20: Phylogenies and the History of Life

Question 1

What is a basal taxon?

Answer 1

A branch on a phylogenetic tree that has not diverged significantly from the root ancestor.

Question 2

What is binomial nomenclature?

Answer 2

A system of two-part scientific names for an organism, which includes genus and species names.

Question 3

What is a branch point?

Answer 3

A node on a phylogenetic tree where a single lineage splits into distinct new ones.

Question 4

What is a class?

Answer 4

A division of phylum in the taxonomic classification system.

Question 5

What is a family?

Answer 5

A division of order in the taxonomic classification system.

Question 6

What is a genus?

Answer 6

Division of family in the taxonomic classification system; the first part of the binomial scientific name.

Question 7

What is a kingdom?

Answer 7

A division of domain in the taxonomic classification system.

Question 8

What is an order?

Answer 8

A division of class in the taxonomic classification system.

Question 9

What is a phylogenetic tree?

Answer 9

A diagram used to reflect the evolutionary relationships among organisms or groups of organisms.

Question 10

What is phylogeny?

Answer 10

The evolutionary history and relationship of an organism or group of organisms.

Question 11

What is a phylum?

Answer 11

A division of kingdom in the taxonomic classification system. Plural: phyla.

Question 12

What is polytomy?

Answer 12

A branch on a phylogenetic tree with more than two groups or taxa. It serves to illustrate where scientists have no definitively determined all of the relationships.

Question 13

What does it mean to be rooted?

Answer 13

A single ancestral lineage on a phylogenetic tree to which all organisms represented in the diagram relate.

Question 14

What are sister taxa?

Answer 14

Two lineages that diverged from the same branch point.

Question 15

What is systematics?

Answer 15

A field of organizing and classifying organisms based on evolutionary relationships.

Question 16

What is a taxon?

Answer 16

A single level in the taxonomic classification system. Plural: taxa.

Question 17

What is taxonomy?

Answer 17

The science of classifying organisms.

Question 18

Who created the Linnaean system?

Answer 18

Carl Linnaeus, a Swedish botanist, zoologist, and physician who invented the taxonomic classification system, or Linnaean system.

Question 19

What is the taxonomic classification of dogs?

Answer 19

The common dog. The species Canis lupus also includes the wolf and dingo.

• Subspecies: Canis lupus familiaris
• Species: Canis lupus
• Genus: Canis
• Family: Canidae
• Order: Carnivora
• Class: Mammalia
• Phylum: Chordata
• Kingdom: Animalia
• Domain: Eukarya

Question 20

What is an analogy?

Answer 20

A characteristic that is similar between organisms by convergent evolution, not due to the same evolutionary path. AKA homoplasy. Some structures are both homologous and analogous, such as the wings of a bat and the wings of a bird.

Question 21

What is cladistics?

Answer 21

A system used to organize homologous traits to describe phylogenies.

Question 22

What is maximum parsimony?

Answer 22

Applying the simplest, most obvious way with the least number of steps.

Question 23

What is molecular systematics?

Answer 23

A technique using molecular evidence to identify phylogenetic relationships.

Question 24

What is a monophyletic group or clade?

Answer 24

Organisms that share a single ancestor.

Question 25

What is a shared ancestral character?

Answer 25

Describes a characteristic on a phylogenetic tree that is shared by all organisms on the tree.

Question 26

What is a shared derived character?

Answer 26

Describes a characteristic on a phylogenetic tree that is shared only by a certain clade of organisms.

Question 27

What is an example of a species that was identified using DNA markers?

Answer 27

Dalbergia sissoo (D. sissoo), a member of the Fabaceae (legume) family. Scientists have found that D. sissoo shares a DNA marker with species within the Fabaceae family that have antifungal properties. Subsequently, D. sissoo was shown to have fungicidal activity, supporting the idea that DNA markers can be used to screen for plants with potential medicinal properties.

Question 28

What is the eukaryote-first hypothesis?

Answer 28

A proposal that prokaryotes evolved from eukaryotes.

Question 29

What is a gene transfer agent (GTA)?

Answer 29

A bacteriophage-like particle that transfers random genomic segments from one species of prokaryote to another.

Question 30

What is genome fusion?

Answer 30

Fusion of two prokaryotic genomes, presumably by endosymbiosis.

Question 31

What is horizontal gene transfer (HGT)?

Answer 31

Transfer of genes between unrelated species. AKA lateral gene transfer.

Question 32

What is the mitochondria-first hypothesis?

Answer 32

A proposal that prokaryotes acquired a mitochondrion first, followed by nuclear development.

Question 33

What is the nucleus-first hypothesis?

Answer 33

A proposal that prokaryotes acquired a nucleus first, and then the mitochondrion.

Question 34

What is the ring of life?

Answer 34

Phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes.

Question 35

What is the web of life?

Answer 35

A phylogenetic model that attempts to incorporate the effects of horizontal gene transfer on evolution.

Question 36

How prevalent is horizontal gene transfer?

Answer 36

It occurs in both prokaryotic and eukaryotic evolution. It is thought that HGT is more prevalent in prokaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process. Some researchers believe such estimates are premature: the actual importance of HGT to evolutionary processes must be viewed as a work in progress. Many scientists believe that HGT and mutation appear to be (especially in prokaryotes) a significant source of genetic variation. These transfers may occur between any two species that share an intimate relationship.

Question 37

What is transduction?

Answer 37

The process by which foreign DNA is introduced into a cell by a virus or viral vector.

Question 38

What is an endosymbiont?

Answer 38

Any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship.

Question 39

What is the Endosymbiont Theory?

Answer 39

A hypothesis that eukaryotes descended from the genome fusion of Archaea and Bacteria by endosymbiosis.

Question 40

How does HGT occur in prokaryotes using GTAs?

Answer 40

GTAs have been shown to be responsible for genetic changes, sometimes at a very high frequency compared to other evolutionary processes. The first GTA was characterized in 1974 using purple, non-sulfur bacteria. These GTAs, which are thought to be bacteriophages that lost the ability to reproduce on their own, carry random pieces of DNA from one organism to another. The ability of GTAs to act with high frequency has been demonstrated in controlled studies using marine bacteria. Gene transfer events in marine prokaryotes, either by GTAs or by viruses, have been estimated to be as high as 10¹³ per year in the Mediterranean Sea alone. GTAs and viruses are thought to be efficient HGT vehicles with a major impact on prokaryotic evolution.

Question 41

What is a transposon (or “jumping gene”)?

Answer 41

A DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell’s genetic identity and genome size.

Question 42

How does HGT occur in eukaryotes?

Answer 42

Transposons have been shown to transfer between rice and millet plant species, and fungal species feeding on yew trees, from which the anti-cancer drug TAXOL® is derived from the bark, have acquired the ability to make taxol themselves.

Question 43

What is an example of HGT in eukaryotes?

Answer 43

Aphids are insects that vary in color based on carotenoid content. Carotenoids are made by plants, fungi and microbes naturally, but aphids have acquired the ability to make carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme called a desaturase is responsible for the red coloration seen in certain aphids, and it has been shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color.

Question 44

What are carotenoids?

Answer 44

Pigments made by a variety of plants, fungi and microbes, and which serve a variety of functions in animals, who obtains these chemicals from their food. Humans require carotenoids to synthesize vitamin A, and we obtain them by eating orange fruits and vegetables: carrots, apricots, mangoes, and sweet potatoes.

Question 45

What is mitochondrial DNA and how is it inherited?

Answer 45

Mitochondrial DNA can be regarded as the smallest chromosome. It is inherited only from the mother. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or in other instances when the mitochondria located in the flagellum of the sperm fails to enter the egg.

Question 46

What is the Eocyte hypothesis?

Answer 46

A hypothesis of genome fusion by endosymbiosis proposed by James Lake of the UCLA/NASA Astrobiology Institute to be responsible for the evolution of the first eukaryotic cells. Using DNA analysis and a new mathematical algorithm called conditional reconstruction (CR), his laboratory proposed that eukaryotic cells developed from an endosymbiotic gene fusion between two species, one an Archaea and the other a Bacteria. This would explain why some eukaryotic genes resemble those of Archaea and others resemble those from Bacteria. Many scientists resist this hypothesis because this work is new and the CR algorithm is relatively unsubstantiated. More recent work by Lake proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, resulted from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized.

Question 47

What are some hypotheses of the origin of eukaryotic nuclei?

Answer 47

One theory is that prokaryotic cells produced an additional membrane that surrounded the bacterial chromosome. Some bacteria have DNA enclosed by two membranes; however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes. If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely related to eukaryotes.

Question 48

Who proposed the web of life model?

Answer 48

It was proposed in 1999 by W. Ford Doolittle.

Question 49

Who proposed the ring of life model?

Answer 49

It was proposed by Lake using the conditioned reconstruction algorithm. HIs laboratory proposes that this structure is the best fit for data from extensive DNA analyses performed in his laboratory, and that the ring model is the only one that adequately takes HGT and genomic fusion into account. However, other phylogeneticists remain highly skeptical of this model.

Question 50

How do computers help to compare DNA sequences between different organisms?

Answer 50

New computer programs not only confirm many earlier classified organisms, but also uncover previously made errors. The DNA sequence can be tricky to read in some cases. In some situations, two very closely related organisms can appear unrelated if a mutation occurred that caused a shift in the genetic code, such an insertion or deletion that shifted all nucleotide bases by a single place. Sometimes two segments of DNA code in distantly related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not. For both of these situations, computer technologies have been developed to help identify the actual relationships and, ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny.