Utility of mitochondrial COI gene for identification of wild ungulate species of conservational importance from Pakistan

Figures & data

Table 1. Sampling details of Pakistani ungulate species used in this study, including accession numbers, source, and conservation status.

S#	Species name	Voucher IDs	No. of samples	Sample type	Accession no.	Source	Conservation status**	Coordinates
1.	Moschus cupreus (Kashmir Musk deer)	KMD-BRC	5	Skin/hair follicles	MG742692, MT251406, MT251407, MT251408, MT251409	i) Pir chinasi (Muzaffarabad, AJK) ii) Gurase Valley, AJK	Endangered	34° 23′16′'N 73° 32′51.9′'E
2.	Muntiacus muntjac (Barking Deer)	BD-BRC	5	Tissue	MG722903, MT251410, MT251411, MT251412, MT251413	Margalla Hills National Park, Pakistan	Endangered	33°43′52″N 72°56′13″E
3.	Axis procinus (Hog Deer)	HD-L	5	Fecal	MG742696, MT251374, MT251375, MT251376, MT251377	Lahore Zoo	Vulnerable	31.556006°N 74.325959°E
4.	Axis axis (Chital Deer)	CHT-L	4	Skin/hair follicles	MG742689, MT251371, MT251372, MT251373	Lahore Zoo	Data Deficient	31.556006°N 74.325959°E
5.	Antilope cervicapra (Black Buck)	BB-BRC	5	Tissue/skin/hair follicles	MG722904, MT251367, MT251368, MT251369, MT251370	Lal-Suhanra National Park, Bahawalpur	Critical Endangered	29°19′N 71°55′E
6.	Gazella subgutturosa (Goitered Gazelle)	GG-BRC	1	Skin/hair follicles	MH261362	Pakistan Museum of Natural History	Critically Endangered	33.686389°N 73.076389°E
7.	Gazella bennettii (Chinkara)	GB-BRC	6	Tissue	MG742693, MT251401, MT251402, MT251403, MT251404, MT251405	Kalabagh game reserve	Vulnerable	32°57′57.6′' N 71°33′10.8′' E
8.	Boselaphus tragocamelus (Nilgai)	BT-J	6	Skin/hair follicles/fecal	MG742691, MT251378, MT251379, MT251380, MT251381, MT251382	i) Pakistan Museum of Natural History, Islamabad; ii) Lahore Zoo; iii) Gatwala Wildlife Breeding Center, Faisalabad.	Endangered	i) 33.686389°N 73.076389°E ii) 31.556006°N 74.325959°E iii) 31°28′41″N 73°12′30″E
9.	Naemorhedus goral bedfordi (Gray Goral)	NGB-BRC	3	Hair follicles	MG742694, MT251414, MT251415	Machiara National Park, AJK	Vulnerable	34°30′18 N 73°33′45 E
10.	Capra aegagrus blythi (Sindh wild goat)	SI-J	6	Tissue	MG742690, MT251383, MT251384, MT251385, MT251386, MT251387	Kirthar National Park	Near Threatened	25°42′N 67°35′E
11.	Capra sibirica (Siberian ibex)	HI-BRC	4	Skin/hair follicles	MH261363, MT251398, MT251399, MT251400	Central Karakoram National Park	Least Concern	35° 54′ 0.33′' N 75° 31′ 39.62′' E
12.	Capra falconeri falconeri (Flared horned Markhor)	AMK-GB	7	Skin/hair follicles	MG742698, MT251388, MT251389, MT251390, MT251391, MT251392, MT251393	Chitral Gol National Park	Endangered	35°56′N 71°40′E
13.	Capra falconeri megaceros (Straight Horned Markhor)	SMK-BL	5	Skin/hair follicles	MG742697, MT251394, MT251395, MT251396, MT251397	Torghar Hills, Baluchistan	Near Threatened	34°36′49″N 72°47′18″E
14.	Pseudois nayaur nayaur (Bharal)	BS-J	5	Skin/hair follicles	MG742688, MT251427, MT251428, MT251429, MT251430	Khunjerab National Park	Endangered	36°35′13.21″N 75°23′59.5″E
15.	Ovis ammon polii (Marcopolo Sheep)	MS-K	1	Skin/hair follicles	MH261364	i) Pakistan Museum of Natural History; ii) Khunjrab National Park	Critically Endangered	i) 33.686389°N 73.076389°E ii) 36°35′13.21″N 75°23′59.5″E
16.	Ovis vignei punjabiensis (Punjab Urial)	PU-BRC	5	Skin/hair follicles/fecal	MG735444, MT251419, MT251420, MT251421, MT251422	Kalabagh Game reserve	Endangered	32°57′57.6′' N 71°33′10.8′' E
17.	Ovis vignei blanfordi (Blandford Urial)	UB-J	4	Tissue	MG735443, MT251416, MT251417, MT251418	Kirthar National Park	Vulnerable	25°42′N 67°35′E
18.	Ovis vignei vignei (Ladakh Urial)	LU-J	5	Skin/hair follicles	MG735445, MT251423, MT251424, MT251425, MT251426	Chitral Gol National Park	Endangered	35°56′N 71°40′E
19.	Sus scrofa cristatus (Wild Boar)	WB-SGD	4	Skin/hair follicles	MF125268, MT251431, MT251432, MT251433,	i) Kirana hills Pakistan*; ii) Lahore Zoo	Least concern	i) 31°57′15″N 72°42′26″E ii) 31.556006°N 74.325959°E

The accession numbers represent the newly generated sequences of Pakistani ungulates submitted to NCBI GenBank.

*Animal was found dead on Sargodha to Sillanwali road (near Kirana hills).

**Conservation status according to data collected from Pakistan (Molur 2003).

Figure 1. Neighbor-Joining phylogenetic tree of ungulates using COI DNA barcodes. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (10000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the p-distance method and are in the units of the number of base differences per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 5). The analysis involved 188 nucleotide sequences. All positions containing gaps and missing data were eliminated.

Molur S. 2003. Status and Red List of Pakistan’s mammals. Pakistan mammal conservation assessment & management plan workshop, 18–22 August 2003.

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