Genetic barrier detection in landscape genetics
Hey,
currently i am working with micro-satellite data from several local populations of Tanzanian elephants and i was wondering if there are somehow borders between my populations that prevent migration and therefore gene-flow. As elephants usually are animals that live quite long (if not killed by poaching right after reaching maturity), detecting actual barriers in field-observations might be difficult and requires a lot of effort. And that is where landscape genetic techniques come into the picture.
As early as in 1973, a french Guy called Monmonier (Monmonier 1973) came up with a very nice idea of barrier-detection using graph-theory and gis-techniques such as Vorronoi tessellations. Although previously intended to be used in a purely geographical context its nowadays has been extended and can be used in multiple cases including population genetics.
What i did:
- I downloaded the program Barrier. Then i calculated centroids of my sampling locations and loaded everything into Barrier
- I then bootstrapped my Microsatellite-data 100x times (Chao et al. 2008) and created pairwise-distance matrices using the D index introduced by Jost (Jost 2008). So i end up with a list of 100 “dist” objects in R.
- I saved the list of dist-matrices into a txt-file and loaded it into Barrier to conduct a barrier significance test (Using replicates of the same matrix).
As you can see especially Point 4 (red arrow -> a national park in central Tanzania) seems to be more genetically isolated than the other sampling locations (the strength of the red lines represent contribution of the bootstrapped barriers). However the whole result was a bit disappointing for me (no really clear barrier) and additional analysis using the popular program structure as well as traditional population differentiation indices like Fst, G’st and Jost’D revealed that the population structure of elephants is indeed quite complex. Still i really like this technique and I’m curious about other use-cases.
In this case I used the very simple and straight-forward program barrier by Manni et al (2004) to produce the above graphic. However the popular R-package adegenet (Jombart 2008) also has a method – monmonier – for genetic barrier detection. See the R graphical website for an example. Still it would be great to see such feature in a real GIS-environment like GRASS or QGIS. Has anyone heard of any extensions or plugins that add landscape genetic methodologies to these programs? I don’t have much time to code right now, but basically all it needs are some point coordinates (from a point layer) and a matrix displaying distance between the points. Great stuff 🙂
References:
- Monmonier, M. (1973) Maximum-difference barriers: an alternative numerical regionalization method. Geographic Analysis, 3, 245–261.
- Manni,F., Guérard, E. & Heyer, E. (2004). Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by “Monmonier’s algorithm”. Human Biology, 76(2): 173-190.
- Jombart T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405
- Chao, A. et al. (2008). A Two-Stage probabilistic approach to Multiple-Community similarity indices. Biometrics, 64:1178-1186
- Jost, L. (2008), GST and its relatives do not measure differentiation. Molecular Ecology, 17: 4015-4026.
Tags
adegenet africa barrier biodiversity biodiversity research biogeography birdlooker Cameroon conservation conservation biology conservation ecology crisis Deforestation dragonflies eastern arc mountains ecological database ecological networks ecology edge effects elephants forests fruit dispersal gbif General News GIS google maps habitat fragmentation Herakles Farms home-range land cover analysis landscape ecology landscape genetics landscape metrics land use lecos lines linux macroecology maps in r model nullmodel openjump ornithology Palm Oil palm oil plantations Phd photovoltaic plants plugin population differentiation PREDICTS protected planet publication python qgis qgis-plugin r-code raster raster statistics remote-sensing research river science scipy sextante snippet solar panel spatial overlaps statistics sustainability taxize taxonomy Tropical Forests unsustainable projects wmsRecent Posts
- New Paper: Local factors mediate the response of biodiversity to land use on two African mountains
- New paper: A first global assessment of remaining biodiversity intactness
- New publication: LecoS now with own reference
- Get credit for your work!
- To all editors, reviewers and authors: time to move on regarding land sparing
Categories
Curlew on Twitter
My TweetsBlogs I Follow
- Quantitative analysis meeting group at the University of Sussex
- Sussex Research Hive
- Small Pond Science
- Landscape Ecology 2.0
- nexus
- Amy Whitehead's Research
- Guy Abel
- Michael McCarthy's Research
- The Rostrum
- marionpfeifer
- Dynamic Ecology
- The Molecular Ecologist
- The Solitary Ecologist
- metvurst
- A Birder´s Blog
- BIOFRAG - Biodiversity responses to habitat degradation & fragmentation
- Trust Me, I'm a Geographer
- Data Analysis Visually Enforced
- Duncan Golicher's weblog
- Daniel J. Hocking