Abstract Physiological increases in energy expenditure frequently occur in response to environmental stress. Although energy limitation is often invoked as a basis for decreased calcification under ...ocean acidification, energy-relevant measurements related to this process are scant. In this study we focus on first-shell (prodissoconch I) formation in larvae of the Pacific oyster, Crassostrea gigas. The energy cost of calcification was empirically derived to be ≤ 1.1 µJ (ng CaCO3)−1. Regardless of the saturation state of aragonite (2.77 vs. 0.77), larvae utilize the same amount of total energy to complete first-shell formation. Even though there was a 56% reduction of shell mass and an increase in dissolution at aragonite undersaturation, first-shell formation is not energy limited because sufficient endogenous reserves are available to meet metabolic demand. Further studies were undertaken on larvae from genetic crosses of pedigreed lines to test for variance in response to aragonite undersaturation. Larval families show variation in response to ocean acidification, with loss of shell size ranging from no effect to 28%. These differences show that resilience to ocean acidification may exist among genotypes. Combined studies of bioenergetics and genetics are promising approaches for understanding climate change impacts on marine organisms that undergo calcification.
INFERRING GENE FLOW AND MIGRATION FROM SPATIAL VARIATION IN ALLELE AND GENOTYPE FREQUENCIES Understanding the connectivity of marine populations is vital for conservation and fisheries management, ...particularly for the strategic design of reserve systems. A recent proliferation of molecular and statistical tools allows increasingly sophisticatecl integration of genetic and geographic data (e.g., Manel et al., 2003). Such advances have fueled considerable hope that the challenging problem of tracking movement of individuals within the vast ocean will soon be solved. Here, we focus on some of the inherent limitations of genetic approaches to inferring connectivity, particularly in marine environments. More optimistically, we also point to a number of situations where genetic approaches have been particularly successful in the past, as well as newer integrative approaches that deserve further attention.
The causes of inbreeding depression and the converse phenomenon of heterosis or hybrid vigor remain poorly understood despite their scientific and agricultural importance. In bivalve molluscs, ...related phenomena, marker-associated heterosis and distortion of marker segregation ratios, have been widely reported over the past 25 years. A large load of deleterious recessive mutations could explain both phenomena, according to the dominance hypothesis of heterosis. Using inbred lines derived from a natural population of Pacific oysters and classical crossbreeding experiments, we compare the segregation ratios of microsatellite DNA markers at 6 hr and 2-3 months postfertilization in F(2) or F(3) hybrid families. We find evidence for strong and widespread selection against identical-by-descent marker homozygotes. The marker segregation data, when fit to models of selection against linked deleterious recessive mutations and extrapolated to the whole genome, suggest that the wild founders of inbred lines carried a minimum of 8-14 highly deleterious recessive mutations. This evidence for a high genetic load strongly supports the dominance theory of heterosis and inbreeding depression and establishes the oyster as an animal model for understanding the genetic and physiological causes of these economically important phenomena.
Studies of linkage and linkage mapping have advanced genetic and biological knowledge for over 100 years. In addition to their growing role, today, in mapping phenotypes to genotypes, dense linkage ...maps can help to validate genome assemblies. Previously, we showed that 40% of scaffolds in the first genome assembly for the Pacific oyster
were chimeric, containing single nucleotide polymorphisms (SNPs) mapping to different linkage groups. Here, we merge 14 linkage maps constructed of SNPs generated from genotyping-by-sequencing (GBS) methods with five, previously constructed linkage maps, to create a compendium of nearly 69 thousand SNPs mapped with high confidence. We use this compendium to assess a recently available, chromosome-level assembly of the
genome, mapping SNPs in 275 of 301 contigs and comparing the ordering of these contigs, by linkage, to their assembly by Hi-C sequencing methods. We find that, while 26% of contigs contain chimeric blocks of SNPs,
, adjacent SNPs mapping to different linkage groups than the majority of SNPs in their contig, these apparent misassemblies amount to only 0.08% of the genome sequence. Furthermore, nearly 90% of 275 contigs mapped by linkage and sequencing are assembled identically; inconsistencies between the two assemblies for the remaining 10% of contigs appear to result from insufficient linkage information. Thus, our compilation of linkage maps strongly supports this chromosome-level assembly of the oyster genome. Finally, we use this assembly to estimate, for the first time in a Lophotrochozoan, genome-wide recombination rates and causes of variation in this fundamental process.
Understanding the genetic bases of inbreeding depression, heterosis, and genetic load is integral to understanding how genetic diversity is maintained in natural populations. The Pacific oyster ...Crassostrea gigas, like many long-lived plants, has high fecundity and high early mortality (type-III survivorship), manifesting a large, overt, genetic load; the oyster harbors an even greater concealed genetic load revealed by inbreeding. Here, we map viability QTL (vQTL) in six interrelated F2 oyster families, using high-density linkage maps of single nucleotide polymorphisms generated by genotyping-by-sequencing (GBS) methods. Altogether, we detect 70 vQTL and provisionally infer 89 causal mutations, 11 to 20 per family. Genetic mortality caused by independent (unlinked) vQTL ranges from 94.2% to 97.8% across families, consistent with previous reports. High-density maps provide better resolution of genetic mechanisms, however. Models of one causal mutation present in both identical-by-descent (IBD) homozygotes and heterozygotes fit genotype frequencies at 37 vQTL; consistent with the mutation-selection balance theory of genetic load, 20 are highly deleterious, completely recessive mutations and 17 are less deleterious, partially dominant mutations. Another 22 vQTL require pairs of recessive or partially dominant causal mutations, half showing selection against recessive mutations linked in repulsion, producing pseudo-overdominance. Only eight vQTL appear to support the overdominance theory of genetic load, with deficiencies of both IBD homozygotes, but at least four of these are likely caused by pseudo-overdominance. Evidence for epistasis is absent. A high mutation rate, random genetic drift, and pseudo-overdominance may explain both the oyster's extremely high genetic diversity and a high genetic load maintained primarily by mutation-selection balance.
Identifying elite inbred parent lines that produce high-performing hybrid Pacific oyster seed requires diallel or factorial test crosses among lines, each acting as both a male and a female parent. ...Previously, we used the generalized linear model with fixed effects (i.e. GLM) to partition variance in yield, among hybrid families produced by a diallel cross, into causal genetic components—principally, general combining ability (GCA), specific combining ability (SCA), and reciprocal effect (R). However, GLM is extremely sensitive to missing information, which arises from loss of hybrid families for random environmental causes or from variation in the reproductive success of parent lines. To resolve this issue, we apply a Bayesian hierarchical model, which partitions yield variance into the familiar causal genetic components, while providing Bayesian shrinkage estimates incorporating the uncertainty of missing data. Our study suggests that correlation between observed yields and those predicted by the Bayesian model is high (r2 ≥ 0.99), for observed offspring, regardless of diallel completeness. Additionally, in analyses of complete diallel crosses, line-specific GCA rankings from GLM and Bayesian models are consistent for parent lines. Finally, comparing simulated complete and incomplete diallel datasets, we show the accuracy of predicted yield for families that are present and of parent-line ranking by GCA and the reliability of parent-line selection for double-cross hybrids, especially when non-parental lines (i.e. the four hybrid parents used to predict the yield of double-cross hybrids) are present. Our study demonstrates that the Bayesian hierarchical model performs as well as GLM in analyzing complete diallel crosses and can properly deal with incomplete diallel crosses for which GLM does not work. Therefore, the Bayesian hierarchical model is powerful in diallel analysis to select superior parent lines for producing high-yielding, hybrid, Pacific oyster seed.
•The Pacific oyster shows dramatic hybrid vigor for yield and potential for rapid improvement through crossbreeding.•Traditional statistical methods for diallel analysis are sensitive to missing information, which is common in practice.•We use simulation to test the ability of a Bayesian hierarchical model to predict offspring and to rank parent lines.•This model accurately predicts yield of offspring present in incomplete diallels and helps identify superior parent lines.
Compared with understanding of biological shape and form, knowledge is sparse regarding what regulates growth and body size of a species. For example, the genetic and physiological causes of ...heterosis (hybrid vigor) have remained elusive for nearly a century. Here, we investigate gene-expression patterns underlying growth heterosis in the Pacific oyster (Crassostrea gigas) in two partially inbred (f = 0.375) and two hybrid larval populations produced by a reciprocal cross between the two inbred families. We cloned cDNA and generated 4.5 M sequence tags with massively parallel signature sequencing. The sequences contain 23,274 distinct signatures that are expressed at statistically nonzero levels and show a highly positively skewed distribution with median and modal counts of 9.25 million and 3 transcripts per million, respectively. For nearly half of these signatures, expression level depends on genotype and is predominantly nonadditive (hybrids deviate from the inbred average). Statistical contrasts suggest almost equal to350 candidate genes for growth heterosis that exhibit concordant nonadditive expression in reciprocal hybrids; this represents only almost equal to1.5% of the >20,000 transcripts. Patterns of gene expression, which include dominance for low expression and even underdominance of expression, are more complex than predicted from classical dominant or overdominant explanations of heterosis. Preliminary identification of ribosomal proteins among candidate genes supports the suggestion from previous studies that efficiency of protein metabolism plays a role in growth heterosis.
Population connectivity, the extent to which geographically separated subpopulations exchange individuals and are demographically linked, is important to the scientific management of marine living ...resources. In theory, the design of a marine protected area, for example, depends on an explicit understanding of how dispersal of planktonic larvae affects metapopulation structure and dynamics (Botsford et al. 2001). In practice, for most marine metazoans with planktonic larvae, the mean and variance of the distances that larvae disperse are unobservable quantities, owing to the small sizes of larvae and the very large volumes through which they are distributed. Simulation of dispersal kernels with models that incorporate oceanography and limited aspects of larval biology and behaviour, coupled with field studies of larval distribution, abundance, and settlement, have provided the best available approaches to date for understanding connectivity of marine populations (Cowen et al. 2006). On the other hand, marine population connectivity has often been judged by spatial variation in the frequencies of alleles and genotypes, although the inherent limitations of this indirect approach to measuring larval dispersal have often been overlooked (Hedgecock et al. 2007). More recently, researchers have turned to genetic methods and highly polymorphic markers that can provide direct evidence of population connectivity in the form of parentage or relatedness of recruits (e.g. Jones et al. 2005). In this issue, Christie et al. (2010) provide a particularly elegant example, in which both indirect and novel direct genetic methods are used to determine the major ecological processes shaping dispersal patterns of larval bicolour damselfish Stegastes partitus, a common and widespread reef fish species in the Caribbean Basin (Fig. 1).
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The bicolour damselfish Stegastes partitus shows substantial self‐recruitment of juveniles to their natal coral reef habitat. Below, a male guarding an artificial nest made from PVC pipe; differential reproductive success of parents or differential survival of egg clutches or the larvae that hatch from them may account for signals of sweepstakes reproductive success in this species (photo credits: top, Bill Harward; bottom, Darren Johnson).
The Molluscan Broodstock Program (MBP) has been selecting Pacific oysters Crassostrea gigas for improved yield for over two decades. Nevertheless, realized gain in yield, the percent difference in ...least-square mean yield between MBP and pooled control families made from “wild” stock, was reported to be zero in the fifth generation. Among the potential explanations for zero realized gain was that MBP-derived stock had spread or reproduced in bays with extensive oyster farming and contributed to the “wild” broodstock used for the control population. This “MBP = wild” hypothesis was tested by analyses of genetic data from four MBP cohorts and 11 wild populations, including founders of MBP cohorts. A new 2016 sample from Willapa Bay, the primary source of MBP's control families, was genotyped by high-resolution melting (HRM) of 45, SNP-containing PCR amplicons and compared to previous HRM data for a 1996 sample. Average temporal variance in allele frequencies for Willapa Bay implies a small, local, effective population size (Ne = 55, 95% CI, 32–159) with very high gene flow among Pacific Northwest populations (migration rate, m = 0.99, 95% CI, 0.25–1.0). These estimates, which are remarkably consistent with previous estimates, also based on 20-y intervals, for populations in Pipestem Inlet and Dabob Bay, support the general conclusion that the North American Pacific oyster metapopulation is evolving by genetic drift, likely owing to local sweepstakes reproductive processes, with high gene flow maintaining spatial similarity. Direct comparison of MBP and wild populations reveals 7× more genetic divergence between selected and wild populations than among wild populations. Evidence for genetic drift within the Willapa Bay wild population that is uncorrelated with genetic drift in Dabob Bay, together with evidence for genetic drift between MBP and all wild populations studied to date, falsifies the hypothesis that gene flow from MBP-derived commercial stocks to wild populations is responsible for a realized gain in yield of zero. Further analyses of parentage and relatedness in four MBP cohorts suggests that pedigree errors may have contributed to inaccuracies in the selective breeding program and resulted in the observed realized gain in yield of zero.
•“Selected oysters = wild controls” does not explain zero realized gain in yield.•Selected stocks and wild populations have diverged by random genetic drift.•Genetic analyses of selected oysters and their parents reveal pedigree errors.•Zero gain likely explained by pedigree errors, inaccurate and inefficient selection.•Genetic markers are needed for pedigree control in shellfish breeding programs.
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