Population Genetics and GIS - Revision history

⚠️Micha: /* Background */

2012-12-04T09:31:49Z

Background

← Older revision		Revision as of 09:31, 4 December 2012
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	== Background ==		== Background ==
	New world Screw-worm ''Cochliomyia hominivorax'' (NWS) is a well known insect pest in South and North America, causing extensive damage to livestock. The females lay eggs into small wounds in warm-blooded ~~vertebrate~~ and the larvae then burrow into the tissue. This injury, known as myasis, weakens the animal, lowers production, and sometimes is severe enough to lead to death of the animal. The "cousin" of NWS, the Old World Screw-worm ''Chrysomya bezziana'' (OWS) causes similar effects throughout the Middle East and South East Asia.		New world Screw-worm ''Cochliomyia hominivorax'' (NWS) is a well known insect pest in South and North America, causing extensive damage to livestock. The females lay eggs into small wounds in warm-blooded vertebrates and the larvae then burrow into the tissue. This injury, known as myasis, weakens the animal, lowers production, and sometimes is severe enough to lead to death of the animal. The "cousin" of NWS, the Old World Screw-worm ''Chrysomya bezziana'' (OWS) causes similar effects throughout the Middle East and South East Asia.

	Typically these insect pests are treated by spraying the livestock directly with pesticides. However they are an ideal candidate for treatment by Sterile Insect Technique (SIT) in the context of an Area-Wide pest management program. See [http://www-naweb.iaea.org/nafa/ipc/screwworm-flies.html the Joint FAO/IAEA program]. An SIT based program requires releasing huge numbers of sterilized male flies throughout the grazing lands, so that the female flies do not encounter a wild male, thus leading to a substantial reduction in the population within a few generations. The method is cost effective when the treated area actually is infested or potentially can be infested with screw-worm. So a successful SIT treatment plan depends on a good understanding of the distribution and possible migration of the pest. This research attempts to address that very question. By merging population genetics and a species habitat model through the use of GIS tools, a procedure is suggested which leads to a geographic data layer representing possible migration corridors of the insect. These corridors are created by combining genetic distance data with environmental data using GRASS GIS.		Typically these insect pests are treated by spraying the livestock directly with pesticides. However they are an ideal candidate for treatment by Sterile Insect Technique (SIT) in the context of an Area-Wide pest management program. See [http://www-naweb.iaea.org/nafa/ipc/screwworm-flies.html the Joint FAO/IAEA program]. An SIT based program requires releasing huge numbers of sterilized male flies throughout the grazing lands, so that the female flies do not encounter a wild male, thus leading to a substantial reduction in the population within a few generations. The method is cost effective when the treated area actually is infested or potentially can be infested with screw-worm. So a successful SIT treatment plan depends on a good understanding of the distribution and possible migration of the pest. This research attempts to address that very question. By merging population genetics and a species habitat model through the use of GIS tools, a procedure is suggested which leads to a geographic data layer representing possible migration corridors of the insect. These corridors are created by combining genetic distance data with environmental data using GRASS GIS.


	== Genetics ==		== Genetics ==

⚠️Micha: /* Create cost maps for each of the locations based on the friction raster */

2012-12-03T19:20:50Z

Create cost maps for each of the locations based on the friction raster

← Older revision		Revision as of 19:20, 3 December 2012
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	</code>		</code>

	By looping through all the locations, cost rasters were created which represent the difficulty, or cost (from the friction map) to reach each of the locations from any other pixel in the region. This "difficulty" is drawn from the original environmental layers as represented in the habitiat suitability model. In the resulting cost raster, pixels with a low value are those where is would be "easy" for an insect to migrate to~~, from~~ the given location. Pixels with a high value represent locations to which it's unlikely that an insect would migrate.		By looping through all the locations, cost rasters were created which represent the difficulty, or cost (from the friction map) to reach each of the locations from any other pixel in the region. This "difficulty" is drawn from the original environmental layers as represented in the habitiat suitability model. In the resulting cost raster, pixels with a low value are those where is would be "easy" for an insect to migrate to the given location. Pixels with a high value represent locations to which it's unlikely that an insect would migrate.

	===== Combine the cost rasters =====		===== Combine the cost rasters =====

⚠️Micha: /* Samples */

2012-12-03T19:17:01Z

Samples

← Older revision		Revision as of 19:17, 3 December 2012
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	===== Samples =====		===== Samples =====
	~~Here~~ are two sample maps of HSM and LCP ~~corridors.resulting~~ predicted migration corridors.		Below are two sample maps of HSM and resulting LCP predicted migration corridors.

	[[File:HSM.jpg\|border\|450px\|left\|Map 1]]		[[File:HSM.jpg\|border\|450px\|left\|Map 1]]
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	''Map 1:'' the HSM for New World Screw-worm in S. America		''Map 1:'' the HSM for New World Screw-worm in S. America

	''Map 2:'' the resulting predicted migration corridors		''Map 2:'' the resulting predicted migration corridors


	== Discussion ==		== Discussion ==

⚠️Micha: /* Finally merge all reclass rasters */

2012-12-03T19:16:07Z

Finally merge all reclass rasters

← Older revision		Revision as of 19:16, 3 December 2012
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	===== Finally merge all reclass rasters =====		===== Finally merge all reclass rasters =====
	~~Create an~~ overall LCP raster for the whole region by summing all the reclass maps, showing possible migration corridors.		An overall LCP raster for the whole region was then created by summing all the reclass maps, thus showing possible migration corridors.

	<code>		<code>

⚠️Micha: /* Combine the cost rasters */

2012-12-03T19:15:15Z

Combine the cost rasters

← Older revision		Revision as of 19:15, 3 December 2012
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	===== Combine the cost rasters =====		===== Combine the cost rasters =====
	~~Use matrix~~ addition to combine two cost rasters, considering only those pairs of locations for which the genetic distance was close (F<sub>st</sub> = 0). The script loops through pairs of locations read from the Fst_zero.csv ASCII text file. In addition to adding the rasters, the result is used to create a '''reclassed''' raster as follows:		Matrix addition was used to combine two cost rasters, while considering only those pairs of locations for which the genetic distance was close (F<sub>st</sub> = 0). The script loops through pairs of locations read from the Fst_zero.csv ASCII text file. In addition to adding the rasters, the result was used to create a '''reclassed''' raster as follows:

	* The minimum value from the combined raster is given value 3.		* The minimum value from the combined raster is given value 3.
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	* all other values are set to null		* all other values are set to null

	This new reclass raster essentially ~~creates~~ a least cost path (LCP), or corridor between pairs of locations. This LCP corridor merges the environmental connectivity, and the genetic distance between locations. A LCP raster is created for each pair of points with the following code:		This new reclass raster essentially created a least cost path (LCP), or corridor between pairs of locations. This LCP corridor merges the environmental connectivity, and the genetic distance between locations. A LCP raster was created for each pair of points with the following code:

	<code>		<code>

⚠️Micha: /* Habitat Suitability Model */

2012-12-03T19:13:42Z

Habitat Suitability Model

← Older revision		Revision as of 19:13, 3 December 2012
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	== Habitat Suitability Model ==		== Habitat Suitability Model ==
	The presence only algorithm employed by MaxEnt ( [http://www.cs.princeton.edu/~schapire/maxent/ software for species habitat modeling] ) was used to create a Habitat Suitability Model (HSM). Environmental predictors were chosen from the BioCLIM data, as well as elevation, landcover (the [http://bioval.jrc.ec.europa.eu/products/glc2000/products.php glc2000 dataset] ) and livestock density from the FAO [http://www.fao.org/AG/againfo/resources/en/glw/home.html Gridded Livestock of the World] data layer. The resulting raster showed the habitat suitability of the NWS based on environmental conditions.		The presence only algorithm employed by MaxEnt ( [http://www.cs.princeton.edu/~schapire/maxent/ software for species habitat modeling] ) was used to create a Habitat Suitability Model (HSM). Environmental predictors were chosen from the BioCLIM data, as well as elevation, landcover (the [http://bioval.jrc.ec.europa.eu/products/glc2000/products.php glc2000 dataset] ) and livestock density from the FAO [http://www.fao.org/AG/againfo/resources/en/glw/home.html Gridded Livestock of the World] data layer. The resulting raster showed the habitat suitability of the NWS based on environmental conditions.


	== GIS ==		== GIS ==

⚠️Micha: /* Genetics */

2012-12-03T19:12:54Z

Genetics

← Older revision		Revision as of 19:12, 3 December 2012
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	== Genetics ==		== Genetics ==
	In this research, we used the pairwise F<sub>st</sub> matrix estimated in [http://pubget.com/paper/21485363 Fresia et al. 2011]. (full text availble on request) as the genetic distance between samples from all pairs of locations. ~~In this study, a~~ total of 227 mitochondrial haplotypes were identified in 282 individuals collected from 29 locations throughout S. America and grouped into two "geographic groups". From the ~~F<sub>st</sub>~~ matrix, those pairs with F<sub>st</sub>=0 (genetically identical samples) were retained for further work. This F<sub>st</sub>=0 value was chosen based on the dispersal capability of the NWS and can be adjusted in any particular case.		In this research, we used the pairwise F<sub>st</sub> matrix estimated in [http://pubget.com/paper/21485363 Fresia et al. 2011]. (full text availble on request) as the genetic distance between samples from all pairs of locations. A total of 227 mitochondrial haplotypes were identified in 282 individuals collected from 29 locations throughout S. America and grouped into two "geographic groups". From the matrix, those pairs with F<sub>st</sub>=0 (genetically identical samples) were retained for further work. This F<sub>st</sub>=0 value was chosen based on the dispersal capability of the NWS and can be adjusted in any particular case.


	== Habitat Suitability Model ==		== Habitat Suitability Model ==

⚠️Micha at 19:10, 3 December 2012

2012-12-03T19:10:11Z

← Older revision		Revision as of 19:10, 3 December 2012
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	</code>		</code>

	===== ~~Sample~~ =====		===== Samples =====
	Here ~~is a~~ sample ~~map~~ of LCP corridors ~~for the state of São Paulo, Brazil~~		Here are two sample maps of HSM and LCP corridors.resulting predicted migration corridors.
	[[File:~~Lcp_merged~~.jpg\|border\|~~400px~~\|right]]
	'''Map 1''': ~~Predicted~~ migration corridors		[[File:HSM.jpg\|border\|450px\|left\|Map 1]]
			[[File:Corridors.jpg\|border\|450px\|right\|Map 2]]
			<br clear=all>
			''Map 1:'' the HSM for New World Screw-worm in S. America

			''Map 2:'' the resulting predicted migration corridors


	== Discussion ==		== Discussion ==

⚠️Micha at 17:41, 3 December 2012

2012-12-03T17:41:32Z

← Older revision		Revision as of 17:41, 3 December 2012
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	= Applying Population Genetics and GIS to create predicted migration corridors for New World Screw-worm =		= Applying Population Genetics, Habitat Suitability Modeling and GIS to create predicted migration corridors for New World Screw-worm =

	== Background ==		== Background ==
	New world Screw-worm ''Cochliomyia hominivorax'' (NWS) is a well known ~~agricultural~~ pest in South and North America, causing extensive damage to ~~cattle~~. The females lay ~~larvae~~ into small wounds in ~~the animal's skin~~ and the larvae then burrow into the tissue ~~and cause~~ myasis, ~~which~~ weakens the animal, lowers production, and sometimes is severe enough to lead to death of the animal. The "cousin" of NWS, the Old World Screw-worm ''Chrysomya bezziana'' (OWS) causes similar effects ~~in cattle and also small ruminants~~ throughout the Middle East and South East Asia.		New world Screw-worm ''Cochliomyia hominivorax'' (NWS) is a well known insect pest in South and North America, causing extensive damage to livestock. The females lay eggs into small wounds in warm-blooded vertebrate and the larvae then burrow into the tissue. This injury, known as myasis, weakens the animal, lowers production, and sometimes is severe enough to lead to death of the animal. The "cousin" of NWS, the Old World Screw-worm ''Chrysomya bezziana'' (OWS) causes similar effects throughout the Middle East and South East Asia.

	Typically these pests are treated by spraying the livestock directly with pesticides. However they are an ideal candidate for treatment by Sterile Insect Technique (SIT) in the context of an Area-Wide pest management program. See [http://www-naweb.iaea.org/nafa/ipc/screwworm-flies.html the Joint FAO/IAEA program]. An SIT based program requires releasing huge numbers of sterilized male flies throughout the grazing lands, so that the female flies do not encounter a wild male, thus leading to a substantial reduction in the population within a few generations. The method is cost effective when the treated area actually is infested or potentially can be infested with screw-worm. So a successful SIT treatment plan depends on a good understanding of the distribution and possible migration of the pest. This research attempts to address that very question. By merging population genetics and a species habitat model through the use of GIS tools, a procedure is suggested which leads to a geographic data layer representing possible migration corridors of the insect. These corridors are created by combining genetic distance data with environmental data using GRASS GIS.		Typically these insect pests are treated by spraying the livestock directly with pesticides. However they are an ideal candidate for treatment by Sterile Insect Technique (SIT) in the context of an Area-Wide pest management program. See [http://www-naweb.iaea.org/nafa/ipc/screwworm-flies.html the Joint FAO/IAEA program]. An SIT based program requires releasing huge numbers of sterilized male flies throughout the grazing lands, so that the female flies do not encounter a wild male, thus leading to a substantial reduction in the population within a few generations. The method is cost effective when the treated area actually is infested or potentially can be infested with screw-worm. So a successful SIT treatment plan depends on a good understanding of the distribution and possible migration of the pest. This research attempts to address that very question. By merging population genetics and a species habitat model through the use of GIS tools, a procedure is suggested which leads to a geographic data layer representing possible migration corridors of the insect. These corridors are created by combining genetic distance data with environmental data using GRASS GIS.


	== Genetics ==		== Genetics ==
	In this research, ~~individuals were collected from 38 locations throughout S. America, and mtDNA analysis isolated over 200 haplotypes. The haplotypes where grouped into four "geographic groups". A~~ pairwise F<sub>st</sub> matrix ~~was created indicating the genetic distance between samples from all pairs of locations. This procedure is fully described~~ in [http://pubget.com/paper/21485363 Fresia et al. 2011]. (~~Full~~ text availble on request). From the F<sub>st</sub> matrix, those pairs with F<sub>st</sub>=0 (genetically identical samples) were ~~isolated~~ for further work.		In this research, we used the pairwise F<sub>st</sub> matrix estimated in [http://pubget.com/paper/21485363 Fresia et al. 2011]. (full text availble on request) as the genetic distance between samples from all pairs of locations. In this study, a total of 227 mitochondrial haplotypes were identified in 282 individuals collected from 29 locations throughout S. America and grouped into two "geographic groups". From the F<sub>st</sub> matrix, those pairs with F<sub>st</sub>=0 (genetically identical samples) were retained for further work. This F<sub>st</sub>=0 value was chosen based on the dispersal capability of the NWS and can be adjusted in any particular case.


	== Habitat Suitability Model ==		== Habitat Suitability Model ==
	The presence only algorithm employed by MaxEnt ( [http://www.cs.princeton.edu/~schapire/maxent/ software for species habitat modeling] ) was used to create a Habitat Suitability Model (HSM). Environmental predictors were chosen from the BioCLIM data, as well as elevation, landcover (the [http://bioval.jrc.ec.europa.eu/products/glc2000/products.php glc2000 dataset] ) and livestock density from the FAO [http://www.fao.org/AG/againfo/resources/en/glw/home.html Gridded Livestock of the World] data layer. The resulting raster showed ~~probabilities for spread~~ of the NWS based on environmental conditions.		The presence only algorithm employed by MaxEnt ( [http://www.cs.princeton.edu/~schapire/maxent/ software for species habitat modeling] ) was used to create a Habitat Suitability Model (HSM). Environmental predictors were chosen from the BioCLIM data, as well as elevation, landcover (the [http://bioval.jrc.ec.europa.eu/products/glc2000/products.php glc2000 dataset] ) and livestock density from the FAO [http://www.fao.org/AG/againfo/resources/en/glw/home.html Gridded Livestock of the World] data layer. The resulting raster showed the habitat suitability of the NWS based on environmental conditions.


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	===== Sample =====		===== Sample =====
	Here is a sample map of LCP corridors for the state of São Paulo, Brazil		Here is a sample map of LCP corridors for the state of São Paulo, Brazil
	[[File:Lcp_merged.jpg\|~~frame~~]]		[[File:Lcp_merged.jpg\|border\|400px\|right]]
	'''Map 1''': Predicted migration corridors		'''Map 1''': Predicted migration corridors

⚠️Micha: /* Sample */

2012-12-01T15:34:30Z

Sample

← Older revision		Revision as of 15:34, 1 December 2012
Line 81:		Line 81:
	Here is a sample map of LCP corridors for the state of São Paulo, Brazil		Here is a sample map of LCP corridors for the state of São Paulo, Brazil
	[[File:Lcp_merged.jpg\|frame]]		[[File:Lcp_merged.jpg\|frame]]
			'''Map 1''': Predicted migration corridors

	== Discussion ==		== Discussion ==