Evolutionary Relationships
Humans have been attempting to properly classify living things since Aristotle made the first attempt during the 4th century BC. Aristotle’s system wa…
Humans have classified and organized biological organisms for thousands of years. Originally, primarily ordering objects necessary for survival. As human history progressed, so did the skill and detail in these classifications. In the fourth century B.C., Aristotle pioneered formal classifications, delineating plants and animals into different groups and then dividing these further based on their physical characteristics and traits like the habitats that they occupy. Later, in the mid 1700s, Linnaeus built on Aristotle's system. He called his highest level of grouping the kingdoms and, from there, divided the groups using synapomorphies, a defining physical feature which splits a branch. For example, if an animal possesses a backbone or a similar structure, it should be placed in the phylum chordata. If it doesn't, then there are many other phyla, which animals without backbones can be split into, including the arthropoda, a large group including insects. Linneaus continued splitting groups of organisms based on their synapomorphies at subsequent levels through the class, order, family, and genus, until reaching the final designation, generally, the species. We refer to Linnaeus' type of classification as cladistics, the classification of organisms based on differences in physical characteristics.
Today, scientists commonly construct trees called dendrograms to give visual representations of these splits and groups. This particular form of dendrogram, the cladogram, visualizes the cladistic relationships between the species so that the tips of the tree represent the species and the branches show how they're related to one another. For example, here the chimpanzee and bear are more closely related to one another and share more common characteristics than either of them do with the sunfish. The places where the branches meet are referred to as nodes and denote common ancestors for the species that follow. A second major dendrogram type is the phylogram. These are different from cladograms because the length of the branches between species varies, representing the degree of change between them. So the longer the branch, the more time has passed since the species diverged from their last common ancestor.
Dendrograms were constructed by simply analyzing the morphology of organisms. With the advent of modern technology, comparing DNA has also become a common way to build trees. DNA is made up of nucleotides associated with one of four different bases. Adenine, guanine, cytosine, or thymine. The order of these bases is the DNA code. This code is passed from parent to offspring. Consequently, if you look across a single species like humans, there is a very high degree of similarity in our genetic code, around 99.9%. We also share some of our DNA code with other species, like chimpanzees and mice, but the degree of overall similarity between our DNA and theirs is vastly different. This means that we can create trees, which group species based on the similarities or difference between their genetic codes. This field of analysis, combining statistics, mathematical modeling, and computer science, is referred to as bioinformatics. To compare DNA sequences, researchers often use a bioinformatics tool called the Basic Local Alignment Search Tool, or BLAST, which was created, and is maintained by, the National Center for Biotechnology Information.
In this laboratory, you will first create a cladogram of animals using morphological information, and then place a fossil species onto this cladogram based on its morphology. You will then use DNA sequences from several different modern-day relatives of the fossil and the BLAST database to verify your positioning of the fossil onto the tree.
Humans have classified and organized biological organisms for thousands of years. Originally, primarily ordering objects necessary for survival. As human history progressed, so did the skill and detail in these classifications. In the fourth century B.C., Aristotle pioneered formal classifications, delineating plants and animals into different groups and then dividing these further based on their physical characteristics and traits like the habitats that they occupy. Later, in the mid 1700s, Linnaeus built on Aristotle's system. He called his highest level of grouping the kingdoms and, from there, divided the groups using synapomorphies, a defining physical feature which splits a branch. For example, if an animal possesses a backbone or a similar structure, it should be placed in the phylum chordata. If it doesn't, then there are many other phyla, which animals without backbones can be split into, including the arthropoda, a large group including insects. Linneaus continued splitting groups of organisms based on their synapomorphies at subsequent levels through the class, order, family, and genus, until reaching the final designation, generally, the species. We refer to Linnaeus' type of classification as cladistics, the classification of organisms based on differences in physical characteristics.
Today, scientists commonly construct trees called dendrograms to give visual representations of these splits and groups. This particular form of dendrogram, the cladogram, visualizes the cladistic relationships between the species so that the tips of the tree represent the species and the branches show how they're related to one another. For example, here the chimpanzee and bear are more closely related to one another and share more common characteristics than either of them do with the sunfish. The places where the branches meet are referred to as nodes and denote common ancestors for the species that follow. A second major dendrogram type is the phylogram. These are different from cladograms because the length of the branches between species varies, representing the degree of change between them. So the longer the branch, the more time has passed since the species diverged from their last common ancestor.
Dendrograms were constructed by simply analyzing the morphology of organisms. With the advent of modern technology, comparing DNA has also become a common way to build trees. DNA is made up of nucleotides associated with one of four different bases. Adenine, guanine, cytosine, or thymine. The order of these bases is the DNA code. This code is passed from parent to offspring. Consequently, if you look across a single species like humans, there is a very high degree of similarity in our genetic code, around 99.9%. We also share some of our DNA code with other species, like chimpanzees and mice, but the degree of overall similarity between our DNA and theirs is vastly different. This means that we can create trees, which group species based on the similarities or difference between their genetic codes. This field of analysis, combining statistics, mathematical modeling, and computer science, is referred to as bioinformatics. To compare DNA sequences, researchers often use a bioinformatics tool called the Basic Local Alignment Search Tool, or BLAST, which was created, and is maintained by, the National Center for Biotechnology Information.
In this laboratory, you will first create a cladogram of animals using morphological information, and then place a fossil species onto this cladogram based on its morphology. You will then use DNA sequences from several different modern-day relatives of the fossil and the BLAST database to verify your positioning of the fossil onto the tree.
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Q1: What is a cladogram and how does it show evolutionary relationships?
A cladogram is a dendrogram that visualizes cladistic relationships between species, with branch tips representing individual species and branches showing how they relate to one another. The points where branches meet, called nodes, denote common ancestors. Species positioned closer together share more recent common ancestors and are more closely related than species positioned farther apart.
Q2: How do phylograms differ from cladograms in representing evolutionary change?
Phylograms differ from cladograms because branch lengths vary, representing the degree of change between species. Longer branches indicate more time has passed since species diverged from their last common ancestor, while shorter branches indicate less evolutionary change. Cladograms, by contrast, show only branching relationships without representing time or change magnitude.
Q3: What are synapomorphies and why are they important in classification?
Synapomorphies are defining physical features shared by groups of organisms that split branches in classification systems. For example, possessing a backbone places animals in phylum Chordata, while lacking one places them in other phyla like Arthropoda. These shared characteristics indicate organisms descended from common ancestors and are fundamental to organizing species into hierarchical groups.
Q4: How does DNA sequence comparison improve upon morphological classification?
DNA sequence comparison allows researchers to identify evolutionary relationships based on genetic similarity rather than physical traits alone. Since DNA is inherited from parents to offspring and species sharing common ancestors have similar nucleotide sequences, comparing DNA codes reveals relationships that morphology might miss. This genetic approach also enables estimation of how long ago different species diverged from common ancestors.
Q5: What is BLAST and how does it help identify evolutionary relationships?
BLAST (Basic Local Alignment Search Tool) is a bioinformatics tool that searches DNA sequences against the NCBI database to find matching sequences from other species. It aligns nucleotide bases from a query sequence with database sequences, listing results by similarity. Species with highly similar sequences are closely related evolutionarily, allowing researchers to construct trees showing evolutionary relationships using genetic data.
Q6: Why is bioinformatics essential for modern evolutionary analysis?
Bioinformatics combines computer science, mathematical modeling, and statistics to analyze large genetic datasets that would be impossible to process manually. Tools like BLAST enable rapid comparison of DNA sequences across thousands of species in databases, revealing evolutionary relationships with precision. This computational approach has become standard for constructing accurate dendrograms and understanding how species diverged from common ancestors.
Q7: How do scientists use fossil morphology to place extinct species on evolutionary trees?
Scientists analyze fossil physical characteristics and compare them to synapomorphies of living species to determine where fossils fit on cladograms. By identifying shared defining features, researchers can position fossils among modern relatives based on morphological similarity. DNA sequences from modern relatives can then verify the fossil's placement, since extinct organisms rarely preserve DNA in soft tissues during fossilization.