West Coast Salamander Tutorial - Revision history

Dparks: /* References */

2012-03-03T14:55:30Z

References

Dparks: /* Loading Data */

2012-03-02T21:38:16Z

Loading Data

Dparks: /* Quantitative Analysis of Non-linear Gradients */

2012-03-02T21:37:46Z

Quantitative Analysis of Non-linear Gradients

Dparks: /* Quantitative Analysis of Non-linear Gradients */

2012-03-02T21:37:29Z

Quantitative Analysis of Non-linear Gradients

Dparks: /* Quantitative Analysis of Non-linear Gradients */

2012-03-02T21:29:43Z

Quantitative Analysis of Non-linear Gradients

Dparks: /* Quantitative Analysis of Non-linear Gradients */

2012-03-02T21:07:32Z

Quantitative Analysis of Non-linear Gradients

Dparks: New page: =Introduction= GenGIS is a free and open-source bioinformatics application that allows geographic data to be merged with information about biological sequences collected from the environm...

2012-03-02T21:03:31Z

New page: =Introduction= GenGIS is a free and open-source bioinformatics application that allows geographic data to be merged with information about biological sequences collected from the environm...

New page

=Introduction=

GenGIS is a free and open-source bioinformatics application that allows geographic data to be merged with information about biological sequences collected from the environment. It consists of a 3D graphical user interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.

The ''Ensatina eschscholtzii'' salamander from the western United States is a classic example of allopatric speciation. In this tutorial, we demonstrate how GenGIS can be used to analyze non-linear geographic gradients (Parks and Beiko, 2009). To follow along with this tutorial download the data:

* [[Media:GenGIS_Salamanders.zip|Download salamander data set]]

This tutorial assumes you have already worked through the [[Katydid Tutorial | ''Banza'' Katydid]] and [[GOS Tutorial | GOS]] tutorials. In particular, it assumes you are familiar with how geophylogenies are analyzed within GenGIS (Parks and Beiko, 2009; Parks ''et al.'', 2009).

=Loading Data=

The Salamander data consists of a 2D map (WestCoast.tif), projection information for the map (WestCoast.tfw), location data (salamander.csv), and a geophylogeny (salamander.tre). Load this data into GenGIS. For basic information on using the GenGIS interface and loading data please see the [[Katydid Tutorial | ''Banza'' Katydid Tutorial]].

=Changing Visual Properties=

The location set properties were so the colour of a location reflects the ''Subspecies'' sampled at that location. The properties of the geophylogeny were set so location colours are discretely propagated through the tree. Other tree properties such as the height of the tree and the size of internal nodes were also set to improve visual clarity. For further details on setting visual properties see the [[Katydid Tutorial | ''Banza'' Katydid]] or [[GOS Tutorial | GOS]] tutorials.

=Quantitative Analysis of Non-linear Gradients=

Non-linear geographic gradients can be evaluated in GenGIS using the ''Geographic Axis'' toolbar button. This allows a polyline to be drawn which represents the non-linear gradient to be evaluated. The polyline is drawn by sequentially clicking on the map to place control points representing the end of each line segment. A polyline can be finalized by hitting the ''Enter'' key. If desired, additional line segments extending from an existing control point can be added by right-clicking on the control point and selecting ''xxx'' from the pop-up menu. The [[Media:GenGIS_Salamander_Tutorial.mp4|video tutorial]] demonstrates the construction of a multi-segment polyline.

Here a non-linear geographic gradient is contrasts with a strictly linear gradient in order to evaluate two alternative hypotheses concerning the biogeographic history of the ''Ensatina eschscholtzii'' salamanders. First the hypothesis that these salamanders originated in the redwood forests of southern Oregon and migrated down the western United States during periods of greater humidity is considered. This hypothesis is illustrated in the left panel of Figure 1 and results in 37 crossings occur between the correlation lines. This is significantly non-random at P ≤ 0.0004, which provides support for this hypothesis. However, by assigning unique colours to each sub-species a heterogeneous distribution of colours along the linear gradient is observed which indicates that sub-species are highly intermixed along this geographic axis.
Alternatively, while moving down the western United States the salamanders may have dispersed down separate coastal and inland ranges (Stebbins, 1949). This hypothesis is shown in the right panel of Figure 1 and results in only 11 crossings (P ≤ 0.0001). Crossings that occur with this geographic axis have important biological and geographic significance. For example, the highlighted geographic point is the cause of several crossings. This point is from the Sierran population of the xanthoptica sub-species which is found primarily along the coast. It is hypothesized that the Sierran population evolved from the coastal population during a mesic (moderately moist) period of the Pleistocene epoch (Mortiz ''et al.'', 1992).

[[Image:Salamanders.png|thumb|center|600px|Figure 1. Geophylogeny of ''Ensatina eschscholtzii'' salamanders from the western United States with each sub-species assigned a unique colour. The visualization on the left tests whether the phylogenetic tree correlates with a linear geographic axis along the coastline. This hypothesis results in 37 crossings. The visualization on the right evaluates a non-linear geographic axis resulting from two diverging migration paths. This hypothesis results in only 11 crossings. The geographic point highlighted in red and marked by an arrow gives rise to 5 of these 11 crossings.]]

=Contact Information=
We encourage you to send us suggestions for new features. GenGIS is in active development and we are interested in discussing all potential applications of this software. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko@cs.dal.ca). If reporting a bug, please provide as much information as possible and, if possible, a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue.

=References=
Moritz C, Schneider CJ, Wake DB. 1992. Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation. ''Syst Biol'', '''41''': 273-291.

Parks DH and Beiko RG. 2009. Quantitative visualizations of hierarchically organized data in a geographic context. ''Geoinformatics 2009'', Fairfax, VA. [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&isnumber=5292806&arnumber=5293552&count=243&index=6 IEEE Xplore]

Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S and Beiko RG. 2009. GenGIS: A geospatial information system for genomic data. ''Genome Research'', '''19''': 1896-1904.

Stebbins RC. 1949. Speciation in salamanders of the Plethodontid genus Ensatina. ''Univ Calif Publ Zool'', '''48''': 377-526.

@@ Line 19: / Line 19: @@
 =Quantitative Analysis of Non-linear Gradients=
-Non-linear geographic gradients can be evaluated in GenGIS using the ''Geographic Axis'' toolbar button. This allows a polyline to be drawn which represents the non-linear gradient to be evaluated. The polyline is drawn by sequentially clicking on the map to place control points representing the end of each line segment. A polyline can be finalized by hitting the ''Enter'' key. If desired, additional line segments extending from an existing control point can be added by right-clicking on the control point and selecting ''Extend geographic axis'' from the pop-up menu. To assign a non-linear geographic axis to a tree, right-click the tree in the ''Layer Tree' and select ''Assign geographic axes to tree'' from the pop-up menu. The [[Media:GenGIS_Salamander_Tutorial.mp4|video tutorial]] demonstrates the construction of a multi-segment polyline.
+Non-linear geographic gradients can be evaluated in GenGIS using the ''Geographic Axis'' toolbar button. This allows a polyline to be drawn which represents the non-linear gradient to be evaluated. The polyline is drawn by sequentially clicking on the map to place control points representing the end of each line segment. A polyline can be finalized by hitting the ''Enter'' key. If desired, additional line segments extending from an existing control point can be added by right-clicking on the control point and selecting ''Extend geographic axis'' from the pop-up menu. To assign a non-linear geographic axis to a tree, right-click the tree in the ''Layer Tree'' and select ''Assign geographic axes to tree'' from the pop-up menu. The [[Media:GenGIS_Salamander_Tutorial.mp4|video tutorial]] demonstrates the construction of a multi-segment polyline.
 Here a non-linear geographic gradient is contrasts with a strictly linear gradient in order to evaluate two alternative hypotheses concerning the biogeographic history of the ''Ensatina  eschscholtzii'' salamanders. First the hypothesis that these salamanders originated in the redwood forests of southern Oregon and migrated down the western United States during periods of greater humidity is considered.  This hypothesis is illustrated in Figure 1a and results in 37 crossings occur between the correlation lines. This is significantly non-random at P ≤ 0.0004, which provides support for this hypothesis. However, by assigning unique colours to each sub-species a heterogeneous distribution of colours along the linear gradient is observed which indicates that sub-species are highly intermixed along this geographic axis.

@@ Line 19: / Line 19: @@
 =Quantitative Analysis of Non-linear Gradients=
-Non-linear geographic gradients can be evaluated in GenGIS using the ''Geographic Axis'' toolbar button. This allows a polyline to be drawn which represents the non-linear gradient to be evaluated. The polyline is drawn by sequentially clicking on the map to place control points representing the end of each line segment. A polyline can be finalized by hitting the ''Enter'' key. If desired, additional line segments extending from an existing control point can be added by right-clicking on the control point and selecting ''Extend geographic axis'' from the pop-up menu. The [[Media:GenGIS_Salamander_Tutorial.mp4|video tutorial]] demonstrates the construction of a multi-segment polyline.
+Non-linear geographic gradients can be evaluated in GenGIS using the ''Geographic Axis'' toolbar button. This allows a polyline to be drawn which represents the non-linear gradient to be evaluated. The polyline is drawn by sequentially clicking on the map to place control points representing the end of each line segment. A polyline can be finalized by hitting the ''Enter'' key. If desired, additional line segments extending from an existing control point can be added by right-clicking on the control point and selecting ''Extend geographic axis'' from the pop-up menu. To assign a non-linear geographic axis to a tree, right-click the tree in the ''Layer Tree' and select ''Assign geographic axes to tree'' from the pop-up menu. The [[Media:GenGIS_Salamander_Tutorial.mp4|video tutorial]] demonstrates the construction of a multi-segment polyline.
 Here a non-linear geographic gradient is contrasts with a strictly linear gradient in order to evaluate two alternative hypotheses concerning the biogeographic history of the ''Ensatina  eschscholtzii'' salamanders. First the hypothesis that these salamanders originated in the redwood forests of southern Oregon and migrated down the western United States during periods of greater humidity is considered.  This hypothesis is illustrated in Figure 1a and results in 37 crossings occur between the correlation lines. This is significantly non-random at P ≤ 0.0004, which provides support for this hypothesis. However, by assigning unique colours to each sub-species a heterogeneous distribution of colours along the linear gradient is observed which indicates that sub-species are highly intermixed along this geographic axis.

@@ Line 19: / Line 19: @@
 =Quantitative Analysis of Non-linear Gradients=
-Non-linear geographic gradients can be evaluated in GenGIS using the ''Geographic Axis'' toolbar button. This allows a polyline to be drawn which represents the non-linear gradient to be evaluated. The polyline is drawn by sequentially clicking on the map to place control points representing the end of each line segment. A polyline can be finalized by hitting the ''Enter'' key. If desired, additional line segments extending from an existing control point can be added by right-clicking on the control point and selecting ''xxx'' from the pop-up menu. The [[Media:GenGIS_Salamander_Tutorial.mp4|video tutorial]] demonstrates the construction of a multi-segment polyline.
+Non-linear geographic gradients can be evaluated in GenGIS using the ''Geographic Axis'' toolbar button. This allows a polyline to be drawn which represents the non-linear gradient to be evaluated. The polyline is drawn by sequentially clicking on the map to place control points representing the end of each line segment. A polyline can be finalized by hitting the ''Enter'' key. If desired, additional line segments extending from an existing control point can be added by right-clicking on the control point and selecting ''Extend geographic axis'' from the pop-up menu. The [[Media:GenGIS_Salamander_Tutorial.mp4|video tutorial]] demonstrates the construction of a multi-segment polyline.
 Here a non-linear geographic gradient is contrasts with a strictly linear gradient in order to evaluate two alternative hypotheses concerning the biogeographic history of the ''Ensatina  eschscholtzii'' salamanders. First the hypothesis that these salamanders originated in the redwood forests of southern Oregon and migrated down the western United States during periods of greater humidity is considered.  This hypothesis is illustrated in Figure 1a and results in 37 crossings occur between the correlation lines. This is significantly non-random at P ≤ 0.0004, which provides support for this hypothesis. However, by assigning unique colours to each sub-species a heterogeneous distribution of colours along the linear gradient is observed which indicates that sub-species are highly intermixed along this geographic axis.

@@ Line 34: / Line 34: @@
 Parks DH and Beiko RG. 2009. Quantitative visualizations of hierarchically organized data in a geographic context. ''Geoinformatics 2009'', Fairfax, VA. [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&isnumber=5292806&arnumber=5293552&count=243&index=6 IEEE Xplore]
-Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S and Beiko RG. 2009. GenGIS: A geospatial information system for genomic data. ''Genome Research'', '''19''': 1896-1904.
+Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S and Beiko RG. 2009. GenGIS: A geospatial information system for genomic data. ''Genome Research'', '''19''': 1896-1904. ([http://genome.cshlp.org/content/19/10/1896 Abstract])
 Stebbins RC. 1949. Speciation in salamanders of the Plethodontid genus Ensatina. ''Univ Calif Publ Zool'', '''48''': 377-526.

@@ Line 11: / Line 11: @@
 =Loading Data=
 The Salamander data  consists of a 2D map (WestCoast.tif), projection information for the map (WestCoast.tfw), location data (salamander.csv), and a geophylogeny (salamander.tre). Load this data into GenGIS. For basic information on using the GenGIS interface and loading data please see the [[Katydid Tutorial | ''Banza'' Katydid Tutorial]].
 =Changing Visual Properties=

@@ Line 21: / Line 21: @@
 Non-linear geographic gradients can be evaluated in GenGIS using the ''Geographic Axis'' toolbar button. This allows a polyline to be drawn which represents the non-linear gradient to be evaluated. The polyline is drawn by sequentially clicking on the map to place control points representing the end of each line segment. A polyline can be finalized by hitting the ''Enter'' key. If desired, additional line segments extending from an existing control point can be added by right-clicking on the control point and selecting ''xxx'' from the pop-up menu. The [[Media:GenGIS_Salamander_Tutorial.mp4|video tutorial]] demonstrates the construction of a multi-segment polyline.
-Here a non-linear geographic gradient is contrasts with a strictly linear gradient in order to evaluate two alternative hypotheses concerning the biogeographic history of the ''Ensatina  eschscholtzii'' salamanders. First the hypothesis that these salamanders originated in the redwood forests of southern Oregon and migrated down the western United States during periods of greater humidity is considered.  This hypothesis is illustrated in the left panel of Figure 1 and results in 37 crossings occur between the correlation lines. This is significantly non-random at P ≤ 0.0004, which provides support for this hypothesis. However, by assigning unique colours to each sub-species a heterogeneous distribution of colours along the linear gradient is observed which indicates that sub-species are highly intermixed along this geographic axis.
+Here a non-linear geographic gradient is contrasts with a strictly linear gradient in order to evaluate two alternative hypotheses concerning the biogeographic history of the ''Ensatina  eschscholtzii'' salamanders. First the hypothesis that these salamanders originated in the redwood forests of southern Oregon and migrated down the western United States during periods of greater humidity is considered.  This hypothesis is illustrated in Figure 1a and results in 37 crossings occur between the correlation lines. This is significantly non-random at P ≤ 0.0004, which provides support for this hypothesis. However, by assigning unique colours to each sub-species a heterogeneous distribution of colours along the linear gradient is observed which indicates that sub-species are highly intermixed along this geographic axis.
-Alternatively, while moving down the western United States the salamanders may have dispersed down separate coastal and inland ranges (Stebbins, 1949). This hypothesis is shown in the right panel of Figure 1 and results in only 11 crossings (P ≤ 0.0001). Crossings that occur with this geographic axis have important biological and geographic significance. For example, the highlighted geographic point is the cause of several crossings. This point is from the Sierran population of the xanthoptica sub-species which is found primarily along the coast. It is hypothesized that the Sierran population evolved from the coastal population during a mesic (moderately moist) period of the Pleistocene epoch (Mortiz ''et al.'', 1992).
+Alternatively, while moving down the western United States the salamanders may have dispersed down separate coastal and inland ranges (Stebbins, 1949). This hypothesis is shown in Figure 1b and results in only 11 crossings (P ≤ 0.0001). Crossings that occur with this geographic axis have important biological and geographic significance. For example, the highlighted geographic point is the cause of several crossings. This point is from the Sierran population of the xanthoptica sub-species which is found primarily along the coast. It is hypothesized that the Sierran population evolved from the coastal population during a mesic (moderately moist) period of the Pleistocene epoch (Mortiz ''et al.'', 1992).
 [[Image:Salamanders.png|thumb|center|600px|Figure 1. Geophylogeny of ''Ensatina eschscholtzii'' salamanders from the western United States with each sub-species assigned a unique colour. The visualization on the left tests whether the phylogenetic tree correlates with a linear geographic axis along the coastline. This hypothesis results in 37 crossings. The visualization on the right evaluates a non-linear geographic axis resulting from two diverging migration paths. This hypothesis results in only 11 crossings. The geographic point highlighted in red and marked by an arrow gives rise to 5 of these 11 crossings.]]