The genomes of ancestral organisms can be inferred, but most can never be directly observed. DNA is very stable compared with most organic molecules, but it is not perfectly stable, and its progressive degradation, even under the best circumstances, means that it is virtually impossible to extract sequence information from fossils that are more than a million years old. Although a modern organism such as the horseshoe crab looks remarkably similar to fossil ancestors that lived 200 million years ago, there is every reason to believe that the horse-shoe-crab genome has been changing during all that time in much the same way as in other evolutionary lineages, and at a similar rate. Selection must have maintained key functional properties of the horseshoe-crab genome to account for the morphological stability of the lineage. However, comparisons between different present-day organisms show that the fraction of the genome subject to purifying selection is small; hence, it is fair to assume that the genome of the modern horseshoe crab, while preserving features critical for function, must differ greatly from that of its extinct ancestors, known to us only through the fossil record.
It is possible to get direct sequence information by examining DNA samples from ancient materials if these are not too old. In recent years, technical advances have allowed DNA sequencing from exceptionally well-preserved bone fragments that date from more than 100,000 years ago. Although any DNA this old will be imperfectly preserved, a sequence of the Neanderthal genome has been reconstructed from many millions of short DNA sequences, revealing—among other things—that our human ancestors interbred with Neanderthals in Europe and
Figure 4–69 A comparison of the β-globin gene cluster in the human and mouse genomes, showing the locations of transposable elements. This stretch of the human genome contains five functional β-globin-like genes (orange); the comparable region from the mouse genome has only four. The positions of the human Alu sequences are indicated by green circles, and the human L1 sequences by red circles. The mouse genome contains different but related transposable elements: the positions of b1 elements (which are related to the human Alu sequences) are indicated by blue triangles, and the positions of the mouse L1 elements (which are related to the human L1 sequences) are indicated by orange triangles. The absence of transposable elements from the globin structural genes can be attributed to purifying selection, which would have eliminated any insertion that compromised gene function. (Courtesy of Ross Hardison and webb miller.)
Figure 4–70 The puffer fish, Fugu rubripes. (Courtesy of byrappa venkatesh.) 0.0 100.0 180.0 thousands of nucleotide pairs that modern humans have inherited specific genes from them (Figure 4–72). The average difference in DNA sequence between humans and Neanderthals shows that our two lineages diverged somewhere between 270,000 and 440,000 years ago, well before the time that humans are believed to have migrated out of Africa.
But what about deciphering the genomes of much older ancestors, those for which no useful DNA samples can be isolated? For organisms that are as closely related as human and chimpanzee, we saw that this may not be difficult: reference to the gorilla sequence can be used to sort out which of the few sequence differences between human and chimpanzee are inherited from our common ancestor some 6 million years ago (see Figure 4–64). And for an ancestor that has produced a large number of different organisms alive today, the DNA sequences of many species can be compared simultaneously to unscramble much of the ancestral sequence, allowing scientists to derive DNA sequences much farther back in time. For example, from the genome sequences currently being obtained for dozens of modern placental mammals, it should be possible to infer much of the genome sequence of their 100 million-year-old common ancestor—the precursor of species as diverse as dog, mouse, rabbit, armadillo, and human (see Figure 4–66).
multispecies Sequence Comparisons Identify Conserved DNA Sequences of Unknown Function