The geography of genetic data: Current status and future perspectives

Peng, Xin; Li, Qiang; Cheng, Zhentao; Huang, Xiaolei

doi:10.3389/fevo.2023.1112636

Cited by 3 publications

(3 citation statements)

References 25 publications

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“…Actually, missing coordinates is not the only issue that can cause the coordinates of sample collection sites to be unreliable; there are other factors to be considered as well. For instance, some data have been recorded with the coordinates of research institutions instead of the natural habitats (Peng et al, 2023). Therefore, collectors should carefully validate the accuracy of the raw information before uploading them, also ensure that all the necessary details of collection data are provided.…”

Section: Discussionmentioning

confidence: 99%

The devil is in the details: Problems in DNA barcoding practices indicated by systematic evaluation of insect barcodes

Cheng

Deng

et al. 2023

Front. Ecol. Evol.

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In recent years, DNA barcoding has rapidly developed as a powerful tool in taxonomy, demonstrating its value in species identification and discovery of cryptic diversity. The number of barcoding sequences of various species continues to grow in the GenBank and BOLD databases; however, the accuracy of sequences and related raw information in public repositories is often questionable. In the present study, based on a dataset of 68,089 Hemiptera COI barcode sequences covering 3,064 species, 1,072 genera, and 48 families, we analyzed genetic differences within and between species and evaluated possible data errors in the insect barcodes. The results showed that errors in the barcode data are not rare, and most of them are due to human errors, such as specimen misidentification, sample confusion, and contamination. A significant portion of these errors can be attributed to inappropriate and imprecise practices in the DNA barcoding workflow. Herein, suggestions are provided to improve the practical operations and workflow of DNA barcoding to reduce human errors.

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Section: Discussionmentioning

confidence: 99%

The devil is in the details: Problems in DNA barcoding practices indicated by systematic evaluation of insect barcodes

Cheng

Deng

et al. 2023

Front. Ecol. Evol.

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“…For species with deep intraspecific divergence, inadequate sampling, incomplete lineage sorting and gene flow may lead to incorrect species delimitation (Lin et al, 2021). Therefore, the final species delimitation requires further comprehensive validation from both morphological and molecular aspects, or even in combination of other types of information such as geography, behavior, and ecological preferences (Cheng et al, 2023). The ancestral area of the clades ranged from E to G and finally to H, indicating that A. aspergillum gradually dispersed toward the east after its origin in Guangxi, and that the Yunnan-Guizhou Plateau, Nanling, and Wuyi Mountains might be the geographical obstacles for its spread to the west and north.…”

Section: Haplotype (Number Of Individuals)mentioning

confidence: 99%

Mitochondrial DNA evidence reflects high genetic divergence of Amynthas aspergillum (Oligochaeta: Megascolecidae) in southern China

Li,

Jiang,

Jin

et al. 2024

Ecology and Evolution

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Amynthas aspergillum (Perrier, 1872), a natural resource used in traditional Chinese medicine (Guang‐dilong) with high economic value, is widely distributed in forests and farmland habitats in the hilly areas of southern China. To investigate the extent of genetic differentiation and diversity in A. aspergillum, a population genetic structure study was performed on 157 samples from 75 locations in southern China using the mitochondrial genes COI, COII, 12S rRNA, 16S rRNA, and NDI. The results indicated that A. aspergillum had a high level of genetic diversity, and variation within populations was the main source of the total variation. Six deeply divergent mitochondrial clades (I–VI) were detected using both phylogenetic tree and haplotype network analyses. This finding was supported by the high Kimura two‐parameter genetic distance and the pairwise fixation index value obtained based on the COI gene. No significant phylogeographic structures were observed. The widespread geographic distribution of clades II, IV, and VI suggested a recent demographic expansion based on multiple analysis results. These results include a high level of Hd and low π, star‐shaped haplotype network structures with a high number of less frequent haplotypes, significantly negative neutrality test values, and a unimodal mismatch distribution pattern. The divergence time estimates and reconstruction of the ancestral area revealed that A. aspergillum originated in Guangxi Province and underwent initial intraspecific diversification in the early Pliocene to generate clade I. Then, it gradually dispersed eastward and rapidly differentiated into clades II–V during the Pleistocene. The Yunnan‐Guizhou Plateau and Nanling and Wuyi Mountains might act as geographical barriers for the spread of A. aspergillum to the west and north.

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“…However, implementing such an approach would require accurate global repositories of species distributions and detailed inventories of regional biodiversity which are often not readily available (Beck et al, 2014;Costello & Berghe, 2006). In addition, an important curation step that would greatly benefit rCRUX reference databases is the removal of incorrect reference sequences in global sequence repositories (Cheng et al 2023;Keck et al, 2022).…”

Section: Broader Applications Of Rcruxmentioning

confidence: 99%

rCRUX: A rapid and versatile tool for generating metabarcoding reference libraries in R

Curd,

Gal,

Gallego

et al. 2023

Environmental DNA

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The sequencing revolution requires accurate taxonomic classification of DNA sequences. The key to making accurate taxonomic assignments is curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa than are currently curated by professional staff. Thus, there is a growing need for an easy‐to‐implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like its predecessor, relies on sequence homology and PCR primer compatibility instead of keyword searches to avoid limitations of user‐defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user‐defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI)‐formatted nt database using a taxonomic rank‐based stratified random sampling approach (blast_seeds()). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer‐specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple‐to‐use tool for the generation of curated, comprehensive reference databases for user‐defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.

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The geography of genetic data: Current status and future perspectives

Cited by 3 publications

References 25 publications

The devil is in the details: Problems in DNA barcoding practices indicated by systematic evaluation of insect barcodes

The devil is in the details: Problems in DNA barcoding practices indicated by systematic evaluation of insect barcodes

Mitochondrial DNA evidence reflects high genetic divergence of Amynthas aspergillum (Oligochaeta: Megascolecidae) in southern China

rCRUX: A rapid and versatile tool for generating metabarcoding reference libraries in R

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