Clocks and Rocks

library(evolved)

The fossil record:

Here we will use data on fossilized organism, which we call “fossil occurrences”. the data was originally obtained from the Paleobiology database, a free-to-use resource that is the standard repository for such data and which has been used by hundreds or thousands of scientific research articles to study the history and dynamics of biodiversity in Deep Time.

data("mammals_fossil")
head(mammals_fossil)

##     phylum    class              order         family        genus
## 1 Chordata Mammalia       Artiodactyla        Bovidae     Brabovus
## 2 Chordata Mammalia            Cetacea   Protocetidae Georgiacetus
## 3 Chordata Mammalia            Sirenia  Prorastomidae    Pezosiren
## 4 Chordata Mammalia       Artiodactyla  Xiphodontidae     Dichodon
## 5 Chordata Mammalia          Carnivora        Canidae   Cynodictis
## 6 Chordata Mammalia NO_ORDER_SPECIFIED Nyctitheriidae   Saturninia
##                   species early_interval late_interval max_ma min_ma midpoint
## 1     Brabovus nanincisus       Pliocene                5.333  2.588   3.9605
## 2 Georgiacetus vogtlensis       Lutetian               47.800 41.300  44.5500
## 3      Pezosiren portelli       Lutetian               47.800 41.300  44.5500
## 4       Dichodon cervinus    Late Eocene               37.200 33.900  35.5500
## 5    Cynodictis lacustris    Late Eocene               37.200 33.900  35.5500
## 6     Saturninia gracilis    Late Eocene               37.200 33.900  35.5500
##         lng      lat
## 1  35.13000 -3.13000
## 2 -81.76056 33.14333
## 3 -77.91666 18.33333
## 4  -1.08560 50.67720
## 5  -1.08560 50.67720
## 6  -1.55000 50.66667

Students can use functions in the package to calculate the diversity of a certain taxonomic rank, and plot it through time.

To make it more fun, we will compare tow different taxonomic levels, and will plot them in a relative, log scale:

spDTT = calcFossilDivTT(mammals_fossil, tax.lvl = "species")
genusDTT = calcFossilDivTT(mammals_fossil, tax.lvl = "genus")
famDTT = calcFossilDivTT(mammals_fossil, tax.lvl = "family")

# And to allow comparisons, we will use relative richness:
plot(x=genusDTT$age, xlim = rev(range(genusDTT$age)),
     y=log(genusDTT$div)-log(max(genusDTT$div)), 
     xlab="Time (Million years ago)",
     ylab="Log relative diversity",
     type="l", col="blue", ylim=c(-7,0))

lines(x=famDTT$age,
     y=log(famDTT$div)-log(max(famDTT$div)), 
     col="red")

lines(x=spDTT$age,
     y=log(spDTT$div)-log(max(spDTT$div)), 
     col="black")

We can also visualize fossil records by running:

# Family-level:
plotRawFossilOccs(mammals_fossil, tax.lvl = "family", knitr = TRUE)

# Genus level:
plotRawFossilOccs(mammals_fossil, tax.lvl = "genus", knitr = TRUE)

# Species level:
plotRawFossilOccs(mammals_fossil, tax.lvl = "species", knitr = TRUE)

Are they different? how could we test? Hint: look at the column names of the fossil object:

colnames(mammals_fossil)

##  [1] "phylum"         "class"          "order"          "family"        
##  [5] "genus"          "species"        "early_interval" "late_interval" 
##  [9] "max_ma"         "min_ma"         "midpoint"       "lng"           
## [13] "lat"

Now, how complete is the record? We can use another dataset to explored this:

data("mammals_spp")

And see the proportion of living species with a fossil occurrence.

sum_w_fossil = sum(mammals_spp %in% mammals_fossil$species)

sum_w_fossil / length(mammals_spp)

## [1] 0.1978531

Students can for instance explore how this varies across different mammal groups, and which type of factors (e.g. biological, geological factors) seem to be influencing this the most.

Results from this dataset can also be compared (when relevant) with other fossil records:

data("trilob_fossil")
data("ammonoidea_fossil")
data("dinos_fossil")
data("birds_spp")

We can also compare the temporal trends of species number, for instance. To help in that way, we also provide biodiversity timeseries for more clades:

data("timeseries_fossil")
head(timeseries_fossil)

##   clade    source stem_age rel_time time_ma richness
## 1  anth Alroy2010      617  617.000   0.000     7138
## 2  anth Alroy2010      617  609.754   7.246     7246
## 3  anth Alroy2010      617  601.030  15.970    12673
## 4  anth Alroy2010      617  593.970  23.030     8485
## 5  anth Alroy2010      617  583.100  33.900    14475
## 6  anth Alroy2010      617  575.800  41.200     9280

It contains many fossil datasets, and we will only plot the first 4 of them

clades = unique(timeseries_fossil$clade)[1:4]

cols= c("#ffd353", "#ef8737", "#bb292c", "#62205f")

par(mfrow=c(2,2))
for(i in 1:length(clades)){
  aux = timeseries_fossil[timeseries_fossil$clade==clades[i], ]
  plot(aux$time_ma, log(aux$richness), col=cols[i], lwd=3,
       main=clades[i], type="l", frame.plot = F,
       xlab="Time (Mya)", ylab="Log richness",
       xlim=rev(range(aux$time_ma)))
}

Students can explore this other dataset, and compare it with the previously discussed ones. They can compare richness thought time, calculate statistics related to richness change. Explore factors (e.g. mass extinction) that might have affected some clades, among other learning problems.

But fossils are not the only way to explore the timescale of evolution. Below, we are going to show how some functions that use this type of data work.

Comparing molecular patterns

With other functions, students can also explore molecular sequences and compare species.

First we load the dataset of protein sequences from the cytochrome oxidase 1 gene. This gene, often known as CO1, is a mitochondrial gene that plays a key role in cellular respiration (e.g., the primary aerobic pathway to energy ( ATP ) generation). CO1 contains approximately 513 aminoacids (AA) and has been used by previous studies for reconstructing phylogenetic trees and estimating divergence times between taxa by assuming a molecular clock:

data(cytOxidase)

summary(cytOxidase)

## 
## 17 amino acid sequences, each with length 513

head(cytOxidase)

## $cnidaria
## [1] "-RWIFSTNHKDIGTLYL"
## 
## $snake
## [1] "TRWLFSTNHKDIGTLYL"
## 
## $echinoderm
## [1] "NRWLFSTNHKDIGTLYL"
## 
## $mollusk
## [1] "MRWLFSTNHKDIGTLYI"
## 
## $alligator
## [1] "HRWFFSTNHKDIGTLYF"
## 
## $lamprey
## [1] "IRWLFSTNHKDIGTLYL"
## 
## $shark
## [1] "NRWLFSTNHKDIGTLYL"
## 
## $bird
## [1] "NRWLFSTNHKDIGTLYL"
## 
## $frog
## [1] "TRWLFSTNHKDIGTLYL"
## 
## $fish
## [1] "TRWLFSTNHKDIGTLYL"
## 
## $platypus
## [1] "NRWLFSTNHKDIGTLYL"
## 
## $human
## [1] "DRWLFSTNHKDIGTLYL"
## 
## $chimpanzee
## [1] "DRWLFSTNHKDIGTLYL"
## 
## $bryozoa
## [1] "MRWLGSTNHKDIGTLYF"
## 
## $annelid
## [1] "MRWLYSTNHKDIGTLYF"
## 
## $insect
## [1] "RQWLFSTNHKDIGTLYF"
## 
## $crustacea
## [1] "RQWLFSTNHKDIGTLYL"

We can compare two sequences in terms AA difference number. For instance if we want to compare a species of snake with one species of bird, we type:

countSeqDiffs(cytOxidase, "snake", "bird")

## [1] 123

And to calculate the proportion of differences, we type:

countSeqDiffs(cytOxidase, "snake", "bird")/nchar(cytOxidase["snake"])

##     snake 
## 0.2397661

We can also quickly visualize the sequences by directly handling all elements in this object:

plotProteinSeq(cytOxidase, c("snake", "bird", "cnidaria"), knitr = TRUE)

And using patterns of molecular divergence, as well as fossil occurrences, we can build and, specially, date, molecular phylogenies.

- The fossil record:
- Comparing molecular patterns