PHYLOGENETIC POSITION OF Taeniolabis

taoensis AND Pantolestes natans AND THEIR ROLES

IN THE DIVERSIFICATION OF MAMMALS
Shivam Khatri and Katherine Turchin
Mentor: Pal Velazco

 ABSTRACT
In this study, specimens of Pantolestes natans and Taeniolabis taoensis were
analyzed and included in a phylogeny of mammals. The order Cimolesta serves as a place
in which early Eutherian mammals that do not fit concretely into other orders due to lack
of information are included. The order includes the family Pantolestidae, which
resembles early rodents, which lived from the Paleocene to the Oligocene eras in North
America. Little is known about this family and in particular the species Pantolestes
natans, and how it fits into the evolutionary mammalian tree of life. On the other hand,
the order Multituberculata contains a group of diverse mammals that reached their apex
in the late Mesozoic and early Paleocene. Taeniolabioidea, the largest members of this
extinct order, which were about the size of a beaver, lived from the Late Cretaceous
through the early Eocene. Though Taeniolabis taoensis is the largest known
multituberculate recorded, very little is actually known about its morphology. This study
aims to map the morphological characteristics of these two species as a model for the two
families and to establish a better context as well as a somewhat complete map of the
mammalian tree of life. We used the OLeary et al. 2013s matrix of 4,541 phonemic
characteristics for 86 mammalian taxa stored in the program Morphobank. Out of these
characteristics, 1,353 were scored for Pantolestes and 1,749 for Taeniolabis. We
combined this data with genetic data for all the non-fossil mammals within this matrix
and used maximum parsimony in the program PAUP to generate the phylogenetic trees.
This methodology produced a structured phylogenetic tree that revealed a better snapshot
of Taeniolabis taoenis and Pantolestes natans in the evolutionary tree of life. Our final
results showed that Taeniolabis taoensis grouped within placental mammals and was
included in Afrotheria. Regarding Pantolestes natans, it was grouped outside of
Placentalia with other early Eutherian mammals such as the family Leptictidae.

INTRODUCTION
In 2013, a study performed by 23 scientists from 13 countries assembled and
analyzed the largest character data set for mammals, which involved scoring 4,541
phenomic characteristics of 86 fossils and living species (OLeary et al. 2013). The study
obtained a phylogenetic tree by combining this morphological data with molecular
sequences, which ultimately showed that placentals originated shortly after the K-Pg
(Cretaceous-Paleogene) boundary, an event that marked the extinction of many species,
an example of whom are the dinosaurs. (OLeary et al. 2013). The study successfully
gathered evidence that disputed the short fuse and long fuse diversification models. The
short fuse diversification model assumes that some ordinal diversification occurred in the
Cretaceous period while the long fuse model proposes that placentals originated long
before the mass extinction, but all other ordinal diversification occurred after the K-Pg
boundary. (OLeary et al. 2013). Rather, evidence gathered from this study supported the
explosive diversification model, which proposes that the diversification of placental
mammals occurred shortly after the Cretaceous-Paleogene boundary. (OLeary et al.
2013). To build the morphological matrix the study utilized a web application known as
MorphoBank, which allowed researchers to input phylogenetic characteristics into a
shared matrix so that these researchers could work concurrently. This matrix contained
scored characters from 86 species representing all living placental orders plus 40 fossil
species, which was coupled with genetic data of 27 nuclear genes (OLeary et al. 2013)..
Currently, new species are being added to this MorphoBank matrix in order to improve
the studys results and form a better snapshot of the mammalian tree of life.
This project focuses on the extinct mammals Pantolestes natans and the
multituberculate, Taeniolabis taoensis. Pantolestes natans which lived predominantly
during the Eocene era in North America and was potentially a semi-aquatic mammal
(Boyer 2007, Rose 2006). P. natans was chosen as a representative of its family,
Pantolestidae, as it combines several different characteristics seen in other species within
the order, particularly a large infraorbital foramen, and a horizontally developed glenoid
fossa (Rose 2006, Matthew 1909). Only one specimen is known for P. natans (holotype)
and is comprised of a mostly complete skull and some postcranial elements (Matthew
1909). Since its description in 1909, Pantolestes has been included into several different
orders, including Insectivora, Carnivora, and even Primata (Matthew 1909). Currently, it
is recognized to belong to Cimolesta, but even that is uncertain and debated (Rose 2006).
Cimolesta is generally regarded as an order in that include species which do not fit
anywhere else; it is likely that some members are more closely related to various other
placental orders than to each other, and the species sorted into Cimolesta generally do not
have a wide range of phylogenetic data available (Boyer 2007). As a result, little is
known or can be inferred about P. natans and the genus and family it represents as
inferences cannot be made based on other members of its order. By analysing the
morphological characteristics of P. natans and cross-referencing them with published
genomic data, a more conclusive evolutionary relationship between it and other species
can be obtained, helping to trace the evolution of placentals and contribute to the
mammalian tree of life.
The earliest known multituberculate is known from the Jurassic period and is
known to have gone extinct in the early Oligocene (Rose 2006). Currently, it remains a
conundrum why a diverse group of species such as multituberculates became extinct.
Competing theories include competition with other species; however they coexisted with
these same species in other time periods. (Rose 2006) Though they became extinct, they
were the most successful Mesozoic mammalian group found throughout most of the
world (Rose 2006). One member of the the multituberculates was Taenolabis. The genus
Taeniolabis was described by Edward Cope in 1882 who based it on T. sulcatus, a
holotype which has a broken upper second incisor (Broom 1914). Taeniolabis taoensis is
the largest known member of the order, Multiculberculata reaching the perhaps the size
of a beaver (Simmons 1987). It went extinct in the early Paleocene. (Simmons 1987). The
species belongs to the family Taeniolabidoidea, which are known to have lived in North
America, Asia and Europe (Rose 2006). T. taoensis has been found in the Puercan
localities in northern New Mexico, Utah, and Montana. (Simmons 1987). The holotype of
T. taoensis includes a mostly complete skull, a complete set of dentition, and a few
postcranial bones specifically the scapula. Since its discovery in 1882, the position of T.
taeonsis has often been disputed; however, current evidence points that the species falling
outside of the clade Placentalia. By analyzing the morphological characteristics of T.
taoenisis, and combining this with molecular data from other mammalian taxa, the
position of the species on the mammalian tree of life can be better determined.

igure 1: An artists rendition of Taeniolabis Taoensis
F
The goal of this research project was to create a more complete mammalian tree
of life. This would be accomplished by inputting two species, Pantolestes natans and
Taeniolabis taeoensis, into the MorphoBank matrix, which would ultimately reveal the
position of these species of the tree of life. It is expected that P. natans will be most
similar to other early Eutherian mammals within the matrix such as Leptictis and
Hyopsodus. Because pantolestids generally resemble very early rodents, a distant
evolutionary relationship between P. natans and the representatives of Rodentia in
Morphobank is also predicted (Rose 2006). It is expected that T. taeonsis will fall out of
the clade Placentalia. Because Kryptobaatar dashzevegi is a multituberculate that is
embedded in our matrix, T. taeonsis and K. dashzevegi should have a close evolutionary
relationship.

MATERIALS AND METHODS
The Specimens and Uploading Photos
The specimens were obtained from the Paleontological collection at the American
Museum of Natural History. The P. natans specimen (12152 and 12153) contained a
mostly complete skull (reconstructed with plaster), with some worn down canines and
several molars; right and left mandibles, with several molars; reconstructed tibia on both
sides; reconstructed humeri on both sides; an incomplete pelvis with fragments from both
the right and left side; a section of fused vertebrae, as well as an assortment of various
vertebra; a largely intact femur on the left side, and a partial femur on the right side;
fragmented ulna on both sides; a well preserved right astragalus. The T. taoensis
specimens (749, 968, 969, 970, 3036, 16310, 16321) included two skulls: one which was
mostly intact because of plaster and a complete skull with minor traces of plaster which
had a complete set of incisors, premolars, and molars. There was also a complete set of
mandibles present, which had well preserved dentition as well. Regarding postcranial
structures, there was only a mediocre scapula present, which was mostly intact due to
plaster, and contained very less detail. Photos of these specimens were taken using a
Nikon 4500 camera, tripod, a camera box, and sandbags. The specimen was placed into
the camera box and the sandbag were utilized in order to takes images of the sample from
different angles. These photos were taken from six different angles: lateral right and left,
ventral, dorsal, posterior and anterior. Next, these images were edited and given better
contrast through the use of the software, Photoshop and uploaded to the MorphoBank
matrix where each photo was placed with its respective fossil number and were scored in
the matrix. These images would eventually be used in order to supplement the
morphological characteristics scored for both specimens, which would enable other
scientist to identify the character scored easily and efficiently.
MorphoBank
MorphoBank was the primary software that was used for this project. It is a web
application that provides centralized hosting of high-resolution images and matrices, as
well as specimen, characters and taxonomic information (MorphoBank 2015).
Furthermore, scientists can simultaneously edit the matrices (MorphoBank 2015). There
is archival backup of all data and images and the project data is web published
(MorphoBank 2015). These features give MorphoBank an edge over traditional desktop
phylogenetics softwares (MorphoBank 2015). All these features and contained the matrix
built from the 2013 study, which contains 4,541 morphological characteristics that ask
users to score detail regarding the skull, braincase, ear, dentition, postcranial, soft tissue
structures (OLeary 2011). Furthermore, behavioral characteristics are presented to users,
many of which are usually not able to be scored because the species has gone extinct
(OLeary 2011). Figure 1 shows an screenshot of the MorphoBank matrix used in this
project. On the left side, there are 101 total column, each of which designated for each
different taxon name. There are 4,541 row presents for each taxon name, which represent
that different characteristics present in the matrix. Each characteristics has different
possibilities of scoring that range from 2-9. However, there are three fundamental
symbols present in each cell. The first symbol is ? which is designated to each cell in
order to show that the cell has not been scored. When the cell is scored, the ? is
replaced with the characteristic feature. The second abbreviation is NPA, which means
Not Presently Available as is used by the researcher when a characteristics cannot be
label because the characteristic is not evident in the original fossil due to plaster or
wearing down. The last symbol is the -, which represent inapplicable is scored when
the species does not have the characteristic being asked. Figure 2 shows that each cell can
be supplemented with a photo of the researchers choice. Figure 3 shows the tools present
in order to supplement the photo with the cell. Each photo is added to the matrix and by
using the line tool on the right, the researcher may be able to give specific label in the
photograph. This enables other researchers to easily identify the structure that is being
asked. The majority of the characteristics are cranial and dental as they are the best tools
available in order to better describes the species. There are 2,735 characteristics that
constitute as dental and cranial characteristics.


Figure 2: Image of the MorphoBank Matrix with various morphological characteristics

Figure 3: Image of the Image Option Window. The line tool boxed in blue can be
used to create labels for each characteristic, which shows exactly where that
characteristic is on the specimen.

Genetic Data Alignment

The morphological characters were supplemented with genetic data for extant species in
order to provide more accurate results for the morphological data. The molecular
sequences used were the same ones as those of the previous study conducted in 2013
(OLeary et al. 2013). The molecular data compiled included 27 nuclear genes gathered
from GenBank (OLeary et al. 2013). To combine these molecular sequences, the
MorphoBank matrix was saved as a NEXUS file format. This file was then opened in
Text Wrangler, a text editing program available for the Mac operating system. Since
2013, the only addition to the database have been extinct species, which have no genetic
available, so the genetic entries added was reduced since the entries were designated as
Not Presently Available. In a text editor, this would be represented with a ?. Figure 4
shows a snippet of the matrix consisting of molecular data opened in Text Wrangler.

Figure 4: The Nexus file opened in Text Wrangler. The blue box shows a snippet of
the genetic data for T. taoensis while the red box shows a snippet of the genetic data
for P. natans.

PAUP
In order to construct a phylogenetic tree that mapped the evolutionary relationship
between the mammals scored, the program PAUP (Phylogenetic Analysis Using
Parsimony) was utilized (Swofford 2002). The software allows users to analyze
molecular sequences, morphological data and other types of the data (Swofford 2002).
PAUPs main objective is to use parsimony analysis, which creates a phylogenetic tree by
minimizing the number of character-state changes (Swofford 2002). This leads to a
statistically accurate tree (Swofford 2002). The algorithm used in the study was the
default one where characters were equally weighted, and a heuristic Tree Bisection and
Reconnection swapping search was performed (Swofford 2002, OLeary 2013). Tree
Bisection and Reconnection is a search which reduces the number of networks searched,
so an exhaustive search of all topologies do not need to be performed. It selects a subtree
and connects it to the main, which produce two disconnected trees (Swofford 2002). 100
iterations were used, which means the tree was bisected and reconnected 100 times, and a
best fit tree was averaged out of the 100 different trees (Swofford 2002).

Fig Tree
Fig Tree is a software that allows users to view phylogenetic trees produced from other
programs like BEAST or PAUP (Rambaut). In addition, it allows users to publish
publication-ready trees (Rambaut). Fig Tree has three different styles for phylogenetic
trees: rectangular, polar, and radial (Rambaut) It allows individual to display node heights
and branch lengths (Rambaut). In terms of creating publication-ready trees, it has many
customization options such as coloring the branch and tip labels. The program is also
compatible with PDF softwares, which makes it easier for users to print and export these
trees into a PDF format (Rambaut). In terms of this project, the default settings were used
to create the tree, although there was expansion setting and some common sense tools
that were used in order to have a more visually appealing tree. The group known as
Pantolestids, which contains P. natans, is colored in red in order to differentiate it from
other mammalian groups. On the other hand, green is used in order to represent the
Placentals, which contains T. taoensis. Figure 5 shows a snapshot of the Fig Tree
Program and some of the features that are presented to users.

Figure 5: The Fig Tree Program and some of the options given to users in order to
manipulate and customize their tree for their needs.

 RESULTS
Images of the Specimens

Figures 6 and 6.1: Dorsal view of skull of P. natans (above), lower right mandible with two molars of P. natans (below).
Labels represent key characteristics indicative of pantolestids: (1) wide long nasals, and anterior widening of snout (2) large
round well-developed infraorbital foramen (3) long and robust zygomatic arch (4) inconspicuous sagittal crest that however
extends almost to nasals (5) broad developed occipital crest (6) low trigonids with subequal protoconid and metaconid cusp (7)
wide basined talonids in lower teeth (8) posterior mental foramen is under molar 1, an unusual feature

These uploaded photographs (Figures 6 and 6.1) are two of 129 that map the P.
natans specimen. Since these pictures are on a public database, once the study containing
them is published, anyone with an account will be able to access them. By publishing
detailed pictures of rare or holotype specimens from multiple views, information about
the specimens and the species they represent can be easily spread and used by
morphologists even if the physical sample cannot be obtained. Using the available
specimen, 1,351 characters of the total 4,541, or 30%, were scored.


Figure 7, 7.1, 7.2: Ventral View of skull (above), dorsal view of skull (middle), and lower right mandible (below). Label
represent characteristic of T. taoensis and multituberculates: (1) Upper Incisor 2 with a spatulate shape and hypsodont, (2)
Upper Incisor 3 with a conical shape, (3) Premolar 4 with no important cusps, (4) Upper Molar 1, (5) Upper Molar 2, (6)
Premaxilla with suture separating from molar not evident, (7) Maxilla with no facial process making frontal contact, (8) Nasal
with suture not evident, (9) Jugal beneath Squamosal, (10) Squamosal that extends to palatine, (11) Lower Incisor 1 (12)
Premolar 4, (13) Lower Molar 1, (14) Lower Molar 2 .

Figure 7, 7.1 and 7.2 are three of the 39 photos taken of T. taoensis. These 39
photos are uploaded to MorphoBank Matrix, which enables other scientists to gain access
to the specimen without having the holotype at hand. For this specimen, 1,749 of the
4,541 characteristics were scored. This represents 39% of cells scored. Out of the 1749
cells scored, 1,174 were designated as inapplicable as multituberculates have a dentition
structure that lack many of the cusps that other species have.

Phylogenetic Tree
When the genetic and phenomic data was analysed using PAUP, the number of
steps was 128714. The consistency index, which is the minimum number of changes
divided by the number required on the tree, was 0.38. The retention index, which is the
maximum steps minus the observed steps over the maximum steps minus the minimum
steps, was 0.40. The parsimony analysis obtained two trees. The tree below is the
consensus of the two. The primary difference between the trees produced was the
position of the Pantolestids, represented by P. natans. The tree created was almost
identical to the tree from the early study in 2013, which indicates the robustness of the
matrix (OLeary et al 2013). The changes and additions to this tree arose the inclusion of
Pantolestes natans and Taeniolabis taoensis as species within the matrix, as well as
several others, for instance Kryptobaatar dashzevegi, bringing the total species within
Morphobank from 86 to 101. The tree was rooted from the outgroup species
Morganucodon oehleri. The tree is color coded to reflect different branches of
mammalian evolution; orange is Monotremata, blue is Marsupialia, red is Pantolestidae,
dark green is other Eutherian mammals, and light green is Placentalia. Pantolestes natans
is highlighted in red and Taeniolabis taoensis is highlighted in green. P. natans was
grouped outside of Placentalia with other early Eutherian mammals such as Leptictidae
(dark green). In one tree, P. natans was grouped above them; in the other, it was grouped
below. The average tree groups Pantolestidae and early Eutherians at the same node to
show that PAUP was uncertain as to where to group it. Earlier in the study, P. natans was
grouped in the Placentalia clade with species belonging to the bat clade such as
Onychonycteris finneyi. It was placed in its own node after more data regarding its nasal
structure was added. P. natans, highlighted in red, has its own node as currently it is the
only pantolestid in this database. Taeniolabis taoensis was grouped with the only
multituberculate in the database, Kryptobaatar dashzevegi, an extinct mammal that dated
back to the early Cretaceous period and was found in Central Asia. The Multituberculata
node was grouped in Placentalia (Fig 9), and most closely linked to Afrotheria, a group of
mammals originating from Africa or currently living in Africa (Rose 2006). At an early
point in the study, when only the cranial characteristics had been scored, T. taoenisis was
mapped on a phylogenetic tree and was grouped with early ungulates, which are hooved
mammals (Rose 2006). However, after adding much of dental morphology, the position
of Taeniolabis taoensis seems to have changed and now is closely related to the other
multituberculate.




Figure 8: Complete PAUP Tree that shows the 101 taxa scored including T. taoensis and P. natans

Figure 9: Close-up node containing P. natans. Dark green represents other early Eutherian mammals.

Figure 10: Close-up node containing T. taoensis. It is most closely grouped with K. dashzevegi, and its wider group is
Placentalia.


DISCUSSION
The evolutionary relationship between Taeniolabis taoensis and placentals is odd
and not in accord with the results that were expected to be received. Multituberculates are
expected to fall outside of Placentalia, the placing obtained by our analysis could be the
result of the presence of homoplastic characters. Homoplastic characters are characters
shared by two or more taxa because of convergent evolution. According to the explosive
diversification model, placentals diversified around 65 million years ago, right after the
K-pG boundary. On the other hand, multituberculates have lived for over 120 million
years. (Rose 2006) This means that Taeniolabis taoensis is considered older than
placentals and have seem to survive the mass extinction, while placentals original right
after the mass extinction. These pieces of data point to the fact that T. taoensis should fall
out of Placentalia. Taeniolabis taoensis was also recovered as sister taxa to the other
multituberculate in the analysis Kryptobaatar dashzevegi. This is expected since both
belong to the same taxon and share many distinct features that set them apart from
placentals and marsupials. Both multituberculates, for instance, share the same dental
formula, which includes Incisors 2 and 3, Premolar 4, and Molars 1 and 2, while lack
canines. We believe that the addition of postcranial information and the inclusion of other
multituberculate taxa will improve the position of multituberculates in the mammal Tree
of Life.
The hypothesis that P. natans would be most closely related to other early
Eutherian mammals was supported by the results. P. natans fell outside of the Placentalia
clade, and was closely grouped with Leptictida (Fig 9), small hedgehog-like North
American mammals (Rose 2006). It was most closely grouped with a node of early
non-placental Eutherian mammals, which included Maelestes gobiensis, Ukhaatherium
nessovi, Prokennalestes trofimovi, and Zalambdalestes lechei, all Cretaceous era
shrew-like mammals from Mongolia (Gobi Desert). The differences between P. natans
and the other early eutherians may be based on geography, as while they were found in
East Asia, pantolestids lived in North America. During the Cretaceous period, the
supercontinent Pangaea broke up into modern continents with what would become North
America separating from Eurasia, offering a possible explanation for a similar origin of
pantolestids and other Eutherians, but separate development leading to the separation of
P. natans from the other Eutherians in the database. While the position of P. natans
within the overall mammalian phylogenetic tree has been approximated, PAUP could not
narrow down its position within non-placental Eutherians, and merely placed P. natans
within its own node. More pantolestids would have to be added to the study in order to
better clarify the position of Pantolestidae within the Mammal Tree of Life.

CONCLUSION
In order to improve the position of Taenolabis taoenisis on the mammalian tree of
life, more multituberculate taxon can be added to this MorphoBank matrix as there are
only two multituberculates in this matrix: Taeniolabis taoensis and Kryptobaatar
dashzvegi. Currently, there are 101 taxa within this matrix, representing the entire
Mammalia clade, and the majority of tax are missing over half of the morphological
characteristics, much of which constitutes as behavioral and postcranial characteristics.
There are over 200 species of multituberculates known to scientists today, and adding a
few more may improve the placement of T. taoensis from placental mammals to its own
group (Broom 1914). Additionally, more of the dental characteristics of T. taoensis can
be mapped since many of the characteristics constitute as inapplicable. Expanding on
the current matrix and adding more taxa will help specify the evolutionary relationships
between different species and give scientists a better snapshot of the placental
mammalian ancestry.
To improve the position of P. natans and specify its relation to other
non-placental Eutherian mammals, more pantolestid species should be added to the
database in order to increase the amount of data available and improve its accuracy. By
adding more specimens that have different morphological characters that can be scored,
the overall pantolestid morphology will be more complete. Overall, the position of P.
natans supports the conclusion of OLeary et al. (2013) that indicates that placentals
diversified as a result of an explosive model of diversification.







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