25. Phylogeny

Phylogeny

How to Analyze Cladograms & Phylogenetic Trees?

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.

"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

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.

What types of molecular comparisons are used to determine the very early branching of the tree of life? Explain.

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?

What important assumption does parsimony make when assessing which phylogenetic tree is most accurate? Why was parsimony misleading in the case of the astragalus during the evolution of artiodactyls?

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.

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.

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?

Fill in the blanks on the phylogenetic tree (on the facing page) to show current hypotheses for the origin of multicellular organisms. 
a. 
b. 
c. 
d. 
e. 
f. <img class="fr-dib" src="https://lightcat-files.s3.amazonaws.com/problem_images/d3327a26cdee734c-1677717218949.jpg" style="width: 300px;">

Which of the following kingdoms or domains is a hodgepodge of different evolutionary lineages?
a. Bacteria;
b. Protista;
c. Archaea;
d. Plantae;
e. Animalia

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 __________.

Which are more likely to be closely related: two species with similar appearance but divergent gene sequences or two species with different appearances but nearly identical genes? Explain.

A paleontologist compares fossils from three dinosaurs and Archaeopteryx, the earliest-known bird. The following table shows the distribution of characters for each species, where 1 means that the character is present and 0 means it is not. The outgroup (not shown in the table) had none of the characters. Arrange these species on the phylogenetic tree below and indicate the derived character that defines each branch point. <img class="fr-dib" src="https://lightcat-files.s3.amazonaws.com/problem_images/57e6ffb6235142fa-1677717117067.jpg" style="width: 300px;">

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?

The traditional tree of life (shown above) presents the three domains as distinct, monophyletic lineages. However, other hypotheses propose different views on the relationships among the Archaea, Bacteria, and Eukarya. In particular, the two-domain hypothesis—or eocyte hypothesis—is emerging as a well-supported alternative to the three-domain hypothesis. The eocyte hypothesis, illustrated below, suggests that eukaryotes evolved from eocytes (also known as the Crenarchaeota—a major lineage of the Archaea). Resolving the relationships among these ancient lineages is difficult, but it has profound implications on our understanding of the origin of eukaryotic cells. 

Why are Archaea considered a monophyletic group according to the three-domain hypothesis?
a. Because this group includes all organisms except eukaryotes.
b. Because this group includes an ancestral population and all of its descendants.
c. Because all members of this group lack membrane-bound organelles.
d. Because this group evolved after the origin of bacteria.<img class="fr-dib" src="https://lightcat-files.s3.amazonaws.com/problem_images/8ec0b8f601427646-1677302753892.jpg" style="width: 300px;">

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 __________.

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

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. <img class="fr-dib" src="https://lightcat-files.s3.amazonaws.com/problem_images/ed79932096dd7222-1677289257721.jpg" style="width: 300px;">

Which of the following could provide the best data for determining the phylogeny of very closely related species?
a. the fossil record
b. their morphological differences and similarities
c. a comparison of nucleotide sequences in homologous genes and mitochondrial DNA
d. a comparison of their ribosomal DNA sequences

If you were using cladistics to build a phylogenetic tree of cats, which would be the best choice for an outgroup?
a. kangaroo
b. leopard
c. domestic cat
d. iguana

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?

Cladistics Part 1: Constructing Cladograms

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

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

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 __________.

Explain why changes in the regulation of developmental genes may have played such a large role in the evolution of new forms.

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

Fill in this concept map about systematics 
a.
b. 
c. 
d. 
e.
f.
g<img class="fr-dib" src="https://lightcat-files.s3.amazonaws.com/problem_images/d26b0b99c31a8204-1677716965885.jpg" style="width: 300px;">

VISUAL SKILLS Based on the tree below, which statement is not correct? <img src="https://lightcat-files.s3.amazonaws.com/problem_images/90228deacc030a80-1665767032885.jpg" alt="" /> a.Goats and humans form a sister group.
b. Salamanders are a sister group to the group containing lizards, goats, and humans.
c. Salamanders are as closely related to goats as to humans.
d. Lizards are more closely related to salamanders than to humans.

4.1.3b Phylogeny vs  Taxonomy

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. 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 __________.

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.

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

Evolutionary relationships among bird families