Dynamics of genetic information

Two week goals:

— Find exactly what we’re measuring: unless we get a really different, concrete parameter, we’ll probably measuring average number of regions visited vs. bridge width

— Decide on a single base version of our map w/o bridges

— Email the Umass prof that did that paper on corridors. sdestef@forwild.umass.edu

— By the end of two weeks, we should be able to have a guess at weather width and (maybe) number matters. Data analysis will be in progress

I think I already have a base version I like, 7_3. It’s 1000 by 700 pixels, has a collision rate of 40% per step on the road, road/non-conservation area width of 200, max age of 600, and max population of 100.

Base version has no bridges, I have 10 sub-versions with bridges increasing in width by 10 per version. I’ll post 7_3 and spare everyone 7_3_1 through 7_3_10. Soon I’ll have versions with multiple bridges as well.

greyscale_7_31

Also, check out these maps of actual wildlife corridors. The first is for Jaguars, the second is a general corridor in Australia:

http://www.panthera.org/images/JaguarRangeSites_000.jpg

http://newcastleonhunter.com/mediapix/2009/bouddi-kincumber-wildlife-corridor.jpg

There seems to be a discussion going on if the width of corridors matters or not. I found  several papers that mentioned that it didn’t while Charles Ross found papers that said that it did.

What we’ll end up with is either a yes or a no on if our model acts the way nature does (also depends on which idea we are following). If the answer is yes we can make  some predictions of if several smaller corridors will work better  (if width doesn’t matter it should). If the answer is no then we can work on figuring out why it does not act like nature and what we can do to model it better.

http://www.springerlink.com/content/x88792055540187m/

Abstract:

An obvious consequence of exurban land development is fragmentation of natural areas. Fragmentation leaves patches of habitat of various sizes, which can become increasingly isolated as development continues. A compelling approach to mitigation is the creation of corridors. Corridors in their simplest form are strips of habitat that connect patches and allow for wildlife movements. Intuitively, corridors make sense and land planners and managers often find them useful in land conservation. However, do wildlife corridors perform as expected? Do they work for all species? And how should they be configured (e.g., width, length, placement)? This chapter addresses these and other questions related to wildlife corridors and exurban land development.

Written by a prof at Umass

Applet (does not feature the data collection)

Where we are:

The simulation is back to greyscale. The current version, greyscale_7, has 3 regions that are all attatched. Each region are attached to both of the others. The regions all have an identifying tag, 1 for the left region, 2 for top right, 3 for bottom right and 0 for the road and bridges.  It starts with 4 circles, all in region 1. Each circle is given a unique id tag. We are recording id, parent, generation (parent’s generation +1), color, birthplace, death place, time of death, and list of regions it has been in.

Download:

greyscale_7

algerian-481

(Algerian needs to be in a folder called data that is in the same folder as greyscale_7)

Where to go from here:

Since we are focusing on the width of the bridge we want to make several simulations with different widths of the bridge (One idea is how does several thinner bridges with a combined width x compare to one big bridge with width x). We can also change the shape of the bridge by making the road wider. A last thing to model is the patch bridge. Instead of a simple bridge like the ones we have in our current model we have several smaller patches that are not quite connected but together form a bridge.

Identifying future research needs in landscape ecology: where to from here.

Landscape genetics is an emerging interdisciplinary field that combines methods and concepts from population genetics, landscape ecology, and spatial statistics. The interest in landscape genetics is steadily increasing, and the field is evolving rapidly. We here outline four major challenges for future landscape genetic research that were identified during an international landscape genetics workshop. These challenges include (1) the identification of appropriate spatial and temporal scales; (2) current analytical limitations; (3) the expansion of the current focus in landscape genetics; and (4) interdisciplinary communication and education. Addressing these research challenges will greatly improve landscape genetic applications, and positively contribute to the future growth of this promising field.

A simulation framework for modeling anthropogenic distubances in habitat networks

Anthropogenic disturbances, like roads, increase the landscape fragmentation and affect wildlife migration and biodiversity. Such disturbances often prevent migration of wildlife due to increased barriers and mortality effects.

The aim of our simulation based approach is to assess the landscape permeability considering anthropogenic disturbances. The developed framework SimapD imposes an abstract view of a habitat network, based on an undirected graph. The simulation is done by an individual-oriented approach, where individuals explore the idealized network. Based on the information gained during the simulation, an overall network permeability index is calculated, which can be used to compare different scenarios of landscape development. Disturbances are represented by sub-models, from which appropriate resistance and mortality rates can be deduced. In this paper this is demonstrated by the construction of a fuzzy road kill model for the federal state of Baden-Wuerttemberg, Germany. The utilization of the network permeability index and a comparison to other fragmentation measures is shown by an exemplary application.

Movement Corridors: Conservation Bargains or Poor Investments
Abstract:
Corridors for movement of organisms between refuges are confounded with corridors designed for other functions, obscuring an assessment of cost-effectiveness. The rationales for movement corridors are (1) to lower extinction rate in the sense of the equilibrium theory, (2) to lessen demographic stochasticity, (3) to stem inbreeding depression, and (4) to fulfill an inherent need for movement. There is a paucity of data showing how corridors are used and whether this use lessens extinction by solving these problems. Small, isolated populations need not be doomed to quick extinction from endogenous forces such as inbreeding depression or demographic stochasticity, if their habitats are protected from humans. In specific instances, corridors could have biological disadvantages. Corridor proposals cannot be adequately judged generically. In spite of weak theoretical and empirical bases, numerous movement corridor projects are planned. In the State of Florida, multi-million-dollar corridor proposals are unsupported by data on which species might use the corridors and to what effect. Similarly, plans for massive corridor networks to counter extinction caused by global warming are weakly supported. Alternative approaches not mutually exclusive of corridors might be more effective, but such a judgment cannot be made without a cost-benefit analysis.

Smith College have access to this publication

Other papers to look at

Do habitat corridors provide connectivity

Evaluating the effectiveness of corridors: a genetic approach

Ecological Principles for the Design of Wildlife Corridors

the area have been divided into 4 regions.

For each marble we are recording  the following: id, generation, parent, birthplace, color, deathplace,  time of death and tag array (which regions this marble has visited)

Last details to finish up before tomorrow:

turn back to grey scale.

Tonje:

Have a working simulation with the new variables, 3 areas, tags for areas and restart if possible.

Contact Charles Ross and Smith profs. and hear their input on the idea.

Comment code and post it here.

Mike:

Post a blurb and links to the relevant papers read so far.

Land corridors

Are they good?

Recent, last few weeks

Use what they are using and see if we can reproduce

Conservation biology

Demo

• Population seperated by a road
• Population seperated by road with bridge

Notes about them

• There is a fence around the road. Each marble has a chance of jumping the fence(1/10), then a chance of getting hit by a car(1/20).
• Data collection: The data is collected into a .txt file. Current variables being collected are birthplace, deathplace, time of death and color.

Future development

• Collect information on who each marble’s parents are.
• Start looking  at the collected data (with Stata?)
• Find and use more realistic numbers for jumping and getting hit by a car