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Research on Ancient DNA Could Test Predictions of Non-Darwinian Speciation Models

ancient DNA

The neo-Darwinian theory of evolution postulates that new species originate mainly from ancestral species by geographic isolation, often leading to a reduction of the ancestral genetic variation by population bottlenecks. This is followed by the accumulation of new mutations (new information) driven by natural selection. Such a model would predict that we find more genetic variation created by accumulated mutations (not only neutral and detrimental mutations, but also new beneficial ones) in recent species than in their ancestors, depending on the size of the bottleneck and how long ago it was.

Independent of each other, different groups of researchers (e.g., Hössjer et al. 2016), more or less skeptical of common ancestry, have recently suggested the alternative model of initial heterozygotic diversity. The common element in these models is the working hypothesis of a large variation of beneficial alleles in terms of heterozygosity, later transformed over time by migration, isolation, and natural and sexual selection into phenotypically different populations or descendent species.

By “heterozygotic,” what do I mean? Briefly, the following: Genes can come in different variants. These are called alleles, always present in pairs in species like ours with two parents, possessing two sets of chromosomes from mother and father respectively. In each organism the pair of genes can either have the same allele (homozygosity) or two different alleles (heterozygosity).

For example, assume a hypothetical gene for hair length. It can come in the allele L for longer hair and S for shorter hair. Organisms with the heterozygotic combination LS can have an intermediate or variable condition, or long or short hair if one of the alleles is dominant. A heterozygotic parent can pass on either allele L or allele S. Therefore, the offspring of two heterozygotic parents can have all possible combinations, either heterozygotic LS / SL or homozygotic LL or SS. The latter will usually differ significantly from the phenotype of their heterozygotic parents. Homozygotic organisms can only pass on a single allele type and thus have less information than heterozygotic parents.

The suggestion, noted above, of initial heterozygotic diversity can explain the origin of genetically different populations and descendent species from an ancestral species in relatively short time. Such a process of speciation would not be evolution in the sense of gradual successive generation of new beneficial information by mutation and selection. Instead, it would represent a process of devolution through partitioning of information that was initially set in the ancestral species. As soon as the original heterozygosity of beneficial alleles is partitioned into separated homozygotic populations, the process of further speciation would slow down or even come to a halt. Genetic decay would then accumulate through mostly neutral and detrimental mutations (Sanford 2014).

Such decay could either increase general heterozygosity or, in the case or bottlenecks and isolated subpopulations, decrease heterozygosity. Obviously, the prediction from this model is that we should find more genetic diversity of beneficial alleles in ancient populations or ancestral species of a lineage, while finding less diversity of such beneficial alleles in recent populations or descendent species. We should also find most beneficial alleles in the ancestral groups and hardly any new beneficial alleles in the descendent groups. Finally, we should find a growing percentage of detrimental alleles in successively more recent populations.

A relatively young field, research on ancient DNA could provide data for empirical tests of the predictions from neo-Darwinian and non-Darwinian models. The first studies on ancient DNA were published in the 1990s. They claimed to have isolated ancient DNA from insect inclusions in Oligocene amber, from Miocene plant remains, from a Cretaceous dinosaur egg, and even from Permian bacteria preserved in salt deposits. Unfortunately, based on findings of recent contamination, all these initial studies were later refuted.

However, in the 2000s, better methods produced more serious results. We now have DNA from a 120,000 year old polar bear (Lindqvist et al. 2010), a 300,000 year old cave bear from Spain (Dabney et al. 2013), a 700,000 year old frozen horse from Yukon (Rohland & Hofreiter 2007), as well as the complete mammoth genome from the last Ice Age (Palkopoulou et al. 2015). Projects on ancient human DNA yielded genetic data from 28-40,000 year old modern humans of the Paleolithic period (Caramelli et al. 2008, Fu et al. 2013), the complete genome of Homo neanderthalensis (Prüfer et al. 2014) from the last Ice Age, genetic data from 41,000 year old Denisovans (Reich et al. 2010), and recently even from 300,000 year old Homo heidelbergensis at Sima de los Huesos cave in Spain (Meyer et al. 2013, 2016). When the common biospecies concept (sensu evolutionary biologist Ernst Mayr) is applied, the discovery of the genetic admixture of modern humans with archaic humans like Neandertals and Denisovans (e.g., Skoglund & Jakobsson 2011. Sankararaman et al. 2012) suggests that all these interbreeding ancient Homo species are indeed conspecific with our own species.

Paleoanthropologist John Hawks has discussed these results on his blog (Hawks 2013). He writes:

Europeans today are largely different from the Europeans of 10,000 years ago, with a massive mtDNA replacement along with the introduction of Neolithic culture, and at least a second later large-scale replacement of genetic diversity. Earlier Neandertals in Europe have different mtDNA diversity than later Neandertals in Europe. Denisova cave was home to an earlier population of hominins with different mtDNA than the later Neandertals who lived there. Mitochondrial DNA has never been a straight line linking earlier and later populations within a single location. Whenever we look at ancient DNA in hominins, the earlier populations have different mtDNA diversity than the later ones. Moreover, wherever we have ancient mtDNA from other species — bison, mammoths, cave bears, and others — we find that later mtDNA sequences do not represent the earlier diversity. The Sima cave bear mtDNA is a direct example of this, but the same phenomenon has happened again and again.

Unfortunately, even though these data from ancient hominine DNA suggest a significant change of genetic diversity over time, they mainly address diversity in mitochondrial DNA. They thus do not allow us to make statements about nuclear heterozygosity. Also there is still hardly any information about the adaptive value of the known genes. We know from available nuclear DNA data of Neandertals and Denisovans that their heterozygosity was lower (only about 31 percent) than in present-day humans (Castellano et al., Prüfer et. 2014). However, this is probably related to the fact that they form a separate lineage (within our biospecies) of small effective population size.

Among recent humans the heterozygosity is significantly larger in African populations, which are usually considered to be derived from earlier branching events in the history of Homo sapiens, thus implying that modern humans suffered a significant loss of heterozygosity while migrating out of Africa. An alternative explanation for African heterozygosity could be that African populations have fragmented into small isolated tribes (subpopulations), in which different genetic variants (mostly neutral) have been fixed.

Apart from ancient human DNA, we now have very good data from the completely reconstructed genomes of two woolly mammoth specimens: a 44,800 year old mammoth from Siberia, and a representative of the last survivors of this species from 4,300 years ago on Wrangel Island. The latter showed a significant 20 percent decrease in heterozygosity and an accumulation of detrimental mutations (Palkopoulou et al. 2015, Rogers & Slatkin 2017). This is as predicted by the non-Darwinian model of initial heterozygosity. However, the fact that the final surviving mammoths on Wrangel Island were only a small relict population would be an alternative explanation for the observed genetic effects, compatible with the Darwinian model. Therefore, concerning the two models, the genetic data from the woolly mammoth are inconclusive.

In short, the available data on ancient DNA can as yet neither confirm nor refute either model. Nevertheless, as more data from paleo-DNA studies are released in coming years, it will be very interesting to more rigorously test the two alternative models. Apart from general interest in the subject, that will address a common unsubstantiated claim of some Darwinian evolutionists. These advocates insist that alternative theories to Darwinism, such as intelligent design, are not science because they make no testable predictions. On the contrary, this example shows that non-Darwinian models definitely qualify as empirical science that is testable and falsifiable.


Caramelli D et al. 2008 A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences. PLoS One 3(7): e2700.

Castellano S et al. 2014 Patterns of coding variation in the complete exomes of three Neandertals. PNAS 111(18): 6666–6671.

Dabney J et al. 2013 Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. PNAS 110(39): 15758–15763.

Fu Q et al. 2013 DNA analysis of an early modern human from Tianyuan Cave, China. PNAS 110(6):2223–2227.

Hawks J 2013 The Denisova-Sima de los Huesos connection. john hawks weblog 4 Dec 2013.

Hössjer O, Gauger AK & Reeves C 2016 Genetic Modeling of Human History Part 1: Comparison of Common Descent and Unique Origin Approaches. BioComplexity 2016.

Lindqvist C et al. 2010 Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. PNAS 107(11): 5053–5057.

Meyer M et al. 2013 A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505: 403–406.

Meyer M et al. 2016 Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature 531: 504–507.

Palkopoulou E et al. 2015 Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth. Current Biology 25(10): 1395–1400.

Prüfer K et al. 2014 The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505: 43–49.

Reich D et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468:1053–1060.

Rohland N & Hofreiter M 2007 Ancient DNA extraction from bones and teeth. Nature Protocols 2(7):1756–1762.

Rogers RL & Slatkin M 2017 Excess of genomic defects in a woolly mammoth on Wrangel island. PLOS Genetics 13 (3): e1006601 DOI: 10.1371/journal.pgen.1006601.

Sankararaman S et al. 2012 The Date of Interbreeding between Neandertals and Modern Humans. PLoS Genetics 8(10): e1002947.

Sanford JC 2014 Genetic Entropy. FMS Publ., 270 pp.

Skoglund P, Jakobson M 2011 Archaic human ancestry in East Asia. PNAS 108(5): 18301–18306.

Photo: Tourists contemplate Denisova Cave, Siberia, by ЧуваевНиколай at ru.wikipedia [GFDL or CC BY-SA 3.0], via Wikimedia Commons.