NATURAL PRODUCTS the secondary metabolites

1. NATURAL PRODUCTS thesecondarymetabolites

2. PHASE 5. PHYLOGENETIC SYSTEMS

3. Charles Darwin(1809-1882)

4. An English naturalistandgeologist. • Charles Darwin was born into a wealthy and well-connected family. His maternal grandfather was porcelain manufacturer Josiah Wedgwood, while his paternal grandfather was Erasmus Darwin, one of the leading intellectuals of 18th century England. • He was the fifth of six children of wealthy society doctor and financier Robert Darwin, whowasquietly a freethinker, andSusannah Darwin (Wedgwood). • His fatherwantedhimtohave a medicalcareer, but he found the study of medicine boring.In time he gained a bigdesireforscience, andafterlots of attemptsandstruggles he wasabletojointhejourney of theBeagle.

5. Inthe 1830s Charles Darwin went on thejourney of theBeaglewithCaptainFitzroy. He travelledaroundthe South AmericaandGallapagosIslands, Tahiti, New Zeland, Australia, South Africa, on thewaybacktoEnglandAzoresIslands, stoppingandcollectingspecimensalongtheway. • Duringthevoyage, Darwin observedtheworldaroundhimandformulatedquestionsabout how it had allhappened, how newspecies had comeintobeing, theorigine of mankind, etc. • AfterreturningtoEngland he startedworkingtowardstheanswers.

6. AlfredRusselWallace(1823-1913)

7. Alfred Russel Wallace was a Britishnaturalist, explorer, geographer, anthropologist, and biologist. • He was the seventh of nine children of Thomas Vere Wallace and Mary Anne Greenell. • Thefinancialdifficultiesforced the family to withdraw him fromGrammar School.Wallace workedfirst as a builder in London, andthen as  a surveyor, spending a lot of time outdoors in the countryside, collecting lots of insects. • He was inspired by the chronicles of earlier travelling naturalists, including Alexander vonHumbold, Charles Darwin and William Henry Edwards, and he decided that he also wanted to travel abroad as a naturalist.

8. About 20 yearsafter Darwin, AlfredRussel Wallace wentto South America. He spentfouryearstherecollectingspecimensmostlybirdsandbutterfliestosellthemtothecollectors in London. • TheVictorianswerefascinatedbyallsorts of exotica, andbynaturalhistory in general; unusualspecimensandrarespeciescouldbring a highprice in theLondon. • He had lots of troublesduring his voyages. Once, thecollectionwasembargoedbycustomsforsome time. • Another time, on thewaybacktoEngland, halfwayacrosstheAtlantic, theshipcaught on fire andsank, alongwiththeentirecollection. Wallace lostabsolutelyeverything--fouryears of hard workandsubstantialfinancialinvestment.  He could save only part of his diary and a few studies.

9. AfterreturningLondon, despite having lost almost all of the notes from his South American expedition, he wrote six academic papers (which included "On the Monkeys of the Amazon") and two books; Palm Trees of the Amazon and Their Uses and Travels on the Amazon. He also made connections with a number of other British naturalists—most significantly, Darwin.

10. Wallace did not giveupand set off on a newexpedition, at the age of 31 to 39. Hetravelled through Singapore, Malaysia and Indonesia, to collect specimens for sale and to study natural history. • He collectedbutterflies, birds of paradise, animalsforwhichtherewas a huge market in England, particularly in London. • Wallace collected more than 126,000 specimens in the Malay Islands. • While he was exploring the islands, he refined his thoughts about evolution and naturalselection.

11. In 1858 Wallace wrote a letterto Darwin outlining a theorythathe'dbeendeveloping, abouttheorigin of speciesandthenature of organicchange. • Darwin wasastonished. Wallace wasdescribingthesamenaturalsystemthat he had beenthinkingfor 20 years, but had never had thenervetopublish it. • It was published, along with a description of Darwin's own theory, in the same year.

12. Darwin and Wallace separatelydevelopedtheevolutiontheory at thesame time andpublisheda joinedpaper but thetheorywascreditedto Darwin. • LaterDarwin wrote his masterwork “TheOrigin of Species”, a bookwithmanywords but onlyonepicture. • Thisimageshowshow, through time, newspeciesariseandexistingspeciesgoextinct. • Darwin’s bookOrigin of Speciespublishedin 1859 marks the beginning of the phylogenetic phase of classification.

13. Thetree of life, reproducedfromDarwin’s On theOrigin of Species byNaturalSelectionpublished in 1859

14. A keyfactorthatdarwinintroducedtothestudy of taxonomywasthe time dimension. • Forthefirst time, scientistsrealisedthatthespecieswas not thesameonethat had alwaysexisted, andthestorywasmuchmorecomplicated. • Taxonomy no longerrepresentedthetask of listingallthespecies. • Thepublication of “TheOrigin of Species” created a revolution in thinking, bothforthescientificcommunityandthesociety. 

15. Darwin’sView of Classification • He advocatedandinsisted on genealogy (familytree) as thecriterionforclassification. • He deniedthatsimilarityshould be thebasis of classification. • He acceptsgenealogy as the supporting ofmost similarity, andonly inheritedsimilaritycan be a basis for taxonomy. • Accordingto Darwin, classiŽficationconsists in groupingof beings according to their actual relationships.

16. Darwin is regarded as “thefounder of evolutionarytaxanomy”. • Darwin’s theory of evolution changed the way of biologists’ thought about classification categories. • Biologists now group organisms into categories that represent lines of evolutionary descent, not just physical similarities. • The goal of phylogenetic systematics is to group organisms based on their evolutionary history, not just their physicalsimilarities and differences.

17. Pheneticclassifications are based on overall similarity. • Phylogeneticclassifications tryto reflect the geneaology or evolutionary history of a particular group of plants. • Darwin’s bookOrigin of Speciespublishedin 1859 marks the beginning of the phylogenetic phase of classification. • Plants (as well as other species) were now recognized as being dynamic entities that change through time, one species giving rise to successive species. • Botanists attempted to reflect these relationships in their classifications.

18. Inaccordancewiththeopinion put forwardby Darwin, innovationsweremadein thegrouping of plantswiththe idea of comingfrom a commonancestor.

19. Invitedspeaker: Prof. Dr. Douglas J. Futuyma; NY StonyBrookUniv. The poster of the"II. Evolution, ScienceandEducationSymposium"forcommemoration of Charles Darwin, organisedbyUniversityCouncilsAssociation, Istanbul. 16-17 May, 2009.

20. InvitedSpeaker : Prof. Dr. Andrew Berry, HarwardUniversity The poster of the"IV. Evolution, ScienceandEducationSymposium"forcommemorationof Alfred Wallace, organisedbyUniversityCouncilsAssociation, Istanbul, 21-22 December 2013.

21. CLADISTICS • Inthefirstdecades of the 20thcentury, a newgeneration of taxonomistsstartedtoquestiontheaccepted dogma, andsuggestedalternatives. • Thisnewway of doingtaxonomywascalledcladistics. Thewordcladisticscomesfromclade, derivedfromtheGreekwordforbranch. • A clade is a group of organismsthatsharecharacters, andbyextension, a commonancestor. • Cladistics, also called phylogeneticsystematics, is a taxonomic theory that is based on cladograms.

22. CLADOGRAM • A diagram that shows the evolutionary relationships among a group of organisms is called acladogram. • A clade includes a common ancestor and all its descendants, living or extinct. • Characteristics shared by members of a clade are calledderivedcharacters.

23. CLADOGRAM The nested hierarchy of clades can be shown as a cladogramthat is a group of species that includes a single common ancestor and all descendants of that ancestor. Aclade must include all species that are descended from a common ancestor, and cannot include any species that are not descended from that common ancestor.

24. POLYPHYLETIC A polyphyletic clade includes many species that lack a common ancestor.

25. PARAPHYLETIC A paraphyletic clade consists of an ancestral species and some, of the descendants, but not all.

26. MONOPHYLETIC A valid clade is monophyletic, it consists of the ancestor species and all its descendants. All taxa must be monophyletic!

27. CLADISTICS VS. EVOLUTIONARY TAXONOMY • The important difference between these two theories of taxonomy is that traditional evolutionary taxonomy sometimes accepts paraphyletic clades, while cladistics does not. • Both accept monophyletic clades. • Both reject polyphyletic clades.

28. PHASE 6: MODERN SYSTEMATICS

29. SYSTEMATICS • Biological systematics(simplysystematics) is the study of the diversification of living forms, both past and present, and therelationshipsamong living things through time. • Systematics is fundamental to biology, because it is the foundation for all studies of organisms, by showing how any organism relates to other living things (ancestor-descendant relationships). • Scientists classify organisms in order to study and understand their diversity. • The goal of systematicsis to group species into larger categories that have biological meaning.

30. Systematics is the study of biological diversity and its origins. • It focuses on • understanding evolutionary relationships among organisms, species, higher taxa, or other biological entities, such as genes, • the evolution of the properties of taxa including naturalinherited traits, ecological interactions, and geographic distributions.

31. Systematics is • the study of systems or ofclassification, • the study and classification of organisms with thegoal of reconstructing theirevolutionaryhistories, andrelationships, • phylogenetic (evolutionaryrelationship) classification of livingorganisms.

32. Systematics is the field that • provides scientific names for organisms, • describesthem, • preservescollections of them,  • provides classifications for the organisms, keys for their identification, and data on their distributions, • investigatestheirevolutionaryhistories, • considerstheirenvironmentaladaptations. Taxonomy is the part of Systematics concerned with topics (a) to (d) above.

33. In systematization, the taxonomist asks whether the characteristics of a species support the hypothesis that it descends from the most recent common ancestor of the taxonomic group: Focus is on evolutionary origin of those features. • Systematics is where taxonomy and nomenclature meet. • Thebiological reviews which organise their material in a taxonomic or phylogenetic manner are referred to as “systematic.” • Althoughnowadays, thesystematicsandtaxonomytermsusedsynonymously, systematics has thebroaddefinition as givenabove, andtaxonomy is restrictedtothestudy of classificationanddetermination.

34. CLASSIFICATION • Classification as a process is to form a logicalsystem of categories, eachcontaining a number of organisms, whichallowseasierreferencetoitscomponents. • In classification, the taxonomist asks whether the species contains the defining features of a certain taxonomic grouping.

35. WHAT ARE THE MAJOR GROUPSWITHIN WHICH ALLORGANISMS ARE CURRENTLY CLASSIFIED? • Prokaryota • Bacteria • Archaea • Eukaryota • Protista • Fungi • Plantae • Animalia Phylogeneticandsymbiogenetictree of livingorganisms, showingtheorigins of eukaryotesandevolutionaryrelationshipsbetweenthegroups.

36. Today we still use a derived form of the categoriesfirst published by Linnaeus, although much of the detail has changed. • For example, many single-celled organisms – none of which were known to Linnaeus –are regarded as belonging to a kingdom of theirown, the Protista, which stands alongside theAnimalia andPlantae. • The fungi are no longer considered plants; they also have a kingdom to themselves. • Most surprising, was the discovery arising from genetic studies that protists, plants, animals and fungi, collectively known as the Eucarya, are all relatively similar to each another. Theyhave far moredifferencesdividing them fromtheArchaeaandBacteria.

37. TAXONOMY • Theterm is derivedfromtheGreektaxis (arrangement) andnomos (law). • The science of organising (= classifying) living things into groups reflecting • their natural, • phylogenetic relationships is calledtaxonomy. • The groups are called taxa (sing. taxon). • The goal of Taxonomy today is to produce a formal system for naming and classifying species to illustrate their evolutionary relationships.

38. TAXON (pl. TAXA) • A taxon is anytaxonomicgrouping, such as a phyllum, a family, or a species. It is a usefulterm, and can be usedtoindicatetherank of a group as well as theorganismscontainedwithinthatgroup. • Taxa (singular = taxon) are the major groups of organisms. • Each rank can be subdivided into additional levels of taxa. • Superclass, suborder, etc.

39. THE HIERARCHY OF TAXONOMY • In the 18th century, Carolus Linnaeus designed the hierarchical classification system still in use today. • Theoroticallythere is no limit tothenumber of levelscontained in a hierarchy.

40. The hierarchy ofbiologicalclassification’seight majortaxonomicranks.Life is divided into domains, which are subdivided into further groups. Intermediate minor rankings are not shown.

41. NOMENCLATURE • The assignment of correct names to taxa. • Thestudy of thesystemsandmethods of namingorganisms. • Since, common names vary among languages and even among regions within a single country,also, different species may share a single common name, plantsmust be givenscientificnames. • A useful scientific name must have two characteristics: • Each name must refer to only one species • Everyone must use the same name.

42. The correct way to write scientific names in the binomial nomenclature system is that the genus starts with a capital letter and the species is lowercased. Both words are written in italics.Thescientific name is followedbytheauthor name. • Homonyms are identical names for two different taxa. • Synonyms are different names for the same taxon.

43. The goals of binomial nomenclature and systematics • To study the great diversity of organisms, biologists must give each organism a name. • Biologists also must organize living things into groups in a logical way. Therefore, biologists need a classification system. The science of naming and grouping organisms is called systematics. • The goal of systematics is to determine the phylogeny – the evolutionary history – of a species or group of related species.

44. Phylogenies are deduced by identifying organismal features, characters, that vary among species.These characters can be: • Morphological • Chromosomal • Molecular • Behavioral or ecological

45. The difference between evolutionary classification and Linnaean classification • Evolutionary Classification : The study of evolutionary relationships among organisms is called phylogeny. Classification based on evolutionary relationships is called phylogeneticsystematics, or evolutionary classification. • Evolutionary classification places organisms into higher taxa whose members are more closely related to one another than they are to members of any other group. The larger the taxon, the further back in time all of its members shared a common ancestor. • In this system, organisms are placed into groups called clades. A clade is a group of species that includes a single common ancestor and all descendants of that ancestor. • Aclade must include all species that are descended from a common ancestor, and cannot include any species that are not descended from that common ancestor.

46. The use of DNA sequences in classification • All organisms have DNA. Because DNA is so similar across all forms of life, this molecule can be compared in different species. • In general, the more derived genetic characters two species share, the more recently the species shared a common ancestorand the more closely related they are.

47. Why can genes be considered derived characters? • Genes are passed on from generation to generation. • Organisms share a number of genes. Because all genes mutate over time, shared genes contain differences that can be used as derived characters. • Both humans and yeasts have a gene that codes for a myosin protein. • Their similarities at the molecular level indicate that humans and yeasts share a common ancestry.

48. Whatarethefourmainphyla of theplantkingdom? • Non-VascularPlants • Mossesand “allies,” orrelatedspecies(Bryophytaandallies) • VascularPlantswithSpores • Fernsandallies (Pteridophytaandallies) 3) VascularPlantswithSeeds • Conifersandallies (Coniferophytaandallies) • FloweringPlants(Magnoliophyta)