02996nas a2200169 4500008004100000245012400041210006900165260001200234300000900246490000700255520244900262100002002711700001602731700001902747700001202766856004802778 2015 eng d00aApplication of DNA barcodes in Asian tropical trees – a case study from Xishuangbanna Nature Reserve, Southwest China0 aApplication of DNA barcodes in Asian tropical trees a case study c06/2015 a1-170 v103 a

Background
Within a regional floristic context, DNA barcoding is more useful to manage plant diversity inventories on a large scale and develop valuable conservation strategies. However, there are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world.


Methodology and Principal Findings
A DNA barcoding database of an Asian tropical trees with high diversity was established at Xishuangbanna Nature Reserve, Yunnan, southwest China using rbcL and matK as standard barcodes, as well as trnH–psbA and ITS as supplementary barcodes. The performance of tree species identification success was assessed using 2,052 accessions from four plots belonging to two vegetation types in the region by three methods: Neighbor-Joining, Maximum-Likelihood and BLAST. We corrected morphological field identification errors (9.6%) for the three plots using rbcL and matK based on Neighbor-Joining tree. The best barcode region for PCR and sequencing was rbcL (97.6%, 90.8%), followed by trnH–psbA (93.6%, 85.6%), while matK and ITS obtained relative low PCR and sequencing success rates. However, ITS performed best for both species (44.6–58.1%) and genus (72.8–76.2%) identification. With trnH–psbA slightly less effective for species identification. The two standard barcode rbcL and matK gave poor results for species identification (24.7–28.5% and 31.6–35.3%). Compared with other studies from comparable tropical forests (e.g. Cameroon, the Amazon and India), the overall performance of the four barcodes for species identification was lower for the Xishuangbanna Nature Reserve, possibly because of species/genus ratios and species composition between these tropical areas.


Conclusions/Significance
Although the core barcodes rbcL and matK were not suitable for species identification of tropical trees from Xishuangbanna Nature Reserve, they could still help with identification at the family and genus level. Considering the relative sequence recovery and the species identification performance, we recommend the use of trnH–psbA and ITS in combination as the preferred barcodes for tropical tree species identification in China.

1 aHuang, Xiao-cui1 aCi, Xiu-Qin1 aConran, J., G.1 aLi, Jie uhttps://lauraceae.myspecies.info/node/2040801993nas a2200253 4500008004100000245008400041210006900125260001200194300001200206490000800218520127200226653002001498653001301518653002201531653001401553653002701567653001801594653001401612100001801626700001201644700001901656700001601675856004801691 2010 eng d00aPhylogeny of the Southeast Asian endemic genus Neocinnamomum H. Liu (Lauraceae)0 aPhylogeny of the Southeast Asian endemic genus Neocinnamomum H L c10/2010 a173-1840 v2903 a

A phylogenetic analysis of Neocinnamomum H. Liu and related genera was conducted using psbA–trnH, trnK cpDNA regions, and the ITS nrDNA segment. Neocinnamomum was confirmed to be monophyletic, and an evolutionary series of inflorescence development within the genus was recognized. The compound thyrse seen in N. caudatum is reduced to the few- to many-flowered condensed inflorescences with a poorly defined branching system seen in most species and ultimately to the 1-flowered inflorescence seen in N. atjehense. Consensus network analysis (CNA) suggested that long-branch attraction is responsible for the observed close relationship between Neocinnamomum and Cassytha L. in a combined analysis of the complete data. In contrast, the sister relationship of Neocinnamomum and Caryodaphnopsis seen in the Bayesian analyses of the partial combined matrix was supported by CNA and is also supported by morphology and wood and bark anatomy. The close similarity of the compound thyrse of less derived Neocinnamomum species to the thyrsoid inflorescences of some Caryodaphnopsis species is also seen as strong support for their affinity.

10aCaryodaphnopsis10aCassytha10aConsensus network10aLauraceae10aLong-branch attraction10aNeocinnamomum10aPhylogeny1 aWang, Zhi-hua1 aLi, Jie1 aConran, J., G.1 aLi, Hsi-Wen uhttps://lauraceae.myspecies.info/node/2040702525nas a2200181 4500008004100000245010100041210006900142260001200211490000700223520197100230100001802201700001602219700001302235700001602248700001902264700001202283856004802295 2017 eng d00aDNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China0 aDNA barcoding evaluation and implications for phylogenetic relat c04/20170 v123 a

Lauraceae are an important component of tropical and subtropical forests and have major ecological and economic significance. Owing to lack of clear-cut morphological differences between genera and species, this family is an ideal case for testing the efficacy of DNA barcoding in the identification and discrimination of species and genera. In this study, we evaluated five widely recommended plant DNA barcode loci matK, rbcL, trnH-psbA, ITS2 and the entire ITS region for 409 individuals representing 133 species, 12 genera from China. We tested the ability of DNA barcoding to distinguish species and as an alternative tool for correcting species misidentification. We also used the rbcL+matK+trnH-psbA+ITS loci to investigate the phylogenetic relationships of the species examined. Among the gene regions and their combinations, ITS was the most efficient for identifying species (57.5%) and genera (70%). DNA barcoding also had a positive role for correcting species misidentification (10.8%). Furthermore, based on the results of the phylogenetic analyses, Chinese Lauraceae species formed three supported monophyletic clades, with the Cryptocarya group strongly supported (PP = 1.00, BS = 100%) and the clade including the Persea group, Laureae and Cinnamomum also receiving strong support (PP = 1.00, BS = 98%), whereas the Caryodaphnopsis-Neocinnamomum received only moderate support (PP = 1.00 and BS = 85%). This study indicates that molecular barcoding can assist in screening difficult to identify families like Lauraceae, detecting errors of species identification, as well as helping to reconstruct phylogenetic relationships. DNA barcoding can thus help with large-scale biodiversity inventories and rare species conservation by improving accuracy, as well as reducing time and costs associated with species identification.

1 aLiu, Zhi-Fang1 aCi, Xiu-Qin1 aLi, Lang1 aLi, Hsi-Wen1 aConran, J., G.1 aLi, Jie uhttps://lauraceae.myspecies.info/node/2035101475nas a2200169 4500008004100000245010200041210006900143260001200212300001200224490000800236520095400244100001301198700001201211700001901223700001501242856004801257 2007 eng d00aPhylogeny of Neolitsea (Lauraceae) inferred from Bayesian analysis of nrDNA ITS and ETS sequences0 aPhylogeny of Neolitsea Lauraceae inferred from Bayesian analysis c10/2007 a203-2210 v2693 a

ITS and ETS-based sequence analyses of 29 Neolitsea, six Actinodaphne and five outgroup ‘core’ Laureae taxa show that Neolitsea is monophyletic with two large subclades, whereas most of the sampled Actinodaphne are paraphyletic below it. Inflorescence features appear to be among the more reliable morphological characters for explaining relationships between Neolitsea and other genera within the ‘core’ Laureae, with the Neolitsea/Actinodaphne clade defined by inflorescences lacking vegetative terminal buds in the main axis. Although the relationships within Neolitsea are still poorly resolved, there is enough structure to suggest that the genus seems to divide into two groups based on fruit shape: elliptic or ovoid, versus globose, although more evidence (both molecular and morphological) and wider taxon sampling are required to confirm this.

1 aLi, Lang1 aLi, Jie1 aConran, J., G.1 aLi, Xi-wen uhttps://lauraceae.myspecies.info/node/2034700620nas a2200181 4500008004100000245012500041210006900166260001200235300001200247490000700259100001200266700001900278700002700297700001700324700001300341700001600354856006800370 2008 eng d00aPhylogenetic relationships of the Litsea complex and core Laureae (Lauraceae) using ITS and ETS sequences and morphology0 aPhylogenetic relationships of the Litsea complex and core Laurea c12/2008 a580-5990 v951 aLi, Jie1 aConran, J., G.1 aChristophel, David, C.1 aLi, Zhi-Ming1 aLi, Lang1 aLi, Hsi-Wen uhttp://www.biodiversitylibrary.org/item/55386#page/596/mode/1up02587nas a2200301 4500008004100000245014200041210006900183300001000252490000700262520164000269653003001909653001701939653002901956653002101985653001402006653002402020100002102044700001302065700002402078700001602102700002102118700002202139700001802161700002702179700001902206700001202225856004802237 2016 eng d00aOrigins and evolution of cinnamon and camphor: A phylogenetic and historical biogeographical analysis of the Cinnamomum group (Lauraceae)0 aOrigins and evolution of cinnamon and camphor A phylogenetic and a33-440 v963 a

Tropical and subtropical amphi-Pacific disjunction is among the most fascinating distribution patterns, but received little attention. Here we use the fossil-rich Cinnamomum group, a primarily tropical and sub-tropical Asian lineage with some species distributed in Neotropics, Australasia and Africa to shed light upon this disjunction pattern. Phylogenetic and biogeographic analyses were carried out using sequences of three nuclear loci from 94 Cinnamomum group and 13 outgroup samples. Results show that although there are three clades within a monophyletic Cinnamomum group, Cinnamomum and previously recognized subdivisions within this genus were all rejected as natural groups. The Cinnamomum group appears to have originated in the widespread boreotropical paleoflora of Laurasia during the early Eocene (ca. 55 Ma). The formation and breakup of the boreotropics seems to have then played a key role in the formation of intercontinental disjunctions within the Cinnamomum group. The first cooling interval (50–48 Ma) in the late early Eocene resulted in a floristic discontinuity between Eurasia and North America causing the tropical and subtropical amphi-Pacific disjunction. The second cooling interval in the mid-Eocene (42–38 Ma) resulted in the fragmentation of the boreotropics within Eurasia, leading to an African–Asian disjunction. Multiple dispersal events from North into South America occurred from the early Eocene to late Miocene and a single migration event from Asia into Australia appears to have occurred in the early Miocene.

10aAmphi-Pacific disjunction10aBiogeography10aBoreotropical paleoflora10aCinnamomum group10aLauraceae10amolecular phylogeny1 aHuang, Jian-Feng1 aLi, Lang1 avan der Werff, Henk1 aLi, Hsi-Wen1 aRohwer, Jens, G.1 aCrayn, Darren, M.1 aMeng, Hong-Hu1 avan der Merwe, Marlien1 aConran, J., G.1 aLi, Jie uhttps://lauraceae.myspecies.info/node/2032000573nas a2200145 4500008004100000245017700041210006900218300001000287490000800297100001200305700002700317700001900344700001600363856004800379 2004 eng d00aPhylogenetic relationships within the 'core' Laureae (Litsea complex, Lauraceae) inferred from sequences of the chloroplast gene matK and nuclear ribosomal DNA ITS regions0 aPhylogenetic relationships within the core Laureae Litsea comple a19-340 v2461 aLi, Jie1 aChristophel, David, C.1 aConran, J., G.1 aLi, Hsi-Wen uhttps://lauraceae.myspecies.info/node/20137