Human Evolution and Genetics

20 Feb 2012

Introduction

Within the last seven million years, the human lineage originated from ancestral primates. Our ancestors evolved a unique pattern of innovations, such as upright walking, complex tool manufacture, a hunting and gathering lifestyle, and language. Each of these human characteristics built upon the anatomical and genetic legacy of primate ancestors, following a distinctive path to the present-day.

Genetic information about living people and other primates has added substantial detail to our knowledge of human evolution. The sequencing of the human genome Venter:2001, Lander:2001, along with genome sequencing projects in other primates made it possible to examine the genetic changes that underlie human anatomy and behavior. Today, anthropologists apply a combination of genetic information and evidence from fossils and artifacts to test hypotheses about our evolution.

Humans among the primates

Comparisons of the genomes of living primates suggest that they last shared a common ancestor sometime during the Late Cretaceous period, around 80 million years ago (Ma) Tavare:2002, and early primates are represented by fossil discoveries dating to the Paleocene and Eocene epochs Hartwig:2002. Early primates gave humans an anatomical legacy: arboreal adaptations such as grasping hands, fingernails, and binocular vision. Today, nearly all primates retain a generalized, broad diet made up of a balance of fruits, leaves, gums, and insects or meat, with some primate lineages specializing to some extent on one or another of these sources. Most living primates form long-term social bonds, and many live in groups with complex patterns of social interactions. These anatomical and social legacies form the foundation of many human adaptations.

Monkeys, apes and humans are grouped together as anthropoid primates. Early anthropoids appeared during the Late Eocene, ca. 40 Ma Kay:1997. Today’s anthropoids share a number of features attributable to their common ancestry. These primates tend to invest more resources and time into their offspring, with longer developmental times and more extensive brain growth. Genetic comparisons of living humans and monkeys show that genes expressed in brain development have evolved rapidly during the last 30 Ma, reflecting the recent evolution of cognitive functions in anthropoids Dorus:2004. Nearly all anthropoids give birth to one offspring at a time, and females have a single-chambered uterus to enable longer gestations and larger fetal size. These changes allowed more sophisticated social behaviors, with more stable social groups that share information more effectively.

Living and fossil apes and humans are called hominoids. Living apes, including chimpanzees, gorillas, orangutans and gibbons, are adapted to a flexible pattern of movement in the trees. Their shoulders and long arms enable climbing vertically and suspending beneath branches. While living apes can all walk or run bipedally, only humans have anatomical specializations to support efficient bipedal walking. Apes diverged from the cercopithecoids (Old World monkeys) around 30 Ma, but initially remained similar to monkeys in habit, body plan, and ecological breadth. Proconsul was an important fossil hominoid lineage in Africa from 24 to 15 Ma, with several species covering a range of from the size of monkeys like macaques up to chimpanzee-sized or larger Walker:1989. Sivapithecus, an early member of the orangutan lineage, shows evidence of a similar pattern of quadrupedal locomotion, indicating that the living great apes may have evolved their body plans and locomotor styles convergently with each other. Suspending below branches, long arms, long fingers, and small thumbs evolved repeatedly in the apes and also in New World monkeys. Likewise, at least one Miocene ape adopted effective upright posture on the ground Rook:1999. The apes represent several independent experiments in the development of larger body size, shifts in diet, and styles of locomotion.

Toward the end of the Miocene, ape diversity declined. South Asian and European apes ultimately became extinct, coincident with climate changes that increased seasonal temperature and rainfall variations and reduced the area of forests Patnaik:2005. These climatic shifts favored the rise of the cercopithecoid (Old World) monkeys, which increased their geographic range during the Late Miocene and Pliocene to include Europe and East Asia. By the Early Pliocene (ca. 5 Ma) apes were largely restricted to their current geographic range, tropical Africa and Southeast Asia, with the addition of south China. By this time, the African apes had differentiated into chimpanzee, gorilla, and hominin lineages. In Asia, the gibbons and ancestors of the orangutans remained, along with a giant terrestrial ape, Gigantopithecus, which survived into the last few hundred thousand years Ciochon:1996.

Genetic comparisons of living hominoids show that the common ancestors of chimpanzees, bonobos and humans lived between 4 Ma and 7 Ma Wildman:2003, Kumar:2005. The African apes all diverged from each other within the last 10 Ma, and orangutans sometime earlier than 12 Ma Glazko:Nei:2003. This sets the timeframe of hominin origins as the Late Miocene. Unfortunately, the chimpanzee and gorilla lineages have no clear fossil representatives during this period of time, or indeed throughout most of their existence. The diversity within living chimpanzees, gorillas, and orangutans attests that the ancient populations that gave rise to these primates were separated into subspecies with great geographic and genetic diversity. Yet no clear fossil ancestor of chimpanzees, bonobos, or gorillas is yet known.

The first hominins

Humans and our fossil relatives, closer to us than to chimpanzees and bonobos, are called hominins. Sometime before 4.2 million years ago, hominins developed the unique form of upright, bipedal walking that humans share today. Paleontologists have recovered an array of fossil apes from before this time, some of which may be ancestors or relatives of hominins. Such apes either do not possess clear evidence of bipedality, or may not have shared the same pattern of bipedality as later hominins. However, they have smaller canine teeth than other living or fossil apes, and some skeletal signs of more vertical posture or time spent on the ground.

Three important samples of fossil hominoids may represent either the earliest members of the hominin lineage or their close fossil relatives: 7 million-year-old Sahelanthropus tchadensis in Chad Brunet:2001, 6 million-year-old Orrorin tugenensis in Kenya Senut:2001, and 5.5 Ma-old Ardipithecus kadabba in Ethiopia Haile-Selassie:2004. Each is a fragmentary sample that presents some evidence of bipedal locomotion or upright posture, including the proximal femur of Orrorin, the cranial base of Sahelanthropus, and the foot of Ardipithecus. The dental remains of these genera are very similar, and except for their smaller canines, within the range of other Late Miocene apes Haile-Selassie:2004. All these fossils are important because of their dates around this key time of hominin origins. But anthropologists do not agree which of these, if any, represents our lineage.

A much more complete fossil sample, including a partial skeleton, has been discovered of the 4.3-million-year old species, Ardipithecus ramidus White:paleobiology:2009. Ardipithecus had a skeleton well-adapted to climbing and quadrupedal walking in trees. With a grasping foot, long curving toes, long arms and fingers, and a small apelike thumb, it seems unlikely to be a close relative of later hominins. But it lacks anatomical specializations of the pelvis and limbs found in chimpanzees, bonobos and gorillas. This suggests that the common ancestors of humans, bonobos and chimpanzees were very different from chimpanzees in locomotion and body form.

The australopithecines

Starting after 4.2 million years ago, early hominin fossils form a rich record that documents the diversification of these bipedal apes. The famous “Lucy” skeleton from Hadar, Ethiopia, represents Australopithecus afarensis. Hundreds of other fossil fragments from Ethiopia, Kenya, and Tanzania also belong to this species, which lived between 3.8 and 2.9 Ma. Later, an additional large sample of hominins from South Africa between 3.0 and 2.3 Ma represents Australopithecus africanus. This was the first of the early hominid species to be discovered, by South African anatomist Raymond Dart in 1924 Dart:Taung:1925. The name, Australopithecus, means “southern ape”, and these early hominins are often called “australopithecines.” The first known australopithecine is Australopithecus anamensis, known from the Turkana Basin of Kenya and nearby Ethiopia White:anamensis:2006.

These samples confirm the importance of bipedal locomotion to the early hominid lineage. The shape of the pelvis, knees and feet had evolved to a humanlike form that precluded efficient quadrupedal locomotion. Footprint trails at 3.5 Ma Laetoli, Tanzania also demonstrate their humanlike bipedality. Several pieces of evidence suggest that these australopithecines retained an adaptation to climbing; in particular, this may explain their short legs, small body sizes, powerful arm bones, and curved hand bones Stern:1983. Their small size especially stands out as a contrast to recent humans, as they averaged only around 1.2 m in height and 35-50 kg in mass McHenry:2000.

Aside from bipedality, the other major anatomical pattern of early hominids involved the teeth. Australopithecines had large molar and premolar teeth compared to living and fossil apes and humans. These teeth were low-crowned and had thick enamel, apparently adapted to a diet of grinding hard foods such as seeds. Isotopic evidence suggests that their diet was varied, with the main difference from other primates being a high consumption of plants with a C4 photosynthetic cycle, which include grasses and some sedges Sponheimer:2005. As primates cannot digest grass, it has been suggested that this component may represent the consumption of grass seeds, termites, and other grass-consuming animals Peters:Vogel:2005. Contrasting with their large molar teeth, early hominids had small canine teeth, which may hint at a shift in social interactions.

A later group of australopithecines greatly emphasized the adaptation to large grinding teeth. These “robust” australopithecines had molar and premolar teeth with as much as four times the area of present-day humans, together with immense jawbones and jaw muscles. Their diet was also varied. presumably included a higher fraction of hard brittle foods, which may have been increasingly important during the drier climates of the Late Pliocene deMenocal:1995. These were the last of the australopithecines to become extinct, shortly after 1.5 Ma.

The first humans

Alongside the robust australopithecines lived the earliest members of our own genus, Homo. Early Homo can be distinguished from contemporary australopithecines by its smaller molar teeth (although still larger than living people) and larger brain size. The transition to large brains and smaller teeth was accompanied by an increased dietary reliance on meat. Because of its high caloric and protein content, meat is more easily digestible and can fuel more substantial brain growth Milton:2003.

The archaeological record provides further evidence for a dietary shift, with the earliest-known stone tools occurring in Ethiopia at 2.6 Ma Semaw:2003. These earliest flaked stone tools were used to cut flesh off animal bones and to break into bones for marrow Dominguez-Rodrigo:2005. Many primates are able to manipulate objects as tools, and wild chimpanzees have traditions involving the use of stones to crack nuts and shaping simple wooden spears or probing sticks. Earlier hominins probably also shared these cultural abilities, but they left no archaeological trace. Meat-eating created a new niche for these hominins that also gave us a new way of tracing their behavior.

Before 2 Ma, both fossil and archaeological evidence of Homo remain rare. The first sample of hominin skeletal remains to show clear evidence of the ability to make and use tools is from Malapa, South Africa at 2 Ma Pickering:Robyn:Malapa:2011. Two skeletons assigned to Australopithecus sediba show a mosaic of australopithecine-like and humanlike characteristics. Small body size, long forelimbs and a small brain place A. sediba alongside other earlier hominins. But its molar teeth were relatively smaller, its pelvis had a more humanlike shape, and its hands were well adapted for tool manufacture and use, unlike any earlier hominin Kivell:sediba:2011. A few fragmentary specimens from around this time and slightly earlier also present humanlike features, but it is not clear which of these may represent ancestors of later humans.

After 1.9 Ma, a species called Homo habilis lived in East Africa and South Africa. With endocranial volumes in the range of 500 to 750 ml, this species represents a clear and substantial increase over other early hominins. The species apparently shared the manipulatory abilities of A. sediba, and details of the the internal surface of the skull suggest similarities with humans Holloway:1996.

A second species of early Homo, called Homo erectus had larger bodies and especially taller stature. an average of 1.4-1.8 m compared to earlier hominids at 1.0-1.4 m McHenry:2000. With its longer legs and larger brain size, Homo erectus was adapted to the use of larger home ranges and more patchily distributed, high-energy food resources Anton:2002. The differences in size between males and females in this species were in the range of recent humans, possibly reflecting more humanlike social interactions than in earlier hominids with greater cooperation, including food sharing.

The use of more open territory and larger home ranges may have enabled Homo erectus to colonize Eurasia for the first time Anton:2002. A series of fossils and archaeological remains from Dmanisi, Republic of Georgia, dates to 1.8 Ma. Hominids also reached Java around this time, and in fact the first fossil specimens of Homo erectus to be found were discovered on Java by Dutch colonial physician and scientist Eugene Dubois, in 1891. These hominins reached both China and Europe by 1.2 Ma.

Pleistocene human evolution

Early in their existence, the populations of Homo erectus in Africa and East Asia started to become different from each other. The form of the cranium, thickness and shape of the browridge, size of neck muscle attachments, and other details differed substantially between regions, though they overlapped. Some researchers view these features as evidence that Homo was divided into different species in different parts of the world. Others consider these morphological differences to be of a similar level to features distinguishing human populations today Asfaw:2002.

After a million years ago, fossil specimens in Africa and Europe represent a change from the characteristics of earlier Homo erectus. The African and early European remains are often referred as “archaic” members of our own species, Homo sapiens, or by another species name, Homo heidelbergensis. It is not clear whether the anatomical evolution was accompanied by biological speciation, or whether it represents an increase in brain size and consequent changes in cranial morphology within a single evolving species. In either case, early European hominids also had morphological features distinguishing them from other regions, including a projecting face and nose, and large sinuses accretion. One of the most important sites of the last million years is Sima de los Huesos, Ataperca, Spain, which preserves the partial skeletal remains of more than 25 individuals, from around 600,000 years ago Arsuaga:1997. The Chinese and Javan fossil records undergo a similar pattern of changes, although Homo erectus features of the skull remain common later into the last 500,000 years in these regions.

Humans evolved larger brain sizes across the Pleistocene. The earliest Homo erectus specimens had endocranial volumes averaging around 750 ml; these increased to an average of 1400 ml by 50,000 years ago Lee:2003. The increase is evident everywhere ancient humans lived, including Africa, Asia, and Europe. Brains are energetically expensive, and the metabolic cost of an increase in brain tissue must be redeemed by more food acquisition or reproduction Aiello:Wells:2002. Human brain evolution reflects the cognitive requirements of social and technological abilities in ancestral humans Dunbar:social:2003.

The archaeological record provides additional evidence about cognitive evolution. Stone tools became more sophisticated gradually over the Pleistocene. First, the development of bifacially flaked handaxes and cleavers in the Acheulean industry shows that hominids could learn and replicate standardized, symmetrical forms by 1.5 Ma Wynn:2002. Later, tools became more standardized, raw materials were obtained across longer distances from their sources, and techniques were shared across wider areas. These changes may reflect more widespread contacts between cultural traditions, or more efficient transfer of information. Finally, by 300,000 years ago, humans had mastered prepared core toolmaking techniques, requiring information transfer not only about finished tool form but also procedure. After this time, the technological properties of different human cultures began to diversify yet further, with industries changing more rapidly and occupying smaller areas McBrearty:2000. The fragmentation and acceleration of change in material culture would continue during the last 50,000 years as the complexity of culture and behavior increased further.

It is likely that the behavioral complexity after 300,000 years ago required some capacity for spoken language. Language is a fundamental basis for human culture and behavior, because people learn and coordinate their activities by talking to each other. But there is very little anatomical evidence relating to the evolution of language, as the necessary structures — tongue, larynx, and brain — do not fossilize. Still, a few hints exist. At least one \emph{Homo habilis</bib> skull includes a marked enlargement of Broca’s area in the frontal cortex, a brain structure important to planning complex activities and carrying out speech in living humans Holloway:1996. The hyoid bone, a small bone in the throat that supports the larynx, rarely fossilizes, but two hyoids from Sima de los Huesos and one from Kebara, Israel have been found. These hyoids are essentially humanlike in shape, in contrast to a preserved hyoid from Australopithecus afarensis, which is apelike Alemseged:2006. And at least one gene related to language, FOXP2, shows evidence of selection during the Pleistocene Enard:2002. Together, these hints suggest a long evolution of language from early, simple communication to the fully human language of today.

Neanderthals, Denisovans and modern humans

The most well-known group of ancient humans are the Neanderthals, inhabitants of Europe and parts of West Asia between 200,000 and 30,000 years ago. The Neanderthals were large game hunting specialists, with sites dominated by the bones of bison, horse, and red deer. Isotopic evidence suggests that their diet included a very high proportion of meat Bocherens:2005. Early humans, including Neanderthals, had short lives compared to recent humans, including recent hunter-gatherers Caspari:2004. They also had a very high rate of traumatic injuries Berger:Trinkaus:1995. These factors may be attributable to their reliance on close-contact hunting of large animals, using thrusting spears Trinkaus:1997. With powerful long bones and muscular necks, the Neanderthals were highly adapted to this strenuous lifestyle. The Neanderthals themselves

Recently, genetic evidence directly from Neanderthal skeletal remains has been recovered. Initially, comparisons of the mitochondrial DNA of living people and Neanderthals suggested that the Neanderthals did not contribute to the ancestry of living people Serre:2004. Later sequencing of the entire genome of Neanderthals revealed that approximately 2.5% of the genealogical ancestry of living people outside Africa can be traced to this population Green:draft:2010. The amount of Neandertal ancestry is approximately the same in different regions outside Africa today, but is substantially less or absent within sub-Saharan Africa. Other genetic evidence from recent people also suggests that genes from archaic humans may have introgressed into the living human population two-s.

A skeletal finger bone from Denisova Cave, Russia, has preserved a whole genome of an individual from a different population from the Neandertals Reich:Denisova:2010. The analysis of this genome indicates that present-day Australians, Melanesians and other Oceanic peoples derive roughly 5% of their ancestry from the “Denisovan” population that included this genome. No fossil remains from other sites have yet been shown to share this genetic pattern, and the anatomical features of the population therefore remain unknown.

African populations of the Middle Pleistocene (780,000-125,000 years ago) were highly diverse in both anatomy and material culture. Africa has a larger habitable land area than other continents, for hunter-gatherers operating with Paleolithic technological strategies diss. Genetic variation within living African populations suggests that Middle Pleistocene Africans lived in several regional populations that were more differentiated from each other than today’s human groups Hammer:archaic:2011.

From this diverse population emerged most of the genetic ancestors of present-day humans. Sometime after 150,000 years ago, Africans began to move into West Asia where they could interact with the Neanderthals. This interaction resulted in the disappearance of Neanderthal, Denisovan, and other archaic human populations. These archaic people were in part assimilated into the succeeding population of modern humans, evident from DNA. The spreading population of modern humans became associated with more advanced technology, larger social groups, more rapid colonization and population growth. Late Neanderthals exhibited some of the technological and social innovations of early modern humans, so that the reason for the success of modern humans remains enigmatic.

Continuing human evolution

Humans have increasingly used culture and technology to adapt to our environments. In some ways, our inventions buffer us from natural hazards such as predators, climate, or the risks of foraging activity. Some anthropologists formerly argued that culture has reduced the force of natural selection upon the human population. A common misconception is that humans have not evolved physically or genetically since the origin of modern humans. The post-Pleistocene evolution of our species has in fact been very rapid accel.

After 100,000 years ago, human dispersals and population growth introduced large populations into environments as varied as the Arctic, the Americas, and Australia. Within the last 10,000 years, our interactions with the environment have further been changed by the introduction of agriculture, domestication of animals, life in villages and cities, and other technical and social innovations. Human populations have diversified during this period by founder effects, establishing differences in the frequencies of genes in different regions of the world.

The rapid recent evolution of our species provides an important context for interpreting genetic and physical differences among human populations. For example, human skin and hair pigmentation vary greatly among populations today, a pattern influenced by an array of genetic changes Sturm:2009. Many of the genetic changes that underlie pigmentation variation have been influenced by selection within the last 20,000 years, occurring by parallel changes in the ancestors of Asians and Europeans Norton:2007. Lactase persistence appeared under strong selection in multiple populations during the past 10,000 years Enattah:2008, as did more than two dozen genetic responses to malaria Hedrick:2011. These examples show that many of the classic traits recognized among human geographic groups are actually very recent evolutionary developments.

Even though most humans live today in large industrialized societies, our evolution continues. Long-term studies of the health of individuals within the United States and Europe show that the chances of having children are different depending on several physical and physiological traits, constituting the pattern of natural selection in living people Stearns:measuring:2010. We cannot assume that the future evolution of our species will proceed in the same direction as its recent or current evolutionary trends. However, we can rely on the observation of ongoing evolution to demonstrate that our future will not be static but will exhibit some of the same kinds of changes as in the human past.