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Evolution (2) (The History of Life on Earth (The Fossil record documents…
Evolution (2)
The History of Life on Earth
Conditions on early Earth made the origin of life possible
chemical and physical processes in "4 stages" produced simple cells
the abiotic synthesis of small organic molecules, such as amino acids and nitrogenous bases
Oparin and Haldane hypothesized that earth's early atmosphere was a reducing environment, where organic compounds could have formed
energy from the synthesis could have come from lightning & UV radiation
early oceans were a solution of organic molecules; a primitive soup
some evidence suggest that the early atmosphere was made up primarily of nitrogen and carbon dioxide
researchers found that numerous amino acids had formed under conditions that simulated a volcanic eruption
another hypothesis is they were first produced in deep sea hydrothermal vents
Hydrothermal vents: areas on the seafloor where heated water and minerals gush from earth's interior into the ocean
Alkaline vents: release water that has a high pH and warm rather than hot
possibly more suitable for the origin of life
the joining of these small molecules into macromolecules, such as proteins and nucleic acids
A 2009 study showed the abiotic synthesis of RNA monomers can occur spontaneously from simple molecules
by dripping solutions of amino acids or RNA nucleotides onto hot sand, clay, or rock, researches produced polymers
we have bigger complex molecules
the packaging of these molecules into protocells, droplets w/ membranes that maintained and internal chemistry different from that of their surroundings
phospholipid forms a bubble in water, that can contain molecules from abiotic synthesis or polymerization
the origin of self-replicating molecules that eventually made inheritance possible
all organisms would have to be able to reproduce and process energy
they thought that RNA was the first genetic material. through natural selection the RNA self-replicated
experiment: built a vesicle and added RNA and enzymes to it
The Fossil record documents the history of life
incomplete chronicle of evolution
many of earth's organisms didn't die in the right place and time to be preserved as fossils
the known fossil record is biased in favor of species that existed for a long time
How rocks and fossils are dated:
Radiometric dating: based on the decay of radioactive isotopes
a radioactive "parent" isotope decays to a "daughter" isotope at a characteristic rate
half-life: the time required for 50% of the parent isotope to decay
fossils contain isotopes of elements that accumulated in the organisms when they were alive
ex: carbon isotope: when the organism dies, it stops accumulating carbon, but the radioactive isotope slowly decays into another element
as lava cools into volcanic rock, radioisotopes from the surrounding environment become trapped in the newly formed rock
some of the trapped radioisotopes have long half-lives, allowing geologists to estimate the ages of ancient volcanic rocks
fossils provide a detailed look at the origin of new groups of organisms
ex: the fossil record shows that the unique features of mammalian jaws and teeth evolved gradually over time, in a series of steps
Key Events in life's history
The geologic record: a standard time scale that divides Earth's history into 4 eons and further subdivisions
4 eons: Hadean, Archaean, Proterozoic, & Phanerozoic
Hadean: origin of Earth
Archaean: concentration of atmospheric oxygen begins to increase and oldest fossils of cells appear
Proterozoic: consist of the era of Neo-proterozoic
diverse algae and soft-bodied invertebrate animal appear & oldest fossils of eukaryotic cells appear
Phanerozoic consist of 3 eras, Paleozoic, Mesozoic, and Cenozoic
Paleozoic: sudden increase in diversity of many animal phyla, early vascular plants, bony fish
mesozoic: "age of retiles"
Cenozoic: major radiation of mammals, birds, and pollinating insects. ice ages, appearance of bipedal human ancestors
3.5 billion years ago: earliest evidence of life
Stromatolites: layered rocks that form when certain prokaryotes bind thin films of sediment together
2.7 billion years ago: bacteria similar to cyanobacteria originated 2.7 billion years ago
1.8 billion years ago: the first eukaryotes
eukaryotes evolved from prokaryotic by endosymbiosis (prokaryotic cell engulfs a small cell that would evolve into an organelle found in all eukaryotes)
eukaryotes don't have plastids, the serial endosymbiosis hypothesis supposes that mitochondria evolved before plastids through endosymbiotic events
inner membranes of mitochondria and plastids both have enzymes and transport systems that are homologous to those found in the plasma membrane of living bacteria
the ribosomes of mitochondria an plastids are more similar to bacterial ribosomes than cytoplasmic ribosomes of eukaryotic cells
mitochondria and plastids replicate by splitting process that is similar to that of certain bacteria
mitochondria and plastids have the cellular machinery needed to transcribe and translate their DNA into proteins
1.2 billion years ago: the oldest known fossil of multicellular eukaryotes
535- 525 million years: many present day animal phyla appear suddenly in fossils
Cambrian explosion caused new defensive adaptations
fossils of several animal groups- sponges, cnidarians, and mollusks appear in even older rocks
500 million years ago: larger forms of life, such as fungi, plants, and animals began to colonize land
The rise and fall of groups of organisms reflect differences in speciation and extinction rates
Plate tectonics: the continents are part of great plates of Earth's crust that essentially float on the hot underlying portion of the mantle
continental drift: movements in the mantle cause the plates to move over time
in some cases, 2 plates are moving away from each other
2 plates sliding past each other, forming regions where earthquakes are common
Pangea (supercontinent) altered the physical environment and climate , led species to extinction
organisms are affected by the climate change that results when a content shifts its locations
they either adapt, move to a new location, or become extinct
promotes allopatric speciation
helps explain puzzles about the geographic distribution of extinct organisms
ex: why fossils of the same species of Permian freshwater reptiles have been discovered in both Brazil and the west African nation of Ghana
explains the current distribution of organisms
ex: Australian fauna and flora contrast so sharply w/ those of the rest of the world
Mass extinctions: which large numbers of species become extinct worldwide
there are 5 mass extinctions that are documented in the fossil record; the Permian & the Cretaceous have received the most attention
The Permian mass extinction occurred during the most extreme episode of volcanism in the past 500 million years
The Cretaceous mass extinction occurred 66 million years ago
affected more than half of all marine species
eliminated many families of terrestrial plants and animals, including dinosaurs
crater that hit Mexico
can alter ecological communities by changing the types of organisms residing there
ex: after the permian and cretaceous mass extinctions, the percentage of marine organisms that were predators increased substantially
Adaptive radiations: periods of evolutionary change in which groups of organisms form many new species whose adaptations allow them to fill different ecological roles in their communities
Major changes in body form can result from changes in the sequences and regulation of developmental genes
Effects of Developmental genes:
heterochrony: an evolutionary change in the rate or timing of developmental events
rate: an organism's shape depends on the relative growth rates of different body parts during development
timing: the timing of reproductive development can be altered
if the development of reproductive organs accelerates compared to other organs, the sexually mature stage of a species may retain body features that were juvenile structures in an ancestral species (pedomorphosis)
substantial evolutionary changes can also result from alterations in genes that control spatial organization of body parts
ex: homeotic genes determine such basic features as where a pair of wings and legs will develop on a bird
changes in Gene sequence:
new morphological forms likely come from gene duplication events that produce new developmental genes
ex: specific changes in the Ubx gene have been identified that can "turn off" leg development
changes in gene regulation:
changes in developmental genes can result in new morphological forms
ex: the loss or reduction of ventral spines in lake populations of 3spine stickleback fish appears to have resulted in primarily from a change in the regulation of Pitx 1 gene expression
Evolution is not goal oriented
Evolutionary novelties:
as new species form, novel and complex structures can arise as gradual modifications of ancestral structures
complex structures have evolved in increments from simpler versions that performed the same basic functions
ex: some organisms eyes have evolved to benefit the organism's ability to see; evolves in a series of steps that benefited the eyes owners at every stage
Evolutionary trends
some evolutionary lineages exhibit a trend toward larger or smaller body size
branching evolution can result in a real evolutionary trend even if some species counter the trend
Phylogeny and the Tree of Life
Phylogenies show evolutionary relationships
Binomial: the 2 part format of the scientific name
first part of the binomial is the name of the genus
second part is called the specific epithet, is unique for each species within the genus
first letter of the genus is capitalized and the entire binomial is italicized
hierarchical classification: grouping organisms into a hierarchy of increasingly inclusive categories
the Linnaean system places related genera in the same family, families into order, orders into classes, classes into phyla, phyla into kingdoms, and kingdoms into domains
taxon: the names taxonomic unit at any level of the hierarchy
does not necessarily reflect evolutionary history
the larger categories often are not comparable between lineages
ex: an order of snails doesn't exhibit the same degree of morphological genetic diversity as an order of mammals
Phylogenetic tree: where the evolutionary history of a group of organisms can be represented in a branching diagram
the evolutionary relationships often are depicted as a 2 way branch point
branch point: each one represents the common ancestor of the 2 evolutionary lineages diverging from it
sister taxa: groups of organisms that share an immediate common ancestor that is not shared by any other group
the branches of a tree can be rotated around branch points without changing the relationships shown in the tree
phylogenic trees can be rooted; that a branch point w/in the tree represents the most recent common ancestor of all taxa in the tree
to show patterns of descent, not phenotypic similarity
we can't infer the ages of the taxa or branch points shown in a tree and we shouldn't assume that a taxon on a tree evolved from the taxon next to it
Phylogenies are inferred from morphological and molecular data
to infer phylogeny, systematists must gather as much information as possible of the morphology, genes, and biochemistry of the relevant organisms
homologies: the phenotypic and genetic similarities due to shared ancestry
ex: the similarity in the # & arrangement of bones in the forelimbs of mammals is due to their common ancestor w/ the same bone structure
organisms that share very similar morphologies or similar DNA sequences are likely to be related
if the species are very closely related, the sequences probably differ at only one or a few sites
2 sequences that resemble each other at many points along their length most likely is homologous
analogy: similarity between organism that is due to convergent evolution
convergent evolution occurs when similar environmental pressures and natural selection produce similar adaptations in organisms from different evolutionary lineages
Shared characters are used to construct phylogenetic trees
Cladistics: common ancestry is the primary criterion used to classify organisms
Clades: groups which includes an ancestral species and all of its descendants
a taxon is equivalent to a clade only if it's monophyletic; that it consists of an ancestral species and all of its descendants
if it doesn't include their most recent common ancestor, its a polyphyletic group
paraphyletic: group which consist of an ancestral species and some but not all of its descendants
shared ancestral character: a character that originated in an ancestor of the taxon
shared derived character: an evolutionary novelty unique to a clade
outgroup: a species or group of species from an evolutionary lineage that is closely related to but not part of species that we're studying
comparing the in-group with the outgroup, we can determine which characters were derived at the various branch points of vertebrate evolution
Phlogenetic trees with proportional branch lengths
branch lengths can be proportional to amount of evolutionary change
branch lengths can be the times at which particular events occurred
maximum parsimony and maximum likelihood
maximum parsimony: the simplest explanation
for phylogenies based on DNA, the parsimonious tree requires the fewest base changes
maximum likelihood: approach that identifies the tree most likely to have produced a given set of DNA data, based on certain probability rules about how DNA sequences change overtime
phylogenetic trees as hypotheses: a phylogenetic hypotheses may be modified when new evidence compels systematists to revise their trees
Ex: fossil support fora phylogenetic prediction; dinosaurs built nests and brooded their eggs
Tree of life continues to change based on new data
from 2 kingdoms to 3 domains
taxonomists once classified all known species into 2 kingdoms: plants and animals
3 domains: bacteria, archaea, and eukarya
bacteria contains most of the currently known prokaryotes
eukarya consists of a ll the organisms that have cells containing true nuclei
contains many groups of single-celled organisms as well as multicellular plants, fungi, and animals
archaea consists of a diverse group of proakaryotic organisms that inhabit a wide variety of organisms
new research continues to change our understanding of the tree of life
ex: the genomes of many new species of archaea, leading to discovery of the Thaumarchaeota and other unknown phyla of archaea
horizontal gene transfer: a process in which genes are transferred from one genome to another
exchange of transposable elements and plasmids
viral infection
fusions of organisms
ex: 80*% of the genes in 181 prokaryotic genomes had moved between species at some point during the course of evolution
Molecular clocks help track evolutionary time
molecular clocks: an approach for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at a constant rate
paralogous genes is the # of substitutions is proportional to the time since the ancestral gene was duplicated
some mutations are selectively neutral, neither beneficial nor bad
such genes change more quickly
don't run as smoothly as would be expected if the underlying mutations were selectively neutral
because of natural selection, where certain DNA changes are favored over others
unsure if the clocks have been constant for all the time
An organism's evolutionary history is documented in its genome
different genes can evolve at different rates, even in the same evolutionary lineage
results: molecular trees can represent short or long periods of times depending on the gene they used
gene duplication and gene families:
gene duplication increase the # of genes in the genome
this provides more opportunities for further evolutionary changes
duplications leads us to distinguish 2 types of homologous genes
orthologous genes: the homology is the result of a spectator event and hence occurs between genes found in different species
ex: the genes that code for cytochrome c in humans and dogs
Paralogous genes: the homology results from gene duplication; hence, multiple copies of these genes have diverged from 1 another w/in a species
ex: gene duplication in veterbrates, humans have 380 functional copies of these paralogous genes, while mice have 1,200
genome evolution:
lineages that diverted long ago often share many orthologous genes
the number of genes a species has doesn't seem to increase through duplication at the same rate as perceived phenotypic complexity