1. Chapter 25 Phylogeny and Systematics

2. The Fossil Record The fossil record is an incomplete chronicle of evolutionary time and change. Most species that have ever lived did not die in the right place at the right time to be preserved in the fossil record. Regardless, the fossil record is remarkably detailed in its account of biological change over geological time.

3. Morphology and Molecular Similarities In addition to the fossil record, scientists also look at various morphological and molecular similarities among living organisms. This helps them determine relatedness.

4. Homologies Homologies are similarities due to a shared ancestry. Morphological homologies are shared anatomical features which perform a similar, basic function. Genes and DNA can be homologous if their similarities suggest they share a common ancestor. Hox genes.

5. Examining Phylogenies When looking at phylogenies, it is important to keep in mind the differences between homologies and analogies. Homologies indicate a shared ancestry. Analogies similarities in function due to convergent evolution.

6. Convergent Evolution Convergent evolution results when similar environmental pressures and natural selection produce similar adaptations in organisms with different evolutionary lineages. Example: Australian and N. American burrowing moles. Both occupy a similar niche. However, one is a eutherian, the other is a marsupial.

7. Phylogenetic Trees Are branching diagrams that show how organisms are related in the tree of life. The shared characters of a phylogeny are grouped into a branch of dichotomous branching taxa. The branches represent a divergence from a common ancestor.

9. Phylogenetic Trees Patterns of shared characters are depicted in a cladogram. The cladogram doesn’t necessarily represent an evolutionary history, but if the homologies represent a shared ancestry, then the cladogram forms the basis of the phylogenetic tree.

11. A Clade A clade is a group of species which includes the ancestor and all of its descendents. The study of this is called cladistics.

13. Cladistics Cladists seek to classify all members of a particular group of organisms into a particular branch on a tree. Ideally, the branch includes all descendents from a common ancestor and the ancestor--a monophyletic clade.

14. A Paraphyletic Clade This is a grouping which lacks some members. It consists of an ancestral species and some, but not all, of the descendents.

15. A Polyphyletic Clade When we can group a number of organisms together but can’t find their common ancestor, we have a polyphyletic clade.

17. The Distinction Between Homologous and Analogous Similarities It becomes difficult when you have to sort through homologies to determine shared primitive and shared derived characters. A shared primitive character is any character that is shared beyond the taxon we are trying to define. Example: the backbone is the homologous structure the predates the branching of the mammalian clade from other vertebrate clades.

19. The Distinction Between Homologous and Analogous Similarities A shared derived character is a evolutionary novelty that is unique to a particular clade. Example: Hair is a character shared by mammals, but not found in non-mammalian vertebrates. The backbone can qualify as a shared derived character at a deeper branch point that distinguishes all vertebrates from other animals.

20. The Distinction Between Homologous and Analogous Similarities Among vertebrates, the backbone is a shared primitive character because it was present in a common ancestor to all vertebrates. Among eukaryotes it is a shared derived character because it is an evolutionary novelty that is unique to a particular clade.

21. A cladogram depitcs patterns of shared characteristics between species.

22. Outgroups To draw comparisons and differentiate between shared derived characters and shared primitive characters, scientists use outgroups. Outgroups comprise a species or group of species that are closely related to the group being studied, but not as closely related as any study-group members are to each other.

23. Outgroups For example we’re going to examine 5 vertebrates: a leopard, a turtle, a salamander, a tuna, and a lamprey.

24. Outgroups We use an outgroup to serve as a basis of comparison which is a species or group of species closely related to the ingroup--the various species we are studying.

25. Outgroup The outgroup is less closely related than any of the ingroup members are to each other (based on the evidence). The lancet in our example is the good choice of an outgroup. It is a member of the phylum Chordata, but it doesn’t have a backbone. We now build our cladogram by comparing the ingroup with the outgroup.

26. Outgroup Comparison The outgroup comparison is based on the assumption that homologies are primitive characters that predate the divergence of both groups--a notochord in our example. Lancets have notochords their whole life, vertebrates only have them during embryonic development.

28. Outgroup Comparison The species in the ingroup display a mix of shared primitive and shared derived characters. Using the outgroup comparison, we can compare only those characters that were derived at the various branch points.

29. Outgroup Comparison All vertebrates in the ingroup have a backbone which is a shared primitive character present in an ancestral vertebrate but not the outgroup. Going back to the lancet, the lancet is in the outgroup and doesn’t have a backbone.

30. Outgroup Comparison For example, let’s look at hinged jaws. These are absent in lampreys, but are found in other members of the ingroup-- this represents a branch point. The cladogram we’ve developed isn’t a phylogenetic tree, we need more information from fossils, etc. to indicate when the groups first appeared.

31. Phylograms and Ultrametric Trees The chronology of events in the evolutionary history of the organism in study can be represented using a phylogram or an ultrametric tree. Phylograms represent information about the sequence of events relative to one another. Ultrametric trees present information about the actual time that given events occurred.

32. A Phylogram The length of any branch represents the number of changes that have taken place in a particular DNA sequence in that lineage. The longer the line, the more changes that have taken place since divergence.

33. An Ultrametric Tree The branching pattern is similar to that of a phylogram, but all the branches can be traced from a common ancestor to the present.

34. An Ultrametric Tree The branching pattern is based on the data from the fossil record, and is placed in the context of geological time.

35. Much of the evolutionary history of an organism can be seen looking through the genome for differences. Molecular trees have the ability to encompass short and long periods of time because genes evolve at different rates.

36. Example: Ribosome encoding DNA The DNA that codes for rRNA evolves very slowly and can be used to analyze organisms that are very old. Example: mtDNA mtDNA evolves very quickly and is often used to analyze more recent evolutionary events.

37. Gene Duplications These are the most important evolutionary events that increase the number of genes within a genome. They are also important from a phylogenetic standpoint because they allow scientists to examine genomes and look for duplications. The information can then be used to show the relatedness of the organisms to each other.

38. Orthologous Genes These are genes which are passed on in a straight line from one generation to the next, but have ended up in the other gene pools due to speciation--divergent events. Example:  -hemoglobin in humans and mice are orthologous.

40. Paralogous Genes These genes result from gene duplication, and more than one copy is found within a genome. Example: olfactory receptor genes have undergone numerous gene duplications in vertebrates.

42. Orthologous Vs. Paralogous Of the two types of homologous genes, only orthologous genes diverge after speciation. Paralogous genes diverge while they are in the same gene pool because they are present in more than one copy.

43. Orthologous Vs. Paralogous Example: The orthologous gene for  - hemoglobin serves a similar function in humans and mice, but their sequences have diverged since their common ancestor.

44. Orthologous Vs. Paralogous Example: The paralogous genes comprising the olfactory receptor diverge while in the same gene pool because there is more than one copy. Our ability to identify a wide variety of odors reflects this.

45. Genome Evolution The commonality of orthologous genes among a wide variety of organisms demonstrates that all living organisms share many biochemical and developmental pathways. Also, gene duplication has not kept up with increasing phylogenetic complexity. The versatility of our genes enables us to carry out a wide variety of tasks as compared to other organisms.

46. Molecular Clock Making an estimate for how long ago a living organism diverged from a common ancestor requires the use of a molecular clock. A molecular clock measures the absolute time of evolutionary change based on the observations that genes and other regions of genomes evolve at seemingly constant rates.

47. Molecular Clock The main assumptions of the molecular clock: 1. The number of substitutions in orthologous genes is proportional to the time since the species has branched from its common ancestor. 2. For paralogous genes, the number of substitutions are proportional to the time since the genes were duplicated.

48. Molecular Clock As long as there are reliable rates of evolution, we can calibrate the molecular clock by graphing the number of nucleotide differences against the times of a series of evolutionary branch points that are known from the fossil record.

49. Molecular Clock The graph line created form this can then be used to estimate evolutionary episodes that can’t be discerned from the fossil record.

50. a. The volcanic origin of the Hawaiian islands has produced a chain of islands of increasing geological age. The phylogenetic relationships of island endemic birds (for example, the drepananine (honeycreeper) species such as the amakihi, Hemignathus virens and the akiapolaau Hemignathus wilsoni, shown in the tree) and fruitflies (Drosophila spp.) reflect this volcanic 'conveyer belt', with the species of the oldest islands forming the deepest branch of the tree, and the younger islands on the tips of the tree. Orange lines represent the outgroups. b,c. Molecular dates for Hemignathus (panel b) and Drosophila (panel c) confirm this order of colonization, and produce a remarkably linear relationship between genetic divergence and time when DNA distance is plotted against island age. My, million years. Figures from © (1998) Blackwell Publishing.

51. Molecular Clock Although we can use the idea of a molecular clock to estimate genes, age, and behavior, some of them evolve at different rates making estimation difficult.

52. Molecular Clock There are many reasons for why molecular clocks are not entirely accurate: Changes in nucleotide sequences aren’t always occurring at a constant rates and their effects aren’t always neutral. Thus, differences in DNA can evolve at different rates. Differences in the rate of DNA evolution make dating extremely old fossils difficult.