The animal(s) within us: life on Earth took many forms before the emergence of mammals and mankind.
ANIMALS DISPLAY an extreme diversity, of form, lifestyle, and body organization. Their ancestors were built simpler than the species existing today. One of the most interesting questions in biology is how these forms evolved over time and which innovations of their body plans helped them adapt to new conditions. The answer is difficult to come by because, in most cases, neither the intermediate forms nor the common ancestors exist anymore. Fossils, which are the only clue to the animals of the past, are very rare and tell us almost nothing about the embryonic development or the genes of these animals.
Animals can be classified based on their similarities and thus their evolutionary relationships into groups known as taxa. Members of a particular taxon all share a common ancestor. The largest taxa are called phyla, and there are approximately 30 of them today, though many more probably existed in the past. The five phyla that include the highest number of animal species are the nematodes, or round worms; annelids, or ringed worms; mollusks; the arthropods; and chordates. These phyla, in turn, are divided into classes and each class then is subdivided into orders, families, genera, and species. For instance, the largest class of the chordates is the vertebrates. The vertebrates themselves are divided into the five orders of fish. amphibians, reptiles, birds, and mammals. The mammals include Homo sapiens--the humans.
The relationship among different species can be recognized more easily in embryos than in adults because, during embryonic development, an animal's basic construction plan becomes apparent. This body plan is displayed most clearly at a stage when the animal is not yet fully developed, and when it is not yet able to feed itself. At this early stage, the body still is comparatively simple, because the structures necessary for adaptation to a specific lifestyle have not yet developed. Therefore, animals often are grouped as similar based on embryonic structures rather than on adult ones. The vertebrates, for example, are subdivided into amniotes (reptiles, birds, and mammals) and anamniotes (fishes and amphibians) based on whether they possess an amnion--a protective embryonic coveting. The amnion, however, is not the only criteria for this classification, as there are insects that form an amnion. The fact that some vertebrates have an amnion is based on homology. in other words, derivation from a common ancestor, while the presence of an amnion in vertebrates and insects is based on analogy, namely similar function that has arisen independently during the evolution of the two phyla.
In many cases, it is difficult to determine whether the animal lacking a particular trait is more basic and its ancestor preceded the one of the animal that has it, or whether the trait had been present originally but subsequently was lost in evolution. Because of these uncertainties, the determination of evolutionary relationships among animals always has to rest on several criteria.
Nowadays, the most reliable criteria no longer are morphological, but molecular characteristics--for instance, number of base exchanges in homologous genes. One reliable approach of molecular phylogeny compares DNA sequences of genes that are present in all animals--in particular, gene segments that do not code for proteins. In such noncoding DNA segments, changes are assumed mainly to be accidental, without an influence on the phenotype and therefore not subject to selection. Once a mutation in noncoding DNA has occurred, it therefore should be passed on to all descendants. At present, variation in the genes encoding ribosomal RNA is the most commonly used criteria for the taxonomic classification of more distantly related species. For the analysis of the differences among more closely related species, and the variation among individuals within them, mitochondrial DNA sequences are employed. Mitochondrial DNA mutates more often than chromosomal DNA, as there are fewer DNA repair mechanisms operating in mitochondria. So, there will be more informative sequence differences occurring in the comparatively short lime after the separation of two closely related species.
When genes among different organisms are compared, one striking observation is how similar they are in sequence and, often, in molecular function. This especially is surprising in the case of developmental genes that regulate how body plans and organs are formed. These genes sometimes are so similar that they can replace each other readily in two animals that look very different. This suggests that all animals arose from one ancestor that already had a set of developmental pathways and a rather detailed body plan, with top and bottom, front and rear, and several organs at specific places. Some such genes even can be traced back further to the single-celled ancestors of animals, which, in turn, are presumed to have their origin in some kind of bacteria-like cell. This is evident from the observation that the elements of the basic metabolic and genetic machinery of a cell are common to organisms with evolutionary paths that separated billions of years ago, such as humans and bacteria.
Bacteria-like cells probably were the first organisms on Earth. Bacteria are relatively simple cells surrounded by rigid cell walls that determine their shape. Bacteria already feature the basic mechanisms for cell replication, such as DNA, RNA, protein synthesis, and ribosomes. They do not yet have a nucleus and, their DNA, a ring-shaped molecule, is arranged loosely in the cytoplasm. While there is no true sex in bacteria, a form of genetic exchange does lake place between individual cells. In fact, DNA sometimes can be transferred among cells of different bacterial species. This phenomenon is known as horizontal gene transfer. Bacteria do not display a particular diversity of shapes and, although some species form aggregates of cells, there are no truly multicellular species. However, they do possess a remarkably diverse biochemical ability to convert and build materials of all kinds, allowing for adaptation to even the most extreme conditions of life; for instance there are bacteria that grow best at 230[degrees]F.
The first organisms containing a cell nucleus, the eukaryotes, are assumed to have developed more than 2,000,000,000 years ago. At first, they were single-celled, just like bacteria, but later several types of multicellular forms evolved. As an evolutionary innovation, eukaryotes have a nucleus that houses the DNA and is surrounded by an envelope. Folding in of the cell membrane allows particles to be moved into the cell, which is subdivided into separated compartments formed by membrane-bounded organelles. This restricts the exchange of molecules and provides chemically separated environments within one cell. Another important component of the eukaryotic cell are the mitochondria, which provide energy, and most likely originated from bacteria that were enslaved by the ancestral eukaryotes. Eukaryotes have a versatile interior cytoskeleton (rather than the exterior rigid cell wall of bacteria) that stabilizes the cell and, at the same time, allows for shape changes and motility. The DNA in the eukaryotic nucleus is packed by certain proteins and partitioned into chromosomes to ensure correct distribution into the daughter cells during division. Most components of the eukaryotic cell have been preserved during evolution: the proteins of the cytoskeleton, the enzymes of the DNA replication, and the regulators of cell division; they remain active in today's single-celled eukaryotes, such as yeast, as well as in mnlticellular eukaryotes, such as plants and animals.
Starting as a single cell
Multicellular organisms developed from single-celled eukaryotes. In fact, multicellularity probably evolved several times in plants and fungi, but only once in animals. The first animals probably looked like a hollow ball and comprised two layers of cells, one on the outside and the other on the inside. The organization of eukaryotic cells into aggregates is facilitated by the loss of rigid cell walls. This allowed for the evolution of cell adhesion and communication. Later, animals evolved a branched blind gut and several cell types, among them simple nerve and sensory cells. Such organisms probably looked similar to today's Cnidarians, such as corals or jellyfish.
The first animals can be traced back to more than 600,000,000 years ago. Then, during the Cambrian period, the atmosphere contained levels of oxygen similar to those today, built up by photosynthetic bacteria and algae. This may have allowed animals to grow and spread faster, and ultimately led to the evolution of a large diversity of forms. During this so-called "Cambrian explosion," new organisms with a great variety of body organization and lifestyles emerged within a relatively short period of about 50,000,-000 years. As fossils show, representatives of animal phyla still alive today developed then: mollusks, arthropods, worms of all kinds, and chordates. Additionally many other forms that have no similarities to any of the phyla living today existed at that time as well. Their lifestyles remain a mystery.
The emergence of different forms was facilitated by the evolution of a robust body organization, allowing for variation in shape and growth. The embryo had become flatter and was composed of three germ layers, now including the mesoderm. The inner cells, derived from the endoderm, formed the through gut. Ectodermal sense organs and a mouth developed at the front, specialized to feed. The mesoderm allowed for formation of muscle and circulatory systems.
This prototypic animal, a kind of roundish flatworm, presumably had all essential developmental mechanisms in place. The once radial symmetric animals now could acquire an elongated shape with a clear front and back, top and bottom, and bilateral symmetry. In other words, this primordial animal already must have had all the genes in the most important signaling cascades--such as Delta/Notch--and the gradient system creating the dorsal-ventral axis with decapentaplegic (DPP) and short gastrulation (SOG). The hox-genes, as well as other selector-genes determining the position of sense organs (eyeless) and the heart (tinman), also probably were included in the early repertoire of developmental genes.
Most animal phyla belong to one of two groups of bilaterians: the protostomes or deuterostomes. Their distinguishing characteristic is whether, during gastrulation, the invagination of the gut eventually will become the mouth (protostomes) or the anus (deuterostomes). Vertebrates and echinoderms, such as the sea urchin, are deuterostomes, while arthropods and mollusks, such as mussels and snails, are protostomes.
In the 19th century, French zoologist Etienne Geoffroy Saint-Hillaire remarked that arthropods are similar to vertebrates with regard to their basic body organization. His example was a lobster. All you had to do to see some fundamental similarities between a lobster and, say, a human, was to lay it on its back and invert the positions of the anus and mouth. The central nervous system in deuterostomes lies on the dorsal side, but on the ventral side in protostomes, such as the lobster. Likewise, deuterostomes have their heart on the ventral side, while protostomes have it on the dorsal side.
Comparing the distribution of certain genes' products in the embryos of vertebrates and arthropods offers many further insights. For instance, the succession of the hox-genes, which pattern the anterior-posterior axis, has been preserved in all animals. DPP and SOG create a gradient that determines the dorsal-ventral axis in arthropods. Vertebrates develop a corresponding dorsal-ventral gradient with bone morphogentic protein (BMP, homologous to DPP) and chordin (homologous to SOG). Many molecular feedback mechanisms of this system have been preserved, suggesting that they already operated in the ancestors of protostomes and deuterostomes. In vertebrates and arthropods, though, they are arranged in opposing orientation. The BMP signal is ventral in vertebrates and dorsal in arthropods (DPP). It is conceivable that a twisting of the body organization would have turned a protostome into a deuterostome. Yet, it also is possible that protostomes and deuterostomes developed independently from a common ancestor.
The variety of animal forms developed due to additional construction principles modifying the basic forms. Segmentation--dividing the body into repetitive units--was one such important innovation. Segmental units, which initially are built based on the same principle, can be modified to form a variety of structures. Indeed, members of many different animal phyla are segmented, but the segments develop in different ways. In annelids and many arthropods, stem ceils in a growth zone form precursors of the segments. In Drosophila, segmentation results from a simultaneous subdivision of the blastoderm. Arthropods use the segment-polarity-genes known from Drosophila in their segmentation. The genes operating early during Drosophila segmentation--such as bicoid, hunchback, and knirps--have not been conserved in other arthropods, and likely are a late innovation of the insects. In vertebrates, segments form in an entirely different way. In this case, a time-delayed pulsating activity translates into spatial waves involving Delta-Notch signaling. In arthropods as well as in vertebrates, mechanisms independent from those creating the body segmentation form the head and the frontal segments.
The development of solid support structures facilitates variation in form and, hence, adaptation. Cuticle built from chitin, calcium shells, and interior skeletons composed of cartilage and bone offers protection and allows the development of new ways of locomotion. The hard calcium shell of snails and mussels attaches to the body muscles. The arthropods' outer chitin-skeleton, with its many flexible joints, allows for sophisticated modes of movement.
The interior skeleton of vertebrates is formed by the mesoderm, which builds cartilage and bones of high strength. Skeletons, by rendering physical support to the body, allow an increase in the size of the animals. Outer skeletons, such as the insect cuticle, provide optimal protection against infection, but they have to be shed when the animal grows. Growth of animals with an inner skeleton, such as vertebrates, occurs continuously, and these animals can reach very large sizes.
Limbs, meanwhile, can function as legs, antennae, claws, jaws, arms, or wings, and thus contribute to the variety of forms. Limb development is guided by similar molecular mechanisms as the early stages of body organization. The limbs of arthropods come in an incredible variety of structures, even though they all am formed according to the same construction principle. As part of the head, they are shaped into sensory or defense organs and a rich spectrum of chewing tools. Vertebrates have two pairs of limbs--fins, legs, arms, or wings. Some limbs are homologous among vertebrates; for instance, forelegs, wings, and pectoral fins of fish. Vertebrate limbs develop from buds that arise from the body wall and their pattern formation involves similar molecules as in arthropods. This either may be due to the common ancestor having had limbs or the fact that these signaling molecules may be particularly suited to forming limbs.
The ancestors of the vertebrates and some other groups of the Cambrium were rather simple chordates: lacking a skull and feeding by filtering prey out of the sea water through their gills. Vertebrates today, by contrast, display a skull protecting a large brain, and a great variety of feeding structures. For this evolutionary innovation, the development of the neural crest was crucial. The neural crest cells emerge from the dorsal ectoderm near the future nervous system, migrate throughout the body, and can differentiate into a number of various structures to furnish the body's periphery with many specialized functions. Vertebrate innovations that depend on cells of the neural crest are some bones of the skull, jawbones, and teeth to facilitate food intake. Neural crest cells also produce the pigmentation of the body--claws, horns, and beaks.
In general, vertebrates are more complex than arthropods. This is partly because the arthropods' outer skeleton requires shedding of the skin to allow growth. The larger the animal, the more difficult and dangerous molting becomes. This puts a limit to growth. In contrast, the inner skeleton of vertebrates allows for continuous growth, and enormous sizes can be reached. Vertebrate structures such as the neural crest and the placodes further the development of the head and the brain, which reaches an unprecedented complexity in humans.
Genetic jigsaw puzzle
The complexity of the body organization of animals is mirrored in the size and number of their genes. The simplest organisms, bacteria, have small genomes with average gene sizes of about 1,000 base pairs. The number of genes per genome varies from species to species: the smallest bacterial genomes comprise only about 600 genes, while Escherichia coli contains 4,300 genes and has a genome size of 4,000,000 base pairs. The human genome, the largest deciphered so far, is about 1,000 times the size of the genome of E. coli.
The genome of the first multicellular organism sequenced--by British biologist John Sulston and colleagues in 1998--was that of the nematode worm Caenorhabditis elegans. It contains 100,000,000 base pairs. For deciphering the genome, big overlapping DNA segments were sequenced and computer programs--which recognize regions that can be translated into proteins--determined the position and number of genes.
The C. elegans genome has about 19,000 genes. In comparison, the single-celled yeast Saccharomyces cerevisiae features about 6,000 genes, and Drosophila contains about 13,000 genes. It was quite surprising to find that the number of genes in mammals--humans and mice--was not much higher than those found in the fly and the worm (about 32,000). However, mammalian genes are larger than the genes of flies and worms. On average, a human gene contains 27,000 base pairs, and about 10 exons with 100 base pairs each, while introns are about 10 times as long.
These comparisons allow for an important conclusion: the growing complexity during evolution does not necessarily correlate with the size of the genome nor does it require a corresponding increase in the number of genes. Although the genes themselves get larger with increasing position along the evolutionary path, the growth in genome size is due mainly to DNA sequences that do not code for proteins and even may have no function at all. About half of the 3,000,000,000 base pairs of a mammalian genome consist of junk-DNA. This term mainly refers to short sequences that occur repeatedly in large numbers, so-called repetitive DNA. These sequences may give interesting insights into the evolutionary history of the genome, although the reason for their existence is not clear at all. It is to be expected that organisms with a short generation lime lose useless genetic material more quickly. However, it is quite possible that the mammalian genome actually collects junk-DNA, because the junk does not cause disadvantages in the process of selection, and thus can be tolerated.
Some vertebrates obviously preserve large DNA regions that have no apparent function. A comparison among fish illustrates this: the pufferfish Fugu lives with a genome one-quarter the size of the zebrafish, although both have about the same number of genes. Comparing the sequence of untranslated DNA regions in two closely related animal species might help to understand their significance. Regions that am similar or the same most likely do have a function, even though this function may not be clear immediately from the DNA sequence. Comparing the genome of mice and humans will give further insight into this problem.
Comparison of sequences among related genes shows how new genes evolve from existing ones. In this process, three principles are at work: mutation of Individual bases; gene duplication; and the new combination of gene parts of different origin. Bacteria feature one additional mechanism: horizontal gene transfer--for example, the exchange of genes among different species. Horizontal gene Wansfer does not seem to be occurring in eukaryotes.
Most proteins are composed in a modular manner, meaning they contain particular domains of short amino acid sequences that confer specific biochemical properties such as DNA binding or enzymatic activity. About 1,200 different protein domains are known; they are used in many different combinations, thus defining many gene families that developed through gene duplication. In homologous genes of different species, often only the sequences coding for these very domains are preserved. The surrounding sequences can be modified greatly, while still retaining the original function of the protein. Of the 1,200 domains known so far, about 200 can be found in the proteins of all organisms, from bacteria to humans.
While the proteins of yeast are rather simple, those of multicellular organisms generally contain several domains per gene. These proteins seem to have evolved by combining parts of different genes, such that proteins with completely new functions may have been created. Mammalian proteins are particularly complex. About one-third of mammalian genes can be spliced in more than one way such that several proteins are produced which may differ in domain composition and thus function. Therefore, in mammals, the number of different proteins is higher than the number of different genes.
Gene families most likely arose from duplications of individual genes. This may have been caused by a rare mistake during recombination or replication, but duplications of entire genomes also are conceivable. The genome of vertebrates, for example, seems to have been duplicated twice in a relatively short period of time during evolution--with one duplication having been completed already before the appearance of fish. Chordates without a skull, like the lancet, merely have one complex of box-genes while most vertebrates have four. There is a whole range of genes that appears in four similar copies in the mouse, but just once in Drosophila. Frequently, such gene duplicates are preserved only if they can take on different functions through a series of mutations. In fish, there has teen an additional genome duplication, but only about 20% of the duplicated genes were preserved.
Many genes and their properties had been known even before systematic international projects managed to sequence entire genomes. Nevertheless, such projects are very important because they allow for elucidating which genes are present in which organism and, more importantly, which ones are not. The resulting dam has made it easier to find homologous genes, which--due to their divergence in sequence--can be identified only through computer-supported search programs.
Two mammalian genomes that have been deciphered, that of the mouse and humans, demonstrate, as expected from their close evolutionary relationship--the last common ancestor lived about 100,0130,000 years ago, as their genomes are relatively similar. At least 99% of the mouse genes have a counterpart in human genes and 78% of the amino acids in the respective proteins are the same. Yet, these numbers do not say much, as the degree of similarity varies considerably from gene to gene, and because functional variations may depend in complex ways on the primary sequence of the protein. This comparison also does not take control regions into account. Important differences between humans and mice are revealed in the number of genes influencing certain protein families. For example, mice have many more genes involved in sensing smell than do humans.
Sequence comparisons among eukaryotes show that more than 60% of Drosophila genes and almost 50% of worm and yeast genes are homologous to mammalian genes. This does not mean that these genes in all cases fulfill a similar function, because many mutations have taken place to adapt proteins to new processes more relevant to the respective organism. It does mean, though, that these genes share a common origin. These numbers stress the conservative nature of evolution. Still, it has brought forth an amazing variety in form, function, and lifestyle of organisms.
Molecular biology can be employed to investigate the origin and evolution of humans. An analysis of the differences in the DNA among individuals is quite revealing. In a few cases, a comparison of the DNA extracted from human fossils with that of humans living today has been successful. However, still most of what we know about ancient human evolution rests on fossil evidence; this naturally is shaky due to the scarcity of human fossils in particular.
Fossils have shown that the first primates existed about 60,000,000 years ago and later evolved into hominids in Africa. The oldest fossils suggesting an upright gait are about 4,000,000 years old. It could not be clarified, however, when and where the modern human, Homo sapiens, arose, because fossils of the genus Homo have been found on several continents.
It's all in the DNA
The analysis of differences among DNA in humans of contrasting ethnic groups riving today has solved the issue. The most extensive data stems from the comparison of mitochondrial DNA. Mitochondria are passed on exclusively by egg cells and, hence, strictly speaking, only reveal the relationships among female ancestors. Male relationships are studied by examining certain regions on the Y-chromosome; these are less variable but do not undergo the process of recombination.
There are variations in about three of 100 base pairs within a mitochondrial DNA sequence. It is possible to reconstruct a family tree from the common variations in humans living today. The largest degree of variation is found among Africans, while only subsets of this variation are found in non-Africans. This indicates that the origin of all modern humans is Africa--it is from there they emigrated and spread all over the world. Considering the relatively small number of variations, the species Homo sapiens can be traced back to a surprisingly small founder population of probably no more than 10,000 individuals. The other striking finding stemming from such comparisons is that there is more variation among people within a given population than among wide-ranging populations. This is surprising because, superficially, people from various parts of the world can look rather different in terms of body size or skin color. However, the overall variance in the genes is tiny compared to the dissimilarities among individuals within one ethnic group. Thus, there is no real genetic basis for the idea of human races.
When did modern humans evolve? One estimate is based on the characteristics of humans and chimpanzees, the human's closest living relative. The DNA variation between humans and chimpanzees is roughly estimated to be about 25 times greater than between any two humans. These arose after the split of the lineages leading to humans and chimps, respectively. According to age determination of fossils, the common ancestor of humans and chimpanzees lived about 5,000,000 years ago. Thus, Homo sapiens emerged about 200,000 years ago (5,000,000 divided by 25 equals 200,000). Also, considering information based on other methods, we end up with an average time span of 150,000 years ago.
Fossil discoveries in Central Europe show that modern humans rived there about 30,000 years ago. These humans already produced art, as is evident from many impressive cave paintings in southwestern Europe. At the same time, members of a different human species, known as Neanderthals--named after the Neanderthal in Germany where their fossils were first found--populated Europe as well. Comparing Neanderthal DNA sequence extracted from fossils with the sequence of modern humans shows 10 times more deviations than within individual modern humans. This means that the Neanderthals most likely have not been a direct ancestor of modern humans. The last common ancestor of modern humans and Neanderthals is assumed to have rived about 500,000 years ago.
The closest living relatives of humans are the great apes: chimpanzee, bonobo, orangutan, and gorilla. Molecular data show that we are most closely related to the chimpanzee, and least closely related to the orangutan. Chimpanzee and human genomic DNA sequences differ only in one of 100 base pairs. By comparison, two nonrelated human beings differ in one of 1,000 base pairs.
Genome research indicates that, although humans differ from chimps by only about one percent of the bases, this still amounts to tens of millions of individual bases because these genomes are so big. About one-third of the proteins present in chimps and humans are identical and most of the rest only differ by one or two amino acids. This means that the disparities at the molecular level are very subtle. Why then are humans and chimps so distinctive? A comparison of the genomes of these species helps answer this question by identifying regions, genes, and regulatory DNA that have been under intense selective pressure, and that differ relatively greatly from chimps but are very similar among various human groups.
It is interesting that the DNA variation within one species of ape living today is three times greater than those among humans, even though the population of living chimpanzees, about 50,000, is much smaller than that of the 6,000,-000,000 humans. This suggests that the ape species are older, and that they never reproduced very fast. Human populations, on the other hand, expanded quickly and, as previously stated, probably originated from a very small founder population 150,000 years ago.
Therefore, all people living today are very closely related genetically. Until, and even after, the emergence of modern humans, the population remained relatively small but, with the end of the last ice age, and with the subsequent invention of farming 11,000 years ago in the fertile crescent now known as Iraq, the human population blossomed.
Christiane Nusslein-Volhard, a Nobel Prize Laureate in Physiology and Medicine, is the author of Coming to Life: How Genes Drive Development, from which this article was excerpted.
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|Title Annotation:||Science & Technology|
|Publication:||USA Today (Magazine)|
|Date:||Sep 1, 2010|
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