AP Biology Ch. 16 Quiz

Phylogenetic tree and the reconstruction of an ancestral state

Phylogenetic trees can aid in knowing how an extinct organism behaved, what its morphology was like, and possibly what its genome was like. Basically, it helps discover the nature of its biology through the phylogenetic methods. For example, the archosaur, which is extinct, can be analyzed through looking at its opsins, the proteins involved in vision. These opsins differ depending on which amino acids are present, and thus differ in which wavelengths of light they are excited by. These different wavelengths of light, colors, could determine the archosaur's behavior. By performing a phylogenetic analysis on the opsins from living vertebrates, scientists estimated the amino acid sequences that would have been present in the archosaur. In this case, in the reconstructed opsin, it leaned towards the more red wavelength, meaning that the archosaur most likely would have been more active at night.

Split vs. node

A split has to directly halt any interbreeding, urging speciation A node just defines a new lineage; interbreeding can still occur

Molecular data

All heritable variation is encoded in DNA, complete genome contains large set of traits (individual nucleotide bases of DNA) Now most widely used sources of data for construction Not limited to DNA: eukaryotes (mitochondrial DNA [mtDNA] genes) plant cells (chloroplast genes [cpDNA]) cpDNA = slow changes over evolutionary time (ancient relationships) mtDNA = rapid changes over evolutionary time (closely related animals) Nuclear gene sequences Entire genomes Gene products = amino acid sequences of proteins

Homologous features

Any features shared by two or more species that have been inherited from a common ancestor May be heritable traits (DNA sequences, protein structures, anatomical structures, behavior patterns) Ex. vertebral column in all living vertebrates and ancestral vertebrate (homologous in all vertebrates)

Taxon

Any group of biological organisms Very minor differences in one species or widespread differences between species

Taxon

Any group of species Exx. humans, primates, mammals, vertebrates (each taxon member of next, more inclusive taxon)

Clade

Any taxon that consists of all the evolutionary descendants of a common ancestor Can be identified by picking any point on a phylogenetic tree and from that point tracking all the descendant lineages to the tips of terminal branches

Occam's razor

Best explanation is the one that best fits the data while making the fewest assumptions; most complicated explanations are accepted only when the evidence requires them

Purposes of phylogeny

Biology helps us understand organisms, which have cells, which have nuclei, which have DNA, which revel the past relationships of taxa. Realization that a trait may arise more that once in evolutionary history Figuring out origin of complex trait (ex. wings) Molecular clocks (allow determination of relatedness of taxa though DNA --> RNA --> protein --> phenoype, but could bypass proteins/phenotypes and use DNA as molecular clock) Use in medicine = specific targeted cancer therapies (not all cancer results from the same mutation)

Mathematical models and simulations

Can be used to illustrate/support evolutionary concepts

Evolutionary tree

Darwinian theory Principle that's become formalized and more specific, now called the phylogenetic tree

Biochemical/genetic similarities

DNA nucleotide and protein sequences

What can be used for the construction of phylogenetic trees?

DNA sequences, protein structures, morphology/anatomy (ex. vertebral column in vertebrates), or behavior (ex. duck mating dance, orphan duck develops dance w/o any guidance as to how; shows this is heritable trait and not cultural)

Evolution of humans from primate ancestors

Darwin believed that we had a common ancestor w/ apes, but wasn't able to prove this because of lack of fossils and scientific abilities to sequence Mary and Richard Leakey traveled to the Olduvai Gorge and found tools, but not their makers. However, on July 17, 1959, they found an early hominid skull that was around 1.76 million years old (not the tool maker, not advanced enough) The next year, though, Olduvai hominid #7, which was about 1.8 million years old was discovered. OH7 was a separate species of early hominid (there were differences in the skull piece, wrist, and finger bones) This indicated two different lineages evolving at the same time Chimp brain size < early hominid brain size < modern brain All traits must have evolved between 1.8 million years ago and when human and chimp lines separated Using biomolecule/DNA evidence, split was calculated to be ~7 million years ago (before Olduvai). However, this evidence could not address when and where our traits emerged (fossils/ancient environmental evidence can) In East Africa, ancient volcanic activity had placed layers of radioactive ash, which had a steady rate of decay, allowing for accurate sediment/fossil dating Don Johanson traveled to Hadar, north of Olduvai, and found Lucy, a 3.2 million year old 1/2 skeleton that represented Australopithecus (bipeds, smaller brains, no evidence of stone tool use [comes in much later]), evidence of bipedalism was in the pelvis, and this is extremely different from great apes. In Tanzania, an Australopithecus older than Lucy was found, and was dated to approx. 3.75 million years old; this fossil was not a skeleton, though, but instead hominid footprints on hardened volcanic ash, which showed researchers more human foot features than primate foot features, indicating that upright walking was a trait much earlier than Lucy; scientists now wanted to find what was before Lucy Found exposed rock layers dating back 6 mill. yrs., found skeleton w/ head-to-toe coverage of "Ardi" who was Ardipithecus; this skeleton was representative of the earliest known phase of human evolution (4.4 mill. yrs. ago) Detailed features, such as teeth scratches, could be seen, as well as an extension of the lower pelvis, showing that she was a tree climber There was a large toe that stuck out from the side, and this is the first time this is seen in a hominid, but it is common in primates Ardi was neither chimp nor human Ardi showed that bipedality did not evolve in a grassland but rather a woodland (already developed bipedality, spent time in trees), and this took away any doubt that bipedality was extremely ancient (preceded by 4 million years expansion of brain, tool usage, etc.)

Fossil dating/providing evidence for evolution

Dating methods can also provide evidence for evolution Age of rocks where fossil is found, rate of decay of isotopes (Carbon-14), relationships within phylogenetic trees, mathematical calculations that take into account information from chemical properties and/or geographical data

Splits and nodes

Define phylogenetic tree Not arbitrary, must find which ones relate Split = new character arising, ancestral, must stop interbreeding, engage in speciation Node = defines new lineage

Synapomorphies

Derived traits that are shared among a group of organisms and are also viewed as evidence of the common ancestry Ex. vertebral column (shared, derived trait; ancestral = undivided supporting rod)

Which traits can be used in the construction of a phylogenetic tree

Derived traits, ancestral traits Derived traits that are shared by the organisms in a group and indicate a common ancestry are called synapomorphies (ex. hawk wing and penguin flipper) and can be used in a phylogenetic tree Homologous features are any heritable (anything encoded for in the genome, protein structures, anatomical, etc.) features that indicate a common ancestry in more than two organisms

Mathematical models

Describe how DNA sequences change over time Account for multiple changes at given positions in sequence, different rates of change at diff. position in gene, diff. position in codon, among diff. nucleotides

Phases of human evolution

Developed through dating of fossils back 6 million years Ardi, Phase 1, Ardipithecus - Climb in woodlands, walk on two legs Lucy, Phase 2, Australopithecus - Biped, small brain, big teeth for chewing, big/robust faces, more open habitats throughout Africa Phase 3, Homo - Technological primate, depending more and more on culture, tools help compete against scavengers/predators, allowing broadening of diet, geographic range

Phylogenetic tree

Diagrammatic reconstruction of the evolutionary history (phylogeny) Commonly used for species, populations, genes Based on physical structures, behaviors, and biochemical attributes, and now genomic sequencing (greater detail) May depict history of major evolutionary group (ex. insects) or closely related species (smaller group)

HIV and phylogeny

Discover changes in HIV genome that make it resistant to certain drug treatments Association of evolution of resistance and genetic change, tested experimentally

Phylogeny

Evolutionary history of related organisms

Phylogeny

Evolutionary history of the relationships between organisms since all life shares a common ancestor

Analogous features

These are convergent characters Unrelated species with similar characters

Root

Formed by the common ancestor of the organisms in the tree Left (earliest), flowing right (most recent)

Paleontology

Fossil record; show us where/when organisms lived in the past, give us idea of what they looked like Important evidence helps us distinguish ancestral vs. derived traits Reveal when lineages diverged/began their independent evolutionary histories Groups w/ few species that survived to the present, info on extinct species is critical to understanding large divergences among surviving species Limitations: few/no fossils have been found for some groups, record often fragmentary for many

Ingroup

Group of organisms of primary interest

When can you use gene as taxon?

Have mutation providing diversity

Why can't homoplasies be considered in phylogenetic trees?

Homoplasies, which consist of traits that result from convergent evolution or evolutionary reversal, cannot be considered applicable data in the construction of a phylogenetic tree due to the fact that they are non-conservative traits and do not indicate any sort of evolutionary relationship (similar solution to similar problem, doesn't indicate common ancestry)

Horizontal vs. time axis

Horizontal = time axis, has meaning as it shows the timing Vertical = no meaning, vertical distances do not correlated w/ degree of similarity or difference between among groups Lineages can be rotated w/o effect

Maximum likelihood

Identify the tree that most likely produced the observed data, given the assumed model fo evolutionary change Can be used for any characters, most often w/ molecular data (easier to develop models of evolutionary change) Advantages: incorporate more info about ev. ch. than parsimony methods Disadvantages: computationally intensive and require explicit models of evolutionary change (may not be avail. for some kinds of character change)

Conservative characters

Important for the construction of phylogenetic trees Cannot be prone to homoplasies Non-conservative characters are characters that are prone to convergent evolution, evolutionary reversal etc.

Morphology

Important source of phylogenetic information Presence, size, shape, and other attributes of body parts Wealth of data (organisms observed, depicted, studied for millennia; museum, herbarium collections) Electron microscope, CT scans help gather more data in much greater detail Data often specific to a certain group (ex. floral structures) Limitations: some taxa exhibit little morphological diversity (despite great species diversity; ex. leopard frogs, many species look similar, even though there are diff. in behavior/physiology), few morphological traits can be compared across distantly related species (earthworms vs. mammals), and some morphological variation has an environmental (rather than genetic) basis so must be excluded from analyses Good phylogenetic analysis requires more data than morphological data

Homologous features

Indicates common ancestor Penguin flipper and hawk wing Diff. functions, same structure, common ancestor

Lamprey Construction of Phylogenetic Tree

Lamprey, perch, salamander, lizard, crocodile, pigeon, mouse, and chimpanzee (all vertebrates) Any derived trait arose only once during evolution (no convergent evolution), no derived trait lost from any descendant groups (no evolutionary reversal) In group = all except lamprey Outgroup = lamprey Lampreys = jawless, separated from lineage leading to other vertebrates before jaw arose Chimpanzee/mouse = mammary glands and fur, absent in both outgroup and in other species of ingroup (derived traits evolved from common ancestor of chimps and mice after lineage separated from lineages leading to other vertebrates; synapomorphies) Lizard/crocodile/pigeon: keratinous scales synapomorphy Pigeon: unique presence of feathers Pigeon/crocodile: gizzards, close relationship

Phylogenetic tree

Lineage = sequence of ancestor and descendant populations Species = has ancestral roots that gave rise to it Ancestor goes left, descendant goes right on horizontal axis Species, population of species (if it has own trajectory; always potential for one population to speciate), genes (nice because with modern genetics you can look at organism genes and determine lineage)

Bacteriophage T7

Lineages allowed to evolve from ancestral virus Initial split into two sep. lins., one of which became ingroup for analysis and the other the outgroup for rooting tree Ingroup lineages split in two every 400 generations, samples saved for analysis at each branching point Allowed to evolve until eight lineages in ingrop Mutagens added to viral cultures, increase mutation rate, amount of change/degree of homoplasy would be typical of organisms analyzed in avg. phylo analy. Sequenced samples from end points of 8 lineages and from ancestors at branching points Gave sequences to investigators for analyzation (not revealing known history of lineages/sequences of ancestral viruses) History reconstructed correctly? Yes. Sequences reconstructed accurately? Yes. Branching order of lineages reconstructed exactly as occurred (98% of nucleotide positions of ancestral reconstructed correctly, 100% amino acid/viral proteins) Demonstrated accuracy of phylogenetic under conditions tested, not under all conditions Computer simulations/other experiments have since tested other conditions, but still confirmed accuracy, refined methods and extended to new applications

What sources of data are phylogenetic trees constructed from?

Morphlogical data, behavioral data, paleontological data, molecular data, embryological data

Parsimony Principle

Preferred explanation of observed data is the simplest explanation Minimizing number of evolutionary changes that need to be assumed over all characters in all groups in the tree Best hypothesis: fewest homoplasies

What can phylogenies help with?

Reconstructing ancestral state and past events, targeted cancer therapies, the usage of molecular clocks, determining if convergent evolution/homoplasies are present, and the understanding of complex traits

Morphological homologies

Represent features shared by common ancestry Vestigial structures are remnants of functional structures, which can be compared to fossils and provide evidence for evolution

Gene sequencing

Sequencing of target genes can improve a phylogenetic tree by finding new data and making changes to the tree

Gene sequencing

Sequencing of target genes improves phylogenetic tree by finding new data and making changes

Lineage

Series of ancestor and descendant populations. Depicted as a line drawn on a time axis Divides in two (geographic barrier, ex.), poss. two descendant population that no longer interact with each other (node in phylogenetic tree)

Derived traits

Show and provide evidence of evolutionary relationships Only traits that give accurate evolutionary history Convergent characters don't work, can't be similar solution to common problem, has to be opposite which is derived trait Morphology, cellular architecture (prokaryotic/eukaryotic differences), organelle morphology, chromosome numbers (helpful w/ animals, not w/plants because conservative w/ animals but not w/ plants) Biochemistry (protein structure, DNA) Embryology (highly conservative) Behavior (only if there is a strong genetic component, biologically inherited, can't be something like language)

Homoplasies

Similar traits generated by convergent evolution and evolutionary reversals

Developmental patterns

Similarities in developmental patterns may reveal evolutionary relationships; some organisms exhibit similarities only during early developmental stages (ex. sea squirts w/ notochord that disappears as they develop into adults, shows similarities w/ vertebrates, as all vertebrate animals have notochord sometimes during development, indicates similarities that would have not been noticed if only adults had been examined)

Behavior

Some traits are culturally transmitted and others are genetically inherited Culturally = not accurate reflection of evolutionary relationships (ex. bird songs) Genetically = acceptable sources of information for reconstructing phylogenies (ex. frog croak)

Outgroup

Species/group that is closely related to the ingroup but is known to be phylogenetically outside it (root of tree located between ingroup and outgroup; any trait present in both must have evolved prior to origination of ingroup (thus ancestral to the ingroup); traits only present in certain members of ingroup must be derived within the ingroup

Molecular clock

Studies the timing of splits Diff. genes evolve at diff. rates, diffs. in evolutionary rates among species related to differing generation times, environments, efficiencies among closly related species, and other bio factors Closely related = gene evolves at reasonably constant rate Uses avg. rate at which given gene/protein accumulates changes to gauge time of divergence for particular split in phylogeny

Convergent evolution

Superficially similar traits may evolve independently in different lineages Ex. wing bones of bats and birds (wing bones are homologous [common tetrapod ancestor], wings are not [evolved independently from forelimbs of different nonflying ancestors])

Archaeopteryx and the evolution of birds

The archaeopteryx was a shocking discovery Darwin was the one who wanted to find missing links for modern species that looked sort of similar but differed with certain traits; wanted to use fossils, but there weren't any The arch. found in Southern Germany had wings (not new) but also had feathers (very new, first) and teeth (birds don't have true teeth, these were like lizard teeth) and claws (birds have tallons, but lizard have claws) Showed that the arch. was very intermediate, it was a missing link, cross between lizard (no flight) and bird (flight) Direct evidence, so the species was real Behavioral inferences mainly include knowing that because of its claws and teeth it could have been predatorial, from its wings we know that it could have had the ability to fly (don't know if it did, could be a sexual selection thing or defense; we do see, though, that the midvein is symmetrical and thus suggests that it could have glided since there are no insertion points for flight muscles)

Derived trait

The condition to which each character of an organism evolves from the ancestral trait

Ancestral trait

The one condition from which each character of an organism evolves to the derived trait

Evolutionary reversal

The process by which a character reverts from a derived state back to an ancestral trait Ex. derived limbs of terrestrial tetrapods evolved from ancestral fins of aquatic ancestors; within mammals = ancestors of modern cetaceans (whales/dolphins) returned to ocean, cetacean limbs evolved to resemble ancestral state -- fins; superficial similarities between fish and cetacean fins does not suggest close relationship, but only evolutionary reversal

Node

The split in a single lineage that results in the division of an ancestral population into two descendant populations that no longer interact with each other. Each gives rise to new lineage, which evolve (new traits form in each) Lineages continue to split = branching tree, can be used to trace evolutionary relationships from ancient common ancestor of group of species to present organism populations Timing of splitting events in lineages is shown by the position of nodes on time axis Possible speciation event (mountain), gene duplication event, or viral transmission event (viral lineages transmitted through host population)

Systematics

The study and classification of biodiversity

Why do biologists use phylogenies?

To make comparisons and predictions about shared traits across genes, populations, and species. Evolutionary relationships among species (tree of life) form the basis for biological classification Knowledge of tree of life is not complete, new species being discovered, analyses being constantly reviewed/revised 1.8/10 million have been classified (formally described and named) Essential for making comparisons in biology, build phylogenies for groups of interest need be (compare species and observe traits that differ within GOI, try to understand when traits evolved; how evolution of trait related to environmental conditions/selective pressures)

Bird feathers

Trait that can be ancestral or derived, depending on point of refernece All birds have feathers (highly modified scales), infer that they were present in common ancestor of modern birds, consider presence of feathers to be ancestral traits for any group of modern birds; feathers aren't present in any other living animals, so reconstruction of phylogeny of all living vertebrates = feathers are derived trait found only among birds (synapomorphy of birds too)

Homoplasies

Trait that may arise more than once in evolutionary history Convergent evolution between 2 lineages, evolutionary reversal

Division of tree

Tree must divide Depends on what you are studying (conservative character vs. non-conservative; prefer conservative) Convergent ev. = non-conservative = quick changes

Sister clades

Two clades that are each other's closest relatives

Sister species

Two species that are each other's closest relatives

Current scientific understanding of biological evolution

Uses information from geographical, geological, physical, chemical, and mathematical applications Molecular, morphological, and genetic information of existing and extinct organisms add to this understanding

Accuracy of phylogenetic methods

reconstructions of past events in which humans were not involved Accuracy-testing computer simulations (bacteriophage T7)