2.3 Usage
The main menu presents the initial options to verify the availability of
data for a species, determine divergence times, a timeline, a time tree,
validate the data, or print the citation for Time Tree, as summarized in Figure 2 . The data availability option brings up a submenu to
specify if availability should be verified for a single species or
species list. When checking a single species, the availability is
printed to the screen as the species name followed by either ‘Available’
or ‘Not Available’. This function was designed to ensure data
availability prior to further data retrieval steps. For a list of
species, the species name and availability are printed on screen and
stored to export results in a CSV file.
The timeline and time tree options will bring up a similar submenu that
provides the option to retrieve information for an individual species,
individual taxon, or a list of species. As before, individual species
will result in a single output. The timeline retrieval function will
retrieve an image in the JPEG format that illustrates the evolutionary
history for the species highlighting the major time points where a
kingdom, order, class, genus, and species first emerged. As an example,
a timeline was retrieved for the Lazuli bunting, Passerina amoena [Say, 1823]. Input given as a list will retrieve
individual images for each species in the list. The time tree option has
similar functionality except that input can either be a larger taxonomic
group, such as family or genus containing several congenic species, or a
list of species as this output provides a time calibrated tree
displaying both the interrelatedness of species as well as the timescale
along which the branches diverged. As an example, two time trees were
generated for the genus Catharus and Malurus respectively.
The individual diversification rate (r ) was calculated for each
genus in R (R Core Team, 2020) using the geiger (version 2.0)
package (Harmon et al. , 2008) with the Magallon-Sanderson
equation (Magallón and Sanderson, 2001).
The Divergence time submenu provides the option to check for the
divergence time between two species e.g., the Neotropical Swainson’s
thrush, Catharus ustulatus [Nuttall, 1840], and the
Australasian Superb fairywren, Malurus cyaneus [Ellis,
1782]. The result will be printed to the screen as the name of
‘Taxon a’ and ‘Taxon b’ followed by the mean divergence time in millions
of years ago (MYA) e.g., 35 MYA. The list option takes a text file with
a list of species names and iterates through the list to determine the
divergence time between each species in the list. The results are stored
in a ‘dataframe’ object which can be exported as a CSV file in the form
of a three column vectorized matrix with the names for ‘Taxa 1’ in the
first column, the names of ‘Taxa 2’ in the second column, and the
divergence times between them in the third column. Additional
functionality is provided in the main menu to validate data. This option
can be used to check output files for missing values, as well as
retrieve and replace such values, in case a server error occurred.
RESULTS
Examples of timelines and time tree data retrieved from the Time tree
resource are illustrated in Figure 3 and Figure 4 . The
timeline was retrieved for the Neotropical bird the Lazuli bunting. The
left panel indicates the major geologic timescales in Eons and Eras
while the right indicates the main divergence times when specific taxa
emerged. This includes the current Phanerozoic Eon as well as the
subdivisions from the Paleozoic Era, which lasted until approximately
250 MYA, and the Mesozoic which lasted until 65 MYA. This period was
marked by the emergence of the first birds (class: Aves) approximately
110 MYA. The specific species, a bunting in the family Cardinalidae,
emerged from a common ancestor shared with other cardinals in the
Cenozoic, while species of the genus Passerina first emerging 4
MYA and subsequently diverged to form species and subspecies.
Time trees were generated for two genera of birds that each contain
several congenic species (11-12 species) but have different evolutionary
histories in terms of the divergence times within their genus. The first
represents the genus Catharus for which 12 species are included
in the time tree. These species diverged over a period spanning
approximately 4.73 million years and have an absolute diversification
rate of 0.38. By comparison, the second tree for the genus Malurus includes a similar number of species, however, these
species diverged over a period of approximately 9 million years and have
a diversification rate (r = 0.19) of nearly half the rate
observed in Catharus .
PAReTT was furthermore used to retrieve data availability and divergence
times for a list of forty bird species, as well as a time tree for
seventy-six species, in a recent review and meta-analysis on clock genes
as candidate genes in migration studies, published in Biological Reviews . This study found a significant relationship between
divergence times and the observed genetic distance in two candidate
genes, illustrating high heritability of genotypes within lineages and a
lack of selection. This illustrates the significance in studying
divergence time data in relation to genetic data in molecular studies.
The results from the benchmarking tests, performed in tandem, showed an
average time for submitting data and retrieving the result ranged from
fifteen to thirty seconds and memory consumption remained low, ranging
from <100 to 400 Megabytes (Supplementary table 1 ).
DISCUSSION
Time is an important variable in the study of evolutionary processes as
it relates both to large scale geographic remodelling that occurred over
millions of years and the timelines for the emergence and
diversification of taxonomic and phylogenetic lineages. Time is also a
key factor in determining the diversification rate within lineages which
may be vastly different even between families in the same class and
order. The Time tree resource provides relevant data that can easily be
incorporated into molecular studies tracking diversification rates as
well as studies comparing the heritability of specific genotypes as
ancestrally inherited or currently undergoing active selection. The
resource does, however, still lack options to facilitate batch retrieval
for lists of species. Here, we illustrate the use of a newly scripted
PYTHON package called PAReTT that provides an added layer of
functionality to the Time Tree resource by enabling the batch retrieval
of data for lists of species in a format that can enhance molecular and
ecological studies.