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Essay on Human Evolutionary Genetics
Essay Contents:
- Essay on the Introduction to Human Evolutionary Genetics
- Essay on the Sources of Human Evolutionary Genetics
- Essay on the Complications Faced by Human Evolutionary Genetics
- Essay on Understanding Phenotypes and Disease
Essay # 1. Introduction to Human Evolutionary Genetics:
We are all curious about our origins. This common interest manifests itself in different ways, at both the personal level and at the level of society. This curiosity is not new- some of the oldest historical texts from different societies detail origin myths, as do oral histories passed down over generations. Distinguishing fact from fiction in these stories is difficult and differences of opinion can be a source of political conflict.
Any scientific investigation of the past should start with a consideration of the different types of evidence available, since this provides the basis for testing hypotheses and refining models. While there was only one past, it is revealed to us in many ways.
I. The historical record comprises written texts, the oldest of which are from Mesopotamia and date from as far back as 4000 years ago. Writing itself goes back another 1000 years but appears to have been mostly associated with accounting practices. These early texts were written in cuneiform symbols indented into clay tablets using reeds, and it is only later that papyrus and modern alphabets were invented.
It must be remembered that very few ancient languages were written down, and some of those that were recorded are presently indecipherable. There are also oral histories, and folklore handed down through the centuries. It is difficult to judge the factual content of these intergenerational ‘Chinese whispers’, let alone their time-depth.
The boundaries between oral and written histories are often blurred; some histories that were initially oral have achieved special prominence through being written down in antiquity.
II. Spoken languages retain evidence of their origins over thousands of years. The discipline of historical linguistics seeks to trace the ancestry of all ∼6500 languages currently spoken in the world. Many of these languages can be traced to a number of ancestral languages known as proto-languages.
For example, English, French, German, Russian and Sanskrit all belong to the Indo-European language family and share a common ancestral language known as proto-Indo- European. Although the origins of spoken languages can be traced back further than historical records, a common ancestry for all human languages cannot be identified, and some historical linguists have suggested that languages do not retain evidence of their origins over more than ∼6000 years.
III. The archaeological record consists of physical objects that have been shaped by human contact. These include not only tools, ornaments, and pottery, but also soils, waste deposits, houses and landscapes. The earliest recognizable stone tools date from about 2.5 million years ago. Humans are not the only animals to make tools, but tools produced by earlier human ancestors or nonhuman species are difficult to distinguish from naturally occurring objects.
IV. The paleontological record comprises the fossilized remains of living organisms or their traces, like preserved footprints. The earliest microfossils are suggested to date from 3500 MYA. These would be roughly three-quarters of the age of the planet itself, suggesting that life on Earth started almost as soon as conditions were suitable.
Paleoanthropologists focus on the remains of humans and their ancestors. The earliest fossils that appear to be more closely related to humans than to any other living species are dated from 5-7 MYA.
V. Paleoclimatology seeks information on past climates and aims to reconstruct paleoenvironments. Data come from physical remains, both organic and geological in origin. An example of geological evidence comes from the cores of ice taken from ice shelves, which at different depths exhibit varying isotope ratios of certain elements that can be related to temperature changes over the past million years.
Similarly, cores of lake sediments reveal the predominance of pollen from different plants at different times, which provide evidence about the biotic environment over shorter time-scales. Geological records in rocks provide information on older climates as far back as 3800 MYA. We will see that climate has varied greatly over the last few million years, and has had a major influence on human populations.
V. In principle, the evolutionary genetic record of life on Earth contained in the genomes of living species could provide evidence on human evolutionary processes and relationships all the way back to the last universal common ancestor of all extant species.
To find out about this lucky individual we have to compare and contrast the most distantly related branches on the tree of life. Comparisons among much more closely related individuals, perhaps from the same species, should provide evidence on much more recent human evolutionary processes.
Essay # 2. Sources of Human Evolutionary Genetics:
Genetic evidence comes from two main sources:
i. The genomes of living individuals that must have been passed down from ancestors;
ii. Ancient DNA from well-preserved organic remains, which may or may not have been, passed down to living descendants.
All Records are Selective:
It is important to bear in mind that none of these records represents an unbiased picture of the past. We do not have a time machine and therefore must rely upon evidence that has survived to the present. This process of survival is selective. In the archaeological record we find many stone tools but few wooden ones-arrowheads but not shafts.
In the paleontological record we find plenty of skeletal fossils, but soft tissues leave traces only very rarely. In the historical record we may not encounter those texts that displeased contemporaneous or subsequent heads of state, either because they were destroyed, or not written in the first place.
Similarly, in the genetic record, survival is quite literally selective. Natural selection and other processes have shaped, and continue to shape, our genome in different ways. Even ancient DNA evidence, although not influenced by subsequent natural selection, is biased- for technical reasons it can tell us far more about the genetic diversity of our female ancestors than it can about our male forebears. Since the survival of ancient DNA is influenced by physical and chemical conditions, samples will be more plentiful from some regions of the world than from others.
The Palimpsest Metaphor:
In times past, when writing materials were in short supply a scribe would often reuse a manuscript rather than obtain a new parchment. The manuscript would be turned through 90°, and overwritten. These overwritten manuscripts bearing the imprint of more than one text are known as palimpsests.
The genetic record is a complex palimpsest. Variation among, modern individuals is shaped by cumulative past processes. Extracting information on any one past period or event requires careful interpretation to isolate it from previous and subsequent processes. In addition, natural selection is ever present, potentially influencing any variation that affects phenotypic fitness.
As a result, researchers have sought loci within our genomes that are selectively neutral, in the hope that these might provide a more representative record of the past. Studies of ancient DNA only partly circumvent the palimpsest problem, since organic remains themselves have complex histories, and there are formidable technical difficulties in extracting information.
Different strata of the past are accessible through the analysis of genetic diversity.
Moving from the most ancient to the most recent, we encounter:
I. Our phylogenetic relationship to other species;
II. The origin of our species;
III. Pre-historical migrations;
IV. Historical migrations;
V. Genealogical studies;
VI. Paternity testing;
VII. Individual identification.
Comparisons between Different Records of the Past:
No single record of the past is more important than any other, but each records different features of the past. Therefore the record chosen for investigation in a given study is largely determined by the specific questions under consideration.
If we want to address a cultural question, such as ‘What was life like for humans 10 000 years ago?’, archaeology will give us more insight than will linguistics or genetics. In contrast, if we want to answer a biological question, such as ‘Which nonhuman species is most closely related to us?’, archaeology and linguistics will be of little use.
To compile a fuller picture of the past we often seek to combine information from multiple records into a single ‘synthesis’. This requires that we consider a little more closely the similarities and unique characteristics of different records. For example, while we can be sure that the speakers of modern languages have ancestors, we cannot be sure that the makers of a certain style of pottery left any descendants.
When similar information is being sought from several records of the past, it becomes particularly critical to appreciate the differences between them. For example, if we are interested in migrations we must appreciate that artifacts can move through trade, without the concomitant movement of genes. Similarly, not all gene flow need be accompanied by the movement of languages.
These different records are independent reflections of a single past – but they need not all tell us the same thing. Rather, conflicting signals allow us to reconstruct subtle and nuanced views of a past that must have been just as complex as the present. Nevertheless, readers should maintain a healthy skepticism of interdisciplinary syntheses.
Each individual discipline that interprets a record of the past contains competing hypotheses and many issues upon which there is no consensus. This could enable researchers in one field to ‘cherry-pick’ hypotheses from other disciplines that agree best with their own thinking.
Stringing together an initial contentious hypothesis from field A with equally contentious theories from fields B and C, may make for a more complete and interesting narrative, but does not make the original hypothesis any less contentious.
We recognize the importance of these ongoing debates and try to give readers a flavour of the diversity of opinions by incorporating ‘Opinion Boxes’ written by active researchers who have new, interesting or challenging theories, or who are particularly well placed to comment on an area of controversy.
Essay # 3. Complications Faced by Human Evolutionary Genetics:
i. Ethical Responsibility:
This places an ethical responsibility upon those who seek to explore the past to do all they can to ensure that their work is not misused. This is not just a theoretical possibility- history is rife with the misuse of anthropological research to justify regimes that have cost the lives and livelihoods of many innocent people.
So much damage has been caused that some have even questioned whether work to reconstruct our evolutionary past should be undertaken at all. We believe that the potential intellectual and medical benefits of this work outweigh the potential dangers, but only when researchers take responsibility for the accurate popularization and public dissemination of this research, including active opposition to misinterpretation.
Having said that, we must acknowledge that much of this work is published by an unrepresentative subset of our species, namely men in developed countries and that this cultural framework undoubtedly has an influence on interpretation.
As scientists, we should recognize that our work rightly depends upon the approval of wider society; indeed, most funding for human evolutionary studies around the world comes from the public purse. Irrespective of the source of funding, public concerns about the wider implications of our work must be addressed.
Although the most notorious historical misuse of anthropology has been the justification of genocide, public anxiety is currently more focused on issues of ownership, commercialization and privacy. When work is being conducted in the public interest, the perception of misuse can be as important as the reality of misuse.
Steps must be actively taken to ensure both that such misuse does not occur, and that misuse is seen not to occur. It is for these reasons that research projects on human subjects, whether they are medical patients or volunteers contributing a few cheek cells, should be scrutinized and approved by ethical committees prior to their initiation.
ii. Fallacy of the Contemporary Ancestor:
We want to find out about our ancestors and to collate information from every source that we can. However, this insatiable thirst for knowledge can lead us to adopt unreliable sources of information. Unfortunately, we cannot dig up a living, breathing ancestor, or use a time machine to study the past directly.
All living organisms are ‘cousins’ that share a common ancestor sometime in the past. Each pair of contemporary organisms is equally derived in terms of time from this common ancestor, yet the concept of a living fossil or a ‘contemporary ancestor’ is pervasive.
This concept insinuates itself implicitly or explicitly into all levels of the tree of life, as illustrated by misguided statements such as these:
I. The first living organisms were like bacteria.
II. The coelacanth is a ‘living fossil’ of the first four- limbed vertebrate.
III. Humans evolved from chimpanzees.
IV. Modern hunter-gatherers resemble humans before the advent of agriculture.
V. The Basques are a Paleolithic relict population.
At the inter-specific level, this concept derives in part from an anthropocentric view of nature- that human have transcended the rest of the natural world, and that we have progressed beyond the bounds that limit other species. Potential dangers lie in the assumption that in the absence of evidence about the common ancestor of humans and any other species, the non-human species is a closer approximation to this common ancestor.
A misconception of inevitable progress also dominates popular thinking about diversity within humans. Ancient populations are often assumed to be less like modern Western societies and more like less-developed indigenous peoples. Yet it is well accepted within anthropology that ethnography can be a poor guide to the past.
If there is any basis to this common misconception, it must lie in some measurement of human evolutionary derivation other than time.
In principle human evolutionary derivation may be measured in terms of:
I. Time;
II. Phenotypic change;
III. Ecological change;
IV. Genetic change.
It could be argued that many of our ‘cousins’, whether human or not, have maintained modes of life more similar to those of our common ancestor, and that this has led them to undergo less phenotypic change. However, it must be remembered that all forms of life are adapted to their present ecological niches. Selection is ongoing, and as a consequence important adaptive changes have taken place in all organisms, which may reveal themselves at the morphological or physiological level.
Mutational change is blind to ecological circumstance; neutral mutations that do not affect the fitness of the individual occur in all organisms. If the annual mutation rate is equal between two species, each will be equally derived from the common ancestor with respect to neutral mutations.
However, annual mutation rates can be shown to have varied between lineages, such that humans have accumulated fewer neutral mutations since their common ancestor with Old World Monkeys, and Rodents. In these cases, it is the humans who are less derived.
iii. Interpretation, Interpretation, Interpretation:
In many fields, as time passes, opinion upon how data should be interpreted changes. Indeed, there are often differences in opinion about data interpretation at any one time. This is particularly true of genetic data on human diversity. Particular methods of analysis, with different underlying paradigms, can be adopted by opposing ‘camps’ within a particular field, and reconciliation becomes difficult. Some methods for analyzing diversity data seem particularly open to different interpretations.
Essay # 4. Understanding Phenotypes and Disease:
What use is an evolutionary perspective on human genetic variation beyond the reconstruction of the past for its own sake?
i. Importance of a Shared Evolutionary History:
The great twentieth century evolutionary biologist Theodosius Dobzhansky wrote that:
“Nothing in biology makes sense except in the light of evolution.”
All the size, shapes, chemistries and genes of organisms alive today derive from ancestors that can be traced back over billions of years. All of these features have been shaped by the environmental challenges faced by these organisms and their ancestors. If it were not the case that humans share a common ancestor with every other species on the planet, there would be no value in performing any form of comparative analyses.
There would be nothing that the Escherichia coli bacterium, brewer’s yeast, fruit fly, nematode worm, zebra fish, mouse or chimpanzee could tell us about ourselves. It is our shared evolutionary heritage with these species that makes them such powerful ‘model organisms’.
To take just one example, sequencing the mouse genome allows us to identify more genes in the human genome than does sequencing the human genome alone. By identifying segments of DNA that are more similar between the two species than could be expected by chance, we can identify regions whose evolution has been constrained by the need to perform a specific function.
In other words, we can identify a gene not because it looks like a gene, nor because an organism treats it like a gene, but because it evolves like a gene. This approach, sometimes called ‘phylogenetic foot printing’ or ‘shadowing’ can be extended by examining genomes from a range of primates.
ii. Understanding the Present:
If we were to take a perspective to the biology of modern humans that neglects human evolutionary history, what might we predict about the genetic diversity of our species, the significance of our phenotypic differences and the prevalence of disease-causing mutations?
First, we would be struck by the huge numbers of humans, especially when compared to other animals of similar body size. We might reasonably think that this should be mirrored by a correspondingly greater genetic diversity. Second, we might be struck by the clustered distribution of phenotypic diversity among modern human groups and might expect this to be matched by a similar structuring of genetic diversity. Third, we might expect that disease-causing mutations would be specific to different continental groups, in a similar manner to some of their easily observable ‘normal’ phenotypes.
To understand why this is so, we must comprehend that the past is not simply something that happened, and is packaged up and studied for its own sake, but is more properly considered as the source of the present.
The present should only be seen as another small step in shaping this past. If we are to improve our present circumstances, we must take account of how that present has come to be. An evolutionary genetics perspective does not just answer the question ‘What happened in the past?’ but also the question ‘Why is the present like it is?’
Once we understand that the obvious differences between peoples’ appearances can be unreliable indicators of biological origins, we start to appreciate the other factors that have shaped and continue to shape human biology. The interaction of humans and their environments comes to the fore, as does an understanding of human adaptability in the face of huge variability in inhabited environments.
iii. Improving the Future:
An evolutionary genetics perspective on human genetic variation also allows us to make predictions about the future, both of biological research and of our species. We are able to pose many more questions within biology than we are presently able to answer. An evolutionary perspective tells us how we might go about answering these questions, and about what kinds of answers we might expect.
Phenotypic traits of humans, be the skin colour, height or disorders such as diabetes, are controlled by a combination of inherited and environmental factors, and stochastic developmental and molecular processes. The easiest traits to dissect genetically are those determined in large part by single genes-so-called Mendelian traits.
However, many of the phenotypic traits of most interest to both anthropologists and physicians are not so simple. These complex traits are governed by interactions between chance events, multiple genes and the environment, and disentangling these interactions will help to relieve the considerable burden of complex diseases on individuals and economies.
Genes involved in complex traits can be identified in one of two ways. In a physiological or biochemical approach, we identify the gene product as a causal factor, based on an understanding of the physiological and molecular basis of the trait. In the alternative positional approach, we locate the position of the gene within the genome by identifying a chromosomal segment that is consistently co-inherited with the trait.
Knowledge of our past allows us to predict something about the numbers and frequencies of gene variants expected to be involved in a given trait and to choose the best strategy of finding them-what populations to choose, and which segments of the genome to concentrate on. Not only that, but an evolutionary genetics perspective helps to understand and predict which individuals will respond best to each therapy and how best to focus limited screening resources.