Exercise 2.2

The Molecular Clock and Dating of the Divergence of Metazoan Lineages

(This exercise is based on Wray, G. A., J. S. Levinton, and L. H. Shapiro. 1996. Molecular evidence for deep Precambrian divergences among metazoan phyla. Science 274: 568–573.)

(Note: The reference above links directly to the article on the journal’s website. In order to access the full text of the article, you may need to be on your institution’s network [or logged in remotely], so that you can use your institution’s access privileges.)

INTRODUCTION

When did metazoans (multicellular animals) first arise? The fossil record is spotty before the Cambrian explosion (circa 545 million years ago) and absent prior to 600 million years ago, yet there is substantial diversity of body forms by the middle of the Cambrian period. Did this diversification occur in just tens of millions of years, or had diversified metazoan lineages existed long before the Cambrian?

A provocative, early molecular study by Greg Wray and colleagues provided support to the notion that metazoans originated and diversified long before their appearance in the fossil record. The researchers examined the extent of divergence between existing lineages that have established dates of divergence to calculate rates of divergence. Then, assuming a molecular clock, the researchers extrapolated an estimated time for the divergence of the major metazoan lineages.

QUESTIONS

Use the information in Figure 1 to answer questions 1 through 3.

 

Figure 1 The graphs show plots for eight genes. In each plot, the x-axis represents time (in millions of years) and the y-axis represents genetic divergence. The dots represent divergences of lineages with known divergence times. The shaded regions represent the range of genetic divergences between invertebrates and vertebrates (y-axis) and the inferred range of divergence times between invertebrates and vertebrates (x-axis).

Question 1. What is the most recent estimated time of divergence between invertebrates and vertebrates, based on the ATPase 6 gene? What is the most distant?

 

Question 2. Based on the most recent plausible age, which gene gives the most recent time for the divergence between invertebrates and vertebrates? According to that estimate, how long ago was this?

 

Question 3. Based on the most distant plausible age, which gene gives the most distant time for the divergence between invertebrates and vertebrates? According to that estimate, how long ago was this?

 

Use the information in Figure 2 to answer questions 4 through 6.

 

Figure 2 Estimated times of divergence for lineages of animals, based on the average of the genes used in this study.

 

Question 4. Which two of the lineages presented diverged most recently? How long ago did they diverge (based on the midpoint of the range)?

 

Question 5. Based on the midpoint of the range, about how long ago did protostomes and deuterostomes diverge?

 

Question 6. Based on these results, what can you conclude about the origins of metazoans?

 

Use the information in Figure 3 to answer questions 7 and 8.

 

Figure 3 One concern about the molecular clock is heterogeneity of rates among lineages. Such heterogeneity could call into question the validity of molecular clock estimates. A common way to test for rate heterogeneity is the relative rates test.

 

Question 7. If there is no rate heterogeneity, what would one expect for the amount of divergence between an invertebrate and a nonmetazoan and a vertebrate and the same nonmetazoan?

 

Question 8. If a gene evolves faster in vertebrates than it does in invertebrates, what would one expect for the amount of divergence between an invertebrate and a nonmetazoan and a vertebrate and the same nonmetazoan?

 

Use the information in Table 1 to answer questions 9 and 10.

 

Reference taxon

Vertebrates

 

Invertebrates

n

Mean

SEM

 

n

Mean

SEM

 

ATPase 6

         

 

Metaphyte

12

1.54

0.034

 

10

1.60

0.058

Yeast

 

1.68

0.030

   

1.83

0.087

Eubacterium

 

1.65

0.030

   

1.82

0.039

 

Cytochrome c

Metaphyte

27

0.50

0.006

 

14

0.44

0.008

Fungus

 

0.52

0.004

   

0.42

0.003

Eubacterium

 

0.79

0.008

   

0.75

0.011

 

Cytochrome oxidase I

Metaphyte

16

0.43

0.003

 

10

0.40

0.007

Fungus

 

0.45

0.003

   

0.42

0.006

Eubacterium

 

0.47

0.003

   

0.49

0.008

 

Cytochrome oxidase II

Metaphyte

26

0.74

0.007

 

22

0.76

0.016

Yeast

 

0.95

0.016

   

0.86

0.017

Eubacterium

 

1.22

0.021

   

1.17

0.017

 

Hemoglobin

Metaphyte

49

4.66

0.084

 

16

3.21

0.083

Protist

 

5.34

0.084

   

6.29

0.475

Eubacterium

 

3.83

0.063

   

3.83

0.155

 

NADH 1

Metaphyte

14

0.76

0.013

 

13

0.91

0.028

Slime mold

 

0.81

0.010

   

0.94

0.024

Eubacterium

 

0.96

0.013

   

1.13

0.022

 

18S rRNA

Metaphyte

8

0.26

0.021

 

43

0.32

0.003

Fungus

 

0.26

0.018

   

0.32

0.003

Alga

0.30

0.018

 

 

0.34

0.008

Table 1 The extent of genetic divergence for seven genes between vertebrates and the reference taxon and invertebrates and the reference taxon. (Metaphytes are multicellular plants.)

 

Question 9. Compare the amount of divergence genes between vertebrates and the reference taxon and invertebrates and the reference taxon for each of the genes and for each of the reference taxa. Are there any genes for which the divergence to invertebrates was markedly (1.5 times or more) greater or markedly less than the divergence to vertebrates?

 

Question 10. Did NADH1 evolve faster in invertebrates or in vertebrates?