Rarefaction Techniques

Question 1

What does classic rarefaction do?

Answer 1

Estimates true species richness from incomplete fossil record

Question 2

How do you perform a classic rarefaction?

Answer 2

Put the total number of taxa into time or locality bins and use the most complete assemblage to infer total number of individuals which might be present.

Question 3

What formula is used for classic rarefaction?

Answer 3

Hurlbert Formula.

Question 4

What does a rarefaction curve show?

Answer 4

How species richness accumulates with increasing sampling effort

Question 5

What R package is used to implement classic rarefaction?

Answer 5

Vegan

Question 6

What is the issue with classic rarefaction when looking at morphological diversity?

Answer 6

Greater fossil record completeness might preserve more features for comparision.

Question 7

Explain the core premise of new suggested rarefaction technique

Answer 7

Using fossil completness and morphological disparity instead of species richness rarefaction

Question 8

What coefficient can be modified or employed for proposed completeness rarefaction?

Answer 8

Gower’s similarity coefficient

Question 9

What is Gower’s similarity coefficient?

Answer 9

The number of shared applicable characters divided by the total number of characters where at least one is applicable to organisms being studied.

Question 10

What is the result format of Gower’s similarity coefficient?

Answer 10

Numbers 0-1 with identical species being 1 and 0 implying zero similarity

Question 11

Explain your new coefficient proposal

Answer 11

Take the total number of characters that are shared by the two species and divide by the shared charaters + total different characters that are present in both.

Question 12

What is Shareholder Quorum Subsampling?

Answer 12

Coverage based rarefaction

Question 13

What is another way to describe coverage based rarefaction?

Answer 13

Shareholder Quorum subsampling

Question 14

How does coverage based rarefaction work?

Answer 14

Good coverage is when there are very few species known from an isolated occurrence. Poor coverage has many species known only from holotype.

Question 15

What is TRiPS?

Answer 15

True Richness estimated by poission sampling

Question 16

What is the principle of Poisson sampling?

Answer 16

Constant probability. Probability of a species being sampled remains constant in a temporal span.

Question 17

What is a TRiPS richness estimation?

Answer 17

Inference of the number of species that must have existed to result in the number of fossils found

Question 18

How do you carry out a TRiPS assessment?

Answer 18

Input the occurrence data, estimate the sampling rate for the time interval, calculate true species richness.

Question 19

What is the estimated sampling rate in a TRiPS analysis?

Answer 19

Average number of fossils per species per interval.

Question 20

What is the output from MrBayes?

Answer 20

Cladogram with the posterior probabilities for each split.

Question 21

What programmes can the MrBayes file output be read by?

Answer 21

FigTree, TreeView and Mesquite

Question 22

What data types can MrBayes process?

Answer 22

DNA, RNA, Protein, binary, 0-9 morphology data.

Question 23

How do you specify the evolutionary model in MrBayes?

Answer 23

lset for structure of model. Prset for prior probability distributions.

Question 24

What model in MrBayes should be used for fossil data?

Answer 24

Mkv

Question 25

What is Tip Dating in MrBayes

Answer 25

Time Calibration

Question 26

How do you use Tip Dating in MrBayes?

Answer 26

Use fossilised birth-death process (FBD) model for tree prior.

Question 27

What is more resilliant to gaps in the fossil reccord than speciation and extinction events?

Answer 27

Functional trait evolution and morphological disparity

Question 28

How do you build a morphometric dataset?

Answer 28

Use 2D standardised photos or 3D photogrammetry or CT scans to plot discrete landmarks.

Question 29

What software can be used to digitise landmarks in morphometrics?

Answer 29

tpsDig or ImageJ

Question 30

What is procrustes superimposition?

Answer 30

used to align and normalise shapes in morphometrics

Question 31

What tools can be used to normalise shapes in morphometrics?

Answer 31

MorphoJ or the R packages geomorph or morpho.

Question 32

Outline the steps for a morphometrics study.

Answer 32

Aquire images or 3d scans, digitise the landmarks, organise in clean data table, perform shape alignement (procrustes), visualise.

Question 33

What does a principle component analysis do?

Answer 33

help to reduce dimensionality to reveal patterns in morphological innovation (morphometrics).

Question 34

Which R package is used for time-calibrated phylogeny?

Answer 34

Paleotree

Question 35

Which lineages could be studied to indicate whether there was divergence in pan-Amniota prior to synapsids and sauropsids diverging?

Answer 35

Temnospondyls, lepospondyls, embolmeres, anthracosaurs and other reptilomorphs.

Question 36

What did Cavin & Forey suggest about the use of ghost lineages to make inferences?

Answer 36

During rapid speciation, ghost lineages would be short.

Question 37

What habitat shift is thought to have prompted reliance on lungs instead of gills?

Answer 37

marine to freshwater

Question 38

What are trait-dependent diversification models?

Answer 38

Designed to examine how specific traits influence the rates of speciation and extinction.

Question 39

How can we examine how specific traits influence speciation and extinction?

Answer 39

Trait-dependent diversification models

Question 40

List the 4 types of trait-dependent diversification models.

Answer 40

binary state (BiSSE), Multistate (MuSSE), Quantative (QuaMMSE), Hidden state (HiSSE).

Question 41

What R package can be used to identify innovative traits from trait-dependent diversification models?

Answer 41

Diversitree

Question 42

What does BiSSE stand for?

Answer 42

Binary state speciation and extinction (trait dependent diversification models).

Question 43

How can you use ghost lineages to make inferences about apparent peaks in biodiversity?

Answer 43

Genuine peaks in biodiversity are accompanied by short ghost lineages. Baseline ghost lineages suggest sampling bias rather than true biodiversity increase.

Question 44

If a more complete fossil reccord suggests higher rates of diversification than an incomplete fossil record, what does that imply?

Answer 44

Potential bias.

Question 45

If diversity trends remain constant across fossil assemblages with different levels of completeness - what does that imply?

Answer 45

That relaible inference can be made from even a patchy reccord.

Question 46

What could be used as a proxy clade for amniotes and/or tetrapods?

Answer 46

For amniotes, the temnospondyls, for all tetrapods it would need to be other terrestrial taxa such as arthropods.

Question 47

What is the R package Phytools for?

Answer 47

Phylogenetic tree manipulation and visualisation. Trait evolution and ancestral state reconstruction. Phylomorphospace plotting

Question 48

What is a phylogenetic generalised least square?

Answer 48

uses knowledge of phylogenetic relationships to produce an estimate of expected covariance in cross-species data.

Question 49

What is meant by higher covariance?

Answer 49

Traits are expected to be more similar (have higher covariance) between species that are more closely related on a phylogenetic tree

Question 50

How do you conduct a phylogenetic generalised least square in R?

Answer 50

Use a phylogenetic tree to model the correlation structure between species due to shared ancestry

Question 51

Explain the difference between Parsimony and Bayesian approaches

Answer 51

Parsimony aims to find the simplest tree that requires the fewest evolutionary changes, Bayesian methods utilise probabilistic models of evolution and incorporate prior information to estimate the most likely tree topology