October 21, 2009
by Tonje Stolpestad (tstolpes)

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
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

State of the Code:

October 20, 2009
by Tonje Stolpestad (tstolpes)

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.

Plans for where we want to be by next week

October 14, 2009
by Tonje Stolpestad (tstolpes)


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.


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

Notes from class

October 7, 2009
by Tonje Stolpestad (tstolpes)

Land corridors

Are they good?

Recent, last few weeks

Use what they are using and see if we can reproduce

Conservation biology

Wednesday presentation of code

October 7, 2009
by Tonje Stolpestad (tstolpes)


  • 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

Class meeting Sept 30

September 30, 2009
by Tonje Stolpestad (tstolpes)

Processing on the cluster

Talk to the cluster people

There have been some problems in the past

Igor people

Ask Lee for a copy of the bridge thingy he showed



Talk to the data analysis

Probably write in .txt

Modeling populations with electrical circuits

Figure out a specific entry point into the litterature

Fill in the Blahs

Possible questions to answer.

September 27, 2009
by Tonje Stolpestad (tstolpes)

-by Tonje

Is using dna evidence (number of neutural mutations) a valid way of dating populations?

  • Lee’s model from wolf paper says no
  • Does geography change this?
  • How does this respond to a changing geography (islands with changing bridges etc.)
  • How would this respond to a disaster (flood, famine etc)? Will we loose important information? (My got feeling is yes)
  • Who would care?

Will landbridges (over roads etc) and wildlife parks (which sort of functions as islands) affect species? If so how? Will we see a string founder effect here? Landscape Paper

  • It feels like this will be easy to answer, my gut instinct says yes.  Might be possible to tie into the previous question.
  • Is it already answered?
  • Model  idea: two areas seperated by one or several roads. Compare what happens when you put land bridges in.
  • Who would care?  The WCS and WCS – living landscapes, other people who deal with wildlife conservation in relation to roads etc?
  • We have chosen to focus on this ( Sun. Sept 27 09)

Other places to present/publish?

  • Smith Colllaborations(“Celebrating Collaborations: Students and Faculty Working Together”). Small, poster and/or powerpoint presentations of research done by students. Will need to check of they will accept this as it is not completely Smith based. Is in the spring.

More ideas on simulations

September 24, 2009
by Tonje Stolpestad (tstolpes)

-by Tonje

last night I was bouncing ideas of my two biology major room mates and got a crash course in genetics.  Here are two things that jumped out at me as easy to model.

Model currently being worked on:

  • has two gene arrays instead of one.
  • color can be one of 4 colors (0,75, 150, 225)
  • Darker color is always dominant.
  • An offspring gets one of the gene array entires from each parent
  • It is random if the gene from a parent is the dominant or the non dominant gene

Second model: co dominace

  • the offspring’s color code is the average of the parents

Todo next: debug these models and do more research of what is in fact goin on here, build in color for a better visual effect (3 genes, R-G-B, darker always dominant a marble has geneBlue1, geneBlue2, geneRed1 etc.  Which of the pair the offspring gets from each parent is random)

If I am messing up here, please tell m.

Notes from class meeting 09/23/09

September 23, 2009
by Tonje Stolpestad (tstolpes)

-by Tonje


Add in obstacles, islands etc

Local made up

Look up a more formal

Ecology how do people measure something like spatial diversity

This mutation is good if you are in an area where people can see you

Hybrid zones

How do you measure diversity in one area vs. another

Who is going to care?




Founder vs. adaptive

What is the point the sim can show

First sim

Use dna evidence to date populations

Add this to founder

What kind of land bridges

Landscape species model

GIS indicator species


Amazon test patches


Where are they not doing mathematical

Simple simulation replication

September 23, 2009
by Tonje Stolpestad (tstolpes)

-by Tonje

Notes for making a replica of the second simulation in “What is a Wolf?

marble lives:

  • A marble dies after 250 timesteps
  • Everytime a marble collide with another it ages 10 steps
  • 1/150 chance of producing offspring
  • Two conditions
  1. Asexual reproduction, gene copied from parent
  2. Mating, gene copied from either a  parent or mate (1/2 chance)
  • mutation happens 1/100