25. Phylogeny

Phylogeny

Cladistics Part 1: Constructing Cladograms

 is a formal grouping in any level from phylum to species 

 No. A taxon is a formal grouping at any given level. 

 No. A taxon may be a clade, but it need not be. 

 of one type of organism at one level is comparable to another type of organism at the same level 

 No. Most likely not. For example, an order of snails would not be compared morphologically to an order of mammals. 

 is a formal grouping at any given level 

"Taxon," as in taxonomy.

A taxon __________.

 No. The correct use of binomial nomenclature requires the genus be capitalized and the species be set lowercase.  

 No. The correct use of binomial nomenclature requires the name be italicized or underlined, and the genus should be capitalized and the species set lowercase. 

 No. The correct use of binomial nomenclature requires the name to be italicized or underlined. 

Consider the proper format of binomial nomenclature.

Which of the following is the correct taxonomic name for the African forest elephant?

How are hypotheses about the evolutionary relationships among living organisms tested?

Phylogenies are created based on the principle that all species descending from a recent common ancestor                   .
a. should be identical;
b. should share characteristics that evolved in that ancestor;
c. should be found as fossils;
d. should have identical DNA sequences;
e. should be no more similar than species that are less closely related

How to Analyze Cladograms & Phylogenetic Trees?

Three living species X, Y, and Z share a common ancestor T, as do extinct species U and V. A grouping that consists of species T, X, Y, and Z (but not U or V) makes up
a. a monophyletic taxon.
b. an ingroup, with species U as the outgroup.
c. a paraphyletic group.
d. a polyphyletic group.

Taxonomy and the Tree of Life

Homology and Homoplasy

 No. Each species is assigned a two-part Latin name, or binomial. The first word is the genus, and the second word is the species. Species that are very similar are grouped into the same genus. 

This system was devised by Linnaeus.

The binomial system assigns to each organism a unique name that describes its __________.

 No. Messenger RNA would not be the most likely choice. 

 No. Ribosomal RNA changes relatively slowly. In 15,000 years, there may not be enough changes to draw any conclusions. 

 No. Transfer RNA would not be the most likely choice. 

 No. Nuclear DNA would not be the most likely choice. 

Think about relative rates of evolution in different types of genes.

If you wanted to determine the lineage of plants that have evolved on a relatively young archipelago&mdash;approximately 15,000 years old&mdash;what type of nucleic acid should you compare?

 Descriptions of various types of limbs (wings, legs, flippers, etc.) 

 No. Such information would be useful in identifying shared primitive characters and shared derived characters. 

 No. These data might contain information regarding shared primitive characters and shared derived characters. 

 The fact that teeth vary among types of mammals 

 No. Variation among the teeth of different types of mammals may be used to distinguish among shared primitive and shared derived characteristics. 

 No. Similarities and differences among DNA-based sequences play an important role in the construction of phylogenetic trees. 

Consider which of these features cannot be used to distinguish among mammals.

Using cladistic analysis, a taxonomist wishes to construct a phylogenetic tree showing the relationships among various species of mammals. Which of the following would be the least useful for this purpose?

 It shows that the common ancestor of birds and mammals must have had a four-chambered heart. 

 No. This would be the most parsimonious assumption. Abundant evidence, however, suggests that birds are more closely related to reptiles than they are to mammals. Thus, the common ancestor of birds and mammals could not have had a four-chambered heart. 

 This represents a problem with the principle of parsimony rather than a problem with the analogy-homology issue. 

 No. Just the opposite is true. A four-chambered heart must have developed independently in birds and mammals. To be the most accurate, a phylogenetic tree should represent several different characters to overcome problems with analogy and homology. 

 The most likely tree is always the most parsimonious. 

 No. Often this is true. But in this situation, evidence shows that the ancestors of mammals diverged from reptiles before the ancestors of birds did. Therefore, there is no common ancestor of birds and mammals that had a four-chambered heart. This character must have evolved twice. 

 None of the listed responses is correct. 

 No. One of the other choices is correct. 

 The most likely tree is not always the most parsimonious. 

During embryonic development, the four chambers do not develop in the same way in birds and mammals.

Birds and mammals have a four-chambered heart, but most reptiles have a three-chambered heart. How does this fact affect the construction of phylogenetic trees for these groups?

Critique the following statement: The absence of a trait cannot be used as a synapomorphy in phylogenetic analysis; only shared derived traits that are present in the clade can be used.

 It is important to use a gene that has been affected by natural selection to ensure that evolution will be observed. 

 No. Genes that have been affected by natural selection are unlikely to have constant rates of change, so they are not good candidates for molecular clocks. 

 It is important to use one gene in which the changes are clearly neutral. 

 No. It is difficult to determine whether all the changes in a gene are neutral; therefore, it is better to use several genes so that directional changes may average out. 

 It is best to use a gene that is essential to survival because they change more slowly. 

 No. The choice of gene will determine the timeframe that can be examined, but an essential gene will still be prone to evolving at different speeds. 

 All of the listed responses are correct. 

 No. Only one of the answers is correct. 

 It is important to use as many genes as possible. With this approach, fluctuations in evolutionary rate will tend to average out. 

As more and more sequence data become available, it is getting easier to apply molecular clock techniques reliably.

The idea of using molecules as clocks to time evolutionary events is very attractive, but there are many problems in actually applying the technique. What seems to be the best way to get reliable results?

In Figure 33.2, which two main clades branch from the most recent common ancestor of the eumetazoans?
a. Porifera and Cnidaria
b. Lophotrochozoa and Ecdysozoa
c. Cnidaria and Bilateria
d. Deuterostomia and Bilateria

 No. The more similar the DNA base sequences, the closer the relationship. 

 No. Homology is indicative of a common ancestry. 

 No. Ancestral-descendant sequences can be traced through the fossil record. 

 No. The more similar the amino acid sequences, the closer the relationship. 

Consider which of these does not provide information about the historical relationships among species.

Which of the following would be the least useful in determining the relationships among various species?

Cladogram

 No. Evolution can be defined as descent with modification. 

 No. Taxonomy is the naming and classification of organisms. 

 No. This refers to a convention that calls for every species name to consist of two parts. 

 No. Phylogeny is the evolutionary history of a species or group of related species. 

It is anything but a haphazard approach.

The analytical approach to understanding the diversity and relatedness of both extant and extinct organisms is called __________.

 are passed from generation to generation in a straight line 

 can only diverge after speciation has taken place 

 are responsible for the differences in beta hemoglobin in humans and mice 

 No. Beta hemoglobin genes are orthologous. 

 No. Unlike orthologous genes, paralogous genes can diverge in the same gene pool. 

Paralogous is from the Greek para, “at the side of.”

Paralogous genes __________.

If you were using cladistics to build a phylogenetic tree of cats, which of the following would be the best outgroup?
a. wolf
b. domestic cat
c. lion
d. leopard

 Analogous traits come about because of convergent evolution. 

 No. This assumption still appears to be valid. 

 Homologous traits come about because of common ancestry. 

 The greater the difference in gene sequences, the longer two species have diverged. 

 No. This assumption appears to be valid overall. 

 Genes are often passed from one organism to another without the occurrence of reproduction. 

 No. This is not one of the assumptions on which phylogenetic trees are based. 

 Genes are passed vertically from one generation to the next. 

In which dimension are phylogenetic trees primarily built?

Universal phylogenetic trees built from different genes sometimes give inconsistent results. What basic assumption on which phylogenetic trees are based has probably been violated during the history of life?

 Comparing morphology (shape and structure) 

 Comparing physiology (the functioning of structures and systems) 

 No. This is a method of observation and could be performed to some extent without the technology we have available today. 

 Comparing the amino acid sequences of proteins and nucleotide sequences of nucleic acids 

Consider which of these involves the most recent technological innovations.

Which of the following methods to establish phylogenetic relationships among organisms has been developed most recently?

Cladograms

 No. Order is less inclusive than class; thus, they could be in the same class and different orders. In fact, guinea pigs are rodents, but rabbits are placed in the order Lagomorpha. 

 No. Genus is less inclusive than class; thus, they could be in the same class and different genera. 

 No. Family is less inclusive than class; thus, they could be in the same class and different families. 

 No. Classification is hierarchical and linear; thus, organisms sharing a rank also share the ranks above it but not necessarily those below it. For example, all of the species found in class Mammalia, including rabbits and guinea pigs, must also be in the same phylum, phylum Chordata, and the same kingdom, kingdom Animalia, but are not necessarily in the same order, family, or genus. 

Consider the hierarchy of classification.

Rabbits and guinea pigs both belong to class Mammalia. This means they must also both belong to __________.

 A branch point represents a split between two phyla. 

 No. A branch point does not have a set rank on a phylogenetic tree. It is a point at which two evolutionary lineages diverge from a common ancestor. 

 A branch point represents a gene duplication event. 

 No. A gene duplication event does not necessarily cause two lineages to split from a common ancestor. 

 A branch point represents a place where one species branches off from another. 

 A branch point represents the absolute time at which two evolutionary lineages split from a common ancestor. 

 No. Without evidence from the fossil record and radiometric dating, it is not possible to put an absolute date on branch points. 

 A branch point represents a point at which two evolutionary lineages split from a common ancestor. 

A branch point is a general term.

What does a branch point in a phylogenetic tree represent?

You can use a “one-snip test” to identify monophyletic groups—meaning that if you “cut” any branch on a tree, everything that “falls off” is a monophyletic group. Why is this valid?

 The most parsimonious tree requires the fewest evolutionary events to have occurred in the form of shared ancestral characters. 

 No. You may want to review the definitions of shared ancestral and derived characters. 

 Given the rules of how morphological traits change over time, a tree can be found that reflects the most likely sequence of evolutionary events. 

 No. There are no true rules about how morphological traits change over time. There are certain rules regarding how DNA changes; however, this statement is more related to the principle of maximum likelihood. 

 Given the rules of how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events. 

 No. This statement is true, but it applies more to the principle of maximum likelihood than it does to maximum parsimony. 

 Trees can be constructed that are the most parsimonious or the most likely, but not both at the same time. 

 No. Although this is a difficult task, especially when working with a large data set, many computerized tools have been devised to search for trees that are the most parsimonious and the most likely. 

 The most parsimonious tree requires the fewest evolutionary events to have occurred in the form of shared derived characters. 

What is meant by "maximum parsimony?"

Which statement below is true of parsimonious trees?

Use the fossil evidence shown in Figure 25.6 to determine whether flight evolved earlier in insects or in birds. Is flight an example of homology or convergent evolution? Explain. <IMAGE>

Cladistics

VISUAL SKILLS In Figure 26.4, which similarly inclusive taxon is represented as descending from the same common ancestor as Canidae?
a. Felidae
b. Mustelidae
c. Carnivora
d. Lutra

 They give the absolute time that the gene duplication occurred. 

 No. It is possible to make some estimate of the time of gene duplication using molecular clock principles, but it is very difficult to get an accurate date with only one gene. 

 They give the absolute time that two species diverged. 

 No. Because paralogous genes result from gene duplication, the duplicated genes can diverge from each other without speciation occurring. Paralogous genes are not very useful in looking at when species diverge. 

 The fact that many paralogous genes are found in vastly different organisms emphasizes the many biochemical and developmental pathways shared by all organisms. 

 They increase the size of the genome and provide more opportunity for the evolution of novel characteristics. 

Do paralogous genes foster evolution or inhibit it?

What is the evolutionary significance of paralogous genes?

Cladistics Part 2: Monophyly, Paraphyly, and Polyphyly

 No. This is true, but there is a better response. 

 each species has a name that is understandable regardless of language barriers among scientists 

 systematists can easily specify the closest relatives of any species 

Think about the problems that could arise without a standardized naming system for organisms.

The two-part format of the scientific name, referred to as binomial, ensures that __________.

To apply parsimony to constructing a phylogenetic tree,
a. choose the tree that assumes all evolutionary changes are equally probable.
b. choose the tree in which the branch points are based on as many shared derived characters as possible.
c. choose the tree that represents the fewest evolutionary changes, in either DNA sequences or morphology.
d. choose the tree with the fewest branch points.

 No. A paraphyletic clade includes individuals derived from a common ancestor. But not all the individuals derived from that ancestor. 

 No. The members of a monophyletic clade share a common ancestor. However, unlike a paraphyletic group, all of the individuals derived from the most recent common ancestor are included. 

 No. The taxon in question would be described as "polyphyletic" because its members are derived from ancestors that are not common to all members. 

Taxa should be equivalent to clades wherever possible.

Many researchers who study the kingdom Protista argue that all of these organisms should not be placed in the same kingdom because these organisms could not have evolved from a common ancestor. In other words, they argue that the kingdom Protista is __________.

Classification of species, taxonomy, phylogenetic classification and binomial system for A-Level Bio

Taxonomy and Phylogeny

Bio 12.1.3-12.2 - Cladistics and Cladograms

4.1.3b Phylogeny vs  Taxonomy

Which of the following is an example of homoplasy?
a. hair in humans and fur in mice
b. astragalus ankle bones in hippos and deer
c. Hox genes in humans and flies
d. streamlined bodies in dolphins and ichthyosaurs

 species A and species B are in the same family 

 No. If they are not in the same order, then they cannot be in the same family. 

 species B and species C share a less recent ancestor than do species A and B 

 No. You cannot make this conclusion from the given information. 

 all three species are members of the same genus 

 No. This is not possible because all three species are not even members of the same order. 

 all three species are not members of the same phylum 

 No. All three species are members of the same phylum. 

 species C could be in the same class as species A and B 

Review the order of categories of classification and draw a quick tree to help yourself visualize the relationships.

Species A and species B are in the same phylum. Species A and species C, but not species B, are in the same order. From this information you can conclude that __________.

Taxonomy "classification of living things" with mnemonic

 No. Although taxonomic observations serve as a basis for evolutionary theory, taxonomy is based primarily on observed relationships. 

 No. Patterns of heredity are the primary focus of genetics. 

 No. Taxonomy is not a historical study. 

No. The study of environmental biology is referred to as ecology.

 The classification of life-forms by their similarities and differences 

What is a taxon?

What is the focus of the branch of biology called taxonomy?

 estimate how long ago the common ancestor lived 

 No. This is not the best answer. The fact that molecules have diverged between species does not in itself tell us how long ago their common ancestor lived. 

 hypothesize about the morphological structures of a common ancestor 

 No. The fossil record is much more useful for this purpose. 

 hypothesize about the behavior of a common ancestor 

 No. This information would not be discernible from studying molecular homologies. 

 No. Only one of the other choices is correct. 

 reveal the number of mutations in a particular sequence that has occurred in each species since they diverged from a common ancestor 

What are we looking at when we examine molecules?

Researchers can use molecular homologies to __________.

Taxonomy: Life's Filing System - Crash Course Biology #19

 Characteristics shared by all bird families 

 No. Characteristics shared by all bird families would not allow for a determination of the relationships among bird families. 

 No. Phylogeny does not necessarily match similarity of appearance. 

 Analogous structures shared by various species 

 No. Analogous structures are excluded from cladistic analysis. 

 Relative ages of living species of birds 

 No. Such information is not necessarily found on a phylogenetic tree. 

 Evolutionary relationships among bird families 

How is a clade defined?

A phylogenetic tree of bird families constructed by cladistic analysis would be a hypothesis about which of the following?

.VISUAL SKILLS  Based on the tree below, which statement is correct? 
(A)Lizards and goats form a sister group.
(B)Salamanders are a sister group to the group containing liz-ards, goats, and humans.
(C)Salamanders are more closely related to lizards than to humans.
(D)Goats and humans are the only sister group shown in this tree.

 hypothesize the relative relatedness between different taxa  

 No. This is true of regular phylogenies. 