Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars

Hu, Guibing; Feng, Junting; Xu, Xiang; Wang, Jiabao; Salojärvi, Jarkko; Liu, Chengming; Wu, Zhongjie; Zhang, Jisen; Liang, Xinming; Jiang, Zide; Liu, Wei; Ou, Lijun; Li, Jiawei; Fan, Guangyi; Mai, Yingxiao; Chen, Chengjie; Zhang, Xingtan; Zheng, Jiakun; Zhang, Yanqing; HongXiang, Peng; Yao, Lixian; Wai, Ching Man; Luo, Xinping; Fu, Jiaxin; Tang, Haibao; Lan, Tianying; Lai, Bo; Sun, Jun; Wei, Yongzan; Huanling, L; Chen, Jiezhen; Huang, Xu-Ming; Yan, Qian; Liu, Xin; McHale, Leah K.; Rolling, William; Guyot, Romain; Sankoff, David; Zheng, Chunfang; Albert, Victor A.; Ming, Ray; Chen, Houbin; Xia, Rui; Li, Jianguo

doi:10.1038/s41588-021-00971-3

Cited by 98 publications

(56 citation statements)

References 96 publications

(131 reference statements)

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“…Reflecting the cladistic progression of our populations ( SI Appendix , Fig. S4), the youngest split time was between the PB and AK modern polar bear populations, followed by the split between the ABC-A and ABC-BC brown bear populations (~11.8 ka), the ABC brown bear split from the mainland Alaskan brown bears (28–36 ka), and the continental (YB) brown bear split from the Alaskan bears (43–46 ka) ( SI Appendix , Fig. S12 and Table S6).…”

Section: Resultsmentioning

confidence: 94%

“…Highly heterozygous regions coalesce further back in time in coalescent modeling. Therefore, this shift, implying much more recent coalescence throughout the genome in polar bears than brown bears, could have resulted from phenomena that reduce genome-level heterozygosity, such as high levels of inbreeding, as has been demonstrated in plant systems (28).…”

Section: Population Demographic Histories Of Highly Inbred Ancient An...mentioning

confidence: 96%

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Insights into bear evolution from a Pleistocene polar bear genome

Lan

Leppälä

Tomlin³

et al. 2021

Preprint

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The polar bear (Ursus maritimus) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population history, including evidence for ancient admixture between polar bears and brown bears (Ursus arctos). Here, we extend our earlier studies of a 130,000-115,000-year-old polar bear from the Svalbard Archipelago using 10X coverage genome sequence and ten new genomes of polar and brown bears from contemporary zones of overlap in northern Alaska. We demonstrate a dramatic decline in effective population size for this ancient polar bear's lineage, followed by a modest increase just before its demise. A slightly higher genetic diversity in the ancient polar bear suggests a severe genetic erosion over a prolonged bottleneck in modern polar bears. Statistical fitting of data to alternative admixture graph scenarios favors at least one ancient introgression event from brown bears into the ancestor of polar bears, possibly dating back over 150,000 years. Gene flow was likely bidirectional, but allelic transfer from brown into polar bear is the strongest detected signal, which contrasts with other published works. These findings have implications for our understanding of climate change impacts: polar bears, a specialist Arctic lineage, may not only have undergone severe genetic bottlenecks, but also been the recipient of generalist, boreal genetic variants from brown bear during critical phases of Northern Hemisphere glacial oscillations.

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Section: Resultsmentioning

confidence: 94%

Section: Population Demographic Histories Of Highly Inbred Ancient An...mentioning

confidence: 96%

Insights into bear evolution from a Pleistocene polar bear genome

Lan

Leppälä

Tomlin³

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Highly heterozygous regions coalesce further back in time in coalescent modeling. Therefore, this shift, implying much more recent coalescence throughout the genome in polar bears than in brown bears, could have resulted from phenomena that reduce genome-level heterozygosity, such as high levels of inbreeding, as has been demonstrated in plant systems ( 28 ).…”

Section: Resultsmentioning

confidence: 96%

Insights into bear evolution from a Pleistocene polar bear genome

Lan

Leppälä

Tomlin

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The polar bear ( Ursus maritimus ) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population history, including evidence for ancient admixture between polar bears and brown bears ( Ursus arctos ). Here, we extend our earlier studies of a 130,000- to 115,000-y-old polar bear from the Svalbard Archipelago using a 10× coverage genome sequence and 10 new genomes of polar and brown bears from contemporary zones of overlap in northern Alaska. We demonstrate a dramatic decline in effective population size for this ancient polar bear’s lineage, followed by a modest increase just before its demise. A slightly higher genetic diversity in the ancient polar bear suggests a severe genetic erosion over a prolonged bottleneck in modern polar bears. Statistical fitting of data to alternative admixture graph scenarios favors at least one ancient introgression event from brown bears into the ancestor of polar bears, possibly dating back over 150,000 y. Gene flow was likely bidirectional, but allelic transfer from brown into polar bear is the strongest detected signal, which contrasts with other published work. These findings may have implications for our understanding of climate change impacts: Polar bears, a specialist Arctic lineage, may not only have undergone severe genetic bottlenecks but also been the recipient of generalist, boreal genetic variants from brown bears during critical phases of Northern Hemisphere glacial oscillations.

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“…A dual origin of domesticated lablab was confirmed, with the localised (to Ethiopia) two-seeded and the widespread four-seeded types being genetically distinct and domestication events occurring in both of these groups. This therefore adds lablab to the relatively ‘exclusive’ list of crops with more than one origin, which includes common bean 13 , lychee 29 , Tartary buckwheat 30 and, potentially, rice 31 and barley 32 . Data on reproductive isolation between the gene pools is unclear, and crosses are only known between four-seeded samples 33–35 , thus any taxonomic reassessment (first suggested by Maass et al 2005 15 ) should begin with assessing reproductive compatibility between the gene pools.…”

Section: Discussionmentioning

confidence: 99%

Chromosome-scale assembly of the lablab genome - A model for inclusive orphan crop genomics

Njaci

Waweru

Kamal

et al. 2022

Preprint

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Orphan crops (also described as underutilised and neglected crops) hold the key to diversified and climate-resilient food systems. After decades of neglect, the genome sequencing of orphan crops is gathering pace, providing the foundations for their accelerated domestication and improvement. Recent attention has however turned to the gross under-representation of researchers in Africa in the genome sequencing efforts of their indigenous orphan crops. Here we report a radically inclusive approach to orphan crop genomics using the case of Lablab purpureus (L.) Sweet (syn. Dolichos lablab, or hyacinth bean) – a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led South-North plant genome collaboration produced a high-quality chromosome-scale assembly of the lablab genome – the first chromosome-scale plant genome assembly locally produced in Africa. We also re-sequenced cultivated and wild accessions of lablab from Africa confirming two domestication events and examined the genetic diversity in lablab germplasm conserved in Africa. Our approach provides a valuable resource for lablab improvement and also presents a model that could be explored by other researchers sequencing indigenous crops particularly from Low and middle income countries (LMIC).

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Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars

Cited by 98 publications

References 96 publications

Insights into bear evolution from a Pleistocene polar bear genome

Insights into bear evolution from a Pleistocene polar bear genome

Insights into bear evolution from a Pleistocene polar bear genome

Chromosome-scale assembly of the lablab genome - A model for inclusive orphan crop genomics

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