iDarwin AS 0022 (2022 AD)

Volume 2

Original Article
iDarwin volume 2, pages 39-51
Published on November 3, AS 0022 (2022 AD)
Phylogenetic analysis of camel complete mitochondrial DNA sequences
Gulnur ZHUNUSSOVA1,2,3, Kairat DOSSYBAYEV1,4, Timothy A. JINAM1, SUZUKI Rumiko1,5, and SAITOU Naruya1,5
1 Population Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
2 Laboratory of Molecular Genetics, Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan
3 Department of Fundamental Medicine, Al-Farabi Kazakh National University, 050040 Almaty, Kazakhstan
4 Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan
5 SAITOU Naruya Laboratory, National Institute of Genetics, Mishima 411-8540, Japan

Note: This study was conducted in AS 0020 when G.Z. and K.D. stayed at Population Genetics Laboratory of NIG for one year. S.N. retired from NIG in March AS
0022, and he is now specially appointed professor of NIG at SAITOU Naruya Laboratory.

Corresponding author: Saitou Naruya (Email: saitounr@nig.ac.jp)

Abstract
One-humped and two-humped camels diverged 4-5 million years ago, however, they produce fertile hybrids. We are thusinterested in the phylogenetic relationship of mitochondrial DNA sequences of these camels to detect any introgression between
these two camel species. We conducted a phylogenetic analysis of complete mitochondrial DNA (mtDNA) sequences of 26 and
156 individuals of one-humped camels (Camelus dromedarius) and two-humped camels (C. bactrianus and C. ferus),
respectively, as well as those of other camelid species. MAFFT was used for multiple alignment, and the neighbor-joining andmaximum likelihood methods were used for phylogenetic tree construction. Seven camel mtDNA sequences from Iran,Kazakhstan, and Russia had statistically signi cant heterogeneity of evolutionary rates using Tajima’s test, though mtDNA
sequences of closely related species are expected to be under a molecular clock. We found that these problematic sequences had

fi39

iDarwin AS 0022 (2022 AD)

Volume 2certain mapping problems. After remapping of short-read sequences, we obtained six mtDNA sequences different frompreviously reported ones. Two of these re-determined mtDNA sequences were originated from morphologically two-humped
camels. However, their mtDNA sequences were very similar to those of one-humped camels. We conclude that these two camel
species have been hybridizing for some time, because introgression of mtDNAs were inferred in this study.
Keywords: mtDNA, bactrian camel, dromedary, introgression, short-read sequences

Introduction
Family Camelidae belongs to Cetariodactyla, and their lineage (Tylopoda) diverged from the common ancestor of Ruminantia
and Cetanodonta more than 60 million years ago (Zurano et al., 2018). Camelidae includes humped type Camelus and nonhumped type Lama and Vicugna. Camelus are distributed in the Old World (Eurasia and Africa), while Lama and Vicugna are
distributed in South America. There are three extant species of genus Camelus; C. bactrianus (bactrian camel), C. ferus (wildcamel), and C. dromedarius (dromedary). C. bactrianus and C. ferus are two-humped camels, and are distributed from East toCentral Asia, including Kazakhstan (Imamura et al., 2017). C. dromedarius is a one-humped camel distributed in Central Asia,
South Asia, North Africa, and Australia (Burgher et al., 2019). C. bactrianus and C. dromedarius are domesticated, but C. ferus
remains wild. Camelidae in South America include domesticated (alpaca and llama) and wild (guanaco and vicuna) populations.
The divergence time between one-humped and two-humped camel lineages was estimated to be 4.4 (con dence intervals 1.9-7.2)
million years ago based on whole nuclear genome sequence data (Wu et al., 2014).
Nowadays, many complete mtDNA sequences were determined for Camelidae. Saitou and Shokat (2017) collected 37
complete mtDNA sequences of camelids available at that time from the DDBJ/ENA/GenBank International Nucleotide Sequence
Database. These mtDNA sequences included those of now-extinct Camelops, which were distributed in North America(Heinzman et al., 2015). Saitou and Shokat (2017) conducted phylogenetic analyses of these camelid mtDNA sequences, andinferred evolution of Camelidae with special reference to genus Camelus.
Recently many more camel mtDNA data were published, especially by Ming et al. (2020), who determined whole-genome
sequences of 128 camels. We thus conducted phylogenetic analyses of complete camelid mtDNA sequences currently available,
and would like to suggest a possibility of frequent introgression of mtDNA between C. bactrianus and C. dromedarius in Eurasia.

fi

40

iDarwin AS 0022 (2022 AD)

Volume 2

Materials and Methods
Data sources
Camelid complete mtDNA genome sequences were obtained from the DDBJ/ENA/GenBank International Nucleotide Sequence
Database. We found that NCBI presents three camel species mtDNA sequences only in their genome database under NCBIspeci c IDs (NC_009628, NC_009629, and NC_009849). All these sequences are listed in Supplementary Table 1 (http://idarwin.org/docs/vol2_suppl_ les_1/Suppl_Table_1.pdf). There are a total of 191 complete mtDNA sequences; 32 individuals of
C. ferus from Mongolia, 124 individuals of C. bactrianus (35 from Mongolia, 56 from China, 7 from Kazakhstan, 10 from
Russia, 14 from Iran, 1 from Austria, and 1 from Japan; see the map shown in Supplementary Figure 1A (http://idarwin.org/docs/
vol2_suppl_ les_1/Suppl_Fig_1.pdf), 26 individuals of C. dromedarius (14 from Iran, 3 from Saudi Arabia, 3 from UAE(Dubai), 1 from Qatar, 1 from Kenya, 1 from Sudan, 1 from Morocco, 1 from Pakistan, and 1 from Austria; see the map shown in
Supplementary Figure 1B (http://idarwin.org/docs/vol2_suppl_ les_1/Suppl_Fig_1.pdf), 3 individuals of extinct Camelops from
North America, 4 individuals of Lama and 2 individuals of Vicugna from South America. Bos taurus (cow), Ovis aries (sheep),and Pantholops hodgsonii (Tibetan antelope) were used as the outgroup. Table 1 shows a summary of the camelid sequence data
used in this study.
Phylogenetic analyses
Multiple alignment of these 191 camelid mtDNA sequences and the three outgroup species was conducted using MAFFT
version 7 (Katoh and Standley, 2013), and pairwise numbers of nucleotide substitutions were estimated by using Tamura andNei’s (1993) method. The neighbor-joining method (Saitou and Nei 1987) and a maximum likelihood method implemented in
MEGAX (Kumar et al., 2018) were used for construction of phylogenetic trees. The reliability of the branches in the tree was
evaluated by the bootstrap method with 1,000 replications. The “complete deletion” option was used for excluding all positions
containing gaps and missing data. These evolutionary analyses were conducted by using MEGAX. Tajima’s (1993) branch length
heterogeneity test was also conducted using MEGAX.
Additionally, mtDNA sequences were extracted from whole-genome Next Generation Sequencing (NGS) raw les.
Paired-end FASTQ les were downloaded from the NCBI BioProject database (accession number PRJNA383081) reported by
Ming et al. (2020). Quality control, adapter trimming and quality ltering were conducted using fastp tool (Chen et al., 2018).

fi

fi

fi

fi

fi

fi

fi

41

iDarwin AS 0022 (2022 AD)

Volume 2

Table 1. List of mtDNA complete sequences of camelid species
Numbers in parentheses after region names are number of camel mtDNA sequences from that region.
———————————————————————————————————————————————————(A) Camelus dromedarius
Austria (1): KU605076
Iran (14): KX554931-KX554934, MH109998-MH1100071
Kenya (1): KU605078
2
Morocco (1): JN632608
Pakistan (1): KU605080
Qatar (1): KU605072
Saudi Arabia (3): KU605073-KU605075
Sudan (1): KU605079
UAE (3): EU159113, KU605077, NC_009849**(B) Camelus bactrianus
Austria (1): KU666460
China: EF2120373, MH109872-MH1099112, MH109931-MH1099452
Iran (14): KX554925-KX554930, MH109990-MH1099972
Japan (1): AP003423
2
Kazakhstan (7): KU666461, MH109984-MH109989
Mongolia (59): EF5077983, EF5077993, KU666462-KU666465, MH109946-MH109972, NC_009628**
Russia (10): MH109974-MH1099832(C) Camelus ferus
Mongolia (32): EF2120383, EF5078003, EF5078013, KU666451-KU666459, MH109912-MH1099302, NC_009629**(D) Cameridae (extinct) from Canada
Camelops sp. (3): KR822420-KR8224224(E) Cameridae from South America
Lama glama (1): AP003426
Lama guanicoe (1): EU6819545
Lama pacos (2): AJ5663646, Y191847
Vicugna pacos (1): KU168760
Vicugna vicugna (1): FJ456892———————————————————————————————————————————————————** NCBI-specific IDs
References: 1) Ming et al. (2020), 2) Hassanin et al. (2012), 3) Ji et al. (2009), 4) Heinzman et al. (2015), 5) di Rocco et al. (2010), 6) Arnason et al. (2004), 7) Ursing et al. (2000)

Trimmed reads were aligned to the mitochondrion complete reference genome of C. ferus (NC_009629), dromedarius(NC_009849) and bactrianus (NC_009628) using the mem-algorithm of the BWA (Li et al, 2009). The mapped reads were sorted
and indexed using SAMtools (Li et al., 2009) and Picard tools (https://broadinstitute.github.io/picard/) was used to mark andremove PCR duplicates from the sorted BAM les. Single-nucleotide variants (SNVs) and indels were called using BCFtools(http://samtools.github.io/bcftools/). VCF format les were converted into FASTA format les by using vcf-consensus option in
VCFtools (https://vcftools.github.io/index.html) developed by Danecek et al. (2011).

fi

fi

fi

42

iDarwin AS 0022 (2022 AD)

Volume 2

Results
We performed a multiple alignment for complete mtDNA sequences
listed in Supplementary Table 1, and eliminated the positions withgaps and missing data. There were a total of 15,739 nucleotide
positions in the nal dataset (data not shown). We then constructed aneighbor-joining tree of 191 mtDNA sequences (Supplementary
Figure 2; http://idarwin.org/docs/vol2_suppl_ les_1/
Suppl_Fig_2.pdf). As the evolutionary distances among many
sequences were very small, we chose only representative 31
sequences, and generated another neighbor-joining tree (Figure 1).
Camelid mtDNA sequences are classi ed into three clusters in thistree; cluster 1 contains one-humped camel (C. dromedarius) and twohumped camel (C. ferus and C. bactrianus), extinct Camelops forms
the second cluster, and South American non-humped camelids (genus
Lama and Vicugna) formed the third cluster. These three clusters are
consistent with the phylogenetic tree shown in Figure 1 of Saitou andShokat (2017).
We focused our phylogenetic analysis on 19 mtDNA
sequences of cluster 1 in Figure 1. The neighbor-joining tree of these
Figure 1. A neighbor-joining tree of representative 31
19 sequences is shown in Figure 2. The root position follows that ofsequences.
cluster 1 in Figure 1 with the mid-point rooting. There are twoclusters, A and B, in Figure 2. Cluster A contains mtDNA sequencesof seven C. bactrianus, three C. ferus, and four C. dromedaries, and Cluster B contains mtDNA sequences of one C. bactrianus
and four C. dromedaries. We also constructed an ML tree (Figure 3) for these sequences, and their branching patterns with highbootstrap values were very similar to those in Figure 2.
Both one-humped camels (C. dromedaries) and two-humped camels (C. bactrianus) are included in these two clusters.

fi

fi

fi

43

iDarwin AS 0022 (2022 AD)

Volume 2

This pattern is quite different from Figure 2 of Saitou and Shokat (2017) in which C. dromedaries and C. bactrianus formed two
distinct monophyletic clusters. The divergence time of one-humped
and two-humped camels was estimated to be 4.4 million years ago(Wu et al., 2014). We expect a clear-cut cluster for mtDNA sequencesof these two camel species as shown by Saitou and Shokat (2017).
Ming et al. (2020) constructed a phylogenetic tree of mtDNA
sequences using a maximum-likelihood method (see their Figure 3C).
They suggested independent introgression events in two C. bactrianus

Figure 2. A neighbor-joining tree of 19 complete
mtDNA sequences of camels. Sequence IDs are the samewith those of Supplementary Table 1.

Figure 3. A maximum likelihood tree using the same
mtDNA sequences used for the neighbor-joining tree in
Figure 2.

mtDNA sequences that are included in our Figure 2; C_bact_85
Kazakhstan (accession number MH109985) and C_bact_74
Russia (accession number MH109974). Interestingly, these twosequences have considerably shorter branches from the root thanthe other sequences (see Figures 2 and 3). The evolutionary rate of
mtDNA among congeneric species is expected to be roughly thesame under the neutral evolution (e.g., Saitou [2018]). Therefore,
some unexpected situation may exist for these two sequences.
We thus used Tajima’s (1993) test for these two sequences
44

iDarwin AS 0022 (2022 AD)

Volume 2(C_bact_85 Kazakhstan and C_bact_74 Russia) as well as ve more mtDNA sequences (C_bact_12, C_drom_17, C_drom_18,
C_drom_22, and C_drom_23) fromIran, whose branch lengths are somewhat shorter than the remaining 12 sequences (seeFigures 2 and 3). The result is shown in Table 2. All the seven sequences were statistically shorter than control sequences. This
result is inconsistent with the expected pattern for mtDNA sequences with the putatively same evolutionary rates.
Table 2. Result of Tajima’s (1993) test for seven sequences––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––-––––––––––––
Set

Short branchControl

Outgroup

Chi-squarepID

sequence

sequence*

sequence*

value

value

–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
1

C_bact_74 Russia

AB

244.98

6.36E-542

C_bact_85 Kazakhstan

BA

383.794.58E-84

3

C_drom_17 Iran

B

A

78.54

8.82E-18

4

C_drom_18 Iran

B

A

45.96

1.05E-10

5

C_drom_22 Iran

B

A

73.93

8.84E-17

6

C_drom_23 Iran

B

A

73.48

1.11E-16

7

C_bact_12 Iran

B

A

17.61

1.50E-04––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––-––––––––––––* Sequence A = C_drom_5_Saudi Arabia, Sequence B = C_bact_1 Japan

Ming et al. (2020) used C. ferus as the reference sequence of mtDNA for morphologically bactrian (two-humped) camel.
We thus remapped all short read data reported by Ming et al. (2020) to the reference dromedary (one-humped camel) mtDNA
sequence (NC_009849), and obtained mtDNA sequences. Somehow, C_bact_12 short read data did not exist in the database, andwe omitted this individual from mapping. Mitochondrial DNA sequences of six camels were quite different from those reportedby Ming et al. (2020). Then we tried mapping of the short read data of the six camels onto mitochondrial sequences of C.

fi

45Volume 2

bactrianus and C. dromedarius. The resulted sequences were all close to C. dromedarius whichever reference was used. The vcf
les of the mapping also showed that variant calls were the least when C. dromedarius was used as the reference (supplementary
vcf les 1 – 18; http://idarwin.org/docs/vol2_suppl_ les_1/Suppl_vcf_ les.pdf).
This means that these six camels aremorphologically two-humped like C. ferus or C. bactrianus but their mitochondria are close to one-hump camel, C. dromedarius,
probably because of maternal hybridization in the past. Therefore, we employed mitochondrial sequences mapped onto C.
dromedarius for these six camels. These re-determined mtDNA sequences were deposited to DDBJ as TPA (third party
annotation), as listed in Table 3.
Table 3. A list of 6 TPA entries for remapped camel mtDNA sequences––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––-–––––––––––––––––––––––
Camel
Short read
Assembly
Morphology
mtDNA lineage––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––-–––––––––––––––––––––––
C_bact_74 Russia
SRR5563521
BR001658
Two-hump
One-hump
MH109974
Cluster B (one-hump)
C_bact_85 Kazakhstan
SRR5563543
BR001659
Two-hump
One-hump
MH109985
Cluster A (one/two mix)
C_drom_17 Iran
SRR5563504
BR001657
One-hump
One-hump
MH110001
Cluster A (one/two mix)
C_drom_18 Iran
SRR5563498
BR001654
One-hump
One-hump
MH110002
Cluster A (one/two mix)
C_drom_22 Iran
SRR5563499
BR001655
One-hump
One-hump
MH110006
Cluster A (one/two mix)
C_drom_23 Iran
SRR5563500
BR001656
One-hump
One-hump
MH110007
Cluster A (one/two mix)––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––-–––––––––––––––––––––––The “assembly” column shows the DDBJ/ENA/GenBank accession numbers of mitochondrial DNA assembled by us (above) and by Ming et al.
(below). The “mtDNA lineage” column indicates the clusters our sequences belonged to in Figure 2 (above) and that of the Ming’s sequences in Figure
1 (below).

We used these new six mtDNA sequences determined by us for phylogenetic tree construction (Figure 4). All the six
mtDNA sequences are now very close to typical dromedary mtDNA sequences (C_drom_1, C_drom_5, C_drom_9, and

fi

fi

46

fi

fi

iDarwin AS 0022 (2022 AD)

iDarwin AS 0022 (2022 AD)

C_drom_15),
clear-cut cluster.
morphologicallyour new mtDNA
C_bact_74

Volume 2

and formed aA l t h o u g h
two-humped,
sequences of

Figure 4. A neighbor-joining tree of 19 complete mtDNA sequences of camels. Numbers in the branches represent thebootstrap values (%) from 1,000 replicates. Two clusters are named as Two-hump Cluster and One-hump Cluster. Six
sequences re-determined from short read data (SRR IDs are given
47 to them) are all belonging to One-hump Cluster.

iDarwin AS 0022 (2022 AD)

Volume 2

and C_bact_85 from Russia and Kazakhstan, respectively, arevery similar to mtDNA sequences of one-humped camels. We
named this cluster as “One-hump Cluster” in Figure 4. The othercluster contains ferus and bactrian mtDNA sequences, and we
named this cluster as “Two-hump Cluster” in Figure 4. The
external branch for the C_bact_12 sequence is still somewhat
shorter than other sequences in this cluster. An ML tree obtained
for the same 19 sequences (Figure 5) had an identical branchingpattern with that for the NJ tree (Figure 4) for branches with highbootstrap values.
There is one possibility that the noncoding region (socalled D-loop) is the major cause of error made by Ming et al.
(2020). We thus eliminated the noncoding region and constructed
phylogenetic trees. Supplementary Figure 3 (http://idarwin.org/
docs/data/vol2_suppl_ les_1/Suppl_Fig_3.pdf) shows four trees
and they correspond to those of Figure 2 (Supp. Fig. 3A), Figure
3 (Supp. Fig. 3B), Figure 4 (Supp. Fig. 3C), and Figure 5 (Supp.
Fig. 3D). In all cases, phylogenetic trees using complete mtDNA
sequence data (Figures 2-5) and those without the noncoding
region (Supp. Figs. 3A-3D) are more or less the same. Therefore,
sequence errors of Ming et al. (2020) are not focused on thenoncoding region.

Figure 5. A maximum likelihood tree using the same
mtDNA sequences used for the neighbor-joining tree in
Figure 4.

Discussion
When we constructed phylogenetic trees for camel mtDNA sequences, we found some unexpected patterns, namely, violationfrom the approximate constancy of the evolutionary rates among closely related species mtDNA. Ming et al. (2020) presented afi

48

iDarwin AS 0022 (2022 AD)

Volume 2phylogenetic tree of mtDNAs, but they did not show branch lengths, and all sequences are located at the same vertical line. This
clearly indicates the importance of branch lengths for phylogenetic analyses in general.
We reanalyzed short read data of these camel sequences submitted to NCBI BioProject database (accession number
PRJNA383081), and found mtDNA sequences different from those reported by Ming et al. (2020). Two of these re-determined
mtDNA sequences, one from Russia (SRR5563521) and the other from Kazakhstan (SRR5563543), were originated frommorphologically two-humped camels. However, their mtDNA sequences were very similar to those of one-humped camels (seeFigure 2). This suggests that these two camel species have been hybridizing for a long time. Ming et al. (2020) also noticed
mtDNA introgression from dromedary to bactrian camels.
If we consider repeated back-crossing to bactrian camels after creating F1 hybrid between C. dromedaries (one-humped
camel) and C. bactrianus (two-humped camel), it is possible to obtain this discrepancy. In fact, Lado et al. (2020) who examined
nuclear genome sequences of many dromedary individuals reported that some dromedaries from Iran and Kazakhstan were foundto have considerable proportion of Bactrian nuclear DNAs. In any case, we have to be careful to choose reference sequences todetermine mtDNA sequences from NGS-generated short read data.
The main point of study is to indicate the erroneously reported camel mtDNA sequences. Unfortunately, camel DNA
researchers do not realize this problem, and just use reported sequences (e.g., Ming et al. [2021]). We thus think this report isuseful for camel mtDNA sequence analyses.

Acknowlegements
We would like to thank Professor Kaoru Imamura at Nagoya Gakuin University, who is P.I. of MEXT Grant-in-Aid for Scienti c
Research “A dynamic analysis of pastoral society in Central Asia: from domestication to climate change” (grant number
18H03608). One of us (N.S.) is co-P.I. of this project, and his visits to Kazakhstan initiated a collaboration with two of us (G.Z.
and K.D.) at the Institute of Genetics and Physiology in Almaty, Kazakhstan. We also like to thank Dr. Zhen Wang at CAS-MPG
Partner Institute for Computational Biology, Shanghai, China to send us his nding, after N.S. visited his laboratory. Funding:This work was supported by MEXT Grant-in-Aid for Scienti c Research given to N.S. as mentioned above, and by the Bolashak
fellowship from the Kazakhstan Government to K.D. and to G.Z.

fi

fi

fi

49

iDarwin AS 0022 (2022 AD)

Volume 2

References
Arnason U., Gulliber A., and Anke A. (2004) Mitogenomic analyses provide new insights into cetacean origin and evolution. Gene, vol. 333, pp. 27-34.
Burger P. A., Ciani E., and Faye B. (2019) Old World camels in a modern world – a balancing act between conservation and genetic improvement.
Animal Genetics, vol. 50, pp. 598–612.
Chen S., Zhou Y., Chen Y., and Gu J. (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, vol. 34, pp. i884-i890.
Danecek P., Auton A., Abecasis G., Albers C. A., Banks E., DePristo M. A., Handsaker R. E., Lunter G., Marth G. T., Sherry S. T., McVean G., DurbinR., and 1000 Genomes Project Analysis Group (2011) The variant call format and VCFtools. Bioinformatics 27: 2156–2158.
di Rocco F., Zambelli A., Mate L., and Vidal-Rioja L. (2010) The complete mitochondrial DNA sequence of the guanaco (Lama guanicoe):comparative analysis with the vicuna (Vicugna vicugna) genome. Genetica, vol. 138, pp. 813-818.
Hassanin A., Delsuc F., Ropiquet A., Hammer C., van Vuuren B. J., Matthee C., Ruiz-Garcia M., Catze is F., Areskoug V., Nguyen T. T., and Couloux
A. (2012) Pattern and timing of diversi cation of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of
mitochondrial genomes. Comptes Rendus Biologies, vol. 335, pp. 32-50.
Heinzman P. D., Zazula G. D., Cahill J. A., Reyes A. V., Macphee R. D., and Shapiro B. (2015) Genomic Data from Extinct North American Camelops
Revise Camel Evolutionary History. Molecular Biology and Evolution, vol. 32, pp. 2433-2440.
Imamura K., Sallmurzauli R., Iklasov M. K., Baibayssov A., Matsui K., and Nurtazin S. T. (2017) The distribution of the two domestic camel species
in Kazakhstan caused by the demand of industrial stockbreeding. Journal of Arid Land Studies, vol. 26, pp. 233-236.
Ji R., Cui P., Ding F., Geng J., Gao H., Zhang H., Yu J., Hu S. and Meng H. (2009) Monophyletic origin of domestic bactrian camel (Camelus
bactrianus) and its evolutionary relationship with the extant wild camel (Camelus bactrianus ferus). Animal Genetics, vol. 40, pp. 377-382.
Katoh K. and Standley D. M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular
Biology and Evolution, vol. 30, pp. 772–780.
Kumar S., Stecher G., Li M., Knyaz C., and Tamura K. (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms.
Molecular Biology and Evolution, vol. 35, pp. 1547-1549.
Lado S., Elbers J. P., Doskocil A., Scaglione D., Trucchi E., Banabazi M. H., Almathen F., Saitou N., Ciani E., and Burger P. A. (2020) Genome-wide
diversity and global migration patterns in dromedaries follow ancient caravan routes. Communications Biology, vol. 3, article number 387.
Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., and Durbin R. (2009) 1000 Genome Project Data Processing
Subgroup. The sequence alignment/map format and SAMtools. Bioinformatics, vol. 25, pp. 2078–2079.
Ming L., Siren D., Yi L., Hai L., He J., and Ji R. (2021) Mitochondrial DNA variation and phylogeography of Old World camels. Animal Bioscience,
vol. 34, pp. 525-532.
Ming L., Yuan L., Yi L., Ding G., Hasi S., Chen G., Jambl T., Hedayat-Evright N., Batmunkh M., Badmaevna G. K., Gan-Erdene T., Bastskh TS,
Zhang W., Zuliplikaer A., Hosblig, Erdemt, Natyrov A., Mamay P., Narenbatu, Meng G., Narangerel C., Khongorzul O., He J., Hai L., Lin W.,
Sarentuya S., Aiyisi, Li Y., Wang Z., and Jirimutu (2020) Whole-genome sequencing of 128 camels across Asia provides insights into origin andmigration of domestic Bactrian camels. Communications Biology, vol. 3, article 1.
Saitou N. and Shokat S. (2017) DNA analyses of camels. Journal of Arid Land Studies, vol. 26, pp. 223-226.

fl

fi

50

iDarwin AS 0022 (2022 AD)

Volume 2

Saitou N. (2018) Introduction to Evolutionary Genomics Second Edition. Springer, London.
Saitou N. and Nei M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, vol.
4, pp. 406-425.
Tajima F. (1993) Simple methods for testing the molecular evolutionary clock hypothesis. Genetics, vol. 135, pp. 599-607.
Tamura K. and Nei M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans andchimpanzees. Molecular Biology and Evolution, vol. 10, pp. 512-526.
Ursing B.M., Slack K.E., and Arnason U. (2000) Subordinal artiodactyl relationships in the light of phylogenetic analysis of 12 mitochondrial proteincoding genes. Zoologica Scripta, vol. 29, pp. 83-88.
Zurano J. P., Magalhães F. M., Asato A. E., Silva G., Bidau C., Mesquita D. O., and Costa G. C. (2019) Cetartiodactyla: updating a time-calibrated
molecular phylogeny. Molecular Phylogenetics and Evolution, vol. 133, pp. 256-262.
Wu H., Guang X., Al-Fageeh M. B., Cao J., Pan S., Zhou H., Zhang L., Abutarboush M. H., Xing Y., Xie Z., …, Al-Swailem A. M., and Wang J.
(2014) Camelid genomes reveal evolution and adaptation to desert environments. Nature Communications, vol. 5, article number 5188.

51