Phylogenetic trees how do the changes in gene sequences answers


How do scientists build phylogenetic trees?

A phylogenetic tree is a diagram used to show how organisms are related to one another. 

There are actually a lot of different ways to make these trees! As long as you have something you can compare across different species, you can make a phylogenetic tree. 

A phylogenetic tree can be built using physical information like body shape, bone structure, or behavior. Or it can be built from molecular information, like genetic sequences. 

In general, the more information you’re able to compare, the more accurate the tree will be. So you’d get a more accurate tree by comparing entire skeletons, instead of just a single bone. Or by comparing entire genomes, instead of just a single gene.

Any DNA, RNA, or protein sequence can be used to generate a phylogenetic tree. But DNA sequences are most commonly used in generating trees today. 

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In a phylogenetic tree, each line is called a branch. The end of each branch is called a tip– this is where you put a species!

Each point where the two branches split is called a node. A node is the most recent common ancestor of all species on those branches.

And if you go all the way down to the bottom of the tree, the last node is called the root. This is the common ancestor of all the species in the tree! 

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You can draw phylogenetic trees in many different shapes. It doesn’t matter whether it’s rectangular or circular. The import part is how it is branched. The branching represents the differences in the relationship of species. 

These trees all show exactly the same information! Just in different shapes.

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Ask a Geneticist

Any DNA, RNA, or protein sequences can be used to draw a phylogenetic tree. But DNA sequences are the most widely used. It’s pretty cheap and easy now to get DNA sequences. Plus DNA contains more information, which can make more accurate trees. For example, some changes in DNA sequences do not lead to changes in proteins. 

To construct a tree, we’ll compare the DNA sequences of different species. 

Evolutionarily related species have a common ancestor. Before they split into separate species, they had exactly the same DNA. But as species evolve and diverge, they will accumulate changes in the DNA sequences. 

We can use these changes in the DNA to tell how closely related two species are. If there aren’t very many differences, they’re probably closely related. If there are a lot of changes, they might be more distant relatives.

The first thing to do is align the two DNA sequences together that you’re going to compare. Make sure you’re comparing the same gene! (Or other sequence.) Otherwise you are comparing apples to oranges.

This sequence alignment is often done with the help of computer programs. The strategy is to find the alignment that has the most matches and the least mismatches. 

You can align and compare as many sequences as you want. Remember, the more information you consider, the more accurate your tree will be!

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Ok, so you’ve got your DNA aligned. Now what? How do you convert that into a tree?

Next you compare the sequences, to see how similar they are to each other.

We can see that Sequence #1 vs #2 have one difference. Sequence #2 vs #3 have 2 differences. Sequences #3 vs #4 has 5 differences. And so on.  

Just by looking at them, we can see that Sequences 1 and 2 are pretty similar. We would group them together in a tree.

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But we can do better than just looking at them. You can actually calculate how similar any two sequences are, and make a table to compare all the differences. This especially helps when you’re comparing a lot of information!

Sequences 1 and 2 differ by 1 nucleotide, out of the 20 total. So the difference between Sequence 1 and 2 is: 

1/20= 0.05

We can calculate the difference between each pair of sequences. If we put the calculated differences in a matrix, it would look like this:

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Now if you look at the matrix, the pairs that have the lowest values are the most similar. As before, we can see that sequences 1 and 2 are very similar. So we can put 1 and 2 together. 

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After we put 1 and 2 together, we will have to recalculate the difference between sequences. Now that we’ve 1-2 together in the tree, we’re going to consider them as a single group. We’ll calculate the differences with other sequences by taking an average. 

For example, the difference between 1&2 vs 3 would be:

Average of (1 vs 3) and (2 vs 3) = 1-2 vs 3
                    ½ * (0.1+0.1)= 0.1

Similarly, we could calculate the differences with other sequences. We would have a table like below: 

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Looking at the table, we can see 3 is most similar with 1-2. So we can group 3 together with 1-2. 

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Now, we will repeat the above steps. We will treat 1, 2, and 3 as one species as we keep building the tree. We’ll use the average of 1-2 vs other and 3 vs other to do this.

For example, the difference between 1-3 and 4 would be:

Average of (1-2 vs 4) and (3 vs 4) = 1-2-3 vs 4
½ * (0.2+0.25) = 0.225

We can calculate the rest with the same method. Now we have a table as below:

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We can see that 1-3 and 4 are most similar. So we can put 4 and 1-3 together. 

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Now we can add in sequence 5 and get our tree!

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You can use this method to build all sorts of trees! Not all trees will look like this one, but the same basic principles will apply.

Phylogenetic Trees | Biology for Majors I

Read and analyze a phylogenetic tree that documents evolutionary relationships

In scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. Phylogeny describes the relationships of an organism, such as from which organisms it is thought to have evolved, to which species it is most closely related, and so forth. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different.

Learning Objectives

  • Identify how and why scientists classify the organisms on earth
  • Differentiate between types of phylogenetic trees and what their structure tells us
  • Identify some limitations of phylogenetic trees
  • Relate the taxonomic classification system and binomial nomenclature

Scientific Classification

Figure 1. Only a few of the more than one million known species of insects are represented in this beetle collection. Beetles are a major subgroup of insects. They make up about 40 percent of all insect species and about 25 percent of all known species of organisms.

Why do biologists classify organisms? The major reason is to make sense of the incredible diversity of life on Earth. Scientists have identified millions of different species of organisms. Among animals, the most diverse group of organisms is the insects. More than one million different species of insects have already been described. An estimated nine million insect species have yet to be identified. A tiny fraction of insect species is shown in the beetle collection in Figure 1.

As diverse as insects are, there may be even more species of bacteria, another major group of organisms. Clearly, there is a need to organize the tremendous diversity of life. Classification allows scientists to organize and better understand the basic similarities and differences among organisms. This knowledge is necessary to understand the present diversity and the past evolutionary history of life on Earth.

Phylogenetic Trees

Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms (Figure 2).

Each group of organisms went through its own evolutionary journey, called its phylogeny. Each organism shares relatedness with others, and based on morphologic and genetic evidence, scientists attempt to map the evolutionary pathways of all life on Earth. Many scientists build phylogenetic trees to illustrate evolutionary relationships.

Structure of Phylogenetic Trees

A phylogenetic tree can be read like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted, which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains—Bacteria, Archaea, and Eukarya—diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and miniscule these groups are compared with other organisms. Unrooted trees don’t show a common ancestor but do show relationships among species.

Figure 2. Both of these phylogenetic trees shows the relationship of the three domains of life—Bacteria, Archaea, and Eukarya—but the (a) rooted tree attempts to identify when various species diverged from a common ancestor while the (b) unrooted tree does not. (credit a: modification of work by Eric Gaba)

In a rooted tree, the branching indicates evolutionary relationships (Figure 3). The point where a split occurs, called a branch point, represents where a single lineage evolved into a distinct new one. A lineage that evolved early from the root and remains unbranched is called basal taxon. When two lineages stem from the same branch point, they are called sister taxa. A branch with more than two lineages is called a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships. It is important to note that although sister taxa and polytomy do share an ancestor, it does not mean that the groups of organisms split or evolved from each other. Organisms in two taxa may have split apart at a specific branch point, but neither taxa gave rise to the other.

Figure 3. The root of a phylogenetic tree indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where two lineages diverged. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister taxa. A branch with more than two lineages is a polytomy.

The diagrams above can serve as a pathway to understanding evolutionary history. The pathway can be traced from the origin of life to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a single species and tracing back towards the “trunk” of the tree, one can discover that species’ ancestors, as well as where lineages share a common ancestry. In addition, the tree can be used to study entire groups of organisms.

Another point to mention on phylogenetic tree structure is that rotation at branch points does not change the information. For example, if a branch point was rotated and the taxon order changed, this would not alter the information because the evolution of each taxon from the branch point was independent of the other.

Many disciplines within the study of biology contribute to understanding how past and present life evolved over time; these disciplines together contribute to building, updating, and maintaining the “tree of life.” Information is used to organize and classify organisms based on evolutionary relationships in a scientific field called systematics. Data may be collected from fossils, from studying the structure of body parts or molecules used by an organism, and by DNA analysis. By combining data from many sources, scientists can put together the phylogeny of an organism; since phylogenetic trees are hypotheses, they will continue to change as new types of life are discovered and new information is learned.

Video Review

Limitations of Phylogenetic Trees

It may be easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. If two closely related lineages evolved under significantly varied surroundings or after the evolution of a major new adaptation, it is possible for the two groups to appear more different than other groups that are not as closely related. For example, the phylogenetic tree in Figure 4 shows that lizards and rabbits both have amniotic eggs, whereas frogs do not; yet lizards and frogs appear more similar than lizards and rabbits.

Figure 4. This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different characters are placed in different groups based on the characteristics they share.

Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not account for length of time, only the evolutionary order. In other words, the length of a branch does not typically mean more time passed, nor does a short branch mean less time passed— unless specified on the diagram. For example, in Figure 4, the tree does not indicate how much time passed between the evolution of amniotic eggs and hair. What the tree does show is the order in which things took place. Again using Figure 4, the tree shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember that any phylogenetic tree is a part of the greater whole, and like a real tree, it does not grow in only one direction after a new branch develops.

So, for the organisms in Figure 4, just because a vertebral column evolved does not mean that invertebrate evolution ceased, it only means that a new branch formed. Also, groups that are not closely related, but evolve under similar conditions, may appear more phenotypically similar to each other than to a close relative.

Head to this website to see interactive exercises that allow you to explore the evolutionary relationships among species.

The Taxonomic Classification System

Taxonomy (which literally means “arrangement law”) is the science of classifying organisms to construct internationally shared classification systems with each organism placed into more and more inclusive groupings. Think about how a grocery store is organized. One large space is divided into departments, such as produce, dairy, and meats. Then each department further divides into aisles, then each aisle into categories and brands, and then finally a single product. This organization from larger to smaller, more specific categories is called a hierarchical system.

The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish botanist, zoologist, and physician) uses a hierarchical model. Moving from the point of origin, the groups become more specific, until one branch ends as a single species. For example, after the common beginning of all life, scientists divide organisms into three large categories called a domain: Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom. After kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species (Figure 5).

Figure 5. The taxonomic classification system uses a hierarchical model to organize living organisms into increasingly specific categories. The common dog, Canis lupus familiaris, is a subspecies of Canis lupus, which also includes the wolf and dingo. (credit “dog”: modification of work by Janneke Vreugdenhil)

The kingdom Animalia stems from the Eukarya domain. For the common dog, the classification levels would be as shown in Figure 5. Therefore, the full name of an organism technically has eight terms. For the dog, it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species, and the genus and species names are italicized. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, in what is called binomial nomenclature. Therefore, the scientific name of the dog is Canis lupus. The name at each level is also called a taxon. In other words, dogs are in order Carnivora. Carnivora is the name of the taxon at the order level; Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, in this case, dog. Note that the dog is additionally a subspecies: the “familiaris” in Canis lupus familiaris. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are considered separate subspecies due to geographic or behavioral isolation or other factors.

Figure 6 shows how the levels move toward specificity with other organisms. Notice how the dog shares a domain with the widest diversity of organisms, including plants and butterflies. At each sublevel, the organisms become more similar because they are more closely related. Historically, scientists classified organisms using characteristics, but as DNA technology developed, more precise phylogenies have been determined.

Practice Question

Figure 6. At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same species because they can breed and produce viable offspring, but they are different enough to be classified as different subspecies. (credit “plant”: modification of work by “berduchwal”/Flickr; credit “insect”: modification of work by Jon Sullivan; credit “fish”: modification of work by Christian Mehlführer; credit “rabbit”: modification of work by Aidan Wojtas; credit “cat”: modification of work by Jonathan Lidbeck; credit “fox”: modification of work by Kevin Bacher, NPS; credit “jackal”: modification of work by Thomas A. Hermann, NBII, USGS; credit “wolf”: modification of work by Robert Dewar; credit “dog”: modification of work by “digital_image_fan”/Flickr)

 

At what levels are cats and dogs considered to be part of the same group?

Show Answer

Visit this website to classify three organisms—bear, orchid, and sea cucumber—from kingdom to species. To launch the game, under Classifying Life, click the picture of the bear or the Launch Interactive button.

Recent genetic analysis and other advancements have found that some earlier phylogenetic classifications do not align with the evolutionary past; therefore, changes and updates must be made as new discoveries occur. Recall that phylogenetic trees are hypotheses and are modified as data becomes available. In addition, classification historically has focused on grouping organisms mainly by shared characteristics and does not necessarily illustrate how the various groups relate to each other from an evolutionary perspective. For example, despite the fact that a hippopotamus resembles a pig more than a whale, the hippopotamus may be the closest living relative of the whale.

Check Your Understanding

Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does not count toward your grade in the class, and you can retake it an unlimited number of times.

Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section.

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"Molecular archaeology" clarified the phylogenetic relationships of vertebrates

Scientists from Konstanz university refined the tree for jawed vertebrates, using transcriptome data from a hundred different species. They found out, among other things, the location on phylogenetic tree of a number of groups that have long been questioned, including turtles, lungfish and salamanders. The article with the study was published in the journal Ecology&Evolution .

The study of evolutionary relationships between different organisms has always attracted the attention of scientists. Phylogenetic trees help to explore such important processes like adaptive radiation or convergent evolution. To build trees kinship, various data are used, including morphological and genetic. Now, in addition to individual genes and genomes, in the phylogenetic The analysis also uses transcriptomes (a set of RNA cells). This science is called phylotranscriptomics and, according to the authors of this article, it helps to resolve some disputes that phylogenomics could not resolve.

Phylogenetic relationships vertebrates is also part of the history of human development, as representative of vertebrate tetrapods. The phylum of vertebrates includes more than 68 thousand species. In this study, scientists studied jawed vertebrates ( Gnathostomata). These include most vertebrates (with the exception of hagfish, lampreys and a number of extinct classes) - fish, amphibians, reptiles, mammals and birds. Vertebrates appeared about 470 million years ago. From the very beginning, the process of speciation was quite intensive for them, so it can be quite difficult to understand their relationship. Some species, in addition, have common features, while being on different branches of the phylogenetic tree. For example, both birds and bats have the ability to fly, and flying snakes and whales use echolocation.

In the new work, scientists took transcriptomes for 100 species of jawed vertebrates, including 23 species for which transcriptomes have not been studied previously. They selected 7,189 genes from which they built a phylogenetic tree calibrated for important geological events. The method of constructing trees from DNA or RNA is called "molecular archeology" because it allows tracking evolutionary changes over time. By examining these changes, one can reconstruct events that happened millions of years ago. Scientists used a number of bioinformatics tools to optimize the method: for example, they were able to take into account sample contamination and the role of paralog genes, ignore poorly sequenced regions, and, using hidden Markov models, minimize the role of incorrectly annotated genes. Scientists note that this method can be used to reconstruct evolutionary relationships not only between vertebrates, but also any other living organisms.

It turned out that the size of the genome did not affect the rate of evolution and speciation. In addition, it was previously believed that the number of small insertions and deletions (indels) affects the size of the genome, but in this study, no significant correlation was observed in this regard, either in the coding or non-coding regions.

The resulting tree suggested that the main groups of cartilaginous and ray-finned fishes appeared in the Ordovician period earlier than previous phylogenetic studies showed, which is consistent with recent paleontological work. The same goes for turtles and birds from the early Cretaceous. Turtles turned out to be a sister group to crocodiles and birds, and their role as an independent group of anapsids was refuted. The researchers also managed to resolve the dispute about lungfish, which turned out to be close relatives of land vertebrates (at the same time, the hypothesis that lobe-finned fish are closer to them was not confirmed). Amphibians turned out to be a monophyletic group, and not paraphyletic, as some researchers thought. The oldest species of salamanders were representatives of group Andrias , not sirens.

Many scientists set themselves the task of understanding and tracing the origin of species and their relationships. Recently, we talked about the presented preliminary version of the "Tree life" as part of a large-scale phylogenetic project that includes data for more than 2.3 million species of living organisms.

Nadezhda Potapova and Anna Kaznadzey

Editor's Note: Initially, a number of inaccuracies were made in the note, which were later corrected.


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