Organizing Information About Species AP Biology Spring 2011

Taxonomy and Cladistics

A Rose by Any Other Name…  Taxonomy is the science of naming and classifying species  Early taxonomy had few rules and led to many variations in English and Latin naming

Carolus Linnaeus  Developed a binomial nomenclature based on an organism’s genus and species  This is an organism’s unique scientific name

Carolus Linnaeus  Linnaeus eventually used more exhaustive categories, or taxa, to organize species  The categories included in order from least to most specific are:  Domain  Kingdom  Plylum  Class  Order  Family  Genus  Species Do Kings Play Chess Or Farm Giant Shrimp?

Carolus Linnaeus  Assignment into a taxon is based on shared similarity

Ranking Versus Grouping  Linnaeus developed his taxonomy before knowledge of evolution  Knowledge of evolution makes classification more difficult

Ranking Versus Grouping  Speciation does not happen at a distinct time  Interbreeding may occur during speciation, or distinct populations may interbreed after diverging

Ranking Versus Grouping  Phylogeny takes evolutionary patterns into account when charting biological diversity  Central question in phylogeny is “who is related to whom?”

Ranking Versus Grouping  Cladistics: one phylogenic method that separates species in to clades (branches) based on shared characteristics like physical, behavioral, physiological, or molecular features

Ranking Versus Grouping  Because organisms have many different characters, groupings will differ based on what type of character is used  The result of cladistic analysis is a cladogram, a diagram that shows a network of evolutionary analysis  Cladograms represent data-based hypotheses about species relationships and are pliable based on new or emerging evidence

Comparing Body Form and Function

Comparative Morphology  Comparative morphology: focuses on the comparative study of body form and structure in different organisms

Morphological Divergence  Populations of a species have diverged when gene flow between them has ceased  Eventually common morphological traits will also diverge  However, the changes often represent some homology within a lineage

Morphological Divergence  Morphological divergence is a macroevolutionary pattern where some morphological homology is retained  Vertebrate forelimbs provide an example

Morphological Divergence  Fossilized evidence shows all land vertebrates have a common ancestor that crouched low on the ground and walked on all four legs  This stem reptile had a 5-toe limb that was a adapted into many different land vertebrate lineages that include flight in bats and birds, fins in penguins and dolphins, and degeneration in snakes

Morphological Divergence  Even though the vertebrate forelimbs are different in size, shape, and function, it is clear that they are alike in positioning and structure of the bony elements  Comparisons of early embryos show resemblance in the bony development. These similarities are evidence of shared ancestry.

Morphological Convergence  Similar body parts may emerge separately from different lineages  This is morphological convergence

Morphological Convergence  In this scenario, analogous structures emerge, and while the structures have the same features, they have different evolutionary lineages  Wings provide an example of this convergent evolution

Morphological Convergence  Wing use is all governed by the same physical constraints that govern flight  Birds and bats have homologous forelimbs, but the wing is a thin membranous extensions of the skin  Bird wings are lined with feathers that are extensions derived from skin  Insect wings develop as fused sacs that flatten and strengthened with chitin  Instead of developing around a forelimb

Morphological Convergence  Analogous structures (morphological convergence) are adaptations that emerge after the divergence of the species

Comparing Patterns of Development

Embryo Development  Embryo development is guided by a set of master genes  Some master genes called homeotic genes are responsible for shaping the developing embryo  Mutations in homeotic genes will have a dramatic effect on the final shape of the organism

Similar Genes in Plants  Mutations to a floral identity gene have a dramatic effect on plant morphology  Consider Apetela 1:  In wild cabbage, Apetela 1 mutation causes mutant flowers  In common wall cress, Apetela 1 leads to no flower petals  Apetela 1 mutations affect a wide range of plant lineages

Developmental Comparisons in Animals  How many legs?  All vertebrates go through similar stages in development  Changes in adult body plans can be attributed to mutations in onset, rate, or completion of early development  Dlx is a homeotic gene that causes limb bud formations  Hox is a master gene that suppresses Dlx

Developmental Comparisons in Animals  How many legs cont.  In pythons, Hox is expressed along the length of the embryo; limb buds form but do not develop into legs  Dlx/Hox regulation may be responsible for variations in number and position of limbs in mature animals

Forever Young  Skull development in humans and chimpanzees shows evidence of relationship  Juvenile skulls for humans and chimps are identical in proportion  The skull morphology changes in later development with human adult skulls more closely resembling a juvenile chimp skull

Comparing DNA and Protein

DNA and Proteins  All lineages have a mix of ancestral and novel characters including biochemical traits observed in DNA sequence and protein structure

DNA and Proteins  Mutation is random and can occur anywhere in the DNA  Most mutations are neutral, that is they have little or no effect on a individual’s reproduction or survival  Neutral mutations help to identify when lineages diverge; more closely related species will have more similar mutations compared to lesser relationships

DNA and Proteins  Further evidence of common lineage can be found by correlating changes in the DNA with morphological changes in the fossil record  Biochemical comparisons by DNA sequencing and footprinting have become faster and more accurate with new technologies  The field of comparative genomics deals with these types of comparisons

Molecular Comparisons  Comparisons of amino acid sequences can be used to determine species relationships  The more identical the protein sequence, the more related the species

Molecular Comparisons  Some essential genes have not changed much over time due to their utility.  Take cytochrome b for example  Cytochrome b is essential for electron transfer chains to function properly  The structure of cytochrome b is fairly conserved over a large number of species (fig. 19.9)

Molecular Comparisons  In amino acid sequences, single substitutions may have large or small effects based on the amino acid that is replaced and what it is replaced with  Most mutations that affect phenotype are selected against, some may prove adaptive  Similarities in proteins do not always equal similarity in DNA sequence because of the redundancy in the genetic code

Molecular Comparisons  Mitochondrial DNA can also be sequencing analysis  Mitochondria can be used to determine familiar relationships because the mitochondrial DNA is passed on intact without the effects of crossing over during meiosis or recombination during fertilization

Making Data Into Trees

Making Data into Trees  In order to elucidate evolutionary relationships evolutionary biologists use genomic analysis, morphological analysis, or biochemical analysis (or even combinations of the 3) to describe the character differences

Making Data into Trees  Parsimony analysis: done to determine he most logical connections between species  Parsimony and the basic rule of cladistics, is that simplicity guides relationships  The closer a relationship between species, the least amount of differences  Evolutionary trees with fewest differences are more likely to be correct

Preview of Life’s Evolutionary History

 Hawaiian Honeycreepers:  A period of adaptive radiation led to a series of new Honeycreeper species emerging  However, now that many of these species are becoming extinct due to predation and competition, their genetic diversity is declining

Preview of Life’s Evolutionary History  Phylogeny is an ongoing field of research  We are constantly refining our understanding of evolutionary relationships

Preview of Life’s Evolutionary History  Several ways of defining he big picture of evolution exist  Some evolutionary biologist use a 6 kingdom model where prokaryotes fit into either the bacteria or Archea Kingdom while Plants, Animals, Protists, and Fungi each have their kingdom  Other evolutionary biologists use a 3 domain system where Archea, Bacteria, and Eukaryotes have their own domain