Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna

Applications of DNA barcoding include identifying species, inferring ecological and evolutionary relationships between species, and DNA metabarcoding. These applications require reference libraries that are not yet available for many taxa and geographic regions. We collected, identified, and vouchered plant specimens from Mpala Research Center in Laikipia, Kenya, to develop an extensive DNA-barcode library for a savanna ecosystem in equatorial East Africa. We amassed up to five DNA barcode markers (rbcL, matK, trnL-F, trnH–psbA, and ITS) for 1,781 specimens representing up to 460 species (~92% of the known flora), increasing the number of plant DNA barcode records for Africa by ~9%. We evaluated the ability of these markers, singly and in combination, to delimit species by calculating intra- and inter-specific genetic distances. We further estimated a plant community phylogeny and demonstrated its utility by testing if evolutionary relatedness could predict the tendency of members of the Mpala plant community to have or lack “barcode gaps”, defined as disparities between the maximum intra- and minimum inter-specific genetic distances. We found barcode gaps for 72–89% of taxa depending on the marker or markers used. With the exception of the markers rbcL and ITS, we found that evolutionary relatedness was an important predictor of barcode-gap presence or absence for all of the markers in combination and for matK, trnL-F, and trnH–psbA individually. This plant DNA barcode library and community phylogeny will be a valuable resource for future investigations.

DNA条形码（DNA barcoding）的应用场景涵盖物种鉴定、推断物种种间生态与演化关联，以及DNA宏条形码（DNA metabarcoding）技术。上述应用依赖参考数据库，但目前许多类群与地理区域仍缺乏此类参考库。本研究采集、鉴定并制备了肯尼亚莱基皮亚地区姆帕拉研究中心的植物凭证标本，旨在为赤道东非稀树草原生态系统构建一套完整的DNA条形码参考库。本研究为1781份标本获取了最多5组DNA条形码标记（rbcL、matK、trnL-F、trnH–psbA及ITS），涵盖至多460个物种（约占已知植物区系的92%），使非洲植物DNA条形码记录总量提升了约9%。本研究通过计算种内与种间遗传距离，评估了这些标记单独使用或组合使用时的物种界定能力。本研究进一步构建了植物群落系统发育树，并通过检验演化亲缘关系能否预测姆帕拉植物群落类群存在或缺失“条形码间隙（barcode gap）”——即最大种内遗传距离与最小种间遗传距离的差值——验证了该系统发育树的应用价值。研究结果显示，根据所使用的单个或组合标记，72%至89%的类群可检测到条形码间隙。除rbcL与ITS标记外，我们发现：对于所有标记的组合使用组，以及matK、trnL-F、trnH–psbA单独使用组，演化亲缘关系均是预测条形码间隙存在与否的重要因素。本研究构建的植物DNA条形码参考库与群落系统发育树，将为后续相关研究提供宝贵的资源支撑。