Documenting decapod biodiversity in the Caribbean from DNA barcodes generated during field training in taxonomy

Abstract

DNA barcoding is a useful tool to identify the components of mixed or bulk samples, as well as to determine individuals that lack morphologically diagnostic features. However, the reference database of DNA barcode sequences is particularly sparsely populated for marine invertebrates and for tropical taxa. We used samples collected as part of two field courses, focused on graduate training in taxonomy and systematics, to generate DNA sequences of the barcode fragments of cytochrome c oxidase subunit I (COI) and mitochondrial ribosomal 16S genes for 447 individuals, representing at least 129 morphospecies of decapod crustaceans. COI sequences for 36% (51/140) of the species and 16S sequences for 26% (37/140) of the species were new to GenBank. Automatic Barcode Gap Discovery identified 140 operational taxonomic units (OTUs) which largely coincided with the morphospecies delimitations. Barcode identifications (i.e. matches to identified sequences) were especially useful for OTUs within Synalpheus, a group that is notoriously difficult to identify and rife with cryptic species, a number of which we could not identify to species, based on morphology. Non-concordance between morphospecies and barcode OTUs also occurred in a few cases of suspected cryptic species. As mitochondrial pseudogenes are particularly common in decapods, we investigate the potential for this dataset to include pseudogenes and discuss the utility of these sequences as species identifiers (i.e. barcodes). These results demonstrate that material collected and identified during training activities can provide useful incidental barcode reference samples for under-studied taxa.

Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches

“…Barcode-based delimitation provides an additional tool for cryptic diversity exploration and can be used to resolve taxonomic validity in morphologically complex organisms including crustacean decapods [35,44,[119][120][121][122][123]. Previously, the proposal of a universal threshold for species delimitation in crustaceans using genetic divergence has been introduced [39].…”

“…However, the use of DNA barcoding has been debated for intensive systematic study [137][138][139]. The nuclear mitochondrial DNA (numts), a common DNA segment found in crustaceans, was suspected to interfere with the COI sequences used in crustacean phylogeny and barcode analysis [122,140,141]. The low quality of COI sequences containing numts may cause misleading results in species genealogies and clustering methods [142].…”

Molecular phylogeny and species delimitation of the freshwater prawnMacrobrachium pilimanusspecies group, with descriptions of three new species from Thailand

“…Molecular systematics based on DNA barcoding regions and species delimitation coupled with DNA sequence variation has been widely used to screen for putative species identification in some highly diversified decapod groups ( Bernardes et al, 2017 ; De Mazancourt et al, 2019 ; Venera-Pontón et al, 2020 ; Fujisawa & Barraclough, 2013 ). In this study, we integrate traditional taxonomic examination and molecular phylogeny using three molecular markers to delimit species boundaries and to illustrate the phylogenetic relationships within the “ pilimanus ” species group collected from Thailand, with further discussion of their distribution and phylogenetic position among mainland Southeast Asian species.…”

Peer Review #1 of "Molecular phylogeny and species delimitation of the freshwater prawn Macrobrachium pilimanus species group, with descriptions of three new species from Thailand (v0.1)"

“…Molecular systematics based on DNA barcoding regions and species delimitation coupled with DNA sequence variation has been widely used to screen for putative species identification in some highly diversified decapod groups (Bernardes et al 2017;de Mazancourt et al 2019;Venera-Pontón et al 2020). In this study, we integrate traditional taxonomic examination and molecular phylogeny using three molecular markers to delimit species boundaries and to illustrate the phylogenetic relationships within the "pilimanus" species group collected from Thailand, with further discussion of their distribution and phylogenetic position among mainland Southeast Asian species.…”