Preserve genetic diversity: Make informed choices for individual reintroductions.
I Choose You helps conservation practitioners select captive individuals for translocation/reintroduction/genetic rescue, based on their theoretical genetic diversity.
ICY considers three input constraints:
- The number of males wanted.
- The number of females wanted.
- A threshold for the level of relatedness between any chosen individuals.
ICY reports the individuals that should be selected for transolcation that would maximise genetic diversity, given the three constraints.
ICY can also generate a downloadable report. The report provides more thorough explanations about the analysis ICY performs, and presents more informationb about the individuals within a given population.
The source code can find ICY on Github here.
ICY is MIT Licensed.
Captive breeding programmes by zoos and other conservation practicioners are critical for conserving species. The purpose of such programmes is to introduce individuals that support endangerd wild populations and help recover. This works because the introduced individuals are often genetically distinct to the wild individuals, and so introducing them increases the genetic diversity of the wild population's gene pool. This helps the population overcome common genetic problems that endangerd and reduced populations have, such as inbreeding depression, which cause all kinds of health problems.
To make the most of these reintroductions individuals that will maximise the genetic diversity in the wild population should be chosen. However, practitioners don't often have access to current sequencing data, or the genomics expertise to be able to interpret such data. Some projects have some form of pedigree data for the wild population as well as the captive one, and this data can be used to infer which individuals may be better to reintroduce than others. However, some projects have none of these data and in such cases the individuals chosen for reintroduction may be picked blindly.
Many projects have a studbook and its information can be used to calculate a measure of theoretical genetic diversity for each individual in the population. This metric is called founder equivalents, and groups of individuals can be selected which are as diverse as possible whilst not being too related to each other.
ICY was designed to allow practitioners to quickly compute such an analysis and obtain a good selection of individuals based on the theoretical genetic diversity of captive individuals being considered for translocation/reintroduction/genetic rescue. It is aimed at practitioners who do not have any genetic data. Whilst ICY does not guarantee THE optimal result, and does not consider pragmatic considerations (those are up to the practitioners), it should result in genetically healthier decisions than choosing individuals blindly (at random).
ICY takes as input three csv files all readily available to download from studbook software such as Sparks or PmX. See the tab 'How to. . .' above to make sure the correct files are generated. ICY then uses Python functions to format the data and calculates the number of founder equivalents (Fe) per individual and ranks birds based on Fe and mean kinship coefficient (MK). Finally given the three input parameters (number of males, number of females, relatedness threshold) it will calulcate a group (where the group size is equal to number of males + number females specified) of individuals which are the highest ranked individuals that are all less related than the specified relatedness threshold. The methods employed by ICY are deisgned to maximise geentic diversity and help prevent inbreeding.
Important to note just because ICY suggests a group of individuals does not necessarily mean these are the best individuals for reintroduction/translocation. This because there are many other pragmatic considerations such as age, location, health that may be relevant that ICY does not consider. Many pragmatic decisions can be thought through before generating the data for ICY (for example age) so that the input data only contains a subset of individuals from the whole population deemed most appropriate by the user. Ultimately the decision of which individuals to reintroduce belongs to the practitioners, ICY is designed to provide an easy way for users to integrate genetic health into their decisions in the hope of promoting healthier and more stable populations.
We've already built and deployed I.C.Y. on Heroku so you don't have to!
Just head over here and use it.
Note: our deployment is currently in a Heroku free dyno, and so sometimes the page-load times are wanting!
I.C.Y is a shiny web-application, and it is packaged into a docker container. To run it locally you can clone this repository, and from the root directory, issue the following shell commands to build and run the container.
export PORT=80 # Set the port for the app to listen on.
docker build -t my-icy-app .
docker run --rm -p 80:80 my-icy-app # Make sure -p argument matches port set above.- Please read the FAQs (below).
- If the FAQs do not help please open an issue Describe your issue as clearly as you can, any printed error messages or screenshots will help.
- Error: index 0 is out of bounds for axis 0 with size 0 - this means it is not possible to have the number or males and number of females at the threshold you have set because they are all more related than that threshold. To solve this you can try decreasing the threshold (ie increasing the allowed realtedness between individuals in a group) or try decreasing either the number or males and/or the number of females.