who the Denisovans are (Wolpoff et al., 2014). Fossils cannot be recognised as Denisovans, and it is also possible that there never was a recognisable sample of Denisovans in the sense there is a recognisable sample of European Neanderthals, though Wolpoff & Lee suggest there are almost certainly Denisovan fossils that are known to paleoanthropologists at the present. Reasons for this are discussed below. In the view of Wolpoff & Lee none of the skeletal remains from the Late Pleistocene (<50 ka: Prüfer et al., 2014) hominids from Denisova Cave have diagnostic anatomy. From the range of modern human populations that contain detectable frequencies of Denisovan nDNA , that are almost invariably from Island Southeast Asia, Australia and Oceania (Reich et al., 2011), where the frequencies of Denisovan genomes are between 1 % and 6%.

The problem is described by Wolpoff & Lee as there being no disparity between the phylogenies that describe Neanderthal mtDNA and their nDNA relationships, as being evidenced by the fact that even the toe phalanx from Denisova Cave with mtDNA close to that of European Neanderthals also has a nuclear genome that resembles closely that of European Neanderthals (Prüfer et al., 2014; Skoglund et al., 2014). According to Wolpoff & Lee this is not necessarily because the mtDNA sand the nDNA relationships differ fundamentally in Neanderthals and Denisovans, but because the groups themselves, Neanderthals and Denisovans were historically defined quite differently. Neanderthals have been identified by their skeletal anatomy for more than 150 years as expressed in Western and Central Europe. The diagnosis of Neanderthals near the edge of their range is not always clear, as has been demonstrated by discussions about specimens from the Levant (Amud, Tabun), North Africa (Jebel Irhoud 1, 2) and Central Asia (Teshik Tash). Some authors have diagnosed each of these examples as Neanderthal, though somewhat different from Neanderthals by others. Though in Central and Western Europe this is rarely the case, where the identification as Neanderthal has been unambiguous and without controversy, in most part. After these anatomical identifications have been made, the mtDNA that was subsequently recovered so far from European and Asian (anatomically identified) Neanderthals are branches of a single mtDNA clade.

On the other hand Denisovans have not been described anatomically. These phylogenetic relationships have been based on mtDNA alone, portrayed by the position of a hand phalanx and 2 molars from the Denisova Cave in Siberia on a mtDNA tree (Krause et al., 2010). But more complex phylogenetic relationships are shown by the subsequent high-coverage nDNA sequence (Meyer et al., 2012). And the relationship of specimens with Denisovan mtDNA to Neanderthals on the tree of mtDNA relationships (Meyer et al., 2014) differs from the relationships that anatomy suggests when Sima de los Huesos is also considered. It is indicated that Sima de los Huesos is 1of the ancestors of European Neanderthals, as noted above, but not necessarily of all living humans (Arsuaga et al., 1997; Martinón-Torres et al., 2012). It is not known whether the fossil specimens with Denisovan mtDNA and anatomically similar to each other, in the sense that European Neanderthals are (Wolpoff, 2014).

Sources & Further reading

1. Habgood, P. J. (2016). "WLH 50: How Australia Informs the Worldwide Pattern of Pleistocene Human Evolution By Milford H. Wolpoff and Sang-Hee Lee PB - PaleoAnthropology 2014: 505−564. DOI:10.4207/PA.2014.ART88." Archaeology in Oceania 51(1): 77-79.