Macroevolution Macroevolution: major patterns and changes among living organisms over long periods of time. The evidence comes from 2 main sources: fossils and comparisons between living organisms.

Examples

How Large Scale Changes Occur The classical Neo-Darwinists thought that the same forces that drive microeveolution also cause macroevolutionary changes, given enough time. That is, selection pressure gradually changes the form of a species, and speciation events cause two species to slowly diverge from each other. This theory can be called the “gradualist” model of macroevolution. A more recent theory, “punctuated equilibrium”, says that the large scale changes occur rapidly in small, isolated groups, due to mutations that significantly alter the form of the organism. Gradual changes occur in between bouts of major changes. This theory’s modern version is due to Stephen Jay Gould and Niles Eldredge.

Fossils Fossils are the remains of living organisms, often converted into rock. Bones, teeth, shells, seeds, footprints, leaf prints, etc. If an organism is buried so that large and small decay organisms don’t destroy it, water slowly dissolves away the organic material and replaces it with inorganic compounds: calcium carbonate is a common form. As sediments accumulate above, pressure squeezes fossils, so they are often distorted and flattened. Some fossils are not turned to rock: insects in amber (fossilized tree sap) and sometimes ancient bones. Occasionally possible to extract DNA from them. Fossils are exposed when erosion removes the overlaying rock, or when people dig them up n rock quarries and road cuts. Becoming a fossil is very unusual: most organisms decay to nothing.

Fossils in Sedimentary layers Two main sources of rock layers: sediments piling up at the bottom of lakes and oceans, and volcanic ash. Disruption of layers is caused by erosion, which can remove whole layers, and mountain-building, which folds the layers and sometimes even turns them over. But, in most cases, older rocks are underneath newer ones. Maps of rock strata show where different layers lie relative to each other, and where they are exposed on the surface. The maps can be used to detect loss of layers by erosion.

What does the Fossil Record Show? It is quite spotty. If you are looking for specific fossils, they are hard to find. Estimated 250,000 fossil species known, mostly from the past 600 million years. Currently alive: estimated 4 million. So, lots are missing. Bias in the fossil record: hard parts are easier to fossilize. Very few insect fossils, for instance, despite their prevalence in the world today. General, obvious trend: living things get more complex over time. There were invertebrates before there were fish, fish before reptiles, reptiles before mammals, for example. Clear intermediate forms are rare: the “missing link” between apes and humans, for example. However, there is a list of 139 examples of gradual species to species transitions that are very well documented in the fossil record. The fossil record is like taking single frames from a movie—we miss much of the action and need to fill in the gaps ourselves. Lack of intermediate forms has stimulated the punctuated equilibrium idea. “Explosions” of new species—adaptive radiation– is a common event in the fossil record. Mass extinctions are also common. Note that mass extinctions can occur over thousands of years are still seem almost instantaneous in the fossil record—sediments are usually laid down slowly.

Plate Tectonics Plate tectonics = slow movement of continents over long periods of time. From the earliest maps of the Atlantic Ocean and surrounding land it was obvious that the bulge of South America appears to fit into the side of Africa. The idea that continents can move, that this isn’t just a coincidence, was proposed in the 1930’s by Albert Wegener. No good mechanism, and it didn’t fit current theories—his theory was ignored or attacked. Mapping of the ocean floors in the 1960’s showed that new ocean floor was being created by volcanoes in the mid-ocean ridge, and then spreading out from there. Rocks get older as you move away from the ridge. Conintental rock is ligher than ocean rock—continents float on top. The plates ocean rocks are pushed underneath continents at deep ocean trenches. Plates can also slide past each other (as in California) or crash into each other (as in India). Volcanoes erupt near plate boundaries: the plates going underneath melt and buddle up to the surface again. The theory is very widely accepted today, and it explains most of the world’s geology.

More Plate Tectonics

Still More

Biogeography How plate tectonics affects life. Biogeography is the study of how the spatial patterns of living things developed. Continents have split apart, moved around, then rejoined, all very slowly. There are coal beds in Antarctica, for example, laid down when that part of the world was near the equator. Identical rock layers with particular fossils in them are found in different continents—they were laid down as one bed, then the continents broke up and now they are widely separated. Distribution of current species can also be explained by continental movements.

Continents Colliding The Great American Interchange. North and South America were not connected until about 3 million years ago. Separate groups of animals developed on each. South America had many marsupials (mammals with pouches, like kangaroos and opossums), armadillos, sloths. North America had rodents, canines, felines, bears. When the continents were joined, it became possible for animals to pass between them Many South American animals became extinct: giant ground sloths, marsupial carnivores—as their habitat was taken over by North American types. Some South American animals have flourished in North America: opossums, armadillos, anteaters.

A More Recent Collision Still ongoing is a collision between the Australian and Asian plates. They are colliding in Indonesia, as a consequence a very volcanic region, home of Krakatoa. Alfred Wallace mapped a line between Borneo and Sulawesi, where entirely different sets of animals, birds, and plants lived, as a result of having evolved on separate plates. Some islands are less than 20 miles apart. On the Australian side, the mammals are marsupials, and on the Asian side, the mammals are placental.

Comparative Morphology Many creatures share characteristics with each other. We have arms and hands, so do monkeys, and other mammals have similar forelegs. The bones among these structures are similar across species. Similarly, all vertebrates have skulls, and the bones among them are quite similar. Morphological divergence: starting form a common ancestor, different species have modified their body parts to fit their situations. The forelimbs of primitive reptiles have been modified to become human hands, rid and bat wings, penguin flippers, horse hooves, dog paws, etc. The basic bones and muscles are all still present, but they have grown or shrunk in the different species. Examining the similarities and differences between structures is one of the main ways species are grouped together. Structures sharing a common origin are called “homologous” structures.

More Divergence Divergent evolution: starting with a common ancestor, then diverging into altered forms. Vertebrate forelimb is an example. Another example: insect wings. Started with 4 wings, equal in size, like a dragonfly. Rear wings have shrunk to tiny balancers in flies. Front wings converted to cases in beetles. All wings expanded in butterflies.

Morphological Convergence Convergent evolution: different organisms developing similar structures independently from each other. Similar solutions to common problems, similar responses to common environmental conditions. Example: the shape of dolphins (mammal), sharks (fish) and icthyosaurs (extinct reptile). All live in the ocean and need to swim fast. Common streamlined body shape. Another example: birds, bats, and insects all have wings with very different structures. Structures with similar functions that have different evolutionary origins are called ‘analogous” structures. Convergence can confound the study of evolutionary relationships. Often attention is paid to small details that seem unimportant to natural selection, to avoid being confused by convergence.

Developmental Patterns To quote Haekel: “Ontology recapitulates phylogeny”. That is, the embryo goes through stages that look a lot like the evolutionary development of species. This idea is better stated as: the early embryos of related species often resemble each other more than the adults do. Why—the basic body plan gets modified from an ancestral pattern as species evolve. Modifications accumulate on top of the original pattern.

Comparative Biochemistry Many genes are found in all living things, because we all use similar metabolism. Ribosomal RNA genes are a common example—all living things make proteins by essentially the same mechanism. Also genes for basic metabolic functions like glycolysis and electron transport. Genes can also be described as homologous and analogous. Homologous genes evolved from a common ancestor; analogous genes perform similar functions, but have different evolutionary origins. Considering homologous genes, the genes of closely related species are or similar than genes from more distantly related species. Increasing time since the divergence of two species gives increasing numbers of random mutations.

Sequence Analysis Example Using a bit of text from the sixth century Irish monk, the Venerable Bede. Manuscripts were copied by hand, leading to errors, just like DNA sequences. Errors are propagated with each successive copying, and new errors appear. The errors can be analyzed to show the order and derivation of the manuscripts. “Before the inevitable journey”

Example MS Century Text 1 9 FORE TH’E NEIDFAERAE 2 10 FORE THAE NEIDFAERAE 3 12 FORE TH_E NEIDFAERAE 4 12 FORE TH_E NEIDFAER_E 5 15 FORE TH_E NEYDFAER_E 6 13 FORE TH_E NEYDFAOR_E 7 12 FORE TH_E NEIDFAOR_E

Cytochrome C Cytochrome C is part of the electron transport system in the mitochondria. It is found in all eukaryotes, and some aerobic prokaryotes as well. The number of amino acid differences between the cytochrome c found in different species is proportional to the time since they diverged.

Protein and DNA Comparisons Genes have functions that are important for life, and so they are subject to natural selection. Mutations that affect critical amino acids will be lethal. This causes some proteins to be almost unvaried between all species. For example, histones are proteins that make up the basic structure of chromosomes. There are only 2 amino acid differences between yeast histone H4 and the same protein in humans. Histone structure is highly conserved, due to a high level of natural selection. However, recall that each amino acid is coded for by a group of 3 DNA bases, a codon. There are more codons (64) than amino acids (20), and several codons code for the same amino acid. Synonymous mutations alter the codon but give the same amino acid. Although the amino acid sequence of histone H4 is virtually identical in all eukaryotes, the number of synonymous changes is very high. Synonymous mutations are selectively neutral. For this reason, most evolutionary studies today try to use DNA and not protein, and they concentrate on synonymous codon changes.

Molecular Clock Mutations happen at random, and synonymous mutations are not subject to selection pressure. So, the accumulation of synonymous mutations should occur at a relatively regular rate. This is the molecular clock concept: the idea that you can date the time since divergence of two species by counting the number of synonymous changes between homologous genes. It tends to work reasonably well as long as you stay within a single type of gene, and if you have some outside evidence to verify it. But, the rate of change varies between genes and between different groups of organism.

Taxonomy How to impose order on the chaos of 4 million species. Attempt to classify them into groups. Some of it is pretty obvious: cats, lions and tigers are all felines; cats, dogs, monkeys, and rats are all mammals; mammals, reptiles, fish are all vertebrates; vertebrates, insects, mollusks are all animals. Carl Linne (Linnaeus) developed the classification scheme we use today, called the binomial system. In it, the first word is the genus (general type), and the second word is the species. Both are in Latin, and the genus is capitalized while the species is not. Thus humans are Homo sapiens. “Homo” is the genus, which we share with some extinct species such as Homo erectus. “sapiens” is the species. Another example: the common black bear is Ursus americanus. Other bears are also part of the genus Ursus: Ursus maritimus (polar bear), Ursus arctos (grizzly bear and Alaska brown bear). Several species in different genera can have the same species name: americanus is a species of Ursus (bear), Homarus (lobster), and Bufo (toad).

Higher Taxa There is clearly order among living things above the level of genus. Taxonomists have developed a hierarchy to describe any organism’s classification: kingdom, phylum, class, order, family, genus, species. “Kings play chess on fine ground sand” is a good mnemonic device for this. For humans: we are in the animal kingdom, the chordate phylum, the class of mammals, the order of primates, family of hominids, genus Homo, species sapiens. The classification scheme roughly indicates evolutionary relationships. But in reality, all evolutionary changes come from one species splitting into 2. A true representation of evolutionary history would be a tree diagram showing when each species split.

Large Scale Classification Schemes Linnaeus originally had two kingdoms: plant and animal. This works OK, but there is no real place for bacteria. They got lumped in with plants, but that isn’t reasonable. A later scheme had 5 kingdoms: the bacteria were in the kingdom Monera, single celled eukaryotes were the kingdom Protista, Fungi had their own kingdom, and the Plants and Animals had separate kingdoms. Recent work with DNA sequencing of the ribosomal RNA genes has shown that the bacteria are deeply divided into 2 groups: the Eubacteria (most of the common bacteria) and the Archaebacteria (dwellers in extreme temperature, pH, salinity, etc.). The Archaebacteria and the Eubacteria are as different from each other as they are from all eukaryotes, as far as the time since they diverged goes. This has led to the “3 domain” model”: life can be classified as Archaebacteria, Eubacteria, or Eukaryote. This scheme is favored by microbiologists. Problem: although the 3 domain model fits evolutionary history well, the differences between Eubacteria and Archaebacteria are not easy to state for non-scientists. I like to think of prokaryote vs. eukaryote as the largest distinction between groups. The book uses a 6 kingdom scheme: eubacteria, archaebacteria, protists, fungi, plants, animals. There is no universal agreement about any scheme, and all schemes are artificial: in all cases, one species split into 2 species are different point in time.

Three Domain Scheme

Five Kingdom Scheme