Survival in the Tropics despite isolation, inbreeding and asexual reproduction: insights from the genome of the world’s southernmost poplar (Populus ilicifolia)

• Published in: The Plant journal : for cell and molecular biology 2020-07, Vol.103 (1), p.430-442
• Main Authors: Chen, Zeyuan, Ai, Fandi, Zhang, Junlin, Ma, Xinzhi, Yang, Wenlu, Wang, Weiwei, Su, Yutao, Wang, Mingcheng, Yang, Yongzhi, Mao, Kangshan, Wang, Qingfeng, Lascoux, Martin, Liu, Jianquan, Ma, Tao
• Format: Article
• Language: English
• Subjects: Asexual reproduction; Breeding; Conservation; conservation genomics; Endangered Species; Evolution; Extinct species; Genetic diversity; genetic load; Genetic Variation - genetics; Genome, Plant - genetics; Genome, Plant - physiology; Genomes; Homozygosity; Homozygote; Inbreeding; Polymorphism, Genetic - genetics; Poplar; Population decline; Population number; Populus - genetics; Populus - physiology; Populus ilicifolia; Prunus ilicifolia; Purging; Reproduction, Asexual - genetics; Species; Species diversity; Survival; Threatened species; tropical adaptation; Tropical Climate; Tropical environments; Wildlife conservation
• ISSN: 0960-7412; 1365-313X; 1365-313X
• DOI: 10.1111/tpj.14744

SUMMARY Species are becoming extinct at unprecedented rates as a consequence of human activity. Hence it is important to understand the evolutionary dynamics of species with already small population sizes. Populus ilicifolia is a vulnerable poplar species that is isolated from other poplar species and is uniquely adapted to the Tropics. It has a very limited size, reproduces partly clonally and is therefore an excellent case study for conservation genomics. We present here the first annotated draft genome of P. ilicifolia, characterize genome‐wide patterns of polymorphisms and compare those to other poplar species with larger natural ranges. P. ilicifolia experienced a more prolonged and severe decline of effective population size (Ne) and signs of genetic erosion than any other poplar species with which it was compared. At present, the species has the lowest genome‐wide genetic diversity, the highest abundance of long runs of homozygosity, high inbreeding levels as well as a high overall accumulation of deleterious variants. However, more effective purging of severely deleterious variants and adaptation to the Tropics may have contributed to its survival. Hence, in spite of its limited genetic variation, it is certainly worth pursuing the conservation efforts of this unique species. Significance Statement Whole‐genome sequencing of Populus ilicifolia, a vulnerable and isolated poplar tree from the Tropics that can reproduce both sexually and asexually, was used to explore how population history and reproduction affected its genetic characteristics, genetic load, and its potential for tropical adaptation.