生物多样性 ›› 2019, Vol. 27 ›› Issue (12): 1291-1297.doi: 10.17520/biods.2019255

• 研究报告:动物多样性 • 上一篇    下一篇

基于基因组SNPs的南极恩克斯堡岛阿德利企鹅繁殖种群的遗传结构

张剑, 董路, 张雁云()   

  1. 生物多样性与生态工程教育部重点实验室, 北京师范大学生命科学学院, 北京 100875
  • 收稿日期:2019-08-16 接受日期:2019-11-20 出版日期:2019-12-20
  • 通讯作者: 张雁云 E-mail:zhangyy@bnu.edu.cn
  • 基金项目:
    南极恩克斯堡岛企鹅保护区项目(23020005);南大洋鸟类多样性和分布格局调查项目(JDXT2019-02)

Population genetic structure of Adélie penguins (Pygoscelis adeliae) from Inexpressible Island, Antarctica, using SNP markers

Jian Zhang, Lu Dong, Yanyun Zhang()   

  1. College of Life Sciences, Beijing Normal University, Beijing 100875
  • Received:2019-08-16 Accepted:2019-11-20 Online:2019-12-20
  • Contact: Zhang Yanyun E-mail:zhangyy@bnu.edu.cn

我国提议在南极恩克斯堡岛新站址北侧3 km的阿德利企鹅(Pygoscelis adeliae)聚集繁殖地建立南极特别保护区, 对保护区边界的划分, 各国尚存争议, 尤其是对南湾(South Bay)的繁殖小种群是否具有遗传独特性, 是否应将其纳入保护区是重点关注的问题。本研究采集了恩克斯堡岛海景湾(Seaview Bay)和南湾的阿德利企鹅样品, 通过全基因组重测序和种群基因组学方法, 分析了恩克斯堡岛不同区域的种群遗传结构。发现恩克斯堡岛海景湾与南湾阿德利企鹅没有显著的遗传分化, 南湾阿德利企鹅不是独特的小种群; 海景湾高海拔区域个体与低海拔区域个体之间也没有显著的遗传差异, 推测该区域阿德利企鹅繁殖群体的分布格局与冰川堆积形成的阶地不具有显著相关性。本工作为恩克斯堡岛保护区和罗斯海新站建设提供了重要科技支撑。

关键词: 恩克斯堡岛, 阿德利企鹅, 遗传结构, 南极特别保护区, SNPs

China has proposed to establish an Antarctic Specially Protected Area (ASPA) to protect the Adélie penguin, Pygoscelis adeliae, colonies on Inexpressible Island. However, the boundary of the proposed ASPA is disputed mainly by whether the South Bay population is a distinct genetic population in need of protection. We collected samples of Adélie penguins from the South Bay and neighboring Seaview Bay on Inexpressible Island and identified SNPs via Illumina sequencing for population structure analysis. Our results indicated that there was no significant genetic difference between the South Bay colonies and the Seaview Bay colonies, or between the higher and lower elevational colonies in the Seaview Bay. Thus, the breeding populations of Adélie penguin on the island could be recognized as a single conservation unit. The currently proposed boundary of the ASPA, which covers the majority of breeding populations in Seaview Bay, would be sufficient to protect the genetic diversity of Adélie penguins in Inexpressible Island.

Key words: Inexpressible Island, Pygoscelis adeliae, population structure, Antarctic Specially Protected Area, SNPs

图1

阿德利企鹅采样区地图。A: 南极地图, 红框示恩克斯堡岛的位置; B: 恩克斯堡岛地图, 红框示拟建保护区的位置; C: 采样区域, 蓝色和红色圆圈分别为海景湾高海拔和低海拔采样区, 绿色圆圈为南湾采样区。"

图2

基于110,451个SNPs利用最大似然法构建的恩克斯堡岛阿德利企鹅的种群遗传结构。(a)交叉验证错误率分布; (b) K = 2; (c) K = 3。图中每一竖条为1个个体, 用颜色表示每个个体基因组中不同祖先所占的比例。"

图3

基于62只阿德利企鹅110,451个SNPs的主成分分析"

图4

阿德利企鹅个体间遗传距离与地理距离的Mantel检验"

[1] Ainley DG, LeResche RE, Sladen WJL ( 1983) Breeding Biology of the Adélie Penguin. University of California Press, Oakland.
[2] Alexander DH, Novembre J, Lange K ( 2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19, 1655-1664.
[3] Baroni C, Hall BL ( 2004) A new Holocene relative sea-level curve for Terra Nova Bay, Victoria Land, Antarctica. Journal of Quaternary Science, 19, 377-396.
[4] Baroni C, Orombelli G ( 1991) Holocene raised beaches at Terra Nova Bay, Victoria Land, Antarctica. Quaternary Research, 36, 157-177.
[5] Borowicz A, McDowall P, Youngflesh C, Sayre-McCord T, Clucas G, Herman R, Forrest S, Rider M, Schwaller M, Hart T, Jenouvrier S, Polito MJ, Singh H, Lynch HJ ( 2018) Multi-modal survey of Adélie penguin mega-colonies reveals the Danger Islands as a seabird hotspot. Scientific Reports, 8, 9.
[6] Bromwich DH, Kurtz DD ( 1984) Katabatic wind forcing of the Terra Nova Bay polynya. Journal of Geophysical Research Oceans, 89, 3561-3572.
[7] Clucas GV, Younger JL, Kao D, Emmerson L, Southwell C, Wienecke B, Rogers AD, Bost CA, Miller GD, Polito MJ, Lelliott P, Handley J, Crofts S, Phillips RA, Dunn MJ, Miller KJ, Hart T ( 2018) Comparative population genomics reveals key barriers to dispersal in Southern Ocean penguins. Molecular Ecology, 27, 4680-4697.
[8] Clucas GV, Younger JL, Kao D, Rogers AD, Handley J, Miller GD, Jouventin P, Nolan P, Gharbi K, Miller KJ, Hart T ( 2016) Dispersal in the sub-Antarctic: King penguins show remarkably little population genetic differentiation across their range. BMC Evolutionary Biology, 16, 211.
[9] Croxall JP, Prince PA ( 1979) Antarctic seabird and seal monitoring studies. Polar Record, 19, 573-595.
[10] Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST ( 2011) The variant call format and VCFtools. Bioinformatics, 27, 2156-2158.
[11] Emslie SD, Coats L, Licht K ( 2007) A 45,000 yr record of Adélie penguins and climate change in the Ross Sea, Antarctica. Geology, 35, 61-64.
[12] Freed D, Aldana R, Weber JA, Edwards JS ( 2017) The Sentieon Genomics Tools—A fast and accurate solution to variant calling from next-generation sequence data. bioRxiv, 115717.
[13] Funk WC, McKay JK, Hohenlohe PA, Allendorf FW ( 2012) Harnessing genomics for delineating conservation units. Trends in Ecology & Evolution, 27, 489-496.
[14] Gorman KB, Talbot SL, Sonsthagen SA, Sage GK, Gravely MC, Fraser WR, Williams TD ( 2017) Population genetic structure and gene flow of Adélie penguins (Pygoscelis adeliae) breeding throughout the western Antarctic Peninsula. Antarctic Science, 29, 499-510.
[15] Li H, Durbin R ( 2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
[16] Lischer HEL, Excoffier L ( 2012) PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics, 28, 298-299.
[17] Lorenzini S, Baroni C, Fallick AE, Baneschi I, Salvatore MC, Zanchetta G, Dallai L ( 2010) Stable isotopes reveal Holocene changes in the diet of Adélie penguins in Northern Victoria Land (Ross Sea, Antarctica). Oecologia, 164, 911-919.
[18] Lynch HJ, LaRue MA ( 2016) First global census of the Adélie penguin. Auk, 133, 236.
[19] Lyver POB, Barron M, Barton KJ, Ainley DG, Pollard A, Gordon S, McNeill S, Ballard G, Wilson PR ( 2014) Trends in the breeding population of Adélie penguins in the Ross Sea, 1981-2012: A coincidence of climate and resource extraction effects. PLoS ONE, 9, e91188.
[20] Manel S, Schwartz MK, Luikart G, Taberlet P ( 2003) Landscape genetics: Combining landscape ecology and population genetics. Trends in Ecology & Evolution, 18, 189-197.
[21] Nielsen R, Paul JS, Albrechtsen A, Song Y ( 2011) Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics, 12, 443-451.
[22] Palsboll PJ, Berube M, Allendorf FW ( 2007) Identification of management units using population genetic data. Trends in Ecology & Evolution, 22, 11-16.
[23] Peakall R, Smouse PE ( 2012) GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics, 28, 2537-2539.
[24] Raj A, Stephens M, Pritchard JK ( 2014) fastSTRUCTURE: Variational inference of population structure in large SNP data sets. Genetics, 197, 573-589.
[25] Ritchie PA, Millar CD, Gibb GC, Baroni C, Lambert DM ( 2004) Ancient DNA enables timing of the Pleistocene origin and Holocene expansion of two Adélie penguin lineages in Antarctica. Molecular Biology and Evolution, 21, 240-248.
[26] Shepherd LD, Millar CD, Ballard G, Ainley DG, Wilson PR, Haynes GD, Baroni C, Lambert DM ( 2005) Microevolution and mega-icebergs in the Antarctic. Proceedings of the National Academy of Sciences, USA, 102, 16717-16722.
[27] Stonehouse B ( 1969) Air census of two colonies of Adélie penguins (Pygoscelis adeliae) in Ross Dependency, Antarctica. Polar Record, 14, 471-475.
[28] Walther GR, Post E, Convey P, Menzel A, Parmesan C, Beebee TJC, Fromentin JM, Hoegh-Guldberg O, Bairlein F ( 2002) Ecological responses to recent climate change. Nature, 416, 389-395.
[29] Woehler EJ, Croxall JP ( 1997) The status and trends of Antarctic and sub-Antarctic seabirds. Marine Ornithology, 25, 43-66.
[30] Younger JL, Clucas GV, Kao D, Rogers AD, Gharbi K, Hart T, Miller KJ ( 2017) The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins. Molecular Ecology, 26, 3883-3897.
[31] Zhang C, Dong SS, Xu JY, He WM, Yang TL ( 2019) PopLDdecay: A fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics, 35, 1786-1788.
[32] Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW ( 2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346, 1311-1320.
[33] Zheng XW, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS ( 2012) A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics, 28, 3326-3328.
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