chapter 19 and 20

Question 1

early classification of organisms

Answer 1

aristotle- species are fixed made the SCALA NATURAE (scale of nature) organisms on scale of increasing complexity and they are fit for their specific environment “god created organisms for each environment”
carolus linnaeus- binomial nomenclature and nested classification kpcofgs
lammarck- use/disuse theory- body parts being used grow and ones that aren’t being used disintegrate or shrink. - inheritance of acquired characteristics and change that an organism acquires in their life time is directly passed on to its offspring (single organism can evolve (wrong))- organisms had a drive to change. people regarded him as very wrong but he did realize that organisms do evolve which is very important

Question 2

Darwin

Answer 2

naturalist, went on the HMS beagle and found evidence that allowed him to make his theory of evolution. he observed an earth quake- fossils can surface and natural processes shape the earth- thats why he found ocean fossils in the andes ( lyell slow earth geological processes)
galapagos-islands off the coast of south america, darwin found similar birds that were different species and that were unique to each island but resembled animals in south america – therefore the galapagos islands were colonized by a species of bird from the mainland. The species adapted to the new environment and new species evolved that are closely related

Question 3

adaptations

Answer 3

• inherited characteristics that enhance survival and reproduction in specific environments – adaptations to new environments can result in a new species closely related to another species
• new species result from a gradual accumulation of adaptations (this happened to the finches-beaks and behaviours adapted to resources available

Question 4

natural selection

Answer 4

process in which individuals with certain inherited traits tend to survive and reproduce more then others because of the traits. this is the mechanism of descent with modification. (evolution)
-substantial modification of a species over many generations- the less favourable traits will disappear
- natural selection increases match between an organism and their environment
-change in environment results in natural selection and adaptation to new conditions and sometimes a new species.
IMPORTANT
** individuals do not evolve ( lamarck wrong) -a population does
** natural selection only increases or diminishes only inheritable traits that differ among individuals in population- if all members in population have a genetically identical trait evolution by natural selection does not occur
**environmental factors vary over time and natural selection is always operating, traits favoured depend on the environmental pressures.

Question 5

ideas from Darwins book

Answer 5

descent with modification by means of natural selection explains why - theres a huge diversity of life -unity of life (shared characteristics of life) -match of organisms to their environments

Question 6

descent with modification

Answer 6

organisms share many characteristics (unity of life) -descent of all organisms from one common ancestor - the descendants all live in varied environments which results in diverse modifications or adaptations that fit to environments. - common ancestor lead to all life today- history of life tree - the gaps in evolution of closely related species can be explained by their extinction - organisms that are similar to one may have gone extinct at some point in time leaving a gap
artificial selection- humans have modified species by selecting and breading individuals with desired traits - a similar process happens in nature

2 observations–1. members of population vary in inherited traits —— advantageous traits allow these animals to survive and reproduce a lot. 2. all species produce more offspring then can survive so many don’t—— leads to accumulation of favourable traits in a population over generations
CONNECTION- natural selection connected to over production of offspring (over production - thomas malthus)
characteristic of all species- organism has advantageous traits it will pass them on to offspring - more survive then others in the species increasing the frequency of this trait throughout generations –natural selection leads to increase in amount of favourable traits in a population

Question 7

support of evolution (plant)

Answer 7

PLANT EXPERIMENT- soapberry bugs use beak(hollow mouth part) to feed on seeds inside fruit- beak length corresponds to seed depth = effective. prediction; fruit with seeds closer to the surface will result in natural selection of bugs with shorter beaks prediction correct. conclusion; change in size of food resulted in evolution by natural selection for matching beak size ( same if fruit was larger)– natural selection caused rapid evolution in a wild population

Question 8

support of evolution ( bacteria)

Answer 8

evolution of bacteria results in bacteria resistant drugs- that can be very harmful like MRSA and there has been an increase of in virulent forms. USA300 form of MRSA is a flesh eating disease
-1943 penicillin used as antibiotic until strains became resistant, other strains became resistant to other antibiotic strains as well.
ex methicillin deactivates proteins used in cell wall and some MRSA populations had variations some could synthesize their cell wall without this protein which could survive and the treatment and reproduce at higher rates once the other bacteria had been killed.
how bacteria become resistant; they exchange genes. present day multi drug resistant strains may have emerged over time as MRSA strains that were resistant to different antibiotics and have exchanged genes.

Question 9

conclusion of support of evolution

Answer 9

natural selection edits organisms and does not create them– the drug selects for resistant individuals in population– it also depends on time and place- favours characteristics in genetically variable population that have advantage in current time and place

Question 10

Homology (evidence of evolution)

Answer 10

-similarity resulting from common ancestor- related species have similar characteristics with a different function
–anatomical homologies- forelimbs of mammals have the same arrangement of bones but appendages of species or even class of mammals have different functions such as flying or walking.
homologous structures- variations on structural them present in common ancestor– embryos also show anatomical homologies- vertebrates all have a posterior tail pharyngeal arches and these and these all develop into structures with different functions

Question 11

vestigial structures ( evidence of evolution)

Answer 11

features present in organisms no longer being used, but their ancestors may have used them- ex; hip bones in snakes no longer used.
molecular level-homologous genes - some have new function but some keep their function-ex; humans and bacteria share same genes but they each do a different thing

Question 12

convergent evolution (evidence of evolution)

Answer 12

indépendant evolution of similar features in different lineages- two animals from two different ancestors evolved independently but have adapted to similar environments resulting in similar characteristics —-ANALOGOUS- similar function but not a common ancestory- similar function- different structure

Question 13

Fossil record ( evidence of evolution

Answer 13

past organisms differed from present day organisms and species have become extinct- show evolutionary changes that have occurred in various groups of organisms- driven by natural selection-ex; fossils of cetaceans ( whales dolphins proposes) show that they are more closely related to even toed ungulates (dear pigs and camels) earliest cetacean was 50-60 million years ago - most mammals terrestrial so cetaceans originated from land mammals. in this case life on land moved to life in the sea. oner time descent with modification produced increasingly large differences among these two related groups of organisms resulting in diversity

Question 14

biogeography

Answer 14

study of geographic distribution of species - influenced by factors such continental drift– (PANGAEA) fossils of different groups of organisms can be found in places corresponding to the previous arrangement of the continents
ENDEMIC SPECIES- species unique to a specific place ( usually island) – Darwin island– island species are closely related to species from nearest mainland- thesis species colonized the island and a new species evolved as the species from the island adapted to the islands environment
— this explains how tow islands with similar environments (far away from each other) are populated by species more closely related to species on the mainland instead of each other (the mainland environment may be very different)– this is also known as convergent evolution ( misleading when classifying organisms)

Question 15

darwin theoretical view of life

Answer 15

darwins theory extremely strong- backed uo by incredible amounts of evidence and fills holes in many questions, however some things are missing- natural selection is only one mechanism for evolution.

Question 16

phylogeny

phylogenetic tree

Answer 16

-evolutionary history of a species or group of species – grouping based on DNA ( i think)

• evolutionary history of a group of organisms- branching tree matches how taxonomists have classified groups of organisms nested within each other-
  but taxonomists may have misplace species because they have lost key features - species looks more closely to another but its actually not( they may have undergone convergent evolution– have analogous structures) DNA evidence determines this
• a phylogenetic tree represents a hypothesis of evolutionary relationships of different group
  -branch points- divergent of two evolutionary lineages
  sister taxa- two most recently related taxons in phylogenetic tree they are most closely related to each other
  -basal taxon- lineage that diverges in early history of group
  -tree rooted- most recent common ancestor of all taxon included

Question 17

hierarchal classification

Answer 17

carolus linnaeus grouped species of increasing exclusive categories in a taxonomic system called the linen system- species in genus in family in order in class in phylum in kingdom- characteristics useful for classifying one group may not work for another group- larger categories not comparable between lineages- two groups may not have the same degree of morphological or genetic diversity

also carolus linnaeus created binomial nomenclature- two part biological name for every species– genus and the specific epithet ( unique for each species)

genus first letter capitalized the rest, species, all lower case, whole thing italicized

Question 18

what do phylogenetic trees show

Answer 18

pattern of descent not phenotypic similarities - related organism may not physically be similar if lineages have diverged at different rates– ex: crocodiles are more closely related to birds then lizards

• sequence of branching of tree does not indicate age of species (unless you fricking make the branch lengths correspond to time)
• • only shows most recent common ancestor of two species (page 384 3rd paragraph)
• taxon on phylogenetic tree did not evolve from the one next to t; they shared a common ancestor with is now extinct

Question 19

applying phylogenetics

Answer 19

infer species identities by analyzing relatedness of DNA sequences from different organisms ( it was done with whale meat)
**phylogenies inferred from morphological and molecular data

Question 20

morphological and molecular homologies`

Answer 20

phenotypic is morphological and genetic similarities due to shared ancestry –animals with same bones have morphological homology- genes and DNA sequences homologous if they are descended from sequences carried by a common ancestor- sometimes morphologic divergence of two species large but genetic divergence small vice versa

Question 21

homology vs analogy

Answer 21

phylogeny based on homology( shared ancestry) analogous animals are very different sharing a distant common ancestor but appear as though they share a recent one due to similar characteristics pressured by convergent evolution.
ex; birds and bats both fly, but birds are more closely related to crocodiles and bats to cats thus a bats wing is analogous to a birds not homologous.
– distinguishing between analogy and homology loin at complicity of characteristics being compared- the more similar elements the more likely it is they shared a common ancestor—- same with genes-if two organisms share many DNA portions the genes are homologous

Question 22

evaluating molecular homologies

Answer 22

closely elated species DNA is similar and distantly related species genes differ greatly –different bases and gene lengths. insertions and deletion mutations accumulate differences indicate lineages diverged a long time ago ( even if morphologically similar) - also organisms closely related if they have similar genes but are morphologically different.

Question 23

molecular homoplasies (analogies)

Answer 23

organisms that do not appear closely related yet have very similar portions of DNA ???? check this one

Question 24

Cladistics

Answer 24

common ancestor is primary criterion to classify organisms- species in group called clades
clade consists of ancestral species plus descendants – clades nested in larger clades - taxon= clade if clade is monophyletic
monophyletic- ancestral species +all of descendants
paraphyletic- ancestor + some but not all descendants
polyphyletic-includes members with different ancestors -most recent common ancestor not in group

Question 25

ancestral+ derived characters (still cladistics)

Answer 25

organisms have specific characteristics +s hare some with ancestors
shared ancestral character– character that originated in ancestor of taxon
shared derived characteristic- character unique to clade
ex; all mammals have hair not ancestor is a derived character but all mammals have vertebra is a shared ancestral characteristic because they do all have that but so do other animals
-it depends on where you’re looking because a shared ancestral character can be considered a shared derived character depending on how far back in the lineage you’re considering it

Question 26

derived characters

Answer 26

unique to a clade - evolutionary relationships inferred from derived characters
outgroup- species or group of species from evolutionary lineage that is known to have diverged before the lineage that includes the lineage that includes the species you are looking at which is considered the in group
- compare the in-group members and the outgroup members to determine which characters were derived at various ranch points - this can make a phylogenetic tree that groups all taxa into hierarchy based on derived characters

Question 27

phylogenetic trees with proportional lengths

Answer 27

phylogenetic trees are chronologic but not absolute if length is not proportional to either time or amount of DNA mutations
-lengths of branches proportional to DNA the longest branch will have the most genetic changes compared to the others
**different length branches- organisms day all have different lineages that descend form a common ancestor have survived for the same number of years - ex; bacteria have not changed much but the they have 3 hundred million years of linage same with humans 3 hundred million years of lineage– these are equal spans of chronological time- -phylogenetic trees with branches proportional to time each lineage has the same total length from branch tips to base of tree
if you merge genetic change with time you have the average rate of genetic change and dates of divergence

Question 28

maximum parsimony

Answer 28

principle to first investigate the simples explanation that is consistent with facts
– trees based on morphology (phenotypic a)- so applying this principle means there would be fewest evolutionary events which is measured by origin of shared derived morphological characteristics
– trees based on DNA- applying principle of parsimony means there would be the fewest base changes
– any trees fewest evolutionary changes is most likely
(from what i understand this is applying probability, if it has a low probability compare to something else, it is less like that it will happen and the probability becomes increasing smaller as the complexity of something increases)

Question 29

hypotheses (about phylogeny)

Answer 29

phylogenetic tree represents hypothesis about how various organisms are related – the best one best fits all data available-and it is modified by new evidence - make and test predictions based on assumption that a phylogeny is correct.

Question 30

phylogenetic bracketing

Answer 30

predict by parsimony that features shared by two groups of closely related species are present in their common ancestor and all of the other descendants. ex; birds and crocodiles share common ancestor – and also share many features-any features shared by birds and crocodiles is most likely present in their common ancestor and all of the descendants( which are extinct dinosaurs) leading to hypothesis that dinosaurs shared some characteristics of bird and crocodiles because they shared the same common ancestor

Question 31

molecular clocks

Answer 31

• measures absolute time of evolutionary change based on the observation that some genes and other regions of genome appear to evolve at constant rates
• assumption*** VERY IMPORTANT- number of nucleotide substations in related genes is proportional to the time elapsed since the genes branched from the common ancestor– average rate of evolution by graphing the number of genetic differences against dates of evolutionary branch points knowns from the fossil record.
• this is not completely precise some parts of genome evolve in irregular bursts ** molecular clocks only show average rate of time ( over time there are deviations) and some genes may evolve ate different rates in different groups of organisms and some may evolve faster than others

Question 32

differences in clock speed

Answer 32

some mutations are selectively neutral which means they have no effect on fitness and there is a regular rate of neutral mutatio
* differences in clock rate depend on how important a gene is – important genes change very slowly because mutations are often lethal and the organisms with these mutations die before reproduction – less crucial genes face more change because the organisms can survive the mutations

Question 33

problems with molecular clocks

Answer 33

-irregularities from natural selection DNA changes favoured over others and the direction of natural selection can repeatedly change ( some clocks can approximately mark the time tho)
- the clocks try to go back farther than fossils, estimates of farther back in time than fossils assumes that clocks have been constant but that is highly uncertain
avoidance of problems;- compare many genes not just one and fluctuations can average out.

Question 34

origin of HIV ( using molecular clocks)

Answer 34

HIV has descended from viruses that infect chimpanzees and primates - the virus spread to humans more than once and there are multiple origins reflected in a variety of the viral strains.–RNA viruses evolve rapidly
- main strain -HIV1M- compared virus samples to various times during the epidemic to find earliert infection- virus evolve in a clocklike fashion so HIV-1M first spread to humans in 1930

Question 35

New info= revise understanding of evolutionary history

Answer 35

older idea- all species into two kingdoms -plant and animal then five kingdoms- monera protista fungi plantae and animalia- problem with that is some prokaryotes differed as much as they do from each other as they do form eukaryotes– current understanding is the three domains eukarya, archea, and bacteria
- much history of life is single celled organisms

Question 36

horizontal gene transfer

Answer 36

movement of genes between organisms in different domains this is known as a process and the genes are transferred from one genome to another through mechanisms such as plasmids and exchange of transposable elements or viral infection or even fusion of the organisms
why this conclusion has been reached:
frist major split is when bacertia diverged from other organisms
eukaryotes and arches are more closely related then bacteria – rRNA gene comparisons- rRNA evolve slowly because RNA is very important which allows homologies to still be detected.
other evidence suggests that eukaryotes are more closely related to bacteria
–conflicting results which leads to the conclusion that eukaryotes originated form fusion between archean and bacterium
-phylogenetic trees assume genes are passed vertically- horizontal gene transfer explains why trees built using different genes can give inconsistent results.
some scientists think- horizontal gene transfer is so common that early history should represented a s and entangled network of connected branches