Genetic connectivity and phylogeography of the night shark (Carcharhinus signatus) in the western Atlantic Ocean: Implications for conservation management

Abstract

The night shark, Carcharhinus signatus, is a mesopelagic, semi‐oceanic shark species found only in the Atlantic Ocean. It is one of the most frequently caught sharks in pelagic longline fisheries and is classified as Vulnerable by the International Union for the Conservation of Nature (IUCN). Despite their prevalence in commercial fisheries, the population genetic structure of the night shark has not been assessed. The present study investigated the genetic diversity, genetic connectivity, and phylogeography of the species throughout the western Atlantic Ocean, based on complete mitochondrial control region (mtCR) sequence data (n = 152) and genotypic data from nine nuclear microsatellites (n = 119). The mtCR sequence revealed 19 haplotypes, with overall haplotype and nucleotide diversities of 0.74 (±0.027) and 0.0034 (±0.0019), respectively, whereas the nuclear microsatellite observed and expected heterozygosities were 0.408 and 0.421, respectively. There was significant population structure (ФST = 0.429; P < 0.01) and isolation by distance (r = 0.65, P = 0.03) based on mtCR sequence data, but no genetic differentiation based on nuclear microsatellite analyses. The phylogenetic analyses support the existence of two matrilineal lineages, which diverged during the Pleistocene. Mitochondrial demographic analyses indicated a historical bottleneck effect followed by population expansion during the Pleistocene, whereas nuclear microsatellites did not detect a recent or a strong bottleneck. For conservation purposes, we advocate that the species should be considered to comprise at least two management units (MUs) in the western Atlantic Ocean. MU‐specific catch quotas should be implemented throughout the range of the species given its low genetic diversity and vulnerability to overexploitation.

Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis)

“…Both mtDNA and nuclear markers often have concordant results in sedentary species ( Lavery, Moritz & Fielder, 1996 ; Avise, 2004 ; Zink & Barrowclough, 2008 ; DiBattista et al, 2015 ) but, when examined alone, may miss key components of population structure, particularly in migratory fauna ( Pardini et al, 2001 ; Bowen et al, 2005 ; Toews & Brelsford, 2012 ). When highly mobile elasmobranchs are examined with both mtDNA and nuclear markers (usually microsatellites), a different picture often emerges in which females are more resident and males are dispersive ( Pardini et al, 2001 ; Schultz et al, 2008 ; Portnoy et al, 2010 ; Karl et al, 2011 ; Daly-Engel et al, 2012 ; Portnoy et al, 2015 : Bernard et al, 2017 ; Domingues et al, 2018 ). Identifying outlier SNPs in the nuclear genome can highlight genes possibly under selection, or show functional responses to environmental changes that have important management consequences ( Jones et al, 2012 ; Fischer et al, 2013 ; Barrio et al, 2016 ; Guo, Li & Merilä, 2016 ).…”

Phylogeography of Acartia tonsa Dana, 1849 (Calanoida: Copepoda) and phylogenetic reconstruction of the genus Acartia Dana, 1846

“…There are several examples of marine organisms that demonstrate close phylogenetic relationships between these two regions. For example, the night shark (Carcharhinus signatus) from the Western Atlantic has two major maternal lineages based on the mitochondrial control region; one lineage is prevalent in Brazil, while the other lineage is prevalent in the USA, including the Gulf of Mexico (Domingues et al 2019). A phylogenetic analysis of Atlantic oyster species, based on mtCOI and mitochondrial 16 s ribosomal RNA revealed that the North American species of the American oyster Crassotrea virginica is sister to the north Brazilian species Crassotrea rhizophorae (Lazoski et al 2011).…”

Regional population genetics and global phylogeography of the endangered highly migratory shark Lamna nasus: Implications for fishery management and conservation

“…For instance, for widely distributed and highly migratory shark species, long thought to form ‘panmictic’ populations, recent studies have shown significant genetic divergence at both global (e.g. Bernard et al, 2016; Clarke et al, 2015; Karl, Castro, Lopez, Charvet, & Burgess, 2011) and regional scales (Domingues et al, 2018; Hernández et al, 2015; Portnoy et al, 2014). Genetic structure observed in these large, widespread, and highly migratory sharks appears to be the effect of glaciation cycles occurring during the Pleistocene (e.g.…”

“…Genetic structure observed in these large, widespread, and highly migratory sharks appears to be the effect of glaciation cycles occurring during the Pleistocene (e.g. Domingues et al, 2018; Hernández et al, 2015; Portnoy et al, 2014) coupled or not with philopatric behaviours (e.g. Bernard et al, 2016; Portnoy et al, 2015; Tillett, Meekan, Field, Thorburn, & Ovenden, 2012).…”

“…Nonetheless, a single, short technical report (Kitamura & Matsunaga, 2010) and one unpublished thesis (Testerman, 2014), both using mitochondrial DNA (mtDNA) markers, suggested that the North Atlantic and South Atlantic populations are genetically distinct. Currently, it is not clear whether L. nasus represents a single panmictic population or two or more genetically dissimilar populations in the SH (see Bernard et al, 2016; Clarke et al, 2015; Domingues et al, 2018; Hernández et al, 2015; Portnoy et al, 2014).…”