Chap 26

family

In Linnaean classification, the taxonomic category above genus.

order

In Linnaean classification, the taxonomic category above the level of family.

class

In Linnaean classification, the taxonomic category above the level of order.

The three domains of life

Bacteria, Archaea, Eukarya This phylogenetic tree is based on sequence data for rRNA and other genes.

rooted

Describing a phylogenetic tree that contains a branch point (often, the one farthest to the left) representing the most recent common ancestor of all taxa in the tree.

paralogous genes

Homologous genes that are found in the same genome as a result of gene duplication.

Homology vs. Analogy

Homology is similarity due to shared ancestry Analogy is similarity due to convergent evolution

What causes trees based on data from different genes to yield such different results?

Horizontal gene transfer

phylogeny (fī-loj′-uh-nē)

The evolutionary history of a species or group of related species.

Suppose a molecular clock dates the divergence of two taxa at 80 million years ago, but new fossil evidence shows that the taxa diverged at least 120 million years ago. Explain how this could happen.

The gene (or genes) used for the molecular clock may have evolved more slowly in these two taxa than in the species used to calibrate the clock; as a result, the clock would underestimate the time at which the taxa diverged from each other.

Why is the kingdom Monera no longer considered a valid taxon?

The kingdom Monera included bacteria and archaea, but we now know that these organisms are in separate domains. Kingdoms are subsets of domains, so a single kingdom (like Monera) that includes taxa from different domains is not valid.

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?

The most likely tree is not always the most parsimonious.

Which statement below is true of parsimonious trees?

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

branch point

The representation on a phylogenetic tree of the divergence of two or more taxa from a common ancestor. A branch point is usually shown as a dichotomy in which a branch representing the ancestral lineage splits (at the branch point) into two branches, one for each of the two descendant lineages.

The reason that paralogous genes can diverge from each other within the same gene pool, whereas orthologous genes diverge only after gene pools are isolated from each other, is that _____.

having an extra copy of a gene permits modifications to the copy without loss of the original gene product

In a comparison of birds and mammals, the condition of having four limbs is

a shared ancestral character.

Keep in mind that no genes mark time precisely some portions of the genome appear to have evolved in irregular bursts that are not at all clocklike and even those genes that seem to act as reliable molecular clocks are

accurate only in the statistical sense of showing a fairly smooth average rate of change.

Note that orthologous genes can only diverge

after speciation has taken place, that is, after the genes are found in separate gene pools

To construct a phylogenetic tree a character table is a useful tool especially in separating

an outgroup from the ingroup.

Systematists depict evolutionary relationships in

branching phylogenetic trees (see fig 26.4)

The genus name is ____ and the species name _______. The scientific name is usually underlined or italicized.

capitalized, begins with a lowercase letter

Linnaeus also developed a scheme where organisms are classified or grouped into

categories. These categories are further divided into smaller and smaller groupings creating an organizational hierarchy (see fig 26.3)

To apply parsimony to constructing a phylogenetic tree,

choose the tree that represents the fewest evolutionary changes, in either DNA sequences or morphology.

Cladistics uses ______ and _______ to show phylogenetic relationships.

cladograms and clades

The discipline of systematics

classifies organisms based on shared relationships.

Generally, similar morphology and similar DNA sequences =

closely related species.

Well-supported phylogenetic hypotheses are

consistent with a wide range of data.

Evolutionary history and the genome Changes in the DNA (mutations) and comparisons between genomes can be used to

construct and evaluate phylogenetic trees.

However analogous structures (a.k.a., homoplasies) may be due to

convergent evolution, not shared ancestry.

These branches were termed

domains (see fig 26.21)

In 1969 Robert Whittaker proposed a means for

easily determining which of the five kingdoms an organism belonged in based on observably different attributes that defined them.

The domain of Eukarya branches into the separate

eukaryotic kingdoms

Systematists use

fossil, molecular, and genetic data to infer these relationships

One type of mutation that can occur is a

gene duplication.

We can calibrate the molecular clock of a gene that has a reliable average rate of evolution by

graphing the number of genetic differences

Nodes closer to the ancestral linage represent

greater amounts of divergence than nodes farther from the ancestral linage.

gene families,

groups of related genes within an organism's genome

Organizing or grouping things

helps in dealing with them. The same idea holds true for the study of life.

In evaluating molecular similarities for evolutionary studies. Two sequences that resemble each other at many points along their length most likely are _____. (see Figure 26.8).

homologous

Plants vs. animals was an

imperfect system and as a result didn't last.

Systematics is an

inexact process.

in a paraphyletic group, the most recent common ancestor of all members of the group ____ part of the group, whereas in a polyphyletic group the most recent common ancestor ___ part of the group.

is, is not

Only monophyletic groups made up of an ancestral species and all of its descendents qualify as

legitimate taxa in cladistics

Changes in the DNA (mutations) and comparisons between genomes can be used to construct and evaluate phylogenetic trees. This type of analysis combines

maximum parsimony and maximum likelihood

But in organisms that do not appear to be closely related, the bases that their otherwise very different sequences happen to share may simply be coincidental matches, called

molecular homoplasies.

DNA similarities, known as _________ can also occur.

molecular homoplasy

In the five-kingdom system, prokaryotes are placed in the kingdom _____.

monera

Using systematic, the more categories two organisms have in common the

more closely they are related.

Phylogenies are inferred from

morphological and molecular data

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

mtDNA (Mitochondrial DNA (mtDNA) evolves rapidly and can be used to explore more recent evolutionary events.)

Gene duplications produce

multiple copies of a gene within the genome.

If organisms (or any items) are to be grouped then they need a

name. In biology this begins with taxonomy.

Each branch point in the tree is a

node represents the divergence of species.

The idea of a molecular clock rests on the assumption that neutral mutations can arise and become fixed in populations. The rate of occurrence of these mutations is _____ by natural selection, so it is assumed that the rate is relatively constant over time.

not affected

There is(are) _____ eukaryotic domain(s).

one The only eukaryotic domain is the domain Eukarya.

Changes in a single gene can result in

orthologous genes

Changes in the genes in an organism's gene family can result in

paralogous genes

Shared characters are used to construct

phylogenetic trees.

The bacteria, fungi and many protists were considered

plants while some of the protists were grouped with the animals.

The character table shows

shared ancestral characteristics that predate the branching of a particular clade from other members of that clade. It also shows shared derived characteristic that are unique to a particular clade.

It was clear from very early that best systematic arrangement would group together organisms with a

shared phylogeny Grouping based on perceived evolution.

Phylogenetic history can be inferred from

similarities in homologous structures and genes when compared among organisms.

The more closely related two organisms are the

smaller the differences between them.

One of the early classification systems placed

the animals in one group and the plants in another.

An organism's genome consists of

the complete complement of its genes along with all of its noncoding DNA sequences. Organisms within a species display some variation within their DNA sequences.

Molecular clock analyses suggest that the most common strain of HIV jumped from primates to humans in

the early 1900s.

The relative lengths of the frog and mouse branches in the phylogenetic tree in Figure 26.13 indicate that

the homolog has evolved more slowly in mice.

The ability to examine the DNA sequences and genes of different organisms resulted in

the kingdom Monera being separated into two distinct groups which are polyphyletic.

The second problem has yet to be resolved. If you examine the kingdoms within domain Eukarya you will see that

the protist kingdom is also polyphyletic.

The lowest two categories of the taxonomic hierarchy (genus and species) make up

the scientific name for an organism.

There were two problems with Whittaker's system that became obvious once DNA technology improved in the 1980's The techniques of molecular biology have aided

the taxonomist in the classification of organisms by allowing the DNA sequences from two organisms to be compared.

Clades can be distinguished by

their shared derived characters

Carl Woese proposed that

these two groups of prokaryotes are as different form each other as they are from the eukaryotes and that these differences arose very early in the process of evolution.

In the two-kingdom system, why were fungi classified in the kingdom Plantae?

they are sedentary

Prokaryotic cells are found in the domain(s) _____.

Bacteria and Archaea

There are two prokaryotic domains

Bacteria and Archaea and a eukaryotic domain Eukarya.

In order to accommodate these differences and place them in the appropriate evolutionary context, Woese and others proposed an

"evolutionary tree" with three main branches.

genus (jē′-nus)

(plural, genera) A taxonomic category above the species level, designated by the first word of a species' two-part scientific name.

phylum (fī′-lum)

(plural, phyla) In Linnaean classification, the taxonomic category above class.

taxon

(plural, taxa) A named taxonomic unit at any given level of classification.

phylogenetic tree

A branching diagram that represents a hypothesis about the evolutionary history of a group of organisms.

shared ancestral character

A character, shared by members of a particular clade, that originated in an ancestor that is not a member of that clade.

binomial

A common term for the two-part, latinized format for naming a species, consisting of the genus and specific epithet; also called a binomen.

clade (klād)

A group of species that includes an ancestral species and all of its descendants. A clade is equivalent to a monophyletic group.

molecular clock

A method for estimating the time required for a given amount of evolutionary change, based on the observation that some regions of genomes evolve at constant rates.

maximum parsimony

A principle that states that when considering multiple explanations for an observation, one should first investigate the simplest explanation that is consistent with the facts.

taxonomy (tak-son′-uh-mē)

A scientific discipline concerned with naming and classifying the diverse forms of life.

systematics

A scientific discipline focused on classifying organisms and determining their evolutionary relationships.

outgroup

A species or group of species from an evolutionary lineage that is known to have diverged before the lineage that contains the group of species being studied. An outgroup is selected so that its members are closely related to the group of species being studied, but not as closely related as any study-group members are to each other.

ingroup

A species or group of species whose evolutionary relationships are being examined in a given analysis.

kingdom

A taxonomic category, the second broadest after domain.

cladistics (kluh-dis′-tiks)

An approach to systematics in which organisms are placed into groups called clades based primarily on common descent.

shared derived character

An evolutionary novelty that is unique to a particular clade.

The origins of taxonomy date back to

Aristotle.

maximum likelihood

As applied to DNA sequence data, a principle that states that when considering multiple phylogenetic hypotheses, one should take into account the hypothesis that reflects the most likely sequence of evolutionary events, given certain rules about how DNA changes over time.

Explain why phylogenies based on different genes can yield different branching patterns for the tree of all life.

Because of horizontal gene transfer, some genes in eukaryotes are more closely related to bacteria, while others are more closely related to archaea; thus, depending on which genes are used, phylogenetic trees constructed from DNA data can yield conflicting results.

Why do researchers use rRNA in investigations of relationships between taxa that diverged hundreds of millions of years ago?

DNA coding for rRNA changes relatively slowly.

The major taxonomic categories from most inclusive (biggest set) to least inclusive (smallest set) are:

Domain - this one was added later (see below) Kingdom Phylum/Division Class Order Family Genus Species Use a phrase (mnemonic device) to help you remember the order of these categories. Dear King Phillip Came Over From Great Spain

Explain how the origin of eukaryotes is thought to have represented a fusion of organisms, leading to extensive horizontal gene transfer.

Eukaryotes are hypothesized to have originated when a heterotrophic prokaryote (an archaeal host cell) engulfed a bacterium that would later become an organelle found in all eukaryotes—the mitochondrion. Over time, a fusion of organisms occurred as the archaeal host cell and its bacterial endosymbiont evolved to become a single organism. As a result, we would expect the cell of a eukaryote to include both archaeal DNA and bacterial DNA, making the origin of eukaryotes an example of horizontal gene transfer.

What other key points do we need to keep in mind when interpreting phylogenetic trees?

First, they are intended to show patterns of descent, not phenotypic similarity. second, we cannot necessarily infer the ages of the taxa or branch points shown in a tree. Third, we should not assume that a taxon on a phylogenetic tree evolved from the taxon next to it.

sister taxa

Groups of organisms that share an immediate common ancestor and hence are each other's closest relatives.

orthologous genes

Homologous genes that are found in different species because of speciation.

How can a particular gene have different functions in different tissues within an organism.

In RNA processing, the exons or coding regions of a gene can be spliced together in different ways, yielding different mRNAs and hence different protein products. As a result, different proteins could potentially be produced from the same gene in different tissues, thereby enabling the gene to perform different functions in these different tissues.

basal taxon

In a specified group of organisms, a taxon whose evolutionary lineage diverged early in the history of the group.

What assumption underlies the use of a molecular clock?

It is based on the assumption that the regions of genomes being compared evolve at constant rates.

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?

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

The five kingdoms and their defining characteristics:

Kingdom Cell Cell Nutritional Type Number Method Monera Prokaryotic Unicellular Absorption/photosynthesis Protista Eukaryotic Unicellular Absorption/photosyn./ingestion Fungi Eukaryotic Multicellular Absorption Plantae Eukaryotic Multicellular Photosynthesis Animalia Eukaryotic Multicellular Ingestion

This and other issues in taxonomy are in the process of being resolved such as

Linking systematics and phylogeny

The foundation for modern classification, binomial nomenclature, was developed by

Linnaeus in the 1700's.

polyphyletic (pol′-ē-fī-let′-ik)

Pertaining to a group of taxa that includes distantly related organisms but does not include their most recent common ancestor.

How can we determine the timing of phylogenies that extend beyond the fossil record?

Molecular clocks

A group of organisms can be:

Monophyletic Paraphyletic Polyphyletic

Many criteria are used by biologists to group organisms

Morphology (size, shape, structure) Anatomy (organs, tissues) Developmental stage (compare the embryos) Cell structure (chromosome number and structure) Behavior (does it fly? Swim? Quack?) Lifecycle (How long does it live? How often does it reproduce?) Ecology (Where does it live? What does it eat?)

Molecular clocks are based on the idea that _____.

On average neutral mutations arise at a constant rate

monophyletic (mon′-ō-fī-let′-ik)

Pertaining to a group of taxa that consists of a common ancestor and all of its descendants. A monophyletic taxon is equivalent to a clade.

paraphyletic (pār′-uh-fī-let′-ik)

Pertaining to a group of taxa that consists of a common ancestor and some, but not all, of its descendants.

In this scheme each Kingdom is divided into either

Phyla (plural of phylum) or Divisions.

analogy

Similarity between two species that is due to convergent evolution rather than to descent from a common ancestor with the same trait.

What causes such differences in the speed at which clocklike genes evolve?

The answer stems from the fact that some mutations are selectively neutral—neither beneficial nor detrimental. Differences in the clock rate for different genes are related to how important a gene is.

horizontal gene transfer

The transfer of genes from one genome to another through mechanisms such as transposable elements, plasmid exchange, viral activity, and perhaps fusions of different organisms.

Suppose gene A is orthologous in species 1 and species 2, and gene B is paralogous to gene A in species 1. Suggest a sequence of two evolutionary events that could result in the following: Gene A differs considerably between species, yet gene A and gene B show little divergence from each other.

These observations suggest that the evolutionary lineages leading to species 1 and species 2 diverged from one another before a gene duplication event in species 1 produced gene B from gene A.

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 __________.

polyphyletic (A taxon is polyphyletic if its members are derived from ancestors that are not common to all members.)

A node with multiple lineages is a

polytomy that requires more data to be resolved.

In the case of paralogous genes, the number of substitutions is

proportional to the time since the ancestral gene was duplicated.

An assumption underlying 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

What kind of evidence has recently made it necessary to assign the prokaryotes to either of two different domains, rather than assigning all prokaryotes to the same kingdom?

rRNA genes (molecular)

Among phylogenies, the most parsimonious tree is the one that

requires the fewest evolutionary changes. The most likely tree is the one based on the most likely pattern of changes.

Researchers can use molecular homologies to __________.

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

Some of these criteria can be misleading because

very different organisms can have similar characteristics which are the result of convergent evolution.

This often means

very small anatomical differences are used to distinguish between two species.