Abstract
The fossil record supplies research with evidence of human origins, offering a crucial insight into the study of palaeoanthropology. This discipline has critically developed our understanding of human origins; however, the fossil record is sporadic and incomplete, often precluding a full assessment to the potential morphological scope of past populations.
Over the past couple of decades, advances in molecular genetics have precipitated a new age for evolutionary studies in human origins. Research on DNA variation in diverse human populations have quickly amassed. The accumulation of such knowledge has propelled a need to understand this variation in for future benefits in medical fields and developmental biology. The obvious benefits, at its core, a desire to recognise the origins of our species drives ongoing human origins research. Progress in functional genomics and population genetic modelling have revealed many factors shaping the human genome such as functional modification to DNA histones, conserved 3D topological chromatin domains, structural variation and heterogonous mutation patterns within the genome. Utilising these occurrences and applying evolutionary theories could potentially lead to significant developments in medicine and recognising what makes us human.
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Despite the obvious benefits of genetic research on discerning human evolution, several problematic ethical, legal and social issues could be raised. DNA and protein sequencing itself has many limitations in terms of the accuracy of computational and statistical approaches. There is no clear-cut way to determine our exact origins with a majority of the data gathered still possessing some subjective judgement.
In this essay, I will the evolution of data sequencing developed in the past 30 years. We will then show that the information collected revolutionized our understanding of our own origins in terms of (i) whether we developed in genetic isolation from archaic hominins, (ii) how our ancestors populated the planet, and (iii) how we became adapted to a wide range of environments.
Human Evolution and Molecular Studies
A history of evolutionary research
During the late 1970s, evolutionary research emerged in the form of molecular studies, revealing insights into the functions, abnormities and differences of Homo sapiens, providing an explanation for the causes of disease and variations among different ethnic groups. One aspect that lead to the evolution of anatomically modern human was the discovery and subsequent effective use of exceedingly refined processes. Development in genetics, genomics and proteomics supports the need for appropriate designs and advanced instruments to recognise discrete benefits to modern humans in their survival as well as serving as a reflection for their greater cognitive capabilities.
Using molecular biology to study diversity in unity was first proposed by evolutionary biologist and geneticist, Theodosius Dobzhansky. DNA within all living organisms, prokaryotes and eukaryotes alike, are comprised of four bases. A small singular mutation at a molecular level in DNA replication and translation processes of sequencing can potentially have drastic outcomes to a species over time in the form of speciation. Despite the seemingly extensive interval in time scale, molecular studies bridged that gap between missing information provided by the fossil record.
Instead of simply relying on morphology, a common ancestry between apes and humans and identification of genetic relationships was required. Despite the discovery of DNA structure in the 60s, scientific and technological approaches were not adequately progressive in the 70s. Professor of Biochemistry Allan Wilson pioneered molecular approaches and phylogenies used to identify evolutionary changes. Wilson based his research on the understanding that protein expression in blood proteins, antigens and antibodies accounted for morphological variation. Wilson’s study supported the past ancestry between humans, apes and chimpanzees and promoted the genetic similarity between the species with slight variation occurring due to gene expression and epigenetics.
Following the completion of the Human Genome Project in 2003, the sequencing of chimpanzee, orangutan, gorilla and bonobos genomes commenced. These studies deduced that genetic variation between humans, chimpanzees and bonobos differed by only 1.2% whilst the genetic relationship between humans and gorillas only differed by 1.6%, concluding that chimpanzees and bonobos were the nearest ape ancestors to modern humans.
The late 80s (Brown, W.M., George, M. Jr. & Wilson, A.C. Rapid evolution of animal mitochondrial DNA.Proc. Natl. Acad. Sci. USA76, 1967–1971 (1979). Johnson, M.J., Wallace, D.C., Ferris, S.D., Rattazzi, M.C. & Cavalli-Sforza, L.L. Radiation of human mitochondrial DNA types analyzed by restrictionendonuclease cleavage patterns. J. Mol. Evol.19, 255–271 (1983)) gave rise to another major historical development in the field of human evolution. Mitochondrial DNA presented a means to trace the origins of modern humanity. The mutation rate of Mitochondrial DNA is approximately ten times greater than that of nuclear DNA (Tang, H., Siegmund, D.O., Shen, P., Oefner, P.J. & Feldman, M.W. Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition. Genetics 161, 447–459 (2002)) and much simpler to analyse as it could only be passed down through a person’s maternal lineage without recombination (Kajander, O.A., Karhunen, P.J., Holt, I.J. & Jacobs, H.T. Prominent mitochondrial DNA recombination intermediates in human heart muscle.EMBO Rep. 2,1007–1012 (2001)). Mitochondrial DNA analysis presented a theory that modern humans originated from a common ancestor, ‘Mitochondrial Eve’ some 100,000 to 200,000 years ago in Africa. Wilson and fellow geneticist, Rebecca Cann reinforced this finding in their studies and further purported that modern humans migrated out of Africa to different parts of the world.
Haploid markers from mitochondrial DNA and the Y chromosome have been irrefutable in creating a standard model for human evolution. Earlier research on protein polymorphisms have been reinforced by more refined DNA analysis. Y chromosome have been used extensively to reconstruct human lineages. Unlike mitochondrial DNA, Y chromosomes can only be passed through paternal descendants. Y chromosomes comprise of genes controlling spermatogenesis, resulting in variance and lasting proliferation. This is substantiated from genealogy studies and hunting-gathering societies, though these lack the meticulousness provided by the modern molecular markers of inheritance. (Cummins et al 2001).
A significant benefit arising from linking medical genomics and human evolutionary genomics is the insight provided to major unresolved biological questions concerning how the human species evolved and why we possessed the ability to contract numerous polygenic diseases. This proposed a challenge for evolutionary geneticists as constructing links required an in-depth knowledge into genetically caused diseases and medical geneticists lacked knowledge about evolutionary processes (Nesse and Stearns 2008; Stearns and Koella 2008; Gluckman et al. 2011).
The discovery of efficient DNA sequencing methods accompanied by the development of prompt use of these processes is gradually leading to the sequencing of the complete human genome (Venter et al. 2001). In 2001, a study of comprehensive nucleotide sequencing involving the euchromatin aspect of human genome was conducted by two teams of researchers. Studies such as these modernised biology, particularly the postgenomic era of biology. The application of these findings has had sweeping effects in medical fields and undoubtedly changed past perspectives on evolution. New research on the nature of human genetic polymorphism has emerged.
This evolutionary evidence supports a more recent finding of African origin (i.e., ∼200,000 years ago) for modern humans, shadowed by a diffusion out of Africa with minimal interbreeding with other hominid populations. Despite this theory, countless inconsistencies and further details remain underdetermined. The geographical finds of mtDNA have been questioned (Maddison 1991; Maddison et al. 1992), giving rise to genetic evidence that supports numerous different models (Templeton 1992, 1993). Furthermore, estimates of the amalgamation time of human β-globin genes have also been used to oppose previous African origin for modern humans (Fullerton et al. 1997), but they are consistent with the recent origin model, as the amalgamation time for a neutral autosomal feature would be expected to be roughly four times that of a mitochondrial gene, revealing the perplexing function of selection. Despite this debate, there is a general underlying pattern: Genetics provides a single African origin for modern humans. This result leads to two important questions: what is the relationship between this evidence and the fossil evidence that allegedly supports the multiregional model and what can palaeoanthropology contribute to genetics? The answer to the first question lies in the fact that there has been morphological evidence that does not support a multiregional view. However, this matter seems to still be in dispute within the genetic community and the ostensible lack of communication between the two disciplines provides an answer to the second question; palaeoanthropology provides evidence that concentrates exclusively on the context in which human genetic evolution occurred.
Interpreting Past Evolutionary Events
One central objective of comparative DNA sequencing aims to reconstruct and interpret past evolutionary events, for instance, examining DNA sequences from multiple species to reveal their genetic relationship, which particular alterations caused deviations in species, and which specific locations were under strong selective pressures and environmental constraints, if any. The standard analysis process for determining answers to these questions occurs through comparing sequences, building phylogenetic trees and running computer scans for different types of selection and recombination. From this analysis, researchers can investigate locations of interest, map them back onto the protein’s structure and carry out supplementary testing. Despite this, initial sequence analysis is but a mere prerequisite for successful studies and additional follow-up work is required.
The analysis approach has been exceptionally fruitful, though it fails to consider aspects of biochemistry that ultimately regulates the environment in which sequences evolves. Approaches that combine sequence data with additional information, such as protein structure, produce more sensitive and accurate estimates than methods based solely on sequence data. Considering these grounds, several researchers have developed models for coding-sequence evolution that integrate exchanges between sites mediated by protein structure [3]–[5]. [6].) Similarly, some researchers have incorporated protein structure research in procedures of ancestral reconstruction [7]. With reference to phylogenetic-tree, evidence is amassing that independent positions may not be a good representation [8] for protein-coding and especially for RNA-coding sequences. Thus, prospective techniques of phylogenetic tree reconstruction may also incorporate structural information in some form.
Besides merely just understanding and interpreting events impacting evolution, evolutionary biologists also attempt to identify ideologies relating to molecular evolution. These principles offer insights into different biological systems; for instance, discovering codon usage bias that relates to gene expression level [10], [11].
Examining past evolutionary events is only one aspect of understanding human evolution. Many practical applications require a projection of future evolutionary events to an extent. For instance, H5N1 avian influenza could possibly result in a disastrous epidemic if it developed the capacity to disperse between humans. What remains unknown [28] is the possibility that the influenza would progress to this stage or whether it may become progressively less pathogenic as it develops more efficient transmission between humans. Additionally, infectious diseases could potentially be remedied with interfering particles (e.g., [29]) allowing for the spread of these particles between infected patients, the safety of such treatments depends solely on precisely calculating how such therapeutic particles might react once discharged into the air.
Evolution is a dynamic process and as such predicting which specific mutations will occur in a given lineage is highly improbable. However, accurately hypothesising future events would serve as an immensely useful tool in understanding human evolution. The ability to develop hypothetical frameworks lies with the involvement of realistic, atom-level computational modelling [30]–[33]. With the increase of technological advancements, accurate modela of biological systems have become an exceedingly probable outcome.
On a molecular level, realistic modelling consists of atom-level approximations of protein structures [34] or protein-folding dynamics [35], [36], and computational enzyme design [37]–[39]. The accuracy of these computational models waver. Computational enzyme design requires designing catalytically active enzymes where crystal structures of enzymes are quite similar to technologically prepared ones [39]. However, only a slight amount of these computational designs operate as anticipated. In a recent study, 84 computationally designed enzymes were assessed by such means [39]. Of those, 50 were comprehensible but only two catalyzed the desired reaction.
Currently, atom-level modelling of proteins is not generally exercised in evolutionary studies ([40]) however the computational research may provide the key to understanding future evolutionary patterns. Identifying mutations that have the likelihood of performing specific functions through computational analysis could give rise to predictions about which mutants are likely to appear under exclusive and distinct selection pressures. It is unlikely that computational analysis of atom-level protein modelling will solve broad issues, such as, predicting specific alterations in the DNA sequence of an intrusive species as when it is presented a new environment. However, the reasonable success of computational analysis is much more likely for more distinct issues. For example, identifying mutations that an animal virus utilises to bind to its human receptor counterpart it uses for cell entry in its host species would have high chance of being computationally graphed. Irrespective of whether atom-level modelling or statistical approaches are utilised, computational postulations have a degree of inaccuracy.
Emerging Issues
Early complications
The arrangement of human populations into races and significant human groups presented itself as one of the first emerging issues. Previously, some classic anthropologists had classed races by implementing unrealistic parameters on the constant variations of morphological features particularly skin colour. For instance, according to this technique, black inhabitants in sub-Saharan Africa and South Asia would be categorised within the same race. This theoretical belief was overruled following the discovery of protein markers and DNA sequencing which demonstrated a substantial disparity between these two groups of geographically distant populations. (Nei M, Roychoudhury AK. Evolutionary relationships of human populations on a global scale. Mol Biol Evol. 1993; 10: 927-943.). Additionally, contemporary human society is strongly against any racial classification, even to a trivial extent. The black skin colour would have been attributable to a genetic adaptation to tropical climates and other environmental influences (Jablonski NG. Living color: The biological and social meaning of skin color. University of California Press, 1ST edition. 2012.). This link between morphological characteristics and environmental facts could result in an amalgamation of evolutionary populations living in analogous climates, potentially obscuring phylogenetic trees.
In addition to the aforementioned classification of race, genetic anthropologists in the 1980s classified race according to three major branches; Caucasoid, Mongoloid and Negroid. Caucasoid referred to the ‘Caucasia’ geographic expanse in the South East region of Europe. However, this term is not representative of present society where ‘white’ societies suggest a predominantly European population. Stemming from the word ‘Negro’, ‘Negroid’ was previously applied to all ‘black’ populations but was now limited to ‘black’ Africans as their genetic profile was significantly different from other ‘black’ populations. ‘Mongoloid’ denoted to populations hailing from Mongolia. The term was nominated for East Asian populations.
Currently, it is implausible, inaccurate and inappropriate to comply with these terms as they do not incorporate all human populations, particularly those living in remote geographical areas and do not account for the stability of genetic variation between populations on different continents. Thus, it is inconceivable to catalogue human populations in three sets as they signify a global multifaceted network of genetic interactions, reflecting their unique origin, migration and isolation tendencies since the rise of modern man (Chaabani H. GM polymorphism and the evolutionary history of modern humans. Ann Genet. 2002; 45: 197-206.. Chaabani H. Recent out of Yemen: new version of the theory of unique and recent origin of modern man. Int J Mod Anthrop. 2014; 7: 13-41). Considering these scientific deliberations, a more precise and adequate model for classifying human populations was required.
Present matters
Currently, research on recent human evolution primarily centres around the place and date of modern human emergence. Much of the confusion, vagueness and debate lies with the definition and origins of anatomically modern man. Traditionally, paleoanthropologists examined universal anatomical characteristics, particularly the discrete cranial traits (DCT) for shaping and describing modern humans and thus distinguishing Homo erectus remnants and modern human remnants apart. Recent studies indicate that the post-cranial topography of Homo erectus, though more robust, falls within the range of Homo sapiens sapiens; DCT however leads to dubious conclusions which result in disagreement with corresponding ancient DNA data (Adcock GJ, Dennis ES, Easteal S, Huttley GA, Jermiin LS, Peacock WJ, et al. Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins. Proc Natl Acad Sci U S A. 2001; 98: 537-542. Relethford JH. Ancient DNA and the origin of modern humans. Proc Natl Acad Sci U S A. 2001; 98: 390-391.) Thus anatomical principles are palpably of inadequate use in the classification and reconstruction of true modern human remains. As a result, there was need for a more appropriate and adequate standard that required a closely fitted definition and identification for modern humans, specifically accounting for the complexity of brain functions including superior cognitive capabilities (Chaabani H. Recent out of Yemen: new version of the theory of unique and recent origin of modern man. Int J Mod Anthrop. 2014; 7: 13-41).
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