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Biology Chapter 27.docx

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McMaster University
Ben Evans

Chapter 27: Phylogenies and the History of Life Tools for Studying History: Phylogenetic Trees  The evolutionary history of a group of organisms is called its phylogeny  Phylogenies are usually summarized and depicted in the form of a phylogenetic tree  A phylogenetic tree shows the ancestor-descendant relationships among populations or species and clarifies who is related to whom  In a phylogenetic tree, a branch represents a population through time  The point where two branches diverge, called a node, represents the point in time when an ancestral group split into two or more descendant groups  A tip, the endpoint of a branch, represents a group living today or one that ended in extinction  How Researchers Estimate Phylogenies o Phylogenetic trees are an effective way of summarizing data on the evolutionary history of a group of organisms o However, the relationships depicted in an evolutionary tree are estimated from data o To infer the historical relationships among species, researchers analyze the species’ morphological or genetic characteristics or both o Ex. To reconstruct relationships among fossil species of humans, scientists analyze aspects of tooth, jaw and skull structure o To reconstruct relationships among contemporary human populations, investigators usually compare the sequences of bases in a particular gene o The fundamental idea in phylogeny inference is that closely related species should share many characteristics, while distantly related species should share fewer characteristics o Two general strategies for using data to estimate trees  Phenetic approach to estimating trees is based on computing a statistic that summarizes the overall similarity among populations, based on data  Ex. Researchers might use gene sequences to compute an overall “genetic distance” between two populations  A genetic distance summarizes the average percentage of bases in a DNA sequence that differ between two populations  A computer program then builds a tree that clusters the most similar populations and places more divergent populations on more distant branches  Cladistic approach of inferring trees is based on a realization that relationships among species can be reconstructed by identifying shared derived characters (synapomorphies) in the species being studied  A synapomorphy is a trait that certain groups of organisms have that exists in no others  Synapomorphies allow biologists to recognize monophyletic groups, also called clades or lineages  Ex. Fur and lactation are synapomorphies that identify mammals as a monophyletic group  Synapomorphies are characteristics that are shared because they are derived from traits that existed in their common ancestor  How Biologists Distinguish Homology from Homoplasy o Problems arise from the two different approaches o The issue is that traits can be similar in two species not because those traits were present in a common ancestor, but because similar traits evolved independently in two distantly related groups o Homology occurs when traits are similar due to shared ancestry o Homoplasy occurs when traits are similar for reasons other than common ancestry  Ex. The aquatic reptiles called ichthyosaurs were very similar to modern dolphins  Both are large marine animals with streamlined bodies and large dorsal fins  Both chase down fish and capture them between elongated jaws filled with dagger-like teeth  However, no one would argue that both are similar because the traits they share existed in a common ancestor  Phylogeny has shown that ichthyosaurs are reptiles whereas dolphins are mammals  Based on these data, it is logical to argue that the similarities between both result from convergent evolution  Convergent evolution occurs when natural selection favours similar situations to the problems posed by a similar way of making a living  But convergent evolution does not occur in the common ancestor of the similar species (streamlined body and sharp teeth help any species chase down fish)  Convergent evolution is a common cause of Homoplasy and it results in what biologists once called analogous traits o In many cases, homology and homoplasy are much more difficult to distinguish than in the previous example o Ex. The Hox genes of insects and vertebrates  Even though insects and vertebrates last shared a common ancestor 600- 700 mya, biologists argue that their Hox genes are derived from the same ancestral sequences  Several lines of evidence  The genes are organized in a similar way  All of the Hox genes share a 180-base-pair sequence called the homeobox o Polypeptide encoded by the homeobox is almost identical in insects and vertebrates and has a similar function, it binds to DNA and regulates the expression of other genes  Products of the Hox genes have similar functions, they identify the locations of cells in embryos o They are also expressed in similar patterns in time and space o In addition, many other animals on lineages that branched off between insects and mammals have similar genes o This is a crucial observation  If similar traits found in distantly related lineages are indeed similar due to common ancestry, then similar traits should be found in many intervening lineages on the tree of life o To reduce the chance that homoplasy will lead to erroneous conclusions about which species are most closely related, biologists who are using cladistic approaches invoke the logical principle of parsimony o Under parsimony, the most likely explanation or pattern is the one that implies the least amount of change o Ex. A biologist might compare all of the branching patterns that are theoretically possible and count the number of changes in DNA sequences that would be required to produce each pattern o Convergent evolution and other causes of homoplasy should be rare compared with similarity due to shared descent, so the tree that implies the fewest overall evolutionary changes should be the one that most accurately reflects what really happened during evolution  Whale Evolution: A Case History o As an example of how a cladistic approach works, consider the evolutionary relationships of whales and lineage of mammals called the Artiodactyla o Cows, deer and hippos are artiodactylas o Members of this group have hooves and an even number of toes o They also share another feature, the unusual pulley shape of an ankle bone called the astragalus o Along with having feet with hooves and an even number of toes, the shape of the astragalus is a synapomorphy that identifies the artiodactyls as a monophyletic group o Whales do not have an astragalus and are an outgroup of the artiodactyls (species is closely related to the monophyletic group, but not part of it) o When researchers began comparing DNA sequences of artiodactyls and other species of mammals, the data showed that whales share many similarities with hippos o The results supported by the DNA data conflicts with the results supported by morphological data because it implies that the pulley-shaped astragalus evolved in artiodactyls and then was lost during whale evolution o If whales are related to hippos, it implies two changes in the astragalus (a gain and a loss) o If whales are not related to hippos, it implies just one change (a gain) o In terms of evolution of the astragalus, the first theory is less parsimonious than the second theory) o The conflict between the data sets was resolved when researchers analyzed the distribution of the parasitic gene sequence called SINEs (short interspersed nuclear elements), which occasionally insert themselves into the genomes of mammals o SINEs are transposable elements o Data shows that whales and hippos share several types of SINES that are not found in other groups o Specifically, whales and hippos share SINEs numbered 4, 5, 6 and 7 o Other SINE genes are present in some artiodactyls, but not in others o The presence of a particular SINE represents a derived character o Because whales and hippos share four of these derived characters, it is logical to conclude that these animals are closely related o Based on this data, most biologists accept the second theory of two changes as the most accurate estimate of evolutionary history o According to this phylogeny, whales are artiodactyls and share a relatively recent common ancestor with hippos Tools for Studying History: The Fossil Record  Only a fossil record provides direct evidence about what organisms that lived in the past looked like, where they lived and when they existed  A fossil is a piece of physical evidence from an organism that lived in the past  The fossil record is the total collection of fossils that have been found throughout the world  How Fossils Form o Most of these processes that form fossils begin when part or all of an organism is buried in ash, sand, mud or some other type of sediment o Ex. A tree lives in a swampy habitat, the tree drops leaves, pollen and seeds into the mud where decomposition is slow  The tree falls, the trunk and branches break up as they rot  Flooding brings in sand and mud, burying the remains of the tree  Over millions of years, mountains erode and swamp is filled with sediment and the habitat dries o One burial occurs, several things can happen  If decomposition does not occur, organic remains can be preserved intact (intact fossil)  Alternatively, if sediments accumulate on top of the material and become cemented into rocks such as mudstone or shale, sediment weight can compress the organic material below into a thin, carbonaceous film (compression fossil)  If the remains decompose after they are buried, the hole that remains can fill with dissolved minerals and create a cast of remains (cast fossil)  If the remains slowly rot, dissolved minerals can gradually infiltrate the interior of the cells and harden into stone, forming a permineralized fossil, such as petrified wood (permineralized fossil)  Limitations of the Fossil Record o Habitat bias  Organisms that live in areas where sediments are actively being deposited (beaches, mudflats, swamps) are much more likely to form fossils than are organisms that live in other habitats  Within these habitants, burrowing organisms such as clams are already underground before death and are therefore much more likely to fossilize  Organisms that live aboveground in dry forests, grasslands and desserts are less likely to fossilize o Taxonomic bias  Slow decay is almost always essential to fossilization so organisms with hard parts such as bones or shells are most likely to leave fossil evidence  Requirement introduces a strong taxonomic bias  Clams, snails and other organisms with hard parts have a much higher tendency to be preserved than do worms  Similar bias exists for tissues within organisms  Ex. Pollen grains are encased in a tough outer coat that resists decay so they fossilize much more readily than flowers  Teeth are the most common mammalian fossil because they are so hard and decay resistant o Temporal bias  Recent fossils are much more common than ancient fossils  When two of Earth’s tectonic plates converge, the edge of one plate usually sinks beneath the other plate  The rocks composing the edge of the descending plate are either melted or radically altered by the increased heat and pressure they encounter as they move downward into Earth’s interior  These alterations obliterate any fossils in the rock  In addition, fossil-bearing rocks on land are constantly being broken apart and destroyed by wind and water erosion  The older a fossil is, the more likely it is to be demolished o Abundance bias  Because fossilization is so improbable, the fossil record is weighted toward common species  Organisms that are abundant, widespread and present on Earth for long periods of time leave evidence much more often than do species that are rare, local or ephemeral  Life’s Time Line o Precambrian  4.6 bya  Divided into the Hadean, Archaean and Proterozoic eons  Life was exclusively unicellular  Oxygen was virtually absent from oceans and atmosphere for almost 2 billion years after the origin of life  Oxygen levels rose just before the Precambrian o Interval between 542 mya and the present is called the Phanerozoic era and is divided into three eras (each era further divided into periods)  Paleozoic era  Begins with appearance of any animal lineages and ends with obliteration of almost all multicellular life-forms at the end of the Permian period  Origin and initial diversification of animals, land plants and fungi as well as appearance of land animals  Mesozoic ear  Nicknamed the Age of Reptiles  Begins with end-Permian extinction events and ends with extinction of dinosaurs (except birds) and other groups at the boundary between the Cretaceous period and Paleogene period  In terrestrial environments, gymnosperms were the dominant plants and dinosaurs were the dominant vertebrates  Cenozoic era  Divided into the Paleogene period and the Neogene period  Sometimes nicknamed the Age of Mammals because mammals diversified after the disappearance of dinosaurs  On land, angiosperms were the dominant plants and mammals were the dominant vertebrates  Events that occur today are considered to be part of the Cenozoic era  Molecular clock o The hypothesis that some nucleotide substitutions occur at a constant rate over long time periods; consequently, DNA sequence comparisons may be used to estimate timing for evolutionary divergences The Cambrian Explosion  The first animals appear in the fossil record about 570 mya  A burst of diversification occurred soon after that, at the start of the Cambrian period, now known as the Cambrian explosion  About 565 mya, the first animals (sponges, jellyfish and simple worms) appear in the fossil record  Just 50 million years later, virtually every major groups of animals had appeared  In a relatively short time, creatures with shells, exoskeletons, internal skeletons, legs, heads, tails, eyes, antennae, jaw-like mandibles, segmented bodies, muscles and brains had evolved  Arguably the most spectacular period of evolutionary change in the history of life  Cambrian Fossils: An Overview o Cambrian explosion is documented by three major fossil assemblages that record the state of animal life at 570 mya, at 565 to 542 mya and at 525 to 515 mya o Species collected from each of these intervals are referred to respectively as the Doushantuo fossils, Ediacarian fossils and Burgess Shale fossils o These three assemblages all break one of the rules of foss
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