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Cladogram

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Cladogram

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A horizontal cladogram, with the root to the left
Two vertical cladograms, the root at the bottom

A cladogram (from Greek clados “branch” and gramma “character”) is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed, so many differing evolutionary trees can be consistent with the same cladogram.[1][2][3][4][5] A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor (not an actual entity) which can be inferred to exhibit the traits shared among the terminal taxa above it.[4][6] This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other evolutionary narratives about ancestors. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational phylogenetics are now very commonly used in the generation of cladograms, either on their own or in combination with morphology.

Generating a cladogram

Molecular versus morphological data

The characteristics used to create a cladogram can be roughly categorized as either morphological (synapsid skull, warm blooded, notochord, unicellular, etc.) or molecular (DNA, RNA, or other genetic information).[7] Prior to the advent of DNA sequencing, cladistic analysis primarily used morphological data. Behavioral data (for animals) may also be used.[8]

As DNA sequencing has become cheaper and easier, molecular systematics has become a more and more popular way to infer phylogenetic hypotheses.[9] Using a parsimony criterion is only one of several methods to infer a phylogeny from molecular data. Approaches such as maximum likelihood, which incorporate explicit models of sequence evolution, are non-Hennigian ways to evaluate sequence data. Another powerful method of reconstructing phylogenies is the use of genomic retrotransposon markers, which are thought to be less prone to the problem of reversion that plagues sequence data. They are also generally assumed to have a low incidence of homoplasies because it was once thought that their integration into the genome was entirely random; this seems at least sometimes not to be the case, however.

Apomorphy in cladistics. This diagram indicates “A” and “C” as ancestral states, and “B”, “D” and “E” as states that are present in terminal taxa. Note that in practice, ancestral conditions are not known a priori (as shown in this heuristic example), but must be inferred from the pattern of shared states observed in the terminals. Given that each terminal in this example has a unique state, in reality we would not be able to infer anything conclusive about the ancestral states (other than the fact that the existence of unobserved states “A” and “C” would be unparsimonious inferences!)
Plesiomorphies and synapomorphies

Researchers must decide which character states are “ancestral” (plesiomorphies) and which are derived (synapomorphies), because only synapomorphic character states provide evidence of grouping.[10] This determination is usually done by comparison to the character states of one or more outgroups. States shared between the outgroup and some members of the in-group are symplesiomorphies; states that are present only in a subset of the in-group are synapomorphies. Note that character states unique to a single terminal (autapomorphies) do not provide evidence of grouping. The choice of an outgroup is a crucial step in cladistic analysis because different outgroups can produce trees with profoundly different topologies.

Homoplasies

A homoplasy is a character state that is shared by two or more taxa due to some cause other than common ancestry.[11] The two main types of homoplasy are convergence (evolution of the “same” character in at least two distinct lineages) and reversion (the return to an ancestral character state). Characters that are obviously homoplastic, such as white fur in different lineages of Arctic mammals, should not be included as a character in a phylogenetic analysis as they do not contribute anything to our understanding of relationships. However, homoplasy is often not evident from inspection of the character itself (as in DNA sequence, for example), and is then detected by its incongruence (unparsimonious distribution) on a most-parsimonious cladogram. Note that characters that are homoplastic may still contain phylogenetic signal.[12]

A well-known example of homoplasy due to convergent evolution would be the character, “presence of wings”. Although the wings of birds, bats, and insects serve the same function, each evolved independently, as can be seen by their anatomy. If a bird, bat, and a winged insect were scored for the character, “presence of wings”, a homoplasy would be introduced into the dataset, and this could potentially confound the analysis, possibly resulting in a false hypothesis of relationships. Of course, the only reason a homoplasy is recognizable in the first place is because there are other characters that imply a pattern of relationships that reveal its homoplastic distribution.

What is not a cladogram

A cladogram is the diagrammatic result of an analysis, which groups taxa on the basis of synapomorphies alone. There are many other phylogenetic algorithms that treat data somewhat differently, and result in phylogenetic trees that look like cladograms but are not cladograms. For example, phenetic algorithms, such as UPGMA and Neighbor-Joining, group by overall similarity, and treat both synapomorphies and symplesiomorphies as evidence of grouping, The resulting diagrams are phenograms, not cladograms, Similarly, the results of model-based methods (Maximum Likelihood or Bayesian approaches) that take into account both branching order and “branch length,” count both synapomorphies and autapomorphies as evidence for or against grouping, The diagrams resulting from those sorts of analysis are not cladograms, either.[13]

Cladogram selection

There are several algorithms available to identify the “best” cladogram.[14] Most algorithms use a metric to measure how consistent a candidate cladogram is with the data. Most cladogram algorithms use the mathematical techniques of optimization and minimization.

In general, cladogram generation algorithms must be implemented as computer programs, although some algorithms can be performed manually when the data sets are modest (for example, just a few species and a couple of characteristics).

Some algorithms are useful only when the characteristic data are molecular (DNA, RNA); other algorithms are useful only when the characteristic data are morphological. Other algorithms can be used when the characteristic data includes both molecular and morphological data.

Algorithms for cladograms or other types of phylogenetic trees include least squares, neighbor-joining, parsimony, maximum likelihood, and Bayesian inference.

Biologists sometimes use the term parsimony for a specific kind of cladogram generation algorithm and sometimes as an umbrella term for all phylogenetic algorithms.[15]

Algorithms that perform optimization tasks (such as building cladograms) can be sensitive to the order in which the input data (the list of species and their characteristics) is presented. Inputting the data in various orders can cause the same algorithm to produce different “best” cladograms. In these situations, the user should input the data in various orders and compare the results.

Using different algorithms on a single data set can sometimes yield different “best” cladograms, because each algorithm may have a unique definition of what is “best”.

Because of the astronomical number of possible cladograms, algorithms cannot guarantee that the solution is the overall best solution. A nonoptimal cladogram will be selected if the program settles on a local minimum rather than the desired global minimum.[16] To help solve this problem, many cladogram algorithms use a simulated annealing approach to increase the likelihood that the selected cladogram is the optimal one.[17]

The basal position is the direction of the base (or root) of a rooted phylogenetic tree or cladogram. A basal clade is the earliest clade (of a given taxonomic rank[a]) to branch within a larger clade.

Statistics

Incongruence length difference test (or partition homogeneity test)

The incongruence length difference test (ILD) is a measurement of how the combination of different datasets (e.g. morphological and molecular, plastid and nuclear genes) contributes to a longer tree. It is measured by first calculating the total tree length of each partition and summing them. Then replicates are made by making randomly assembled partitions consisting of the original partitions. The lengths are summed. A p value of 0.01 is obtained for 100 replicates if 99 replicates have longer combined tree lengths.

Measuring homoplasy
Further information: Convergent evolution

Some measures attempt to measure the amount of homoplasy in a dataset with reference to a tree,[18] though it is not necessarily clear precisely what property these measures aim to quantify[19]

Consistency index

The consistency index (CI) measures the consistency of a tree to a set of data – a measure of the minimum amount of homoplasy implied by the tree.[20] It is calculated by counting the minimum number of changes in a dataset and dividing it by the actual number of changes needed for the cladogram.[20] A consistency index can also be calculated for an individual character i, denoted ci.

Besides reflecting the amount of homoplasy, the metric also reflects the number of taxa in the dataset,[21] (to a lesser extent) the number of characters in a dataset,[22] the degree to which each character carries phylogenetic information,[23] and the fashion in which additive characters are coded, rendering it unfit for purpose.[24]

ci occupies a range from 1 to 1/[n.taxa/2] in binary characters with an even state distribution; its minimum value is larger when states are not evenly spread.[23][18] In general, for a binary or non-binary character with n.states{\displaystyle n.states}, ci occupies a range from 1 to (n.states−1)/(n.taxa−⌈n.taxa/n.states⌉){\displaystyle (n.states-1)/(n.taxa-\lceil n.taxa/n.states\rceil )}.[23]

Retention index

The retention index (RI) was proposed as an improvement of the CI “for certain applications”[25] This metric also purports to measure of the amount of homoplasy, but also measures how well synapomorphies explain the tree. It is calculated taking the (maximum number of changes on a tree minus the number of changes on the tree), and dividing by the (maximum number of changes on the tree minus the minimum number of changes in the dataset).

The rescaled consistency index (RC) is obtained by multiplying the CI by the RI; in effect this stretches the range of the CI such that its minimum theoretically attainable value is rescaled to 0, with its maximum remaining at 1.[18][25] The homoplasy index (HI) is simply 1 − CI.

Homoplasy Excess Ratio

This measures the amount of homoplasy observed on a tree relative to the maximum amount of homoplasy that could theoretically be present – 1 − (observed homoplasy excess) / (maximum homoplasy excess).[22] A value of 1 indicates no homoplasy; 0 represents as much homoplasy as there would be in a fully random dataset, and negative values indicate more homoplasy still (and tend only to occur in contrived examples).[22] The HER is presented as the best measure of homoplasy currently available.[18][26]

See also

Phylogenetics
Dendrogram
Basal (phylogenetics)

References

^ .mw-parser-output cite.citation{font-style:inherit}.mw-parser-output .citation q{quotes:”\”””\”””‘””‘”}.mw-parser-output .id-lock-free a,.mw-parser-output .citation .cs1-lock-free a{background:linear-gradient(transparent,transparent),url(“//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg”)right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited a,.mw-parser-output .id-lock-registration a,.mw-parser-output .citation .cs1-lock-limited a,.mw-parser-output .citation .cs1-lock-registration a{background:linear-gradient(transparent,transparent),url(“//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg”)right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription a,.mw-parser-output .citation .cs1-lock-subscription a{background:linear-gradient(transparent,transparent),url(“//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg”)right 0.1em center/9px no-repeat}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration{color:#555}.mw-parser-output .cs1-subscription span,.mw-parser-output .cs1-registration span{border-bottom:1px dotted;cursor:help}.mw-parser-output .cs1-ws-icon a{background:linear-gradient(transparent,transparent),url(“//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg”)right 0.1em center/12px no-repeat}.mw-parser-output code.cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;font-size:100%}.mw-parser-output .cs1-visible-error{font-size:100%}.mw-parser-output .cs1-maint{display:none;color:#33aa33;margin-left:0.3em}.mw-parser-output .cs1-format{font-size:95%}.mw-parser-output .cs1-kern-left,.mw-parser-output .cs1-kern-wl-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right,.mw-parser-output .cs1-kern-wl-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}Mayr, Ernst (2009). “Cladistic analysis or cladistic classification?”. Journal of Zoological Systematics and Evolutionary Research. 12: 94–128. doi:10.1111/j.1439-0469.1974.tb00160.x.

^ Foote, Mike (Spring 1996). “On the Probability of Ancestors in the Fossil Record”. Paleobiology. 22 (2): 141–51. doi:10.1017/S0094837300016146. JSTOR 2401114.

^ Dayrat, Benoît (Summer 2005). “Ancestor-Descendant Relationships and the Reconstruction of the Tree of Life”. Paleobiology. 31 (3): 347–53. doi:10.1666/0094-8373(2005)031[0347:aratro]2.0.co;2. JSTOR 4096939.

^ a b Posada, David; Crandall, Keith A. (2001). “Intraspecific gene genealogies: Trees grafting into networks”. Trends in Ecology & Evolution. 16: 37–45. doi:10.1016/S0169-5347(00)02026-7.

^ Podani, János (2013). “Tree thinking, time and topology: Comments on the interpretation of tree diagrams in evolutionary/phylogenetic systematics” (PDF). Cladistics. 29 (3): 315–327. doi:10.1111/j.1096-0031.2012.00423.x.

^ Schuh, Randall T. (2000). Biological Systematics: Principles and Applications. ISBN 978-0-8014-3675-8.

^ DeSalle, Rob (2002). Techniques in Molecular Systematics and Evolution. Birkhauser. ISBN 978-3-7643-6257-7.

^ Wenzel, John W. (1992). “Behavioral homology and phylogeny”. Annu. Rev. Ecol. Syst. 23: 361–381. doi:10.1146/annurev.es.23.110192.002045.

^ Hillis, David (1996). Molecular Systematics. Sinaur. ISBN 978-0-87893-282-5.

^ Hennig, Willi (1966). Phylogenetic Systematics. University of Illinois Press.

^ West-Eberhard, Mary Jane (2003). Developmental Plasticity and Evolution. Oxford Univ. Press. pp. 353–376. ISBN 978-0-19-512235-0.

^ Kalersjo, Mari; Albert, Victor A.; Farris, James S. (1999). “Homoplasy Increases Phylogenetic Structure”. Cladistics. 15: 91–93. doi:10.1111/j.1096-0031.1999.tb00400.x.

^ Brower, Andrew V.Z. (2016). “What is a cladogram and what is not?”. Cladistics. 32 (5): 573–576. doi:10.1111/cla.12144.

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Kitching, Ian (1998). Cladistics: The Theory and Practice of Parsimony Analysis. Oxford University Press. ISBN 978-0-19-850138-1.

^ Stewart, Caro-Beth (1993). “The powers and pitfalls of parsimony”. Nature. 361 (6413): 603–7. Bibcode:1993Natur.361..603S. doi:10.1038/361603a0. PMID 8437621.

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^ a b c Archie, J. W. (1989). “HOMOPLASY EXCESS RATIOS : NEW INDICES FOR MEASURING LEVELS OF HOMOPLASY IN PHYLOGENETIC SYSTEMATICS AND A CRITIQUE OF THE CONSISTENCY INDEX”. Systematic Zoology. 38 (3): 253–269. doi:10.2307/2992286. JSTOR 2992286.

^ a b c Hoyal Cuthill, Jennifer F.; Braddy, Simon J.; Donoghue, Philip C. J. (2010). “A formula for maximum possible steps in multistate characters: Isolating matrix parameter effects on measures of evolutionary convergence”. Cladistics. 26: 98–102. doi:10.1111/j.1096-0031.2009.00270.x.

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^ Hoyal Cuthill, Jennifer (2015). “The size of the character state space affects the occurrence and detection of homoplasy: Modelling the probability of incompatibility for unordered phylogenetic characters”. Journal of Theoretical Biology. 366: 24–32. doi:10.1016/j.jtbi.2014.10.033. PMID 25451518.

External links

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PDF  Cladogram Worksheet

PDF Cladogram Worksheet – In the past, biologists would group organisms based solely on their physical appearance. CLADISTICS is form of analysis that looks at features of organisms that are considered "innovations", or newer features that serve some kind In the box below, create a cladogram based off your matrix.Building Cladograms. A cladogram's branching patterns indicate degrees of relatedness among organisms. Because lineages 3 and 4 share a common ancestor more recently with each other than they do with lineage 2, you know that lineages 3 and 4 are more closely related to each other than…of groups of organisms; the organisms are assigned to groups based on similarities and A cladogram is a type of phylogenetic tree that only shows tree topology—the shape indicating Cladogram refers to the branching tree diagram, which is generated to show the similarities between…

PDF Slide 1 | Building Cladograms – A clade is a group of organisms that includes an ancestor species and all of its descendants. According to this cladogram, beetles were the first insect to branch off from a common ancestor. What other evolutionary relationships does the cladogram reveal? Generating Cladograms.Cladograms – . what is a cladogram ?. a cladogram shows evolutionary relationships between groups of living things. it is. Using these patterns of shared derived characters, a cladogram can be constructed as a series of branches. • At every branch, one of the organisms that does not share a…Get an answer for 'What does a branch point in a cladogram represent?' and find homework help for other Science questions at eNotes. They consist of horizontal or vertical lines connecting various organisms. These different lines branch off from a common point on the cladogram.

PDF  Slide 1 | Building Cladograms

What is the difference between a cladogram and a phylogram? – Quora – Tugadeola Tugadeola. When a new trait evolve.In a cladogram, a group of organisms branches off: when a new trait evolves. One 200 gram bag of rice cost $8.12 how much does 1 kilogram of riceA cladogram (from Greek clados 'branch' and gramma 'character') is a diagram used in cladistics to show relations among organisms. What is a Cladogram and what does it tell us? Biologists use cladograms and phylogenetic trees to illustrate How is the in group determined in a Cladogram?

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AP Bio Chapters 26-27 Part 1 – .

1 B 2 Phylogenetic Trees and Cladograms – .

Cladograms – This is a big biology with mr..
Rock and today we are going to be talking about lotta grams First question obviously as always we asked. What is a plotter in a Cladogram is a branching diagram that shows evolutionary relationships between species What this being said a lot of times evolutionary biologists will use the word? evolutionary tree a Phylogenetic tree and sometimes it use these different words, and they're talking about the image below Clutter grams are synonymous with evolutionary tree so if you ever hear about an evolutionary tree They're talking about what you see in front of you so the purpose of this diagram is to show evolutionary relationships So work I'm starting off with the cladogram here and In the one you saw previously You saw species on top sharks fish amphibians primates rabbits crocodiles birds Up here. Uh it could be the same, so these species up here are just a letter you don't know what species They are but you don't need to know which ones. They are to understand what we need to learn from the cladogram so the first thing that I want to point out is a node and a node is also known as a branch point a Branch point is going to indicate a common ancestor between Two species so it's where two species diverged The next thing that you would need to know about a Cladogram is that the species that you see on top so before it was like an alligator of rabid primate you see ABCDEF up there These are modern species so species that are alive today And then the species that were interested in so we're studying the species evolutionary relationship The next thing that you need to know about a pata gram is we start off on the bottom and on the bottom is going To be the very very oldest point of time and as you go up the cladogram You get to the modern-day the present-day so the species that are on top ABCDEF. This is modern-day 2018 this is happening right now Oldest point in time goes way way way back millions of years and that's at the bottom of the quadrant The next thing you need to know is what a branch is a branch It comes from a branch point so anytime you like there are two branches here Okay, so there's multiple branches as well as nodes like there's a lot of nodes on this cloud Tata Graham And there's a lot of branches The branches this is typically where we put traits that separate the species As soon as the trait goes on the pata gram Anything that follows This point in this traits all of these species cdef are going to have that trait and I'll explain that more in a bit And then finally and I'm just putting this up here common ancestor between E. And F So this just loops back to what I was speaking about the node the nodes Represent common ancestors so I can point to two species than I could say what is the common ancestor between E. And F, and It's this red point right here on the cladogram, so I actually want to put a Claddagh ground up here, and show you What this looks like because I was just explaining some things. I want to give some practical examples So number one what a node is we have lots of nodes on this cladogram So these are branch points And they indicate a common ancestor so the common ancestor of a mouse and chimp is right here The common ancestor between a salamander in a chimp is right here This is down. Here is the oldest and we go home to present day The last thing I'll point out is with the trace notice that the traits are on branches So this is a treat and this is a trait that separates all of these species All of these species moving forward are going to have jobs So the perch has a job the salamander has a job the lizard has a job pigeon mouse chimp The hagfish does not have a job So because it is to the left it does not have a job and we could keep on doing this as we move down so claws and nails Moving forward lizards have claws or nails pigeons have claws Mouse have claws or nails chimps have claws or nails so if you see a tree it carries on to the branch After that and then same thing with feathers here you see only feather despoiling birds are going to have feathers So the traits tell you this not only shows evolutionary relationships, but it also shares What kind of traits different species can have and it doesn't have to do that? But it's kind of a nice feature about the plot agree Okay, so the last thing I want to tell you about is What is a clade because we're never referred to clades quite frequently when we're looking at programs And it is a group of organisms evolved from a common ancestor, so When you're looking at a clade? All of the organisms and need to be included if that stem from the common ancestor, so When we're looking looking at examples here This is the common ancestor so this is a claim because all of the species are included Same thing here, this is a very simple example, but this is a clade, so we're good there However, this is not the clay This is not a clade down here on the left in order for this to be a clade. What should be shaded in is Like if you're going to include this species of this species of this species That the clade has to be the whole entire thing because the common ancestor goes all the way back to this point Same thing what's here on the right? This is not a clade it because you left out this species over here So clade is all of the species that come from a common answer Closing thoughts on this would be number one. What is a clade? So if I asked you what is the clade four c d e and f species C D en F. What is the claim? You should be able to draw a circle or point to the common ancestor where the claim begins Up where's the claim the clade is right here, so all of these organisms are in a clade Another thing that I want to point out is relationships to each other So when I'm asking you about what species are most related You need to look at the common ancestor, so what common trick question is is D and E species D and More related then C and F So I'm trying to figure out evolutionary relationships, and which one is more related okay, this is kind of a trick question because If you're trying to look at D, and E. It looks like they're more closely related because they are closer to each other But you always need to go back to the common ancestor so D and E. If you go back to the common ancestor They are just as related as see and although they are further apart on the cloud ram They are just as related because you always need to go back to the common ancestor When you're trying to determine the relationship between the species This has been a bit of biology with mr.. Rock. I'm signing off .