Introduction to Phylogenies: Analyzing the History of Life

1. Ch 27 Introduction - Phylogenies • In biology we must consider profound changes in the nature of life on Earth over immense periods of time. • There are two major analytical tools that biologists use to reconstruct the history of life: phylogenetic trees and the fossil record.

2. Reading a Phylogenetic Tree • A branch represents a population through time. • The point where two branches diverge, called a node (or fork), represents the point in time when an ancestral species split into two or more descendant species • A tip (or terminal node), the endpoint of a branch, represents a group (a species or larger taxon) that is living today or ended in extinction.

3. How Do Researchers Estimate Phylogenies? • Phylogenetic trees are an extremely effective way of summarizing data on the evolutionary history of a group of organisms. • Researchers analyze morphological and/or genetic characteristics to infer phylogenetic relationships among species. • There are two general strategies for using data to estimate trees: the phenetic and the cladistic approaches.

4. The Phenetic Approach to Estimating Phylogenies • The pheneticapproach is based on computing a statistic that summarizes the overall similarity among populations. • A computer program then compares the statistics for different populations and builds a tree that clusters the most similar populations and places more divergent populations on more distant branches.

5. The Cladistic Approach to Estimating Phylogenies • The cladistic approach to inferring trees focuses on synapomorphies, the shared derived characters of the species under study. • Synapomorphies allow biologists to recognize monophyletic groups—also called clades or lineages. Synapomorphies are characteristics that are shared because their common ancestor had them. • When many such traits have been measured, traits unique to each clade are identified and the groups are placed on a tree in the appropriate relationship to one another.

6. Ancestral and Derived Characters • An ancestral trait is a characteristic that existed in an ancestor. • A derived trait is one that is a modified form of the ancestral trait, found in a descendant. • Ancestral and derived traits are relative.

8. Distinguishing Homology from Homoplasy • Problems can arise with both phenetic and cladistic analyses because similar traits can evolve independently in two distant species rather than from a trait present in a common ancestor. • Homology occurs when traits are similar due to shared ancestry. • Homoplasy occurs when traits are similar for reasons other than common ancestry (e.g. convergence). • For example, ichthyosaurs (extinct aquatic reptiles) and dolphins (extant mammals) are very similar, but these similarities are not due to common ancestry.

10. Distinguishing Homology from Homoplasy • Convergent evolution occurs when natural selection favors similar solutions to the problems posed by a similar way of life. • Convergent evolution is a common cause of homoplasy. • [Devil’s Advocate: 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.]

11. Evidence for Homology • Even though insects and vertebrates diverged some 600–700 million years ago, biologists argue that their Hox genes are derived from the same ancestral sequences. • There are several lines of evidence to support this hypothesis: • Groups of Hox genes are organized on chromosomes in a similar way. • All of the Hox genes share a 180-base-pair sequence called the homeobox. • The products of the Hox genes have similar functions.

13. Evidence for Homology • 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—because all of the species in question inherited the trait from the same common ancestor.

14. Using Parsimony • Parsimony is a principle of logic stating that the most likely explanation or pattern is the simplest one (the one that requires the least amount of change). • 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 happened during evolution.

16. Whale Evolution: A Case History • Artiodactyls, including hippos, cows, deer, and pigs, are mammals that have hooves, an even number of toes, and an unusual pulley-shaped ankle bone (astragalus). • Traditionally, phylogenetic trees based on morphological data place whales as the outgroup—that is, a species or group that is closely related to the monophyletic group but not part of it.

17. Whale Evolution: A Case History • DNA sequence data, however, suggest a close relationship between whales and hippos. This tree would require two changes to the astragalus trait. • Recent data on gene sequences called short interspersed nuclear elements (SINEs) show that whales and hippos share several SINE genes that are absent in other artiodactyl groups. • These SINEs are shared derived traits (synapomorphies) and support the hypothesis that whales and hippos are indeed closely related.

22. Tools for Studying History: The Fossil Record • A fossil is the physical trace left by an organism that lived in the past. • The fossil record is the total collection of fossils that have been found throughout the world. • The fossil record provides the only direct evidence about what organisms that lived in the past looked like, where they lived, and when they existed.

23. How Do Fossils Form? • Fossilization preserves traces of organisms that lived in the past. • Most of the processes that form fossils begin when part or all of an organism is buried in ash, sand, mud, or some other type of sediment.

24. Preservation after Burial • There are four main types of fossils: • Intact fossils form when decomposition does not occur. • Compression fossils form when sediments accumulate on top of the material and compress it into a thin film. • Cast fossils form when the remains decompose after burial and dissolved minerals create a cast in the remaining hole. • Permineralized fossils form when the remains rot extremely slowly and dissolved minerals infiltrate the interior of the cells and harden into stone.

25. Fossilization Is a Rare Event • Fossilization only occurs under ideal conditions. • There are 10 specimens of the first bird to appear in the fossil record, Archaeopteryx. • As far as researchers currently know, only 1 out of every 200,000,000 individuals fossilized.

26. Limitations of the Fossil Record • Paleontologists—scientists who study fossils—recognize that they are limited to studying tiny and scattered segments on the tree of life, yet they also know that this is the only way to get a glimpse of what extinct life was like. • There are several limitations of the fossil record: • Habitat bias occurs because organisms that live in areas where sediments are actively being deposited are more likely to fossilize than are organisms that live in other habitats.

27. Limitations of the Fossil Record • Taxonomic bias is due to the fact that some organisms (e.g., those with bones) are more likely to decay slowly and leave fossil evidence. • Temporal bias occurs because more recent fossils are more common than ancient fossils. • Abundance bias occurs because organisms that are abundant, widespread, and present on Earth for a long time leave evidence much more often than do species that are rare, local, or ephemeral.

28. Life's Timeline • The best data available indicate that the Earth started to form about 4.6 billion years ago, and that life began around 3.4 billion years ago. • To organize the tremendous sweep of time between then and now, researchers divide Earth history into segments called eons, eras, and periods. • Radiometric dating allows researchers to assign absolute dates—expressed as years before the present—to events in the fossil record.

29. The Precambrian • The Precambrian encompasses the Hadean, Archaean, and Proterozoic eons. This period spans from the formation of the Earth to the appearance of most animal groups about 542 million years ago (mya). • In the Precambrian era, almost all life was unicellular and hardly any oxygen was present.

34. The Phanerozoic Eon • The Phanerozoic eon spans the interval between 542 mya and the present. It is divided into three eras—the Paleozoic, the Mesozoic, and the Cenozoic—that are further divided into periods. • The Paleozoic era covers the interval from 542 to 251 mya. • Many animal groups—including fungi, land plants, and land animals—appeared in the Paleozoic era.This era ends with the obliteration of almost all multicellular life-forms at the end of the Permian period.

35. The Phanerozoic Eon • The Mesozoic era (Age of Reptiles) covers the interval from 251 to 65.5 mya. • This era saw the rise and dominance of the dinosaurs and ended with their extinction. • The Cenozoic era (Age of Mammals) includes the interval from 65.5 mya to the present. • During this time the mammals diversified after the disappearance of the dinosaurs. • Events that occur today are considered to be part of the Cenozoic era.

41. Changes in the Oceans and Continents • Earth’s crust is broken into enormous plates that are in constant motion, driven by heat rising from the planet’s core. • Movement of these plates has dramatically shifted the extent and position of the continents over time. • There have been major changes in climate as well.

45. Adaptive Radiations • An adaptiveradiation is when rapid speciation in a single lineage is followed by divergence into many different adaptive forms. • The Hawaiian silverswords fulfill the three hallmarks of an adaptive radiation: • They are a monophyletic group. • They speciated rapidly. • They diversified ecologically. • Biologists use the term nicheto describe the range of resources that a species can use and the range of conditions that it can tolerate. Silverswords occupy a wide array of niches.

47. Why Do Adaptive Radiations Occur? • Two general mechanisms can trigger adaptive radiations: new resources, and new ways to exploit resources.

48. Ecological Opportunity as a Trigger • One of the most consistent triggers of adaptive radiations is ecological opportunity—the availability of new types of resources. • For example, biologists have documented adaptive radiations of the Anolis lizards of the Caribbean islands. • On the two islands studied, the same four ecological types eventually evolved, because the islands had similar varieties of habitats. Therefore, similar adaptive radiations took place independently on the two islands, triggered by the available environment and lack of competition.