Isolation of microsatellite loci for the endangered vermetid gastropod Dendropoma lebeche using Illumina MiSeq next generation sequencing technology

Abstract

Dendropoma petraeum, considered the primary vermetid reef-building species in the Mediterranean, has recently been shown to be a species complex of at least four cryptic species. These species have highly restricted, non-overlapping distributions, causing concern for their conservation status. To better study the genetic diversity of these populations, we selected one of these species, Dendropoma lebeche (Templado et al. in Mediterr Mar Sci 17(1):13-31, 2016), which is restricted to the western Mediterranean, for microsatellite marker development using Illumina MiSeq. We provide an initial survey of 29 polymorphic microsatellite loci for D. lebeche. Genetic analyses identified 2-11 alleles per locus across the 30 samples examined. Observed and expected heterozygosities ranged from 0.067 to 0.800 and 0.064 to 0.770, respectively. None of the loci deviated from Hardy-Weinberg equilibrium or showed signs of being under selective pressure. Significant linkage disequilibrium was found between two loci. We also show the cross-species amplification of these microsatellite markers in the other three species of the complex, the Tyrrhenian-Sicilian lineage, D. cristatum (Biondi, 1859), the Levantine lineage, D. anguliferum (Monterosato, 1878) and Dendropoma sp. found along the Ionian-Aegean coasts, suggesting their potential utility for future phylogenetic and evolutionary studies.

Dispersal ability, habitat characteristics, and sea-surface circulation shape population structure of Cingula trifasciata (Gastropoda: Rissoidae) in the remote Azores Archipelago

“…In addition to being highly informative, this newly generated set of SSR markers retrieved overall diversity parameters consistent with values reported for other marine gastropods [ 64 , 76 , 77 ]. Deviations from HWE in some populations – Caloura, Pico, São Jorge, and Vigo –, are frequently reported in marine invertebrates [ 70 , 72 , 73 , 102 ].…”

“…During the past decades, microsatellite sets have been developed and characterized for marine gastropods, especially for abundant, commercially interesting or threatened species (e.g. [ 57 – 64 ]). These sets of SSR markers appear to be skewed towards large-sized genera, such as Nucella, Littorina , Buccinum , Haliotis and Concholepas .…”

Genetic connectivity of two marine gastropods in the Mediterranean Sea: seascape genetics reveals species‐specific oceanographic drivers of gene flow

“…Dendropoma lebeche species identification followed a previous study (Templado et al, 2016) where the species showed a clearly delimited geographical distribution and was highly divergent at both levels of mitochondrial and nuclear genes (Calvo et al, 2009). Twenty-three polymorphic microsatellites for G. divaricata (López-Márquez et al, 2016) and D. lebeche (López-Márquez et al, 2018), respectively, were initially tested using nested PCR (polymerase chain reaction), a method successfully applied in other species including the nemertean Malacobdella arrokeana (Alfaya et al, 2014) and the mollusc Panopea abbreviata (Ahanchédé et al, 2013).…”

“…Twenty-three polymorphic microsatellites for G. divaricata (López-Márquez et al, 2016) and D. lebeche (López-Márquez et al, 2018), respectively, were initially tested using nested PCR (polymerase chain reaction), a method successfully applied in other species including the nemertean Malacobdella arrokeana (Alfaya et al, 2014) and the mollusc Panopea abbreviata (Ahanchédé et al, 2013).…”

How we study cryptic species and their biological implications: A case study from marine shelled gastropods

“…Studying multiple species of interest in the same group (e.g., the Mediterranean reef-building Dendropoma species; worm shells, Vermetidae; Calvo et al, 2009Calvo et al, , 2015López-Márquez et al, 2018;Templado et al, 2016), or following up an initial cryptic species report with a formal description (e.g., Chilean intertidal slipper shells, Calyptraeidae, Véliz et al, 2003Véliz et al, , 2012 illustrates the importance of continued efforts to understand a species.…”