



































Unraveling the Tree of Life


DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

73 

Article 
 

The Tree of Life: Tangled Roots and Sexy Shoots 
Tracing the genetic pathway from the first Eukaryotes to Homo sapiens 

 
Chris King* 

 

 ABSTRACT 

The picture conveyed by the significance of endosymbiosis, genome fusion and horizontal transfer as 

key evolutionary processes complementing the vertical transmission of the tree of life, makes clear 

that evolution is not just a matter of competitive survival of the fittest gene, individual, or species, 

but of dynamic survival of genes in a surviving ecosystem. Although Dawkins' (1978) notion of the 

"selfish gene" was pivotal in drawing attention to the fact that it was the survival of genes and not 

organisms, or even species, that was the key evolutionary process, attributing the human sentiment of 

selfishness to a gene is somewhat of a self-serving advertising distraction on the part of the author, 

which diminishes the subtlety and complexity of the sometimes apparently paradoxical ways genes 

actually interact to bring about beneficial outcomes in the evolutionary dynamics of the ecosystem. 

Although the idea of selection of genes has been pivotal in defining the need to consider 

evolutionarily stable strategies under genetic variation in ways which have been subsequently 

confirmed time and time again in situations such as the sexual genetics of social insects such as bees 

and ants, social selection is by no means ineffectual, or much of sociobiology, including the 

biological basis of morality as an extension of reciprocal altruism, would cease to exist. Moreover, 

from what we have seen, particularly about horizontal gene transfer, and the capacity of mobile 

elements to induce modulated changes in nuclear genomes, it is not the 'selfishness' of a genetic 

element alone that results in survival of both a gene and its hosts, but dynamic feedbacks,, and 

relationships which ultimately contribute to a massive sharing of information in the manner of 

parallel genetic algorithms fundamental to the replicative genetic process, which enable global forms 

of genetic and genome optimization central to the overall viability of life as complex systems. 

Key Words: tree of life, genetic pathway, Eukaryotes, Homo Sapien, DNA, RNA, evolution. 

Introduction 

This article is a fully referenced research review to overview progress in unraveling the details of the 

evolutionary Tree of Life, from life's first occurrence in the hypothetical RNA-era, to humanity's 

own emergence and diversification, through migration and intermarriage, using research diagrams 

and brief discussion of the current state of the art, as of 2009, in response to summaries of some of 

these developments (Lawton 2009, Lane 2009). 

The Tree of Life, in biological terms, has come to be identified with the evolutionary tree of 

biological diversity. It is this tree which represents the climax fruitfulness of the biosphere and the 

genetic foundation of our existence, embracing not just higher Eukaryotes, plants, animals and fungi, 

but Protista, Eubacteria, and Archaea, the realm, including the extreme heat and salt-loving 

organisms, which appears to lie almost at the root of life itself. 

                                                           

*
 Correspondence: Chris King  http://www.dhushara.com E-Mail: chris@sexualparadox.org  

http://en.wikipedia.org/wiki/Evolutionary_tree
http://en.wikipedia.org/wiki/Tree_of_life
http://en.wikipedia.org/wiki/Eukaryote
http://en.wikipedia.org/wiki/Protista
http://en.wikipedia.org/wiki/Eubacteria
http://en.wikipedia.org/wiki/Archaea
http://www.dhushara.com/
mailto:chris@sexualparadox.org


DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

74 

 

Fig 1: The Tree of Life (King http://www.dhushara.com/book/unraveltree/life4CK.jpg) 

http://www.dhushara.com/


DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

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75 

The Universal Common Ancestor 

Following a phase of biogenesis possibly based on cosmic symmetry-breaking (King 1978, 2004), 

based on new breakthroughs concerning RNA synthesis (Sutherland et. al. 2009) recent research 

suggests that the last universal common ancestor (LUCA) of all life on the planet may have arisen 

from a phase interface between alkaline hydrogen-emitting undersea vents and the archaic acidified 

iron-rich ocean (Martin and Russel 2003), giving rise to an active iron-sulphur reaction phase still 

present in living cells and associated with electron transport and some of the most ancient proteins, 

such as ferredoxin, in which differential dynamics in membranous micropores in the vents managed 

to concentrate polypeptides and polynucleotides to biologically sustainable levels (Baaske et. al. 

2007, Budin et. al. 2009), giving rise to the RNA era, while at the same time providing a free energy 

source based on proton transport across membranous microcellular interfaces resulting from fatty 

acids also being concentrated above their critical aggregate concentration .  

 

Fig 1a: Proposed scheme for the universal common ancestor (Martin and Russel 2003)  

The universal common ancestor of the three domains of life may have thus been a proton-pumping 

membranous interface from which archaea and bacteria emerged as free-living adaptions. This is 

suggested by fundamental differences in their cell walls and other details of evolutionary 

relationships among some of the oldest genes. 

It has also been proposed, on the basis of the highly-conserved commonality of transcription and 

translation proteins to all life, but the apparently independent emergence of distinct DNA replication 

enzymes in archaea/eucaryotes and eubacteria, that the last universal common ancestor had a mixed 

RNA-DNA metabolism based on reverse transcriptase, pinpointing it to the latter phases of the RNA 

era (Leipe et. al. 1999). 



DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
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76 

 

Fig 1b: Hypothetical branching and evolution of RNA and DNA replication machinery 

(Leipe et. al. 1999).  

 

Three Domains of Life 

Life today is informationally based on the sequences of the four bases A, G, T and C in DNA, with 

messenger copies of the genetic sequence in mRNA forming intermediates in the assembly of 

proteins, as the cell's primary active chemical and structural agents. This is achieved through a 

process of translation at the ribosome - a supra-molecular complex composed of some 50 

chaperoning proteins surrounding a core composed of three rRNA units, fed by amino-acid coupled 

tRNAs. The RNAs carry out the essential function, supporting the idea that translation was at first a 

purely RNA-based process of protein construction. In line with this and other RNA fossils found 

particularly in Eukaryotes, it is widely believed that life began based on RNA, which shares both the 

capacity for complementary replication of DNA and the formation of 3-dimensional chemically 

reactive conformations, similar to proteins, after which the ribosome evolved, transferring the 

reactive burden on to proteins sequenced through the genetic code. Some time later, the 

informational genome was consolidated into more stable DNA. 

 

Fig 2: The initial tree of rRNAs shows three distinct founding domains (Woese 1987) 



DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

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77 

Originally the Bacteria and Archaea were thought to be one large diverse family of prokaryotes until 

Carl Woese (1977, 1978, 1987, 1990) and others investigated the evolutionary tree of ribosomal 

RNAs and found that there were three distinct founding evolutionary domains, then named 

eubacteria, archaebacteria along with the eukaryotes. 

This gave the Eukaryotes a closer founding status as well, by contrast with the idea that the 

procaryotic bacteria came first and then, somehow the higher Eukaryote organisms with their 

complex cellular structures, including among others - the endoplasmic reticulum, along with the 

nuclear envelope and Golgi apparatus - all parts of a common complex of internal membranous 

partitions - and the architecture of microtubules, including centrioles, and the Eukaryote flagellum, 

as well as the Eukaryotes endosymbiont mitochondria and chloroplasts 

 
Fig 3: Key structural differences separating the larger rRNA units of the three domains 

(Woese 1987). 

In addition to their evolutionary sequence divergence, the smaller 30s ribosomal RNAs of each 

domain, show distinct structural features characteristic of their own domain, but also emphasizing 

structural links between Bacteria and Archaea on the one hand and Archaea and Eukaryotes on the 

other, qualitatively confirming the central place of the Archaea in the divergence.  

 

Fig 4: Small and large rRNA subunits of the eubacteia Thermus thermophilus and the 

archaeon Haloarcula marismortui. RNA orange and yellow, protein blue and active site 

green. (Wikipedia Ribosome) 

The validity of the RNA-era concept and the capacity for RNAs to be both replicating informational 

and active ribo-enzymes is emphasized by the continuing dependence of the ribosome on rRNA 

http://www.dhushara.com/book/unraveltree/10_small_subunit.gif
http://www.dhushara.com/book/unraveltree/10_small_subunit.gif
http://en.wikipedia.org/wiki/Ribosome


DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

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78 

rather than the protein components is emphasized by the 3-dimensional realizations of the two 

subunits in fig 4, which show that the rRNA molecules are still carrying out the central task of 

protein assembly with only minor modification due to the 'chaperoning' proteins, despite 3.8 billion 

years of evolution. 

Norman Pace subsequently enlarged the scope and accuracy of the rRNA tree, including a greater 

diversity of organisms. This tree has become the basis of several other studies (see e.g. fig 10). 

The Copernican principle asserts that the Earth is a typical rocky planet in a typical planetary system, 

located in an unexceptional region of a common barred-spiral galaxy, hence it is probable that the 

universe teems with complex life. This is supported to a reasonable extent by the discovery of an 

increasing number of planets including some putative "Goldilocks" zone planets where water would 

be liquid and life as we know it could potentially exist. Set against this, the Rare Earth hypothesis 

argues that the emergence of complex life requires a host of fortuitous circumstances including a 

galactic habitable zone, a central star and planetary system having the requisite character, the 

circumstellar habitable zone, the size of the planet, the advantage of a large satellite, conditions 

needed to assure the planet has a magnetosphere and plate tectonics, the chemistry of the lithosphere, 

atmosphere, and oceans, the role of "evolutionary pumps" such as massive glaciation and rare bolide 

impacts, and whatever led to the still mysterious Cambrian explosion of animal phyla. This might 

mean that planets able to support a bacterial level of life are not so uncommon, but those supporting 

complex multicellular life might be.  

 

Fig 5: Further elaboration of the rRNA tree (Pace 1997) 

http://en.wikipedia.org/wiki/Rare_Earth_hypothesis


DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
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79 

 
Fig 6: Lower right: A third rRNA tree which suggests Archaea lie very close to the root is 

contrasted with that for the enzyme HMGCoA reductase, which also shows evidence of 

horizontal transfer to an Archaean (ex Doolittle 2000). 

Bringing this question to a pivotal crux in our context, the emergence of mitochondria as 

endosymbionts has been proposed to be a critical bottleneck which allowed complex life to evolve 

only once, because, only in this effectively fractal cellular architecture, can the membrane surface 

areas necessary to support the chemical reactions enabling the vastly larger number of genes in a 

complex organism's genome to maintain metabolic stability (Lane and Martin 2010). Whether such 

endo-symbiosis is rare. or a common extreme of parasitic relationships would then determine how 

likely or unlikely complex life might be. 

Offset against both the uniqueness of the mitochondrial endo-symbiosis and the closely linked, but 

independent question of the origin of the nucleus and nuclear envelope, has been the discovery of 

mimiviruses and mamaviruses infecting amoeba (Raoult et, al. 2004) and related very large aquatic 

viruses such as CroV infecting single celled plankton species, which despite their recent discovery, 

appear from ocean gene analyses to be potentially ubiquitous and widespread in the oceans and 

possibly playing a crucial role in regulating the atmospheric-oceanic pathways, such as carbon 

sequestration (Fisher, Allen, Wilson and Suttle 2010). These form an intermediate genetic position 

between viruses and cells, having the largest genomes, with extensive cellular machinery and larger 

than the smallest completely autonomous bacterial and archaeal genomes. 

As an illustration of genes in mimivirus normally appearing only in cellular genomes, the mimivirus 

has genes for central protein-translation components, including four amino-acyl transfer RNA 

synthetases, peptide release factor 1, translation elongation factor EF-TU, and translation initiation 

factor 1. The genome also exhibits six tRNAs. Other notable features include the presence of both 

type I and type II topoisomerases, components of all DNA repair pathways, many polysaccharide 

synthesis enzymes, and one intein-containing gene. Inteins are protein-splicing domains encoded by 

mobile intervening sequences (IVSs). They self-catalyze their excision from the host protein, ligating 

their former flanks by a peptide bond. They have been found in all domains of life (Eukaria, 

Archaea, and Eubacteria), but their distribution is highly sporadic. Only a few instances of viral 

inteins have been described. Self-splicing type I introns are a different type of mobile IVS, self-

http://www.newscientist.com/article/dn18734-why-complex-life-probably-evolved-only-once.html
http://www.newscientist.com/article/dn18734-why-complex-life-probably-evolved-only-once.html
http://www.k8science.org/news/news.cfm?art=1288
http://en.wikipedia.org/wiki/Mimivirus
http://en.wikipedia.org/wiki/Mamavirus
http://www.newscientist.com/article/dn19625-giant-virus-with-tiny-victims-carries-a-monster-genome.html


DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

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80 

excising at the mRNA level. They are rare in viruses. Mimivirus exhibits four instances of self-

excising intron, all in RNA polymerase genes. 

Evolutionary diversification of Mimiviruses from nucleocytoplasmic large DNA viruses 

(Fisher et. al.) and in relation to the three domains of cellular life based on the concatenated 

sequences of seven universally conserved protein sequences (Raoult et. al.) 

Mimiviruses also host parasitic virophages, affectionately named sputnik as viral satellites, which 

piggy back on the metabolism of the large viral factories set up by these giant viral genomes causing 

the mimiviruses to sicken, and these virophages also contains genes that are linked to viruses 

infecting each of the three domains of life Eukarya, Archaea and Bacteria (La Scola et. al. 2008). It 

has thus been suggested that they have a primary role in the establishment of cellular life and that 

they may have been instrumental in the emergence of the nuclear envelope. 

 

Fig 7: Evolution of iron-sulphur cluster proteins of mitochondria is linked to α-

proteobacteria (Emelyanov 2003) 

http://www.nature.com/news/2008/080806/full/454677a.html


DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

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81 

Tangled Roots of Horizontal Transfer 

Despite the division into three domains, further investigations of proteins in the three domains began 

to reveal a much more confused and complicated picture. Firstly the ribosomal proteins, like the 

rRNAs show distinct, easily differentiated morphologies with some correspondences linking one pair 

of domains and other another pair (Forterre 2006b, Woese 2000). Secondly, the proteins in 

Eukaryotes appear to have a mixed origin with the informational ones having an evolutionary 

relationship with Archaea but the metabolic enzymes appearing to have a bacterial origin. This 

suggests that the Eukaryote genome has either resulted from one, or more symbiotic fusions e.g. an 

Archaeal and a bacterial genome and/or that there has been a high degree of horizontal gene transfer 

between bacteria and Eukaryotes. 

The evidence for symbiotic inclusions is clear from the fact that all Eukaryotes, except for a few 

primitive anaerobic varieties, such as the metamonad human gut parasite Giardia lamblia, all have 

endosymbiotic respiring mitochondria, which are evolutionarily related to α-proteobacteria such as 

Rickettsiae (Emelyanov 2003). Plants also have photosynthetic chloroplasts derived from 

cyanobacteria. α-proteobacteria, including Rickettsiae (and related Wollbachia and Agrocbacterium), 

obligately live in the cytoplasm of other cells and so are naturally adapted to becoming an endo-

symbiont of a glycolytic organism by providing respiring energy to the host's metabolism resulting in 

the mitochondrion. Giardia still retains traces of mitochondrial proteins so appears to have lost its 

respiring organelles, rather than occupying a place in the tree before mitochondria were incorporated 

into eucarya (Adam 2000). 

 
Fig 8: Tangled roots (Doolittle 2000) 

http://en.wikipedia.org/wiki/Giardia
http://en.wikipedia.org/wiki/Proteobacteria
http://en.wikipedia.org/wiki/Rickettsiae
http://en.wikipedia.org/wiki/Cyanobacteria


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King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
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82 

The picture of horizontal transfer is even more tangled in bacterial and archaeal genomes, which 

contain a great number of shared and exchanged genes, probably through viral transfer. 

This has led generally to Doolittle (1998), Woese (2002), and others, proposing a tangled root to the 

tree of life involving a transition from a regime in which thre was a much higher rate of horizontal 

exchange and effective global optimization of genomes, to tree-like vertical evolution of genomes, 

once the more complex genomes of the Eukaryote domains became established. 

Subsequently, to try to clarify the taxonomic relationships founding the tree of life, Peer Bork and 

his team produced a refined evolutionary tree by selecting only universal proteins that had not been 

subjected to horizontal transfer, providing the most detailed tree root diagram to date, although 

admittedly on only a skeleton gene set comprising some 1% of the respective genomes. The 

phylogenetic tree has its basis in a cleaned and concatenated alignment of 31 universal protein 

families and covers 191 species whose genomes have been fully sequenced. 

 

Fig 9: High resolution tree of the three domains of life (Ciccarelli, Bork et. al. 2006).Purple 

eubacteria, green archaea, red Eukaryotes. 



DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
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83 

 
 

Fig 9b: Tree diagram of the birth, transfer, duplication and loss of key genes in the redox 

and electron transport pathways, in a founding burst of gene evolution between 3.3 and 2.7 

billion years ago (David and Alm 2010). 

Then Lawrence David and Eric Alm (2010) produced the above tree investigating the central genes 

common to a wide spectrum of life forms, involving the founding steps of redox reactions and 

electron transport, demonstrating a rapid evolutionary innovation during an Archaean genetic 

expansion between 3.3 and 2.7 billion years ago. They mapped the evolutionary history of 3983 gene 

families that occur in a wide range of modern species. They were able to show that 27 per cent of 

these gene families appeared in a short evolutionary burst. Many of the genes from this time were 

involved in electron transport - a key step in respiration and photosynthesis, which ultimately led to 

oxygen-producing photosynthesis and the "great oxygenation event" 2.4 billion years ago, when the 

atmosphere became oxygen rich. 

This lends support to the idea that the collective primordial genome functioned as a supercomputer 

(King 2010) based on parallel genetic algorithms combined with horizontal genetic transfer, whose 

bit computation rate through mutation and recombination is sufficient to generate the functional 

conformations, through protein folding, to solve the key metabolic pathways over a period no longer 

than 300 million years. 

Bacteria engage in much more radical forms of pan-sexuality than higher organisms, involving 

viruses and plasmids, themselves separate mobile genetic elements, acting as agents of genetic 

transfer, accelerating the pace of bacterial evolution (Maxmen 2010). This enables the genetic 

sequences of bacteria, archaea and protists to move around in the genome and to be exchanged 

between cells, and even between different species. Sexual exchange of material can happen both 

through viral exchange and through a conjugation plasmid, which can spool DNA from one 

bacterium into another, resulting in a net donation of genes from one strain or species to another, 

which ensures a broad exchange of genetic material throughout bacterial ecosystems, resulting in 

rapid accumulation of advantageous genes exemplified by plasmid borne infectious drug resistance. 



DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

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84 

To give a very rough idea of the computing power of the combined bacterial genome alone, taking 

into account bacterial soil densities (~10
9
/g), effective surface area (~10

18
 cm

2
), genome sizes (~10

6
), 

combined reproduction and mutation rates (~10
-3

/s) gives a combined presentation rate of new 

combinations of up to 10
30

 bits per second, roughly 10
13

 times greater than the current fastest 

computer at 2 petaflops or about 10
17

 bit ops per second. Corresponding rates for complex life forms 

would be much lower, at around 10
17

 per second because they are fewer in total number and have 

lower reproduction rates and longer generation times, but they are still vying with the computation 

rates of the fastest supercomputer on earth. 

 

Fig 10: Horizontal transfers across the bacterial tree under two thresholds 10, 5 genes 

(Dagan et. al.). 

This picture of bit rates coincides closely with the Archaean expansion scenario noted above and 

suggests that evolution has been a two-phase process in which the much higher bit rates of the 

collective single-celled genome under promiscuous sexuality and horizontal transfer has arrived at a 

global genetic solution to the protein folding problems of the central metabolic, electro-chemical and 

even root developmental pathways, which are then later capitalized on by multi-celled organisms, 

through gene duplication and loss as well as the creation of new specialized genes at a much lower 

rate. 

The massive extent of horizontal transfer in eubacteria, as well as archaea has also become clear 

suggesting large components of procaryote genomes are effectively globally optimized for their 

niches by frequent genetic transfer. Dagan et. al. have characterized the extent of horizontal transfer 



DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
King, C., The Tree of Life: Tangled Roots and Sexy Shoots  

ISSN: 2159-046X DNA Decipher Journal 
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85 

for a series of thresholds as well as establishing specific modularity of horizontal transfer of 

functions between 

groups.  

Fig 11: Evolutionary root of the tree of life and its diversification into archaea, bacteria and 

Eukaryotes appears to have gone through an early period of cool temperature consistent with an 

RNA era, followed by a hot period (Anathaswamy, Boussau et. al.)  

Surviving Archaea are known to inhabit extreme environments, including hot volcanic pools, 

hydrothermal vents and extreme salty environments and several arrangements of the root of the tree, 

including Bork's team's work suggest a hot origin for life. However other research (Brochier and 

Philippe, Boussau et. al.), concludes the base root may have been at about 25
o
C, a more viable 

temperature for a simple RNA metabolism, with a succeeding period of high temperature adaptions 

shortly after the differentiation of the three domains in evolutionary time. 

 

Fig 12: Genetic diffusion at the root of the tree (Dagan and Martin) 

Critics of the validity of the tree root concept, such as Dagan and Martin emphasize the small 

proportion (1%) of the genome used in Bork's study and stress both the lateral (or horizontal) gene 

transfer events uniting the prokaryote realms and the apparent chimaeric nature of the Eukaryote 

http://en.wikipedia.org/wiki/Archaea


DNA Decipher Journal | January 2011 | Vol. 1 | Issue 1 | pp. 073-109 
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86 

genome, which appears to contain both archaea-related informational genes and eubacterial 

metabolic ones, in addition to obvious endosymbiont events of the mitochondrion and chloroplast. 

 

Fig 13: Pattern of invasions of the SPIN element (Lisch) 

The case for horizontal transfer of genes between unrelated Eukaryote species through infectious 

elements invading new and hence non-resistant species is also well established. The SPIN element is 

present in a diverse unrelated set of species, spanning amphibians, reptiles, marsupials and mammals 

while absent from closely related species (Lisch). 

 

The Eukaryote Nuclear Genome as a Genetic Fusion 

 
Fig 14: The proposed ring of life (Rivera and Lake) 

In a further study, Rivera and Lake used a new algorithm to take account of possible genetic fusion 

events by forming a genetic ring through matching partial trees into a most parsimonious whole, 

inferring that the Eukaryote genome has arisen from a fusion of an archaeal (possibly eocyte) 

genome with that of either a cyanobacterium or possibly a γ-proteobacterium. 

http://en.wikipedia.org/wiki/Eocyte


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87 

The method used cannot definitively determine whether or not the eubacterial genome could have 

come from the mitochondrial event, which, to an even greater extent than the more recent 

chloroplast, has resulted in a high net transfer of genes from the mitochondrial chromosome to the 

nucleus, leaving open the possibility that in addition to the mitochondrial symbiosis, and the later 

chloroplast one, there may have been an additional genetic fusion. Lane and Archibald have cited 

further major endosymbiosis events involving complex three genome interaction in protista, where 

both green and red algae have been incorporated by endosymbiosis into other protists, which 

demonstrate both that endosymbiois has occurred many times and the genomic complexity of nuclear 

symbiont gene exchange. 

 
 

Fig 15: Proposed fusion between two genomes - informational, from Archaea (red), and 

metabolic, from Eubacteria (blue) as well as mitochondrial genes migrating to the nucleus 

(green) (Horiike et. al.). Up to 75% of nuclear genes whose ancestry has been elucidated 

may come from bacteria (Lane). 

The idea of a genetic fusion between an archaea and a γ-proteobacterium is also supported by several 

other lines of research including evolution of glycolytic enzymes (Emelyanov), ‘homology-hit 

analysis’ of non-mitochondrial genes determined the number of yeast orthologous ORFs in each 

functional category to the ORFs in six Archaea and nine Bacteria at several thresholds, suggesting an 

archaeal parasite engulfed by a eubacterium (Horiike et. al.) the proposal that close association 

between a central methanogenic archaebacterium (archaea) and a close-knit surrounding clump of 

ancestral sulfate-respiring δ-proteobacteria could have also led to the nucleus and endoplasmic 

reticulum (Moreira and Lopez-Garcia). 

http://www.newscientist.com/article/mg20227121.600-has-the-mystery-of-sex-been-explained-at-last.html?full=true


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88 

 

Fig 16: Gene replacement tree root (Makarova) Hartman and Federov's list of putative 

chronocyte genes correspond to the 359 above. 

Other theories stick to the three domain paradigm and propose that a primitive Eukaryote precursor 

possibly still retaining an RNA-based genome, as suggested by Woese (1998) might be the case for 

the progenote (first root life form) to be the last universal common ancestor of all three domains, 

possibly including genes for endoplasmic reticulum and microtubules, engulfed both and archaea and 

a eubacterium. Hartman and Federov cite a collection of such genes, including those for ribosomal 

proteins as well, naming the organism as a chronocyte. 

This is also consistent with the much greater complexity of use of RNA in Eukaryotes, including 

alternative splicing, the use of introns, interfering-RNAs in gene regulation, micro-RNAs and the use 

of the nucleus to contain a diversely functioning RNA informational metabolism not unlike that of a 

putative progenote. 

Viral Influences on the Nuclear Genome 

 

Fig 17: Proposed viral contribution of DNA polymerases FvA etc. founder viruses 

(Forterre). Other cellular and viral genealogies are possible and the scheme is merely 

representative. 



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Forterre looks likewise to a three component origin, but his emphasis is on the idea that viruses have 

contributed major components to the genome of all three groups, possibly providing each of three 

RNA-based cell lineages with independent transitions to DNA-based genomes by contributing DNA-

polymerases, thus radically improving the stability and competitiveness of these cell lines who 

became the eventual survivors. In addition to the ribosomal proteins and rRNAs having distinct 

qualitative features in each domain, many DNA informational proteins exist in different non-

homologous families (usually with several versions for one family). There are already six known 

non-homologous families of cellular DNA polymerases. In the case of DNA polymerases of the B 

family, there is one version in Bacteria (only found in some proteobacteria), one in Archaea, and 

several in Eukarya. The distribution of the different versions and families of cellular DNA 

informational proteins among domains is erratic most of the time and does not fit with any of the 

models proposed for the universal tree, suggesting abrupt insertion into the cellular genomes by viral 

transfer. 

 

Fig 18: Evolutionary tree of DNA polymerase amino termini (Villareal and Defilippis). 

Villareal and Defilippis have likewise investigated the idea that DNA viruses are the origin of DNA 

replication proteins, by investigating the amino terminus and constructing an evolutionary tree which 

shows DNA polymerases of DNA viruses, eukaryotes (α,δ), archaea, E coli and two phages rooted in 

a tree consistent with a viral origin. 

This idea has a great deal of plausibility because viruses are now know to have a potentially primal 

origin, rather than being recent escapees from cellular genomes which have undergone reductive 

parasitic changes to their genome. Viruses clearly also have retained both RNA-RNA, DNA-DNA 

and retrotranscription DNA-RNA-DNA using both RNA and DNA stages in their capsid viral forms, 

so they retain all the transitional states between RNA and DNA-based replication. 



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Fig 19: Bacterial DNA polymerases also show viral members (underlined) close to the root 

of the tree (File et. al.). 

Furthermore the retroviruses and related mobile genetic elements have a common ancient 

evolutionary origin, which is related to telomerase, which itself uses an RNA primer to initiate 

chromosome duplication. There is thus a plausible case that telomerase is in fact a biological fossil of 

a retroviral conversion of the founding Eukaryote cell line to a DNA genome. 

 

The Symbiotic Face of Eukaryote Mobile Elements 

In 1978, following the work of Darryl Reanny (1974-6), I proposed (1978, 1992) that viruses and 

transposable elements, far from just being selfish genes (Dawkins 1976), formed part of a dynamical 

system of genetic symbiosis between the hosts and the mobile genetic elements, because the mobile 

elements permitted forms of coordinated gene expression and the formation of new genes in a 

modular manner, which would otherwise be impossible, achieving in return perpetuation of their 

own genomes over evolutionary time scales. Most of the details of this proposal have proved to be 

realized. 

By some reckonings, 40 to 50 per cent of the human genome consists of DNA imported horizontally 

by viruses, some of which has taken on vital biological functions. Coding sequences comprise less 

than 5% of the human genome, whereas repeat sequences account for at least 50% and probably 



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much more. Transposable LINE or long-intermediate repeat retroelements common to vertebrates, 

with a history running back to the Eukaryote origin are specifically activated in both sperms and eggs 

during meiosis (Branciforte and Martin, Tchénio et. al., Trelogan and Martin). These replicate from 

transcribed RNA copies of themselves thus using RNA to instruct DNA copies, indicating an origin 

in RNA-based life, as does the active RNA processing of our own Eukaryote cells. Their RNA-based 

reverse transcriptase shows homologies with the telomerase essential for maintaining immortality in 

our germ line, indicating a common and symbiotic origin. 100,000 partially defective LINEs and 

their 300,000 dependent smaller fellow traveler Alu SINEs make up a significant portion of the 

human and mammalian genomes, along with pseudogenes, apparently defective copies of existing 

genes translocated by elements such as LINEs. 

 

Fig 20: Human transposable element evolutionary history of L1-LINEs (cream), Alu 

elements (lt. blue), retrovirus-like LTR (long-terminal repeat) elements (green) and DNA 

transposons (dk. brown). Older LINEs and SINEs are in yellow and dk. blue. This history 

extends back over 200 million years indicating the very ancient basis of this potentially 

symbiotic relationship (Human Genome Consortium). 

These elements travel passively down the germ line with chromosomal DNA, so their specific 

activation during meiosis suggests they may perform a role of coordinated regulatory mutation. This 

suggests that the type of symbiotic sexuality embraced by bacteria and plasmids also continues to 

function in higher organisms in a form of sexual symbiosis between our chromosomes and 

transposable genetic elements. This is consistent with the 1.4% point mutation divergence between 

humans and chimps, being overshadowed by an additional 3.9% divergence to 5.4% overall 

(Britten), when insertions and deletions are accounted. 

SINEs, such as human Alu, a free-rider on the LINE reverse transcriptase derived from the small 

cellular RNA used to insert nascent proteins through the membrane, are in turn implicated in active 

functional genes (Reynolds, Schmid) particularly some involved in cellular stress reactions, again 

suggesting genetic symbiosis. Humans have about 13 times as many RNA edits as non-primate 

species, including inosine insertions associated with Alu elements, as well as intron deletions 

(Holmes ) and newly inserted exons (Ast), which may differentiate humans from other apes through 

alternative splicing of genes expressed in the brain. RNA editing is abundant in brain tissue, where 

editing defects have been linked to depression, epilepsy and motor neuron disease. There is a new 



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Alu insert about every 100 births. As many as three quarters of all human genes are subject to 

alternative splice editing. 

 

Fig 21: Pseudogene-mediated production of endogenous small interfering RNAs (endo-

siRNAs). Pseudogenes can arise through the copying of a parent gene (by duplication or by 

retrotransposition). (a) An antisense transcript of the pseudogene and an mRNA transcript 

of its parent gene can then form a double-stranded RNA. (b) Pseudogenic endo-siRNAs can 

also arise through copying of the parent gene as in a and then nearby duplication and 

inversion of this copy. The subsequent transcription of both copies results in a long RNA, 

which folds into a hairpin, as one half of it is complementary to its other half. In both a and 

b, the double-stranded RNA is cut by Dicer into 21-nucleotide endo-siRNAs, which are 

guided by the RISC complex to interact with, and degrade, the parent gene's remaining 

mRNA transcripts. The mRNA from genes is in red and that from pseudogenes is in blue. 

Green arrows indicate DNA rearrangements (Sasidharan and Gerstein). 

Recent explosion of the area of interfering miRNAs as regulatory elements in gametogenesis and 

development (Großhans) has provided an explanation of how pseudogenes, including those 

retrotransposed via LINE elements, can gain functional regulatory significance even though they do 

not produce translatable mRNAs. 

Although the data from the human genome project indicated that human LINEs are becoming less 

active as a group by comparison with the corresponding elements in the more rapidly evolving 

mouse genome, there remain about 60 active human LINE elements which are known to be 

responsible for mutations in humans. More recent investigation (Boissinot et. al.) shows that the 

most recent families are highly active. Around four million years ago shortly after the chimp-human 

split, a new family Ta-L1 LINE-1 emerged and is still active, with about half the Ta insertions being 

polymorphic, varying across human populations. Moreover 90% of Ta-1d, the most recent subfamily 

are polymorphic, showing highly active lines remain present. LINEs are more heavily distributed on 

the sex chromosomes with X chromosomes containing 3 times as many full length potentially active 

elements and the Y chromosome 9 times as many! This is consistent with a continuing mutational 



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load on humans which is removed more slowly from the sex chromosomes by crossing over in 

proportion to the degree to which crossing over is inhibited in each (i.e. totally on the Y and largely 

in males in the X but not in females). Sexual recombination is a protection from mutational error in a 

process called Muller's ratchet. 

 

Fig 22: Evolution of reverse transcriptases from a common ancestor bearing a LINE 

archetype (Xiong and Eickbush, Nakamura et. al.). The root of their evolution goes back to 

the transfer from RNA to DNA at the beginning of life. They form a complementary 

evolutionary tree to that of cellular life as genetic symbionts of metazoa travelling down the 

germ line. Their group includes telomerases essential to the reproductive cycle. 

LINEs are preferentially expressed in both steriodogenic and germ-line tissues in mice (Branciforte 

and Martin, Trelogan and Martin), suggesting stress could interact with meiosis. L1 expression 

occurs in embryogenesis, at several stages of spermatogenesis including leptotene, and in the 

primary oocytes of females poised at prophase 1. Conversely the SRY-group male determining gene 

SOX has been found to regulate LINE retrotransposition (Tchénio et. al.). Similarly LINE elements 

have been proposed to be 'boosters' in the inactivation of one X chromosome that happens in female 

embryogenesis (Lyon). This could enable somatic stress to have a potential effect on translocation in 

the germ-line which might enable form of genetic adaption in long-lived species such as humans. 

Both L1 and Alu elements may be able to self-regulate rates of replication, through the existence of 

stealth drivers, viable elements which maintain a low transcription rate of active elements, with little 

genomic impact and hence little negative selection. These occasionally seed daughter master 

elements, which may replicate actively to form new families when conditions permit. This picture is 

consistent with long periods of quiescence, punctuated by bursts of 'saltatory' replication leading to 

large copy numbers (Han et. al.). 

 



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Endogenous Retroviruses and the Placenta 

Endogenous retroviruses, or ERVs, which also travel down the germ line as free-riders, although 

some may retain infectious capacity, may be essential for placental function, as every mammal tested 

has placental blooms of endogenous retroviruses which appear to both aid the formation of the 

syncytium, the super-cellular fused membrane that enables diffusion from the mother to the baby and 

the immunity suppression, which prevents rejection of the embryo, both characteristics of 

retroviruses such as HIV.  

Mi and colleagues (2000) found a placental gene whose sequence was homologous to several 

retroviral envelope proteins. The sequence, now called syncytin, is identical to the envelope protein 

of the HERV-W retrovirus (Blond et. al.) which exists in around 40 apparently defective viral copies, 

including those in which the two syncytin viral env genes are fully functional (Mi et. al.). Syncytin is 

expressed at high levels in the syncytiotrophoblast (and at low levels in the testes) and nowhere else. 

Most of the other genes of the provirus have been mutated, suggesting that the envelope glycoprotein 

function was specifically selected. If cultured cells are made to express syncytin, they will fuse 

together, and this fusion can be blocked with antibodies against syncytin. HERV-W is only found in 

primates, but mice have similar retroviral blooms and ERV-related Syncytin genes have also been 

found in them (Dupressoir et. al.). The ability of mammals and thus ourselves to form a viable 

placenta and give birth to live young may thus depend on the mammals having harnessed a viral 

gene somewhere in our evolutionary lineage. 

The defective copies of endogenous retroviruses may also serve to protect the host against further 

infection by becoming transcribed and causing incorporation of defective elements into the 

replicating virus (Best et. al.). 

 

Fig 23: The evolutionary tree of endogenous retrovirus classes along with other infectious 

retroviruses such as HIV span virtually all metazoa. When retrotranspons are included (fig 

22) they extend to all Eukaryote realms. 

http://en.wikipedia.org/wiki/Endogenous_retrovirus


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Emergence and Diversification of Modern Humans 

 

Fig 24: One hypothetical evolutionary tree for humans and related apes. There is much 

debate about the actual form of such a tree. 

Homo sapiens appears to have evolved into a single dominant species on the planet, after preceding 

period in which fossil evidence suggests there were several different anthropoid species coexistent. 

The final stage of this process was the disappearance of Homo erectus and Neanderthal, the latter 

after a well-defined period of coexistence in Europe at the end of the last ice age. 

Our own evolutionary and cultural roots appear to lie in Africa, with evidence of culture and 

cosmetics running back over 100,000 years, in addition to evidence for tools and weapons. An 

alternative regional development theory has proposed that humans evolved through a considerable 

amount of interbreeding over the whole African and Asian continental region, however genetic 

evidence is coming to point towards an African origin with only at most very occasional cross 

fertilization with related species. 

 

Fig 25: Human-Neanderthal-Chimp divergences (Green et. al.) 

According to genetic analysis, Neanderthals diverged from homo sapiens ~500,000 years ago. There 

has been no major interbreeding, but possibly some transfer of genes e.g. from human males to 

Neanaderthal females, although candidate human genes conferring natural advantage do have a 

profile consistent with transfer from Neanderthals (Green et. al.). 



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Fig 26: The "Out of Africa" hypothesis may be consistent with a degree of regional 

development involving some sexual interbreeding with Neanderthals and Homo erectus 

(New Scientist). 

Specific genes such a s PDHA1 consist of two families with the last common ancestor 1.8 million 

years ago, and microcephalin variants appearing 40,000 years ago also have differences suggesting 

an original divergence 1 million years ago suggesting 'introgression' from Neanderthals (Jones). An 

even more ancient divergence in the pseudogene RRM2P4 in East Asian people suggests 

interbreeding with Homo Erectus. Some evidence from skeletons is also consistent with this picture. 

However more recent sequencing of the Neanderthal nuclear genome (Callaway) suggests little or no 

interbreeding with Homo sapiens and has cast doubt on the existence of the microcephalin variant in 

Neanderthals, as well as a gene associated with increased fertility in Icelanders also attributed to 

transfer from Neanderthals. 

 

Comprehensive investigation of the Neanderthal genome (Green, R. E. et al. (2010) Science 328, 

710-722., Nature | doi:10.1038/news.2010.225) suggests that there was a period of interbreeding 

between Neanderthals and humans in the Near East around the time of the first migration out of 



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Africa, rather than more recently in Europe, as the putative sequences are shared by non-African 

French, Han and Papuan, but not by the African Yoruba or San. It is estimated that among the 

former, 1-4% of the genome derives from Neanderthal sequences, although there is little evidence for 

these corresponding to the specific genes suggested by Lahn's team. Other transfers could have 

occurred but are not apparent in the research. 

The situation has been complicated by two finds. Firstly we have the 'hobbit' human remains found 

on Flores, named Homo floresiensis. These are variously claimed to be a Separate human species 

possibly related to Homo erectus, or disclaimed as microcephalic human pygmy peoples. More 

recently we have the discovery of remains of Denisovians, a further species branching off from the 

Neanderthals. Genetic analysis of the remains indicates a significant interbreeding specifically with 

Melanesian people of some 6% (Reich D, et. al. 2010 Genetic history of an archaic hominin group 

from Denisova Cave in Siberia Nature doi:10.1038/nature09710). 

Chromosomes contain a variety of markers that can be used to compare diverse populations and infer 

an evolutionary relationship between them. These include the slowly varying protein polymorphisms 

of coding regions which are useful for long-term trends, single nucleotide polymorphisms, and non-

coding region changes (mutation rates about 2.5 x 10
-8

 per base pair per generation and useful for 

reconstructing evolutionary history only over millions of years) insertion and deletion events (about 

8% of polymorphisms, extending from one to millions of nucleotides), particularly those driven by 

transposable elements such as the LINEs and even more frequent SINEs, non-coding micro-satellites 

(mutation rate 10
-5

 - 10
-2

 due to repeat slippage) and mini-satellite regions of repeating DNA 

(mutation rates as high as 2 x 10
-1

 due to meiotic recombination in sperm) that both evolve rapidly 

and are not subject to the strong selection of coding regions which can differentiate changes over the 

much shorter time scales of modern human migration. 

The insertions and deletions of the million or so Alu elements in the human genome are particularly 

useful, as the most active sub-population of about 1000 Alu is actively transcribing and undergoing 

rapid change. A subpopulation of Alu are capable of generating new coding regions (exons), when 

inserted into non-coding introns between spliced sections of a translated mRNA, because one base-

pair change within Alu leads to formation of a new exon reading into the surrounding DNA. This is 

not necessarily deleterious because alternative splicing still allows the original protein to be made as 

well. We have the highest number of introns per gene of any organism, and thus have to have gained 

an advantage from this costly error-prone process. Alus may have given rise, through alternative 

splicing, to new proteins that drove primates' divergence from other mammals. Recent studies have 

shown that the nearly identical genes of humans and chimps produce essentially the same proteins in 

most tissues, except in parts of the brain, where certain human genes are more active and others 

generate significantly different proteins through alternative splicing of gene transcripts. Our 

divergence from other primates may thus be due in part to alternative splicing. 

If we consider the likely effects of the out of Africa hypothesis, we would expect that founding 

African populations not subject to active expansion and migration would have greater genetic 

diversity and that the genetic makeup of other world populations would come from a subset of the 

African diversity, consisting of those subgroups who migrated. 

In the case of mitochondrial mtDNA (mutation rate about 2.5 x 10
-7

) and its hyper-variable D-loop 

(mutations rates as high as 4 x 10
-3

), which is transmitted only down the maternal line (see Tishkoff 

and Verrelli for caveat) and the non-recombining majority of the Y-chromosome which is 

transmitted only down the paternal line, each with no recombination, we would expect greater 

diversity going deeper into the historical tree of divergence, with certain existing groups who have 

http://en.wikipedia.org/wiki/Homo_floresiensis
http://www.nature.com/news/2010/101222/full/4681012a.html


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retained the founding patterns of survival and have not undergone rapid population expansions to 

retain an increasingly diverse source variation. All these features are broadly observed in the genetic 

data to date. 

 
Fig 27: (a) MtDNA tree for African groups showing haplotypes of !Kung, Mbuti and Biaka as well 

as the line coming out of Africa (Chen et. al.). (b) Diagram of world migration and regional 

differentiation of successive mtDNA haplotypes (Gilbert). (c) mtDNA distances between founding 

African groups including Hadza (clicks) Khwe is from (Knight et. al.). Recent mtDNA evidence 

suggests a first wave of migration down the coast of Asia all the way to Australia (Forster et. al.). 

Most studies of non-coding regions of autosomal, X-chromosome, and mitochondrial mtDNA 

genetic variation (which are desirable markers because they are not so subject to selection and thus 

have relatively neutral drift) show higher levels of genetic variation in African populations compared 

to non-African populations, using many types of markers. Although some studies of Y-chromosome 

variation have observed higher heterozygosity levels in non-African populations, the African 

populations have higher levels of pairwise sequence differences, consistent with these populations 

being ancestral. High levels of diversity in African populations alone do not prove that African 

populations are ancestral. A recent bottleneck event and/or colonization and extinction events among 

non-African populations, or a more recent onset of population growth in non-Africans, could also 

cause a decrease in genetic diversity (Tishkoff and Verrelli). In fact the complete inter-fertility of all 

human populations and the relative lack of genetic divergence by comparison with the few remaining 

chimp colonies in the wild (Hrdy 183) does indicate a significant bottleneck. The genetic data is 

consistent with a human emergence from a population of only 10,000 around 100,000 years ago. 

This is also consistent with the delayed maturation, long birth spacings as a result of prolonged 

lactation and high infant mortality seen in gather-hunter populations such as the !Kung. At such low 

growth rates a population of 100 would take 50,000 years to reach 10,000 (Hrdy 183). 

 



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Fig 28: Patterns of male migration. The Genographic Project - a partnership between 

National Geographic and IBM - will collect DNA samples from over 100,000 people 

worldwide to provide a high-resolution genetic map of human migration. 

However studies of protein polymorphisms as well as mtDNA haplotypes, X-chromosome and Y-

chromosome haplotypes, autosomal microsatellites and minisatellites, Alu elements, and autosomal 

haplotypes indicate that the roots of the population trees constructed from these data are composed of 

African populations and/or that Africans have the most divergent lineages, as expected under a 

recent African origin rather than a multi-regional emergence model. Additionally, studies of 

autosomal, X-chromosomal haplotype and mtDNA variation indicate that Africans have the largest 

number of population-specific alleles and that non-African populations harbor a subset of the genetic 

diversity that is present in Africa, as expected if there was a genetic bottleneck when modern humans 

migrated out of Africa. Analysis of genetic variation among ethnically diverse human populations 

indicates that populations cluster by geographic region (i.e., Africa, Europe/Middle East, Asia, 

Oceania, New World) and that African populations are highly divergent. The mtDNA studies 

hypothesize a primal female ancestor - the African Eve - around 150,000 years ago (Chen et. al.) 

while the Y-chromosome Adam is more recent, at around 90,000 years ago (Underhill et. al.) 

consistent with the greater reproductive variance of males than females. Differences between the Y- 

and mtDNA distributions indicate how migration, intermarriage and female exogamy have affected 

the gene pool.  

 

Fig 29: (Right) Genographic project study of mitochondrial origins shows a deep split 

separating Khoisan mitochondrial inheritance from other groups, including those migrating 

out of Africa, suggesting a separation of some 100,000 years possibly caused by long term 

drought in Africa (Behar et al.) 

The genetic patterns of both these and autosomal microsatellites (Zhivotovsky et. al.) are consistent 

with founding African diversity with migratory radiations to form other world populations, with deep 

founding radiations to the forest people such as the Biaka and Mbuti, Khoisan click-language 

speaking !Kung-san bushmen of Botswana and the Sandawe of Tanzania, and possibly the Hadzabe, 



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as well as the forest people such as the Mbuti and Biaka 'pygmies' who have adopted the Bantu 

languages of the farming neighbours with which they now share semi-symbiotic relationships. Along 

with some Ethiopian and Sudanese sub-populations, these groups may represent some of the oldest 

and deeply diversified branches of modern humans.Such recent genetic evidence has laid bare the 

relationships between some of the founding human groups spread across Africa from the 'Cushite' 

horn of Ethiopia to the southern Kalahari. Mitochondrial DNA studies have highlighted the ancient 

origin of the !Kung San and of pygmy peoples of the Congo Basin such as the Mbuti and the Biaka. 

Y-chromosome studies have shown the !Kung share a most ancient haplotype with sub-populations 

from Ethiopia and the Sudan. According to an overall survey of genetic research by Sarah Tishkoff 

of the University of Maryland, the most deeply ancestral known human DNA lineages may be those 

of East Africans, such as the Sandawe, who share many phenotypic features and a click language 

with the !Kung. This suggests southern Khoisan-speaking peoples originated in East Africa. The 

most ancient populations are now believed to also include the Sandawe, Burunge, Gorowaa and 

Datog people of Tanzania. The Burunge and Gorowaa migrated to Tanzania from Ethiopia within the 

last 5,000 years consistent with an ancient founding population in this area. Echoes of the earliest 

language spoken by ancient humans tens of thousands of years ago may have been preserved in the 

distinctive clicking sounds still spoken by some existing African tribes. 

 

Fig 30: (a) Non-recombining Y-chromosome evolutionary tree (Underhill et. al.) (b) 

Geographical distribution showing the ancient haplotype shared by the San and Ethiopian 

and Sudanese sub-populations. (c) Genetic distances between Khoisan and forest peoples 

sharing M112 a Y-chromosome allele common only in these groups showing great genetic 

distance between Hadzabe and San peoples (Knight et. al.) . (d) Autosome satellite analysis 

confirming ancient divergence of San and forest peoples leading to migration from Africa 

(Zhivotovsky et. al.). 



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Highlighting unique features of human genetic evolution, are two key genes whose mutations cause 

microcephaly, consistent with increased brain size, whose rapid spread through the human 

population may coincide with spurts in human culture. Microcephalin (Evans et. al.) appeared 

~37,000 years ago coinciding with the birth of culture and ASPM spread from the Near East around 

5000 years ago (Mekel-Bobrov et. al.). However studies linking these variants have failed to find 

differences in intelligence and results remain highly controversial 

(DOI:10.1126/science.314.5807.1872). Nevertheless, these results are consistent with an overall 

examination of linkage disequilibrium in single nucleotide polymorphisms (Moyzis et. al.) which 

indicate that about 7% of our genes have been subject to selection in the last 50,000 years, a figure 

similar to domestication of maize, including genes for protein metabolism, disease resistance and 

brain function. 

In a counterpoint to these studies, (Hein, Rohde et. al.) estimate that the repeated spreading of family 

trees by sexually recombining mobile populations and differences in reproductive rates leads to an 

estimate of the most recent common ancestor of our global populations existing just 3,500 years ago, 

excepting these most isolated groups. 

 

Fig 31: Human divergence trees calculated by single nucleotide polymorphisms (SNPs) top 

left (Li et. al.) lower right (Jakobsson et. al.) and for haplotypes and copy number variation 

between populations (Li et. al.). 

Further studies of the nuclear genome, using SNPs (single nucleotide polymorphisms), CNVs (copy 

number variation) and haplotype have thrown up reasonably consistent maps of regional divergence 

of principal human groups, demonstrating correspondence to the "Out of Africa" hypothesis and 

consistent with major patterns of migration. 



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The evolutionary tree of human ethnic and migratory peoples bears an interesting relationship with 

the corresponding tree of languages, which has been resolved at least as far as the founding Indo-

European languages (Gray and Atkinson). 

 

 

Fig 31a: In 2009, Tishkoff et. al. reported on a major study of African and African 

American evolution containing the most detailed information on African diversity to date. 



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Fig 32: Evolutionary tree of Indo-European languages suggests a possible radiation 

corresponding to the Kurgans occurred around 4,900 BC (6,900 BP) and that they were 

preceded by Hittite migrations into Anatolia. Time scales in red are BP (Gray and 

Atkinson). Significantly Tocharian appears in Buddhist writings from China's Xinjiang 

province, indicating early far-eastern spread. Inset: hypothetical relationship between Indo-

European and wider language groups such as Afro-Asiatic. 



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Fig 33: Hypothetical core of all human languages from "The Shape and Fabric of Language 

Evolution" further work associated with Gray and Atkinson's research. 

 



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Conclusion: The Tree of Life, the Selfish Gene, and Climax Genetic Diversity 

The picture conveyed by the significance of endosymbiosis, genome fusion and horizontal transfer as 

key evolutionary processes complementing the vertical transmission of the tree of life, makes clear 

that evolution is not just a matter of competitive survival of the fittest gene, individual, or species, 

but of dynamic survival of genes in a surviving ecosystem. Although Dawkins' (1978) notion of the 

"selfish gene" was pivotal in drawing attention to the fact that it was the survival of genes and not 

organisms, or even species, that was the key evolutionary process, attributing the human sentiment of 

selfishness to a gene is somewhat of a self-serving advertising distraction on the part of the author, 

which diminishes the subtlety and complexity of the sometimes apparently paradoxical ways genes 

actually interact to bring about beneficial outcomes in the evolutionary dynamics of the ecosystem. 

 

The Mandala of Evolution (Dion Wright) (detail). 

Although the idea of selection of genes has been pivotal in defining the need to consider 

evolutionarily stable strategies under genetic variation in ways which have been subsequently 

confirmed time and time again in situations such as the sexual genetics of social insects such as bees 

and ants, social selection is by no means ineffectual, or much of sociobiology, including the 

biological basis of morality as an extension of reciprocal altruism, would cease to exist. 

Moreover, from what we have seen, particularly about horizontal gene transfer, and the capacity of 

mobile elements to induce modulated changes in nuclear genomes, it is not the 'selfishness' of a 

genetic element alone that results in survival of both a gene and its hosts, but dynamic feedbacks,, 

and relationships which ultimately contribute to a massive sharing of information in the manner of 

parallel genetic algorithms fundamental to the replicative genetic process, which enable global forms 

of genetic and genome optimization central to the overall viability of life as complex systems. 

Just as a predator, such as a lion survives, not because it is a selfish beast thinking only of eating the 

next gazelle, but because the predator, although it is surviving by killing individual antelopes, is 

maintaining a degree of stability in population dynamics, without which, the herbivores might 

multiply causing a massive famine, leading to cycles of boom and bust and the potential extinction or 

attrition of antelopes, lions and the grasslands. 



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Likewise, although we may think of individual genes, transposable elements, or viruses as 'selfish' 

for reproducing sufficiently to ensure their own survival, and sometimes behaving as noxious 

parasites, the overall effects of this process, in evolution can be to enrich the genetic potential of 

many unrelated organisms along the way, changing forever the face of the ecosystems in which they 

exist, enabling organisms of far greater complexity to evolve and to survive in the closing circle of 

the biosphere. 

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