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Phylogenies and
the History of Life
Organizing Life on Earth
Determining Evolutionary Relationships
Perspectives on the Phylogenetic Tree
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Phylogenies and the History of Life > Organizing Life on Earth
Organizing Life on Earth
• Phylogenetic Trees
• Limitations of Phylogenetic Trees
• The Levels of Classification
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Phylogenies and the History of Life > Determining Evolutionary Relationships
Determining Evolutionary Relationships
• Distinguishing between Similar Traits
• Building Phylogenetic Trees
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Phylogenies and the History of Life > Perspectives on the Phylogenetic Tree
Perspectives on the Phylogenetic Tree
• Limitations to the Classic Model of Phylogenetic Trees
• Horizontal Gene Transfer
• Endosymbiotic Theory and the Evolution of Eukaryotes
• Web, Network, and Ring of Life Models
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Appendix
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Phylogenies and the History of Life
Key terms
• analogous when similar similar physical features occur in organisms because of environmental constraints and not due to a
close evolutionary relationship
• ancestral of, pertaining to, derived from, or possessed by, an ancestor or ancestors; as, an ancestral estate
• basal taxon a lineage, displayed using a phylogenetic tree, that evolved early from the root and from which no other branches
have diverged
• binomial nomenclature the scientific system of naming each species of organism with a Latinized name in two parts
• clades groups of organisms that descended from a single ancestor
• clonal pertaining to asexual reproduction
• conjugation the temporary fusion of organisms, especially as part of sexual reproduction
• derived of, or pertaining to, conditions unique to the descendant species of a clade, and not found in earlier ancestral species
• endosymbiosis when one symbiotic species is taken inside the cytoplasm of another symbiotic species and both become
endosymbiotic
• genome fusion a result of endosymbiosis when a genome consists of genes from both the endosymbiont and the host.
• homologous when similar physical features and genomes stem from developmental similarities that are based on evolution
• horizontal gene transfer the transfer of genetic material from one organism to another one that is not its offspring; especially
common among bacteria
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Phylogenies and the History of Life
• Linnaeus Swedish botanist, physician and zoologist who laid the foundations for the modern scheme of nomenclature; known
as the "father of modern taxonomy"
• maximum parsimony the preferred phylogenetic tree is the tree that requires the least evolutionary change to explain some
observed data
• molecular systematics molecular phylogenetics is the analysis of hereditary molecular differences, mainly in DNA sequences, to
gain information on an organism's evolutionary relationships
• monophyletic of, pertaining to, or affecting a single phylum (or other taxon) of organisms
• phenotypical of or pertaining to a phenotype: the appearance of an organism based on a multifactorial combination of genetic
traits and environmental factors
• phylogenetic of, or relating to the evolutionary development of organisms
• phylogeny the evolutionary history of an organism
• phylogeny the visual representation of the evolutionary history of organisms; based on rigorous analyses
• polytomy a section of a phylogeny in which the evolutionary relationships cannot be fully resolved to dichotomies
• ring of life a phylogenetic model where all three domains of life (Archaea, Bacteria, and Eukarya) evolved from a pool of
primitive prokaryotes
• symbiotic of a relationship with mutual benefit between two individuals or organisms
• systematics research into the relationships of organisms; the science of systematic classification
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Phylogenies and the History of Life
• taxon any of the taxonomic categories such as phylum or subspecies
• transduction horizontal gene transfer mechanism in prokaryotes where genes are transferred using a virus
• transformation the alteration of a bacterial cell caused by the transfer of DNA from another, especially if pathogenic
• web of life a phylogenetic model that resembles a web or a network more than a tree
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Phylogenies and the History of Life
Homologous structures
Bat and bird wings are homologous structures, indicating that bats and birds share a common evolutionary past.
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Phylogenies and the History of Life
Mechanisms of prokaryotic and eukaryotic horizontal gene transfer
Horizontal gene transfer is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission
from parent(s) to offspring. These transfers allow even distantly-related species (using standard phylogeny) to share genes, influencing their phenotypes.
Examples of mechanisms of horizontal gene transfer are listed for both prokaryotic and eukaryotic organisms.
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Phylogenies and the History of Life
Analogous structures
The (c) wing of a honeybee is similar in shape to a (b) bird wing and (a) bat wing, and it serves the same function. However, the honeybee wing is not
composed of bones and has a distinctly-different structure and embryonic origin. These wing types (insect versus bat and bird) illustrate an analogy:
similar structures that do not share an evolutionary history.
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Phylogenies and the History of Life
Three hypotheses of eukaryotic and prokaryotic evolution
Three alternate hypotheses of eukaryotic and prokaryotic evolution are (a) the nucleus-first hypothesis, (b) the mitochondrion-first hypothesis, and (c) the
eukaryote-first hypothesis.
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Phylogenies and the History of Life
Limitations of phylogenetic trees
This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different
characters are placed in different groups based on the characteristics they share.
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Phylogenies and the History of Life
HGT within the aphid species
(a) Red aphids get their color from red carotenoid pigment. Genes necessary to make this pigment are present in certain fungi. Scientists speculate that
aphids acquired these genes through HGT after consuming fungi for food. If genes for making carotenoids are inactivated by mutation, the aphids revert
back to (b) their green color. Red coloration makes the aphids much more conspicuous to predators, but evidence suggests that red aphids are more
resistant to insecticides than green ones. Thus, red aphids may be more fit to survive in some environments than green ones.
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Phylogenies and the History of Life
Phylogenetic trees
Both of these phylogenetic trees shows the relationship of the three domains of life (Bacteria, Archaea, and Eukarya), but the (a) rooted tree attempts to
identify when various species diverged from a common ancestor, while the (b) unrooted tree does not.
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Phylogenies and the History of Life
Rooted phylogenetic trees
The root of a phylogenetic tree indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where two lineages
diverged. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister
taxa. A branch with more than two lineages is a polytomy.
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Phylogenies and the History of Life
Examples of clades
All the organisms within a clade stem from a single point on the tree. A clade may contain multiple groups, as in the case of animals, fungi, and plants, or
a single group, as in the case of flagellates. Groups that diverge at a different branch point, or that do not include all groups in a single branch point, are
not considered clades.
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Phylogenies and the History of Life
Common ancestors
Lizards, rabbits, and humans all descend from a common ancestor that had an amniotic egg. Thus, lizards, rabbits, and humans all belong to the clade
Amniota. Vertebrata is a larger clade that also includes fish and lamprey.
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Phylogenies and the History of Life
Endosymbiosis in eukaryotes
The theory that mitochondria and chloroplasts are endosymbiotic in origin is now widely accepted. More controversial is the proposal that (a) the
eukaryotic nucleus resulted from the fusion of archaeal and bacterial genomes; and that (b) Gram-negative bacteria, which have two membranes,
resulted from the fusion of Archaea and Gram-positive bacteria, each of which has a single membrane.
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Phylogenies and the History of Life
Levels in taxonomic classification
At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same species because they can
breed and produce viable offspring, but they are different enough to be classified as different subspecies.
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Phylogenies and the History of Life
Hierarchical models
The taxonomic classification system uses a hierarchical model to organize living organisms into increasingly specific categories. The common dog,
Canis lupus familiaris, is a subspecies of Canis lupus, which also includes the wolf and dingo.
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Phylogenies and the History of Life
Phylogenetic ring of life model
According to the "ring of life" phylogenetic model, the three domains of life evolved from a pool of primitive prokaryotes.
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Phylogenies and the History of Life
Phylogenetic web of life model
In the (a) phylogenetic model proposed by W. Ford Doolittle, the "tree of life" arose from a community of ancestral cells, has multiple trunks, and has
connections between branches where horizontal gene transfer has occurred. Visually, this concept is better represented by (b) the multi-trunked Ficus
than by the single trunk of the oak, similar to the tree drawn by Darwin.
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Phylogenies and the History of Life
Tree of life
The (a) concept of the "tree of life" goes back to an 1837 sketch by Charles Darwin. Like an (b) oak tree, the "tree of life" has a single trunk and many
branches.
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Phylogenies and the History of Life
Attribution
• Wiktionary. "polytomy." CC BY-SA 3.0 http://en.wiktionary.org/wiki/polytomy
• Boundless Learning. "Boundless." CC BY-SA 3.0 http://www.boundless.com//biology/definition/basal-taxon
• Wiktionary. "systematics." CC BY-SA 3.0 http://en.wiktionary.org/wiki/systematics
• Wiktionary. "phylogeny." CC BY-SA 3.0 http://en.wiktionary.org/wiki/phylogeny
• OpenStax CNX. "OpenStax College, Biology. October 16, 2013." CC BY 3.0
http://cnx.org/content/m44588/latest/?collection=col11448/latest
• Wiktionary. "phenotypical." CC BY-SA 3.0 http://en.wiktionary.org/wiki/phenotypical
• OpenStax CNX. "OpenStax College, Biology. October 16, 2013." CC BY 3.0
http://cnx.org/content/m44588/latest/?collection=col11448/latest
• Wiktionary. "taxon." CC BY-SA 3.0 http://en.wiktionary.org/wiki/taxon
• Wiktionary. "Linnaeus." CC BY-SA 3.0 http://en.wiktionary.org/wiki/Linnaeus
• Wiktionary. "binomial nomenclature." CC BY-SA 3.0 http://en.wiktionary.org/wiki/binomial+nomenclature
• OpenStax CNX. "OpenStax College, Biology. October 16, 2013." CC BY 3.0
http://cnx.org/content/m44588/latest/?collection=col11448/latest
• Wikipedia. "molecular systematics." CC BY-SA 3.0 http://en.wikipedia.org/wiki/molecular%20systematics
• Wiktionary. "phylogeny." CC BY-SA 3.0 http://en.wiktionary.org/wiki/phylogeny
• Wiktionary. "homologous." CC BY-SA 3.0 http://en.wiktionary.org/wiki/homologous
• Wiktionary. "analogous." CC BY-SA 3.0 http://en.wiktionary.org/wiki/analogous
• OpenStax CNX. "OpenStax College, Biology. October 16, 2013." CC BY 3.0
http://cnx.org/content/m44591/latest/?collection=col11448/latest
• Wikipedia. "maximum parsimony." CC BY-SA 3.0 http://en.wikipedia.org/wiki/maximum%20parsimony
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Phylogenies and the History of Life
• Wiktionary. "ancestral." CC BY-SA 3.0 http://en.wiktionary.org/wiki/ancestral
• Wiktionary. "derived." CC BY-SA 3.0 http://en.wiktionary.org/wiki/derived
• Wiktionary. "monophyletic." CC BY-SA 3.0 http://en.wiktionary.org/wiki/monophyletic
• Boundless Learning. "Boundless." CC BY-SA 3.0 http://www.boundless.com//biology/definition/clades
• OpenStax CNX. "OpenStax College, Biology. October 16, 2013." CC BY 3.0
http://cnx.org/content/m44591/latest/?collection=col11448/latest
• Wiktionary. "horizontal gene transfer." CC BY-SA 3.0 http://en.wiktionary.org/wiki/horizontal+gene+transfer
• Wiktionary. "clonal." CC BY-SA 3.0 http://en.wiktionary.org/wiki/clonal
• Wiktionary. "phylogenetic." CC BY-SA 3.0 http://en.wiktionary.org/wiki/phylogenetic
• OpenStax CNX. "OpenStax College, Biology. November 5, 2013." CC BY 3.0
http://cnx.org/content/m44593/latest/?collection=col11448/latest
• OpenStax CNX. "OpenStax College, Biology. October 16, 2013." CC BY 3.0
http://cnx.org/content/m44593/latest/?collection=col11448/latest
• Wiktionary. "conjugation." CC BY-SA 3.0 http://en.wiktionary.org/wiki/conjugation
• Wiktionary. "transduction." CC BY-SA 3.0 http://en.wiktionary.org/wiki/transduction
• Wiktionary. "transformation." CC BY-SA 3.0 http://en.wiktionary.org/wiki/transformation
• OpenStax CNX. "OpenStax College, Biology. October 16, 2013." CC BY 3.0
http://cnx.org/content/m44593/latest/?collection=col11448/latest
• Boundless Learning. "Boundless." CC BY-SA 3.0 http://www.boundless.com//biology/definition/genome-fusion
• Wiktionary. "endosymbiosis." CC BY-SA 3.0 http://en.wiktionary.org/wiki/endosymbiosis
• Wiktionary. "symbiotic." CC BY-SA 3.0 http://en.wiktionary.org/wiki/symbiotic
• OpenStax CNX. "OpenStax College, Biology. October 16, 2013." CC BY 3.0
http://cnx.org/content/m44593/latest/?collection=col11448/latest
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• Boundless Learning. "Boundless." CC BY-SA 3.0 http://www.boundless.com//biology/definition/ring-of-life
Phylogenies and the History of Life
• Boundless Learning. "Boundless." CC BY-SA 3.0 http://www.boundless.com//biology/definition/web-of-life
• OpenStax CNX. "OpenStax College, Biology. October 23, 2013." CC BY 3.0
http://cnx.org/content/m44593/latest/?collection=col11448/latest
• OpenStax CNX. "OpenStax College, Biology. October 16, 2013." CC BY 3.0
http://cnx.org/content/m44593/latest/?collection=col11448/latest
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