ScienceWeek

EVOLUTION: ON THE EVOLUTION OF HUMANS AND CHIMPANZEES

The following points are made by Hans Ellegren (Current Biology 2005 15:R919):

1) The field of molecular evolution was born in the 1950s when it became possible to determine the amino acid sequence of proteins, and to compare these sequences among related species. Subsequent advances in DNA sequencing technology allowed homologous genes to be analyzed at the nucleotide level and, from this, we could start to infer how mutation and selection had contributed to molecular evolution. Today, the availability of full genome sequences and computational methods for comparing them means that the full spectrum of evolutionarily accumulated mutations distinguishing two species can be studied. As reported in new work [1-4], the human genome has now been lined up against that of our closest living relative, the chimpanzee. A comparison of the two genomes reveals a number of important features.

2) In addition to the biological and medical interest in the human and chimpanzee genomes, their sequences are important to molecular evolution for several reasons. First, with two species as closely related as these two hominids, their sequences will almost always be sufficiently similar to make alignment of homologous regions unambiguous. Notably, this is true not only for conserved regions, like genes, but also for neutral sequences, as in the intergenic landscape. Second, over such a short evolutionary distance, the incidence of multiple mutational hits at individual sites is negligible, so it is usually straightforward to infer which evolutionary changes have been made since the two genomes split.

3) What does the chimpanzee genome sequence tell us about the role of natural selection in human evolution? Purifying selection is clearly evidenced by the fact that mutations that alter the amino acid sequence, which in many cases presumably have a deleterious effect, have gone to fixation at a much lower rate than those that do not. Traditionally, this is expressed in terms of the ratio of non-synonymous (dN) to synonymous (dS) substitutions, dN/dS, where dS is here used as an index of the rate of unconstrained, neutral evolution. When dN/dS is less than 1, the usual interpretation is that negative selection has taken place on non-synonymous substitutions. When dN/dS is greater than 1, positive selection is likely to have accelerated the rate of fixation of non-synonymous substitutions. Note that purifying selection is the conservative force in molecular evolution, whereas positive selection is the diversifying force that drives molecular adaptation. dN/dS is estimated to be ~0.25, on average, for the human chimp comparison. In other words, about 75% of all amino acid replacements seem to be removed by purifying selection.

4) The initial comparison of two more or less fully sequenced hominid genomes represents a milestone event in molecular evolutionary studies. The coming in-depth analyses of these genomes are likely to offer a route towards the most challenging question: what does it take to make a human? It can be foreseen that future work in this area will have to integrate information from observations of sequence as well as expression divergence. Moreover, advances in analytical methods will be necessary to be able to disentangle divergence caused by random genetic drift from divergence caused by natural selection.[5]

References (abridged):

1. T.S. Mikkelsen, L.W. Hillier, E.E. Eichler, M.C. Zody, D.B. Jaffe, S.-P. Yang, W. Enard, I. Hellmann, K. Lindblad-Toh and T.K. Altheide et al., Initial sequence of the chimpanzee genome and comparison with the human genome, Nature 437 (2005), pp. 69 87

2. Z. Cheng, M. Ventura, X. She, P. Khaitovich, T. Graves, K. Osoegawa, D. Church, P. DeJong, R.K. Wilson and S. Pääbo et al., A genome-wide comparison of recent chimpanzee and human segmental duplications, Nature 437 (2005), pp. 88 93

3. E.V. Linardopoulou, E.M. Williams, Y. Fan, C. Friedman, J.M. Young and B.J. Trask, Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication, Nature 437 (2005), pp. 94 100

4. J.F. Hughes, H. Skaletsky, T. Pyntikova, P.J. Minx, T. Graves, S. Rozen, R.K. Wilson and D.C. Page, Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee, Nature 437 (2005), pp. 101 104

5. The international HapMap project, The international HapMap project, Nature 426 (2003), pp. 789 796

Current Biology http://www.current-biology.com

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COGNITIVE SCIENCE: NUMBERS AND COUNTING IN A CHIMPANZEE

Notes by ScienceWeek:

In this context, let us define "animals" as all living multi-cellular creatures other than humans that are not plants. In recent decades it has become apparent that the cognitive skills of many animals, especially non-human primates, are greater than previously suspected. Part of the problem in research on cognition in animals has been the intrinsic difficulty in communicating with or testing animals, a difficulty that makes the outcome of a cognitive experiment heavily dependent on the ingenuity of the experimental approach.

Another problem is that when investigating the non-human primates, the animals whose cognitive skills are closest to that of humans, one cannot do experiments on large populations because such populations either do not exist or are prohibitively expensive to maintain. The result is that in the area of primate cognitive research reported experiments are often "anecdotal", i.e., experiments involving only a few or even a single animal subject.

But anecdotal evidence can often be of great significance and have startling implications: a report, even in a single animal, of important abstract abilities, numeric or conceptual, is worthy of attention, if only because it may destroy old myths and point to new directions in methodology. In 1985, T. Matsuzawa reported experiments with a female chimpanzee that had learned to use Arabic numerals to represent numbers of items. This animal (which is still alive and whose name is "Ai") can count from 0 to 9 items, which she demonstrates by touching the appropriate number on a touch-sensitive monitor. Ai can also order the numbers from 0 to 9 in sequence.

The following points are made by N. Kawai and T. Matsuzawa (Nature 2000 403:39):

1) The author report an investigation of Ai's memory span by testing her skill in numerical tasks. The authors point out that humans can easily memorize strings of codes such as phone numbers and postal codes if they consist of up to 7 items, but above this number of items, humans find memorization more difficult. This "magic number 7" effect, as it is known in human information processing, represents an apparent limit for the number of items that can be handled simultaneously by the human brain.

2) The authors report that the chimpanzee Ai can remember the correct sequence of any 5 numbers selected from the range 0 to 9.

3) The authors relate that in one testing session, after choosing the first correct number in a sequence (all other numbers still masked), "a fight broke out among a group of chimpanzees outside the room, accompanied by loud screaming. Ai abandoned her task and paid attention to the fight for about 20 seconds, after which she returned to the screen and completed the trial without error."

4) The authors conclude: "Ai's performance shows that chimpanzees can remember the sequence of at least 5 numbers, the same as (or even more than) preschool children. Our study and others demonstrate the rudimentary form of numerical competence in non-human primates."

Nature http://www.nature.com/nature

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ANIMAL BIOLOGY: ON HUMANS AND CHIMPANZEES

The following points are made by Linda Vigilant (Current Biology 2004 14:R369):

1) The name "chimpanzee" usually refers to members of a species designated Pan troglodytes and found in a broad but discontinuous distribution across equatorial Africa. Such "common chimpanzees" are distinguished from their close relative the pygmy chimpanzee or bonobo (Pan paniscus), which lives only south of the Congo River in the current-day Democratic Republic of Congo. But for other taxa, genetic similarity as close as that between humans and chimpanzees leads routinely to classification in the same genus. Adopting that logic would make us all chimpanzees, or all chimpanzees members of the genus Homo.

2) Chimpanzees and humans are not distinguished by tool use, hunting, or coalitionary aggression -- both species are known for those kinds of things. Attributes unique to humans include hallmarks of advanced culture and technology, such as complex spoken language, art, and sophisticated tool use. We can also count susceptibility to malaria, a habitual upright gait, and certain cancers as human specific features. A handful of genetic or biochemical differences have been identified. But chimps and humans shared a common ancestor only approximately 5 million years ago, and it is not simple to find genes that hint at selection over such a short time. The list currently includes FOXP2, a gene for a transcription factor that apparently plays a role in developing the ability to produce articulate speech, and ASPM, a gene involved in determining brain size. Humans also have a higher proportion of disrupted olfactory receptor genes --pseudogenes -- suggesting that selection for olfactory abilities may have been reduced in the human lineage.

3) The central idea of the chimpanzee genome project is that comparison of the chimpanzee and human genomes will uncover genetic differences underlying the molecular, morphological, and cultural differences between the two species. The power of such an approach was illustrated by a recent study comparing more than 7000 genes from the chimpanzee to those from humans and mice. Signs of positive selection on the human lineage were shown by genes influencing hearing and those encoding catabolic enzymes that could play a role in adaptation to dietary novelties.

4) Of importance is that the newly completed chimpanzee genome sequence will allow testing of hypotheses about the relationship between genetic and observed species differences. In 1975, Mary-Claire King and Allan Wilson proposed that changes in gene regulation are likely to be more important than changes in the sequences of proteins. Evidence in support of this view came from a recent survey of tissue-specific levels of gene expression in humans, chimpanzees, and other primates, which suggested that the rate of change in expression in the human brain is increased. Gene insertions, deletions, and duplications are also likely to have differentially shaped the human and chimpanzee genomes.(1-3)

References (abridged):

1. Mitani, J.C., Watts, D.P., and Muller, M. (2002). Recent developments in the study of wild chimpanzee behavior. Evolutionary Anthropology 11, 9-25

2. Olson, M.V. and Varki, A. (2003). Sequencing the chimpanzee genome: insights into human evolution and disease. Nat. Rev. Genet. 4, 20-28

3. Tomasello, M., Call, J., and Hare, B. (2003). Chimpanzees understand psychological states- the question is which ones and to what extent. Trends Cogn. Sci. 7, 153-156

Current Biology http://www.current-biology.com

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