Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots

To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (G[subscript]m/G[subscript]t and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.Supplementary information accompanies this paper at http://www.nature.com/srep. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Nature Publishing Group. The published article can be found at: http://www.nature.com/articles/srep1512

Distribution and Source Apportionment of Polycyclic Aromatic Hydrocarbons (PAHs) in Forest Soils from Urban to Rural Areas in the Pearl River Delta of Southern China

The upper layer of forest soils (0–20 cm depth) were collected from urban, suburban, and rural areas in the Pearl River Delta of Southern China to estimate the distribution and the possible sources of polycyclic aromatic hydrocarbons (PAHs). Total concentrations of PAHs in the forest soils decreased significantly along the urban–suburban–rural gradient, indicating the influence of anthropogenic emissions on the PAH distribution in forest soils. High and low molecular weight PAHs dominated in the urban and rural forest soils, respectively, implying the difference in emission sources between the areas. The values of PAH isomeric diagnostic ratios indicated that forest soil PAHs were mainly originated from traffic emissions, mixed sources and coal/wood combustion in the urban, suburban and rural areas, respectively. Principal component analysis revealed that traffic emissions, coal burning and residential biomass combustion were the three primary contributors to forest soil PAHs in the Pearl River Delta. Long range transportation of PAHs via atmosphere from urban area might also impact the PAHs distribution in the forest soils of rural area

Dominant Species in Subtropical Forests Could Decrease Photosynthetic N Allocation to Carboxylation and Bioenergetics and Enhance Leaf Construction Costs during Forest Succession

It is important to understand how eco-physiological characteristics shift in forests when elucidating the mechanisms underlying species replacement and the process of succession and stabilization. In this study, the dominant species at three typical successional stages (early-, mid-, and late-succession) in the subtropical forests of China were selected. At each stage, we compared the leaf construction costs (CC), payback time (PBT), leaf area based N content (NA), maximum CO2 assimilation rate (Pmax), specific leaf area (SLA), photosynthetic nitrogen use efficiency (PNUE), and leaf N allocated to carboxylation (NC), and to bioenergetics (NB). The relationships between these leaf functional traits were also determined. The results showed that the early-succession forest is characterized with significantly lower leaf CC, PBT, NA, but higher Pmax, SLA, PNUE, NC, and NB, in relation to the late-succession forest. From the early- to the late-succession forests, the relationship between Pmax and leaf CC strengthened, whereas the relationships between NB, NC, PNUE, and leaf CC weakened. Thus, the dominant species are able to decrease the allocation of the photosynthetic N fraction to carboxylation and bioenergetics during forest succession. The shift in these leaf functional traits and their linkages might represent a fundamental physiological mechanism that occurs during forest succession and stabilization

JonesFrankBotanyPlantPathCloselyRelatedTaxaSupplementaryInfo.pdf

To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (G[subscript]m/G[subscript]t and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities

JonesFrankBotanyPlantPathCloselyRelatedTaxa.pdf

To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (G[subscript]m/G[subscript]t and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities

Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots

To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (G(m)/G(t) and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities