Reconstructing and Using Phylogenies

1. Chapter 22 Sadava Reconstructing and Using Phylogenies

2. Phylogeny • Evolutionary history of relationships among organisms or their genes

3. Systematics • Scientific study of the diversity of organisms, • Reveals evolutionary relationships between organisms. • Taxonomy • Subdivision of systematics • Theory and practice of classifying organisms. • Organizing them into groups

4. A phylogeny is a hypothesis • Describes evolutionary history of relationships among organisms from their common ancestor • A phylogenetic tree (or cladogram) represents that history • A clade is a branch of phylogentic tree from single common ancestor

5. The timing of divergences is shown by the position of nodes on a time or divergence axis Lineages can be rotated around nodes; the vertical order of taxa is largely arbitrary These two cladograms are the same

6. A taxon (plural taxa) is any group of species that we designate to talk about at that time e.g., vertebrates, Animalia A taxon that consists of all descendents of a single common ancestor is called a clade Blue arrow represents common ancestor to the tetrapods Yellow arrow represents common ancestor to the mammals

7. Two species that are each other’s closest relatives are sister species Two clades that are each other’s closest relatives are sister clades

8. All life is connected through evolutionary history The “Tree of Life” is complete, 4-billion-year history of life Knowledge of evolutionary relationships is essential for making comparisons in understanding all levels of biology http://www.ecplanet.com/pic/2006/04/1145173301/treeoflife_haeckel.jpg A modern tree of life from the European Molecular Biology Laboratory (left), and Haeckel’s tree, circa 1879 http://www.scienceinschool.org/repository/images/issue2tree2_large.jpg

9. Phylogenists try to determine traits that differ within a group of interest (taxon) Then hypothesize when and why traits evolved Often, we wish to know how the trait was influenced by environmental conditions or selection pressures http://taggart.glg.msu.edu/isb200/BISTOND.JPG

10. Some Terminology • Ancestral traits – inherited from common ancestor • Homologous trait – trait that is the same in 2 or more species, inherited from common ancestor • Vertebrate in Subphylum Vertebrata • Derived trait – trait that differs from ancestral form • All organisms in Phylum Chordata have notochord, but only forms into vertebrate in organisms in Subphylum vertebrata • Synapomorphy – derived trait shared by group of organisms • Vertebrate in Subphylum Vertebrata • Homoplasies – when talking about convergent evolution, traits that are similar for reason OTHER than inheritance from common ancestor • Leglessness in snakes and worms • Wings in bats and birds

11. Examples • Derived traits • Common ancestor to birds had flight, secondarily lost in penguins • No flight is synapomorphy in Order Sphenisciformes • Common ancestor to mammals was tetrapod but secondarily lost in dolphins and whales • No legs is synapomorphy in Cetacea • Derived traits are recent traits

12. Traits first appearing in more recent ancestor should be shared by fewer species • Trait E showed up recently and is only in crocs and birds • These shared traits, inherited from a common ancestor, are called ancestral traits • Trait A is anscestral trait found in all of the animals in figure • Trait F is ancestral trait only in primates and rodents http://www.msu.edu/course/isb/202/ebertmay/images/Vert%20Tree%20Redrawn.jpg

13. Comparison www.imp.univie.ac.at/hartmann/images Homologous • Features (DNA sequences, behavior, or anatomical feature) shared by two or more species that descended from a common ancestor • e.g. vertebral column is homologous in all vertebrates (derived from common ancestor) Derived trait – trait that differs from its ancestral form • e.g. – verterbral column derived from ancestral notochord (vertebral column not shared with all chordates) Trait present in ancestor of a group is ancestral trait www.microscopy-uk.net/mag/imgdec00

14. Comparison • Derived or Ancestral? • Depends on point of reference in a phylogeny • Example: Looking at the vertebrates • Bird feathers – modified scales • Present in common ancestor of birds • Ancestral trait for modern birds • Not present in other vertebrates • Therefore, feathers are a derived trait found in only birds • Also, since it’s a derived trait found only in birds, it is a synapomorphy for birds

15. Comparison • Derived or Ancestral??? • Two processes make this determination of what traits are ancestral or derived difficult: • Convergent evolution – independently evolved features subjected to similar selective pressures become superficially similar (a.k.a. analogous structures) • Evolutionary reversal (see below)

16. Comparison – Convergent Evolution • An example of covergence – independently-derived • Snakes (a reptile) are vertebrates that lack legs • Caecilians are also vertebrates (amphibians) that lack legs – completely different evolutionary history • Can you think of other legless animals? Coral snake http://www.l-costaricalink.com/costa_rica_fauna/wildlife _images/purple_caecilian.jpg http://static.howstuffworks.com/gif/willow/coral-snake-info0.gif

17. Comparison – Convergent Evolution

18. Comparison – Evolutionary reversal http://www.theage.com.au/ffximage/2007/04/16/snake,0.jpg • Evolutionary reversal – character reverts from a derived state back to an ancestral state • Leglessness in snakes and caeciliansis a reversal to the ancestor of tetrapods (with legs) to no legs • While most frogs have lost their lower jaw teeth (their common ancestor had lower teeth), one (Gastrotheca) has “re-evolved” lower teeth – reversing character state Whip snake Gastrotheca guentheri http://www.puce.edu.ec/zoologia/vertebrados/amphibiawebec/especies/anura/Hemiphractidae/guentheri/guentheri_f_f_p_tng.gif

19. http://www.theage.com.au/ffximage/2007/04/16/snake,0.jpg Convergent evolution and evolutionary reversal generate homoplastic traits, orhomoplasies: • Traits that are similar for some reason other thaninheritance from common ancestor • Snakes and worms have a homoplasy of leglessness Whip snake Gegeneophis mhadeiensis http://www.puce.edu.ec/zoologia/vertebrados/amphibiawebec/especies/anura/Hemiphractidae/guentheri/guentheri_f_f_p_tng.gif http://scienceblogs.com/zooillogix/caecilian.bmp

20. Comparison Distinction between ancestral and derived traits is critical in reconstructing phylogenies. • Particular trait may be ancestral or derived, depending on the group or level of interest. • E.g. In rodents, continuously growing incisors are ancestral because all rodents have them. • But in phylogeny of all mammals, continuously growing incisors are derived trait unique to rodents http://www.unk.edu/acad/biology/Faculty.Biology/Springer

21. Distinguishing derived traits from ancestral traits may be difficult because traits often become very dissimilar • For example – leaves have specific functions but can look very different from plant to plant

22. How Are Phylogenetic Trees Constructed? Computer programs are now used to analyze traits and construct trees Systematists use many characters to reconstruct phylogenies, including • structural characters of living and fossil organisms • developmental characters • physiological • behavioral • Molecular – DNA sequence of genes http://www.fossils.duke.edu/research

23. Morphology Most species have been described on basis of morphological data – size and shape of body parts E.g. features of the skeletal system in vertebrates, floral structures in plants Limitations: comparing distantly related species some morphological variation is caused by environment some species show few morphological differences http://www.calacademy.org/exhibits/skulls/structure_function/

24. Developmental stages reveal similarities among organisms Taking a look at growing embryos • but similarities may be lost in adulthood • For example – larval form of sea squirt resembles other chordates but notochord is lost in adult (pictured right) http://www.umanitoba.ca/faculties http://www.sms.si.edu

25. The Evolutionary Relationship between Sea Squirts and Vertebrates

26. Paleontology Fossils provide information about morphology of past organisms, and where and when they lived Important in determining derived and ancestral traits, and when lineages diverged Limitations: fossil record is fragmentary and missing for some groups http://www.biologycorner.com/resources/fossil_collage.jpg

27. Behavior Behavior can be inherited or culturally transmitted Bird songs are often learned, and may not be a useful trait for phylogenies Frog calls are genetically determined and can be used in phylogenetic trees http://darwin.biology.utah.edu/Images/Critters/Swift.jpg http://darwin.biology.utah.edu/Images/Projects/BehaviorFig2.jpg

28. Molecular data DNA sequences have become most widely used data for constructing phylogenetic trees Mitochondrial and chloroplast DNA is used as well as nuclear DNA. RNA sequences often used for higher-level relationships Gene product information, such as amino acid sequences, are also used www.mun.ca/biology/scarr http://lectures.molgen.mpg.de/ProteinStructure/Levels

29. http://ejournal.sinica.edu.tw/bbas • Comparing the primary structure of proteins: • Homologous proteins are obtained and number of amino acids changed since lineages diverged from common ancestor are determined. • DNA base sequences: • Chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) have been used extensively to study evolutionary relationships • Mitochondrial DNA is used to map relationships between closely related species and individuals MtDNA used to map human migrations http://abagond.files.wordpress.com/2010/01/ftdna-map.gif

30. Example: Relationships among apes and humans • Investigated using hemoglobin pseudogene • Hemoglobin gene was duplicated but is now nonfunctional because of mutation but it is present • Sequence is compared with humans, chimps, and gorillas • Indicates chimpanzees and humans share a more recent common ancestor with each other than they do with gorillas. • Therefore, chimps and humans are more closely related than chimps and gorillas. http://www.pubmedcentral.nih.gov

31. How Do Biologists Use Phylogenetic Trees? Phylogenetic analysis can be important in understanding zoonotic diseases (infectious organisms are transmitted to humans from another animal host) Example: HIV was acquired from chimpanzees and sooty mangabeys. Sooty mangabey http://pin.primate.wisc.edu/fs/sheets/images/450med.jpg

32. Rate of evolution of influenza virus is high Phylogenetic analysis helps biologists predict which currently circulating strain are most likely to survive and leave descendents This information is then used to formulate influenza vaccines http://www.ifpma.org/Influenza/content/images/diagram_virus_thumb.jpg

33. Explicit rules govern the use of scientific names Ensures that there is only one correct scientific name for any taxon.

34. Binomial nomenclature • Two-name system of biological classification • Developed by Carolus Linnaeus in 1758 • Common names vary by location and language • Scientific names are universal • Genus species • Genus is capitalized, species is not • Has to be italicized (Genus species) or underlined (Genusspecies)

35. Abbreviations in taxonomy • For references to multiple species in a genus • Abbreviation “spp.” is often used • Drosophila spp. • If identity of species is uncertain, the abbreviation “sp.” may be used • Drosophila sp. • If organism is referred to numerous times, the genus is abbreviated, after first reference. • D. melanogaster for Drosophila melanogaster http://www.lightblog.com/member/premenopaws/images/drosophila.jpg

36. Biological Classification andEvolutionary Relationships Any group of organisms treated as a unit is called a taxon (plural, taxa), at any taxonomic level • Species and genera are further grouped into higher taxonomic categories • Category above genus is family. Family names end with the suffix “-idae” for animals and “-aceae” for plants. • Families in turn are grouped into higher taxa: orders, classes, phyla, and kingdoms • Application of these levels is somewhat subjective

37. Figure 25.6 Hierarchy in the Linnaean System

38. Biological classification systems and unique names are important for several reasons. • They are aids to memory and precise communication. • They improve the ability to infer relationships among organisms, and are also useful for predictions in scientific investigations

39. Most taxonomistsbelieve biological classification systems should reflect evolutionary relationships • Taxonomic units should be monophyletic • Can create confusion with traditional groupings • A monophyletic group (taxon or clade) contains… • all descendants of a particular ancestor and… • no other organisms • A polyphyletictaxon contains members with more than one recent common ancestor • A paraphyletic group contains some, but not all, of the descendants of a particular ancestor

40. Paraphyletic taxon– contains some but not all descendants (missing A) • Polyphyletic taxon – contains organisms that do not share same recent common ancestor (E+F, but not G) • Monophyletic taxon– contains all descendants of single ancestor, but no others

41. A true clade or monophyletic group can be removed from the tree by making a single “cut” Taxonomists agree that polyphyletic and paraphyletic groups are not appropriate taxonomic units (not a “single cut”) These groups are gradually being eliminated and taxonomic classifications revised – though it can upset traditionalists

42. The traditional “Reptilia” is paraphyletic • It does not include all descendants of its common ancestor -birds are excluded. • Birds considered a distinct grade because they evolved unique derived traits since they separated from reptiles

43. Current tendency is to change classifications to eliminate paraphyletic groups; • however, some familiar taxonomic categories (e.g. reptiles) are paraphyletic and will probably remain in use