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Case Study 22. The Cutting Edge of Science: Kissing Cousins Revealed Through Ancient DNA

Case Study 22. The Cutting Edge of Science: Kissing Cousins Revealed Through Ancient DNA

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Case Study 22. The Cutting Edge of Science: Kissing Cousins Revealed Through…

housed. Any technique to extract and copy the original DNA will act on the DNA

from all of these sources. Chimpanzee DNA is approximately 97 % identical to that

of a human, and we can be certain that any hominin DNA is even closer. Therefore,

if DNA is being extracted from a fossil human, it is usually possible to distinguish

that from contaminating bacteria or mold. If the DNA sequence that was extracted

does not look similar to human, it must be contamination. Unfortunately, people in

the museum and the laboratory are a likely source of extraneous DNA, so if the

extracted sequence appears similar to humans it may still be contamination.

The German geneticist Svante Pääbo found ways to overcome contamination and

piece together the genome of human ancestors, including Neanderthals. After numerous

failures, strict protocols have been worked out to maintain a clean laboratory that minimizes the presence of bacteria or the tendency of humans to shed their own cells.

Specimens are only handled with clean gloves, and attempts are made to recover DNA

from the center, not from the surface of the bones and teeth. It is also practice to maintain

a profile of everyone potentially in contact with the lab and specimens, so that modern

human contamination can be identified. Pääbo’s work has led to new understanding

about past relationships among different species of humans and hint at the existence of

populations not currently known from the fossil record.

Neanderthal Genes

Svante Pääbo was the first to obtain a partial sequence of mitochondrial DNA

from an extinct hominin in 1997. He looked for mtDNA first, because it is much

more common than nuclear DNA, with potentially thousands of mitochondria in

a single cell. He chose, appropriately, the type specimen of Neanderthal from the

Feldhofer Quarry in Germany, which was estimated to be 30,000–100,000 years

old. The resulting sequence was sufficiently distant from modern humans to suggest a long separate history for our two species with a divergence time between

550 and 690 Ka. It seemed to negate the long-debated possibility that Neanderthals

were our ancestors.

MtDNA from a second Neanderthal, this time from Mezmaiskaya Cave in the

Caucasus, was sequenced in 2000 and proved similar, but not identical to the first.

Within a decade sequences, including complete mtDNA, were available for at least

15 individuals from Germany, Russia, France, Spain, Croatia, Belgium, and Italy,

and the number continues to grow. Most of them date from near the end of the

Neanderthal era, less than 50,000 years old, but one was nearly 100,000 years old.

With a number of individuals sampled, it became possible to ask different questions.

All of the fossils showed similarities, indicating they came from the same matrilineage distinct from that of modern humans. However, not unexpectedly, there were

differences among the Neanderthals. At last three clusters are apparent that correspond to Western and Southern Europe and the Middle East.

Pääbo then tackled the nuclear DNA, announcing an outline of the Neanderthal

genome in 2006, with increasingly complete sequencing in subsequent years. The

Neanderthal genome proved to be 99.5 % identical as modern humans and equally

Neanderthal Genes


distinct from the Upper Paleolithic peoples that replaced them in Europe. A common

ancestor with us was calculated to have existed between 390,000 and 500,000 years ago.

In order to learn more about the Neanderthals themselves, the researchers began

by looking for genes of known functions in humans. They found, for example, that

at least some Neanderthals had pale skin and red hair. Interestingly, they also carried a modern variant of the gene FOXp2 that some researchers had suggested

corresponded to modern speech.

The issue of Neanderthal language had eluded researchers for a century, residing

more in imagination than in evidence. Many researchers had attempted to find indicators in the skeleton that would tell us whether Neanderthals could talk like we can.

For example, as early as 1971 Philip Lieberman attempted to use the base of a

Neanderthal cranium to reconstruct the pharynx and identify the range of sounds a

Neanderthal could make. Other studies focused on the shape of the hyoid bone or

the size of the canal through which the hypoglossal nerve passes on its way to the

tongue. Although this work generally failed to find convincing functional differences from humans, all of the indicators were controversial and inconclusive.

Where anatomical studies failed, genetics offered a different approach. In 2001

clinicians identified a family with heritable language disorders that could be traced

to the FOXp2 gene. This codes for a membrane protein expressed in neurons. Its

relationship to language is not understood, but it may facilitate certain patterns of

neural communication. Studies by Pääbo’s laboratory reported that the normal

sequence of the gene in modern humans is unique among living primates and

acquired two mutations quite recently, probably within the past 100,000 years. If the

new allele could become fixed in the human population so rapidly, it must have been

under strong positive selection. The date appeared to coincide with the migration of

modern humans out of Africa (see Case Study 16) and fit with models suggesting

some extraordinary advantage enabled them to displace archaic populations in

Europe and Asia. While at first glance the discovery of the modern form of the

FOXp2 gene in Neanderthals suggests they had language, that same find undermines the previous work. Neanderthals and therefore our immediate ancestors likely

acquired it well before 1000,000, and the trait could not explain a competitive


The genetic differences between Neanderthals and modern populations are distinct, but quite small. They have not led us to any greater understanding of why

Neanderthals are extinct and why we are the only species alive today. The possibility

remains that we may yet discover explanations for the skeletal peculiarities of

Neanderthals and other archaic forms of humans. It is likely that such important shifts

in function reflect modifications to controls that up-regulate or down-regulate metabolic pathways in the brain or other tissues rather than changes in structural genes.

Overall the sequences from different Neanderthal individuals that have been

observed show a low degree of genetic variability, consistent with the hypothesis

that the Neanderthal population in glacial Europe was never very large. One sample

from Denisova Cave, Siberia, in the extreme eastern edge of the Neanderthal range

shows evidence of extensive inbreeding, probably because of isolation. Examination

of the mtDNA of 12 individuals at El Sidron in Spain shows that normally females


Case Study 22. The Cutting Edge of Science: Kissing Cousins Revealed Through…

moved between social groups. The three adult males in this cave shared the same

mtDNA, but the three females and six children did not.

Denisovan Genes

In 2008 a fragment of a 40,000-year-old finger bone was found in Denisova Cave in

central Siberia. Such a small fossil had little to tell us anatomically, but it yielded

some interesting DNA. Remarkably, it represents a population of humans as distinct

from Neanderthals as both are from modern humans. Because the only other remains

associated with the finger bone were two teeth, we cannot associate these bones and

this genome with fossils from other localities or from any known type of human.

They are being referred to simply as the Denisovans. Nonetheless, we now know

that, along with Homo floresiensis, there were at least four and most likely more species of humans alive at this time. As modern humans spread across the Old World,

they interbred to some extent with the archaic populations they encountered.

A clue to the origin of the Denisovans came with the sequencing of a much older

individual. Sima de los Huesos in northern Spain is one of the richest sites in the

world for premodern hominins. This population appears to be transitional between

H. heidelbergensis and H. neanderthalensis, more than 300,000 years old. In 2014,

Pääbo’s lab published the mtDNA sequence from one of the bones found there, the

oldest mtDNA recovered and sequenced to date. The mtDNA more closely resembled that from Denisova than it did Neanderthals. The simplest explanation is that a

single population gave rise to both Neanderthals and Denisovans, or at least to the

two corresponding matrilineages. Since none of the later Neanderthal samples

match the Denisovan sample, current evidence suggests the latter genome type

became rare in the west but persisted in Asia.

The Fate of Neanderthals and Other Archaic Humans

The revelations from ancient DNA now make it possible to address the Neanderthal

problem from a new angle. Did the Neanderthal genome disappear entirely? No.

Modern Eurasians share some genes with Neanderthals that are not seen in modern

Africans. Neanderthal genes make up to 1–4 % of the genome of different individuals and must have entered the modern population through limited interbreeding,

although we now know that there were a number of hybridization events.

There were many opportunities for the two populations to mingle. We know that

moderns appeared in Israel 60,000 years ago while Neanderthals were still living

there. A cranium and mandible from Oase Cave in Rumania about 40,000 years ago

show Neanderthal traits on a fundamentally modern morphology. Chunks of

Neanderthal DNA sequence in the genome of the mandible indicate interbreeding

had occurred within a half dozen generations. In western France, changes in the

The Fate of Neanderthals and Other Archaic Humans


archaeological remains associated with Neanderthals suggest cultural changes,

which would have provided opportunities for cross-breeding. In Spain and the

Caucasus the last Neanderthals persisted in refuges where they might have

overlapped in time with moderns. It would be most surprising if the two populations

did not interbreed in many places.

Given these observations, it would also be surprising if modern genes had not

entered the Neanderthal population. Interaction at some level had long been suspected on the basis of cultural innovations among late surviving Neanderthals and

from a few skeletal finds that mixed archaic cranial features with more modern

postcrania. A 2016 study identified modern genes in the Neanderthal bone from

Denisova that were not present in Western European Neanderthals. Comparison

with modern humans shows this genetic material is most closely related to that

found in African populations and that it likely entered the Neanderthal population

before 68,000 years ago. This indicates contact between the two peoples occurred

significantly earlier than the time modern fossils have appeared in Western Asia and

Europe. Possibly there was an earlier migration out of Africa that left no descendants or the main migration did not spread as rapidly as has been assumed.

Denisovan DNA can also be detected among modern populations. It comprises

1–6 % of the genome of people of Australia, New Guinea, and Melanesia and in

lesser amounts in India and East Asia. Again, there is evidence for several separate

interbreeding events. There are many reasons, however, why such a small percentages of archaic DNA survives today. It is possible that selection acted against most

Neanderthal genes. It is also likely that any specific societies on the frontier of

expansion by the moderns went extinct long ago and were replaced by later migrations; thus more highly hybridized populations may have disappeared by chance.

However, the borrowed genes that persisted in the modern genome may have been

kept for a reason.

It is possible now to scan the modern human genome for these borrowed genes

and to use the comparisons between our species to explore the meaning of the differences. While exact functions of specific genes are generally difficult to understand at this time, we have some clues according to the tissues where they are

expressed. We know, for example, Neanderthals had a number of genetic changes

involved in bone development and the skin. In contrast, the modern genome had

undergone more change relating to pigmentation. There are very few Neanderthal

genes on our X chromosome and none on the Y and the modern genome has more

unique genes expressed in the testis. All of this suggests heavy selection against

potential fertility problems caused by hybridization.

A number of genes inherited from Neanderthals have medical implications,

including a greater risk of heart attack because of rapid blood clotting and increased

risk of depression, sun sensitivity, and susceptibility to nicotine. On the other hand,

three genes have been identified that boost our immune defenses. The latter genes

probably were selected for, and the others may be connected with some subtle benefits. One functional gene inherited from the Denisovans helps people adapt to high

altitude. Ironically, while this might have been adaptive in the Altai Mountains of

Siberia where the Denisovan finger bone was found, it is less useful in Southeast

Asia or Pacific Islands where Denisovan genes are more common today.


Case Study 22. The Cutting Edge of Science: Kissing Cousins Revealed Through…

We have learned from the Human Genome Project that a listing of human genes

is not sufficient to understand how our chromosomes determine human structure

and function. Chemical modification of the DNA strands, including the attachment

of methyl groups, can regulate or silence individual genes. These epigenetic

changes are critical for cell differentiation and normal development patterns.

Methylation affects the way DNA degrades over time and thus leaves a signature

in ancient DNA. Geneticists were able to recover some patterns from the

Neanderthal genome. In particular, there was excess methylation near HOX genes

involved in limb development. It was suggested that this might explain Neanderthals’

proportionately shorter arms and legs.

Beyond Ancient DNA

The discovery of Denisovans was a complete surprise, but perhaps it should not

have been. Eurasia has been populated, albeit sparsely, for nearly 2 Ma. Current

models understand that modern humans emerged from Africa within the past hundred thousand and Neanderthals were restricted to Europe and Western Asia. We

should have been asking who occupied the rest of the hemisphere. The fossil record

for Africa, pre-Neanderthal Europe, and Eastern Asia is complex and fossils refuse

to be easily sorted into lineages. Multiple morphological groups appear to coexist in

time within each of these regions. Moreover, most of South Asia and Southeast Asia

as well as West Africa have no fossil record, but the presence of stone tools tells us

these were not uninhabited. Many of these peoples must have interbred with our

ancestors. If we are able to recover more ancient DNA, we will certainly discover

populations that are currently unknown. In the meantime, we can scan our own

DNA for evidence of past interbreeding.

There is evidence within the Denisovan genome of an introgression of genes

from still another unknown people. Some of these genes can be found in modern

East Asian peoples. A similar discovery was made in 2011 by Michael Hammer in

a 13,000-year-old cranium from Iwo Eleru in Nigeria. While considered fully modern by age, this skull still has a primitive overall elongated shape consistent with its

mixed genetic heritage. There is no evidence that hybridization event left its mark

on people today; however, another introgression was later found by Hammer in a

Central African Pygmy population. The Pygmies, along with the Bushmen of South

Africa, are peoples native to African long assumed on the basis of unique language

distinct body statute to have had a long separate history and partial isolation from

their neighbors. Hammer’s team estimates an admixture with an unidentified population as recently as 30,000 years ago.

Odd hominins were found in Red Deer Cave (Maludong) in China in 1989 as

recent as 12,000 years old. They are considered modern humans and not primitive,

but anatomically unique. Homo floresiensis existed until only 13,000 years ago. The

most recently named species, Homo naledi is undated. While its morphology and

small brain size suggest a separate lineage as far back as the earliest Pleistocene,

Additional Reading


the evidence for deliberate disposal of the dead in Rising Star Cave in South Africa

would not be expected until the Late Pleistocene. Anthropologists have been most

reluctant to abandon the nineteenth-century paradigm that describes human evolution as a chain of species ascending to Homo sapiens, but evidence is accumulating

that the story is far more interesting than Haeckel could have imagined. With the

help of new genetic tools we will be able to see the fossil record in a different light

and likely find cousins we never suspected we had.

Questions for Discussion

Q1: How would you expect the presence of multiple species of coexisting hominins

to appear in the fossil and archaeological records? Is that what we observe?

Q2: DNA from archaic hominin lineages is responsible for only small proportions

of the modern genome. What reasons might explain this?

Q3: If multiple hominin species existed at any one time until recently, why is there

only one species now?

Q4: What other kinds of information might we hope to obtain by studying ancient


Additional Reading

Bustamante CD, Henn BM (2010) Shadows of early migrations. Nature 468:1044–1045

Callaway E (2011) Ancient DNA reveals secrets of human history. Nature 476:136–137

Castellano S et al (2014) Patterns of coding variation in the complete exomes of three Neandertals.

Proc Natl Acad Sci U S A 111:6666–6671

Fabre V et al (2009) Genetic evidence of geographical groups among Neanderthals. PLoS One


Gibbons A (2011) African data bolster new view of modern human origins. Science 334:167

Gibbons A (2016a) Neandertal genes linked to modern diseases. Science 351:648–649

Gibbons A (2016b) Five matings for modern Neandertals. Science 351:1250–1251

Hammer MF (2013) Human hybrids. Sci Am 308(5):66–71

Hawks J (2013) Significance of Neandertal and Denisovan genomes in human evolution. Annu

Rev Anthropol 42:433–449

Holden C (1998) No last word on language origins. Science 282:1455–1458

Hsieh PH et al (2016) Model-based analyses of whole-genome data reveal a complex evolutionary

history involving archaic introgression in Central African Pygmies. Genome Res 26:291–300

Krause J et al (2007) The derived FOXP2 variant of modern humans was shared with Neandertals.

Curr Biol 17:1908–1912

Krings M et al (1997) Neandertal DNA sequence and the origin of modern humans. Cell


Kuhlwilm M et al (2016) Ancient gene flow from early modern humans into Eastern Neanderthals.

Nature 530:429–433

Lalueza-Fox C et al (2011) Genetic evidence for patrilocal mating behavior among Neandertal

groups. Proc Natl Acad Sci U S A 108:250–253


Case Study 22. The Cutting Edge of Science: Kissing Cousins Revealed Through…

Meyer M et al (2014) A mitochondrial genome sequence of a hominin from Sima de los Huesos.

Nature 505:403–406

Pääbo S (2014) Neanderthal man: in search of lost genomes. Basic Books, New York

Pennisi E (2014) Ancient DNA holds clues to gene activity in extinct humans. Science


Reich D et al (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia.

Nature 468:1053–1060

Sankararaman S et al (2014) The genomic landscape of Neanderthal ancestry in present-day

humans. Nature 507:354–357

Skogland P, Jakobsson M (2011) Archaic human ancestry in East Asia. Proc Natl Acad Sci U S A


Case Study 23. Is Humanity Sustainable?

Tracking the Source of our Ecological


Abstract Behind all of our attempts to understand human evolution is our curiosity

about ourselves. “Human nature,” the innate drives and desires that define us as a

species, has always been constructed according to our own prejudices and aspirations, but it is rarely possible to investigate such models through science. A common

approach has been to compare ourselves to other animal species for clues of what

lies beneath our cultural veneer. Choosing the appropriate animal model is not less

subjective. In this study, humans are compared to other mammals seeking ecological similarities and differences to clarify which might be appropriate models for us

as we ask the question, “When did humans become unique?”

In 2003, marine ecologists Charles W. Fowler and Larry Hobbs asked the question,

“Is humanity sustainable?,” contemplating the immediate economic and ecological

issues of modern human society. Specifically, Fowler and Hobbs tested the hypothesis that “the human species falls within the normal range of natural variation

observed among species for a variety of ecologically relevant measures.” By comparing humans with a wide range of terrestrial and marine mammals and birds, they

demonstrated that humans are outliers with respect to many ecological parameters,

including CO2 production, energy and biomass consumption, geographical range

size, and population size. Fowler and Hobbs rejected their hypothesis and observed

that by behaving outside the range of normal parameters we disrupt the equilibrium

of our ecosystem in ways that are not sustainable.

One of the core premises of the discipline is that paleoanthropologists view

humans as another species of primate, subject to the same biological principles as

any other species. When in the course of human evolution did such abnormality

arise? Is it a property of the species or only a consequence of a complex agricultural

or industrial society? While Fowler and Hobbs evaluated industrial society, this

chapter compares samples of modern and prehistoric hunter-gatherers with other

medium-sized mammals. It looks at life history and other ecological parameters for

109 living genera of medium-sized placental mammals. Humans are represented by

prehistoric and hunter-gatherer populations.

© Springer International Publishing Switzerland 2016

J.H. Langdon, The Science of Human Evolution,

DOI 10.1007/978-3-319-41585-7_23


Case Study 23. Is Humanity Sustainable? Tracking the Source of our Ecological…


Life History Strategies

Life history strategies concern the allocation of energy to development, maintenance,

and reproduction. Species may choose to mature and reproduce earlier, skimping on

the opportunity to grow larger and store more resources or delay reproduction until

later in life, using the additional years to become bigger, stronger, more competitive,

or more intelligent. It is not surprising, therefore, that body size correlates with a

longer lifespan. Large brains demand a great diversion of resources and shape themselves through early experience; thus, brain size also correlates with longevity.

From body and brain size, it is possible to calculate an expected rate of development.

Having relatively large brains for their body size, the great apes develop slowly

and live a long time compared to other mammals. Humans take this trend to an

extreme degree; however, in terms of longevity and age of maturation, we are most

like the apes (Figs. 1 and 2). In one parameter, however, humans depart from the

depicted values. Our gestation length is only 9 months instead of the extrapolated

14–18 months. While it is argued that the human brain merely continues its

development outside the womb, the period of infancy (defined by nursing) is not

extended. When gestation length and weaning age are added together, humans are

nourished by their mothers for less time than the other great apes and much less than

might be expected (Fig. 3). Instead, humans have a unique period of dependency

called childhood, in which they must continue to be fed and protected by other

members of the social group for a considerable period after weaning. Individuals

who stand in for parents and assist with childcare are called alloparents. Other






Homo sapiens
















Fig. 1 Longevity. Homo sapiens is on the left. Modified from Langdon (2013)


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Case Study 22. The Cutting Edge of Science: Kissing Cousins Revealed Through Ancient DNA

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