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Divergence in Elymus sibiricus is related to geography and climate oscillation: A new look from pan‐chloroplast genome data 西伯利亚羊草的分化与地理和气候振荡有关:来自全叶绿体基因组数据的新认识
Pub Date : 2023-09-27 DOI: 10.1111/jse.13020
Yi Xiong, Yan‐Li Xiong, Xue‐Jie Jia, Jun‐Ming Zhao, Li‐Jun Yan, Li‐Na Sha, Lin Liu, Qing‐Qing Yu, Xiong Lei, Shi‐Qie Bai, Xiao Ma
Abstract Quaternary glacial climate oscillation and geographical isolation have significantly influenced the geographic distribution pattern and lineage evolution history of species. However, understanding how these factors specifically impact the genealogical structure of dominant Gramineous species in the Qinghai–Tibet Plateau (QTP) remains a subject of investigation. Elymus sibiricus L. (Gramineae), indigenous to the QTP and widely distributed in Eurasia, exhibits remarkable environmental adaptation and phenotypic diversity, making it an ideal candidate for phylogeographic studies. Based on the analysis of 175 complete chloroplast genome sequences, our results indicated that the ancestors of E. sibiricus originated from the QTP and underwent a complex migration history. After the speciation of E. sibiricus , several geo‐groups exhibited independent differentiation, showing minimal gene flow among them. The current phylogeographic patterns of E. sibiricus are a result of frequent climate alternations and the cold climate during the Quaternary glacial, as well as the presence of several geographical barriers that have restricted the gene flow among different geo‐groups. Our research has revealed for the first time that E. sibiricus has a multilineage origin, and its maternal donors are not limited to a single species. Furthermore, the high quality and mapping depth of the variant file provided reliable data for analyzing the patterns based on raw sequencing data. These findings enhance our understanding of the relationship between plant differentiation and climatic and geographical factors of Eurasia.
第四纪冰川气候振荡和地理隔离对物种的地理分布格局和谱系演化史产生了重大影响。然而,这些因素如何影响青藏高原禾本科优势种的家谱结构仍有待进一步研究。禾本科羊草(Elymus sibiricus L., Gramineae)是青藏高原的土生植物,广泛分布于欧亚大陆,具有显著的环境适应性和表型多样性,是系统地理学研究的理想对象。基于175个完整的叶绿体基因组序列分析,我们的研究结果表明,西伯利亚家鼠的祖先起源于QTP,并经历了一个复杂的迁徙历史。在西伯利亚大鼠形成物种后,几个地理类群表现出独立的分化,它们之间的基因流动最小。第四纪冰期频繁的气候变化和寒冷的气候,以及限制不同地理类群间基因流动的若干地理障碍,共同导致了西伯利亚野鼠目前的系统地理格局。我们的研究首次揭示了西伯利亚伊蚊具有多系起源,其母系供体并不局限于单一物种。此外,变体文件的高质量和映射深度为基于原始测序数据的模式分析提供了可靠的数据。这些发现增强了我们对欧亚大陆植物分化与气候地理因素关系的认识。
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引用次数: 0
Spatial patterns and drivers of native plant diversity in Hainan, China 海南原生植物多样性的空间格局及其驱动因素
Pub Date : 2023-09-21 DOI: 10.1111/jse.13017
Guo‐Qing Wang, Rosa A. Scherson, Diego Vera, Yun‐Hao Bai, Jun Wen, Lin‐Yuan Guo, Alice C. Hughes, Hua‐Feng Wang
Abstract Hainan Island has the most extensive and well‐preserved tropical forests in China. With rapid economic development of Hainan, biodiversity is increasingly at risk. Determining the spatial patterns of plant diversity in Hainan and explaining the drivers behind plant diversity are important considerations in assessing and maximizing the effectiveness of national parks, such as the newly designated Hainan Rainforest National Park. We assessed phylogenetic diversity patterns, and species richness using 106 252 georeferenced specimen records and a molecular phylogeny of 3792 native plant species. Based on phylogenetic range‐weighted turnover metrics, we divided Hainan flora into four major floristic units. The Grade of Membership model was used to further verify the four units, and to understand their boundaries and the internal structure of each floristic unit. Finally, the best combination model was used to explore the driving mechanisms underlying the division. Our results reveal that central Hainan is the most important hotspot for plant endemism and diversity, followed by the southern area. Environmental energy is the main factor determining the spatial patterns of native plant diversity on the island, and accessibility has the greatest impact on native plant diversity among social factors. We explore patterns of spatial phylogenetics and biogeography to identify potential priorities for management and conservation drivers of plant diversity patterns across Hainan, to provide the basis for the effective protection of native plant diversity and the improvement of national parks of Hainan Island.
海南岛是中国热带森林面积最大、保存最完好的地区。随着海南经济的快速发展,生物多样性面临的威胁日益严重。确定海南植物多样性的空间格局和解释植物多样性背后的驱动因素是评估和最大化国家公园效益的重要考虑因素,例如新指定的海南雨林国家公园。我们利用106 252份地理参考标本记录和3792种本地植物的分子系统发育,评估了系统发育多样性模式和物种丰富度。基于系统发育范围加权周转指标,我们将海南植物区系划分为4个主要区系单元。利用隶属度模型进一步验证了这4个单元,并了解了它们的边界和每个区系单元的内部结构。最后,利用最优组合模型来探讨分工背后的驱动机制。结果表明,海南中部是植物特有和多样性最重要的热点地区,其次是南部地区。环境能量是决定岛上原生植物多样性空间格局的主要因素,可达性对岛上原生植物多样性的影响最大。研究海南植物多样性格局的空间系统发育和生物地理特征,为海南本土植物多样性的有效保护和海南国家公园的建设提供依据。
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引用次数: 0
Morphology, molecular phylogeny and biogeography revealed two new Pseudo‐nitzschia (Bacillariophyceae) species in Chinese waters 形态、分子系统发育和生物地理研究揭示了中国水域2个伪尼契亚(硅藻科)新种
IF 3.7 Pub Date : 2023-09-06 DOI: 10.1111/jse.13016
Biaobiao Niu, Qi‐Xiang Zheng, Yang Liu, N. Lundholm, S. Teng, Xu‐Dan Lu, Rui‐Wei Ran, Li Zhang, Yang Li
Pseudo‐nitzschia is a group of widely distributed planktonic diatoms. Some species produce the neurotoxin domoic acid. Herein, two new Pseudo‐nitzschia species were described from Chinese coastal waters and the South China Sea after combining morphological and molecular data, together with biogeographical traits. Pseudo‐nitzschia punctionis sp. nov. was similar to Pseudo‐nitzschia bipertita morphologically, but differed in poroid structure, which was undivided in P. punctionis but divided in two sectors in P. bipertita. This difference corresponded to the presence of two hemicompensatory base changes (HCBCs) in the secondary structure of internal transcribed spacer 2. Pseudo‐nitzschia polymorpha sp. nov. was sister to Pseudo‐nitzschia limii phylogenetically, but distinct by the various shapes of perforations on the valve and copula, which was supported by four HCBCs. In a metabarcoding analysis, multiple new ribotypes were identified within the two new species, and intraspecific genetic divergences were analyzed. Metabarcoding data revealed that P. punctionis had a broader temperature range (12.9–30.5 °C) than P. polymorpha (22.3–30.5 °C). Within the two new species, different traits were found among the amplicon sequence variants regarding temperature and biogeography, representing different microevolutionary directions under environmental selection. The two new species had different biogeographical traits when compared to their closely related species. Domoic acid was detected in strains of P. punctionis at a concentration of 13.5–17.7 fg/cell, but the toxin was not found in strains of P. polymorpha. A combination of characters based on laboratory strains and field metabarcoding data provided more data for delimiting Pseudo‐nitzschia species and gave new insights into their diversity and biogeography.
伪尼茨藻是一种分布广泛的浮游硅藻。有些种类产生神经毒素软骨藻酸。本文将形态、分子和生物地理特征相结合,在中国沿海和南海海域分别描述了2个伪尼奇亚虫新种。针刺伪尼契虫与两带假尼契虫形态相似,但孔结构不同,针刺伪尼契虫的孔结构不分裂,而两带假尼契虫的孔结构分为两段。这种差异与内部转录间隔器2的二级结构中存在两种半代偿性碱基变化(HCBCs)相对应。多形伪尼茨schia sp. 11 .是有限伪尼茨schia的姐妹,但在阀和轴上有不同形状的穿孔,这是由四个HCBCs支撑的。在元条形码分析中,在两个新种中发现了多个新的核糖型,并分析了种内遗传差异。元条形码数据显示,刺点假单胞菌的温度范围(12.9 ~ 30.5°C)比多形假单胞菌(22.3 ~ 30.5°C)更宽。在两个新种中,扩增子序列变异在温度和生物地理方面表现出不同的特征,代表了环境选择下不同的微观进化方向。这两个新种与近缘种相比具有不同的生物地理特征。在刺点假单胞菌中检测到软骨藻酸浓度为13.5 ~ 17.7 fg/细胞,而在多形假单胞菌中未检测到软骨藻酸。基于实验室菌株和野外元条形码数据的特征组合为伪尼茨氏菌的物种划分提供了更多的数据,并为其多样性和生物地理学提供了新的见解。
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引用次数: 1
Lineage‐specific trait variations and plasticity of obligate parthenogenetic animals following the expansion of distribution range to a continental archipelago 分布范围向大陆群岛扩展后专性孤雌生殖动物的谱系特异性性状变异和可塑性
IF 3.7 Pub Date : 2023-09-04 DOI: 10.1111/jse.13015
Xiao‐Fei Tian, Maki Toyota, Hajime Ohtsuki, Jotaro Urabe
Evolutionary theory suggests the hypothesis that among genetically isolated populations, phenotypic variation should be smaller in populations with smaller ratios of nonsynonymous to synonymous substitutions (dN/dS) because smaller dN/dS ratios occur under greater purification selections. Two distinct lineages (JPN1 and JPN2) of panarctic Daphnia cf. pulex sensu Hebert (1995), invaded independently into Japan from North America, provide an excellent opportunity to test this hypothesis because the earlier invader JPN1 has a lower dN/dS ratio than JPN2. Therefore, we examined phenotypic variations in fitness‐related traits, including digestive, life‐history, and morphological traits, among several genotypes within these two lineages. We found that phenotypic variations were smaller within the JPN1 lineage than within the JPN2 lineage. Furthermore, within‐lineage variation of the phenotypic plasticity to changing food levels was smaller in the JPN1 lineage than in the JPN2 lineage. These results support the hypothesis that the JPN1 lineage has been more efficiently subjected to negative selection. However, the magnitude of the phenotypic plasticity of these traits was, on average, at the same level between the JPN1 and JPN2 lineages and its direction differed among genotypes of these lineages, suggesting that the JPN2 genotypes might have exploited niches that were different from those of the JPN1 genotypes.
进化理论提出了这样的假设:在遗传隔离的群体中,非同义与同义替换(dN/dS)比例较小的群体中,表型变异应该更小,因为在更大的纯化选择下,dN/dS比例更小。从北美独立入侵日本的泛北极水蚤(panarctic Daphnia cf.pulex sensu Hebert, 1995)的两个不同谱系(JPN1和JPN2)为验证这一假设提供了很好的机会,因为较早的入侵者JPN1的dN/dS比JPN2低。因此,我们研究了这两个世系中几个基因型的适应度相关性状的表型差异,包括消化、生活史和形态性状。我们发现JPN1谱系的表型变异比JPN2谱系的表型变异要小。此外,与JPN2谱系相比,JPN1谱系对食物水平变化的表型可塑性变异更小。这些结果支持了JPN1谱系更有效地经受负选择的假设。然而,这些性状的表型可塑性在JPN1和JPN2间的平均水平相同,但其方向在不同的基因型间存在差异,表明JPN2基因型可能利用了不同于JPN1基因型的生态位。
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引用次数: 0
Mid‐Pleistocene events influenced the current spatial structure of genetic diversity in Scots pine (Pinus sylvestris L.) 中更新世事件对苏格兰松遗传多样性空间结构的影响
IF 3.7 Pub Date : 2023-08-07 DOI: 10.1111/jse.13013
Bartosz Łabiszak, W. Wachowiak
Scots pine (Pinus sylvestris L.) is one of the most important tree species of the temperate and boreal zones in Eurasia. Its wide distribution range and current patterns of genetic variation have been influenced by Quaternary climatic oscillations and the demographic processes connected to them. In order to better understand the relationship between evolutionary history and demographic factors in a widespread species with a large genome, we used the single‐nucleotide polymorphism (SNP) array to genotype thousands of SNP markers across 62 natural populations (N = 686 trees) of Scots pine in Eurasia. This provides the largest range‐wide SNPs' genetic diversity assessment of Scots pine to date. Our findings show evidence of past admixture events between genetic clusters that were retained despite the potential for effective pollen‐mediated gene flow across the species' distribution range. We also examined the contemporary population structure of the species and analyzed the range‐wide genetic diversity patterns. Phylogenetic analyses and demographic modeling suggest that the observed divergence patterns between genetic lineages likely predate the last glaciation events. Two of the most distinctive groups are represented by trees from the eastern parts of Fennoscandia and Eastern Russia, which have remained separated since the mid‐Pleistocene. The patterns of genetic variation also confirm the dual colonization of Fennoscandia and the existence of an admixture zone in Central Europe that was formed during multiple waves of postglacial recolonization. This study provides insights into the genetic relationships of Scots pine populations from Europe and Asia and offers a more comprehensive understanding of the species' history.
苏格兰松(Pinus sylvestris L.)是欧亚大陆温带和寒带地区最重要的树种之一。其广泛的分布范围和当前的遗传变异模式受到第四纪气候波动及其相关的人口统计过程的影响。为了更好地了解具有大基因组的广泛物种的进化史与人口统计学因素之间的关系,我们使用单核苷酸多态性(SNP)阵列对欧亚大陆62个自然种群(N = 686棵树)的数千个SNP标记进行了基因型分析。这提供了迄今为止最大范围的苏格兰松snp遗传多样性评估。我们的研究结果表明,尽管花粉介导的基因在物种分布范围内有效流动,但遗传集群之间过去的混合事件仍被保留。我们还研究了该物种的当代种群结构,并分析了全范围的遗传多样性模式。系统发育分析和人口统计学模型表明,观察到的遗传谱系之间的分化模式可能早于最后一次冰期事件。芬诺斯坎迪亚东部和俄罗斯东部的树木代表了两个最独特的群体,它们自中更新世以来一直保持分离。遗传变异的模式也证实了芬诺斯坎迪亚的双重殖民化和中欧存在的混合区,这是在冰川后的多次再殖民化浪潮中形成的。这项研究为欧洲和亚洲苏格兰松种群的遗传关系提供了见解,并为该物种的历史提供了更全面的了解。
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引用次数: 0
Linked selection and recombination rate generate both shared and lineage‐specific genomic islands of divergence in two independent Quercus species pairs 连锁选择和重组率在两个独立的栎树物种对中产生了共享的和谱系特异性的基因组分化岛
IF 3.7 Pub Date : 2023-08-02 DOI: 10.1111/jse.13008
Yong Shi, Biao‐Feng Zhou, Yiming Liang, Baosheng Wang
A fundamental question in speciation genomics is how evolutionary processes shape the genomic landscape of differentiation between species. Regions of elevated differentiation, referred to as genomic islands, could be shared among closely related species (shared islands) or specific to a lineage (lineage‐specific islands). Shared islands are typically assumed to result from background selection. However, simulations and empirical studies have suggested that positive selection contributes to both shared and lineage‐specific islands. Here, we utilized comparative population genomics to examine the contributions of different evolutionary processes to patterns of genetic differentiation when gene flow and incomplete lineage sorting are minimal. We used whole‐genome resequencing data for 135 individuals from four oak species, including two independent species pairs, Quercus variabilis Blume and Quercus acutissima Carruth. in the subgenus Cerris, and Quercus dentata Thunb. and Quercus griffithii Hook.f. & Thomson ex Miq. in the subgenus Quercus. We found that both shared and subgenus‐specific islands were caused by positive selection, including selective sweeps in current populations and in their most recent common ancestors. Moreover, the recombination rate was a better predictor of genomic differentiation than gene density. Overall, our results reveal that recombination and positive selection impacted genomic differentiation considerably and provide a more precise grasp of how genomic islands formed in Quercus.
物种形成基因组学的一个基本问题是进化过程如何塑造物种间分化的基因组景观。分化程度较高的区域,被称为基因组岛,可以在密切相关的物种之间共享(共享岛)或特定于一个谱系(谱系特异性岛)。共享岛屿通常被认为是背景选择的结果。然而,模拟和实证研究表明,正向选择对共享岛屿和谱系特异性岛屿都有贡献。在这里,我们利用比较群体基因组学来研究当基因流动和不完全谱系分选最小时,不同进化过程对遗传分化模式的贡献。我们使用了来自4个栎种的135个个体的全基因组重测序数据,包括两个独立的种对,Quercus variabilis Blume和Quercus acutissima Carruth。属于栎亚属和栎属。和栎木。& Thomson ex Miq。属于栎亚属。我们发现,共有岛和亚属岛都是由正选择引起的,包括对当前种群及其最近共同祖先的选择性清除。此外,重组率比基因密度更能预测基因组分化。总的来说,我们的研究结果揭示了重组和正选择对基因组分化的影响,并提供了更精确的掌握基因组岛是如何在栎树中形成的。
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引用次数: 0
Phylogenetic and taxonomic relationships between morphotypes related to Elymus caninus (Poaceae) based on sequence of a nuclear gene GBSS1 (waxy) and sexual hybridization 基于核基因GBSS1(蜡质)序列和性杂交的犬Elymus caninus (Poaceae)相关形态型的系统发育和分类关系
IF 3.7 Pub Date : 2023-07-31 DOI: 10.1111/jse.13006
Alexander V. Agafonov, E. Shabanova, M. Emtseva, S. Asbaganov, Igor V. Morozov, A. Bondar, O. Dorogina
{"title":"Phylogenetic and taxonomic relationships between morphotypes related to Elymus caninus (Poaceae) based on sequence of a nuclear gene GBSS1 (waxy) and sexual hybridization","authors":"Alexander V. Agafonov, E. Shabanova, M. Emtseva, S. Asbaganov, Igor V. Morozov, A. Bondar, O. Dorogina","doi":"10.1111/jse.13006","DOIUrl":"https://doi.org/10.1111/jse.13006","url":null,"abstract":"","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"1 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2023-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86180284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
DNA barcoding of recently diverging legume genera: Assessing the temperate Asian Caragana (Fabaceae: Papilionoideae) 新近分化的豆科属的DNA条形码研究:亚洲温带锦鸡儿(蚕豆科:凤蝶科)
IF 3.7 Pub Date : 2023-07-26 DOI: 10.1111/jse.13009
S. Rather, Josphat K. Saina, A. Adit, Hong‐Mei Liu, Zhao-Yang Chang, Harald Schneider
{"title":"DNA barcoding of recently diverging legume genera: Assessing the temperate Asian Caragana (Fabaceae: Papilionoideae)","authors":"S. Rather, Josphat K. Saina, A. Adit, Hong‐Mei Liu, Zhao-Yang Chang, Harald Schneider","doi":"10.1111/jse.13009","DOIUrl":"https://doi.org/10.1111/jse.13009","url":null,"abstract":"","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"70 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2023-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73194639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A haplotype‐resolved genome for Rhododendron × pulchrum and the expression analysis of heat shock genes 杜鹃(Rhododendron x pulchrum)单倍型解析基因组及热休克基因表达分析
IF 3.7 Pub Date : 2023-07-21 DOI: 10.1111/jse.13007
Jianmin Shen, Lan Lan, S. Kan, Hefeng Cheng, D. Peng, Z. Wan, Yue Hu, Xiao‐Ling Huang, Xue-qin Li, Yuanjun Ye, L. Tembrock, Zhide Wu, Song-Heng Jin
{"title":"A haplotype‐resolved genome for Rhododendron × pulchrum and the expression analysis of heat shock genes","authors":"Jianmin Shen, Lan Lan, S. Kan, Hefeng Cheng, D. Peng, Z. Wan, Yue Hu, Xiao‐Ling Huang, Xue-qin Li, Yuanjun Ye, L. Tembrock, Zhide Wu, Song-Heng Jin","doi":"10.1111/jse.13007","DOIUrl":"https://doi.org/10.1111/jse.13007","url":null,"abstract":"","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"131 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2023-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74541984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Next‐generation sequencing reveals hidden genomic diversity in glacial relicts: A case study of Meesia triquetra 新一代测序揭示了冰川遗迹中隐藏的基因组多样性:以三叶草为例
IF 3.7 Pub Date : 2023-07-20 DOI: 10.1111/jse.13005
E. Mikulášková, T. Peterka, Jakub Šmerda, M. Hájek
{"title":"Next‐generation sequencing reveals hidden genomic diversity in glacial relicts: A case study of Meesia triquetra","authors":"E. Mikulášková, T. Peterka, Jakub Šmerda, M. Hájek","doi":"10.1111/jse.13005","DOIUrl":"https://doi.org/10.1111/jse.13005","url":null,"abstract":"","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"20 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87909711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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