Genetic Diversity Activity

Overview

In this activity, we will be examining diversity in the Sonoran desert bark beetle, Araptus attenuatus, included in the gstudio library.

library( tidyverse )

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──

✓ ggplot2 3.3.5     ✓ purrr   0.3.4
✓ tibble  3.1.6     ✓ dplyr   1.0.7
✓ tidyr   1.1.4     ✓ stringr 1.4.0
✓ readr   2.1.1     ✓ forcats 0.5.1

── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()

library( gstudio )
data( arapat )
summary( arapat )

      Species      Cluster      Population        ID         Latitude    
 Cape     : 75   CBP-C :150   32     : 19   101_10A:  1   Min.   :23.08  
 Mainland : 36   NBP-C : 84   75     : 11   101_1A :  1   1st Qu.:24.59  
 Peninsula:252   SBP-C : 18   Const  : 11   101_2A :  1   Median :26.25  
                 SCBP-A: 75   12     : 10   101_3A :  1   Mean   :26.25  
                 SON-B : 36   153    : 10   101_4A :  1   3rd Qu.:27.53  
                              157    : 10   101_5A :  1   Max.   :29.33  
                              (Other):292   (Other):357                  
   Longitude          LTRS          WNT            EN           EF     
 Min.   :-114.3   01:01 :147   03:03  :108   01:01  :225   01:01 :219  
 1st Qu.:-113.0   01:02 : 86   01:01  : 82   01:02  : 52   01:02 : 52  
 Median :-111.5   02:02 :130   01:03  : 77   02:02  : 38   02:02 : 90  
 Mean   :-111.7                02:02  : 62   03:03  : 22   NA's  :  2  
 3rd Qu.:-110.5                03:04  :  8   01:03  :  7               
 Max.   :-109.1                (Other): 15   (Other): 16               
                               NA's   : 11   NA's   :  3               
     ZMP           AML           ATPS          MP20    
 01:01 : 46   08:08  : 51   05:05  :155   05:07  : 64  
 01:02 : 51   07:07  : 42   03:03  : 69   07:07  : 53  
 02:02 :233   07:08  : 42   09:09  : 66   18:18  : 52  
 NA's  : 33   04:04  : 41   02:02  : 30   05:05  : 48  
              07:09  : 22   07:09  : 14   05:06  : 22  
              (Other):142   08:08  :  9   (Other):119  
              NA's   : 23   (Other): 20   NA's   :  5  

Activity Questions

Overview

In this activity, we will be examining diversity in the Sonoran desert bark beetle, Araptus attenuatus, included in the gstudio library.

library( tidyverse )
library( gstudio )
data( arapat )
summary( arapat )

      Species      Cluster      Population        ID         Latitude    
 Cape     : 75   CBP-C :150   32     : 19   101_10A:  1   Min.   :23.08  
 Mainland : 36   NBP-C : 84   75     : 11   101_1A :  1   1st Qu.:24.59  
 Peninsula:252   SBP-C : 18   Const  : 11   101_2A :  1   Median :26.25  
                 SCBP-A: 75   12     : 10   101_3A :  1   Mean   :26.25  
                 SON-B : 36   153    : 10   101_4A :  1   3rd Qu.:27.53  
                              157    : 10   101_5A :  1   Max.   :29.33  
                              (Other):292   (Other):357                  
   Longitude          LTRS          WNT            EN           EF     
 Min.   :-114.3   01:01 :147   03:03  :108   01:01  :225   01:01 :219  
 1st Qu.:-113.0   01:02 : 86   01:01  : 82   01:02  : 52   01:02 : 52  
 Median :-111.5   02:02 :130   01:03  : 77   02:02  : 38   02:02 : 90  
 Mean   :-111.7                02:02  : 62   03:03  : 22   NA's  :  2  
 3rd Qu.:-110.5                03:04  :  8   01:03  :  7               
 Max.   :-109.1                (Other): 15   (Other): 16               
                               NA's   : 11   NA's   :  3               
     ZMP           AML           ATPS          MP20    
 01:01 : 46   08:08  : 51   05:05  :155   05:07  : 64  
 01:02 : 51   07:07  : 42   03:03  : 69   07:07  : 53  
 02:02 :233   07:08  : 42   09:09  : 66   18:18  : 52  
 NA's  : 33   04:04  : 41   02:02  : 30   05:05  : 48  
              07:09  : 22   07:09  : 14   05:06  : 22  
              (Other):142   08:08  :  9   (Other):119  
              NA's   : 23   (Other): 20   NA's   :  5  

Activity Questions

1. Create a leaflet map showing the levels of effective allelic diversity (\(A_e\)) as bars by Populations for loci \(LTRS\), \(WNT\), and \(EN\).

2. Estimate effective allelic diversity for all populations of the individuals where Species == Peninsula at the locus MP20. Is there the same indication of “Allele Surfing” in the beetle as shown for its host plant? How do you interpret this pattern?

3. Is there more effective allelic diversity in the Cape or Peninsula groupings?

4. Is there a correlation between genetic effective allelic diversity (\(A_e\)) and genotypic diversity (\(H_e\)) in these data? Do you expect there to be one? Why?