Reconstruction of phylogenetic history to resolve the subspecies anomaly of Pantherine cats



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Title: Reconstruction of phylogenetic history to resolve the subspecies anomaly of 

Pantherine cats 



 

Authors: Ranajit Das

1

, Priyanka Upadhyai



 

1



Manipal Centre for Natural Sciences, Manipal University, Manipal, Karnataka 576104, 

India 


 

2

Department of Medical Genetics, Kasturba Medical College, Manipal University, 



Manipal, Karnataka 576104, India 

 

Email address: 

ranajit.das@manipal.edu 

 

Running title: Mitogenome phylogeny of Pantherine cats 

 

Abstract 

 

All charismatic big cats including tiger (Panthera tigris), lion (Panthera leo), leopard 



(Panthera pardus), snow leopard (Panthera uncial), and jaguar (Panthera onca) are 

grouped into the subfamily Pantherinae. Several mitogenomic approaches have been 

employed to reconstruct the phylogenetic history of the Pantherine cats but the phylogeny 

has remained largely unresolved till date. One of the major reasons for the difficulty in 

resolving the phylogenetic tree of Pantherine cats is the small sample size. While 

previous studies included only 5-10 samples, we have used 43 publically available taxa to 

reconstruct Pantherine phylogenetic history. Complete mtDNA sequences were used 

from all individuals excluding the control region (15,489bp). A Bayesian MCMC 

approach was employed to investigate the divergence times among different Pantherine 

clades. Both maximum likelihood and Bayesian phylogeny generated a dendrogram: 



Neofelis nebulosa (Panthera tigris (Panthera onca (Panthera uncia (Panthera leo

Panthera pardus)))), grouping lions with leopards and placing snow leopards as an 

outgroup to this clade. The phylogeny revealed that lions split from their sister species 

leopard ~3 Mya and the divergence time between snow leopards and the clade including 

lions and leopards was estimated to be ~5 Mya. Our study revealed that the morphology-

based subspecies designation for both lions and tigers is largely not valid. The estimated 

tMRCA of 2.9 Mya between Barbary lions and Sub-Saharan African lions depicts the 

restriction of female-mediated gene flow between the lion populations in the backdrop of 

the habitat fragmentation taking place from late Pliocene to early to mid-Pleistocene 

creating islands of forest refugia in central Africa. 

 

 



Key wordsPanthera, Bayesian MCMC, mitogenome, subspecies anomaly 

 

 



 

 

 



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peer-reviewed) is the author/funder. It is made available under a

The copyright holder for this preprint (which was not

http://dx.doi.org/10.1101/082891



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bioRxiv preprint first posted online Oct. 24, 2016; 




Introduction 

 

The charismatic big cats: tiger (Panthera tigris), lion (Panthera leo), leopard (Panthera 



pardus), snow leopard (Panthera uncial), and jaguar (Panthera onca) are grouped into 

the subfamily Pantherinae (Bagatharia, et al., 2013). All of these big cats are endangered 

and are found in small fragmented populations in the world. Tigers are given an 

endangered status by IUCN (IUCN, 2015). They are currently found in Siberian taiga and 

grasslands (Siberian tiger, 

P. t. altaica)

, small pockets in Southeast Asia (Indochinese 

tiger, 

P. t. corbetti

, and Malayan tiger, 



P. t. jacksoni),

 Southern China (South China tiger, 



P. t. amoyensis

), island of Sumatra (Sumatran tiger, 



P. t. sumatrae)

, and the mangrove 

swamps of Indian subcontinent (Bengal tiger, 

P. t. tigris) (Luo, et al., 2004)

. Lions are 

given a vulnerable conservation status (IUCN, 2015). They are found in two widely 

isolated geographical areas: various parts of Africa (African lion), and the Gir forest of 

Southwestern Gujarat, India (Asiatic lion) (Hemmer, 1966). While all Asiatic lion belong 

to the same subspecies (P. l. persica), the African lions are grouped into five separate 

subspecies: Barbary lion (Northern Africa, P. l. leo), Senegal lion (West-central Africa, 

P. l. senegalensis), Masai lion (East African lion, P. l. nubica), Katanga lion (Southwest 

Africa, 


P. l. bleyenberghi), and Transvaal lion (Southeast Africa, P. l. krugeri) (Hemmer, 

1966)


. Leopards are designated as near threatened by IUCN (IUCN, 2015). These 

charismatic cats have a wide range of distribution from in sub-Saharan Africa to 

Southeast Asia and Siberia. There are currently nine recognized subspecies of leopard: 

African leopard (P. p. pardus), Arabian leopard (P. p. nimr), Persian leopard (P. p. 



saxicolor), Indian leopard (P. p. fusca), Sri Lankan leopard (P. p. kotiya), Indochinese 

leopard (P. p. delacouri), North-Chinese leopard (P. p. japonensis), Siberian leopard (P. 



p. orientalis), and Javan leopard (P. p. melas) (Uphyrkina, et al., 2001). Snow leopards 

are listed as endangered in IUCN Red List of Threatened Species (IUCN, 2015). They are 

native to mountains of Central and South Asia. Jaguars are nearly endangered according 

to IUCN Red List (IUCN, 2015) and they are native to southern North America, Central 

and South America. There are three recognized subspecies of jaguar: Amazon jaguar (P. 

o. onca), Mexican jaguar (P. o. hernandesii), and Brazilian jaguar (P. o. palustris

(Seymour, 1989).  

Reconstruction of the phylogenetic history of these charismatic cats can provide us a 

plethora of information about their species, subspecies, and population genetic status, 

which can be helpful for the conservation of these threatened animals. 

Several morphological, biochemical, and molecular approaches have been 

employed to resolve the phylogenetic history of the Pantherine cats such as 

morphological (Salles, 1992), cytogenetic (Wurster-Hill and Gray, 1975), immunological 

(Collier and O'Brien, 1985), biochemical (Slattery, et al., 1994), sex-chromosome based 

(Slattery and O'Brien, 1998), chemical (Bininda Emonds, Decker Flum and 

Gittleman, 2001), and molecular genetic (Bagatharia, et al., 2013; Johnson, et al., 2006; 

Johnson and O’brien, 1997; Wei, et al., 2011). In spite of several trials to reconstruct the 

phylogenetic history of Pantherine cats, their phylogeny has remained largely unresolved. 

Johnson et al. (2006) grouped snow leopards with tigers based on 

18,853 bp of nuclear 

DNA concatenated data 

(Johnson, et al., 2006)

. In contrast, a later phylogenetic analysis 

grouped snow leopards with lions based on their complete mtDNA sequences (Wei, et 

al., 2011). They estimated that 

N. nebulosa shared a common ancestor with other 

.

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peer-reviewed) is the author/funder. It is made available under a

The copyright holder for this preprint (which was not

http://dx.doi.org/10.1101/082891



doi: 

bioRxiv preprint first posted online Oct. 24, 2016; 




Pantherine cats about 8.66 Mya and that the leopards shared a common ancestor with the 

lion-snow leopard clade about 4.35 Mya. Recently, another mitogenomic study grouped 

lion and leopards together and placed snow leopard as the sister taxa to this clade 

(Bagatharia, et al., 2013). Although Panthera phylogeny has been reconstructed multiple 

times, none of these studies used multiple subspecies of Pantherine cats. So, the 

subspecies anomaly remained unresolved. 

All previous phylogenetic studies were performed using 5-10 Pantherine cats, 

taking one individual from each species, which made it difficult to assess the 

phylogenetic tree at a high resolution and determine the subspecies level genetic 

diversity. In the present study we have used complete mitochondrial DNA sequences 

excluding the control region (15,489bp) from 43 publicly available Pantherine taxa 

including multiple individuals and subspecies of big cats to resolve the phylogenetic 

history of the gennus Panthera and to genetically validate the ‘subspecies’ status of 

various Pantherine taxa. This study thus offers an unparalleled and in-depth view of 

Pantherine phylogeny and genetically assess the ‘subspecies’ question that has remained 

elusive till date, which can aid in providing more effective conservation measures for 

these charismatic big cats. 

Methods 

Molecular phylogenetic analysis 

 

We retrieved 43 publicly available Pantherine mitogenomes including all available 



subspecies of six charismatic cats: tiger, lion, leopard, snow leopard, jaguar, and Neofelis 

from GenBank (Benson, et al., 2004) (Table 1). The mitogenome sequences were first 

aligned using Clustal Omega online server (Sievers, et al., 2011). The fasta alignment of 

the complete mitogenome sequences was then exported to MEGA v6.06, where the 

control region (D-loop) sequences were eliminated. Pair-wise genetic distances among 

the Pantherine taxa were calculated in MEGA v6.06 (Tamura, et al. 2013). A model test 

was performed to determine the best fitting nucleotide substitution model for the dataset, 

using Akaike’s information criteria with correction (AICc) and Bayesian information 

criteria (BIC) using jModelTest v2.1.4 (Guindon and Gascuel, 2003). The alignment of 

43 Pantherine taxa was used for maximum likelihood phylogenetic reconstruction, with 

1000 bootstrap replicates, using MEGA v6.06. Bayesian phylogenetic tree was 

reconstructed using MrBayes v3.2.5 (Huelsenbeck and Ronquist, 2001). 



Dating the phylogenetic tree 

!

For dating, we used a Bayesian Markov Chain Monte Carlo approach (MCMC) 



implemented in BEAST v1.8.2 (Drummond, et al., 2012). The BEAST input file was 

generated using BEAUTi v1.8.2 (Drummond, et al., 2012). An uncorrelated lognormal 

relaxed molecular clock was used to allow the evolutionary rate to vary from branch to 

branch. Previous studies have shown that has showed that relaxed molecular clock 

provides better estimate of time to most recent common ancestor (tMRCA) over the strict 

molecular clock that does not allow the evolutionary rate to vary among branches 

(Drummond, et al., 2006). SRD06 model of nucleotide substitution was used to partition 

.

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peer-reviewed) is the author/funder. It is made available under a

The copyright holder for this preprint (which was not

http://dx.doi.org/10.1101/082891



doi: 

bioRxiv preprint first posted online Oct. 24, 2016; 




the nucleotide data by codon position. The rate of evolution was calibrated using 

lognormally distributed priors with lognormal means of zero and lognormal standard 

deviation of 0.56. Since lognormally distributed priors sample values from the more 

distant past more frequently than recent values, it performs better than both normally 

distributed and exponentially distributed priors, when using fossil calibration points for 

dating a phylogenetic tree (Ho, 2007). We offset the lognormal distributions of the priors 

at the internal node of Panthera-Neofelis split by 7 Mya, so that the median values of the 

sampled distributions were equal to and the mean values were slightly greater than the 

split date of ~8 Mya between the two. This calibration method has been previously 

employed for reconstructing phylogenetic history of other mammalian subfamily level 

taxa (Bjork, et al., 2011; Das, et al., 2014; Raaum, et al., 2005). Yule speciation process, 

which has been shown to be more appropriate when analyzing sequences from different 

species, was used for the divergence estimation (Stone, et al., 2010). 

MCMC simulation ran for 10 million generations, sampling every 500 steps. 10% 

of the trees were removed as ‘burnin’. The maximum clade credibility (MCC) tree was 

identified and annotated using TreeAnnotator v1.8.2 (Drummond, et al., 2012). Nodes 

with posterior probabilities exceeding 90% (P > 0.9) were used for the tree building. The 

MCC tree generated by TreeAnnotator v1.8.2 was visualized and graphically represented 

using FigTree v1.4.2 (

http://tree.bio.ed.ac.uk/software/figtree

). The posterior estimates of 

the parameters sampled by the Markov Chain was summarized in Tracer v1.6 (Rambaut 

and Drummond, 2013). tMRCA means, medians, and 95% highest posterior density 

(95% HPD) intervals (all in Myr) were also calculated in Tracer v1.6.  



Results 

Sequence divergence and the subspecies dilemma 

 

Among lions, identical nucleotide sequences were observed among P. l. senegalensis 



(KP001502), P. l. azandica (KP001506), P. l. nubica (KP001495), and P. leo 

(NC_028302), raising questions about the validity of the different subspecies status for 

these individuals. The two Barbary lions (KF776494 and KF907306) are genetically most 

distant from the rest of the clade, showing 2.2 - 3% divergence of the mitogenome. The 

remaining lion subspecies shows 0 - 0.6% genetic divergence among each other. Our 

results thus indicate that the morphological variation among the different African lion 

populations may not be enough to consider them as different ‘subspecies’. 

The validity of the subspecies status is also questionable in case of the tigers with 



P. t. amoyensis (HM589215) and P. t. altaica (HM185182) showing identical nucleotide 

sequences. The mean tiger mitogenome divergence was 0.5% and the largest divergence 

was observed between the Amoy tigers (HM589214 and HM589215) and the rest of the 

tree (1.2%). Thus, similar to lions, most of the tiger subspecies are also potentially not 

valid genetically. 

Leopard subspecies show 0 – 0.9% genetic divergence among each other with the 

highest divergence between P. p. pardus (KP001507) and P. p. japonensis (EF551002) 

(0.9%).  

.

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peer-reviewed) is the author/funder. It is made available under a

The copyright holder for this preprint (which was not

http://dx.doi.org/10.1101/082891



doi: 

bioRxiv preprint first posted online Oct. 24, 2016; 




 

Phylogenetic analyses 

!

The maximum likelihood (ML) tree was constructed using Hasegawa-Kishino-Yano 



model of nucleotide substitution with gamma distribution and invariable sites 

(HKY+G+I), which was selected to be the best fitting model for the dataset by 

jModelTest v2.1.4. The ML based phylogeny grouped lions (N = 16) and leopards (N = 

5) together with 100% bootstrap support and placed show leopards (N = 3) as the sister 

taxa to this clade (100% bootstrap support) (Figure 1). Jaguars (N = 4) were designated to 

be the sister taxa of the lion-leopard-snow leopard clade (Figure 1). The deepest root 

within the lions was observed between the Barbary lions (P. l. leo) and the rest of the 

subspecies with 100% bootstrap support (Figure 1). For the tigers (N = 13), the deepest 

root was observed between the Amoy tigers and the rest (100% bootstrap support) 

(Figure 1). Similar grouping of the Patherine taxa was revealed in the Bayesian 

phylogenetic tree (Figure 2). Overall, the phylogenetic analyses revealed a dendrogram: 

Neofelis nebulosa (Panthera tigris (Panthera onca (Panthera uncia (Panthera leo

Panthera pardus)))). 

Estimates of divergence dates 

 

As mentioned before (see methods) a single calibration point of Neofelis-Panthera split 



of 8 Mya was used to estimate the divergence time. Similar to the ML tree, the Bayesian 

tree also grouped lions and leopards together and placed snow leopard as the sister taxa to 

this clade. The MCMC analysis employed in BEAST revealed that lions split from its 

sister species leopard 3.45 Mya (1.75 – 5.17) (Table 2). The divergence time between 

snow leopards and the clade including lions and leopards was estimated to be 4.97 Mya 

(2.9 -7.24) (Table 2). Tigers appeared to split from the rest four charismatic big cats 7.47 

Mya (4.97 – 9.24) (Table 2). The deepest roots within the tigers was estimated to be ~2 

Mya between the Amur tiger and the remainder of the tiger clade (Table 2). As revealed 

by the ML tree, the deepest split within lions was between the Barbary lions and the 

remainder of the subspecies (including all Sub-Saharan African and Asian subspecies) 

(2.87 Mya). The divergence between the Asian lions from the East-Central African 

subspecies is relatively new 1.39 Mya (0.63 – 4.2) (Table 2). 



Discussion 

mtDNA based phylogeny: advantages of large sample size 

 

For the last two decades mtDNA is being used to reconstruct Pantherine phylogeny. 



However, all previous phylogenetic analyses in this regard were employed using 5 – 10 

Pantherine taxa. Moreover, none of them included multiple subspecies and/or individuals 

from a species. Consequently, the deepest root within the species remained largely 

unknown. Also, due to low resolution, the Pantherine species were often wrongly 

grouped, often generating contrasting results. For instance, Johnson et al (2006) grouped 

.

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peer-reviewed) is the author/funder. It is made available under a

The copyright holder for this preprint (which was not

http://dx.doi.org/10.1101/082891



doi: 

bioRxiv preprint first posted online Oct. 24, 2016; 




snow leopards with tigers and Wei et al. (2011) grouped

 them with lions 

(Johnson, et al.

2006; Wei, et al., 2011)

.

  

We used 43 Pantherine taxa in this study, including individuals and subspecies 



from all charismatic big cats. Complete mtDNA sequences excluding the control regions 

(15,489bp) were used for phylogenetic analysis. The control regions were excluded in 

this study on two major accounts: i) this area of the mitogenome is very difficult to align 

across the big cats and ii) the repeat sequences found in this region results in different 

mitogenome sizes across the Pantherine cats (Bagatharia, et al., 2013). Therefore several 

recent phylogenetic studies on Pantherine cats have either included only the protein 

coding genes or the complete mtDNA sequence excluding the control region (Bagatharia

et al., 2013; Wei, et al., 2011). Proper and systematic sampling method employed here 

aids to the robustness of the analyses by increasing the statistical power. Both ML and 

Bayesian based phylogeny revealed the same grouping of all Pantherine taxa.  

Overall, the current study revealed a dendrogram: Neofelis nebulosa (Panthera 



tigris (Panthera onca (Panthera uncia (Panthera leoPanthera pardus)))). The inclusion 

of multiple individuals and subspecies from all species and incorporation of jaguars has 

helped to reconstruct hitherto unresolved Pantherine phylogeny with high confident. 

Snow leopards are genetically distant from the tigers with 7.5 – 8.1% sequence 

divergence and therefore grouping them with tigers is potentially an artifact of improper 

and inadequate sampling (Johnson, et al., 2006). Lions are genetically close to both 

leopards (4 – 5% sequence divergence) and snow leopards (5.5 – 6.1% sequence 

divergence). So, if multiple individuals from all species are not included in the analyses, 

lions can be, at random, wrongly grouped with snow leopards, and this is what has 

potentially occurred in case of the phylogeny described in Wei et al. (2011) 

who used 

only six Pantherine taxa in their study (Wei, et al., 2011). Unlike the aforementioned 

studies, the recent-most Pantherine tree described in Bagatharia et al. (2013) revealed 

correct species level phylogeny by grouping lions and leopards together and placing snow 

leopards as the sister species to the lion-leopard clade. But 

the low sample size (six 

Pantherine cats) of the study and the exclusion of jaguars in all analyses resulted in a low-

resolution phylogeny. 



Subspecies anomaly  

 

Our study raised question on ‘subspecies’ designation based on morphology. In most 



cases we found that the current ‘subspecies’ designation is not genetically valid and 

needs serious taxonomic change.  

For instance, current lion subspecies status is largely based on morphological 

characteristics mentioned in Hemmer (1966) (Hemmer, 1966). The current study raises 

questions about the authenticity of the subspecies status of various Sub-Saharan African 

lion subspecies based on morphology. Although currently geographically isolated, P. l. 



senegalensis (KP001502), P. l. azandica (KP001506), P. l. nubica (KP001495), and P. 

leo (NC_028302) share identical nucleotide sequences. In contrast, the two P. l. 

senegalensis individuals (KP001497 and KP001502) show 0.3% nucleotide divergence. 

Similar nucleotide divergence (0.4%) was observed between the two P. l. bleyenberghi 

individuals (KP001504 and KP001505). These results indicate recent geographical 

isolation of Sub-Saharan African lion populations, who potentially have not yet 

accumulated subspecies level genetic divergence. For decades’ authors have debated on 

.

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peer-reviewed) is the author/funder. It is made available under a

The copyright holder for this preprint (which was not

http://dx.doi.org/10.1101/082891



doi: 

bioRxiv preprint first posted online Oct. 24, 2016; 




the exact number of lion subspecies (eight vs. ten). Our study conclusively revealed that 

there are potentially only three ‘subspecies’ of lion currently exists in this planet: North 

African Barbary Lion, Sub-Saharan African Lion, and Asiatic Lion. The genetic 

variations observed among the Sub-Saharan African Lions are potentially mere individual 

variations. 

The validity of the subspecies status is also questionable in case of the tigers with 



P. t. amoyensis (HM589215) and P. t. altaica (HM185182) showing identical nucleotide 

sequences and two P. t. altaica individuals (HM185182 and JF357973) showing high 

(1.1%) nucleotide divergence. The aforementioned results clearly indicate more 

individual level variation (intra-population) than subspecies level variation (inter-

population), raising questions about the validity of morphology-based subspecies 

designation. It can be speculated that if more samples were analyzed, individuals from 

different populations would have grouped together disobeying their current ‘subspecies’ 

status.  



 

Migration and isolation of Pantherine taxa 

!

Tigers potentially split from other five big cats sometime in late Miocene. As speculated 



in previous studies, Panthera species such as lions potentially migrated into America and 

Africa from Asia in the Pliocene (Werdelin and Lewis, 2005). The migration path of the 

Pantherine cats mentioned in Johnson et al. (2006) fits with the divergence times of 

Pantherine cats mentioned in this study 

(Johnson, et al., 2006). Snow leopards potentially 

got isolated from lions and leopards in early Pliocene (~5Mya), when these cats started 

migrating to Africa.

 

The estimated tMRCA of 2.9 Mya between Barbary lions and the 



Sub-Saharan African lions is an indication of potential restriction of female-mediated 

gene flow between these populations. The habitat fragmentation from late Pliocene to 

early to mid-Pleistocene resulted in the islands of forest refugia in central Africa, 

isolating Barbary lions from other lion populations. However, migration and intermixing 

potentially continued among the Sub-Saharan African subspecies till forests were 

converted into the savannas during late Pleistocene. Additionally it is interesting to note 

that be noted here that the mitogenome divergence among the lion populations potentially 

began at the same time as other African mammals such as chimpanzees, bonobos, and 

gorillas. Overall, this study provides a holistic and in-depth view of Pantherine 

phylogeny, indicating the importance of using large number of samples for confident 

resolution of mammalian phylogenetic history. 

.

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Table 1. Gen Bank IDs, common, and scientific names of the Pantherine samples used in this study 

 

 

Species 

Common name 

Subspecies 

Common name 

Gen Bank IDs 

1. Panthera tigris (N = 13) 

Tiger 

a) Panthera tigris amoyensis (N= 2) 



Amoy tiger 

HM589214, HM589215 

 

 

b) Panthera tigris altaica (N= 4) 



Siberian tiger 

HM185182, JF357973, JF357974, KF297576 

 

 

c) Panthera tigris tigris (N= 3) 



Bengal tiger 

JF357967, JF357968, NC_010642 

 

 

d) Panthera tigris sumatrae (N= 1) 



Sumatran tiger 

JF357969 

 

 

e) Panthera tigris jacksoni (N= 1) 



Malayan tiger 

KJ508413 

 

 

f) Panthera tigris corbetti (N= 1) 



Indochinese tiger 

KJ508412 

 

 

g) Not mentioned (N= 1) 



Not mentioned 

KP202268 

2. Panthera leo (N = 16) 

Lion 


a) Panthera leo leo (N= 2) 

Barbary lion 

KF776494, KF907306 

 

 



b) Panthera leo persica (N= 4) 

Asiatic lion 

JQ904290, KC834784, KP001501, NC_018053 

 

 



c) Panthera leo senegalensis (N= 2) 

West African lion 

KP001502, KP001497 

 

 



d) Panthera leo azandica (N= 1) 

Congo lion 

KP001506 

 

 



e) Panthera leo nubica (N= 3) 

Masai lion 

KP001495, KP001498, KP001499 

 

 



f) Panthera leo bleyenberghi  (N= 2) 

Southwast African lion 

KP001504, KP001505 

 

 



g) Panthera leo krugeri  (N= 1) 

Transvaal lion 

KP001500 

 

 



h) Not mentioned (N= 1) 

Not mentioned 

NC_028302 

3. Panthera pardus (N = 5) 

Leopard 

a) Panthera pardus pardus (N= 1) 

African leopard 

KP001507 

 

 

b) Panthera pardus japonensis (N= 2) 



North-Chinese leopard 

EF551002, KJ866876 

 

 

h) Not mentioned (N= 2) 



Not mentioned 

KP202265, NC_010641 

4. Panthera uncia (N = 3) 

Snow leopard 

NA 

NA 


EF551004, KP202269, NC_010638 

5. Panthera onca (N = 4) 

Jaguar 

NA 


NA 

KF483864, KM236783, KP202264, NC_022842 

6. Neofelis nebulosa (N = 2) 

Clouded leopard 

NA 

NA 


KP202291, NC_008450 

.

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Table 2. tMRCA dates with confidence intervals 

 

 



Taxon divergence 

tMRCA mean

a

 

95% HPD

b

 

Median 

Neofelis - Panthera 

8.03 


7.222 - 9.213 

7.894 


Tiger - Lion/Leopard/Snow leopard/Jaguar 

7.467 


4.972 - 9.236 

7.655 


Jaguar - Lion/Leopard/Snow leopard 

6.708 


3.923 - 8.850 

6.94 


Snow leopard - Lion/Leopard 

4.968 


2.9 - 7.243 

4.852 


Lion - Leopard 

3.45 


1.746 - 5.166 

3.398 


Deepest root within tiger 

2.333 


0.932 - 3.868 

2.252 


Asian and East-Central African lions 

1.39 


0.63 - 4.2 

0.85 


a

Time to most recent common ancestor, in Myr. 

b

95% highest posterior density 



 

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Figure 1. Consensus maximum likelihood tree (HKY+I+G model) of 43 Pantherine taxa. 

Percentage of bootstrapped replicates supporting each node (out of 1,000 bootstraps) are 

shown. The nodes with less than 50% bootstrap support are not shown. The Neofelis cats 

were used as the outgroup to the genus Panthera. The individuals with unknown 

subspecies status are marked with an asterisk.

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Figure 2. Phylogeny of 43 Pantherine taxa based on complete mtDNA sequences 

excluding the control region. The dates were inferred using a Bayesian MCMC approach 

implemented in BEAST with Neofelis-Panthera divergence offset by 7 Myr to 

approximate a 8 Mya date for Neofelis-Panthera split. Individuals with uknown 

subspecies status are indicated with an asterisk.

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