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- Torres Jimenez, Maria Fernanda, et al.
(författare)
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Phylogenomics of the Palm Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New Species of Mauritiella
- 2021
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Ingår i: Systematic Botany. - : American Society of Plant Taxonomists. - 0363-6445. ; 46:3, s. 863-874
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Tidskriftsartikel (refereegranskat)abstract
- The palm tribe Lepidocaryeae (Arecaceae) comprises seven genera and 51 currently accepted species that are distributed in lowland tropical forests and savannas across Africa and the Americas. Subtribal relationships within Lepidocaryeae have been a persistent challenge, limiting our understanding of its systematics, morphology, and biogeography. Several aspects make the tribe an ideal system to study plant evolution and diversity: it is well-represented in the fossil record as a prolific pollen producer, its continental diversity contradicts common biodiversity patterns of lower species richness in Africa in comparison to South America, and it contains one of the most abundant Amazonian tree species, Mauritia flexuosa. Here, we investigated the systematics of the tribe by sampling 122 individuals representing 42 species (82% of the tribe), using target sequence capture. We recovered nearly 10,000 single nucleotide polymorphisms from nuclear and plastid DNA across 146 target sequences to separately infer a phylogenomic tree. Our results strongly support inter-generic and inter-specific relationships, where a majority of nodes were resolved with over 90% bootstrap support. We also identify strong phylogenetic support for the recognition of a new species from central and south Amazonia, Mauritiella disticha. The distichous phyllotaxy is diagnostic of the species within the genus. Rare and currently only known from the middle-lower Madeira River basin in the state of Amazonas, Brazil, M. disticha is restricted to open vegetation and forest edges growing in white sand habitats with saturated or well-drained soils. Our preliminary red list assessment suggests its threatened status to be vulnerable (VU). We use our phylogenomic inference to define and contextualize systematic relationships in the tribe, and present a formal species description.
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| 2. |
- Perez-Escobar, O. A., et al.
(författare)
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Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication
- 2021
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Ingår i: Molecular Biology and Evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 38:10, s. 4475-4492
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Tidskriftsartikel (refereegranskat)abstract
- The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by similar to 2,200years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a similar to 2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.
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| 3. |
- Cowell, C., et al.
(författare)
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Uses and benefits of digital sequence information from plant genetic resources: Lessons learnt from botanical collections
- 2022
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Ingår i: Plants People Planet. - : Wiley. - 2572-2611. ; 4:1, s. 33-43
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Tidskriftsartikel (refereegranskat)abstract
- Societal Impact Statement Digitized molecular data are vital to numerous aspects of scientific research and genetic resource use. The Convention on Biological Diversity currently refers to this as "Digital Sequence Information" (DSI), a term not widely adopted by science and lacking a clear definition. There are concerns over the access to genetic resources and absence of benefit sharing by provider countries. Open access to DSI might exacerbate this, which is leading to increasing policy interventions and restricted access to genetic resources and DSI. We analyze current international debate and proposed solutions and provide case studies of DSI use producing tangible benefits for the provider countries and scientific research, demonstrating the importance of open access DSI to achieving conservation goals. Substantial advances in DNA sequencing over the last decades hold great potential to enhance food security and sustainable use of global biodiversity, benefiting the world's poorest people. Digital Sequence Information (DSI) plays a crucial role in catalyzing research applications that can contribute to international societal and biodiversity conservation targets. However, benefit sharing relating to DSI is difficult to identify and hindered by the lack of clear international governance and legislation, which in turn has led to a reluctance to make DSI publicly and freely available. Critically, no precise definition exists under the Convention on Biological Diversity (CBD), the Nagoya Protocol (NP), or the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA). The key difference between DSI and biological resources, for which access and use are highly regulated under those frameworks, is that information is nonphysical. Information can be replicated and used without movement of, or access to, physical specimens. Thus, regulating the use of DSI is extremely challenging and remains controversial. Here, we review the regulation of DSI and the possible future steps by the international community, in the context of the benefit-sharing obligations of the CBD, NP, and ITPGRFA. We highlight how multilateral agreements work in practice and are a solution to this impasse. We provide case studies demonstrating how the Royal Botanic Gardens, Kew, and its collaborators address the uncertainty surrounding the use of DSI, illustrating tangible and equitable benefits that have arisen from such use. We conclude that open access to DSI is needed for scientific research and international policy.
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