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Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications
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Delimiting Species with Single-Locus DNA Sequences.

Nicolas Hubert1, Jarrett D Phillips2,3, Robert H Hanner3

  • 1UMR ISEM (IRD, UM, CNRS), Université de Montpellier, Montpellier, France. nicolas.hubert@ird.fr.

Methods in Molecular Biology (Clifton, N.J.)
|April 29, 2024
PubMed
Summary

DNA barcoding aids biodiversity inventories by using genetic data for species delimitation. This guide compares distance, network, and tree-based methods, highlighting parameter settings for reliable results.

Keywords:
ASAPAssemble Species by Automatic PartitioningBINBarcode Index NumberGMYCGeneral Mixed Yule Coalescent modelMultiple thresholdPTPPoisson Tree ProcessesSingle threshold

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Area of Science:

  • Molecular Biology
  • Taxonomy
  • Bioinformatics

Background:

  • DNA sequences are increasingly utilized for large-scale biodiversity inventories, offering an alternative to traditional specimen sorting.
  • The integration of genetic data into taxonomic workflows has spurred the development of various species delimitation models.
  • Existing species delimitation methods often yield discordant results due to differing assumptions about lineage history.

Purpose of the Study:

  • To provide a comprehensive, step-by-step guide to DNA-based species delimitation methods.
  • To aggregate essential information for conducting analyses using distance-, network-, and tree-based models.
  • To critically evaluate and categorize methods based on reliability, availability, scalability, understandability, and usability.

Main Methods:

  • Exploration of distance-based methods (e.g., Automatic Barcode Gap Discovery [ABGD], Assemble Species by Automatic Partitioning [ASAP]).
  • Examination of network-based methods (e.g., REfined Single Linkage [RESL] for Barcode Index Numbers [BINs]).
  • Review of tree-based methods (e.g., Poisson Tree Processes [PTP], General Mixed Yule Coalescent [GMYC]), including phylogenetic reconstruction options (e.g., RAxML, BEAST).

Main Results:

  • Detailed procedures for preparing input files, sequence alignment, and phylogenetic reconstruction are presented.
  • Analysis options for distance-, network-, and tree-based species delimitation models are outlined.
  • Parameter setting is identified as crucial for achieving consistent and reliable species delimitation outcomes.

Conclusions:

  • The study offers a structured approach to navigating the complexities of DNA-based species delimitation.
  • A comparative framework based on key indicators is proposed to aid method selection within the DNA barcoding community.
  • Future developments and limitations of current species delimitation approaches are discussed.