Population-Genomic Analysis Identifies a Low Rate of Global Adaptive Fixation in the Proteins of the Cyclical Parthenogen Daphnia magna.

Daphnia are well-established ecological and evolutionary models, and the interaction between D. magna and its microparasites is widely considered a paragon of the host-parasite coevolutionary process. Like other well-studied arthropods such as Drosophila melanogaster and Anopheles gambiae, D. magna is a small, widespread, and abundant species that is therefore expected to display a large long-term population size and high rates of adaptive protein evolution. However, unlike these other species, D. magna is cyclically asexual and lives in a highly structured environment (ponds and lakes) with moderate levels of dispersal, both of which are predicted to impact upon long-term effective population size and adaptive protein evolution. To investigate patterns of adaptive protein fixation, we produced the complete coding genomes of 36 D. magna clones sampled from across the European range (Western Palaearctic), along with draft sequences for the close relatives D. similis and D. lumholtzi, used as outgroups. We analyzed genome-wide patterns of adaptive fixation, with a particular focus on genes that have an a priori expectation of high rates, such as those likely to mediate immune responses, RNA interference against viruses and transposable elements, and those with a strongly male-biased expression pattern. We find that, as expected, D. magna displays high levels of diversity and that this is highly structured among populations. However, compared with Drosophila, we find that D. magna proteins appear to have a high proportion of weakly deleterious variants and do not show evidence of pervasive adaptive fixation across its entire range. This is true of the genome as a whole, and also of putative 'arms race' genes that often show elevated levels of adaptive substitution in other species. In addition to the likely impact of extensive, and previously documented, local adaptation, we speculate that these findings may reflect reduced efficacy of selection associated with cyclical asexual reproduction.

Understanding connectivity of pearl oyster populations within Tuamotu atoll semi-closed lagoons: Cumulative insight from genetics and biophysical modelling approaches.

Connectivity affects species demography, (meta)population dynamics, evolution, phylogeny and biogeography. Various methodological approaches are applied to measure connectivity. Biophysical modelling can explore systematically the influence of atmospheric, oceanic and ecological forcing, while genetics measures connectivity patterns within the sampling strategy limit. In the Pacific Ocean pearl farming lagoons, the activity relies on spat collecting of the black lipped pearl oyster Pinctada margaritifera occurring after the larval dispersal phase, which follows spawning from wild or farmed populations. Biophysical 3D modelling and genomic studies have both separately brought insights on within-lagoon connectivity and on the origin of spats. Here, we combined previous genetics results with new realistic biophysical modelling scenarios to elucidate connectivity in Ahe Atoll lagoon. When combined, we identified the weather sequence likely explaining the realized connectivity observations. We discuss the strengths, weaknesses, opportunities and threats of combining these two approaches considering specific pearl farming demographic connectivity questions.

Environmentally Driven Color Variation in the Pearl Oyster Pinctada margaritifera var. cumingii (Linnaeus, 1758) Is Associated With Differential Methylation of CpGs in Pigment- and Biomineralization-Related Genes.

Today, it is common knowledge that environmental factors can change the color of many animals. Studies have shown that the molecular mechanisms underlying such modifications could involve epigenetic factors. Since 2013, the pearl oyster Pinctada margaritifera var. cumingii has become a biological model for questions on color expression and variation in Mollusca. A previous study reported color plasticity in response to water depth variation, specifically a general darkening of the nacre color at greater depth. However, the molecular mechanisms behind this plasticity are still unknown. In this paper, we investigate the possible implication of epigenetic factors controlling shell color variation through a depth variation experiment associated with a DNA methylation study performed at the whole genome level with a constant genetic background. Our results revealed six genes presenting differentially methylated CpGs in response to the environmental change, among which four are linked to pigmentation processes or regulations (GART, ABCC1, MAPKAP1, and GRL101), especially those leading to darker phenotypes. Interestingly, the genes perlucin and MGAT1, both involved in the biomineralization process (deposition of aragonite and calcite crystals), also showed differential methylation, suggesting that a possible difference in the physical/spatial organization of the crystals could cause darkening (iridescence or transparency modification of the biomineral). These findings are of great interest for the pearl production industry, since wholly black pearls and their opposite, the palest pearls, command a higher value on several markets. They also open the route of epigenetic improvement as a new means for pearl production improvement.

Correction: Reisser, C.M.O. et al. Population Connectivity and Genetic Assessment of Exploited and Natural Populations of Pearl Oysters within a French Polynesian Atoll Lagoon. Genes 2020, 11, 426.

The authors wish to make the following corrections to this paper [...].

Population Connectivity and Genetic Assessment of Exploited and Natural Populations of Pearl Oysters within a French Polynesian Atoll Lagoon.

In French Polynesia, the production and exportation of black pearls through the aquaculture of the black-lip pearl oyster Pinctada margaritifera provide the second largest economic income for the country after tourism. This industry entirely relies on the collection of natural spats from few highly recruiting lagoons. In recent years, pearl oyster producers have experienced variable success rates in spat collection, with significant spatial and temporal variability in spat supply, driving uncertainty in the future of pearl production. This study combines, for the first time in a farmed lagoon, genetic (SNPs), demographic (sex ratio, age), and biophysical data (larval dispersal modelling) to shed new light on population dynamics, connectivity, and spat recruitment in Ahe Atoll, a well-studied pearl farming site. Our results indicate that the geographical structuring of the natural populations and the contribution of both natural and exploited stocks to the production of spats result from the interaction of hydrodynamic features, life history traits and demographic parameters: the northeastern natural populations are older, not well connected to the southwestern natural populations and are not replenished by larvae produced by adjacent exploited populations. Moreover, we observe that the exploited populations did not contribute to larval production during our experiment, despite a sampling period set during the most productive season for spat collection. This is likely the result of a strong male bias in the exploited populations, coupled with a sweepstakes reproductive strategy of the species. Our results warrant further investigations over the future of the northeastern older natural populations and a reflection on the current perliculture techniques.

Evolution of Gene Expression during a Transition from Environmental to Genetic Sex Determination.

Genetic sex determination (GSD) can evolve from environmental sex determination (ESD) via an intermediate state in which both coexist in the same population. Such mixed populations are found in the crustacean Daphnia magna, where non-male producers (NMP, genetically determined females) coexist with male producers (MP), in which male production is environmentally inducible and can also artificially be triggered by exposure to juvenile hormone. This makes Daphnia magna a rare model species for the study of evolutionary transitions from ESD to GSD. Although the chromosomal location of the NMP-determining mutation has been mapped, the actual genes and pathways involved in the evolution of GSD from ESD remain unknown. Here, we present a transcriptomic analysis of MP and NMP females under control (female producing) and under hormone exposure conditions. We found ∼100 differentially expressed genes between MP and NMP under control conditions. Genes in the NMP-determining chromosome region were especially likely to show such constitutive expression differences. Hormone exposure led to expression changes of an additional ∼100 (MP) to ∼600 (NMP) genes, with an almost systematic upregulation of those genes in NMP. These observations suggest that the NMP phenotype is not determined by a simple "loss-of-function" mutation. Rather, homeostasis of female offspring production under hormone exposure appears to be an active state, tightly regulated by complex mechanisms involving many genes. In a broader view, this illustrates that the evolution of GSD, while potentially initiated by a single mutation, likely leads to secondary integration involving many genes and pathways.

Identification of General Patterns of Sex-Biased Expression in Daphnia, a Genus with Environmental Sex Determination.

Daphnia reproduce by cyclic-parthenogenesis, where phases of asexual reproduction are intermitted by sexual production of diapause stages. This life cycle, together with environmental sex determination, allow the comparison of gene expression between genetically identical males and females. We investigated gene expression differences between males and females in four genotypes of Daphnia magna and compared the results with published data on sex-biased gene expression in two other Daphnia species, each representing one of the major phylogenetic clades within the genus. We found that 42% of all annotated genes showed sex-biased expression in D. magna This proportion is similar both to estimates from other Daphnia species as well as from species with genetic sex determination, suggesting that sex-biased expression is not reduced under environmental sex determination. Among 7453 single copy, one-to-one orthologs in the three Daphnia species, 707 consistently showed sex-biased expression and 675 were biased in the same direction in all three species. Hence these genes represent a core-set of genes with consistent sex-differential expression in the genus. A functional analysis identified that several of them are involved in known sex determination pathways. Moreover, 75% were overexpressed in females rather than males, a pattern that appears to be a general feature of sex-biased gene expression in Daphnia.

Transition from Environmental to Partial Genetic Sex Determination in Daphnia through the Evolution of a Female-Determining Incipient W Chromosome.

Sex chromosomes can evolve during the evolution of genetic sex determination (GSD) from environmental sex determination (ESD). Despite theoretical attention, early mechanisms involved in the transition from ESD to GSD have yet to be studied in nature. No mixed ESD-GSD animal species have been reported, except for some species of Daphnia, small freshwater crustaceans in which sex is usually determined solely by the environment, but in which a dominant female sex-determining locus is present in some populations. This locus follows Mendelian single-locus inheritance, but has otherwise not been characterized genetically. We now show that the sex-determining genomic region maps to the same low-recombining peri-centromeric region of linkage group 3 (LG3) in three highly divergent populations of D. magna, and spans 3.6 Mb. Despite low levels of recombination, the associated region contains signs of historical recombination, suggesting a role for selection acting on several genes thereby maintaining linkage disequilibrium among the 36 associated SNPs. The region carries numerous genes involved in sex differentiation in other taxa, including transformer2 and sox9. Taken together, the region determining the genetic females shows characteristics of a sex-related supergene, suggesting that LG3 is potentially an incipient W chromosome despite the lack of significant additional restriction of recombination between Z and W. The occurrence of the female-determining locus in a pre-existing low recombining region illustrates one possible form of recombination suppression in sex chromosomes. D. magna is a promising model for studying the evolutionary transitions from ESD to GSD and early sex chromosome evolution.

Uncovering Cryptic Asexuality in Daphnia magna by RAD Sequencing.

The breeding systems of many organisms are cryptic and difficult to investigate with observational data, yet they have profound effects on a species' ecology, evolution, and genome organization. Genomic approaches offer a novel, indirect way to investigate breeding systems, specifically by studying the transmission of genetic information from parents to offspring. Here we exemplify this method through an assessment of self-fertilization vs. automictic parthenogenesis in Daphnia magna. Self-fertilization reduces heterozygosity by 50% compared to the parents, but under automixis, whereby two haploid products from a single meiosis fuse, the expected heterozygosity reduction depends on whether the two meiotic products are separated during meiosis I or II (i.e., central vs. terminal fusion). Reviewing the existing literature and incorporating recombination interference, we derive an interchromosomal and an intrachromosomal prediction of how to distinguish various forms of automixis from self-fertilization using offspring heterozygosity data. We then test these predictions using RAD-sequencing data on presumed automictic diapause offspring of so-called nonmale producing strains and compare them with "self-fertilized" offspring produced by within-clone mating. The results unequivocally show that these offspring were produced by automixis, mostly, but not exclusively, through terminal fusion. However, the results also show that this conclusion was only possible owing to genome-wide heterozygosity data, with phenotypic data as well as data from microsatellite markers yielding inconclusive or even misleading results. Our study thus demonstrates how to use the power of genomic approaches for elucidating breeding systems, and it provides the first demonstration of automictic parthenogenesis in Daphnia.

Permanent genetic resources added to Molecular Ecology Resources Database 1 December 2011-31 January 2012.

This article documents the addition of 473 microsatellite marker loci and 71 pairs of single-nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Barteria fistulosa, Bombus morio, Galaxias platei, Hematodinium perezi, Macrocentrus cingulum Brischke (a.k.a. M. abdominalis Fab., M. grandii Goidanich or M. gifuensis Ashmead), Micropogonias furnieri, Nerita melanotragus, Nilaparvata lugens Stål, Sciaenops ocellatus, Scomber scombrus, Spodoptera frugiperda and Turdus lherminieri. These loci were cross-tested on the following species: Barteria dewevrei, Barteria nigritana, Barteria solida, Cynoscion acoupa, Cynoscion jamaicensis, Cynoscion leiarchus, Cynoscion nebulosus, Cynoscion striatus, Cynoscion virescens, Macrodon ancylodon, Menticirrhus americanus, Nilaparvata muiri and Umbrina canosai. This article also documents the addition of 116 sequencing primer pairs for Dicentrarchus labrax.

Connectivity, small islands and large distances: the Cellana strigilis limpet complex in the Southern Ocean.

The Southern Ocean contains some of the most isolated islands on Earth, and fundamental questions remain regarding their colonization and the connectivity of their coastal biotas. Here, we conduct a genetic investigation into the Cellana strigilis (limpet) complex that was originally classified based on morphological characters into six subspecies, five of which are endemic to the New Zealand (NZ) subantarctic and Chatham islands (44-52°S). Previous genetic analyses of C. strigilis from six of the seven island groups revealed two lineages with little or no within-lineage variation. We analysed C. strigilis samples from all seven island groups using two mitochondrial (COI and 16S), one nuclear (ATPase ß) and 58 loci from four randomly amplified polymorphic DNA markers (RAPDs) and confirmed the existence of two distinct lineages. The pronounced genetic structuring within each lineage and the presence of private haplotypes in individual islands are the result of little genetic connectivity and therefore very high self-recruitment. This study supports the significance of the subantarctic islands as refugia during the last glacial maximum and adds to the knowledge of contemporary population connectivity among coastal populations of remote islands in large oceans and the distance barrier to gene flow that exists in the sea (despite its continuous medium) for most taxa.

Multiple paternity and competition in sympatric congeneric reef fishes, Embiotoca jacksoni and E. lateralis.

The black surfperch Embiotoca jacksoni and the striped surfperch E. lateralis (Embiotocidae, Perciformes) are livebearing temperate reef fishes that live sympatrically over a large portion of their distribution range, where they exhibit strong ecological competition. In order to assess whether mating strategies reflect competition, we investigated multiple paternity in these two species in an area of sympatry. We sampled 24 pregnant females (12 for each species) in Monterey Bay, California, used microsatellite analysis and assessed paternity with the COLONY software. While broods are relatively small (12 to 36 offspring), they were always sired by multiple fathers (2 to 9), with no correlation between the size of a brood and the number of fathers. The number of sires for each brood was not significantly different between the two species (approximately 3.5 sires per brood). We tested the deviation from stochasticity of fathered offspring for each father in one brood. Results showed a significant deviation for both E. jacksoni and E. lateralis. However, this deviation was not found to be significant between species. The striking similarity in the dynamics of multiple paternity in these species, when sampled in sympatry, may result from several alternative scenarios, including phylogenetic inertia, reproductive behaviour, and ecological competition.