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LIFE CLASSIFICATION OR TAXONOMY OR BIOLOGICAL CLASSIFICATION Taxonomy: Classifying Life Taxonomy: Classifying LifeAt least 1.7
million species of living organisms have been discovered, and the list grows longer every year (especially of insects in the tropical rain forest). How are they to be classified? Timeline of evolution
The basic timeline is a 4.5 billion
year old Earth, with (very approximate) dates: §
3.8 billion years of simple cells (prokaryotes), §
3 billion years of photosynthesis, §
2 billion years of complex cells (eukaryotes), §
1 billion years of multicellular life, §
600 million years of simple animals, §
570 million years of arthropods (ancestors of insects, arachnids and crustaceans), §
550 million years of complex animals, §
500 million years of fish and proto-amphibians, §
475 million years of land plants, §
400 million years of insects and seeds, §
360 million years of amphibians, §
300 million years of reptiles, §
200 million years of mammals, §
150 million years of birds, §
130 million years of flowers, §
65 million years since the non-avian dinosaurs died out, §
2.5 million years since the appearance
of the genus Homo, §
200,000 years since humans started looking like they do today, §
25,000 years since the disappearance of Neanderthal traits from the fossil record. §
13,000 years since the disappearance of Homo floresiensis from the fossil record. Detailed timelineMa, ("megaannum") means "million years ago". ka means "thousand years ago" and yameans "years ago" 3800 Ma and earlier. Date | Event | 4600 Ma | The planet Earth forms from the accretion discrevolving around the young Sun. | 4500 Ma | According to the giant impact hypothesis the moon is formed when the planet Earth and the planet Theia collide, sending a very large number
of moonlets into orbit around the young Earth which eventually coalesce to form the Moon.[1]The gravitational pull of the new Moon stabilises the Earth's
fluctuating axis of rotation and sets up the conditions in which life formed.[2] | 4100 Ma | The surface of the Earth cools enough for thecrust to solidify. The atmosphere and the oceansform.[3] PAH infall,[4] and iron sulfide synthesis along deep ocean platelet boundaries, may have led to the RNA world of competing organic compounds. | Between 4500 and 3500 Ma | The earliest life appears, possibly derived fromself-reproducing RNA molecules.[5][6] The replication of these organisms requires resources like energy,
space, and smaller building blocks, which soon become limited, resulting in competition, with natural selection favouring those molecules which are more efficient at replication. DNA molecules then take over as the main replicators and these archaic genomessoon develop inside enclosing membranes which provide a stable physical and chemical environment conducive to their replication: proto-cells.[7][8][9] | 3900 Ma | Late Heavy Bombardment: peak rate of impact events upon the inner planets by meteoroids. This constant disturbance may have obliterated any life that had evolved to that point, or
possibly not, as some early microbes could have survived in hydrothermal vents below the Earth's surface;[10] or life might have been transported to Earth by a meteoroid.[11] | Somewhere between 3900 and 2500 Ma | Cells resembling prokaryotes appear.[12] These first organisms are chemoautotrophs: they usecarbon dioxide as a carbon source and oxidizeinorganic materials to extract energy. Later, prokaryotes evolve glycolysis, a set of chemical reactions that free the energy of organic molecules such as glucose and store it in the chemical bonds of ATP. Glycolysis (and ATP) continue to be used in almost all organisms,
unchanged, to this day.[13][14] |
3800 Ma – 2500 Ma Date | Event | 3500 Ma | Lifetime of the last universal ancestor;[15][16] the split between bacteria and archaea occurs.[17] Bacteria develop primitive forms of photosynthesis which at first do not produce oxygen.[18] These organisms generate ATP by exploiting a proton gradient, a mechanism still used in virtually all organisms. | 3000 Ma | Photosynthesizing cyanobacteria evolve; they use water as a reducing agent, thereby producing oxygen as waste product.[19] The oxygen initially oxidizes dissolved iron in the oceans, creating iron ore. The oxygen concentration in the atmosphere slowly rises,
acting as a poison for many bacteria. The Moon is still very close to Earth and causes tides 1,000 feet (305 m) high. The Earth is continually wracked by hurricane-force winds. These extreme mixing influences are thought to
stimulate evolutionary processes. (See Oxygen catastrophe). |
2500 Ma – 542 Ma [edit]Phanerozoic Eon542 Ma – present The Phanerozoic Eon, literally the "period of well-displayed life", marks
the appearance in the fossil record of abundant, shell-forming and/or trace-making organisms. It is subdivided into three
eras, the Paleozoic, Mesozoic and Cenozoic, which are divided by major mass extinctions. 542 Ma – 251.0 Ma Date | Event | 535 Ma | Major diversification of living things in
the oceans: chordates, arthropods (e.g. trilobites, crustaceans), echinoderms, mollusks,brachiopods, foraminifers and radiolarians, etc. | 530 Ma | The first known footprints on land date to 530 Ma, indicating that early animal explorations may have predated the development
of terrestrial plants.[33] | 525 Ma | Earliest graptolites. | 510 Ma | First cephalopods (Nautiloids) and chitons. | 505 Ma | Fossilization of the Burgess Shale. | 485 Ma | First vertebrates with true bones (jawless fishes). | 450 Ma | Land arthropod burrows (millipedes) appear, along with the first complete conodonts and echinoids. | 440 Ma | First agnathan fishes: Heterostraci, Galeaspida, and Pituriaspida. | 434 Ma | The first primitive plants move onto land,[34] having evolved from green algae
living along the edges of lakes.[35] They are accompanied by fungi[citation needed], which may have aided the colonization of land through symbiosis. | 420 Ma | Earliest ray-finned fishes, trigonotarbid arachnids, and land scorpions. | 410 Ma | First signs of teeth in fish. Earliest nautiid nautiloids, lycophytes, and trimerophytes. | 395 Ma | First lichens, stoneworts. Earliest harvestman, mites, hexapods (springtails) and ammonoids. The first known tetrapod tracks on land. | 363 Ma | By the start of the Carboniferous Period, the Earth begins to be recognisable. Insects roamed the land and would soon take to the skies; sharks swam the oceans as top predators,[36] and vegetation covered the
land, with seed-bearing plants and forests soon to flourish. Four-limbed tetrapods gradually gain adaptations which will help them occupy a terrestrial
life-habit. | 360
Ma | First crabs and ferns. Land flora dominated by seed ferns. | 350 Ma | First large sharks, ratfishes, and hagfish. | 340 Ma | Diversification of amphibians. | 330 Ma | First amniote vertebrates (Paleothyris). | 320
Ma | Synapsids separate from sauropsids (reptiles) in late Carboniferous.[37] | 305 Ma | Earliest diapsid reptiles (e.g. Petrolacosaurus). | 280
Ma | Earliest beetles, seed plants and conifers diversify while lepidodendrids and sphenopsids decrease. Terrestrial temnospondyl
amphibians and pelycosaurs (e.g. Dimetrodon) diversify in species. | 275 Ma | Therapsids separate from synapsids. | 251.4
Ma | The Permian-Triassic extinction event eliminates over 90-95% of marine species. Terrestrial organisms were
not as seriously affected as the marine biota. This "clearing of the slate" may have led to an ensuing diversification,
but life on land took 30M years to completely recover.[38] |
Date | Event | From 251.4 Ma | The Mesozoic Marine Revolution begins: increasingly well-adapted and diverse predators pressurise
sessile marine groups; the "balance of power" in the oceans shifts dramatically as some groups of prey adapt more
rapidly and effectively than others. | 245 Ma | Earliest ichthyosaurs. | 240 Ma | Increase in diversity of gomphodont cynodonts and rhynchosaurs. | 225 Ma | Earliest dinosaurs (prosauropods), first cardiid bivalves, diversity in cycads, bennettitaleans,
and conifers. First teleostfishes. | 220
Ma |
Eoraptor, among the earliest dinosaurs, appeared in the fossil record 230
million years ago. Gymnosperm forests dominate the land; herbivores grow to huge sizes in order
to accommodate the large guts necessary to digest the nutrient-poor plants.[citation needed], first flies and turtles (Odontochelys). First Coelophysoiddinosaurs | 215
Ma | First mammals (e.g. Eozostrodon), minor vertebrate extinctions occur | 200 Ma | The first accepted
evidence for viruses (at least, the group Geminiviridae) exists.[39] Viruses are still poorly understood and may have arisen before "life"
itself, or may be a more recent phenomenon. Major extinctions in terrestrial vertebrates and large amphibians. Earliest examples
of Ankylosaurian dinosaurs | 195 Ma | First pterosaurs with specialized feeding (Dorygnathus). First sauropod dinosaurs. Diversification in small, ornithischian dinosaurs: heterodontosaurids, fabrosaurids, and scelidosaurids. | 190 Ma | Pliosaurs appear in the fossil record. First lepidopteran insects (Archaeolepis), hermit crabs, modern starfish, irregularechinoids, corbulid bivalves, and tubulipore bryozoans. Extensive development of sponge reefs. | 176 Ma | First members of the Stegosauria group of dinosaurs | 170 Ma | Earliest salamanders, newts, cryptoclidid & elasmosaurid plesiosaurs, and cladotherian mammals. Cynodonts become extinct while sauropod dinosaurs diversify. | 165 Ma | First rays and glycymeridid bivalves. | 161 Ma | Ceratopsian dinosaurs appear in the fossil record (Yinlong) | 155 Ma | First blood-sucking insects (ceratopogonids), rudist bivalves, and cheilosome bryozoans. Archaeopteryx, a possible ancestor to the birds, appears in the fossil record,
along with triconodontid and symmetrodont mammals. Diversity instegosaurian and theropod dinosaurs. | 130 Ma | The rise of the Angiosperms: These flowering plants boast structures that attract insects and other animals to
spread pollen. This innovation causes a major burst of animal evolution
through co-evolution. First freshwater pelomedusid turtles. | 120 Ma | Oldest fossils of heterokonts, including both marine diatoms and silicoflagellates. | 115 Ma | First monotreme mammals. | 110 Ma | First hesperornithes, toothed diving birds. Earliest limopsid, verticordiid, and thyasirid bivalves. | 106 Ma | Spinosaurus, the largest theropod dinosaur, appears in the fossil record. | 100 Ma | Earliest bees. | 90 Ma | Extinction of ichthyosaurs. Earliest snakes and nuculanid bivalves. Large diversification in
angiosperms: magnoliids, rosids,hamamelidids, monocots, and ginger. Earliest examples of ticks. | 80 Ma | First ants. | 70 Ma | Multituberculate mammals increase in diversity. First yoldiid bivalves. | 68 Ma | Tyrannosaurus, the largest terrestrial predator of North America appears
in the fossil record. First species of Triceratops. |
65.5 Ma – present Date | Event | 65.5 Ma | The Cretaceous–Tertiary extinction event eradicates about half of all animal species, including mosasaurs, pterosaurs,plesiosaurs, ammonites, belemnites, rudist and inoceramid bivalves, most planktic foraminifers,
and all of the dinosaurs excluding their descendants the birds [40] | From 65 Ma | Rapid dominance of conifers and ginkgos in high latitudes, along with mammals becoming the dominant species. Firstpsammobiid bivalves. Rapid diversification in ants. | 63 Ma | Evolution of the creodonts, an important group of carnivorous mammals. | 60 Ma | Diversification of large, flightless birds. Earliest true primates, along with the first semelid bivalves, edentates, carnivorous andlipotyphlan mammals, and owls. The ancestors of the carnivorous mammals (miacids) were alive. | 56
Ma | Gastornis, a large, flightless bird appears in the fossil record, becoming
an apex predator at the time. | 55 Ma | Modern bird groups diversify (first song birds, parrots, loons, swifts, woodpeckers), first whale (Himalayacetus), earliestrodents, lagomorphs, armadillos, appearance of sirenians, proboscideans, perissodactyl and artiodactyl mammals in the fossil record. Angiosperms diversify. The ancestor
(according to theory) of the species in Carcharodon, the early mako sharkIsurus hastalis, is alive. | 52 Ma | First bats appear (Onychonycteris). | 50
Ma | Peak diversity of dinoflagellates and nanofossils, increase in diversity
of anomalodesmatan and heteroconch bivalves,brontotheres, tapirs, rhinoceroses, and camels appear in the fossil record, diversification of primates. | 40 Ma | Modern-type butterflies and moths appear. Extinction of Gastornis. Basilosaurus, one of the first of the giant whales, appeared in the fossil record. | 37 Ma | First Nimravid carnivores ("False Saber-toothed
Cats") - these species are unrelated to modern-type felines | 35 Ma | Grasses evolve from among the angiosperms; grasslands begin to expand. Slight increase in diversity
of cold-tolerantostracods and foraminifers, along with major extinctions of gastropods, reptiles, and amphibians. Many modern mammal groups begin to appear: first glyptodonts, ground sloths, dogs, peccaries, and the first eagles and hawks. Diversity in toothedand baleen whales. | 33 Ma | Evolution of the thylacinid marsupials (Badjcinus). | 30
Ma | First balanids and eucalypts, extinction of embrithopod and brontothere mammals, earliest pigs and cats. | 28 Ma | Paraceratherium appears in the fossil record, the largest terrestrial mammal that
ever lived. | 25
Ma | First deer. | 20 Ma | First giraffes and giant anteaters, increase in bird diversity. | 15 Ma | Mammut appears in the fossil record, first bovids and kangaroos, diversity in Australian megafauna. | 10 Ma | Grasslands and savannas are established, diversity in insects, especially ants and termites, horses increase in body size and develop high-crowned teeth, major diversification
in grassland mammals and snakes. | 6.5 Ma | First hominin (Sahelanthropus). | 6
Ma | Australopithecines diversify (Orrorin, Ardipithecus) | 5 Ma | First tree sloths and hippopotami, diversification of grazing herbivores, large carnivorous
mammals, burrowing rodents, kangaroos, birds, and small carnivores, vultures increase in size, decrease in the number of perissodactyl mammals.
Extinction of Nimravid carnivores | 4.8 Ma | Mammoths appear in the fossil record. | 4 Ma | Evolution of Australopithecus, Stupendemys appears in the fossil record
as the largest freshwater turtle. | 3 Ma | The Great American Interchange, where various land and freshwater faunas migrated between
North and South America.Armadillos, opossums, hummingbirds, and vampire bats traveled to North America while horses, tapirs, saber-toothed cats, and deer entered South America. The first short-faced bears
(Arctodus) appear. | 2.7 Ma | Evolution of Paranthropus | 2.5 Ma | The earliest species of Smilodon evolve | 2 Ma | First members of the genus Homo appear in the fossil record. Diversification of conifers in high
latitudes. The eventual ancestor of cattle, Bos primigenius evolves in India | 1.7 Ma | Extinction of australopithecines. | 1.2 Ma | Evolution of Homo antecessor. The last members of Paranthropus die out. | 600 ka | Evolution of Homo heidelbergensis | 350 ka | Evolution of Neanderthals | 300 ka | Gigantopithecus, a giant relative of the orangutan dies out from Asia | 200 ka | Anatomically modern humans appear in Africa.[41][42][43] Around 50,000 years before present they start colonising the other
continents, replacing the Neanderthals in Europe and other hominins in Asia. | 40 ka | The last of the giant monitor lizards (Megalania) die out | 30 ka | Extinction of Neanderthals | 15 ka | The last Woolly rhinoceros (Coelodonta) are believed to have gone extinct | 11 ka | The giant short-faced bears (Arctodus) vanish from North America, with the last Giant Ground Sloths dying out. All Equidaebecome extinct in North America | 10 ka | The Holocene Epoch starts 10,000[44] years ago after the Late Glacial Maximum. The last mainland species of Woolly mammoth (Mammuthus primigenius) die out, as does the last Smilodon species | 6 ka | Small populations of American Mastodon die off in places like Utah and Michigan | 4500 ya | The last members of a dwarf race of Woolly Mammoths vanish from Wrangel Island near Alaska | 384 ya (1627) | The last recorded wild Aurochs die out | 75 ya (1936) | The Thylacine goes extinct in a Tasmanian zoo,
the last member of the family Thylacinidae |
http://en.wikipedia.org/wiki/Timeline_of_evolution Ideally,
classification should be based on homology; that is, shared characteristics that have been inherited from a common ancestor. The more recently two species have shared a common ancestor, - the more homologies they share, and
- the more similar these homologies are.
Until recent decades, the study of homologies
was limited to However,
since the birth of molecular biology, homologies can now also be studied at the level of Anatomical homology: an example The figure shows the bones in the forelimbs of three mammals: human, whale, and bat (obviously not
drawn to the same scale!). Although used for such different functions as throwing, swimming, and flying, the same basic structural
plan is evident in them all. In each case, the bone shown in color is the radius. Body parts are considered homologous if they have - the same basic structure
- the same relationship to other body parts, and, as it turns out,
- develop in a similar manner in the embryo.
It
seems unlikely that a single pattern of bones represents the best possible structure to accomplish the functions to which
these forelimbs are put. However, if we interpret the persistence of the basic pattern as evidence of inheritance from a common
ancestor, we see that the various modifications are adaptations of the plan to the special needs of the organism. It tells
us that evolution is opportunistic, working with materials that have been handed
down by inheritance. Protein Sequences Protein
sequencing provides a tool for establishing homologies from which genealogies can be constructed and phylogenetic trees drawn. Here are two examples. Hemoglobins Human beta chain | 0 | Gorilla | 1 | Gibbon | 2 | Rhesus monkey | 8 | Dog | 15 | Horse, cow | 25 | Mouse | 27 | Gray kangaroo | 38 | Chicken | 45 | Frog | 67 | Lamprey | 125 | Sea slug (a mollusk) | 127 | Soybean (leghemoglobin) | 124 |
An example of molecular homology. The numbers represent the number of amino acid differences between
the beta chain of human hemoglobin and the hemoglobins of the other species.
In general, the number is inversely proportional to the closeness of kinship. All the
values listed are for the beta chain except for the last three, in which the distinction between alpha and beta chains does
not occur. The
human beta chain contains 146 amino acid residues, as do most of the others.
Cytochrome c Cytochrome c is part of the electron
transport chain down which electrons are passed to oxygen during cellular respiration. [Discussion] Cytochrome c is found in the mitochondria of every aerobic eukaryote — animal, plant, and protist. The amino acid sequences
of many of these have been determined, and comparing them shows that they are related. Human
cytochrome c contains 104 amino acids, and 37 of these have been found at equivalent positions in every cytochrome c that
has been sequenced. We assume that each of these molecules has descended from a precursor cytochrome in a primitive microbe
that existed over 2 billion years ago. In other words, these molecules are homologous. The first step in comparing cytochrome c sequences is to align them to find
the maximum number of positions that have the same amino acid. Sometimes gaps are introduced to maximize the number of identities
in the alignment (none was needed in this table). Gaps correct for insertions and deletions that occurred during the evolution of the molecule. This table shows the N-terminal 22 amino acid residues of human cytochrome c with the corresponding
sequences from six other organisms aligned beneath. A dash indicates that the amino acid is the same one found at that position
in the human molecule. All the vertebrate cytochromes (the first four) start with glycine (Gly). TheDrosophila, wheat, and yeast cytochromes have several amino acids that precede the sequence
shown here (indicated by <<<). In every case, the heme group of the cytochrome is attached to Cys-14. and Cys-17 (human numbering).
In addition to the two Cys residues, Gly-1, Gly-6, Phe-10, and His-18 are found at the equivalent positions in every cytochrome
c that has been sequenced. Molecular homology of cytochrome c (see three-letter code of amino acids) | | | 1 | | | | | 6 | | | | 10 | | | | 14 | | | 17 | 18 | | 20 | | | Human | | Gly | Asp | Val | Glu | Lys | Gly | Lys | Lys | Ile | Phe | Ile | Met | Lys | Cys | Ser | Gln | Cys | His | Thr | Val | Glu | Lys | Pig | | - | - | - | - | - | - | - | - | - | - | Val | Gln | - | - | Ala | - | - | - | - | - | - | - | Chicken | | - | - | Ile | - | - | - | - | - | - | - | Val | Gln | - | - | - | - | - | - | - | - | - | - | Dogfish | | - | - | - | - | - | - | - | - | Val | - | Val | Gln | - | - | Ala | - | - | - | - | - | - | Asn | Drosophila | <<< | - | - | - | - | - | - | - | - | Leu | | Val | Gln | Arg | | Ala | - | - | - | - | - | - | Ala | Wheat | <<< | - | Asn | Pro | Asp | Ala | - | Ala | - | - | - | Lys | Thr | - | - | Ala | - | - | - | - | - | Asp | Ala | Yeast | <<< | - | Ser | Ala | Lys | - | - | Ala | Thr | Leu | - | Lys | Thr | Arg | - | Glu | Leu | - | - | - | - | - | - |
We assume that the more identities there are between two molecules, the more recently they have evolved from a common
ancestral molecule and thus the closer the kinship of their owners. Thus the cytochrome c of the rhesus monkey is identical
to that of humans except for one amino acid, whereas yeast cytochrome c differs from that of humans at 44 positions. (There
are no differences between the cytochrome c of humans and that of chimpanzees.) Phylogenetic trees With such information, one can reconstruct an evolutionary history of the molecule and thus of their respective owners.
This requires - using the genetic code to determine the minimum number of nucleotide substitutions in the DNA of the gene needed
to derive one protein from another and
- a powerful computer
program to search for the shortest paths linking the molecules together.
The
result is a phylogenetic tree. This one (the work of Walter M. Fitch and Emanuel Margoliash) shows the relationship between
20 species of eukaryotes. The numbers represent the minimum
number of nucleotide substitutions in the gene for cytochrome c needed to produce these 20 proteins from a series of hypothetical
ancestral genes at the various branching points (nodes). The tree corresponds quite well to what we
have long believed to be the evolutionary relationships among the vertebrates. But there are some anomalies. It indicates,
for example, that the primates (humans and monkeys) split off before the split separating the kangaroo, a marsupial, from
the other placental mammals. This is certainly wrong. But sequence analysis of other proteins can resolve such discrepancies. Cytochrome c is an ancient molecule, and it has evolved very slowly. Even after more than 2 billion
years, one-third of its amino acids are unchanged. This conservatism is a great help in working out the evolutionary relationships
between distantly-related creatures like fish and humans. But what of humans and the great apes? Their
cytochrome c molecules are identical and can tell us nothing about evolutionary relationships. However, some proteins have evolved much more rapidly than cytochrome c, and these can be used to decipher recent
evolutionary events. During blood clotting, short peptides are cut from fibrinogen converting it into insoluble fibrin. Once removed, thesefibrinopeptides have no further function. They have been pretty much free from the rigors
of natural selection and have, consequently, diverged rapidly during evolution. So they provide data useful in sorting out
the twigs of phylogenetic trees of mammals, for example. DNA-DNA Hybridization As
we saw in the comparison of human and kangaroo cytochrome c, a single molecule provides only a narrow window for glimpsing
evolutionary relationships. The technique of DNA-DNA hybridization provides a way of comparing
the total genome of two species. Let us examine the procedure as it might be used to assess the evolutionary relationship
of species B to species A: - The total DNA is extracted from the cells of each species and purified.
- For each, the DNA is heated so that it becomes denatured into single strands (ssDNA).
- The temperature is lowered just enough to allow the multiple short sequences of repetitive DNA to rehybridize back into double-stranded DNA (dsDNA).
- The mixture of ssDNA (representing single genes) and dsDNA (representing repetitive DNA)
is passed over a column packed with hydroxyapatite. The dsDNA sticks to the hydroxyapatite; ssDNA does not and
flows right through. The purpose of this step is to be able to compare the information-encoding portions of the genome —
mostly genes present in a single copy — without having to worry about varying amounts of noninformative repetitive DNA.
- The ssDNA of species A is made radioactive.
- The radioactive
ssDNA is then allowed to rehybridize with nonradioactive ssDNA of the same species (A) as well as —
in a separate tube — the ssDNA of species B.
- After hybridization is
complete, the mixtures (A/A) and (A/B) are individually heated in small (2°–3°C)
increments. At each higher temperature, an aliquot is passed over hydroxyapatite. Any radioactive strands (A)
that have separated from the DNA duplexes pass through the column, and the amount is measured from their radioactivity.
- A graph showing the percentage of ssDNA at each temperature is drawn.
- The temperature at which 50% of the DNA duplexes (dsDNA) have been denatured
(T50H) is determined.
As the figure shows, the curve for A/B is to the left of A/A, i.e., duplexes of A/B separated at a lower
temperature than those of A/A. The sequences of A/A are precisely complementary so all the hydrogen bonds between complementary
base pairs (A-T, C-G) must be broken in order to separate the strands. But
where the gene sequences in B differ from those in A, no base pairing will have occurred and denaturation
is easier. Thus DNA-DNA hybridization provides genetic comparisons integrated over the
entire genome. Its use has cleared up several puzzling taxonomic relationships. DNA-DNA hybridization can also be used to compare genomes of mixed populations of organisms. For example, - when all the bacteria are extracted from 10 g of uncontaminated soil (there
are about 1010 cells in it!);
- the DNA extracted and purified from the bacteria and
- subjected to DNA-DNA hybridization analysis,
the resulting curves indicate that there are
over a million different species in the soil sample, although the population is dominated by only a few of these. Chromosome Painting Another
way to compare entire genomes is to - attach a fluorescent label to the DNA of individual chromosomes of one species
(e.g., human) and
- expose the chromosomes of another species
to it.
- Regions of gene homology will hybridize taking up the fluorescent
label and the "painted" chromosomes can be examined under the microscope.
The method is a modification of fluorescence in situ hybridization (FISH) and is also called Zoo-FISH. Chromosome painting has shown, for example, that large sections of human chromosome 6 (which includes hundreds of genes in the major histocompatibility complex(MHC) have their counterpart; i.e. homologous genes, in - chromosome 5 of the chimpanzee
- chromosome B2 of the domestic
cat
- chromosome 7 of the pig
- chromosome 23 of the cow
- etc.
Comparing DNA Sequences Proteins
are the expression of genes so why not compare the actual gene sequences? There are several advantages: - DNA is much
easier to sequence than protein. [Link to DNA sequencing.]
- Genes contain sites that are much freer to change during evolution than protein sequences are. These include:
- nucleotides that produce synonymous codons. For example, even if the amino acid at position
20 in two proteins is the same, the codons for that amino acid might be different in the two species.
- Introns and flanking sequences. These regions are relatively free to vary without hurting the final protein
product. In other words, these regions of the genome are under much less pressure from natural selection.
- DNA is more stable than protein in the environment. This raises the possibility of doing DNA sequencing on the remains
of extinct organisms. Neaderthal remains over 38,000 years old have yielded samples of DNA that were successfully sequenced.
Some of the most informative studies using comparative DNA sequencing have been done with In both cases, the genes are present in multiple copies making their isolation easier. Cladistics Ideally,
a system of classification should reflect the genealogies of the organisms. Darwin realized this when he wrote: "our
classifications will come, as far as they can be so made, genealogies". A classification
based strictly on the rule that all members of a group must have shared a common ancestor more recently than they have with
any species outside the group is called cladistics. This phylogenetic tree or cladogram depicts
the evolutionary relationships of 4 hypothetical species. - They are all descended from an ancestor with 5 traits (1,2,3,4,5) to be used in drawing the tree.
- Over the course of time, 3 speciation events occurred producing the branches.
- During this time, several of the ancestral traits evolved into a modified or derived form; each one indicated by a
different color.
Taxonomists who use cladistic
methods have created an extraordinary vocabulary to help them (not necessarily us). o
Ancestral traits are called plesiomorphic(shown
here as black numbers). o
Derived traits are called apomorphic (shown
here as colored numbers). All the members of a clade must share one or more apomorphic traits not found in any other species. o
Derived traits shared by two or
more species are called synapomorphic. Here species A and B share the synapomorphic trait designated
with a blue 3 . o
Ancestral traits shared by two
or more species are called symplesiomorphic. Here, the trait shown as black 1 is a symplesiomorphic
trait retained by all 4 species. |
- Note that in comparing the species, the more recent the common ancestor, the more apomorphic traits they share. Thus
species C and D share 4 of the 5 traits but only three (1, 2, and 5) with species A and only two (1 and 5)
with species B.
Even if we reconstruct a precise genealogy and draw a phylogenetic
tree to represent it, taxonomic problems may still remain. 1. The species is the only taxonomic category that exists in nature. All higher categories (e.g., genus,
family, and order) are purely arbitrary. They are created by taxonomists. For example, o
Should species C and D be placed in a single genus with A and B in another? o
Or are all four
sufficiently closely related that they belong in a single genus? o
Or are all four
so distantly related that they should be placed in separate genera? o
Note that none
of these options (and others besides) violates the fundamental rule that all the members of any one group (or "clade")
must have had a common ancestor more recent than any they share with species in other groups. Those taxonomists who are particularly impressed by the differences between species tend
to increase the number of higher categories. Those with this bias are known fondly as "splitters". "Lumpers",
those taxonomists who marvel at the uniformities they see among species, tend to create fewer higher categories. Thus, splitters
might put each of the 4 species in separate genera while lumpers would put them in a single genus. |
2. Classifications based strictly on cladistics are too complex for convenience. In principle, a separate
category has to be created for all the branches derived from each node of the tree. The box shows the conventional classification
of Homo sapiens (in the order Primates of the class Mammalia). Compare it with the graphic above the box
showing a classification of just the primates based more closely on cladistics.
Scientific names. The Swedish naturalist Carolus Linnaeus — the "father of taxonomy"
— created the system for naming species that is used by biologists throughout the world. The scientific name of each
species consists of two parts: o
the name of the genus to which
it is assigned and o
the "specific epithet"
which identifies the particular species within the genus. Latin names were used by Linnaeus, but so many species have
been discovered since then that now taxonomists simply coin new words and cast the genus name in the form of a Latin noun
and the specific epithet as a Latin adjective. By tradition, both names are printed in italics, and the genus name is capitalized,
but not the specific epithet. Note, too, that the characters of the Roman alphabet are always used even by biologists in countries
where different characters are used for ordinary purposes. | Here is a description of a common jellyfish as it appears in a Japanese guide to marine life. (Reprinted with permission from Hoikusha Publishing Co., Ltd.,
Tokyo, Japan.) |
3. A classification based strictly on evolutionary kinship (cladistics) also may often seem to violate
common sense. Thus a phylogenetic tree showing the evolutionary history that gave rise to the salmon (a fish), the lungfish, and the cow requires — according
to cladistics — that the lungfish and cow be placed in aclade separate from the salmon. Even though the lungfish is a fish, the cow has shared a common ancestor with
it more recently than its common ancestor with the salmon. Although it is traditional to classify the lungfish and the salmon
together in the class Pisces (fishes), and to assign the cow to the class Mammalia, this violates the rule of cladistics. The lungfish and the cow with their apomorphic traits of
o internal nostrils and o
epiglottis are descended from a common ancestor (red arrow) that is also the ancestor of all land-living
vertebrates (including ourselves!). Even Darwin recognized that kinship alone
was not always enough for a sound taxonomy so he added a second criterion — degree of similarity — to be used
in assigning species to a taxonomic category. Other Problems to Drawing Phylogenetic
Trees 1. Deducing the evolutionary history of animals is particularly difficult because all the 24 or more
phyla of animals appeared within a short time before and during the Cambrian and have since evolved along separate lines. This means that all
the branches on the phylogenetic tree are long and bunched so closely at their base that it is difficult to determine their
relationships. 2. Computer power. More data would help, but as more data become available, the ability of computer programs to sort out the
most likely tree becomes overwhelmed. 3. Changing rate of evolution. There is considerable evidence that mutation rates are not steady from branch
to branch in phylogenetic trees. Thus a branch based on molecules that have evolved rapidly would seem longer than otherwise. 4. Back mutations. These
mask the changes that preceded them and make branches look shorter than they should be. 5.
Gene transfer
between species. The recent availability of complete gene sequences
for many bacteria have revealed genes that appear to have passed from one group to another rather than having been descended
from a common ancestor. Most of these "horizontal" gene transfers are between two different species of bacteria,
but the gene sequence of Mycobacterium tuberculosis reveals 8 genes that it appears to have picked up from its human
host! So many horizontal gene transfers have occurred that some bacterial taxonomists despair that a proper phylogenetic tree
can ever be deduced for them. 6. Convergent evolution. Evolution in which two species from different genealogies come to resemble each other is called convergent
evolution and structures that resemble each other superficially (and may serve the same function) are called analogous. There are many examples of marsupial mammals in Australia which bear a striking resemblance to placental mammals
of Europe and North America. The North American woodchuck or groundhog and the Australian wombat (photo courtesy of the Australian
News and Information Bureau), for examples, look superficially to be close relatives. But their similarities are analogous,
not homologous, and have arisen as a result of similar selection pressures in similar ecological niches. The wombat has no
placenta, cares for its young in a pouch as other marsupials do, and should be classified with them. In fact we are more closely
related to the North American woodchuck than the wombat is! In the language
of cladistics, the wombat is placed in a clade with all marsupials because they share the marsupial pouch (an apomorphic trait)
but are nonetheless mammals because they, too, have hair (a plesiomorphic trait). Convergent evolution also occurs at the level of molecules. Examples: o
Cows and langur
monkeys both synthesize a lysozyme that share the same activity, but comparison of their amino acid
sequences indicates that each has evolved from a different ancestral molecule. o
Cows and the bacterium Yersinia both synthesize a tyrosine phosphatase with similar three-dimensional structures around their active site and similar
activity. However, each has evolved from a totally different ancestral molecule. o
The bacterium Bacillus subtilis synthesizes a serine protease that acts just like those synthesized by mammals but not only
has an entirely different primary structure but its three-dimensional structure (tertiary) structure is different as well. 7.
Evolution
of mammals. The first true mammals appeared in the Late Triassic (ca. 200 million
years ago), over 70 million years after the first therapsids and approximately 30 million years after the first mammaliaformes.
The rat-like Hadrocodium appears to be in the middle of the transition to true mammal status — it had a mammalian jaw joint (formed
by the dentary and squamosal bones), but there is some debate about whether its middle ear was fully mammalian.[11] The majority of
the mammal species that existed in the Mesozoic Era were characterized
byMultituberculates.
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