Null alleles of microsatellites for Manila clam <i>Ruditapes philippinarum</i>

Chiesa, Stefania; Lucentini, Livia; Freitas, Rosa; Marzano, F.; Ferrari, Claudio; Filonzi, Laura; Breda, Silvia; Minello, Fabiola; Figueira, Etelvina; Argese, Emanuele

doi:10.1111/age.12382

Cited by 15 publications

(12 citation statements)

References 11 publications

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“…Null allele frequencies estimates ranged between 0% and 29.3% (, σ = 0.090; Table 3). This high frequency of null alleles found in this study is consistent with many reports in other bivalve species (Launey et al, 2002; Nantón et al, 2014; Chiesa et al, 2016). Clams are filter feeders and thus, are prone to accumulate xenobiotic compounds (Tlili et al, 2010; Yawetz et al, 2010; Bouzas et al, 2011; Company et al, 2011; Hamdani & Soltani-Mazouni, 2011; Tlili et al, 2011).…”

Section: Resultssupporting

confidence: 93%

“…Another study aiming to examine the genetic variability and relationships between two Manila clam ( Ruditapes philippinarum ) populations in Korea also suggested the occurrence of null alleles in 7 loci out of 10 (Kim et al, 2014). More recently Chiesa et al (2016) demonstrated the occurrence of null alleles through rigorous analytical tests in this species. The presence of null alleles has also been reported in a study that assessed the genetic diversity of four wild and six hatchery stocks of the hard clam ( Mercenaria mercenaria) in Florida.…”

Section: Introductionmentioning

confidence: 99%

“…Recent studies have reported an unusually high frequency of non-amplifying alleles, also known as null alleles, at microsatellite loci in bivalves (Hargrove et al, 2015; Chiesa et al, 2016) including the wedge clam (Nantón et al, 2014). Null alleles occur when mutations in the binding site of the targeted DNA sequence prevent the efficient annealing of at least one primer resulting in failure of amplification during the PCR reaction.…”

Section: Introductionmentioning

confidence: 99%

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Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)

Rico

Cuesta

Drake

et al. 2017

PeerJ

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Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations.

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Section: Resultssupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)

Rico

Cuesta

Drake

et al. 2017

PeerJ

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“…The high incidence of null alleles found in this study is consistent with many reports in natural populations of bivalve species analysed with DNA markers such as microsatellites264445. In a previous study on D. trunculus , Nanton et al 26.…”

Section: Discussionsupporting

confidence: 91%

Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries

Marie

Lejeusne

Karapatsiou

et al. 2016

Sci Rep

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In a resource management perspective, the understanding of the relative influence of the physical factors on species connectivity remains a major challenge and is also of great ecological and conservation biology interest. Despite the overfishing threat on the wedge clam Donax trunculus in Europe, relatively little information is known about its population genetic structure and connectivity and their consequences on conservation policies. We employed 16 microsatellite loci to characterise the genetic diversity and population structure of D. trunculus. A total of 514 samples from seven different localities along the Atlantic-Mediterranean transition, from the Atlantic (Gulf of Cádiz) to the north-western Mediterranean were genotyped. The analysis of the population genetic structure displayed a clear distinction along the Atlantic-Mediterranean transition with different clusters in the Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean. Consequently, we recommend that these three areas should be considered as different management units. We showed that all populations seem to be at high long-term risk of extinction with the exception of the protected Doñana National Park population which still seems to have evolutionary potential. Therefore, our results emphasized the necessity of protection of this economic resource and the validity of molecular tools to evaluate the population dynamics.

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“…In fact, whole genome reference sequences, high-density SNP genotyping arrays or genotyping-by-sequencing have been developed especially for fish (Yáñez et al, 2015). As for Manila clam, few studies have been devoted to the genetic diversity and structure of populations in its native range (see as examples Sekine et al, 2006;Vargas et al, 2008;Liu et al, 2007;Mao et al, 2011;An et al, 2012;Kitada et al, 2013, Nie et al, 2015 and in introduced ecosystems (Chiesa et al, 2011;2016;Mura et al, 2012;Hurtado et al, 2012). Yet a comparative study of native and introduced populations has not previously been undertaken and no genetic information is available concerning the differences occurring among productive stocks worldwide, or potential invasion pathways that might compromise the ability to perform predictions of genetic diversity and population structure of nonindigenous taxa (Holland, 2000).…”

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confidence: 99%

A history of invasion: COI phylogeny of Manila clam Ruditapes philippinarum in Europe

et al. 2017

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1The Manila clam Ruditapes philippinarum -synonym Venerupis philippinarum (Adams and Reeve, 2 1850) is now one of the top 5 most commercially valuable bivalve species worldwide. Originally 3 from the Indo-Pacific region, it has been introduced in many countries for fisheries and aquaculture, 4 including estuarine environments along Atlantic and Mediterranean European coasts. Yet despite its 5 commercial value and widespread distribution, the precise origins of stocks remain speculative and 6 the genetic diversity of introduced populations is poorly known. Thus, the aim of this work was to

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Null alleles of microsatellites for Manila clam Ruditapes philippinarum

Cited by 15 publications

References 11 publications

Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)

Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)

Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries

A history of invasion: COI phylogeny of Manila clam Ruditapes philippinarum in Europe

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