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Chapter 25-26 (History of Life on Earth (Conditions of Early Earth &…
Chapter 25-26
History of Life on Earth
Conditions of Early Earth & Origin of Life
Synthesis of Early Organic Compounds
A.I. Oparin & J.B.S. Haldane (1920's)
Hypothesized earth's early atmosphere was a reducing environment, and that organic compounds formed from simpler compounds exposed to lightning
Early oceans were a "primitive soup" of organic molecules, from which life arose
Stanley Miller & Harold Urey (1953)
Tested Oparin-Haldane Hypothesis
Organic compounds first produced in Deep Sea?
Hydrothermal Vents
Area of the sea floor where heated water and minerals from the earths interior produce a dark, hot, oxygen-deficient environment
Alkaline Vents
Hypothetically and environment more suitable for the origin of life
Deep-sea hydrothermal vents that release warm water with a high pH
Production of Simple Cells Through Four Main Stages
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Abiotic Synthesis of small organic molecules
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Joining of small molecules into macro molecules, such as proteins and nucleic acids
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Packaging of molecules into Protocells with membranes that maintain an internal chemistry different from their surroundings
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Origin of Self-replicating molecules, eventually making inheritance possible
Abiotic Synthesis of Macromolecules
Abiotic synthesis of RNA monomers can occur spontaneously from simple precursor molecules
Possible that RNA polymers acted as a weak catalyst for a variety of chemical reactions
ProtoCells
Abiotically produced vesicles have been shown to exhibit proprieties of life
Simple Reproduction
Metabolism
Maintenance of internal chemical environment different from surroundings
Can "grow" without dilution of their contents
Self Replicating DNA
Ribosomes
Makes complementary copies of short strands of RNA
RNA molecules with the greatest ability to replicate itself will leave the most descendant molecules
A vesicle that could grow, split, and pass it's RNA to it's "daughters", the daughters would then be protocells
Likely carried only limited amounts of genetic information, specifying for only a few properties
Double-stranded DNA is more chemically stable that RNA, and can be replicated more accurately
History of Life Documented by Fossil Record
Fossil Record
Shows the great changes in the types of organisms on earth at different points in time
Incomplete Chronicle of Evolution
Biased toward species that existed for a long time, were abundant and widespread, had hard shells/skeletons/or other parts that facilitated fossilization
How Rocks are Dated
Radiometric Dating
Based on the decay of radioactive isotopes
Half-life
The rate of decay
The time required for 50% of the parent isotope to decay
Indirect Methods
Fossils sandwiched between two layers of volcanic rock
Cooled volcanic rock can trap radioactive isotopes in the surrounding environment, which allows for the estimation of the ages of ancient volcanic rocks
Origin of New Groups of Organisms
Some fossils provide a detailed look at the origin of new groups of organisms
illustrates how new features arise and how long it takes for such changes to occur
Key Events in Life's History
First Single Celled Organisms
Photosynthesis & Oxygen
Oxygen gas originated from the water splitting step of photosynthesis of photosynthetic prokaryotes
First Eukaryotes
Endosymbiosis
Prokaryotic cells engulfed a smaller cell that later evolved into organelles (mitochondrion & chloroplasts)
Serial Endosymbiosis
Mitochondria evolved before Plastids through a sequence of endosymbiotic events
Replicate by splitting processes similar to bacteria, contains circular DNA molecules
Have Cellular machinery, such as ribosomes needed to transcribe & translate DNA into proteins
Inner membrane of both have enzymes & transport systems homologous to those found in plasma membranes of bacteria
Ribosomes are more similar to bacterial ribosomes than cytoplasmic ribosomes of eukaryotic cells
Stromatolites
Layers of rock that form when prokaryotes bind into thin films of sediment
Origin of Multicellularity
Geologic Record
Standard time scale that divides Earth's history
Eons
Hadean (4,600-4,000 million years ago)
Archean (4,000-2,500 mil. ago)
Prokaryotes begin to appear (3,500)
Atmospheric oxygen concentration increases (2,700)
Proterozoic (2,500-541)
Eukaryotic cells appear (1800)
Neo-protozoic (1000-541)
Algae & soft bodied invertebrates appear (635-541)
Phanerozoic (541-now)
Paleozoic (541-252)
Silurian (444-419)
Diversification of vascular plants
Devonian (419-359)
Diversification of bony fish & tetrapods/insects appear
Ordovician (485-444)
Abundance of marine algae: land colonization
Permian (299-252)
radiation of reptiles, extinction of many marine & terrestrial animals
Cambrian (541-485)
Cambrian explosion: sudden increase in biodiversity
Carboniferous (359-299)
Extensive forests; seed plants and reptiles appear, amphibians dominate
Mesozoic (252-66)
Jurassic (201-145)
Gymnosperms dominate, dinosaurs diverse & abundant
Cretaceous (145-66)
Flowering plants appear, many organisms go extinct by end of period
Triassic (252-201)
Cone-bearing plants, dinosaurs evolve, mammals appear
Cenozoic (66-now)
Neogene (23-2.6)
Miocene (23-5.3)
Earliest direct human ancestor
Pliocene (5.3-2.6)
Bipedal human ancestors
Quaternary (2.6-now)
Pleistocene (2.6-.01)
Ice ages; genus
Homo
appears
Holocene (.01-now)
Historical time
Paleogene (66-23)
Paleocene (66-56)
Radiation of mammals. birds & insects
Eocene (56-34)
Angiosperms dominate, continued radiation of mammals
Oligocene (34-23)
Origin of many primate groups
Origin of Multicellularity
Cambrian Explosion
many animal phyla suddenly appear in fossils
Colonization of land
Early Multicellular eukaryotes
Rise and Fall of Groups of Organisms
Plate Tectonics
Continents are part of plates on earth's crust. Movements in the earth's mantle cause the plates to move, known as continental drift
Continental Drift
Pangaea
Plate movements brought separated land masses together into a super continent
Mass Extinctions
"Big Five"
In each mass extinction event, 50% or more of marine species become extinct
Permian Mass Extinction
Defined boundary between Paleozoic & Mesozoic eras
Occurred during extreme episode of volcanism
Cretaceous Mass Extinction
Defined boundary between Mesozoic & Cenozoic eras
Sixth Mass Extinction?
Human actions are modifying the global environment to such an extent that many species are threatened with extinction
Sudden disruptive changes that cause extinction rate to increase dramatically
Consequences of Mass Extinctions
Elimination of large numbers of species, can reduce thriving and complex ecological communities to a shadow of it's former self
Once an evolutionary lineage disappears in cannot reappear
The course of evolution is permanently changed forever
Adaptive Relations
World Adaptive Radiations
Mammals where mostly small and not morphologically diverse, restricted due to being eaten or out competed by larger & more diverse dinosaurs
Disappearance of dinosaurs allowed for mammals to expand in diversity and size to fill ecological roles once occupied by terrestrial dinosaurs
Regional Adaptive Relations
Adaptive relations occurring over more limited geographical areas
Periods of evolutionary change in which groups of organisms form many new species with adaptations allowing them to fill ecological roles, niches, in their communities
Major Changes in Body Form Resulting from Changes in Developmental Genes
Effects of Developmental Genes
Slight genetic differences can produce major morphological differences between species
Large morphological differences can result from genes that alter the rate, timing, and spatial pattern of change in a organism's form as it develops
Changes in Rate and Timing
Heterochrony
Evolutionary change in the rate or timing of developmental events
Changes to these rates can alter the adult form of a species
Can also alter the timing of reproductive development relative to the development of non-reproductive organs.
Paedomorphosis
Sexually mature stage of a species retains features that were juvenile structures
Changes in Spatial Pattern
Homeotic Genes
Control the spatial organization of body parts such as where basic features will develop
Evolution of Development
Changes in Gene Sequence
New developmental genes arise after gene duplication events , probably facilitated the origin of novel morphological forms
Changes in Gene Regulation
Changes in the nucleotide sequence of a gene may affect it's function wherever the gene is expressed, while changes in regulation of a gene can be limited to one cell type
A change in the regulation of a developmental gene may have fewer harmful side effects than a change in the gene sequence
Evolution is not Goal Orientated
Evolutionary Novelties
As new species form, novel and complex structures can arise as gradual modifications to ancestral structures
Complex structures evolved in increments from simpler versions that performed the same basic function
Evolutionary novelties can arise from structures that originally played one role and gradually acquired a different one
Exaptations
Structures that evolve in one context but become co-opted for another function
Natural selection cannot predict the future; it can only improve a structure in the context of it's current utility
Novel features arise gradually via a series of intermediate stages, each of which has some function to the organism's current context
Evolutionary Trends
Branching evolution can result in evolutionary trends even if some species counter the trend
One model views species as analogous to individuals
Populations of individuals organisms undergo natural selection, species undergo species selection
The species that endures the longest and generates the most new offspring species, determines the direction of evolutionary trends
Evolutionary trends can result directly from natural selection
An evolutionary trend does not imply that there is some intrinsic drive toward a particular phenotype
Evolution is the result of the interactions of organisms and their current environment
If environmental conditions change, an evolutionary trend may cease or reverse itself
Phylogeny and Tree of Life
Phylogenies show evolutionary relationships
Binomial Nomenclature
Biologists refer to organisms by Latin names in a two part format
First part of the name is the genus which the species belongs to
The first letter of the genus is always capitalized, and both parts are always italicized.
The second part of the name is the specific epithet, which is unique to each species in a genus
Hierarchical Classification
Organisms are grouped into increasingly inclusive categories
The named taxonomic unit at any level is called a taxon
Species
Genus
Family
Order
Class
Phylum
1 more item...
Linking Classification & Phylogeny
Phylogenetic Tree
The evolutionary history of a group of organisms represented in a branching diagram
Sometimes taxonomists have placed a species within a genus (or other group) that is it not most closely related to.
a mistake may occur because over the course of evolution the species lost a key feature shared by it's close relatives
DNA or other new evidence indicates that an organism has been misclassified, the organism may be reclassified to accurately reflect it's evolutionary history
What Cannot be Learned from Phylogenetic Trees
A phylogenetic tree represents a hypothesis about evolutionary relationships, depicted as a series of dichotomies
Each branch point represents a common ancestor of the two evolutionary lineages diverging from it
The order in which the taxa appear at the right side of the tree does not represent a sequence of evolution
Sister Taxa
Groups of organisms that share an immediate common ancestor that is not shared by any other group
Rooted Branches
A branch point (often drawn farthest left) represents the most recent common ancestor of all taxa in the tree
Basal Taxon
The lineage that diverges from all other members of it's group early in history of the group
Keep in Mind
Cannot necessarily infer the ages of the taxa or branch points shown in a tree
Should not assume that a taxon on a phylogenetic tree evolved from the taxon next to it
Can infer that the lineage leading to humans and the lineage leading to chimpanzees both evolved from a common ancestor, which was neither a human or a chimpanzee
Intended to show patterns of decent, not phenotypic similarity.
Closely related organisms often resemble one another through common ancestry
Applying Phylogenies
Can be used to infer species identities by analyzing the relatedness of DNA sequences from different organisms
Phylogeny
The evolutionary history of a species or group of species
Phylogenies are Inferred from Data
Morphological & Molecular Homologies
Homology
Phenotypic and genetic similarities due to shared ancestry
Organisms that share similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences
Some cases the morphological divergence between related species can be great and their genetic divergence small (or vise versa)
Sorting Homology from Analogy
Analogy vs Homology
Analogy: phylogeny similarities due to convergent evolution
Homology: phylogenetic similarities due to shared common ancestor
Convergent evolution occurs when similar environmental pressures and natural selection produce similar adaptations in organisms with different evolutionary lineages
The more elements that are similar in two complex structures, the more likely that the structures evolved from a common ancestor
Genes are sequences of thousands of nucleotides, each of which represents and inherited character in the form of the four DNA bases
If genes in two organisms share many portions of their nucleotide sequences, it is likely that the genes are homologous
Evaluating Molecular Homologies
After sequencing the molecules, then comparable sequences, from the species being studied, are aligned
If the species are closely related, the sequences differ in only one or a few sites
Comparable nucleic acid sequences in distantly related species usually have different bases at many sites and may have different lengths
Researchers developed computer programs to estimate the best way to align comparable DNA segments of differing lengths
Two sequences that resemble each other at many points along their length most likely are homologous
In organisms that do not appear to be closely related, the bases at their otherwise very different sequences happen to share may be coincidental matches, or molecular homoplasies
Shared Characters Used to Construct Phylogenetic Trees
Cladistics
Uses common ancestry as the primary criterion to classify organisms
Biologists place species into groups, clades, each of which includes an ancestral species and all its descendants
Taxon is equivalent to a clade only if it is monophyletic
Consists of an ancestral species and all of it's descendants
Paraphyletic
Consists of an ancestral species and some, not all, of it's descendants
Polyphyletic
Includes distantly related species but does not include their most recent common ancestor
Biologists avoid polyphyletic groups; if new evidence indicates that an existing group is polyphyletic, it's members are reclassified
Shared Ancestral & Derived Characters
Inferring Phylogenies Using Derived Characters
Shared derived characters are unique to a particular clade, meaning the features arised at some point
It can be determined which clade the shared derived character first appeared
Can be used to infer evolutionary relationships
Outgroup
a species or group of species from an evolutionary lineage that is closely related to but not part of the group of species being studied, the ingroup
Can be determined based on evidence from morphology, paleontology, embryonic development, and gene sequences
Comparing members of the ingroup with each other and the outgroup can determine which characters were derived at the various branch points of evolution
Organisms have characteristics they share with their ancestors, and they also have characters that different from those of their ancestors
Shared Ancestral Characters
A character that originated in an ancestor taxon
Shared Derived Characters
an evolutionary trait novelty unique to a clade
Can refer to the loss of a feature
It is a relative matter whether a character is considered ancestral and derived
Phylogenetic Trees with Proportional Branch Lengths
The lengths of a tree's branches do not indicate the degree of evolutionary change in each lineage
The chronology represented by the branching pattern of the tree is relative
In some diagrams, branch lengths are proportional to amount of evolutionary change or to the times at which particular events occurred
Even though the branches of a phylogenetic tree may have different lengths, among organisms alive toady, all the different lineages that descend from a common ancestor have survived the same number of years
Equal spans of chronological time can be represented in a phylogenetic tree whose branch lengths are proportional to time
It is possible to combine the two types of trees by labeling branch points with information about rates of genetic change or dates of divergence
Maximum Parsimony & Likelihood
Principle of Maximum Parsimony
First investigate the simplest explanation that is constant with the available facts
Maximum Likelihood
Identifies the tree most likely to have produced a given set of DNA data, based on certain probability rules about how DNA sequences change over time
Phylogenetic Tree Hypotheses
Any phylogenetic tree represents a hypothesis about how the organisms in the tree are related to one another
A phylogenetic hypothesis may be modified when new evidence compels revision of trees
Organism's Evolutionary History Documented by it's Genome
Gene Duplication & Families
Gene Duplication
plays a particularly important role in evolution because it increases the number of genes in the genome
proves more of an opportunity for further evolutionary change
Orthologous Genes
Homology as the result of a speciation event and hence occurs between genes found in different species
Paralogous Genes
Homology resulting from gene duplication, multiple copies of these genes have diverged from one another within a species
Genome Evaluation
Lineages that diverged long ago often share many orthologous traits
such commonalities explain why disparate organisms nevertheless share many biochemical and developmental pathways
The number of genes a species has doesn't seem to increase through duplication at the same rate as perceived phenotypic complexity
Different genes can evolve at different rates, even in the same evolutionary linage
Molecular trees can represent short or long periods of time, depending on which genes are used
Molecular Clocks Track Evolutionary Time
Applying Molecular Clocks: Origin of HIV
Molecular clocks can be used to date the origin of HIV infections in humans
Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates
The virus has spread to humans more than once, the multiple origins of HIV are reflected in the variety of strains of the virus
Like other RNA viruses, it evolves quickly
A comparison of gene sequences showed that the virus has evolved in a clock like fashion
Molecular Clocks
Differences in Clock Speed
Some mutations are selectively neutral, neither beneficial nor detrimental
Many mutations are harmful and are removed quickly by selection
Most of the rest are neutral and have little and have little to no effect on fitness, the the rate of evolution of those neutral mutations should indeed be regular, like a clock
Differences in the clock rate for different genes are related to how important a gene is
Because the direction natural selection may change repeatedly over long periods of time, some genes experiencing selection can nevertheless serve as approximate markers of elapsed time
molecular clocks can be used to date evolutionary divergences that occurred a billion years or so ago
Assumes that the clocks have been consistent for all that time, such estimates are highly uncertain
Problems may be avoided by calibrating molecular clocks with data on the rates that which genes have evolved in different taxa
Fluctuations in evolutionary rate due to natural selection or other factors that vary over time may average out
Molecular clocks can aid our understanding of evolutionary relationships
Potential Problems with Molecular Clocks
Molecular clocks do not run as smoothly as would be expected if the underlying mutations were selectively neutral
Irregularities are likely to be the result of natural selection in which certain DNA changes are favored over others
An approach for measuring the absolute time of evolutionary change based on the observation that some genes appear to evolve at constant rates
Underlying assumption of the molecular clock is that the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the genes branched from their common ancestor
Paralogous genes, the number of substitutions is proportional to the time since the ancestral gene was duplicated
Molecular clocks can be calibrated based on a gene that has a reliable average rate of evolution by graphing the number of genetic differences against the dates of evolutionary branch points that are known from the fossil record
No gene marks time with complete precision, some portions of the genome appear to have evolved in irregular bursts that are not clock like
Even those genes that act as reliable molecular clocks are accurate only in the statistical sense of showing a fairly smooth average rate of change
When comparing genes that are clock like, the rate of the clock may vary greatly from one gene to another
Some genes evolve a million times faster than others
The goal of evolutionary biology is to understand the relationship among all organisms, including those for which there is no fossil record