Mozal 1

Evolutionary Relationships in Family

Ochotonidae
Raegan Mozal
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Introduction

Reason for Study

Ochotones are the sole living genus within the family Ochotonidae (Lagomorpha,
Mammalia). The evolutionary relationships and followed phylogeny remain obscure and
unsolidified (Ge et al., 2012, Lissovsky 2014, Mohammadi et al., 2018, Lissovsky et al., 2007, Niu
et al., 2004, Yu et al., 2000). Many of these studies have focused on a selection of mitochondrial
genes; cytochrome c oxidase subunit 1 (COI) as well as cytochrome b (CYTB). However, most
lagomorphs, through hybridization, experience mitochondrial introgression (Lissovsky et al.,
2017). Based on this information we can make the valid assumption that mitochondrial DNA
may not show the most accurate representation of Ochotona evolution. For my analysis of the
phylogeny of ochotones, I chose to focus on 3 specific gene sequences; COI, CYTB, and
interleukin 1 receptor accessory protein-like 1 (IL1RAPL1). The goal I wanted to reach while
using these gene regions was to ensure my samples resembled previously published
relationships, determine the relationships between the di erent subgenera, and place the
locations of three newly named species (most likely subspecies/conspecifics).

Morphological/Behavioral Background
Ochotones are relatively small mammals and tend to be between 15-25 cm long and only
weigh around 400g. Evolutionarily wise, lagomorphs used to be classified within Rodentia,
however, now they are a sister taxa. This is important to mention because it lays the
groundwork for understanding the morphological similarities between these organisms.
Ochotones have unique dentition as they have two sets of continually growing upper incisors.
To ensure that these teeth do not become a hindrance during growth, pikas will use vertical
and transverse jaw movements to maintain a short and proper length (Gidley 1912). The upper
incisors are a common morphological feature among rabbits, hares, and rodents so it is not
surprising that these species were once classified together. The evolution of the pika body
structure includes but is not limited to the following: no visible tail, rounded ears rather than
pointy, thick hair on the soles of feet. These are the features that ultimately separate pikas
from other lagomorphs, the hair on the soles of their feet is especially important given their
niche environments.
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Most extant pikas live throughout North America and Eurasia, inhabiting the high
altitude peaks of mountains, basins, and plateaus with cool and moist environments.
Ochotones have many ways of thermoregulating to maintain homeostasis, due to their small
size they compensate with diurnal habits and thick insulating fur (MacArthur & Wang 1974). As
mentioned above, the thick fur on the soles of their feet keeps the organism warm and allows
them to survive in these cold temperatures.
With a niche environment comes niche behaviors and there are two main pika
ecotypes: meadow dwelling and tallus dwelling. Meadow-dwelling pikas are not as specific
when it comes to habitat characteristics, they are found in a variety of locations where they
can create burrows (Smith 2008). Some meadow dwelling species would include Ochotona
census (Gansu pikas), Ochotona dauurica (Daurian pikas), Ochotona nubrica (Nubra pikas),
Ochotona pusilla (steppe pikas) and more. These species are typically subgenera Ochotona and
can be found all throughout Asia. Tallus dwelling pikas often inhabit small crevices in between
the larger boulder rocks on mountain slopes, they forage in the alpine meadows and rely on
vegetation growing between rocks (Nowak 1999). Some tallus dwelling species would include
Ochotona alpina (alpine pikas), Ochotona collaris (collared pikas), Ochotona gloveri (Glover’s
pikas), Ochotona himalayana (Himalayan Pikas) and more. These species are typically
subgenera Pika and Conothoa and can be found throughout Eurasia and North America, it’s
important to note that North America only has tallus dwellers. Given that both of these
ecotypes are found at high elevations with rocky terrain the brown and black spotted
coloration aids in camouflage from the predators which include organisms such as wolves,
hawks/eagles, bears, etc.
These habitat di erences can also explain the behavioral di erences as well (Reese et
al., 2013). Ochotones are very territorial animals and they have two main behaviors to keep
their territory marked. It was discovered that they secrete an apocrine chin-gland onto the
rocks surrounding their crevices (Svendsen 1979). These scents help deter neighbors as well as
possible predators. Ochotones are also very vocal animals, they have two distinct calls used for
di erent situations. The short call or a caach are tiny ‘bleats’ used during daily activities.
Whether it is used to ward o predators, warn encroaching pika neighbors, or used during
chasing, pikas can let out up to 1000 caachs a day (Svendsen 1979). The second vocalization that
has been characterized is the long call or song. This call is important for mating behaviors, the
territorialization habits of ochotones would suggest that they mate guard, however, this is not
the case. The mating season for these animals is in the spring season, oftentimes the males will
leave their territory to find and seek out and long call sedentary females. The location of
ochotones tends to limit the animals from participating in a polygynandrous mating system as
there are costs associated with leaving the territory for too long, the most significant being an
increased risk of mortality. The location of these species also supports a sex-biased dispersal,
below I will discuss the Tibetan Plateau theory which detailed diversification via dispersal, and
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therefore conspecifics tend to live in the same habitat resulting in specific mating (Zgurski
2011).
I have mentioned several times that ochotones have filled a very specific niche and
again, because of this, their environments have developed a dependency on these organisms
controlling vegetative diversity. Using Ochotona curzoniae as an example, this is a keystone
species for the Tibetan Plateau. Taking both the position of predator and prey they are
essential for the ecosystem to survive. They are a grazing species that create hay piles of
vegetation, when making these piles they are promoting specific plant growth and in turn
provide habitat for smaller rodents, bugs, birds, etc. As prey they are important for the bird
and large mammal populations in the area, they are the target food choice of many large birds
such as eagles, hawks, and owls (Bagchi et al., 2006).

Previous Phylogeny and Story of Origin

Species in the family Ochotonidae used to be very widely diversified and spread
throughout Eurasia, Africa, and the New World. However, over time the most ancient genus
went extinct and we are now left with just one, Ochotona. There are many debates on how the
evolution of these ochotones occurred but the most proven is the Tibetan Plateau Theory.
Through fossil records, we can likely place origination within Central Asia. This theory
supports the idea that as the early ochotones dispersed through plateaus and mountains they
di erentiated via altitude, as they traveled up the Qinghai Tibetan Plateau they formed
individual communities (Dawson 1967). A recent study done by Wang et al., 2o2o assessed the
full mitochondrial DNA (roughly 15,000-16,000 base pairs per sample) between several extant
species of pika to both determine evolutionary relatedness and possible origin story. What was
found in the study was that the genes that were positively selected in the early stages of
evolution with ochotones were categorized based on cold tolerance. The positive selection of
those genes suggests that the Qinghai Tibetan Plateau served as a ‘training ground’ in early
species. This gave ochotones a significant advantage when the global climate was cooling after
the Miocene. When analyzing these sequences and comparing them to each other as well as
distant lagomorph relatives, four subgenera of Ochotonidae were recognized: Alienauroa,
Conothoa, Ochotona, and Pika (Wang et al., 2020). These new subgenera can largely be
di erentiated by habitat location which is mutually exclusive with age.
Alienauroa is a forest taxon that crossed a significant mountain range to reach central
China. Conothoa is a mountain group mainly spread amongst the Himalayan Mountains and
entered Central Asia. Pika is the northernmost group that spread northward through the Tian
Shan Mountains and Ochotona is the shrub-steppe group that spread through the Tibetan
Plateau. This study hits a significant question about both the diversity within the family of
Ochotonidae and how that diversity came to be. The origin story of these species can
determine future migration behavior as well as provide insight into evolutionary relatedness.
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The researchers still addressed faults within their study as there were a few outgroup taxons
that very well could be new species and further experimentation and analysis are required.
Given that this specific study was done by Wang et al,. 2020 and they created phylogenies with
the entire mitochondrial genome and that is not the genome I am specifically focusing on in
this paper it does include the gene regions of COI and CYTB. The results discussed below will
draw parallels between the individual region trees as well as the concatenated trees with the
data from Wang et al., 2020.

Materials and Methods

Description of Species
Given that the species within Ochotonidae are somewhat poorly sampled and there is a
discrepancy between individual species and conspecifics I arranged a list of 38 species to
analyze. Three total genes were looked at; mitochondrial COI, mitochondrial CYTB, and
chromosomal IL1RAPL1. These sequences were obtained from GenBank and aligned via
Geneious Prime 20221.1 (Figure 1). Alignments of individual gene sequences as well as
alignments of the concatenated sequences were run through ModelTeller.tau.ac.il to find the
best substitution model in regards to tree building. The pre-selected outgroup for all analyses
was Oryctolagus cuniculus, the European rabbit. The phylogenetic trees showing the individual
COI gene (Figure 2) and the individual IL1RAPL1 gene (Figure 3) used the
Hasegawa-Kishino-Yano (HKY) substitution model, neighbor-joining building method,
bootstrap resampling methods, 500 replicates, and a randomly generated seed as suggested by
ModelTeller. The remaining trees: individual CYTB gene (Figure 4), COI/CYTB concatenation
(Figure 5), CYTB/IL1RAPL1 concatenation (Figure 6), COI/IL1RAPL1 concatenation (Figure 7),
and the COI/CYTB/IL1RAPL1 concatenation (Figure 8) were analyzed using the Jukes-Cantor
( JC) substitution model, neighbor-joining building method, bootstrap resampling methods,
500 replicates, and a randomly generated seed as suggested by ModelTeller.
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Figure 1. Current taxonomic classification of members within Family Ochotonidae. Includes

COI, CYTB, and IL1RAPL1 sequence codes, used within this study, all sequences were obtained
through NCBI's GenBank.

Results

COI Gene
The results obtained in this analysis (Figure 2) support the subgenus Pika as being a
potential monophyletic group, this is deduced by the placement of O. manchuria. The red
boxes show two important points I would like to point out on all trees. The first box shows O.
sp. being the closest relative to O. thomasi in a nearly monophyletic group of subgenus
Ochotona. The confidence in the consensus sequence should lead us to believe that this
unclassified species of O. sp. could be classified in the Ochotona subgenus, however, this does
not support the findings of Wang et al., 2o2o. The second red box drawn in Figure 2 is there to
highlight the relationship between three species; O. rufescens, O. rutilla, and O. roylei. A pattern
has shown up within the trees suggesting that these species are closely related, however, based
on previous studies this claim is not supported. The COI gene region used was roughly 620
base pairs in length for the alignment and the tree produced using the HKY substitution model
displayed no monophyletic subgenera clades.
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Figure 2. Results of the HKY substitution method analyzing the COI mitochondrial DNA of
family Ochotonidae. The pre-selected outgroup was Oryctolagus cuniculus (European Rabbit)
shown at the top. Purple indicates subgenus Pika, green indicates subgenus Ochotona, blue
indicates subgenus Conothoa, orange indicates subgenus Alienauroa and black represents
unclassified species/possible conspecifics.

IL1RAPL1 Gene
The results obtained in this analysis (Figure 3) again are similar to the above, however,
in this analysis, we see subgenus Conothoa as a monophyletic group which is something we did
not see with the mitochondrial DNA analyses. This analysis also indicates that the species O.
sp. should be classified within the Ochotona subgenera, in this case, the closest relative is
again, O. thomasi. As mentioned earlier I want to focus on the red boxes containing O.
rufescens, O. rutilla, and O. roylei. In this analysis, we see that subphyla Ochotona is almost a
monophyletic group with the exception of O. rufescens and O. syrinx. In this case, we can see
that that claim is not possible to the close relationships between the species of focus. The
IL1RAPL1 gene region used was around 910 base pairs in length for the alignment and the tree
produced using the HKY substitution model. In this case, a single monophyletic subgenus is
displayed.
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Figure 3. Results of the HKY substitution method analyzing the IL1RAPL1 DNA of family
Ochotonidae. The pre-selected outgroup was Oryctolagus cuniculus (European Rabbit) shown at
the top. Purple indicates subgenus Pika, green indicates subgenus Ochotona, blue indicates
subgenus Conothoa, orange indicates subgenus Alienauroa and black represents unclassified
species/possible conspecifics.

CYTB Gene
The sequencing for this gene was found for most species within the family Ochotonidae
providing us with a nearly complete tree (Figure 4). This phylogeny provides us with some solid
results that are similar to Wang et al., 2020, which makes sense given they aligned the entirety
of the mitochondrial genome. We can see a monophyletic group of subgenera Pika with the
exception of a single species. We can again see these new, unclassified samples of O. sp. and O,
morosa being closely related to species in the subgenera Ochotona. Another one of these
species used in this analysis, O. xunhuaensis, is placed in a clade containing species of multiple
subgenera, a valid claim can not be made here. Still following the pattern we can see that the
subgenera Conothoa is a monophyletic group with the addition of O. rufescens. The CYTB gene
region used was roughly 310 base pairs in length for the alignment and the tree produced
using JC substitution models displayed a significant relationship between three existing
species and 2 unclassified species.
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Figure 4. Results of the JC substitution method analyzing the CYTB mitochondrial DNA of
family Ochotonidae. The pre-selected outgroup was Oryctolagus cuniculus (European Rabbit)
shown at the top. Purple indicates subgenus Pika, green indicates subgenus Ochotona, blue
indicates subgenus Conothoa, orange indicates subgenus Alienauroa and black represents
unclassified species/possible conspecifics.

COI/CYTB Genes
This phylogeny highlights the relationships in the family Ochotonidae when the COI
and CYTB genes are concatenated into a single alignment (Figure 5). Here we see once again
that subgenera Conothoa can be classified as a monophyletic group with a significant
relationship to/addition of O. rufescens. We can also see that O. sp. has fallen into a clade
containing species within subgenera Ochotona. The alignment of the COI and CYTB gene
regions was around 1600 base pairs in length and the phylogeny was analyzed using the JC
substitution model. From these results, we have a strong indication that O. rufescens should be
classified within the subgenus Conothoa and that the new species O. sp. can be classified within
subgenera Ochotona.
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Figure 5. Results of the JC substitution method analyzing the concatenation of COI and CYTB
mitochondrial DNA of family Ochotonidae. The pre-selected outgroup was Oryctolagus
cuniculus (European Rabbit) shown at the top. Purple indicates subgenus Pika, green indicates
subgenus Ochotona, blue indicates subgenus Conothoa, orange indicates subgenus Alienauroa
and black represents unclassified species/possible conspecifics.

CYTB/IL1RAPL1 Genes
This phylogeny highlights the relationships in the family Ochotonidae when the CYTB
and IL1RAPL1 genes are concatenated into a single alignment (Figure 6). We see some
di erences in data here which supports the claims made by Lissovsky et al., 2017 that
mitochondrial introgression can alter the analysis of evolutionary relationships. This analysis
can show subgenus Pika as a monophyletic group which we were unable to do for trees only
analyzing single gene regions. The other data we were looking for stands here as well, we can
also see subgenus Conothoa as a monophyletic group with the edition of O. rufescens. The last
bit of significant information we can take from this tree is that the new species/conspecifics
are closely related to and should be classified within the subgenus Ochotona. The alignment of
the CYTB and IL1RAPL1 gene regions was roughly 1900 base pairs in length and the phylogeny
was analyzed using the JC substitution models. From these results, we have a strong indication
that subgenus Conothoa may require the addition of a previously described species as well as
the new species being added to the subgenus Ochotona classification.
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Figure 6. Results of the JC substitution method analyzing the concatenation of CYTB

mitochondrial DNA and IL1RAPL1 DNA of family Ochotonidae. The pre-selected outgroup was
Oryctolagus cuniculus (European Rabbit) shown at the top. Purple indicates subgenus Pika,
green indicates subgenus Ochotona, blue indicates subgenus Conothoa, orange indicates
subgenus Alienauroa and black represents unclassified species/possible conspecifics.

COI/IL1RAPL1 Genes
This phylogeny highlights the relationships in the family Ochotonidae when the COI
and IL1RAPL1 genes are concatenated into a single alignment (Figure 7). The data produced
here follows this study's trend that species O. sp. can be classified within subgenera Ochotona.
The major discrepancy I want to point out here is the relationships between the three species I
have been focusing on: O. rufescens, O. rutilla, and O. roylei. This analysis is able to show
subgenera Conothoa as a complete monophyletic group and O. rufescens is not present or
closely related. However, O. rufescens was previously classified within subgenera Ochotona, and
that relationship is not proved by this tree either. The alignment of the COI and IL1RAPL1 gene
regions was around 1550 base pairs in length and the phylogeny was analyzed using the JC
substitution model. From these results, we have the confidence of a monophyletic Conothoa
subgenus as well as our new species being classified within subgenus Ochotona.
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Figure 7. Results of the JC substitution method analyzing the concatenation of COI

mitochondrial DNA and IL1RAPL1 DNA of family Ochotonidae. The pre-selected outgroup was
Oryctolagus cuniculus (European Rabbit) shown at the top. Purple indicates subgenus Pika,
green indicates subgenus Ochotona, blue indicates subgenus Conothoa, orange indicates
subgenus Alienauroa and black represents unclassified species/possible conspecifics.

COI/CYTB/IL1RAPL1 Genes
The final phylogeny used in this analysis of evolutionary relationships in the family
Ochotonidae is a concatenation of all three genes: COI, CYTB, and IL1RAPL1 (Figure 8). This
data greatly resembles what we have looked at throughout this paper. The species O. sp. is
closely related to and can be classified as a species within subgenera Ochotona. We also see
similar results with subgenus Conothoa being a monophyletic group with the addition of O.
rufescens. The alignment of the COI, CYTB, and IL1RAPL1 gene regions was roughly 2500 base
pairs in length and the phylogeny was analyzed using the JC substitution model. From these
results, we continue to have confidence in the classification of species O. rufescens and O. sp.
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Figure 8. Results of the JC substitution method analyzing the concatenation of COI and CYTB
mitochondrial DNA with IL1RAPL1 DNA of family Ochotonidae. The pre-selected outgroup was
Oryctolagus cuniculus (European Rabbit) shown at the top. Purple indicates subgenus Pika,
green indicates subgenus Ochotona, blue indicates subgenus Conothoa, orange indicates
subgenus Alienauroa and black represents unclassified species/possible conspecifics.

Discussion

Subgenus Conothoa as a monophyletic clade with O. rufescens

One of the main focuses of this study was to understand the relationships between
three previously described species: O. rufescens, O. rutila, and O. roylei. In 5 of the 7 trees
created with multiple gene sequences and concatenations, it is shown that O. rufescens, which
was previously classified within subgenera Ochotona, could be classified within subgenus
Conothoa as a monophyletic group. This was an interesting finding within my research given
that Zgurski 2011 claims O. rufescens is more closely related to species within subgenus Pika
when analyzing CYTB genes. This species is a perfect example of the undecided phylogeny of
ochotones, every paper studying the genome of these species results in di erent
classifications. The claim that O. rufescens should be classified within subgenus Conothoa as a
monophyletic clade is supported by Khalilipour et al., 2017 with even higher consensus
 Mozal 13

percentages than I present in my arguments. Given that this monophyletic clade was only
shown in 5 of the trees I am presenting I would like to suggest further experimentation by
looking at the COI/IL1RAPL1 concatenation as well as the individual analysis of the IL1RAPL1
gene region. I am especially interested in this specific species due to the common claim that it
should be classified within the subgenus Ochotona and many studies published recently are
beginning to find data that does not support this.

Subgenus Ochotona as a monophyletic clade

The second set of data I was heavily focusing on throughout this study was the ability to
classify subgenus Ochotona as a monophyletic clade. Since the first classifications of these
animals, it was known that there was only a single genus, Ochotona. As technologies have
advanced researchers have wanted to further classify these species to understand their
dispersal behavior and understand their evolutionary relationships. Many papers (Wang et al.,
2020, Zgurski 2011, and Lissovky 2018) have found proper data to create an Ochotona
monophyletic clade. The gene regions and samples used in my studies may have altered these
predicated results, specifically the placements of O. syrinx and O. pusilla. Further investigation
should be done on this specific subgenera, analyze more than just mitochondrial DNA given
mitochondrial introgression, and use as many samples as provided to create an accurate tree
analysis.

New species or conspecifics?

A component that I wanted to focus on was the addition of new species into these
analyses. The last few years of research have published new DNA sequences that have been
thrown around the subgenera classifications with no solid claims. For this study, I chose four
of these possible new species: O. morosa, O. sp., O. xunhuaensis, and O. yarlungensis. The most
significant result that we can take from the analyses of these specific gene regions is that O. sp.
and O. morosa can be classified within the subgenus Ochotona. These two species show strong
evolutionary relationships with the species in this subgenus. O. xunhuaensis and O.
yarlungensis did not have as solid results, these species did not have many public samples,
therefore, limiting the number of analyses I could run with them. However, we can see in
Figure 4 that O. sp., O. morosa, and O. xunhuaensis are shown to be related to species in
subgenus Ochotona. These results support the classification of O. sp. and O. morosa as
described in Wang et al., 2020. We can also see that Figure 4 is the only phylogeny showing
relationships between species in subgenera Alienauroa. This clade is not monophyletic and
includes the new species O. xunhuaensis. From my analysis, I do not have enough data or
confidence to claim that O. xunhuaensis is either classified as Alienauroa or a new species at all.
Further data and experimentation would be needed as those claims are beyond my knowledge.
 Mozal 14

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