Chloroplast trnL Research Articles

Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities.

DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site.

Comparison and association of winter diets and gut microbiota using trnL and 16S rRNA gene sequencing for three herbivores in Taohongling, China

Food provides essential nutrients and energy for wildlife and directly influences the compositional patterns of the gut microbiota in natural reservoirs. Little is known about the interspecific differences and correlations between diet and microbial communities in sympatric herbivores. We conducted chloroplast trnL and 16S rRNA genes amplicon sequencing of 90 faecal samples from sika deer (Cervus nippon kopschi), Reeve’s muntjac (Muntiacus reevesi), and a Chinese hare (Lepus sinensis). Diet analysis revealed that sika deer predominantly foraged on Rubus (36.5 %), Loropetalum (25.5 %), and Eurya (13.4 %) at the genus level; Reeve’s muntjac favoured Rubus (51.8 %), Eurya (11.0 %), and Euonymus (6.1 %); Chinese hare showed dominance in Rubus (15.8 %), Smilax (15.6 %), and Rhus (10.6 %) consumption, with all these forage plants being shrubs. The gut microbiota of the three herbivores was characterised by Firmicutes, Bacteroidetes, and Proteobacteria, although the relative abundances of these taxa differed across herbivore species. Alpha diversity indicated no significant differences between sika deer and Reeve’s muntjac, whereas alpha indices showed significant differences between sika deer and Chinese hare (p < 0.05). Beta diversity analysis indicated significant differences between the Chinese hare and sika deer, as well as between the Chinese hare and Reeve’s muntjac (p < 0.05), with no significant difference found between the two cervid species, which may be attributed to the influence of interspecific genetics and evolutionary factors. Due to seasonal shifts, the food availability for herbivores decreased, resulting in the convergent adaptation of shrubs consumed by the three species. Furthermore, PICRUSt functional profile prediction indicated that the gut microbiota of the three species were mainly enriched in metabolic functions. Mantel correlation analysis suggested that the gut microbiota of sika deer showed a significant positive correlation with five genera of plants, one genus of Reeve’s muntjacs, and three genera of Chinese hare (p < 0.01), suggesting that the gut microbiota of sika deer may be more susceptible to changes in food abundance. Our study emphasises how the winter climate affects the foraging strategies and microbial communities of the three herbivores, as well as their correlations. These results may further contribute to the food selection, regulation of gut microbiota, disease prevention, conservation, and management of sika deer and other sympatric herbivores.

A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia).

Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated insitu temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.

DNA metabarcoding reveals the seasonal variation of dietary composition of Taihangshan macaque (Macaca mulatta tcheliensis), Jiyuan, north China.

Dietary analysis in wildlife is fundamental for understanding their flexible response to seasonal changes and developing effective conservation management measures. Taihangshan macaque (Macaca mulatta tcheliensis) is the northernmost population of rhesus macaque, currently only distributed in the southern Mt. Taihangshan area. This area belongs to a semi-arid region resulting in limited plant food availability for Taihangshan macaques, with seasonal variation. Herein, we used a chloroplast trnL DNA metabarcoding approach to identify the plant diet diversity and composition from 100 fecal samples of Taihangshan macaque in four seasons (spring, summer, autumn, and winter) from 2020 to 2021. The results revealed that (1) a total of 48 distinct families, 88 genera, and 52 species within the 105 food items that were consumed by Taihangshan macaques throughout the year; (2) the diversity of food items exhibited significant differences across the four seasons; (3) Rosaceae, Rhamnaceae, Fagaceae, and Poaceae are the preferential food items for Taihangshan macaques and have different relative abundances, fluctuating with seasonal variation. DNA metabarcoding can expand our understanding of the repertoire of food items consumed by Taihangshan macaques by detecting some consumed food items in this population that were not yet discovered using traditional methods. Therefore, the integrative results from traditional methods and DNA metabarcoding can provide a fundamental understanding of dietary composition to guide the conservation management of Taihangshan macaques.

Phylogenetic analysis of the endemic Bornmuellera Hausskn. spp. (Brassicaceae) in Türkiye based on nuclear ITS and chloroplast trnL intron, trnL-F, rbcL and trnQ-rps16 DNA sequences

Phylogenetic analysis of the endemic Bornmuellera Hausskn. spp. (Brassicaceae) in Türkiye based on nuclear ITS and chloroplast trnL intron, trnL-F, rbcL and trnQ-rps16 DNA sequences

Environmental DNA of aquatic macrophytes: The potential for reconstructing past and present vegetation and environments

Abstract Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Macrophytes are especially good environmental indicators, thus their environmental DNA palaeorecord might shed light on past postglacial environments. Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding and metabarcoding markers, in order to explore how each of these methods can be used to capture aquatic vegetation diversity and change. We then investigate the extent to which such a record can be leveraged for reconstructing local environmental conditions, using a case study based on macrophyte ecological niches. We find that, with state‐of‐the‐art DNA barcode reference libraries, using metabarcoding to target the P6 loop region of the chloroplast trnL (UAA) intron is optimal to maximise taxonomic resolution and the diversity of past macrophyte communities. Shotgun sequencing also retrieves a high proportion of aquatic macrophyte diversity, but has the lowest taxonomic resolution, and targeted capture needs to be more widely applied before comparisons can be made. From our case study, we infer past aquatic habitats from sedimentary ancient DNA records of macrophyte taxa. We reconstructed Holocene thermal range, continentality, water pH, trophic status, and light conditions in northern Fennoscandia. We show an overall stability since 9,000 years ago, even though individual lakes display different trends and variation in local climatic and physico‐chemical conditions. Combined with the availability of near‐exhaustive barcode and traits databases, metabarcoding data can support wider ecological reconstructions that are not limited to aquatic plant taxonomic inventories but can also be used to infer past changes in water conditions and their environmental drivers. Sedimentary DNA is also a powerful tool to measure present diversity, as well as to reconstruct past lacustrine and fluvial communities of aquatic macrophytes.

Metabarcoding of soil environmental DNA to estimate plant diversity globally.

Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.

Metabarcoding of eDNA for tracking the floral and geographical origins of bee honey

Authentic honey products have a high commercial value and are often falsified via adulteration. Metabarcoding of environmental DNA (eDNA) from bacterial, floral, and entomological sources has recently been proposed as a useful tool for identifying and authenticating floral and geographical origins of bee honey. In this study, eDNA metabarcoding was applied to reveal the bacterial, plant, and honey bee DNA signatures of 48 commercial honey products from six different geographical origins. Bacterial DNA composition in commercial honey showed different relative abundance of Paenibacillus and Bacillus in geographically different samples, and high abundance of Methylobacterium in chestnut honey implying potential use of bacterial DNA composition for honey authentication. Using the chloroplast trnL (UAA) as a DNA marker, floral origins of commercial honey were investigated. Based on floral DNA signatures, 12 monofloral honey samples were identified among the 45 samples tested. Targeted amplicon sequencing of cytochrome oxidase I (COI) gene from entomological DNA identified three different Apis mellifera sequence variants, specific to geographic origin of honey, suggesting that COI can be implemented as a DNA marker to trace the origin of honey. Therefore, the current study demonstrated the potential of eDNA based metabarcoding as a robust tool for evaluating commercial bee honey by exploring their floral and geographical origins.

Temporal and interspecific dietary variation in wintering ducks in agricultural landscapes.

Farmlands are becoming more important as waterfowl foraging habitats, while natural wetlands are being lost globally. However, it is unclear how waterfowl coexist in agricultural landscapes by resource partitioning. We evaluated the diets of seven sympatric dabbling ducks foraging in rice paddy and lotus fields around Lake Kasumigaura, the second largest lake in Japan, during two wintering seasons (from November to February) by faecal DNA metabarcoding using chloroplast trnL and mitochondrial CO1 region sequences. We examined 420 faecal samples and found different patterns of dietary diversity and composition among the duck species. The pattern also differed between plant and invertebrate food. Dietary niche partitioning was clear in plant food. Large-bodied ducks intensively use crop plants, and other ducks might mediate competition by using terrestrial and aquatic plants that are suitable for their foraging behaviours or microhabitats. Dietary segregation among species was the most apparent in February, when the abundance of foraging ducks was the largest. This study illustrated the complex pattern of dietary niche partitioning of dabbling ducks in agricultural landscapes, which might be difficult to evaluate by conventional approaches. The availability of crop plants, as well as other plant food resources in flooted areas and farmland dikes, may enable ducks to coexist by spatial or behavioural resource partitioning.

Flavonoid-producing tomato plants have a direct negative effect on the zoophytophagous biological control agent Orius sauteri.

Orius sauteri (Poppius) (Hemiptera: Anthocoridae) is often used for biological control of small arthropod pests in greenhouse vegetable production systems in Asia. In addition to feeding on arthropod prey, O. sauteri consumes small quantities of plant material. Previous studies demonstrated that tomato plant chemistry confers antixenosis resistance to phloem-feeding whiteflies, but the potential nontarget effects of phytochemicals on the beneficial predator O. sauteri are unknown. Comparison of O. sauteri confined to near-isogenic lines (NILs) of tomatoes producing high levels of flavonoids (NIL-purple hypocotyl; resistant to whiteflies) and low levels of flavonoids (NIL-green hypocotyl; susceptible to whiteflies) revealed that O. sauteri had reduced oviposition, nymphal survival, and development on resistant plants, even if they were also provided with prey that did not feed on the host plant. Moreover, O. sauteri showed a significant ovipositional preference in choice assays, laying significantly more eggs on susceptible than on resistant plants. Molecular gut content analysis using the specific chloroplast trnL gene from tomato confirmed that adult and immature O. sauteri feed on both resistant and susceptible genotypes, and feeding behavior assays revealed that resistance did not affect plant feeding or prey acceptance by O. sauteri adults. These results demonstrate a direct negative effect of phytochemicals on a nontarget beneficial species and indicate that resistance mediated by phytochemicals can affect organisms that do not solely feed on phloem sap. The results also indicate that the mode of action and the potential ecological effects of phytochemical-mediated resistance are broader than previously recognized.

Phylogenetic analysis using SCoT markers and chloroplast trnL intron in some Eriobotrya japonica (Thunb.) Lindl. (Rosaceae) populations from the Aegean region of Turkey

In this study, phylogenetic analyses of some Eriobotrya japonica (Thunb.) Lindl. populations based on SCoT marker technique and cpDNA trnL intron sequence analysis were performed. Specimens from the populations were collected from the Aegean region of Turkey and brought to the laboratory for genomic DNA isolation. To determine the phylogenetic analysis of Eriobotrya japonica populations, seven SCoT primers were used. In the SCoT analysis, a total of 54 bands were obtained, 49 of which were polymorphic and 5 were monomorphic. In chloroplast trnL intron region, trnC, trnD primers were used for PCR amplification. Eriobotrya japonica trnL intron sequence lengths were determined to be between 530 and 547 nucleotides. The average nucleotide rate detected as 38.9% for thymine, 18.1% for cytosine, 28.2% for adenine and 14.8% for guanine. Rosaceae family trnL intron sequences belonging to Rhaphiolepis Lindl., Heteromeles M.Roem., Photinia Lindl. Cotoneaster Medik, Sorbus L., Malus Miller, Pyrus L., Prunus L. and Rosa L. were retrieved from NCBI and their phylogenetic relationship with Eriobotrya japonica populations were revealed. As a result of the study, polymorphism rate was determined as 90.74% in SCoT analysis. According to cpDNA trnL intron results, Eriobotrya japonica populations were identified in the same group with Rhaphiolepis indica, a finding supported by past phylogenetic analyzes.

DNA metabarcoding uncovers the diet of subterranean rodents in China.

A type of rodent called a zokor causes great harm to agriculture and forestry production due to its large and sophisticated diet. As this rodent lives subterrane for most of its life, researchers know little about its dietary habits. Further understanding of its diet is important for developing green and sustainable control strategies for the zokor. Chloroplast trnL gene and internal transcription spacer 1 primers were selected for high-throughput sequencing of stomach contents of captured zokor by DNA metabarcoding. A total of 25 zokors were selected, the food list of 32 families, 80 genera, and 154 species was obtained. At the family level, it was found that zokors mainly fed on Asteraceae, Poaceae, Rosaceae, Pinaceae, Brassicaceae, and Apiaceae. At the genus level, zokors mainly fed on Echinops, Littledalea, Artemisia, Picea, Cirsium, and Elymus. The diet alpha diversity of Eospalax cansus was slightly higher than that of Eospalax cansus (P>0.05). The zokor's diet is highly phconsistent with the resources of its habitat. Most food choices tend to be the same between the two zokors. They fed primarily on Calamagrostis, Cirsium, Echinops, Medicago, Sanguisorba, and Taraxacum. Zokors mainly fed on the roots of perennial herbs, which are important source of energy. High-throughput sequencing-based DNA metabarcoding technology has effectively revealed the diet of zokors and indicated that zokors are food generalists.

DNA-Based Identification of Eurasian Vicia Species Using Chloroplast and Nuclear DNA Barcodes

Many legume species of the Vicia L. genus (Fabaceae Lindl.) are key components of the Mediterranean diet and have an integral role in sustainable agriculture. Given the importance of the Vicia species for Eurasian culture, it is necessary to implement methodologies, such as DNA barcoding, that can enable the effective authentication and identification of species in the genus. In this study, we analysed the chloroplast trnL and rpoC1, as well as the nuclear ITS2 DNA barcoding regions, to identify 71 Vicia specimens of Eurasian descent. Both the trnL and ITS2 regions were highly effective in discriminating the analysed taxa, while the more conserved rpoC1 region could not identify all of the selected species due to high sequence conservation or non-annotated or absent rpoC1 species sequences in GenBank. A dendrographic representation of the generated trnL data showed sufficient clustering for most of the analysed taxa, although some topological discrepancies were observed. ITS2 and rpoC1 reconstructions were also used for resolving the topological discrepancies observed in the trnL tree. Our analysis suggests that a combination of DNA barcoding regions is essential for accurate species discrimination within the Vicia genus, while single-locus analyses do not provide the necessary resolution.

Genetic diversity and phylogenetic analyses of Vitex agnus castus L. populations using ISSR-PCR and chloroplast DNA trnL intron and trnL-F sequences

In this study, genetic diversity and phylogenetic analysis of some Vitex agnus-castus L. populations were conducted based on ISSR-PCR and chloroplast DNA trnL intron, and trnL-F sequence analyses. Vitex agnus-castus populations were detected in Aydın province, Turkey. Fresh leaf samples from the populations were collected and brought to the laboratory for genomic DNA isolation. 15 ISSR primers were used to determine the genetic diversity ofe Vitex agnus-castus populations. A total of 138 bands were obtained in ISSR analysis, 85 of which were polymorphic and 53 were monomorphic. Polymorphism rate was determined as 61.59 %. trnC, trnD, trnE, and trnF primers were used for PCR amplification of the chloroplast trnL intron and trnL-F region. A total of 138 bands were obtained by ISSR analysis. For trnL intron analyses, nucleotide lengths of 13 populations were between 508 and 516. The average nucleotide composition consisted of 38.5 % T, 18.3 % C, 27.5 % A and 15.7 % G. In trnL-F assays, the nucleotide lengths of the 13 populations ranged from 330 to 353. The average nucleotide composition consisted of 29.4 % T, 18.1 % C, 32.9 % A and 19.6 % G. The results of the phylogenetic trees constructed using some trnL intron and trnL-F sequences of Vitex doniana, Vitex trifolia, Vitex triflora, Vitex turczaninowii, Vitex queenslandica, Vitex axillariflora, Vitex rotundifolia and Vitex negundo species obtained from NCBI were compared. As a result of the study, polymorphisms were obtained at a rate of 61.59% from the ISSR analysis. In addition, the phylogenetic relationship between chloroplast trnL intron and trnL-F sequences of Vitex agnus-castus populations along with the other species was revealed.

Metabarcoding of soil environmental DNA replicates plant community variation but not specificity

AbstractWhile metabarcoding of plant DNA from their environment is an exciting method that can supplement inventorying of live plant species, the accuracy and specificity has yet to be fully assessed over complex continuous landscapes. In this work, we evaluate plant community profiles produced via metabarcoding of soil by comparing them to a morphological survey. We assessed plant communities by metabarcoding of soil DNA in 130 sites along ecological gradients (nutrients, succession, moisture) in Denmark using chloroplast trnL region (10–143 bp) primer set and compared the resulting communities to communities produced with a longer nuclear ITS2 region (~216 bp) and a morphological survey. We found that the community variation observed within the morphological survey was well represented by molecular surveys, with significant correlation with both community composition and richness using both primer sets. While the majority of the ITS2 sequences could be assigned to species (over 80%), we had less success with the trnL sequences (70%), which was only possible after restricting the reference database to local species. We conclude that the community profiles produced by metabarcoding can be highly effective in performing large‐scale macroecological studies. However, the discovery rates and taxonomic assignments produced via metabarcoding remained inferior to morphological surveys, but manual curation of databases improves the specificity of assignments made by the trnL primers, and improves the accuracy of the assignments made with the ITS2 primers. Finally, we suggest that a greater percentage of named diversity would be recovered by increasing soil sampling with the use of additional universal primer sets.

DNA metabarcoding of faecal pellets reveals high consumption of yew (Taxus spp.) by caribou (Rangifer tarandus) in a lichen-poor environment

Woodland caribou ( Rangifer tarandus caribou) are threatened in Canada because of the drastic decline in population size caused primarily by human-induced landscape changes that decrease habitat and increase predation risk. Conservation efforts have largely focused on reducing predators and protecting critical habitat, whereas research on dietary niches and the role of potential food constraints in lichen-poor environments is limited. To improve our understanding of dietary niche variability, we used a next-generation sequencing approach with metabarcoding of DNA extracted from faecal pellets of woodland caribou located on Lake Superior in lichen-rich (mainland) and lichen-poor (island) environments. Amplicon sequencing of fungal ITS2 region revealed lichen-associated fungi as predominant in samples from both populations, but amplification at the chloroplast trnL region, which was only successful on island samples, revealed primary consumption of yew ( Taxus spp.) based on relative read abundance (83.68%) with dogwood ( Cornus spp.; 9.67%) and maple ( Acer spp.; 4.10%) also prevalent. These results suggest that conservation efforts for caribou need to consider the availability of food resources beyond lichen to ensure successful outcomes. More broadly, we provide a reliable methodology for assessing ungulate diet from archived faecal pellets that could reveal important dietary shifts over time in response to climate change.

Plant Sedimentary Ancient DNA From Far East Russia Covering the Last 28,000 Years Reveals Different Assembly Rules in Cold and Warm Climates

Woody plants are expanding into the Arctic in response to the warming climate. The impact on arctic plant communities is not well understood due to the limited knowledge about plant assembly rules. Records of past plant diversity over long time series are rare. Here, we applied sedimentary ancient DNA metabarcoding targeting the P6 loop of the chloroplast trnL gene to a sediment record from Lake Ilirney (central Chukotka, Far Eastern Russia) covering the last 28 thousand years. Our results show that forb-rich steppe-tundra and dwarf-shrub tundra dominated during the cold climate before 14 ka, while deciduous erect-shrub tundra was abundant during the warm period since 14 ka. Larix invasion during the late Holocene substantially lagged behind the likely warmest period between 10 and 6 ka, where the vegetation biomass could be highest. We reveal highest richness during 28–23 ka and a second richness peak during 13–9 ka, with both periods being accompanied by low relative abundance of shrubs. During the cold period before 14 ka, rich plant assemblages were phylogenetically clustered, suggesting low genetic divergence in the assemblages despite the great number of species. This probably originates from environmental filtering along with niche differentiation due to limited resources under harsh environmental conditions. In contrast, during the warmer period after 14 ka, rich plant assemblages were phylogenetically overdispersed. This results from a high number of species which were found to harbor high genetic divergence, likely originating from an erratic recruitment process in the course of warming. Some of our evidence may be of relevance for inferring future arctic plant assembly rules and diversity changes. By analogy to the past, we expect a lagged response of tree invasion. Plant richness might overshoot in the short term; in the long-term, however, the ongoing expansion of deciduous shrubs will eventually result in a phylogenetically more diverse community.

Preservation of sedimentary plant DNA is related to lake water chemistry

AbstractLittle is currently known about preservation of plant DNA in lake sediments. Most prior information originates from laboratory experiments while systematic field‐based studies are still lacking. Here, we used the “g” and “h” universal primers for the P6 loop region of the chloroplast trnL (UAA) intron to amplify plant DNA from 219 lake surface sediments from China and Siberia. We introduce (i) the percentage of sequence counts with the best identity ≥95%, (ii) weighted average identity, (iii) weighted average DNA fragment length, and iv) rarefied richness of terrestrial seed plants of plant DNA metabarcoding as proxies for sedimentary DNA preservation and relate them to five environmental variables (lake water conductivity, lake water pH, mean July air temperature, and sampling depth, lake size) using boosted regression tree (BRT) analyses. Our results suggest that lake water chemical characteristics, that is, electrical conductivity and pH, are the most important variables for the preservation of plant DNA in lake sediments. Intermediate water conductivities (100–500 μS cm−1) and neutral to slightly alkaline water pH (7–9) may facilitate plant DNA preservation. Furthermore, deep lakes seem to support plant DNA preservation as indicated by relatively high rarefied richness. We also find high rarefied richness in small lakes compared with large lakes, but this result needs to be assessed by more studies in the future. None of our BRT models shows that mean July air temperature is a key variable to limit plant DNA preservation. To conclude, our results suggest that sedimentary DNA studies can preferentially select deep lakes characterized by intermediate water conductivities and neutral to slightly alkaline pH conditions.

A revised infrageneric classification of Bellevalia Lapeyr. (Asparagaceae: Scilloideae) based on molecular analysis

Within the genus Bellevalia (Asparagaceae: Scilloideae: Hyacintheae), flower shape and colour, the ratio of leaf to scape length, and the orientation of the pedicels were traditionally used to delimit sections, subsections and species. We conducted a phylogenetic analysis of representative species from sections Bellevalia, Conicae, Nutantes and Oxydontae, representing four out of the six sections that are currently recognised, using the four chloroplast regions rbcL, matK, trnL intron, and trnL-F spacer. Our results indicate that the sections are not monophyletic as currently circumscribed. Our analyses retrieve two major, well-supported clades. The first clade (sect. Conicae) includes only species with ciliate leaves and green-veined perianth lobes, and the second clade (sect. Bellevalia) includes the species lacking these characteristics. Within the second clade, the species with yellow anthers are separated from those with violet anthers. Our molecular analysis does not support the traditional subdivisions of the genus but establishes the value of cilia on the leaf margin, green veins in the perianths lobes, and the colour of the anthers as indicators of relationships among the species. We recommend that the current four sections and six subsections of Bellevalia be reduced to two sections without subsections and we provide an updated and corrected nomenclature for these sections and subsections, designating lectotypes where necessary.

The identification of plants used to make tapa artefacts: development of a reference DNA database and trial of non-destructive DNA extraction methods

ABSTRACT Tapa (barkcloth) is a non-woven textile made from the inner bark of some plant species. Tapa manufacture was once widespread throughout the Pacific and tapa from the eighteenth and nineteenth century form part of Pacific collections in many museums. Here we examined the feasibility of DNA identification of the plants used to make tapa artefacts by developing and testing a DNA reference database of chloroplast trnL intron P6 loop sequences from many of the plant species used to make tapa, as well as other New Zealand textile plants. This database enabled identification to genus for most species but many species shared identical sequences. Despite the lack of species-level resolution, this technique will still aid with identifying the origins of tapa artefacts made from plants with restricted distributions, such as endemic New Zealand and Hawaiian Islands plants. A second aim was to test a number of DNA extraction methods, including non-destructive methods of interest to the heritage sector, on tapa samples. Only one of the non-destructive sampling methods produced amplifiable DNA. However, we did find variation in the success of the destructive methods tested, with the Qiagen DNeasy Plant Mini Kit having the highest success rate.