ESS 221 Assignment 1 Crop Species Niche Modeling

ESS 221 Assignment 1 Crop species niche modeling

Part 1: Getting started with your crop species niche modeling assignment

1.1: Downloading crop species occurrence data from the GBIF portal

Each student will have to choose a different crop species for their assignment (please download the list linked on the blog)

Steps for downloading data from the GBIF portal

GBIF - Global Biodiversity Information Facility is an international organisation funded by governments which helps to facilitate the sharing of biodiversity data. South Africa (classed a mega-biodiverse county with global biodiversity hotspots – the fynbos, succulent Karoo and maputaland, podoland and Albany Hotspot is an important role player in GBIF and we contribute many millions of specimen and observational records the South African Biodiversity Institute facilitates (SABIF) facilitates South Africa’s involvement and is funded by DST and located within SANBI (South African National Biodiversity Institute).

·  Using your favourite browser go to http://www.GBIF.org (GBIF - Global Biodiversity Information Facility

·  Create a user account (really quick and easy just five fields to fill in on the form). You will not be able to download data without an account.

·  Click on “Data” and then “Explore species” in the top menu bar to the right of any of the sites pages. It may seem like you should use “Explore occurrences” but it is necessary to check that you have the right species, subspecies or variety first.

·  Enter the species you have chosen in the search block and click search e.g. Arachis hypogaea L. the peanut or groundnut.

·  The site will return a list of species names which correspond. It is import to check that you have chosen the correct species, subspecies or variety for your assignment as in crop plant a single species may have been bred into numerous very different cultivars or a wild type of a SPECIES may have now have no significance as a food crop.

·  When you are sure you have chosen the correct species/subspecies check the number of occurrence records under “Georeferenced data”.

·  Biodiversity georeferenced data are data where each record of a species (a specimen in a collection or an observation usually others as well) has a latitude and longitude which places it on the surface of the earth as a point. It may have been recorded by the collector directly or calculated from the description provided by the collector.) You preferably want over five hundred georeferenced records. There are many common species with only few records should this be the case choose another species for your assignment. If the number of georeferenced records is sufficient click on the “All [number of records]” link.

·  This will take you to the “Search occurrences” page where you can click on the large “Download” button which will down load a zipped file containing the georeferenced specimen or observational records GBIF has for your crop species. Along with each location (latitude and longitude) of the species record is a large amount of taxonomic and collections data we will first have to clean up.

·  Note that you will have to register on the site before you can download the data. It will take about 10 -15minutes to prepare the download as a zipped file and an email reminder will be sent to your registration email.

·  You can use this time to find out information about your crop species for you assignment by examining the information about the species (go back to the “Explore species”) and following of the links.

·  Unzip your downloaded species location data into a folder on your computer or memory stick.

1.2: Importing the species occurrence data into excel and creating a GIS useable data set.

When you unzip your downloaded species occurrence zip file you will see the following files and folders

·  dataset (folder)

·  citations.txt

·  meta.xml

·  metadata.xml

·  occurrence.txt

·  rights.txt

You will import the occurrence dataset into excel by following these steps:.

1.  Open excel and click on the data tab

2.  Click on the “From text” button in the “Get external data” on the fat left of the toolbar and choose the occurrence.txt file and click on import. The “Text import wizard” will appear as a popup.

3.  Choose the “Delimited” option on the first screen click “Next”

4.  Check “Tab” on the second screen for tab delimited data click “Next”.

5.  Don’t do anything on the third screen and click finish. Accept the import data defaults by clicking “Okay”. The data should appear from block A1 with the column headings in row 1.

THERE ARE A LOT of columns or fields in the download and hopefully as many rows or records as you were promised by GDIF.

You will now tidy up the data set to make it more usable for GIS modeling we are going to do in the DIVA GIS program. First save the excel spreadsheet as it is and make a copy of the data in another worksheet in case you make an error or later decide you want something you delete back.

Using the copied data you can now delete many of the columns all the higher taxa and their id columns, all the verbatim columns, depth columns, author and identified by columns etc.

REMEMBER! don’t delete the latitude, longitude, id, dataset_id, country columns they are the most important.

If you have many thousands of records you may have to make a subset choosing 1000 records or rows to work with as DIVA GIS doesn’t seem to handle very large datasets very well. Cut and paste the subset into a third worksheet.

Rename all your remaining column headings to less than 10 characters for the GIS software we are using DIVA GIS or it will do so for you and you may not understand what it provides.

SAVE your workbook as an .xlsx, xls and the worksheet of the data you wish to import as a tab delimited text file. The reason for doing this is that DIVA GIS will import your data as .xls allowing you to choose the worksheet or tab delimited text files which I find works best.