# Analytical Paleobiology Short Course: Diversity estimation and multivariate methods

Jessica Blois and Michal Kowalewski
1 - 4 August 2018

### Day 1 Overview

(Led by Jessica)

- Introduction to material
  - Data types
  - Types of diversity
  - Challenges
- Estimating richness
- Estimating diversity and evenness
- SAD, RAD

### Day 2 Overview

(Led by Michal and Jessica)

- Intro: similarity vs dissimilarity (Michal)
- Diversity partitioning and beta diversity (Michal)
- Cluster analysis (Jessica)
- Example: Generalized dissimilarity modeling (Jessica)

### Day 3 Overview

(Led mostly by Michal)

- Intro to matrix algebra, PCA (Michal)
- PCO, CA/DCA, NMDS (Michal)
- Canonical Methods: CVA, RDA, CCA, CAP (Michal)
- Multivariate tests (as time allows, Michal)
- Example: Functional data (Jessica)

### Day 4 Overview

- Spillover
- Practicum

### Multivariate Techniques

Major Goals

- Summarize complex patterns within and across assemblages
- Determine dominant drivers/correlates of those patterns

### Multivariate Techniques

Main Data Types

- Assemblage information for a single site
- Species* x site matrices
  - Occurrence or abundance of species at each site
  - *Species here is a surrogate for any unit of taxonomic information

Auxiliary Data Types

- Attributes of sites: Location, habitat, climate
- Attributes of species: Functional type, phylogenetic information

### What do we mean by diversity?

Diversity is an often vague word that describes how individuals are partitioned into species within sites and across the landscape.

We recognize three types of diversity:

- gamma: the overall diversity of the landscape, which can be partitioned into:
  - alpha: the diversity of individual locations within that landscape
  - beta: how diversity changes across the landscape

Today's exercises will focus on alpha diversity, and we'll focus on beta diversity tomorrow.

### Overview of estimating richness and diversity

Fundamental goal:

- Describe how and why assemblages change across space and time

First step:

- Estimate the following:
  - Who / how many species are present in an assemblage?
  - How do we adequately characterize the structure of assemblages?

### Overview of estimating richness and diversity

Aspects of assemblage structure

- Number of species (ie, richness)
- Distribution of abundance across species (Evenness, dominance measures)
- Types/attributes of species

### Challenges of estimating richness and diversity

- Difficult to estimate the true number of species present in a location for many groups and habitats
  - This is even more challenging in the fossil record due to preservation and taphonomic issues that alter what information is preserved.
- Difficult to make apples-to-apples comparisons across space or through time
  - Uneven sampling effort
  - Different deposition/preservation contexts