37  Included Data Sets

The content of this book includes several data sets that come with the gstudio and popgraph libraries. Here is a brief overview of those data sets with references to the manuscripts from which they were analyzed.

37.1 The Sonoran desert bark beetle, Araptus attenuata

knitr::include_graphics("media/araptus.png")

Arapatus attenuatus is a bark beetle endemic to the Sonoran desert. It is known only from the senescing stems of the desert plant, Euphorbia lomelii (syn Pedilanthus macrocarpus). Samples for this data set were collected from 39 populations throughout the species range.

library(leaflet)
library(gstudio)
data(arapat)
coords <- strata_coordinates(arapat)
coords |>
  leaflet() |>
  addTiles() |>
  addMarkers(~Longitude, ~Latitude, popup=~Stratum)

Figure 37.1: Sampling locales for the arapat data set.

37.1.1 Nuclear Markers

The markers in the arapat data set consist of eight polymorphic and codominant nuclear markers.

library(gstudio)
data(arapat)
column_class( arapat, "locus")

[1] "LTRS" "WNT"  "EN"   "EF"   "ZMP"  "AML"  "ATPS" "MP20"

These markers span a range of allelic diversity and richness.

df <- merge( genetic_diversity(arapat,mode="A"), genetic_diversity(arapat,mode="He"))
df <- merge( df, genetic_diversity(arapat, mode="Ae"))
knitr::kable(df,align=c("l","c","c","c"),digits=3)

Locus	A	He	Ae
AML	13	0.829	5.861
ATPS	10	0.719	3.563
EF	2	0.436	1.774
EN	5	0.449	1.815
LTRS	2	0.499	1.996
MP20	19	0.819	5.512
WNT	5	0.653	2.880
ZMP	2	0.339	1.514

37.1.2 Methylation Markers

In addition to codominant nuclear markers, an msAFLP analysis was performed on the major clade and paired sequence and \(C_pG\) methylation markers were derived.

37.2 The Flowering Dogwood Cornus florida

knitr::include_graphics("media/dogwood_flower.png",)

Figure 37.2: Inflorescence for flowering dogwood with conspicuous showy bracts and many small flowers in the center.

Flowering dogwood is an ubiquitous feature of eastern north american forests.

The data set contains five microsatellite loci.

data(cornus)
column_class( cornus, "locus")

[1] "Cf.G8"  "Cf.H18" "Cf.N5"  "Cf.N10" "Cf.O5" 

of roughly equal genetic diversity.

df <- merge( genetic_diversity(cornus,mode="A"), genetic_diversity(cornus,mode="He"))
df <- merge( df, genetic_diversity(cornus, mode="Ae"))
knitr::kable(df,align=c("l","c","c","c"),digits=3)

Locus	A	He	Ae
Cf.G8	28	0.931	14.482
Cf.H18	20	0.925	13.325
Cf.N10	18	0.903	10.349
Cf.N5	11	0.453	1.827
Cf.O5	15	0.860	7.146