Characterization of the Sperm Molecule Bindin in the Sea Urchin Genus Paracentrotus

Calderón, Isabel L.; Turon, Xavier; Lessios, Harilaos A.

doi:10.1007/s00239-009-9219-4

Cited by 24 publications

(29 citation statements)

References 65 publications

(95 reference statements)

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“…Departures from Hardy-Weinberg equilibrium and inbreeding coefficients F IS were computed and tested using Genetix (Belkhir et al 2004). Previous studies with PAML (Yang 2007) confirmed a scattered action of positive selection along the bindin gene in Paracentrotus lividus (Calderón et al 2009a). Of the 12 codons identified by Calderón et al (2009a) as being under positive selection, 3 are located within the analyzed region.…”

Section: Methodsmentioning

confidence: 77%

“…Previous studies with PAML (Yang 2007) confirmed a scattered action of positive selection along the bindin gene in Paracentrotus lividus (Calderón et al 2009a). Of the 12 codons identified by Calderón et al (2009a) as being under positive selection, 3 are located within the analyzed region. To assess the role of selection upon the genetic structure of cohorts, measures of differentiation were also computed only for neutrally evolving sites.…”

Section: Methodsmentioning

confidence: 77%

“…With regard to bindin, we sequenced a total of 316 individuals ( This fragment coded from amino acid 24 in the conserved core (which corresponds to amino acid 144 in the mature bindin sequence; Calderón et al 2009a) down to the stop codon. A total of 56 variable positions (excluding presence/absence of indels) were observed, of which 11 were located within the core region and corresponded to synonymous substitutions.…”

Section: Results Based On Nuclear Bindinmentioning

confidence: 99%

“…A fragment of the second coding region of the nuclear protein bindin was also analyzed. This fragment was amplified using specific primers designed for Paracentrotus lividus (Calderón et al 2009a): Bindin2F2 (5'-GCC ACC AAG ATT GAC CTA CCA-3') and EndCodeR (5'-CCC TTC CCC TA(AT) ACA ATT CA -3') with the following PCR protocol: 94°C for 3 min, 35 cycles of 94°C for 45 s, 58°C for 30 s, and 72°C for 1.5 min, and a final elongation step of 8 min at 72°C. GoTaq ® polymerase (Promega) was used in all PCR reactions.…”

Section: Methodsmentioning

confidence: 99%

“…Mutations that appeared only once in the whole data set of cloned sequences were considered to be PCR and cloning artefacts and were replaced so as to match the consensus sequence (Villablanca et al 1998, Calderón et al 2009a.…”

Section: Methodsmentioning

confidence: 99%

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Temporal genetic variability in the Mediterranean common sea urchin Paracentrotus lividus

Calderón¹,

Turon

2010

Mar. Ecol. Prog. Ser.

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In sedentary benthic invertebrates with pelagic larval stages, the genetic composition of individuals that recruit at a given site is determined by the interaction between factors such as nonrandom mating, differential reproductive success, dispersal ability, selective pressures, and environmental factors. We studied the temporal variation of genetic structure of several cohorts of the sea urchin Paracentrotus lividus (Lamarck) collected over 2 consecutive years (2006, 2007) from a locality in the NW Mediterranean. Sea urchins bigger than ca. 1 cm in diameter were collected and aged using growth bands visible in the tests. Small recruits of the year were collected by scraping off algal substrates. A fragment of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) and a fragment of the nuclear gene of the gamete recognition protein bindin were sequenced for 374 and 316 urchins, respectively. Differentiation between cohorts was smaller than between spatially separated populations for both markers. Likewise, our results do not show a reduction of diversity within cohorts over time or a reduced diversity of the juveniles relative to adult populations. No significant changes in allelic frequencies were detected between cohorts for COI, indicating that sweepstake episodes-in which few individuals dominate reproductive events, resulting in high levels of genetic variance-are not common in this species. In contrast, a stronger signal of differentiation was found for bindin, with many pairwise comparisons among cohorts being significant. This differentiation was mainly due to positively selected codons in this gamete recognition protein, which suggests some degree of non-random mating in Paracentrotus lividus. This can be due to spatial and temporal heterogeneity in the pool of gametes resulting in inter-cohort differences in the composition of bindin alleles that maximized fertilization. Our results indicate that processes occurring previous to fertilization are important in shaping the genetic structure of populations. This information is relevant if management plans are to be designed for this commercially interesting species.

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Section: Methodsmentioning

confidence: 77%

Section: Methodsmentioning

confidence: 77%

Section: Results Based On Nuclear Bindinmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Temporal genetic variability in the Mediterranean common sea urchin Paracentrotus lividus

Calderón¹,

Turon

2010

Mar. Ecol. Prog. Ser.

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Selection and demographic history shape the molecular evolution of the gamete compatibility protein bindin in Pisaster sea stars

Popovic

Marko

Wares

et al. 2014

Ecology and Evolution

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Reproductive compatibility proteins have been shown to evolve rapidly under positive selection leading to reproductive isolation, despite the potential homogenizing effects of gene flow. This process has been implicated in both primary divergence among conspecific populations and reinforcement during secondary contact; however, these two selective regimes can be difficult to discriminate from each other. Here, we describe the gene that encodes the gamete compatibility protein bindin for three sea star species in the genus Pisaster. First, we compare the full-length bindin-coding sequence among all three species and analyze the evolutionary relationships between the repetitive domains of the variable second bindin exon. The comparison suggests that concerted evolution of repetitive domains has an effect on bindin divergence among species and bindin variation within species. Second, we characterize population variation in the second bindin exon of two species: We show that positive selection acts on bindin variation in Pisaster ochraceus but not in Pisaster brevispinus, which is consistent with higher polyspermy risk in P. ochraceus. Third, we show that there is no significant genetic differentiation among populations and no apparent effect of sympatry with congeners that would suggest selection based on reinforcement. Fourth, we combine bindin and cytochrome c oxidase 1 data in isolation-with-migration models to estimate gene flow parameter values and explore the historical demographic context of our positive selection results. Our findings suggest that positive selection on bindin divergence among P. ochraceus alleles can be accounted for in part by relatively recent northward population expansions that may be coupled with the potential homogenizing effects of concerted evolution.

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Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas

Paterno

Schiavina

Aglieri

et al. 2017

Ecology and Evolution

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Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long‐distance dispersal, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic–Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b‐RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic–Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic–Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic–Ionian locations indicates species‐specific differences in genetic connectivity patterns and warns against generalizing single‐species results to the entire community of rocky shore habitats.

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Characterization of the Sperm Molecule Bindin in the Sea Urchin Genus Paracentrotus

Cited by 24 publications

References 65 publications

Temporal genetic variability in the Mediterranean common sea urchin Paracentrotus lividus

Temporal genetic variability in the Mediterranean common sea urchin Paracentrotus lividus

Selection and demographic history shape the molecular evolution of the gamete compatibility protein bindin in Pisaster sea stars

Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas

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