Introduction

This lecture provides a brief introduction to the field of landscape genetics, what it is, and what it isn’t. I provide an overview of the field and some of the main conceptual ideas we will be going over during this activity as well as the logistics of the course. The activity for this topic will mostly focus on making sure your computer is set up properly, the correct set of packages are installed, and you have downloaded the data for the entire course.

Background

For this topic, we are going to start by looking at the following papers from the literature.

Dyer R, 2015. Is there such a thing as as landscape genetics. Molecular Ecology, 24 3518-3528.

This manuscript examines the body of literature pertaining to landscape genetics by lexicographically analyzing every published manuscript and comparing the way researchers introduce their work (Introduction) and perform the analyses (Methods) to determine if the current approaches are truly a mixture of landscape ecology and population genetics or is something more emergent. From this, the following inferences were gained.

  1. Focus of Research

composition of focus

  1. Overlap of Context and Implementation

Ovderlap of Landscape Ecology, Population Genetics, and Landscape Genetics

  1. Nascent partitions.

clustering

Lecture Content

For this topic, I will be spending a bit of time covering the broad foundational theory as well as giving some concrete examples. To do so, you have access to the following slide set1.

The content of the slides are based upon a larger narrative document, which is embedded below2. You can use this narrative document as a general work-flow for this topic. It has all the code necessary to perform the basic operations covered in the talk and reinforced in the activity included below.

Supplemental Materials

In addition to this lecture content, you may find the following information helpful as you go though these exercises.
- Cheatsheet 1
- Cheatsheet 2 - Blogpost

Activity

Here is the activity associated with this particular project


  1. This is a presentation writing in Xaringan, an RMarkdown presentation type. It is an active embed in this page (and hosted elsewhere). It can be extracted my clicking on the slide and hitting the c key on your keyboard—to clone it into its own window (more commands available using ? for viewing).↩︎

  2. This is an R-Notebook document you can download directly to your computer. To do so, pull down the Code menu on the top right and right-click the Download RMD option and save it to your Landscape Genetics Project folder.↩︎

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