The discovery of the past To study evolution means to dig in the past. The science of past organims is paleontology (greek: palaews: old, logos: science) Paleontology deal with fossils (lat. fodere = to dig) Charles Lyell Georges Cuvier Early paleontology mainly described ancient life within the Linnean framework Modern paleontology tries to reconstruct ancient life. It links therefore ecology and taxonomy. Mary Anning (1799-1847) Richard Owen (1804-1892)

How do animals fossilize? Taphonomy (Greek: tafos: burial; nomos: law) Immediate burial Living organism Death Fossil Remains Buried remains Mineralization Decomposition Decay Bleaching Delayed burial Exposed remains Stratinomy Ginkgo biloba Ginkgo adiantoides Much less than 1% of all organisms fossilize Coral fish Coral fish from Jura Bioerosion

Fossilized Cyanobacteria (stromatolites) from South Africa A fossil forest in Dorset, England formed by fossilized bacteria around old tree stumps. Fossilized Cyanobacteria (stromatolites) from South Africa A fossilized dinosaur footprint from New Mexico A mammoth coprolith (fossilized excrements)

What fossilizes? Hard body materials Soft body materials Soft tissues very seldom fossilize (of about half of all major evolutionary lines no fossils are known) Exceptions are Fast drying out in very arid climates Permanent frozen Preservation in amber or asphalt Substance Examples Calcite (CaCO3) Octocorallia Bryozoa Brachiopoda Polychaeta Ammonita Belemnita Echinodermata Aragonite (CaCO3) Hydrozoa Gastropoda Calciumphosphate Vertebrata (Ca5(OH)(PO4)3) Trilobita Crustacea Opal (SiO2.H2O) Radiolaria Diatomea Porifera Chitin Algae Fungi Arthropoda Cnidaria Priapulida Annelida Cellulose Plantae Tunicata A feathered Dinosaur: Sinosauro-pteryx

Under what conditions do organisms fossilize? Probability of fossilization Moisture gradient Nutrient rich soils River sediments Anaerobic conditions (moorlands) Volcanic ashes Salinity gradient

How complete is the fossil record? Benton MJ, Willis MJ,  &  Hitchin R. 2000. Quality of the fossil record through time. Nature 403: 534-537. Divergence time inferred from cladogram Divergence time inferred from fossils SCI: Quotient of consistent to inconsistent nodes RCI: Relative completeness index GAP: Gap excess index 100% ? Completeness At the family level about 50% of all taxa are known from fossils. 50% Fossils of soft-bodied types are not well known 0% Species Family Order Class Type Taxonomic levels

The tectonic plates (from David Sanfwell, Scripps Inst. Oceanography) Continental drift Alfred Lothar Wegener (1880-1930) The tectonic plates (from David Sanfwell, Scripps Inst. Oceanography) Evidence for plate tectonics: Fit of coastlines Distribution of mountains Continuity of fossils Continuity of geological features Isostasy: Earth acts like a fluid From Press et al.. 2004. Understanding earth, http://www.whfreeman.com/presssiever/con_index.htm?99iex

Continental drift From C. R. Scotese: http://www.scotese.com/future.htm

How to match phylogeny and plate tectonics

Relative dating methods Fossil dating Relative dating methods Relative dating uses geological strata to infer whether fossils are older or younger than a given stratum Layer 1 Younger Layer 2 Time Layer 2 Older Stratigraphy Morphological primitivism

Radiometric absolute dating Absolute dating methods Radiometric absolute dating Most minerals which contain radioactive isotopes are in igneous rocks. The dates they give indicate the time the magma cooled. Potassium 40 is found in: potassium feldspar (orthoclase) muscovite amphibole glauconite Volcanic rocks Sometimes in sediments Uranium may be found in: zircon urananite monazite apatite sphene Surviving atoms C14 Daugther atoms N14 Carbon 14 is used for bones

Calibrating geological time Radiometric dating Absolute time scale Stratigraphy Relative time scale Geological time scale Calibrating geological time Recognition of unique events to subdivide time Radiomtric dating of layers Raw data Post eruption 2 time Post fossil B time Volcanic ash 2 160 ± 10 mya 165 mya Fossil B time Last occurrence of B: Depth [m] First occurrence of 180 mya Pre fossil B time Volcanic ash 1 190 ± 8 mya Pre eruption 1 time Last occurrence of A: Fossil B time Older than 190 mya First occurrence of Pre fossil B time Modified from Andy MacRae: Radiometric Dating and the Geological Time Scale. http://www.talkorigins.org/faqs/dating.html

Dendrochronology analyses tree-ring growth patterns. Fission track Dendrochronology Fission Tracks (FT) are micrometer-sized, linear damage tracks that occur in insulating minerals and that are caused by the spontaneous fission of heavy, unstable nuclides (mostly 238U in natural minerals). Dendrochronology analyses tree-ring growth patterns.

History of the earth Steno founded stratigraphy by stating that geological layers are horizontal and superposed. Deeper layers are older. Nicolas Steno (1638-1686) The Red Rock Canyon, California

The geological time scale Eon Era Period Age at Base (Mya) Duration (Mya) Phanerozoic Cenozoic Quarternary 2 Neogene 23 21   Paleogene 65 42 Mesozoic Cretaceous 140 75 Jurassic 205 Triassic 250 45 Paleozoic Permian 290 40 Carboniferous 355 Devonian 410 55 Silurian 440 30 Ordovician 490 50 Cambrian 540 Proterozoic Neoproterozoic Ediacaran (Vendian) 630 90 Cryogenian 850 220 Tonian 1000 150 Mesoproterozoic 1600 600 Palaeproterozoic 2500 900 Archean 3800 2950 Hadean 4550 750 http://en.wikipedia.org/wiki/Geologic_time_scale

Phylogenetic systematics The reconstruction of phylogeny The first Darwinian principle told that every phylogenetic tree has one common ancestor. Phylogenetic analysis is the study of taxonomic relationships among lineages. Phylogenetic systematics Cladistics (greek κλάδος: branch) Numerical taxonomy Robert Sokal (1926-2012) Willi Hennig (1913-1976)

http://www.faunaeur.org/ http://tolweb.org/tree/phylogeny.html http://www.eol.org/

The cladistic methodology Apomorphies are common derived characters. Autapomorphies are characters that are restricted to single lineages. A B C D adf ade abc abd Plesiomorphies are ancestral derived characters. e c f e d b e: Autapomorphy of lineage D b: Synapomorphy of lineage C+D a d: Plesiomorphy of lineage A It is a symplesiomorphy Ancestor a: Apomorphy of the whole tree It is the ancestral state. The collective set of plesiomorphies defines the ground plan of a phylogenetic tree.

Monophyletic taxon Paraphyletic taxon Polyphyletic taxon B C C is the sister taxon of A and B adf ade abd Character d in lineages A, B, and C is not homologous because it derived twice. It is homoplasious e d f Character a in lineages A, B, and C is homologous because it synapomorph d b a Ancestor Monophyletic taxon Paraphyletic taxon The ultimate aim of taxonomy is to group higher taxa into monophyletic subtaxa. For this task we have to infer autapomorphies Autapomorphy defines monophyly A B C D E f d e f Polyphyletic taxon b b d Ancestor

Reptilia (paraphyletic) Tetrapoda The diversification of an evolutionary tree is called cladogenesis Amniota Archosauria Actino-pterygia Dipnoi Anura Urodela Mammalia Squamata Aves Therosauria Loss of tail apomorph Mammae autapomorph Reptilia (paraphyletic) Feathers apomorph Amnion apomorph Tetrapod limbs apomorph The evolutionary change within a lineage is called anagenesis Common ancestor Lungs plesiomorph

Linnean systematics and cladistics Linnean approach Hierachical encaptive system Phenomenological method based on similarity It uses grades (groups of similar body plan) Different taxonomies are possible There is no clear decision intrument for taxonomies The number of higher taxa is rather small (Pisces, Amphibia, Reptilia, Aves, Mammalia) It does not assume common evolutionary history It does not reconstruct evolution Taxonomy is independent of evolution Hennigean approach Hierachical encaptive system Analytical method based on lineage branching It uses clades (groups of identical root) Only one taxonomic solution is allowed Autapomorphies decide about taxonomic position The number of higher taxa is large (Pisces, Amphibia, Reptilia are not valid taxa ) It is based on common evolutionary history It does reconstruct evolution Taxonomy is a part of evolutionary theory High resolution trees Low resolution trees

The construction of phylogenetic trees from numerical methods The principle of maximum parsimony (Occam’s razor) holds that we should accept that phylogenetic tree that can be constructed with the least number of morphological changes. The raw data A B D E C 110111 001101 101101 010010 8 changes Distance matrix 111111 A B D E C 001101 Outgroup 101101 010010 111111 We are looking for such a tree that minimizes the sum of distances. How to define the root? 010111 110111 7 changes

The number of possible trees Parsimony analysis To find the most parsimonious tree we have to cross all combinations of lineages (trees) with all character combinations at the root. The number of possible trees

Assumption of the numerical methods Characters (or transitions) have to be independent. Impossible character states have to be excluded. Birds Mammals Fish Loss of hairs Loss of feathers Hairs Incompatible Feathers Scales Characters are assumed to have equal importance. In reality transitions are not comparable. To overcome this problem you give character weights. Technically you multiply the occurrence of a character in a distance matrix

Trees from molecular data Distance matrix

Evolutionary time scales The molecular clock Numbers of amino acid substitutions and therefore trespective numbers of nucleotide substitutions are for many proteins and genomes approximately proportional to time. Hence, numbers of substitutions are a measure of time of divergence from the latest common ancestor. Linus Pauling (1901-1994) Motoo Kimura (1924-1994) Emile Zuckerkandl (1922-2013) Tomoko Ohta (1933-) Substitutions alone provide a relative time scale Fitch W. M., Ayala F. J. 1994. The superoxide dismutase molecular clock revisited. Proc. Natl. Acad. Sci. USA 91: 6802-6807. Errors An appropriate calibration adds the absolute time scale Superoxide dismutase

Paleontological versus molecular timescales Molecular estimates point frequently much more ancient divergences of lineages than estimates based on the fossil record. The reason are different speeds of morhological and genetical changes. Changes in genetic constitution accumulate to a point where basic regulatory elements are involved Changes in genetic constitution involve first basic regulatory elements. Gene flow up to 2 mya Time axis Time axis First fossils of placental orders (65 mya) Genetical change Genetical change Molecular divergence (4-5 mya) Eomaia (125 mya) First fossils of erect hominids (6-7 mya) Molecular divergence of placental orders (120-140 mya) Morphological change Morphological change

Paleontological versus molecular timescales Matching of molecular and paleontological timescales in Echinodermata Smith A. B. et al. (2006) Testing the Molecular Clock: Molecular and Paleontological Estimates of Divergence Times in the Echinoidea (Echinodermata). Molecular Biol. Evol. 23: 1832-1851. For the majority of Echinoderm subtaxa molecular divergence estimates are higher than the paleontological estimates. Data from Smith et al. (2006)

Paleontological versus molecular timescales Qun Y., Yunye M., XiaoyanS., Peiyun C. 2007. Phylochronology of early metazoans: combined evidence from molecular and fossil data. Geol. J. 42: 281-295. Data from Qun et al. (2007)

Have all phylogenetic trees a single root? Darwin’s first principle: All species of a given taxon have a common ancestor. Parsimony analysis cannot answer this question. A brush would always have a lower number of character changes Theory of Lamarck A brush means: No speciation. If we except that extinction occurs this would mean a constant decrease in the number of species. Character change within whole species. No genetic (character) variability within populations. Extreme longevity of lineages. Scale of organization Scala naturae Spontaneous origin of simple life forms Time But horizontal gene transfer and might at least in bacteria result in networks and rings!

Today’s reading History of palaeontology: http://en.wikipedia.org/wiki/History_of_paleontology History of earth: http://wiki.cotch.net/index.php/History_of_the_Earth Radiometric dating details: http://www.tulane.edu/~sanelson/eens211/radiometric_dating.htm Geological time scale: http://en.wikipedia.org/wiki/Geologic_time_scale Phylogenetic systematics: http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01 Cladistics: http://en.wikipedia.org/wiki/Cladistics Ernst Haeckel: Kunstformen der Natur (Internet exhibition of original drawings: http://caliban.mpiz-koeln.mpg.de/~stueber/haeckel/kunstformen/liste.html The modern molecular clock: http://awcmee.massey.ac.nz/people/dpenny/pdf/BromhamPenny_2003.pdf