Genotyping-by-sequencing informs conservation of Andean palms sources of non-timber forest products

IF 3.5 2区 生物学 Q1 EVOLUTIONARY BIOLOGY Evolutionary Applications Pub Date : 2024-07-31 DOI:10.1111/eva.13765
Nicolás Peñafiel Loaiza, Abigail H. Chafe, Mónica Moraes R, Nora H. Oleas, Julissa Roncal
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Abstract

Conservation and sustainable management of lineages providing non-timber forest products are imperative under the current global biodiversity loss. Most non-timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species' conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus Parajubaea (Arecaceae) has only three species despite the genus' origin 22 million years ago. Two of the three palm species, P. torallyi and P. sunkha, are non-timber forest species endemic to the Andes of Bolivia and are listed as IUCN endangered. The third species, P. cocoides, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of Parajubaea species and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low-copy nuclear genes (3753 bp) challenged the hypothesis that P. cocoides is a cultigen that originated from the wild Bolivian species. We further obtained up to 15,134 de novo single-nucleotide polymorphism markers by genotyping-by-sequencing of 194 wild Parajubaea individuals. Our total DNA sequencing effort rejected the taxonomic separation of the two Bolivian species. As expected for narrow endemic species, we observed low genetic diversity, but no inbreeding signal. We found three genetic clusters shaped by geographic distance, which we use to propose three management units. Different percentages of missing genotypic data did not impact the genetic structure of populations. We use the management units to recommend in situ conservation by creating new protected areas, and ex situ conservation through seed collection.

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通过基因分型测序为保护安第斯棕榈非木材森林产品提供信息。
在当前全球生物多样性丧失的情况下,保护和可持续管理提供非木材森林产品的物种系势在必行。然而,大多数非木材森林物种缺乏基因组研究来描述其种内变异和进化历史,而这些研究可为物种保护实践提供依据。与安第斯生物多样性热点地区许多表现出高度多样化的品系相反,棕榈科 Parajubaea 属只有三个物种,尽管该属起源于 2200 万年前。这三个棕榈物种中的两个,P. torallyi 和 P. sunkha,是玻利维亚安第斯山区特有的非木材森林物种,被列为世界自然保护联盟(IUCN)濒危物种。第三个物种 P. cocoides 是一个野生种群未知的易危物种。我们研究了Parajubaea物种的进化关系以及玻利维亚野生种群的遗传多样性和结构。对五个低拷贝核基因(3753 bp)的测序挑战了 P. cocoides 是起源于玻利维亚野生种的栽培种的假设。通过对 194 个野生 Parajubaea 个体进行基因分型测序,我们进一步获得了多达 15,134 个新的单核苷酸多态性标记。我们的整个 DNA 测序工作否定了这两个玻利维亚物种在分类学上的分离。正如预期的那样,对于狭窄的地方性物种,我们观察到遗传多样性较低,但没有近交信号。我们发现了由地理距离形成的三个基因群,并据此提出了三个管理单元。不同比例的基因型数据缺失不会影响种群的遗传结构。我们利用这些管理单元建议通过建立新的保护区进行原地保护,并通过种子采集进行异地保护。
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来源期刊
Evolutionary Applications
Evolutionary Applications 生物-进化生物学
CiteScore
8.50
自引率
7.30%
发文量
175
审稿时长
6 months
期刊介绍: Evolutionary Applications is a fully peer reviewed open access journal. It publishes papers that utilize concepts from evolutionary biology to address biological questions of health, social and economic relevance. Papers are expected to employ evolutionary concepts or methods to make contributions to areas such as (but not limited to): medicine, agriculture, forestry, exploitation and management (fisheries and wildlife), aquaculture, conservation biology, environmental sciences (including climate change and invasion biology), microbiology, and toxicology. All taxonomic groups are covered from microbes, fungi, plants and animals. In order to better serve the community, we also now strongly encourage submissions of papers making use of modern molecular and genetic methods (population and functional genomics, transcriptomics, proteomics, epigenetics, quantitative genetics, association and linkage mapping) to address important questions in any of these disciplines and in an applied evolutionary framework. Theoretical, empirical, synthesis or perspective papers are welcome.
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