Background:The Emei Shan Liocichla(Liocichla omeiensis) is an endemic bird species to southwestern China with a small geographic range. However, little was known about the genetic status of this threatened species.Met...Background:The Emei Shan Liocichla(Liocichla omeiensis) is an endemic bird species to southwestern China with a small geographic range. However, little was known about the genetic status of this threatened species.Methods:We applied restriction-site-associated DNA sequencing(RAD-Seq) for rapid mass identification of microsatellite markers of the Emei Shan Liocichla.Results:A total of 11,564 microsatellite sequences were obtained, 600 random loci were designed for screening and 24 polymorphic microsatellite loci were selected for further validation. The average allele number, average observed heterozygosity and average expected heterozygosity were relatively low in our samples, which were 6.08, 0.6618 and 0.7048, respectively, indicating that the Emei Shan Liocichla might have lost some genetic diversity. Further analyses suggested that the populations distributed on two mountains(Daxiangling and Xiaoliangshan) showed a modest degree of genetic differentiation.Conclusions:These novel microsatellite markers provided valuable preliminary knowledge regarding the genetic status of the Emei Shan Liocichla and can be useful in further studies, as well as in the management and conservation of this species.展开更多
Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships.In this study,785 singl...Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships.In this study,785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato,an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events.The nuclear phylogeny recovered the monophyly of Malus s.l.(including Docynia);however,the genus was supported to be biphyletic in the plastid phylogeny.An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance.Our conflict analysis demonstrated that ILS,hybridization,and allopolyploidy could explain the widespread nuclear gene tree discordance.One deep hybridization event(Malus doumeri)and one recent event(Malus coronaria)were detected in Malus s.l.Furthermore,our historical biogeographic analysis integrating living and fossil data supported a widespread East Asianwestern North American origin of Malus s.l.in the Eocene,followed by several extinction and dispersal events in the Northern Hemisphere.We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.展开更多
基金supported by the National Natural Science Foundation of China (Grant No. 31272330) to YFthe National Key Programme of Research and Development, Ministry of Science and Technology (2016YFC0503200) to ZZ
文摘Background:The Emei Shan Liocichla(Liocichla omeiensis) is an endemic bird species to southwestern China with a small geographic range. However, little was known about the genetic status of this threatened species.Methods:We applied restriction-site-associated DNA sequencing(RAD-Seq) for rapid mass identification of microsatellite markers of the Emei Shan Liocichla.Results:A total of 11,564 microsatellite sequences were obtained, 600 random loci were designed for screening and 24 polymorphic microsatellite loci were selected for further validation. The average allele number, average observed heterozygosity and average expected heterozygosity were relatively low in our samples, which were 6.08, 0.6618 and 0.7048, respectively, indicating that the Emei Shan Liocichla might have lost some genetic diversity. Further analyses suggested that the populations distributed on two mountains(Daxiangling and Xiaoliangshan) showed a modest degree of genetic differentiation.Conclusions:These novel microsatellite markers provided valuable preliminary knowledge regarding the genetic status of the Emei Shan Liocichla and can be useful in further studies, as well as in the management and conservation of this species.
文摘综述了有关线粒体基因组 (m t DNA)多态性与运动能力的研究 :mt DNA为 16 5 6 9bp的双链闭环分子 ,含有 37个基因 ,排列紧密 ,无内含子。其转录、复制受核 DNA调控 ,同时也不同程度地影响核 DNA表达 ;mt DNA的多样性很高的结论被进一步证实 ,且 m t DNA的差异主要分布在群体内的个体间 ,而群体间的差异较小 ;目前研究认为 ,m t DNA多态性可能造成群体中有氧代谢能力的个体差异 ,是决定有氧能力和训练敏感性的可能分子机制之一。展示了中国运动员和汉人 m t DNA HVR 多态性 ,及其与运动能力关联性研究的结果 ,并对比分析了限制性酶切、直接测序、活细胞培养等方法对 mt DNA多态性与运动能力的研究结果 ,发现众多研究结果还存在不少争议 ,仍需进一步深入研究。 m t DNA作为良好的遗传标记 ,对其单核苷酸多态性(SNP)的分析及其与运动能力表型的关联研究和分子遗传学探讨具有重要意义和研究前景。
基金National Natural Science Foundation of China supports this research (32000163 and 31620103902)
文摘Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships.In this study,785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato,an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events.The nuclear phylogeny recovered the monophyly of Malus s.l.(including Docynia);however,the genus was supported to be biphyletic in the plastid phylogeny.An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance.Our conflict analysis demonstrated that ILS,hybridization,and allopolyploidy could explain the widespread nuclear gene tree discordance.One deep hybridization event(Malus doumeri)and one recent event(Malus coronaria)were detected in Malus s.l.Furthermore,our historical biogeographic analysis integrating living and fossil data supported a widespread East Asianwestern North American origin of Malus s.l.in the Eocene,followed by several extinction and dispersal events in the Northern Hemisphere.We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.
