The use of DNA barcoding to monitor the marine mammal biodiversity along the French Atlantic coast

Abstract

In the last ten years, 14 species of cetaceans and five species of pinnipeds stranded along the Atlantic coast of Brittany in the North West of France. All species included, an average of 150 animals strand each year in this area. Based on reports from the stranding network operating along this coast, the most common stranding events comprise six cetacean species (Delphinus delphis, Tursiops truncatus, Stenella coeruleoalba, Globicephala melas, Grampus griseus, Phocoena phocoena)and one pinniped species (Halichoerus grypus). Rare stranding events include deep-diving or exotic species, such as arctic seals. In this study, our aim was to determine the potential contribution of DNA barcoding to the monitoring of marine mammal biodiversity as performed by the stranding network.We sequenced more than 500 bp of the 5’ end of the mitochondrial COI gene of 89 animals of 15 different species (12 cetaceans, and three pinnipeds). Except for members of the Delphininae, all species were unambiguously discriminated on the basis of their COI sequences. We then applied DNA barcoding to identify some “undetermined” samples. With again the exception of the Delphininae, this was successful using the BOLD identification engine. For samples of the Delphininae, we sequenced a portion of the mitochondrial control region (MCR), and using a non-metric multidimentional scaling plot and posterior probability calculations we were able to determine putatively each species. We then showed, in the case of the harbour porpoise, that COI polymorphisms, although being lower than MCR ones, could also be used to assess intraspecific variability. All these results show that the use of DNA barcoding in conjunction with a stranding network could clearly increase the accuracy of the monitoring of marine mammal biodiversity.

Interspecific Hybridization in Pilot Whales and Asymmetric Genetic Introgression in Northern Globicephala melas under the Scenario of Global Warming

“…In 1988 it was described in the western edge of the Cantabrian Sea within Spanish waters at 43°36’ N [ 69 ], while in 2010 it occurs in Charente-Maritime in France at 46°06’ N [ 70 ]. Moreover, strandings of this species (confirmed by genetic analyses) have been recently reported in this area of France providing another unequivocal signal of the northward displacement of this species [ 71 , 72 ]. Climate change could therefore facilitate mating between G .…”

Molecular identification of cetaceans from the West Atlantic using the E3-I5 region of COI

“…Species in the Delphininae subfamily have been through recent and rapid processes of speciation and potential hybridization (Amaral et al, 2012). Not surprisingly, it is difficult to successfully apply molecular markers for identification of Delphininae, especially between those from the genera Stenella, Tursiops, and Delphinus (Dizon et al, 2000, Amaral et al, 2007Viricel and Rosel, 2012;Alfonsi et al, 2013). Due to this, the use of multiple mitochondrial regions or the development of new markers for identification of Delphininae species has been proposed (Viricel and Rosel, 2012).…”

“…This method has been efficient for identification of several cetacean species (Tsai et al, 2013;Chang et al, 2014;Cypriano-Souza et al, 2016). However, there have been cases in which the Folmer region was not useful for differentiating Delphinus delphis, D. capensis, Stenella coeruleoalba, S. frontalis, and Tursiops truncatus, all of which are species in the family Delphinidae, more specifically in the subfamily Delphininae (Amaral et al, 2007;Viricel and Rosel, 2012;Alfonsi et al, 2013). Therefore, researchers frequently use more than one gene region for species identification (Amaral et al, 2007;Viricel and Rosel, 2012;Alfonsi et al, 2013;Cypriano-Souza et al, 2016).…”

Review: Progress and potential of DNA barcoding for species identification of fish species

“…A 650 base pairs region of mitochondrial COI is considered as a universal barcode for animals because of its comparatively fast mutation rate over a relatively short time scale, has a high number of exons, high availability throughout cells and maternal inheritance (Steinke et al 2009b). Due to these characteristic, the mitochondrial COI gene is a perfect universal barcode for species-level identification in sponges (Vargas et al 2012), Platyhelminthes (Van Steenkiste et al 2015), annelids (Achurra et al 2013), molluscs (Layton et al 2014), insects (Park et al 2011), oysters (Zainal Abidin et al 2016), echinoderms (Hemery et al 2012), fish (Basheer et al 2016), amphibians (Xia et al 2012), reptiles (Hawlitschek et al 2013), birds (Saitoh et al 2015) and mammals (Alfonsi et al 2013) (Table 1).…”