Genetic variation in rusty-necklaced partridge (Alectoris magna) detected by mitochondrial DNA

doi:10.3724/SP.J.1003.2012.09221

Abstract

Abstract:

The rusty-necklaced partridge (Alectoris magna) is a bird species endemic to China that has been threatened by habitat fragmentation and hunting. To examine the conservation status of this species, we examined the intraspeciﬁc variation in the mitochondrial DNA (mtDNA) control region and cytochrome b 234 individuals from 12 representative populations throughout the species’ range. Forty-four haplotypes were defined by 34 variable sites with the mean haplotype diversity of 0.916 ± 0.011 and nucleotide diversity of 0.00449 ± 0.00242 in the 1,127 bp mtDNA control region. Haplotype diversity was maximized in the Jing- yuan and Minhe populations (0.894 ± 0.063) and was minimized in the Haiyuan population (0.476 ± 0.155). Fourteen haplotypes were defined by 14 variable sites with a mean haplotype diversity of 0.738 ± 0.024 and a nucleotide diversity of 0.00216 ± 0.00009 in mtDNA cytochrome b．Haplotype diversity was the highest in the Gonghe population (0.763 ± 0.059) and did not differ in the Delingha population. Correlation between genetic diversity indices and sample size did not result in statistically significant differences. We found that neighbour-joining methods revealed limited phylogenetic distinction between geographically distant populations of the rusty-necklaced partridge, and provided tentative support for a single evolutionarily signiﬁcant unit. AMOVA revealed that the most genetic variation was distributed within populations; However, the genetic variation among groups and populations was also statistically significant, indicating that the appropriate short-term management unit for the rusty-necklaced partridge is a the level of the local population. Therefore, edge populations with lower genetic diversity, including Delingha, Dulan, Lixian, Zhangjiachuan and Haiyuan, have higher conservation value. We recommend that strengthening protection of populations with lower genetic diversity, including Gonghe, Guide and Jingyuan, is advantageous to retain the general level of genetic diversity in this species.

Key words: genetic diversity, genetic differentiation, phylogeny, evolutionarily significant unit, management unit

Rong Zhou, Jiaqi Li, You Li, Naifa Liu, Fengjie Fang, Limin Shi, Ying Wang. Genetic variation in rusty-necklaced partridge (Alectoris magna) detected by mitochondrial DNA[J]. Biodiv Sci, 2012, 20(4): 451-459.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2012.09221

https://www.biodiversity-science.net/EN/Y2012/V20/I4/451

Figures/Tables 5

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种群 Populations	经纬度 Locality	所属亚种 Subspecies	样本量 Sample size
种群 Populations	经纬度 Locality	所属亚种 Subspecies	控制区 D-loop	细胞色素b CYTB
青海 Qinghai
德令哈 Delingha (DLH)	37.22°N, 97.37°E	A. m. magna	12	12
乌兰 Wulan (WL)	36.93°N, 98.48°E	A. m. magna	18	23
都兰 Dulan (DL)	36.30°N, 98.10°E	A. m. magna	25	34
共和 Gonghe (GH)	36.28°N, 100.62°E	A. m. lanzhouensis	21	20
贵德 Guide (GD)	35.93°N, 101.48°E	A. m. lanzhouensis	11	12
互助 Huzhu (HZ)	36.85°N, 102.15°E	A. m. lanzhouensis	16	15
民和 Minhe (MH)	36.33°N, 102.80°E	A. m. lanzhouensis	12	12
甘肃 Gansu 靖远 Jingyuan (JY)	36.34°N, 104.81°E	A. m. lanzhouensis	12	40
会宁 Huining (HN)	35.91°N, 104.80°E	A. m. lanzhouensis	8	16
礼县 Lixian (LX)	34.20°N, 105.13°E	A. m. lanzhouensis	14	18
张家川 Zhangjiachuan (ZJC)	34.99°N, 106.21°E	A. m. lanzhouensis	9	10
宁夏 Ningxia 海原 Haiyuan (HY)	36.57°N, 105.64°E	A. m. lanzhouensis	15	18
总计 Total			173	230

种群 Populations	经纬度 Locality	所属亚种 Subspecies	样本量 Sample size
种群 Populations	经纬度 Locality	所属亚种 Subspecies	控制区 D-loop	细胞色素b CYTB
青海 Qinghai
德令哈 Delingha (DLH)	37.22°N, 97.37°E	A. m. magna	12	12
乌兰 Wulan (WL)	36.93°N, 98.48°E	A. m. magna	18	23
都兰 Dulan (DL)	36.30°N, 98.10°E	A. m. magna	25	34
共和 Gonghe (GH)	36.28°N, 100.62°E	A. m. lanzhouensis	21	20
贵德 Guide (GD)	35.93°N, 101.48°E	A. m. lanzhouensis	11	12
互助 Huzhu (HZ)	36.85°N, 102.15°E	A. m. lanzhouensis	16	15
民和 Minhe (MH)	36.33°N, 102.80°E	A. m. lanzhouensis	12	12
甘肃 Gansu 靖远 Jingyuan (JY)	36.34°N, 104.81°E	A. m. lanzhouensis	12	40
会宁 Huining (HN)	35.91°N, 104.80°E	A. m. lanzhouensis	8	16
礼县 Lixian (LX)	34.20°N, 105.13°E	A. m. lanzhouensis	14	18
张家川 Zhangjiachuan (ZJC)	34.99°N, 106.21°E	A. m. lanzhouensis	9	10
宁夏 Ningxia 海原 Haiyuan (HY)	36.57°N, 105.64°E	A. m. lanzhouensis	15	18
总计 Total			173	230

种群 Population	控制区 D-loop		细胞色素 b CYTB
种群 Population	h	π	h	π
德令哈 DLH	0.652 ± 0.133	0.00257 ± 0.00046	0.000 ± 0.000	0.00000 ± 0.00000
乌兰 WL	0.712 ± 0.074	0.00370 ± 0.00040	0.553 ± 0.080	0.00158 ± 0.00029
都兰 DL	0.663 ± 0.075	0.00386 ± 0.00046	0.508 ± 0.055	0.00124 ± 0.00014
共和 GH	0.800 ± 0.062	0.00342 ± 0.00035	0.763 ± 0.059	0.00202 ± 0.00022
贵德 GD	0.818 ± 0.119	0.00329 ± 0.00068	0.727 ± 0.113	0.00244 ± 0.00037
互助 HZ	0.700 ± 0.080	0.00303 ± 0.00068	0.467 ± 0.148	0.00090 ± 0.00032
民和 MH	0.894 ± 0.063	0.00330 ± 0.00055	0.591 ± 0.108	0.00207 ± 0.00037
靖远 JY	0.894 ± 0.063	0.00436 ± 0.00062	0.708 ± 0.062	0.00193 ± 0.00022
会宁 HN	0.750 ± 0.139	0.00219 ± 0.00105	0.508 ± 0.126	0.00154 ± 0.00036
礼县 LX	0.495 ± 0.151	0.00156 ± 0.00055	0.745 ± 0.079	0.00197 ± 0.00041
张家川 ZJC	0.694 ± 0.147	0.00197 ± 0.00064	0.644 ± 0.152	0.00173 ± 0.00054
海原 HY	0.476 ± 0.155	0.00208 ± 0.00087	0.471 ± 0.130	0.00116 ± 0.00045
平均 Average	0.916 ± 0.011	0.00449 ± 0.00242	0.738 ± 0.024	0.00216 ± 0.00009

种群 Population	控制区 D-loop		细胞色素 b CYTB
种群 Population	h	π	h	π
德令哈 DLH	0.652 ± 0.133	0.00257 ± 0.00046	0.000 ± 0.000	0.00000 ± 0.00000
乌兰 WL	0.712 ± 0.074	0.00370 ± 0.00040	0.553 ± 0.080	0.00158 ± 0.00029
都兰 DL	0.663 ± 0.075	0.00386 ± 0.00046	0.508 ± 0.055	0.00124 ± 0.00014
共和 GH	0.800 ± 0.062	0.00342 ± 0.00035	0.763 ± 0.059	0.00202 ± 0.00022
贵德 GD	0.818 ± 0.119	0.00329 ± 0.00068	0.727 ± 0.113	0.00244 ± 0.00037
互助 HZ	0.700 ± 0.080	0.00303 ± 0.00068	0.467 ± 0.148	0.00090 ± 0.00032
民和 MH	0.894 ± 0.063	0.00330 ± 0.00055	0.591 ± 0.108	0.00207 ± 0.00037
靖远 JY	0.894 ± 0.063	0.00436 ± 0.00062	0.708 ± 0.062	0.00193 ± 0.00022
会宁 HN	0.750 ± 0.139	0.00219 ± 0.00105	0.508 ± 0.126	0.00154 ± 0.00036
礼县 LX	0.495 ± 0.151	0.00156 ± 0.00055	0.745 ± 0.079	0.00197 ± 0.00041
张家川 ZJC	0.694 ± 0.147	0.00197 ± 0.00064	0.644 ± 0.152	0.00173 ± 0.00054
海原 HY	0.476 ± 0.155	0.00208 ± 0.00087	0.471 ± 0.130	0.00116 ± 0.00045
平均 Average	0.916 ± 0.011	0.00449 ± 0.00242	0.738 ± 0.024	0.00216 ± 0.00009

变异来源 Source of variations	变异组成 Variance components	变异百分比 % of variation	P	固定指数(99% IC) Fixation indices
D-loop
地理群组间 Among groups	0.279	10.21	0.041	F_CT= 0.102
地理种群间 Among populations within groups	0.534	19.54	0.000	F_SC= 0.218
种群内 Within populations	1.921	70.25	0.000	F_ST= 0.298
CYTB
地理群组间 Among groups	0.120	12.49	0.038	F_CT= 0.125
地理种群间 Among populations within groups	0.205	21.33	0.000	F_SC= 0.244
种群内 Within populations	0.635	66.18	0.000	F_ST= 0.338