基于线粒体DNA的大石鸡种群遗传变异

doi:10.3724/SP.J.1003.2012.09221

摘要/Abstract

摘要：

大石鸡(Alectoris magna)是我国的特有鸟类, 其种群数量由于受到栖息地片断化和人类狩猎的影响而日益减少。本文以mtDNA的控制区部分序列(1,127 bp)和细胞色素b部分序列(807 bp)为分子标记, 研究了大石鸡分布区内12个种群234个样本的遗传变异。173个样本的控制区序列中共发现了34个多态位点, 定义了44种单倍型, 平均单倍型多样性和核苷酸多样性分别为0.916 ± 0.011和0.00449 ± 0.00242, 所有种群中单倍型多样性最高的是靖远和民和种群 (0.894 ± 0.063), 最低的是海原种群(0.476 ± 0.155)。230个样本的细胞色素b序列中共发现了13个多态位点, 定义了14种单倍型。平均单倍型多样性为0.738 ± 0.024, 平均核苷酸多样性为0.00216 ± 0.00009, 所有种群中单倍型多样性最高的是共和种群(0.763 ± 0.059), 最低的为德令哈种群(0.000 ± 0.000)。所有遗传多样性参数与样本量均无显著相关性。控制区和细胞色素b的单倍型邻接树均显示大石鸡在系统发生树上没有互为单系发生的种群存在, 因此应该将大石鸡作为一个独立的进化显著单元(ESU)来对待。AMOVA结果显示大部分遗传变异分布于种群内, 但种群间和群组间也存在显著的遗传变异, 所以应该把各个种群作为独立的管理单元(MU)来实现短期内的管理和保护。对德令哈、都兰、礼县、张家川、海原等遗传多样性较低的边缘种群应重点保护, 另外, 对共和、贵德和靖远3个遗传多样性较高的种群也应重点加以保护。

关键词: 遗传多样性, 遗传分化, 系统发生, 进化显著单元, 管理单元

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

周蓉, 李佳琦, 李铀, 刘迺发, 房峰杰, 施丽敏, 王莹 (2012) 基于线粒体DNA的大石鸡种群遗传变异. 生物多样性, 20, 451-459. DOI: 10.3724/SP.J.1003.2012.09221.

Rong Zhou, Jiaqi Li, You Li, Naifa Liu, Fengjie Fang, Limin Shi, Ying Wang (2012) Genetic variation in rusty-necklaced partridge (Alectoris magna) detected by mitochondrial DNA. Biodiversity Science, 20, 451-459. DOI: 10.3724/SP.J.1003.2012.09221.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2012.09221

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

图/表 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