DNA barcoding reveals cryptic diversity in the peanut worm Sipunculus nudus

Abstract

Peanut worm (Sipunculus nudus) is a cosmopolitan species mainly distributed in tropical and subtropical coastal waters. Analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences among S. nudus from GenBank revealed high genetic variation (p-distance, 0.115-0.235; k2p, 0.128-0.297) and paraphyletic relationships. These indicated misidentification and/or cryptic diversity may be present in the genus Sipunculus. To understand the genetic diversity and to manage the recourse of S. nudus, we collected specimens from coastal waters of southern China and Taiwan. In the phylogenetic topology, specimens can be separated into four distinct clades; three of these clades (clade A, B and C) were only represented from this region (southern China and Taiwan), but the clade D grouped with individuals from Central America (Atlantic coast). Furthermore, individuals of clades A and D were collected at the same location, which does not support the hypothesis that this genetic break reflects contemporary geographical isolation. The four distinct clades observed among coastal waters of southern China and Taiwan indicated underestimated diversity. It is noteworthy that the cryptic diversity is vulnerable under high pressure of human activity.

DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River

“…; Hsu et al. ). K2P is computationally fast and yields consistent results for many species that exhibit the necessary disparity between intra‐ and interspecific variation.…”

“…Species identification with DNA barcodes is reliable only if a significant difference between the average intraspecific and the average interspecific genetic distances can be consistently detected (Hebert et al 2003a(Hebert et al ,b, 2004Ward et al 2005). The use of Kimura's two-parameter (K2P) model (Kimura 1980) in DNA barcoding studies began with (Hebert et al 2003a,b) and is now widely used to assign an unknown specimen to a known species, to detect novel sequences, and to determine whether an unknown specimen is a distinct new species (Pereira et al 2011;Hsu et al 2013). K2P is computationally fast and yields consistent results for many species that exhibit the necessary disparity between intra-and interspecific variation.…”

Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta‐analysis of COI data from previous phylogeographical studies

“…However, using the fixed empirical threshold of genetic divergence to delimit species is controversial (Meier et al 2006; Species richness can be overestimated or underestimated using a fixed empirical threshold in DNA barcoding studies, which depends on the evolutionary rate of the COI gene within specific taxa and the threshold selected. The morphologically defined species with high genetic variation were usually merit further investigation as potentially cryptic species (Hebert et al 2004b;Smith et al 2005Smith et al , 2006Witt et al 2006;Smith et al 2008;Vieites et al 2009;Goetze 2010;Hsu et al 2013;Dinca et al 2015;von Beeren et al 2016). If the genetic divergence of COI is used to estimate species diversity, distinguishing whether a high variation in COI is intraspecific or interspecific becomes a serious concern.…”

Taxonomic assessment of sharks, rays and guitarfishes (Chondrichthyes: Elasmobranchii) from south-eastern Arabia, using the NADH dehydrogenase subunit 2 (NADH2) gene

“…The underlying assumption of molecular‐assisted taxonomy is that genetic variability between species will be much greater than genetic variability within species (Moritz & Cicero, ; Greig et al ., ; Ward et al ., ). Studies on mitochondrial DNA (mtDNA) have found this to be true for many taxa (Hebert et al ., ; Vences et al ., ; Ward et al ., ; Clare et al ., ; Kumar, Srinivasan & Jambulingam, ; Hsu et al ., ), although there have been exceptions (Coulson et al ., ; León‐Romero, Mejía & Soto‐Galera, ; McCusker et al ., ). In their pioneering research on the molecular taxonomy of birds, Hebert et al .…”