Evolutionary relationships among the living apes and humans were difficult to determine when paleontologists had only their morphology to compare them. Darwin believed that the closest relatives of humans were the African apes, both because of the many features they shared with us and because Africa seemed to be a suitable location for ancient humans to have arisen. But great disagreement about which apes might be our closest relatives continued until the 1960's. Many people did not share Darwin's assumption that Africa was the original location of human origins, and suggested locations from Europe to Australia. These ideas initially were not based on any fossil evidence but instead on ideas about which living human populations might be more "primitive" or "advanced" in form or behavior. Today paleontologists recognize that the locations of fossil apes and humans may not provide accurate information about their evolutionary origins because populations of people or apes could have moved in the past.
Few morphological resemblances make any ape species stand out as a close human relative, though each of the other living hominoids has been proposed at one time or another to be our closest cousin. Studies that include many different features have shown that chimpanzees share more derived features with humans than with gorillas (Collard and Wood 1999), but this case is very difficult to make on the basis of morphology alone. The lack of any fossil record for these living apes has complicated the study of their relationships as all comparisons must span a long evolutionary gap. Without a genetic perspective, the phylogenetic relationships among the living apes were simply too subtle to discover.
For a time, some ancient fossil apes appeared to be closer to humans than to any living African apes, raising the possibility of a long period of hominid divergence. For example, Louis Leakey suggested in the 1950's that each of the later human, chimpanzee, and gorilla lineages were represented 20 million years ago by different species of Proconsul from Kenya. Later, discoveries from Pakistan of an ancient ape, called Ramapithecus, with some dental similarities to ancient hominids appeared to present evidence that hominids had diverged from chimpanzees at least 10 million years ago. If Ramapithecus had been a hominid, its presence in Eurasia instead of Africa and its very early date would make it appear unlikely that either living chimpanzees or gorillas were very close to humans. Later discoveries showed that neither of these ancient fossil apes represented hominid ancestors, but each newer find is closely compared to the known fossil hominids to evaluate whether a relationship may be found between them.
Genetics and phylogeny
Since the 1960's, researchers have applied molecular genetic information from living hominoids to unravel their relationships. After examining many different kinds of genetic information, paleoanthropologists learned the sequence of divergences among hominoid species. Chimpanzees and humans are sister species, with gorillas, orangutans, and gibbons successively more divergent from the human line. Within this arrangement, the three-fold division between humans, chimpanzees, and gorillas is especially close. While most genes show a greater similarity between humans and chimpanzees than between either species and gorillas, the relative differences are very small. Some genes actually show greater similarity between humans and gorillas than between humans and chimpanzees. This pattern likely means that the gorilla lineage diverged only slightly before the split between the human and chimpanzee lineages (Marks 1994). The three lines may have originated as subpopulations within a single large species, having substantial differences like chimpanzee subspecies, but with the possibility of genetic exchanges between them.
Although geneticists have learned much about the sequence of hominoid divergences, it has remained difficult to establish the dates at which those divergences happened. To estimate divergence times, geneticists must know the rate of evolutionary change in the genes that they examine. But different genes evolve at different rates, and learning about these rates over timescales of millions of years is difficult. Genes that evolve very rapidly may accumulate so many changes that new mutations tend to affect changes that already occurred. Other genes change so slowly that only a few mutations happen in several million years. Many genes have been strongly affected by natural selection over the course of hominoid evolutionand geneticists have few ways to tell which genes these are. Thus, when geneticists use the differences between these genes to estimate divergence between species, such estimates may be very inaccurate.
The molecular clock
<br /> Geneticists infer rates of genetic change by comparing different species with each other. If there is good paleontological evidence that two lineages diverged at a particular date in the past, then the current genetic differences between the two lineages can be used to estimate the rate of genetic change in the past. The process of estimating dates in this way, assuming that genes diverge at a more or less constant rate from a known common ancestor, is called the molecular clock.
Many scientists have questioned the validity of the molecular clock assumption, pointing out a number of problems that complicate determining the divergence times among living hominoids. Perhaps the most frequently noted problem is that different lineages appear to have experienced different rates of genetic change in the past. For example, according to some measures rats and mice are more than ten times more genetically different from each other than chimpanzees and humans are from each other. Assuming a simple molecular clock, some geneticists have concluded that humans and chimpanzees diverged from each other only four million years ago or less, and rats and mice diverged over forty million years ago (Easteal et al. 1994). Others have noted the evidence for rapid evolution among the rodents, including a divergence of rats and mice perhaps as recently as 10 million years ago (Catzeflis et al. 1987). Although the times of divergence of these branches are not fully known from fossil evidence, it is clear that human and chimpanzee genes have not evolved at the same rate as rodent genes. Primate genes appear to have evolved at a slower rate than most other kinds of mammals (Li et al. 1987). These differences in rates may have occurred among different kinds of primates also, casting doubt on whether genes can accurately indicate the times that different lineages diverged from each other.
Problems with genetic variation
<br /> For closely related species, a more serious problem with estimating the times of divergences is created by the genetic variation within species themselves. The speciations that split a single ancient lineage into three lineages (humans, chimpanzees, and gorillas) by definition are the times that those lineages stopped interbreeding with each other. But genetic changes do not necessarily accompany the time of speciationthey can precede speciation or follow it by long periods of time. At the time that a single ancestor divides into two descendant species, it already has some degree of genetic variation. The alleles that enter the gene pool of each descendant species may be very different from each other, because they may sample different parts of the variation in the ancestor species. Thus, genes will nearly always have more differences than can be explained by the divergence of species. Furthermore, when species divergence is very recent, genetic differences may greatly misestimate the time of species divergence. For example, different alleles of the <i>PDHA1</i> gene in living people have evolved from a single ancestral allele as long as 1.9 million years ago in the ancient population ancestral to living people (Harris and Hey 1999). If, hypothetically, humans speciated tomorrow into different lineages, future paleoanthropologists would determine that the descendant species had genetic divergences around 1.9 million years earlier than their true speciation time.
Fossils and genetics in conflict?
<br /> Geneticists have estimated of the times that the living hominoid species diverged from each other, based on fossil evidence for earlier branching events among the primates--such as the divergence between the African and Asian apes and the divergence between the hominoids and the Old World monkeys. Beginning in the 1970's and continuing until the present day, these estimates have indicated that human and chimpanzee genes share a common ancestor around 5 million years ago, about a million years later than the divergence of this human-chimpanzee ancestor from the gorilla lineage (Yu 2002). Depending on the level of genetic variation in this ancient human-chimpanzee ancestor species, the speciation that created the human and chimpanzee lineages may have occurred from 1 to 2 million years later--as recent as 3 million years ago. But there is a problem with these estimates: the first fossil members of the human lineage, the hominids, are found as early as 6 million years ago (Senut et al. 2001). While no fossil record of chimpanzee or gorilla ancestors exists, the strong evidence for ancient hominids shows that the last common ancestor of humans and chimpanzees much have existed earlier than 6 million years ago. Thus, human and chimpanzee genes actually must have diverged 1 or 2 million years earlier than the speciation that created the two lineages--in other words, a minimum of 7 to 8 million years instead of 5 million.
In terms of relative chronology, the genetic evidence supports the inference from fossils and anatomy that orangutans are distant relatives of the hominids and African apes, and establishes a closer relationship between hominids and chimpanzees than between either and gorillas. A major goal of further genetic research is to narrow down the possible times of hominid origins within the span from 10 to 7 million years ago, by discovering the evolutionary factors that have influenced human and chimpanzee molecular evolution since that time.
Ancient population size
Geneticists can also analyze genetic variation in terms of the demographic conditions of the ancient common ancestors of living hominoids. The population size and structure of such ancient species influence the divergence times of genes in their descendants. While the mismatch between genetic divergence times and speciation causes problems in estimating the times of speciations, it also may provide information about the sizes of ancient species. For example, geneticists can use the small discrepancies between the expected times of species divergence, which are the same for all genes, and the actual times of genetic divergences, which vary between genes, to estimate how much genetic variation existed in a common ancestor species. For humans and chimpanzees, it appears that the common ancestor may have had substantial genetic variation (Takahata et al. 1995; Yu 2002).
Comparing such genetic variation to living hominoid species, one hypothesis is that the ancient ancestors of humans, chimpanzees, and gorillas may have belonged to a single species spread across a broad area of the African continent. Similar to living chimpanzees and gorillas, different subpopulations across this broad area may have developed substantial genetic differentiation due to the low gene flow between them. These genetically differentiated subspecies may have divided into different reproductively isolated populations, which ultimately were ancestral to the different living species of chimpanzees, gorillas, and humans. This area of research is steadily developing to find more insight into the ancient population structures that led to hominid origins.