Phylogeny and Systematics

chapter 25

WARM UP: What evidence would you use to create a cladogram?

STANDARDS:

8. Evolution is the result of genetic changes that occur in constantly changing environments.

• d. Students know reproductive or geographic isolation affects speciation.

• e. Students know how to analyze fossil evidence with regard to biological diversity, episodic speciation, and mass extinction.

• f.* Students know how to use comparative embryology, DNA or protein sequence comparisons, and other independent sources of data to create a branching diagram (cladogram) that shows probable evolutionary relationships.

• g.* Students know how several independent molecular clocks, calibrated against each other and combined with evidence from the fossil record, can help to estimate how long ago various groups of organisms diverged evolutionarily from one another.

Figure 25.1 A gallery of fossils

Figure 25.0 Fossil of a fish: perch

Figure 25.1a Dinosaur National Monument

Figure 25.1b Skulls of Australopithecus and Homo erectus

Figure 25.1c Petrified trees

Figure 25.1d Leaf impression

Figure 25.1e Ammonite

Figure 25.1f Dinosaur tracks

Figure 25.1g Scorpion in amber

Figure 25.1h Mammoth tusks

Figure 25.1x1 Sedimentary deposit

Figure 25.1x2 Barosaurus

Phylogeny • Greek phylon, tribe & genesis, origin• The evolutionary history of a species or group of related

species.Systematics• The study of biological diversity in an evolutionary

context.• Reconstruct phylogeny.• Name and classify species.Taxonomy• The branch of biology concerned with naming and

classifying diverse forms of life.

Figure 25.18 Modern systematics is shaking some phylogenetic trees

Fossil record• The ordered array in which fossils appear within layers, or

strata, of sedimentary rocks that mark the passing of geologic time.

Geologic time scale• Consistent sequence of historical periods based on fossils

collected from many sites.• Tells the order in which groups of species present in a strata

evolved but not absolute age.• 4 Eras:

1) Precambrian (4,600 mya - 543 mya) life evolves2) Paleozoic (543 mya - 245 mya) life leaves water3) Mesozoic (245 mya - 65 mya) reptiles4) Cenozoic (65 mya - present) age of mammals

Geologic Time Scale

Radiometric dating• Measurement of certain radioactive isotopes in fossils

or rocks.• Method most often used to determine the ages of

rocks and fossils on scale of absolute time.1) organism accumulates isotopes of elements

while alive- stops upon death. 2) isotopes decay at a fixed rate.3) half-life is the number of years it takes for

50% of the original sample to decay. ex. Carbon-14 / 5,730 years / Nitrogen-14

Uranium-238 / 4.5 billion years / Lead

Figure 25.2 Radiometric dating

Plate tectonics

• Geologic processes resulting from plate movement

• Modern continents are passengers on crustal plates that are swept across Earth’s surface by convection currents of the hot mantle below.

Figure 25.3 Earth’s crustal plates and plate tectonics (geologic processes resulting from plate movements)

Figure 25.3x1 Crustal plate boundaries

Figure 25.3x2 San Andreas fault

Figure 25.4 The history of continental drift

Pangaea• Supercontinent “all land” • Existed 250 million years ago, near the end of the

Paleozoic era• Species that had been evolving in isolation came

together and competed.• Formation had tremendous environmental impact that

reshaped biological diversity by causing extinctions and providing new opportunities for surviving taxonomic groups.

• Began to break up 180 million years ago- divergent evolution.

• ex. Australia isolated for 50 million years (marsupials)

Punctuated mass extinctions• Fossil record reveals an episodic history of:

- Long, relatively quiescent periods- briefer intervals of species turnover.

• Mass extinctions are followed by extensive diversification of surviving taxonomic groups.

-ex. Permian Mass Extinction 250 mya 90% of marine animals (& land) perished-ex. Cretaceous Mass Extinction 65 mya more than 1/2 of all species- dinosaurs

Yucatan crater• Impact Hypothesis- Walter & Luis Alvarez, UCBerkeley• Chicxulub 180 km (10 km)- asteroid/meteorite impact

was enough to darken the Earth for years.

Figure 25.6 Trauma for planet Earth and its Cretaceous life

Continental drift, volcanism, and asteroid impacts may have all played a role in mass extinctions.

Figure 25.6x Chicxulub crater

Figure 25.5 Diversity of life and periods of mass extinction

Taxonomic System of Classification• Developed by Linnaeus in the 18th century• It is a hierarchical system placing species into

broader and broader groups of organisms.• The groups include (from broad to specific)

- Kingdom (keep)- Phylum (pots)- Class (clean)- Order (or)- Family (family)- Genus (gets)- Species (sick)

Figure 25.7 Hierarchical classification

Recently, Domains have been added:• Archeae• Bacteria• EukaryaLinnaeus also developed a system of binomial

nomenclature• All organisms are given two-part latinized name• The genus is the first name and is capitalized • the species is the second name• The names are italicized For example: Canis lupis

• Eukarya Domain• Animalia Kingdom• Chordata Phylum• Mammalia Class• Carnivora Order• Canidae Family• Canis Genus• Lupis Species

Phylo-genetic trees reflect the hierarchical classification of taxonomic groups nested within more inclusive groups.

Cladistics = creating a phylogenic tree based on:a) Anatomical traits that appear as dichotomies, or two-

way branching pointsb) Each branch point represents the divergence of two

species from a common ancestorVarious branches in a cladogram indicate a clade

(from Greek clados, branch) • Consists of an ancestral species and all of its

descendents• New branches or clades are designated by a shared

derived character• Backbone contains the shared primitive characters

Unnumbered Figure (page 494) Cladograms

Ability to pur

Retractable claws

Figure 25.12 Cladistics and taxonomy

Figure 25.11 Constructing a cladogram

A problem with anatomical traits:

convergent evolution

• different species possess common characteristics because they have similar ecological roles and natural selection pressures.

• Some organisms have analogous structures/ adaptations • i.e. wings of butterfly/wings of a bird are analogous

flight equipment.

Molecular changes• Many organisms share similar sequences of DNA and amino acids

(polypeptides)• Mutations- insertions/deletions occur over time• Databases & computer programs are used to assess phylogenetic

relationships that cannot be measured by comparative anatomy or other methods.

Molecular clock: using differences in the sequence of DNA and in protein amino acid sequence to place the origin of taxonomic groups in time.

• Based on the observation that at least some regions of genomes evolve at constant rates.

• The number of nucleotide and amino acid substitutions is proportional to the time that has elapsed since the lineages branched.

Figure 25.19 When did most major mammalian orders originate?

The end.

Figure 25.13 Aligning segments of DNA

Figure 25.14 Simplified versions of a four-species problem in phylogenetics

Figure 25.15a Parsimony and molecular systematics

Figure 25.15b Parsimony and molecular systematics (Layer 1)

Figure 25.15b Parsimony and molecular systematics (Layer 2)

Figure 25.15b Parsimony and molecular systematics (Layer 3)

Figure 25.16 Parsimony and the analogy-versus-homology pitfall

Figure 25.17 Dating the origin of HIV-1 M with a molecular clock