Population genomics of the critically endangered kakapo

被引：145

作者：

Dussex, Nicolas ^{[1
,2
,3
,4
]}

van der Valk, Tom ^{[1
,2
]}

Morales, Hernan E. ^{[5
]}

Wheat, Christopher W. ^{[3
]}

Diez-del-Molino, David ^{[1
,2
]}

von Seth, Johanna ^{[1
,2
,3
]}

Foster, Yasmin ^{[6
]}

Kutschera, Verena E. ^{[7
]}

Guschanski, Katerina ^{[8
,9
]}

Rhie, Arang ^{[10
]}

Phillippy, Adam M. ^{[10
]}

Korlach, Jonas ^{[11
]}

Howe, Kerstin ^{[12
]}

Chow, William ^{[12
]}

Pelan, Sarah ^{[12
]}

Damas, Joanna D. Mendes ^{[13
]}

Lewin, Harris A. ^{[13
]}

Hastie, Alex R. ^{[14
]}

Formenti, Giulio ^{[15
,16
,17
]}

Fedrigo, Olivier ^{[15
]}

Guhlin, Joseph ^{[18
]}

Harrop, Thomas W. R. ^{[18
]}

Lec, Marissa F. Le ^{[18
]}

Dearden, Peter K. ^{[18
]}

Haggerty, Leanne ^{[19
]}

Martin, Fergal J. ^{[19
]}

Kodali, Vamsi ^{[20
]}

Thibaud-Nissen, Francoise ^{[20
]}

Iorns, David ^{[21
]}

Knapp, Michael ^{[4
]}

Gemmell, Neil J. ^{[4
]}

Robertson, Fiona ^{[6
]}

Moorhouse, Ron ^{[22
]}

Digby, Andrew ^{[22
]}

Eason, Daryl ^{[22
]}

Vercoe, Deidre ^{[22
]}

Howard, Jason ^{[15
,23
]}

Jarvis, Erich D. ^{[15
,16
,17
]}

Robertson, Bruce C. ^{[6
]}

Dalen, Love ^{[1
,2
,3
]}

机构：

[1] Ctr Palaeogenet, Svante Arrhenius vag 20C, S-10691 Stockholm, Sweden

[2] Swedish Museum Nat Hist, Dept Bioinformat & Genet, Box 50007, SE-10405 Stockholm, Sweden

[3] Stockholm Univ, Dept Zool, S-10691 Stockholm, Sweden

[4] Univ Otago, Dept Anat, POB 913, Dunedin 9016, New Zealand

[5] Univ Copenhagen, GLOBE Inst, Sect Evolutionary Genom, Copenhagen, Denmark

[6] Univ Otago, Dept Zool, POB 56, Dunedin 9054, New Zealand

[7] Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Natl Bioinformat Infrastruct Sweden, Box 1031, S-17121 Solna, Sweden

[8] Univ Edinburgh, Inst Evolutionary Biol, Sch Biol Sci, Edinburgh, Scotland

[9] Uppsala Univ, Dept Ecol & Genet, Anim Ecol, SE-75236 Uppsala, Sweden

[10] Natl Human Genome Res Inst, NIH, Genome Informat Sect Computat & Stat Genom Branch, Bethesda, MD 20892 USA

[11] Pacific Biosci, 1305 OBrien Dr, Menlo Pk, CA 94025 USA

[12] Wellcome Trust Genome Campus, Wellcome Sanger Inst, Hinxton CB10 1SA, England

[13] Univ Calif Davis, Dept Evolut & Ecol, Davis, CA 95616 USA

[14] Bionano Genom, 9540 Towne Ctr Dr, San Diego, CA 92121 USA

[15] Rockefeller Univ, Vertebrate Genome Lab, New York, NY 10065 USA

[16] Rockefeller Univ, Lab Neurogenet Language, Box 54, New York, NY 10065 USA

[17] Howard Hughes Med Inst, Chevy Chase, MD 20815 USA

[18] Univ Otago, Genom Aotearoa, POB 56, Dunedin 9016, Aotearoa, New Zealand

[19] European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England

[20] Natl Ctr Biotechnol Informat, NIH, Natl Lib Med, Bethesda, MD 20894 USA

[21] Genet Rescue Fdn, Wellington, New Zealand

[22] Dept Conservat, Kakapo Recovery, POB 743, Invercargill 9840, New Zealand

[23] BioSkryb Genom, 701 W Main St, Suite 200, Durham, NC 27701 USA

来源：

CELL GENOMICS | 2021年 / 1卷 / 01期

基金：

美国国家卫生研究院; 英国惠康基金; 欧盟地平线“2020”; 瑞士国家科学基金会; 瑞典研究理事会;

关键词：

NEW-ZEALAND; INBREEDING DEPRESSION; GENETIC DIVERSITY; RECOMBINATION RATES; MUTATION; ASSOCIATION; EXTINCTION; FRAMEWORK; INFERENCE; INSIGHTS;

D O I：

10.1016/j.xgen.2021.100002

中图分类号：

Q2 [细胞生物学];

学科分类号：

071009 ; 090102 ;

摘要：

The ka ⠁ka ⠁po ⠁ is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 indi-viduals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for ka ⠁ka ⠁po ⠁, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in ka ⠁ka ⠁po ⠁ indicate that present-day island ka ⠁ka ⠁po ⠁ have a reduced number of harmful muta-tions compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ⠁10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of gen-erations. This work provides key insights into ka ⠁ka ⠁po ⠁ breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.

引用

页数：20

共 94 条

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