Chapter 25: Phylogeny and SystematicsLecture OutlineOverview: Investigating the Tree of Life• Evolutionary biology is about both process and history.◦ The processes of evolution are natural selection and other mechanisms that change the genetic composition of populations and can lead to the evolution of new species.◦ A major goal of evolutionary biology is to reconstruct the history of life on earth.• In this chapter, we will consider how scientists trace phylogeny, the evolutionary history of a group of organisms.• To reconstruct phylogeny, scientists use systematics, an analytical approach to understanding the diversity and relationships of living and extinct organisms.◦ Systematics have traditionally studied morphological and biochemical resemblances among organisms as a basis for inferring evolutionary relationships. ◦ In recent decades, systematists have gained a powerful new tool in molecular systematics, whichuses comparisons of DNA, RNA, and other molecules to infer evolutionary relationships betweenindividual genes or even entire genomes.• This information explosion is enabling evolutionary biologists to construct a universal tree of life, which will be refined as the database of DNA and RNA sequences grows.Concept 25.1: Pylogenies are based on common ansestries inferred from fossil, morphological, and molecular evidence• Fossils are the preserved remnants or impressions left by organisms that lived in the past.• Fossils can establish relationships between living organisms because they reveal ancestral characteristics that may have been lost over time in certain lineages.The Fossil Record• Sedimentary rocks are the richest source of fossils.• Sedimentary rocks form from layers of sand and silt that are carried by rivers to seas and swamps, where the minerals settle to the bottom along with the remains of organisms.◦ As deposits pile up, they compress older sediments below them into layers called strata.- The fossil record is based on the sequence in which fossils have accumulated in such strata. - Though sedimentary fossils are the most common, paleontologists also study other types of fossils. ◦ Fossils can be used to construct phylogenies only if we can determine their ages, clarifying the order in which various characteristics appeared and disappeared. - The fossil record is a substantial, but incomplete, chronicle of evolutionary change.◦ The majority of living things were not captured as fossils upon their death.▪ Of those that formed fossils, later geological processes destroyed many.▪ Only a fraction of existing fossils have been discovered.◦ The fossil record is biased in favor of species that existed for a long time, were abundant and widespread, and had hard shells or skeletons that fossilized readily.Morphological and Molecular Homologies• In addition to fossil organisms, certain morphological and molecular similarities among living organisms can indicate phylogenetic history. • Similarities due to shared ancestry are called homologies.• Organisms that share similar morphologies or DNA sequences are likely to be more closely related than organisms without such similarities.• Morphological divergence between closely related species can be small or great.◦ Morphological diversity may be controlled by relatively few genetic differences.Sorting Homology from Analogy• Similarity due to convergent evolution is called analogy.◦ Convergent evolution occurs similar environmental pressures and natural selection produce similar (analogous) adaptions in organisms from different evolutionary lineages. ▪ Similar analogous adaptations may evolve in such organisms.◦ Analogies are not due to shared ancestry.• Distinguishing homology from analogy is critical in the reconstruction of phylogeny.◦ For example, both birds and bats have adaptations that allow them to fly.◦ However, a close examination of a bat’s wing shows a greater similarity to a cat’s forelimb that toa bird’s wing.◦ Fossil evidence also documents that bat and bird wings arose independently from walking forelimbs of different ancestors.◦ Thus a bat’s wing is homologous to other mammalian forelimbs but is analogous in function to a bird’s wing.• Analogous structures that have evolved independently are also called homoplasies.• In general, the more points of resemblance that two complex structures have, the less likely it is that they evolved independently. (comparing complexity of characters being compared) ◦ For example, the skulls of a human and a chimpanzee are formed by the fusion of many bones.◦ The two skulls match almost perfectly, bone for bone.◦ It is highly unlikely that such complex structures have separate origins.◦ More likely, the genes involved in the development of both skulls were inherited from a common ancestor.• The same argument applies to comparing genes, which are sequences of thousands of nucleotides.• Systematists compare long stretches of DNA and even entire genomes to assess relationships betweenspecies.◦ If genes in two organisms have closely similar nucleotide sequences, it is highly likely that the genes are homologous.Evaluating Molecular Homologies• It may be difficult to carry out molecular comparisons of nucleic acids.◦ The first step is to align nucleic acid sequences from the two species being studied.◦ In closely related species, sequences may differ at only one or a few sites.◦ Distantly related species may have many differences or sequences of different length.▪ Over evolutionary time, insertions and deletions accumulate, altering the lengths of the gene sequences.• Deletions or insertions may shift the remaining sequences, making it difficult to recognize closely matching nucleotide sequences.◦ To deal with this, systematists use computer programs to analyze comparable DNA sequences of differing lengths and align them appropriately.• The fact that molecules have diverged between species does not tell us how long ago their common ancestor lived.◦ Sometimes the fossil record provides data about when their common ancestor probably lived. ◦ In species where few fossils have been found, researchers may be able to compare their moleculardivergence with that found in other plant lineages that have more complete fossil records. ▪ These fossil records can serve as a molecular yardstick to measure the appropriate time span of various degrees of divergence.• Just as