Developing DNA barcodes for species identification in Podophylloideae (Berberidaceae)

Species of Podophyllum, Dysosma, Sinopodophyllum, and Diphylleia, genera from Podophylloideae of Berberidaceae, have long been used in traditional herbal medicine in East Asia and/or North America. Accurate identification of the species of these four genera is crucial to their medicinal uses. In this study, we tested the utility of nine barcodes (matK, rbcL, atpH-atpI, rpl32-trnL^UAG, rps18-clpp, trnL-trnF, trnL-ndhJ, trnS-trnfM, and internal transcribed spacer (ITS)) to discriminate different species of Podophylloideae. Thirty-six individuals representing 12 species of Podophylloideae were collected from different locations in China, Japan, and North America. We assessed the feasibility of amplification and sequencing of all markers, examined the levels of the barcoding gap based on DNA sequence divergence between ranges of intra- and interspecific variation using pairwise distances, and further evaluated successful identifications using each barcode by similarity-based and tree-based methods. Results showed that nine barcodes, except rps18-clpp, have a high level of primer universality and sequencing success. As a single barcode, ITS has the most variable sites, greater intra- and interspecific divergences, and the highest species discrimination rate (83%), followed by matKwhich has moderate variation and also high species discrimination rates. However, these species can also be discriminated by ITS alone, except Dysosma versipellis (Hance) M. Cheng ex T. S. Ying and D. pleiantha (Hance) Woodson. The combination of ITS + matK did not improve species resolution over ITS alone. Thus, we propose that ITS may be used as a sole region for identification of most species in Podophylloideae. The failure of ITS to distinguish D. versipellis and D. pleiantha is likely attributed to incomplete lineage sorting due to recent divergence of the two species.     

DNA barcodes identify Chinese medicinal plants and detect geographical patterns of Sinosenecio (Asteraceae)

DNA barcodes have proved to be efficient for plants species discrimination and identification using short and standardized genomic regions. The genus Sinosenecio(Asteraceae) is used for traditional medicinal purposes in China. Most species of the genus occur in restricted geographical regions and exhibit a wide range of morphological variations within species, making them difficult to differentiate in the field. Previously, taxonomic revisions have been made based on morphological and cytological evidence. In the present study, barcoding analysis was performed on 107 individuals representing 38 species in this genus to evaluate the performance of four candidate barcoding loci (matK, rbcL, trnH-psbA and internal transcribed spacer [ITS]) and detect geographical patterns. Three different methods based on genetic distance, sequence similarity, and the phylogenetic tree were used. Comparably high species discrimination power was detected in species-level taxonomic process by the ITS dataset alone or combined with other loci, which was suggested to be the most suitable barcode for Sinosenecio. Our results are congruent with previous taxonomic studies concerning the monophyly of the S. oldhamianus group. The present study provides an empirical paradigm for the identification of medicinal plant species and their geographical patterns, ascertaining the congruence between taxonomical studies and barcoding analysis inSinosenecio.     

梅花草属四个种的新异名

将丽江梅花草(Parnassia lijiangensis Ku)处理为凹瓣梅花草(P．mysorensis Heyne ex Wight et Am．)的异名;彝良梅花草(P．yiliangensis Ku)处理为大叶梅花草(P．monochorifolia Franch．)的异名;思茅梅花草(P．simaoensis Y．Y．Qian)处理为鸡眼草(P．wightiana Wall．ex Wight ＆ Am．)的异名;龙胜梅花草(P．longshengensis Ku)处理为宽叶梅花草(P．dilatata Hand．-Mazz．)的异名。     

中国梅花草属( 梅花草科) 一些种类的订正

在标本研究和野外观察的基础上, 对中国分布的梅花草属( Parnassia) 的一些种类进行了修订, 将披针瓣梅花草( P. lanceolata) 、窄瓣梅花草( P . angustipetala) 与德格梅花草( P. degeensis) 归并入云南梅花草( P. yunnanensis) ; 将贵州梅花草( P. petimenginii ) 归并入峨眉梅花草( P. faberi ) ; 将矮小梅花草( P. humillis ) 归并入三脉梅花草( P. trinervis) ; 将青海梅花草( P . qinghaiensis) 归并入高山梅花草( P. cacuminum); 将康定梅花草( P . kangdingensis) 归并入类三脉梅花草( P. pusilla) 。     

Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China

The genus Curcuma L. is commonly used as spices, medicines, dyes and ornamentals. Owing to its economic significance and lack of clear‐cut morphological differences between species, this genus is an ideal case for developing DNA barcodes. In this study, four chloroplast DNA regions (matK, rbcL, trnH‐psbA and trnL‐F) and one nuclear region (ITS2) were generated for 44 Curcuma species and five species from closely related genera, represented by 96 samples. PCR amplification success rate, intra‐ and inter‐specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in matK (89.7%), rbcL (100%), trnH‐psbA (100%), trnL‐F (95.7%) and ITS2 (82.6%) regions. The results further showed that four candidate chloroplast barcoding regions (matK, rbcL, trnH‐psbA and trnL‐F) yield no barcode gaps, indicating that the genus Curcuma represents a challenging group for DNA barcoding. The ITS2 region presented large interspecific variation and provided the highest correct identification rates (46.7%) based on BLASTClust method among the five regions. However, the ITS2 only provided 7.9% based on NJ tree method. An increase in discriminatory power needs the development of more variable markers.     

中国梅花草属(梅花草科)一些种类的订正

在标本研究和野外观察的基础上,对中国分布的梅花草属(Parnassia)的一些种类进行了修订,将披针瓣梅花草(P.lanceolata)、窄瓣梅花草(P.angustipetala)与德格梅花草(P.degeensis)归并入云南梅花草(P.yunnanensis);将贵州梅花草(P.petimenginii)归并入峨眉梅花草(P.faberi);将矮小梅花草(P.humillis)归并入三脉梅花草(P.trinervis);将青海梅花草(P.qinghaiensis)归并入高山梅花草(P.ca-cuminum);将康定梅花草(P.kangdingensis)归并入类三脉梅花草(P.pusilla)。     

Nuclear simple sequence repeat markers are superior to DNA barcodes for identification of closely related Rhododendron species on the same mountain

Accurate species delimitation of sampled biological material is critical for a range of studies. Although the DNA barcodes developed in recent years are useful for identifying numerous well differentiated species that have not experienced frequent gene flow, they fail to delimit recently diverged species, especially those with extensive introgressions. Here we use five Rhododendron species growing together on the same mountain as a model system to compare the species delimitation effectiveness of the DNA barcodes (internal transcribed spacer, matK, psbA‐trnH, and rbcL) previously proposed versus 15 pairs of microsatellite markers. Using these markers, we genotyped 129 individuals, which were members of five species according to morphological identification. We identified five simple sequence repeat genetic clusters (independently evolving lineages) corresponding to the morphological identification. However, we found that numerous individuals contained cryptic hybrid introgressions from the other species. The four DNA barcodes could not delimit three out of four closely related species that showed clear morphological differentiation and cryptic introgressions. Even after excluding all cryptic hybrids, two closely related species could not be successfully identified. The low discrimination ability of the DNA barcodes for closely related Rhododendron species could result from two, not mutually exclusive factors: introgressive hybridization and incomplete lineage sorting. Our results highlight the importance of simple sequence repeat markers in delimiting closely related species and identifying cryptic introgressions in the absence of morphological changes.     

中国梅花草属植物的叶表皮特征及其系统学意义

利用光学显微镜和扫描电镜对梅花草属Parnassia 30种植物的叶表皮进行了观察。结果表明:气孔器普遍存在于叶的下表皮,少数种的上表皮也有分布,均为无规则型。叶表皮细胞形状为多边形或不规则形;垂周壁式样可区分为近平直、浅波状和波状。在扫描电镜下,叶表皮气孔器外拱盖内缘为近平滑、浅波状或波状;一些种的保卫细胞两端有加厚;角质膜条纹状,有的条纹隆起,有的条纹上附有颗粒或小孔穴。气孔器类型及下表皮细胞形状的一致性表明梅花草属是一个自然分类群;sect. Saxifragastrum叶表皮特征具有多样性显示该组可能是一个复合群;突隔梅花草P. delavayi属于subsect. Xiphosandra,其气孔下陷,与其细胞学特征相似,支持独立为一组;此外,气孔器的分布、保卫细胞两端加厚、气孔器外拱盖内缘形态以及角质膜等特征对该属部分种的区分有一定的参考价值。     

Species identification of aphids (Insecta: Hemiptera: Aphididae) through DNA barcodes

A 658-bp fragment of mitochondrial DNA from the 5' region of the mitochondrial cytochrome c oxidase 1 (COI) gene has been adopted as the standard DNA barcode region for animal life. In this study, we test its effectiveness in the discrimination of over 300 species of aphids from more than 130 genera. Most (96%) species were well differentiated, and sequence variation within species was low, averaging just 0.2%. Despite the complex life cycles and parthenogenetic reproduction of aphids, DNA barcodes are an effective tool for identification.     

Pollen Morphology of Parnassia L. （Parnassiaceae） and Its Systematic Implications

The pollen morphology of 28 species of Parnassia L. was investigated with light microscopy and scanning electron microscopy (SEM). The shape of pollen grains in this genus varies from subspheroidal to prolate in equatorial view and is three-lobed circular in the polar view. Pollen grains are usually radially symmetrical, isopolar, tricolporate or syntricolporate, with reticulate sculpture. The pollen characteristics among species are fairly similar to each other. Morphological information regarding the pollen grains shows that Parnassia is a natural genus. Based on exine ornamentation observed under SEM, three types of pollen grains were recognized: (i) type I, with foveolate-reticulate sculpture; (ii) type II, with a finely reticulate sculpture; and (iii) type III, with a coarsely reticulate sculpture. Most sections of this genus have one type of sculpture of pollen morphology, but Sect. Nectarotrilobos has three types of sculpture and Sect.Saxifragastrum has two types of sculpture. All three types of sculpture can be found in Southwest China,with species with the longest (Parnassia delavayi Franch.) and shortest (Parnassiafaberi Oliv.) colpi,implying that Southwest China is the center of diversification of the genus.     

Assessment of candidate plant DNA barcodes using the Rutaceae family

DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention.Here,seven regions (psbA-trnH,matK,ycf5,rpoC1,rbcL,ITS2,and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae.To evaluate each barcode’s utility for species authentication,PCR amplification efficiency,genetic divergence,and barcoding gaps were assessed.We found that the ITS2 region exhibited the highest inter-specific divergence,and that this was significantly higher than the intra-specific variation in the "DNA barcoding gap" assessment and Wilcoxon two-sample tests.The ITS2 locus had the highest identification efficiency among all tested regions.In a previous study,we found that ITS2 was able to discriminate a wide range of plant taxa,and here we confirmed that ITS2 was also able to discriminate a number of closely related species.Therefore,we propose that ITS2 is a promising candidate barcode for plant species identification.     

Assessing the diversity of New Zealand freshwater harpacticoid copepods (Crustacea: Copepoda) using mitochondrial DNA (COI) barcodes

Taxonomic and ecological studies of freshwater harpacticoid copepods are limited globally by the ability to easily and accurately identify specimens. Here, we test the use of the mitochondrial cytochrome c oxidase subunit I (COI) gene locus as a tool for assessing the diversity of freshwater Harpacticoida. We obtained sequences from New Zealand harpacticoid copepods, representing two families, five genera and nine species, including the non-indigenous Elaphoidella sewelli. All species were delineated by the COI gene. However, high intraspecific diversity was evident among populations of Elaphoidella bidens (>12%), and between North and South Island populations of Bryocamptus pygmaeus (>18%), potentially indicating the presence of morphologically cryptic taxa. We suggest that mitochondrial DNA (COI) sequences can provide a useful tool for the routine identification of freshwater harpacticoid copepods. Applications of these data will include assessing species diversity and biogeography as well as assisting with the detection of non-indigenous species.     

DNA barcodes for 1/1000 of the animal kingdom

This study reports DNA barcodes for more than 1300 Lepidoptera species from the eastern half of North America, establishing that 99.3 per cent of these species possess diagnostic barcode sequences. Intraspecific divergences averaged just 0.43 per cent among this assemblage, but most values were lower. The mean was elevated by deep barcode divergences (greater than 2%) in 5.1 per cent of the species, often involving the sympatric occurrence of two barcode clusters. A few of these cases have been analysed in detail, revealing species overlooked by the current taxonomic system. This study also provided a large-scale test of the extent of regional divergence in barcode sequences, indicating that geographical differentiation in the Lepidoptera of eastern North America is small, even when comparisons involve populations as much as 2800 km apart. The present results affirm that a highly effective system for the identification of Lepidoptera in this region can be built with few records per species because of the limited intra-specific variation. As most terrestrial and marine taxa are likely to possess a similar pattern of population structure, an effective DNA-based identification system can be developed with modest effort.     

Pollen Morphology of Parnassia L. (Parnassiaceae) and Its Systematic Implications

The pollen morphology of 28 species of Parnassia L. was investigated with light microscopy and scanning electron microscopy (SEM). The shape of pollen grains in this genus varies from subspheroidal to prolate in equatorial view and is three-lobed circular in the polar view. Pollen grains are usually radially symmetrical, isopolar, tricolporate or syntricolporate, with reticulate sculpture. The pollen characteristics among species are fairly similar to each other. Morphological information regarding the pollen grains shows that Parnassia is a natural genus. Based on exine ornamentation observed under SEM, three types of pollen grains were recognized: (i) type Ⅰ, with foveolate-reticulate sculpture; (ii) type Ⅱ, with a finely reticulate sculpture; and (iii) type Ⅲ, with a coarsely reticulate sculpture. Most sections of this genus have one type of sculpture of pollen morphology, but Sect. Nectarotrilobos has three types of sculpture and Sect.Saxifragastrum has two types of sculpture. All three types of sculpture can be found in Southwest China,with species with the longest (Parnassia delavayi Franch.) and shortest (Parnassia faberi Oliv.) colpi,implying that Southwest China is the center of diversification of the genus.     

DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago

DNA barcoding using a partial region (648 bp) of the cytochrome c oxidase I (COI) gene is a powerful tool for species identification and has revealed many cryptic species in various animal taxa. In birds, cryptic species are likely to occur in insular regions like the Japanese Archipelago due to the prevention of gene flow by sea barriers. Using COI sequences of 234 of the 251 Japanese‐breeding bird species, we established a DNA barcoding library for species identification and estimated the number of cryptic species candidates. A total of 226 species (96.6%) had unique COI sequences with large genetic divergence among the closest species based on neighbour‐joining clusters, genetic distance criterion and diagnostic substitutions. Eleven cryptic species candidates were detected, with distinct intraspecific deep genetic divergences, nine lineages of which were geographically separated by islands and straits within the Japanese Archipelago. To identify Japan‐specific cryptic species from trans‐Paleartic birds, we investigated the genetic structure of 142 shared species over an extended region covering Japan and Eurasia; 19 of these species formed two or more clades with high bootstrap values. Excluding six duplicated species from the total of 11 species within the Japanese Archipelago and 19 trans‐Paleartic species, we identified 24 species that were cryptic species candidates within and surrounding the Japanese Archipelago. Repeated sea level changes during the glacial and interglacial periods may be responsible for the deep genetic divergences of Japanese birds in this insular region, which has led to inconsistencies in traditional taxonomies based on morphology.     

Parnassia zhengyuana sp. nov. and P. simianshanensis sp. nov.: two new species of Parnassia (Celastraceae) from karst caves and Danxia landform in southwest China

Two new species of Parnassia, Parnassia zhengyuana M.X. Ren & J. Zhang and P. simianshanensis M.X. Ren, J. Zhang & Z.Y. Liu, have been found in mountainous areas of Chongqing City, southwest China, and are described and illustrated here. Parnassia zhengyuana is found in a limestone cave near Mt Jinfo, Nanchuan District, Chongqing City. This tiny plant has special spoon‐shaped leaves and undivided staminodes with green apices. Parnassia simianshanensis was discovered in Mt Simian, Jiangjin County, Chongqing City. This species grows along streams on red sandstones, i.e. in Danxia landform. It can be easily identified by its unique rhombic leaves and the five‐ or four‐branched staminodes. The conservation status of P. zhengyuana and P. simianshanensis are assessed respectively as ‘Critically Endangered’ (CR) and ‘VU’ (Vulnerable) according to IUCN criteria. The roles of karst and Danxia landforms in the speciation process are discussed.     

Deep genetic divergences in Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi): a widespread 'mite harvestman' defies DNA taxonomy

Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi, Pettalidae), a widespread 'mite harvestman' endemic to the South Island of New Zealand, is found in leaf littler habitats throughout Nelson and Marlborough, and as far south as Arthur's Pass. We investigated the phylogeography and demographic history of A. denticulata in the first genetic population-level study within Opiliones. A total of 119 individuals from 17 localities were sequenced for 785 bp of the gene cytochrome c oxidase subunit I; 102 of these individuals were from the Aoraki subspecies A. denticulata denticulata and the remaining 17 were from the subspecies A. denticulata major. An extraordinarily high degree of genetic diversity was discovered in A. denticulata denticulata, with average uncorrected p-distances between populations as high as 19.2%. AMOVA, average numbers of pairwise differences, and pairwise F(ST) values demonstrated a significant amount of genetic diversity both within and between populations of this subspecies. Phylogenetic analysis of the data set revealed many well-supported groups within A. denticulata denticulata, generally corresponding to clusters of specimens from single populations with short internal branches, but separated by long branches from individuals from other populations. No haplotypes were shared between populations of the widespread small subspecies, A. denticulata denticulata. These results indicate a subspecies within which very little genetic exchange occurs between populations, a result consistent with the idea that Cyphophthalmi are poor dispersers. The highly structured populations and deep genetic divergences observed in A. denticulata denticulata may indicate the presence of cryptic species. However, we find a highly conserved morphology across sampling localities and large genetic divergences within populations from certain localities, equivalent to those typically found between populations from different localities. Past geological events may have contributed to the deep genetic divergences observed between sampling localities; additionally, the high divergence within populations of A. denticulata denticulata suggests that the rate of COI evolution may be accelerated in this taxon. In contrast, the larger subspecies A. denticulata major shows much less differentiation between and within sampling localities, suggesting that it may disperse more easily than its smaller counterpart. The fact that the remarkable genetic divergences within populations of A. denticulata denticulata from certain localities are equivalent to divergences between localities poses a challenge to the rapidly spreading practice of DNA taxonomy.     

Testing the potential of proposed DNA barcodes for species identification of Zingiberaceae

In 2009, the Consortium for the Barcode of Life (CBOL) recommended the combination of rbcL and matK as the plant barcode based on assessments of recoverability, sequencing quality, and levels of species discrimination. Subsequently, based on a study of more than 6600 samples belonging to 193 families from seven phyla, the internal transcribed spacer (ITS) 2 locus was proposed as a universal barcode sequence for all major plant taxa used in traditional herbal medicine. Neither of these two studies was based on a detailed analysis of a particular family. Here, Zingiberaceae plants, including many closely related species, were used to compare the genetic divergence and species identification efficiency of ITS2, rbcL, matK, psbK-psbI, trnH-psbA, and rpoB.The results indicate that ITS2 has the highest interspecific divergence and significant differences between inter- and intraspecific divergence, whereas matK and rbcL have much lower divergence values. Among 260 species belongingto 30 genera in Zingiberaceae, the discrimination ability of the ITS2 locus was 99.5% at the genus level and 73.1% at the species level. Thus, we propose that ITS2 is the preferred DNA barcode sequence for identifying Zingiberaceae plants.     

甘肃省鱼类资源现状及DNA条形码在鱼类物种鉴定中的应用

为了摸清甘肃省土著鱼类资源与分布现状, 探索DNA条形码在鱼类辅助物种鉴定中的适用性, 2012年6-9月对甘肃境内黄河水系、嘉陵江水系和河西内陆河水系进行了较全面的鱼类调查。共采集鱼类标本3,087尾, 隶属于5目10科38属64种, 以鲤科种类最多, 为30种, 占总种数的46.88%。物种多样性分析表明, 在黄河水系的夏河和庄浪河多样性指数是所有调查点中最低的, 分别为1.38和1.09。嘉陵江水系各河段的多样性指数较高(H = 2.15-3.27), 其次为河西内陆河水系(H = 2.01-2.83)。在河西内陆河水系中, 疏勒河的均匀度指数最高, 为1.10, 黑河最低(0.68)。庄浪河的优势度指数最高, 为0.34, 而嘉陵江干流两当段的优势度指数在所有调查点中最低, 为0.04。利用DNA条形码分析了49种662尾标本的COI基因部分序列, 大部分种类在neighbor-joining系统树中形成各自的单系, 种内平均遗传距离0.88%, 种间平均遗传距离为9.99%, 在种内和种间COI序列遗传距离之间形成明显的条形码间隙, 斯氏高原鳅(Triplophysa stoliczkae)与达里湖高原鳅(T. dalaica), 甘肃高原鳅(T. robusta)与似鲇高原鳅(T. siluroides), 嘉陵裸裂尻鱼(Schizopygopsis kialingensis)与黄河裸裂尻鱼(S. pylzovi)之间的遗传距离低于2%, 甘肃高原鳅与似鲇高原鳅不能通过COI基因片段区分开, 其他两对物种可以采用核苷酸诊断法来进一步区分。斯氏高原鳅和拉氏鱼岁(Phoxinus lagowskii)种内遗传分歧较大, 揭示种内可能存在隐存种。结果表明, 对某些近缘种和不同地理种群差异较大的物种, 要将分子、形态和地理分布特点结合起来才能准确鉴定。