Recent Changes for "Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite" - Bodega Phylogenetics Wiki

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

BobThomson — 2010-09-08 12:25:24

(quick edit)

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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- ''2010-09-07 18:38:08'' [[nbsp]] Please change that to Aquilegia. --59.177.197.241

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

BobThomson — 2010-09-08 12:25:11

typos

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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- A group of plants from western North American known as [http://en.wikipedia.org/wiki/Aquilegia columbines] represent another classic example of adaptive radiation. Much like anoles, columbines (genus [http://en.wikipedia.org/wiki/Aquilegia ''Aquiligia'']) have diverged along several distinct ecological axes. Two important axes of divergence involve specialization to different pollinators and habitats. Here we will categorical data for these two axes to ask similar questions to those considered above in ''Anolis''. For more details on pollinator evolution, check out Justen Whittal's rad paper on this topic ([[File(Whittall_etal_2007.pdf)]]).	+ A group of plants from western North American known as [http://en.wikipedia.org/wiki/Aquilegia columbines] represent another classic example of adaptive radiation. Much like anoles, columbines (genus [http://en.wikipedia.org/wiki/Aquilegia ''Aquilegia'']) have diverged along several distinct ecological axes. Two important axes of divergence involve specialization to different pollinators and habitats. Here we will categorical data for these two axes to ask similar questions to those considered above in ''Anolis''. For more details on pollinator evolution, check out Justen Whittal's rad paper on this topic ([[File(Whittall_etal_2007.pdf)]]).
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- '''1.''' Open the file “Aquiligia.nex” in Mesquite. This file contains data on two ecological traits for 31 species of columbines. After opening this file, you should see a Character Matrix with two columns labeled ‘pollinator’ and ‘habitat’. In the pollinator column: 0=bee, 1=hummingbird, and 2=hawkmoth. This file should already include the tree file that you will be using for these analyses.	+ '''1.''' Open the file “Aquilegia.nex” in Mesquite. This file contains data on two ecological traits for 31 species of columbines. After opening this file, you should see a Character Matrix with two columns labeled ‘pollinator’ and ‘habitat’. In the pollinator column: 0=bee, 1=hummingbird, and 2=hawkmoth. This file should already include the tree file that you will be using for these analyses.
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- ''2010-03-26 11:20:36'' [[nbsp]] When I do the maximum likelihood ancestral reconstruction in Mesquite of pollinator character in Aquiligia there are nodes that differ significantly from Whittall estimation. What could be the reason? --132.248.207.161	+ ''2010-03-26 11:20:36'' [[nbsp]] When I do the maximum likelihood ancestral reconstruction in Mesquite of pollinator character in Aquilegia there are nodes that differ significantly from Whittall estimation. What could be the reason? --132.248.207.161

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

2010-09-07 18:38:08

Comment added.

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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	+ ------ + ''2010-09-07 18:38:08'' [[nbsp]] Please change that to Aquilegia. --59.177.197.241

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

2010-03-26 11:20:36

Comment added.

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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	+ ------ + ''2010-03-26 11:20:36'' [[nbsp]] When I do the maximum likelihood ancestral reconstruction in Mesquite of pollinator character in Aquiligia there are nodes that differ significantly from Whittall estimation. What could be the reason? --132.248.207.161

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

2009-04-09 02:34:44

Comment added.

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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	+ ------ + ''2009-04-09 02:34:44'' [[nbsp]] i would want to learn more --137.158.152.206

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-13 15:42:05

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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- ==='''Introduction: More on Ancestral Reconstruction & Testing Phylogenetic Signal'''===	+ ==Introduction: More on Ancestral Reconstruction & Testing Phylogenetic Signal== + -----
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- ==='''Reconstructing Ecological Specialization in Adaptive Radiations of Caribbean ''Anolis'' lizards and Columbine Flowers'''=== - ====What ecological attributes characterized the ancestor of the Greater Antillean anole radiation?====	+ ==Reconstructing Ecological Specialization in Adaptive Radiations of Caribbean ''Anolis'' lizards and Columbine Flowers== + ===What ecological attributes characterized the ancestor of the Greater Antillean anole radiation?=== + -----
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- =====Part 1: Open project in Mesquite & reconstruct ancestral states=====	+ ====Part 1: Open project in Mesquite & reconstruct ancestral states==== + '''1.''' Open the file titled “GA_Anolis_Characters.txt” in Mesquite (NOTE: Mesquite will permit you to have multiple projects open simultaneously, but it might be best to close the finch datasets prior to proceeding with subsequent exercises to avoid confusion). This file contains data for 85 species of ''Anolis'' lizards found on the four large Greater Antillean islands of the northern Caribbean. After opening this file, you should see a Character Matrix with three columns. The first two columns represent two distinct types of ecological specialization. The first represents the categories of microhabitat specialists that are commonly referred to as “ecomorphs”: 0=grass-bush, 1=trunk-ground, 2=trunk, 3=trunk-crown, 4=crown-giant, 5=twig. The second column represents macrohabitat specialization: 0=lowland mesic forest, 1=lowland xeric forest, 2=montane forest. The final column identifies the island that each species is found on: 0=Cuba, 1=Hispaniola, 2=Jamaica, 3=Puerto Rico.
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- (1) Open the file titled “GA_Anolis_Characters.txt” in Mesquite (NOTE: Mesquite will permit you to have multiple projects open simultaneously, but it might be best to close the finch datasets prior to proceeding with subsequent exercises to avoid confusion). This file contains data for 85 species of ''Anolis'' lizards found on the four large Greater Antillean islands of the northern Caribbean. After opening this file, you should see a Character Matrix with three columns. The first two columns represent two distinct types of ecological specialization. The first represents the categories of microhabitat specialists that are commonly referred to as “ecomorphs”: 0=grass-bush, 1=trunk-ground, 2=trunk, 3=trunk-crown, 4=crown-giant, 5=twig. The second column represents macrohabitat specialization: 0=lowland mesic forest, 1=lowland xeric forest, 2=montane forest. The final column identifies the island that each species is found on: 0=Cuba, 1=Hispaniola, 2=Jamaica, 3=Puerto Rico.	+ '''2.''' As in the previous exercise, we want to include a linked tree file by going to the “File” tab, selecting “Include file...”, and then selecting “GA_Anolis_Tree.nex”. To view this tree you can either go to the “Taxa&Trees” tab and open a new window or simply click on the Tree block in the Projects and Files window.
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- (2) As in the previous exercise, we want to include a linked tree file by going to the “File” tab, selecting “Include file...”, and then selecting “GA_Anolis_Tree.nex”. To view this tree you can either go to the “Taxa&Trees” tab and open a new window or simply click on the Tree block in the Projects and Files window.	+ '''3.''' We now want to reconstruct ancestral states. To do this with parsimony, just follow steps 7-8 from the previous Mesquite ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise]. What does parsimony tell us about the microhabitat of the ancestral anole? If all has gone according to plans, you should have found that the twig ecomorph is the most likely ancestral state. This is a very curious conclusion as the twig anoles are among the most narrowly specialized of all anoles. Let’s see what maximum likelihood has to say...
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- (3) We now want to reconstruct ancestral states. To do this with parsimony, just follow steps 7-8 from the previous Mesquite ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise]. What does parsimony tell us about the microhabitat of the ancestral anole? If all has gone according to plans, you should have found that the twig ecomorph is the most likely ancestral state. This is a very curious conclusion as the twig anoles are among the most narrowly specialized of all anoles. Let’s see what maximum likelihood has to say...	+ '''4.''' Follow step 9 from the previous Mesquite ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] to reconstruct ancestral states using maximum likelihood. After doing this, you will see that likelihood reconstructs considerable uncertainty in the state of the ancestor to the Greater Antillean radiation. Thus, the surprising conclusion that the ancestor of the anole radiation is a twig anole is no longer supported.
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- (4) Follow step 9 from the previous Mesquite ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] to reconstruct ancestral states using maximum likelihood. After doing this, you will see that likelihood reconstructs considerable uncertainty in the state of the ancestor to the Greater Antillean radiation. Thus, the surprising conclusion that the ancestor of the anole radiation is a twig anole is no longer supported.	+ '''5.''' To view ancestral reconstructions for macrohabitat, follow the steps above and simply click the blue arrow in the “Trace Character” palette to view the second character in the Character Matrix. What do parsimony and likelihood tell you about the most likely macrohabitat of the radiation’s ancestor? Although both methods suggest a lowland mesic ancestor, the states appear to somewhat randomly distributed across the tips. Could it be that we are reconstructing a mesic ancestor simply because this is the most common state rather than due to some information present in the phylogeny itself. To address this question, we’ll test the amount of phylogenetic signal present in this, and other, characters.
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- (5) To view ancestral reconstructions for macrohabitat, follow the steps above and simply click the blue arrow in the “Trace Character” palette to view the second character in the Character Matrix. What do parsimony and likelihood tell you about the most likely macrohabitat of the radiation’s ancestor? Although both methods suggest a lowland mesic ancestor, the states appear to somewhat randomly distributed across the tips. Could it be that we are reconstructing a mesic ancestor simply because this is the most common state rather than due to some information present in the phylogeny itself. To address this question, we’ll test the amount of phylogenetic signal present in this, and other, characters.	+ ====Part 2: Testing Phylogenetic Signal==== + '''6.''' Go to the “Analysis” tab and select “New Bar & Line Chart For:Trees”.
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- ====Part 2: Testing Phylogenetic Signal===== - (6) Go to the “Analysis” tab and select “New Bar & Line Chart For:Trees”.	+ '''7.''' Select: Randomly modify current tree:Reshuffle terminal taxa:Steps in character:Stored Characters:Current Parsimony Model.
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- (7) Select: Randomly modify current tree:Reshuffle terminal taxa:Steps in character:Stored Characters:Current Parsimony Model.	+ '''8.''' After the following series, you should be prompted with an alert, click “OK” and enter the number of times you want to reshuffle the data (the default of 100 should be fine for our purposes) and click “OK”.
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- (8) After the following series, you should be prompted with an alert, click “OK” and enter the number of times you want to reshuffle the data (the default of 100 should be fine for our purposes) and click “OK”.	+ '''9.''' To identify outliers go to the “Chart” tab and select “Analysis:Percentiles”. Select the desired threshold (the default of 0.05 is suitable here) and click “OK”. Values that fall outside of these bounds contain significantly more or less structure than expected by chance. Values that have fewer changes than the red line on the left are characterized by significant phylogenetic signal. Based on the number of changes in microhabitat/ecomorph inferred in the most parsimonious reconstruction of the original data, does microhabitat exhibit significant phylogenetic signal?
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- (9) To identify outliers go to the “Chart” tab and select “Analysis:Percentiles”. Select the desired threshold (the default of 0.05 is suitable here) and click “OK”. Values that fall outside of these bounds contain significantly more or less structure than expected by chance. Values that have fewer changes than the red line on the left are characterized by significant phylogenetic signal. Based on the number of changes in microhabitat/ecomorph inferred in the most parsimonious reconstruction of the original data, does microhabitat exhibit significant phylogenetic signal?	+ '''10.''' To investigate signal in macrohabitat go to the “Chart” tab and select “Next Character”. Does macrohabitat exhibit significant phylogenetic signal? Given the results of this analysis what are we able to say about signal? What does a lack of phylogenetic signal mean for our ability to infer the most likely ancestral state?
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- (10) To investigate signal in macrohabitat go to the “Chart” tab and select “Next Character”. Does macrohabitat exhibit significant phylogenetic signal? Given the results of this analysis what are we able to say about signal? What does a lack of phylogenetic signal mean for our ability to infer the most likely ancestral state? - - ====2B: What were the ancestral pollinator syndrome and habitat for columbines?==	+ ===What were the ancestral pollinator syndrome and habitat for columbines?=== + -----
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- =====Part 1: Open project in Mesquite & reconstruct ancestral states===== - (1) Open the file “Aquiligia.nex” in Mesquite. This file contains data on two ecological traits for 31 species of columbines. After opening this file, you should see a Character Matrix with two columns labeled ‘pollinator’ and ‘habitat’. In the pollinator column: 0=bee, 1=hummingbird, and 2=hawkmoth. This file should already include the tree file that you will be using for these analyses.	+ ====Part 1: Open project in Mesquite & reconstruct ancestral states==== + '''1.''' Open the file “Aquiligia.nex” in Mesquite. This file contains data on two ecological traits for 31 species of columbines. After opening this file, you should see a Character Matrix with two columns labeled ‘pollinator’ and ‘habitat’. In the pollinator column: 0=bee, 1=hummingbird, and 2=hawkmoth. This file should already include the tree file that you will be using for these analyses.
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- (2) By now you should be familiar enough with ancestral reconstruction and the simple reshuffling test of phylogenetic signal to experiment on your own (or you can just refer back to the instructions for the previous anole example).	+ '''2.''' By now you should be familiar enough with ancestral reconstruction and the simple reshuffling test of phylogenetic signal to experiment on your own (or you can just refer back to the instructions for the previous anole example).
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- (3) What have you learned about the ancestor of the columbine radiation? Do pollinator syndrome and habitat exhibit phylogenetic signal?	+ '''3.''' What have you learned about the ancestor of the columbine radiation? Do pollinator syndrome and habitat exhibit phylogenetic signal?
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- ====References====	+ ==References== + -----

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-11 11:47:42

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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- ==='''Introduction: More on Ancestral Reconstruction & Testing Phylogenetic Signa'''===	+ ==='''Introduction: More on Ancestral Reconstruction & Testing Phylogenetic Signal'''===
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- ==='''Excercise 2: Reconstructing the History of Ecological Specialization in Adaptive Radiations of Caribbean ''Anolis'' lizards and Columbine Flowers'''=== - ====2A: What ecological attributes characterized the ancestor of the Greater Antillean anole radiation?====	+ ==='''Reconstructing Ecological Specialization in Adaptive Radiations of Caribbean ''Anolis'' lizards and Columbine Flowers'''=== + ====What ecological attributes characterized the ancestor of the Greater Antillean anole radiation?====

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-11 11:46:26

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- \|\|[[File(Exercise_2.zip)]]\|\|Finch ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] in Mesquite]\|\|\|\|	+ \|\|[[File(Exercise_2.zip)]]\|\|Finch ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] in Mesquite\|\|\|\|

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-11 11:46:13

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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- [[File(Exercise_2.zip)]]\|\|Finch ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] in Mesquite]\|\|\|\|	+ \|\|[[File(Exercise_2.zip)]]\|\|Finch ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] in Mesquite]\|\|\|\|

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-11 11:46:00

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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- \|\|<bgcolor='#E0E0FF'>'''Example Datafile'''\|\|<bgcolor='#E0E0FF'>'''Prerequisites'''\|\|\|\| - [[File(Exercise_2.zip)]]\|\|Finch ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] in Mesquite]\|\|	+ \|\|<bgcolor='#E0E0FF'>'''Example Datafile'''\|\|<bgcolor='#E0E0FF'>'''Prerequisites'''\|\|<bgcolor='#E0E0FF'>\|\| + [[File(Exercise_2.zip)]]\|\|Finch ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] in Mesquite]\|\|\|\|

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-11 11:45:34

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- \|\|<bgcolor='#E0E0FF'>'''Example Datafile'''\|\|<bgcolor='#E0E0FF'>'''Prerequisites'''\|\| - [[File(Exercise_2.zip)]]\|\|Finch ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] in Mesquite]	+ \|\|<bgcolor='#E0E0FF'>'''Example Datafile'''\|\|<bgcolor='#E0E0FF'>'''Prerequisites'''\|\|\|\| + [[File(Exercise_2.zip)]]\|\|Finch ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] in Mesquite]\|\|

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-11 11:45:12

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- \|\|<bgcolor='#E0E0FF'>'''Primary Contact(s)'''\|\|<bgcolor='#E0E0FF'>'''Created'''\|\|<bgcolor='#E0E0FF'>'''Required Software'''\|\|<bgcolor='#E0E0FF'>'''Example Datafile'''\|\| - \|\|["Users/glor" Rich Glor]\|\|28 March 2008\|\|[http://mesquiteproject.org/mesquite/mesquite.html Mesquite]\|\|[[File(Exercise_2.zip)]]\|\|	+ \|\|<bgcolor='#E0E0FF'>'''Primary Contact(s)'''\|\|<bgcolor='#E0E0FF'>'''Created'''\|\|<bgcolor='#E0E0FF'>'''Required Software'''\|\| + \|\|["Users/glor" Rich Glor]\|\|28 March 2008\|\|[http://mesquiteproject.org/mesquite/mesquite.html Mesquite]\|\| + \|\|<bgcolor='#E0E0FF'>'''Example Datafile'''\|\|<bgcolor='#E0E0FF'>'''Prerequisites'''\|\| + [[File(Exercise_2.zip)]]\|\|Finch ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] in Mesquite]

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-11 11:42:44

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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- In this exercise, we will expand on the lessons learned in the ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] on reconstruction of ancestral diets of Darwin's finches by using three datasets to further explore ancestral reconstruction. These datasets are larger and more complicated than the finch datasets considered ["Basic ancestral reconstruction with_parsimony & maximum likelihood in Mesquite" previously] (and also more realistic). In addition to investigating ancestral reconstruction (as we did with the ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" finch example]), we will also learn a basic test for phylogenetic signal (or phylogenetic inertia). This test reshuffles tips to ask whether the distribution of character states is determined, at least in part, by the phylogeny. Put another way, this test ask whether related species are more similar than expected by chance. Such tests of phylogenetic signal should be conducted in association with any phylogenetic comparative analysis. A lack of signal can be a blessing or a curse. In the realm of ancestral reconstruction, it tends to be more of a curse because we can’t reasonably use the phylogeny to reconstruct the evolution of traits that have no relationship to the tree.	+ In this exercise, we will expand on the lessons learned in the ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] on reconstruction of ancestral diets of Darwin's finches by using three datasets to further explore ancestral reconstruction. These datasets are larger and more complicated than the finch datasets considered ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" previously] (and also more realistic). In addition to investigating ancestral reconstruction (as we did with the ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" finch example]), we will also learn a basic test for phylogenetic signal (or phylogenetic inertia). This test reshuffles tips to ask whether the distribution of character states is determined, at least in part, by the phylogeny. Put another way, this test ask whether related species are more similar than expected by chance. Such tests of phylogenetic signal should be conducted in association with any phylogenetic comparative analysis. A lack of signal can be a blessing or a curse. In the realm of ancestral reconstruction, it tends to be more of a curse because we can’t reasonably use the phylogeny to reconstruct the evolution of traits that have no relationship to the tree.

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-11 11:42:19

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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- In this exercise, we will expand on the lessons learned in the ["Basic_ancestral_reconstruction_with_parsimony_&_maximum_likelihood_in_Mesquite" exercise] on reconstruction of ancestral diets of Darwin's finches by using three datasets to further explore ancestral reconstruction. These datasets are larger and more complicated than the finch datasets considered by ["Exercise 1: Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" Exercise 1] (and also more realistic). In addition to investigating ancestral reconstruction (as we did with the finch example in ["Exercise 1: Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" Exercise 1]), we will also learn a basic test for phylogenetic signal (or phylogenetic inertia). This test reshuffles tips to ask whether the distribution of character states is determined, at least in part, by the phylogeny. Put another way, this test ask whether related species are more similar than expected by chance. Such tests of phylogenetic signal should be conducted in association with any phylogenetic comparative analysis. A lack of signal can be a blessing or a curse. In the realm of ancestral reconstruction, it tends to be more of a curse because we can’t reasonably use the phylogeny to reconstruct the evolution of traits that have no relationship to the tree.	+ In this exercise, we will expand on the lessons learned in the ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] on reconstruction of ancestral diets of Darwin's finches by using three datasets to further explore ancestral reconstruction. These datasets are larger and more complicated than the finch datasets considered ["Basic ancestral reconstruction with_parsimony & maximum likelihood in Mesquite" previously] (and also more realistic). In addition to investigating ancestral reconstruction (as we did with the ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" finch example]), we will also learn a basic test for phylogenetic signal (or phylogenetic inertia). This test reshuffles tips to ask whether the distribution of character states is determined, at least in part, by the phylogeny. Put another way, this test ask whether related species are more similar than expected by chance. Such tests of phylogenetic signal should be conducted in association with any phylogenetic comparative analysis. A lack of signal can be a blessing or a curse. In the realm of ancestral reconstruction, it tends to be more of a curse because we can’t reasonably use the phylogeny to reconstruct the evolution of traits that have no relationship to the tree.
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- (3) We now want to reconstruct ancestral states. To do this with parsimony, just follow steps 7-8 from ["Exercise 1: Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" Exercise 1]. What does parsimony tell us about the microhabitat of the ancestral anole? If all has gone according to plans, you should have found that the twig ecomorph is the most likely ancestral state. This is a very curious conclusion as the twig anoles are among the most narrowly specialized of all anoles. Let’s see what maximum likelihood has to say...	+ (3) We now want to reconstruct ancestral states. To do this with parsimony, just follow steps 7-8 from the previous Mesquite ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise]. What does parsimony tell us about the microhabitat of the ancestral anole? If all has gone according to plans, you should have found that the twig ecomorph is the most likely ancestral state. This is a very curious conclusion as the twig anoles are among the most narrowly specialized of all anoles. Let’s see what maximum likelihood has to say...
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- (4) Follow step 9 from exercise I to reconstruct ancestral states using maximum likelihood. After doing this, you will see that likelihood reconstructs considerable uncertainty in the state of the ancestor to the Greater Antillean radiation. Thus, the surprising conclusion that the ancestor of the anole radiation is a twig anole is no longer supported.	+ (4) Follow step 9 from the previous Mesquite ["Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" exercise] to reconstruct ancestral states using maximum likelihood. After doing this, you will see that likelihood reconstructs considerable uncertainty in the state of the ancestor to the Greater Antillean radiation. Thus, the surprising conclusion that the ancestor of the anole radiation is a twig anole is no longer supported.

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-11 09:17:30

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- ==='''Introduction: More on Ancestral Reconstruction & Testing Phylogenetic Signa''']]'''===	+ ==='''Introduction: More on Ancestral Reconstruction & Testing Phylogenetic Signa'''===

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-11 09:17:15

Differences for Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

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- \|\|<bgcolor='#E0E0FF'>'''Primary Contact(s)'''\|\| - \|\|["Users/glor" Rich Glor]\|\| - \|\|<bgcolor='#E0E0FF'>'''Created'''\|\| - \|\|28 March 2008\|\| - \|\|<bgcolor='#E0E0FF'>'''Required Software'''\|\| - \|\|[http://mesquiteproject.org/mesquite/mesquite.html Mesquite]\|\| - \|\|<bgcolor='#E0E0FF'>'''Example Datafile'''\|\| - \|\|[[File(Exercise_2.zip)]]\|\|	+ \|\|<bgcolor='#E0E0FF'>'''Primary Contact(s)'''\|\|<bgcolor='#E0E0FF'>'''Created'''\|\|<bgcolor='#E0E0FF'>'''Required Software'''\|\|<bgcolor='#E0E0FF'>'''Example Datafile'''\|\| + \|\|["Users/glor" Rich Glor]\|\|28 March 2008\|\|[http://mesquiteproject.org/mesquite/mesquite.html Mesquite]\|\|[[File(Exercise_2.zip)]]\|\|
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- =Introduction: More on Ancestral Reconstruction & Testing Phylogenetic Signal=	+ ==='''Introduction: More on Ancestral Reconstruction & Testing Phylogenetic Signa''']]'''===
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- =Excercise 2: Reconstructing the History of Ecological Specialization in Adaptive Radiations of Caribbean ''Anolis'' lizards and Columbine Flowers= - ==2A: What ecological attributes characterized the ancestor of the Greater Antillean anole radiation?==	+ ==='''Excercise 2: Reconstructing the History of Ecological Specialization in Adaptive Radiations of Caribbean ''Anolis'' lizards and Columbine Flowers'''=== + ====2A: What ecological attributes characterized the ancestor of the Greater Antillean anole radiation?====
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- ===Part 1: Open project in Mesquite & reconstruct ancestral states===	+ =====Part 1: Open project in Mesquite & reconstruct ancestral states=====
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- ===Part 2: Testing phylogenetic signal===	+ ====Part 2: Testing Phylogenetic Signal=====
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- ==2B: What were the ancestral pollinator syndrome and habitat for columbines?==	+ ====2B: What were the ancestral pollinator syndrome and habitat for columbines?==
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- ===Part 1: Open project in Mesquite & reconstruct ancestral states===	+ =====Part 1: Open project in Mesquite & reconstruct ancestral states=====
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- =References=	+ ====References====

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2009-03-09 19:43:49

Renamed from "Exercise 2: Ancestral reconstruction and phylogenetic signal in Mesquite"

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	+ \|\|<bgcolor='#E0E0FF'>'''Primary Contact(s)'''\|\| + \|\|["Users/glor" Rich Glor]\|\| + \|\|<bgcolor='#E0E0FF'>'''Created'''\|\| + \|\|28 March 2008\|\| + \|\|<bgcolor='#E0E0FF'>'''Required Software'''\|\| + \|\|[http://mesquiteproject.org/mesquite/mesquite.html Mesquite]\|\| + \|\|<bgcolor='#E0E0FF'>'''Example Datafile'''\|\| + \|\|[[File(Exercise_2.zip)]]\|\| + + =Introduction: More on Ancestral Reconstruction & Testing Phylogenetic Signal= + In this exercise, we will expand on the lessons learned in the ["Basic_ancestral_reconstruction_with_parsimony_&_maximum_likelihood_in_Mesquite" exercise] on reconstruction of ancestral diets of Darwin's finches by using three datasets to further explore ancestral reconstruction. These datasets are larger and more complicated than the finch datasets considered by ["Exercise 1: Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" Exercise 1] (and also more realistic). In addition to investigating ancestral reconstruction (as we did with the finch example in ["Exercise 1: Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" Exercise 1]), we will also learn a basic test for phylogenetic signal (or phylogenetic inertia). This test reshuffles tips to ask whether the distribution of character states is determined, at least in part, by the phylogeny. Put another way, this test ask whether related species are more similar than expected by chance. Such tests of phylogenetic signal should be conducted in association with any phylogenetic comparative analysis. A lack of signal can be a blessing or a curse. In the realm of ancestral reconstruction, it tends to be more of a curse because we can’t reasonably use the phylogeny to reconstruct the evolution of traits that have no relationship to the tree. + + =Excercise 2: Reconstructing the History of Ecological Specialization in Adaptive Radiations of Caribbean ''Anolis'' lizards and Columbine Flowers= + ==2A: What ecological attributes characterized the ancestor of the Greater Antillean anole radiation?== + With nearly 400 species distributed across the neotropics, [http://en.wikipedia.org/wiki/Anolis ''Anolis''] lizards (anoles) are a classic example of adaptive radiation. The anole radiation is particularly diverse and abundant on Caribbean islands, where as many as 12 species may be found living sympatrically. Ecological specialization has long been considered key to explaining this diversity. For many years, anole biologists have been interested in knowing what traits characterized the ancestral anole that spawned the impressive Caribbean radiation. + + ===Part 1: Open project in Mesquite & reconstruct ancestral states=== + + (1) Open the file titled “GA_Anolis_Characters.txt” in Mesquite (NOTE: Mesquite will permit you to have multiple projects open simultaneously, but it might be best to close the finch datasets prior to proceeding with subsequent exercises to avoid confusion). This file contains data for 85 species of ''Anolis'' lizards found on the four large Greater Antillean islands of the northern Caribbean. After opening this file, you should see a Character Matrix with three columns. The first two columns represent two distinct types of ecological specialization. The first represents the categories of microhabitat specialists that are commonly referred to as “ecomorphs”: 0=grass-bush, 1=trunk-ground, 2=trunk, 3=trunk-crown, 4=crown-giant, 5=twig. The second column represents macrohabitat specialization: 0=lowland mesic forest, 1=lowland xeric forest, 2=montane forest. The final column identifies the island that each species is found on: 0=Cuba, 1=Hispaniola, 2=Jamaica, 3=Puerto Rico. + + (2) As in the previous exercise, we want to include a linked tree file by going to the “File” tab, selecting “Include file...”, and then selecting “GA_Anolis_Tree.nex”. To view this tree you can either go to the “Taxa&Trees” tab and open a new window or simply click on the Tree block in the Projects and Files window. + + (3) We now want to reconstruct ancestral states. To do this with parsimony, just follow steps 7-8 from ["Exercise 1: Basic ancestral reconstruction with parsimony & maximum likelihood in Mesquite" Exercise 1]. What does parsimony tell us about the microhabitat of the ancestral anole? If all has gone according to plans, you should have found that the twig ecomorph is the most likely ancestral state. This is a very curious conclusion as the twig anoles are among the most narrowly specialized of all anoles. Let’s see what maximum likelihood has to say... + + (4) Follow step 9 from exercise I to reconstruct ancestral states using maximum likelihood. After doing this, you will see that likelihood reconstructs considerable uncertainty in the state of the ancestor to the Greater Antillean radiation. Thus, the surprising conclusion that the ancestor of the anole radiation is a twig anole is no longer supported. + + (5) To view ancestral reconstructions for macrohabitat, follow the steps above and simply click the blue arrow in the “Trace Character” palette to view the second character in the Character Matrix. What do parsimony and likelihood tell you about the most likely macrohabitat of the radiation’s ancestor? Although both methods suggest a lowland mesic ancestor, the states appear to somewhat randomly distributed across the tips. Could it be that we are reconstructing a mesic ancestor simply because this is the most common state rather than due to some information present in the phylogeny itself. To address this question, we’ll test the amount of phylogenetic signal present in this, and other, characters. + + ===Part 2: Testing phylogenetic signal=== + (6) Go to the “Analysis” tab and select “New Bar & Line Chart For:Trees”. + + (7) Select: Randomly modify current tree:Reshuffle terminal taxa:Steps in character:Stored Characters:Current Parsimony Model. + + (8) After the following series, you should be prompted with an alert, click “OK” and enter the number of times you want to reshuffle the data (the default of 100 should be fine for our purposes) and click “OK”. + + (9) To identify outliers go to the “Chart” tab and select “Analysis:Percentiles”. Select the desired threshold (the default of 0.05 is suitable here) and click “OK”. Values that fall outside of these bounds contain significantly more or less structure than expected by chance. Values that have fewer changes than the red line on the left are characterized by significant phylogenetic signal. Based on the number of changes in microhabitat/ecomorph inferred in the most parsimonious reconstruction of the original data, does microhabitat exhibit significant phylogenetic signal? + + (10) To investigate signal in macrohabitat go to the “Chart” tab and select “Next Character”. Does macrohabitat exhibit significant phylogenetic signal? Given the results of this analysis what are we able to say about signal? What does a lack of phylogenetic signal mean for our ability to infer the most likely ancestral state? + + ==2B: What were the ancestral pollinator syndrome and habitat for columbines?== + A group of plants from western North American known as [http://en.wikipedia.org/wiki/Aquilegia columbines] represent another classic example of adaptive radiation. Much like anoles, columbines (genus [http://en.wikipedia.org/wiki/Aquilegia ''Aquiligia'']) have diverged along several distinct ecological axes. Two important axes of divergence involve specialization to different pollinators and habitats. Here we will categorical data for these two axes to ask similar questions to those considered above in ''Anolis''. For more details on pollinator evolution, check out Justen Whittal's rad paper on this topic ([[File(Whittall_etal_2007.pdf)]]). + + [[anchor(Figure1)]] + [[Image(pollinator_evolution.jpg, thumbnail, noborder, 400, "Figure 1 (Figure 3 from Whittall et al. 2007) - Reconstructed history of pollinator syndromes in Columbine flowers. Blue indicates bee pollinated, red indicates hummingbird pollinated, and yellow indicates hawkmoth pollinated.")]] + + ===Part 1: Open project in Mesquite & reconstruct ancestral states=== + (1) Open the file “Aquiligia.nex” in Mesquite. This file contains data on two ecological traits for 31 species of columbines. After opening this file, you should see a Character Matrix with two columns labeled ‘pollinator’ and ‘habitat’. In the pollinator column: 0=bee, 1=hummingbird, and 2=hawkmoth. This file should already include the tree file that you will be using for these analyses. + + (2) By now you should be familiar enough with ancestral reconstruction and the simple reshuffling test of phylogenetic signal to experiment on your own (or you can just refer back to the instructions for the previous anole example). + + (3) What have you learned about the ancestor of the columbine radiation? Do pollinator syndrome and habitat exhibit phylogenetic signal? + + =References= + Whittall, J. B., and S. A. Hodges. 2007. Pollinator shifts drive increasingly long nectar spurs in columbine flowers. Nature 447:706-709. [[File(Whittall_etal_2007.pdf)]] + + + + [[Comments]]

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2008-04-28 22:19:09

Upload of file Whittall_etal_2007.pdf.

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

glor — 2008-04-28 22:11:47

Upload of image pollinator_evolution.jpg.

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

2008-03-27 22:44:16

Upload of file Exercise_2.zip.