Biology subjects

Feng, V.

Publications and source records attributed to Feng, V..

6 recordsLinked to original sources

bioRxiv2026

Beyond DNA barcodes: an open-source workflow for recovering and organizing barcoded vouchers for ecological and evolutionary research

1. Most species are neither discovered nor named, let alone included in analyses that require biological information such as trait measurements, images, ecological information and genome-scale data. Specimen-level DNA barcoding can help discover many of these species rapidly, but everything beyond discovery requires vouchers organized into putative species. Yet, existing barcoding workflows lack efficient techniques for voucher recovery, creating a post-barcoding bottleneck that limits the ability of converting barcoded specimens into biological knowledge. 2. Here we present a low-cost, open-source workflow consisting of two stages. The first safeguards barcoded specimens by separating them from DNA extracts and transferring them from microplates into ethanol-filled glass vials. The second converts the resulting voucher collection into a searchable physical resource by linking barcode-derived molecular Operational Taxonomic Unit (mOTU) assignments to vial positions and enabling specimens to be sorted into putative species either manually or automatically using a newly developed open-access robot (SORTER). 3. We evaluated the workflow using 2,024 insect specimens distributed across 21 96-well plates. For the first stage, DNA separation and specimen transfer required approximately 15 minutes per plate. For the second stage, MOTUmapper generated retrieval coordinates in a few seconds, after which the 2,024 vouchers belonging to the 452 putative species could be recovered manually in 5 days or with SORTER in 5 hours. Throughout both stages, specimen identities remained linked to barcode sequences, metadata and storage positions. 4. Vouchers are the Rosetta stones of biology because they connect different kinds of data to the same specimens. By safeguarding these vouchers and making them searchable, the workflow converts barcode projects from one-time molecular surveys into reusable resources for ecological and evolutionary research.

molecular biology↗

bioRxiv2025

Integrative Taxonomy: From FASTA Pain to Species Gain with the interactive ''IntegraTax''

Here we present IntegraTax, a tool for analysing and managing taxonomic projects that combine DNA data with other evidence such as morphology to arrive at integrative species boundaries. IntegraTax visualizes genetic clusters through single-linkage clustering ("Objective Clustering") and provides an interactive browser interface that allows users to record taxonomic decisions regarding species limits. Projects can be saved at any stage, thus allowing continuous tracking of annotations and taxonomic decisions across many sessions. A typical IntegraTax session starts with a set of sequences that are visualized as a cluster fusion diagram revealing the genetic distances between the sequences and clusters. Users can define an "instability zone" to distinguish clusters that are clearly distinct, likely representing separate species, from those whose status is uncertain based on genetic data alone. Based on the instability zone setting, IntegraTax then suggests which and how many specimens should be studied with a second source of data to validate species hypotheses. This process is facilitated by an interactive html environment that enables detailed specimen-level annotations. For example, a taxonomist can label which specimens have been studied, which clusters have been validated as species, and which species can be identified. By combining clustering, intuitive visualization, and easy annotation in one interactive framework, IntegraTax treats species hypotheses as annotated objects that can be inspected, revised, and exported at any stage, with documentation of examined specimens. It simultaneously allows researchers to manage taxonomy projects with tens of thousands of specimens and hundreds of species. This will become increasingly important as taxonomists start resolving the species boundaries of the millions of undescribed species particularly within hyperdiverse dark taxa.

zoology↗

bioRxiv2025

Balancing Barcoding and Genomics: gDNA Quality in Insect Vouchers after HotSHOT DNA extraction

DNA extraction with an alkaline buffer system called "HotSHOT" is widely used for barcoding because it is rapid, inexpensive, and voucher preserving, but it remains unclear whether sufficient genomic DNA (gDNA) remains in small vouchers for downstream use in genomics. We here evaluate gDNA quality and quantity before and after HotSHOT treatment of 11 insect families representing six orders. Some specimens were flash frozen immediately after collection, while others were kept for one week at tropical temperatures in ethanol to mimic Malaise trap conditions. Encouragingly, we show that gDNA of sufficiently high quality and quantity for genomic sequencing remained in specimens treated with HotSHOT. We also show that DNA integrity was strongly influenced by field storage with specimens exposed to Malaise trap conditions showing such pronounced degradation that the standard HotSHOT treatment no longer significantly altered DNA quality. For control material, HotSHOT treatments involving longer exposure to high temperature led to smaller fragment lengths with the effect apparently being influenced by the degree of specimen sclerotization. Our results thus suggest that optimized HotSHOT treatments, together with carefully controlled pre-extraction storage, preserve voucher gDNA of sufficient quality for downstream genomic analyses with both short-read and possibly even some long-read sequencing technologies. Our protocol selection guidelines improve voucher gDNA preservation in HotSHOT-treated samples. This is particularly important for many species which are only known from one or few specimens discovered during barcoding projects.

molecular biology↗

bioRxiv2024

Megabarcoding reveals a tale of two very different dark taxa along the same elevational gradient

AbstractOur planet is entering the sixth mass extinction without detailed spatio-temporal distribution and abundance information for most insect species. Particularly lacking is this information for dark taxa although they contain most animal species. This problem can be addressed with high-throughput single specimen barcoding (megabarcoding), but it remain unknown to what extent one dark taxon can be used as a proxy for another because of similar biodiversity patterns. This is here tested and we show that two Diptera taxa (Phoridae, Mycetophilidae) have very different spatio-temporal distributions across the same elevational gradient. We applied COI megabarcoding to samples collected every 14 days over three seasons at six elevations (800 to 1,800 m) in a temperate forest ecosystem in Northern China (Baihua Mountain Reserve). Elevation, precipitation, and temperature were used as environmental variables to understand the data obtained for 17,179 specimens representing 492 mOTUs of Phoridae and 2,281 specimens of 148 mOTUs of Mycetophilidae. Congruent is that the alpha diversity for both taxa increased in the summer and there is evidence for a mid-domain effect and phylogenetic clustering in high elevations. However, the extent and pattern of seasonal variation differed considerably. Phorid communities exhibited shifts between spring, summer and autumn seasons, but surprisingly little difference between elevations. In contrast, mycetophilid communities were structured along the elevational gradient and dependent on precipitation. Our study highlights the urgent need for obtaining detailed spatio-temporal information for the most diverse dark taxa, but also illustrates that these data can be readily obtained with megabarcoding.

ecology↗

bioRxiv2023

Rapid species discovery and identification with real-time barcoding facilitated by ONTbarcoder 2.0 and Oxford Nanopore R10.4

Most arthropod species are undescribed and hidden in biodiversity samples that are difficult to sort to species using morphological characters. Sorting specimens to putative species with DNA barcodes is an attractive alternative, but needs cost-effective techniques that are suitable for use in many laboratories around the world. Barcoding with Oxford Nanopores portable and inexpensive MinION sequencers could be a good presorting approach because it reduces the space and capital cost of a fully functional barcoding laboratory. Similarly important would be user-friendly and reliable software for analysis of the ONT data. It is here provided in the form of an updated ONTbarcoder that is available for all commonly used operating systems and includes a GUI. The new version of ONTbarcoder has three key improvements related to the higher read quality obtained with ONTs latest basecallers and chemistry (R10.4 flow cells, Q20+ kits). Firstly, ONTbarcoder can now deliver real-time barcoding to complement ONTs real-time sequencing. This means that the first barcodes are obtained within minutes of starting a sequencing run and a significant proportion of barcodes are available before sequencing completes. This real-time feature of ONTbarcoder can be configured to handle both Mk1B and Mk1C sequencers. The input is a demultiplexing sheet and sequencing data (raw or basecalled). Secondly, the improved read quality of ONTs latest flow cells (R10.4) allows for the use of primers with shorter indices than those previously needed (9 bp vs. 12-13 bp). This decreases primer cost and improves PCR success rates. Thirdly, we demonstrate that the availability of R10.4 chemistry in the low-cost Flongle flow cell is an attractive option for users who require only 200-250 barcodes at a time.

ecology↗

bioRxiv2023

Express barcoding with NextGenPCR and MinION for species-level sorting of ecological samples

O_LIDNA barcodes are useful for species-level sorting of specimen samples, but rarely used in time-sensitive projects that require species richness estimates or identification of pest or invasive species within hours. The main reason is that existing express barcoding workflows are either too expensive or can only be carried out in very well equipped laboratories by highly trained staff. C_LIO_LIWe here introduce a simple workflow that combines rapid DNA extraction with HotSHOT, amplicon production with the aid of NextGenPCR(R) thermocyclers, and sequencing with low-cost MinION sequencers. C_LIO_LIWe demonstrate the power of the approach by generating and identifying 250 barcodes for 285 specimens within 6 hours. The workflow only required the following major equipment that easily fits onto a lab bench: Conventional thermocycler, NextGenPCR(R) thermocycler, microplate sealer, Qubit, and MinION. C_LIO_LIWe argue that species-level sorting with simplified barcoding workflows is now faster, more accurate, and sufficiently cost-effective that it can and should replace morphospecies sorting in many projects. C_LI

ecology↗