Interrelationships of heterozygosity, growth rate and heterozygote deficiencies in the coot clam, Mulinia lateralis

Consequences of domestication in eastern oyster: Insights from whole genomic analyses

Selective breeding for production traits has yielded relatively rapid successes with high-fecundity aquaculture species. Discovering the genetic changes associated with selection is an important goal for understanding adaptation and can also facilitate better predictions about the likely fitness of selected strains if they escape aquaculture farms. Here, we hypothesize domestication as a genetic change induced by inadvertent selection in culture. Our premise is that standardized culture protocols generate parallel domestication effects across independent strains. Using eastern oyster as a model and a newly developed 600K SNP array, this study tested for parallel domestication effects in multiple independent selection lines compared with their progenitor wild populations. A single contrast was made between pooled selected strains (1-17 generations in culture) and all wild progenitor samples combined. Population structure analysis indicated rank order levels of differentiation as [wild - wild] < [wild - cultured] < [cultured - cultured]. A genome scan for parallel adaptation to the captive environment applied two methodologically distinct outlier tests to the wild versus selected strain contrast and identified a total of 1174 candidate SNPs. Contrasting wild versus selected strains revealed the early evolutionary consequences of domestication in terms of genomic differentiation, standing genetic diversity, effective population size, relatedness, runs of homozygosity profiles, and genome-wide linkage disequilibrium patterns. Random Forest was used to identify 37 outlier SNPs that had the greatest discriminatory power between bulked wild and selected oysters. The outlier SNPs were in genes enriched for cytoskeletal functions, hinting at possible traits under inadvertent selection during larval culture or pediveliger setting at high density. This study documents rapid genomic changes stemming from hatchery-based cultivation of eastern oysters, identifies candidate loci responding to domestication in parallel among independent aquaculture strains, and provides potentially useful genomic resources for monitoring interbreeding between farm and wild oysters.

Genetic structure, UV-vision, wing coloration and size coincide with colour polymorphism in Fabriciana adippe butterflies

Colour polymorphisms have long served as model systems in evolutionary studies and continue to inform about processes involved in the origin and dynamics of biodiversity. Modern sequencing tools allow for evaluating whether phenotypic differences between morphs reflect genetic differentiation rather than developmental plasticity, and for investigating whether polymorphisms represent intermediate stages of diversification towards speciation. We investigated phenotypic and genetic differentiation between two colour morphs of the butterfly Fabriciana adippe using a combination of ddRAD-sequencing and comparisons of body size, colour patterns and optical properties of bright wing spots. The silvery-spotted adippe form had larger and darker wings and reflected UV light, while the yellow cleodoxa form displayed more green scales and reflected very little UV, showcasing that they constitute distinct and alternative integrated phenotypes. Genomic analyses revealed genetic structuring according to source population, and to colour morph, suggesting that the phenotypic differentiation reflects evolutionary modifications. We report 17 outlier loci associated with colour morph, including ultraviolet-sensitive visual pigment (UVRh1), which is associated with intraspecific communication and mate choice in butterflies. Together with the demonstration that the wings of the adippe (but essentially not the cleodoxa) morph reflect UV light, that UV reflectance is higher in females than males and that morphs differ in wing size, this suggests that these colour morphs might represent genetically integrated phenotypes, possibly adapted to different microhabitats. We propose that non-random mating might contribute to the differentiation and maintenance of the polymorphism.

Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica

The eastern oyster Crassostrea virginica is a major aquaculture species for the USA. The sustainable development of eastern oyster aquaculture depends upon the continued improvement of cultured stocks through advanced breeding technologies. The Eastern Oyster Breeding Consortium (EOBC) was formed to advance the genetics and breeding of the eastern oyster. To facilitate efficient genotyping needed for genomic studies and selection, the consortium developed two single-nucleotide polymorphism (SNP) arrays for the eastern oyster: one screening array with 566K SNPs and one breeders' array with 66K SNPs. The 566K screening array was developed based on whole-genome resequencing data from 292 oysters from Atlantic and Gulf of Mexico populations; it contains 566,262 SNPs including 47K from protein-coding genes with a marker conversion rate of 48.34%. The 66K array was developed using best-performing SNPs from the screening array, which contained 65,893 oyster SNPs including 22,984 genic markers with a calling rate of 99.34%, a concordance rate of 99.81%, and a much-improved marker conversion rate of 92.04%. Null alleles attributable to large indels were found in 13.1% of the SNPs, suggesting that copy number variation is pervasive. Both arrays provided easy identification and separation of selected stocks from wild progenitor populations. The arrays contain 31 mitochondrial SNPs that allowed unambiguous identification of Gulf mitochondrial genotypes in some Atlantic populations. The arrays also contain 756 probes from 13 oyster and human pathogens for possible detection. Our results show that marker conversion rate is low in high polymorphism species and that the two-step process of array development can greatly improve array performance. The two arrays will advance genomic research and accelerate genetic improvement of the eastern oyster by delineating genetic architecture of production traits and enabling genomic selection. The arrays also may be used to monitor pedigree and inbreeding, identify selected stocks and their introgression into wild populations, and assess the success of oyster restoration.

Monitoring of genetically close Tsaiya duck populations using novel microsatellite markers with high polymorphism

OBJECTIVE

A set of microsatellite markers with high polymorphism from Tsaiya duck were used for the genetic monitoring and genetic structure analysis of Brown and White Tsaiya duck populations in Taiwan.

METHODS

The synthetic short tandem repeated probes were used to isolate new microsatellite markers from the genomic DNA of Tsaiya ducks. Eight populations, a total of 566 samples, sourced from Ilan Branch, Livestock Research Institute were genotyped through novel and known markers. The population genetic variables were calculated using optional programs in order to describe and monitor the genetic variability and the genetic structures of these Tsaiya duck populations.

RESULTS

In total 24 primer pairs, including 17 novel microsatellite loci from this study and seven previously known loci, were constructed for the detection of genetic variations in duck populations. The average values for the allele number, the effective number of alleles, the observed heterozygosity, the expected heterozygosity, and the polymorphism information content were 11.29, 5.370, 0.591, 0.746, and 0.708, respectively. The results of analysis of molecular variance and principal component analysis indicated a contracting Brown Tsaiya duck cluster and a spreading White Tsaiya duck cluster. The Brown Tsaiya ducks and the White Tsaiya ducks with Pekin ducks were just split to six clusters and three clusters when K was set equal to 6 and 3 in the Bayesian cluster analysis. The individual phylogenetic tree revealed eight taxa, and each individual was assigned to its own population.

CONCLUSION

According to our study, the 24 novel microsatellite markers exhibited a high capacity to analyze relationships of inter- and intra-population in those populations with a relatively limited degree of genetic diversity. We suggest that duck farms in Taiwan could use the new (novel) microsatellite set to monitor the genetic characteristics and structures of their Tsaiya duck populations at various intervals in order to ensure quality breeding and conservation strategies.

New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean

Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ± 0.02) and the expected heterozygosity (He = 0.73 ± 0.01) were high across loci and populations indicating high microsatellite variation. Pairwise F_ST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.

Genomic Tools and Selective Breeding in Molluscs

The production of most farmed molluscs, including mussels, oysters, scallops, abalone, and clams, is heavily dependent on natural seed from the plankton. Closing the lifecycle of species in hatcheries can secure independence from wild stocks and enables long-term genetic improvement of broodstock through selective breeding. Genomic techniques have the potential to revolutionize hatchery-based selective breeding by improving our understanding of the characteristics of mollusc genetics that can pose a challenge for intensive aquaculture and by providing a new suite of tools for genetic improvement. Here we review characteristics of the life history and genetics of molluscs including high fecundity, self-fertilization, high genetic diversity, genetic load, high incidence of deleterious mutations and segregation distortion, and critically assess their impact on the design and effectiveness of selective breeding strategies. A survey of the results of current breeding programs in the literature show that selective breeding with inbreeding control is likely the best strategy for genetic improvement of most molluscs, and on average growth rate can be improved by 10% per generation and disease resistance by 15% per generation across the major farmed species by implementing individual or family-based selection. Rapid advances in sequencing technology have resulted in a wealth of genomic resources for key species with the potential to greatly improve hatchery-based selective breeding of molluscs. In this review, we catalog the range of genomic resources currently available for molluscs of aquaculture interest and discuss the bottlenecks, including lack of high-quality reference genomes and the relatively high cost of genotyping, as well as opportunities for applying genomics-based selection.

Population structure and connectivity of the mountainous star coral, Orbicella faveolata, throughout the wider Caribbean region

As coral reefs continue to decline worldwide, it becomes ever more necessary to understand the connectivity between coral populations to develop efficient management strategies facilitating survival and adaptation of coral reefs in the future. Orbicella faveolata is one of the most important reef-building corals in the Caribbean and has recently experienced severe population reductions. Here, we utilize a panel of nine microsatellite loci to evaluate the genetic structure of O. faveolata and to infer connectivity across ten sites spanning the wider Caribbean region. Populations are generally well-mixed throughout the basin (F_ST = 0.038), although notable patterns of substructure arise at local and regional scales. Eastern and western populations appear segregated with a genetic break around the Mona Passage in the north, as has been shown previously in other species; however, we find evidence for significant connectivity between Curaçao and Mexico, suggesting that the southern margin of this barrier is permeable to dispersal. Our results also identify a strong genetic break within the Mesoamerican Barrier Reef System associated with complex oceanographic patterns that promote larval retention in southern Belize. Additionally, the diverse genetic signature at Flower Garden Banks suggests its possible function as a downstream genetic sink. The findings reported here are relevant to the ongoing conservation efforts for this important and threatened species, and contribute to the growing understanding of large-scale coral reef connectivity throughout the wider Caribbean.

Allozyme variation and population genetic structure in the carpet shell clam Ruditapes decussatus across the Siculo-Tunisian Strait

This study reports on the polymorphism of 15 allozyme loci in Ruditapes decussatus clams collected from 11 locations along the Tunisian coasts. We concentrated our sampling effort around the Siculo-Tunisian region to verify if any population structuring exists in this region and to identify the factors that have shaped this structure. Measurements of genetic diversity were quantified both within and between populations, and the geographic variability of gene frequencies was analyzed. Our study shows that the Siculo-Tunisian Strait is an important genetic boundary between eastern and western regions, which agrees with findings for a variety of other species. We suggest that vicariance is a predominant factor shaping the current distribution of genetic diversity of R. decussatus, and the mixing of divergent gene pools from the eastern and western regions still seems to be limited by some physical and/or biological factors.

Mating system, bottlenecks and genetic polymorphism in hermaphroditic animals

A loss of neutral genetic polymorphism is theoretically expected for many reasons in inbreeding organisms when compared to outbreeders. The first reason derives from the decrease of the effective population size, down to a halving, in purely selfing species. Other genetical reasons include hitchhiking and background selection. A loss can also be caused by ecological processes, that is by any kind of process provoking a genetic bottleneck. These theoretical expectations have been empirically confirmed in hermaphroditic plants for which selfing species exhibit both a lower gene diversity and number of alleles per population. Here I extend the analysis to hermaphroditic animals, mainly terrestrial and freshwater snails. The decrease of variability in selfers is far greater than what is expected under the halving of the effective size of populations only. Hitchhiking and background selection certainly cannot be rejected as causes of this extra loss. Bottlenecks can clearly be invoked in tropical freshwater snails. However a crude theoretical analysis using Ewens's sampling formulae shows that the relative loss of variability estimated by the number of alleles is smaller in inbreeders than in outbreeders assuming populations with the same number of individuals. This suggests that bottlenecks contribute less to the loss in selfers than in outcrossers. Variability lost within selfing populations of hermaphroditic animals is also lost at the level of a group of populations (metapopulation). This is theoretically not always expected. Indeed, I calculate the ratio of the effective size of a selfing metapopulation to be greater than that of an outcrossing one using previously derived equations. The large variation of this ratio which depends on both migration and effective size of subpopulations prevents prediction of the relative amount of genetic variability stored by selfing and outcrossing metapopulations.

The negative correlation between somatic aneuploidy and growth in the oysterCrassostrea gigasand implications for the effects of induced polyploidization

This study extends previous observations that chromosome loss in somaticcells of juveniles of the pacific oysterCrassostrea gigasis associated with reduced growth rate. All four studies designed to examine this association (two usingrandom population samples and two using full sibs) produced the same result. This consistent effect appears to be unrelated with the commonly, but not consistently, observed correlation between degree of allozyme heterozygosity and growth. We propose thatthe inverse relationship between aneuploidy and growth is due to the unmasking of deleterious recessive genes caused by ‘progressive haploidization’ of somatic cells. Because unmasking of deleterious recessive genes by random chromosome lossisunlikely in polyploid cells, this hypothesis may also provide an explanation for theobservation that artificially produced polyploid shellfish usually grow at faster rates than normal diploid ones.

The apparent selection on neutral marker loci in partially inbreeding populations

Deterministic computer calculations were used to investigate the effects on the fitnesses of genotypes at neutral loci that are caused by associations with several linked or unlinked selected loci, in partially self fertilizing populations. Both mutation to partially recessive alleles and heterozygote advantage at the selected loci were studied. In the heterozygote advantage models, either arbitrary linkage between all loci was modelled, with a single neutral locus, or many unlinked selected and neutral loci were modelled. Large apparent overdominance could be generated in all types of model studied. As has previously been suggested, these types of effect can explain the observed associations between fitness and heterozygosity in partially inbreeding populations. There were also apparent fitness differences between the genotypes at the neutral locus among the progeny produced by selfing, especially with linkage between the neutral and selected loci. There is thus no genotype-independent fitness value for these progeny. Marker based methods for estimating the relative fitness of selfed and outcrossed progeny assume equality of these fitnesses, and will therefore be inaccurate (with in most cases a bias towards overestimating the degree of inbreeding depression) when there is linkage between the neutral marker loci and loci determining fitness.

Reliable selfing rate estimates from imperfect population genetic data

Genotypic frequencies at codominant marker loci in population samples convey information on mating systems. A classical way to extract this information is to measure heterozygote deficiencies (FIS) and obtain the selfing rate s from FIS = s/(2 - s), assuming inbreeding equilibrium. A major drawback is that heterozygote deficiencies are often present without selfing, owing largely to technical artefacts such as null alleles or partial dominance. We show here that, in the absence of gametic disequilibrium, the multilocus structure can be used to derive estimates of s independent of FIS and free of technical biases. Their statistical power and precision are comparable to those of FIS, although they are sensitive to certain types of gametic disequilibria, a bias shared with progeny-array methods but not FIS. We analyse four real data sets spanning a range of mating systems. In two examples, we obtain s = 0 despite positive FIS, strongly suggesting that the latter are artefactual. In the remaining examples, all estimates are consistent. All the computations have been implemented in a open-access and user-friendly software called rmes (robust multilocus estimate of selfing) available at http://ftp.cefe.cnrs.fr, and can be used on any multilocus data. Being able to extract the reliable information from imperfect data, our method opens the way to make use of the ever-growing number of published population genetic studies, in addition to the more demanding progeny-array approaches, to investigate selfing rates.

Population genetics of Collisella subrugosa (Patellogastropoda: Acmaeidae): evidence of two scales of population structure

Marine invertebrate populations usually show high levels of genetic variability that has frequently been associated with spatial and temporal environmental heterogeneity. One of the most heterogeneous marine environments is the intertidal zone, the habitat of Collisella subrugosa, the most widespread and abundant Brazilian limpet. C. subrugosa has planktonic larvae that can disperse over long distances, what can promote gene flow among shores, working against interpopulational differentiation. In this study we investigated the genetic variability and populational substructure of C. subrugosa through analysis of 24 allozyme loci in 14 samples (590 individuals) collected along 2,700 km of the Brazilian coast. The genetic variability was high ([Formula: see text] and [Formula: see text]), as expected for intertidal species. Genetic differentiation among samples was low (F (ST) = 0.03) what may reflect intensive gene flow associated with larval dispersal. However, we detected an isolation-by-distance pattern of population substructure in one sampled region. High levels of heterozygote deficiency were also observed for many loci in each sample. Alternative hypothesis are discussed, and the "breeding groups" is suggested to explain these pattern, indicating the main cause as environmental heterogeneity.

Allozyme and morphometric variability in the dogwhelk, Nucella heyseana (Gastropoda:Muricidae) from Russian and Japanese waters: evidence for a single species under different names

A complicated issue of very variable shell morphology in dogwhelks has led to a detailed discussion and set of complex analyses based on the methods of biochemical genetics, molecular genetics, and morphometrics. In this investigation, 29 allozyme loci and five morphometric shell characters were analysed for six samples of Nucella heyseana (Dunker, 1882) from Sakhalin Island, Primorye (Russia) and Onagawa Bay (Japan). An unweighted pair group method with arithmetic mean dendrogram was constructed using genetic distances for the six populations of N. heyseana sampled, and when combined with an earlier study of N. freycinetti Deshayes, 1841, indicated that two separate species are present. However, the population genetic analysis in combination with multivariate analysis of variance, discriminant and factor analyses for morphometric traits lead us to conclude that all six samples taken from Russian and Japanese waters belong to a single species. The taxon, known in Japanese and Korean literature as N. freycinetti, is actually N. heyseana and N. freycinetti is the appropriate name for another species discovered earlier. For N. heyseana Nei’s minimal unbiased genetic distances were examined at three hierarchical levels: (1) within Onagawa Bay (Pacific coast of Honshu), Dm = 0.0059 ± 0.0056; (2) within the group of populations in Peter the Great Bay (Japan Sea, Russia), Dm = 0.0083 ± 0.0067 (Kartavtsev et al., 2000), and (3) within the whole area investigated in the north-western Pacific, Dm = 0.1550 ± 0.0209. Allele frequency heterogeneity and hierarchical variability showed that each bay contains a genetically distinct population of this species.

Patterns of genetic variation do not correlate with geographical distance in the reef-building coral Pocillopora meandrina in the South Pacific

Dispersal may be a critical factor in the ability of reef-building corals to recover after major disturbances. We studied patterns of geographical structure using four microsatellite markers in seven South Pacific populations of Pocillopora meandrina, a major coral species from Polynesia. Variation within populations showed evidence of heterozygote deficiency. Genetic differentiation between populations was detected at a large scale (2000 km) between the Tonga and the Society Islands. Within the Society Islands, four of the five studied populations from Bora Bora, Moorea and Tahiti were not significantly different from each other. Unexpectedly, one of the three populations surveyed in Moorea was genetically different from the other two populations of this island (that were 5 and 10 km apart), and from the populations of the other two surveyed islands in this archipelago. We cannot rule out the possibility that this pattern is an equilibrium state, whereby short-range dispersal is locally more differentiating than long-range dispersal, as has been suggested by similar patterns reported in other studies. An alternative explanation that is globally consistent with all observations is that this is the signature of a large-scale destruction event, as for instance a bleaching event, followed by the recent restoration of populations by new colonists.

Low effective population size and evidence for inbreeding in an overexploited flatfish, plaice (Pleuronectes platessa L.)

Overexploitation and subsequent collapses of major worldwide fisheries has made it clear that marine stocks are no inexhaustible. Unfortunately, the perception remains that marine fished are resilient to large population reductions, as even a commercially 'collapsed' stock will still consist of millions of individuals. Coupled with this notion is the idea that fisheries can, therefore, have little effect on the genetic diversity of stocks. We used DNA from archived otoliths collected between 1924 and 1972 together with 2002 juvenile;s tissue to estimate effective population size (Ne) in plaice (Pleuronrctes platessa). Ne was estimated at 20,000 in the North Sea and 2000 in Iceland. These values are five orders of magnitude smaller than the estimated census size foe the two locations. Populations examined between 1924 and 1960 were in Hardy-Weinberg equilibrium, whereas populations examined after 1970 were not. Extensive testing was performed to rule out genotyping artefacts and Wahlund effects. The significant heterozygote deficiencies found from 1970 onward were attributed to inbreeding. The emergence of inbreeding between 1905 and 19070 coincides with the increase in fishing mortality after World War II. Although the biological mechanisms remain speculative, our demonstration of inbreeding signals the need for understanding the social and mating behaviour in commercially important fishes.

Ontogenetic change in relative performance of allozyme genotypes influences detection of heterosis in the earthworm Eisenia andrei

The effect of ontogeny on relationships between allozyme genotypes and fresh weight was measured weekly throughout the life history of the earthworm Eisenia andrei to test the hypothesis that there is an ontogenetic component to variation in such relationships. Two of six allozyme loci showed a significant increase in apparent heterosis with ontogeny, while one locus showed a significant decrease in apparent heterosis. Three loci showed a significant decrease in the performance of common homozygotes with ontogeny. Patterns of relative genotypic performance varied among loci, but the cumulative effect was an increase in apparent allozyme heterosis later in ontogeny coinciding with a series of positive relationships between multilocus heterozygosity and fresh weight. The results could not be used to determine whether these patterns were caused by selection acting on the loci directly or on loci tightly linked to allozyme loci. However, because the same individuals were used throughout this study and thus allele frequencies and heterozygote deficiency were constant, the presence of both ontogenetic effects and differences in such patterns among loci is not compatible with a general inbreeding effect. Examining relative genotypic performance repetitively using the same individuals through ontogeny or in different environments is a very powerful experimental design for testing the effects of inbreeding or other populational factors.

Population genetic structure of Pacific white shrimp (Litopenaeus vannamei) from Mexico to Panama: microsatellite DNA variation

Genetic variation and population structure of wild white shrimp (Litopenaeus vannamei) from 4 geographic locations from Mexico to Panama were investigated using 5 microsatellite DNA loci. The genetic diversity between populations was indicated by the mean number of alleles per locus and mean observed heterozygosity, which ranged from 7.4 to 8.6 and from 0.241 to 0.388, respectively. Significant departures from Hardy-Weinberg equilibrium were found at most locations at each locus, with the exception Guatemala at Pvan0013, and were caused by high heterozygote deficiencies. Genetic differences between localities were detected by pairwise comparison based on allelic and genotypic frequencies, with the exception of locus Pvan1003. Significant pairwise F (ST) values between locations and total F (ST) showed that the white shrimp population is structured into subpopulations. However, population differentiation does not follow an isolation-by-distance model. Knowledge of the genetic diversity and structure of L.vannamei populations will be of interest for aquaculture and fisheries management to utilize and preserve aquatic biodiversity.

A hybrid zone between hydrothermal vent mussels (Bivalvia: Mytilidae) from the Mid-Atlantic Ridge

This study provides the first example of a hybrid zone between animal taxa distributed along the mid-ocean ridge system. We examined the distribution and genetic structure of deep-sea hydrothermal vent mussels (Bivalvia: Mytilidae) along a 2888-km portion of the Mid-Atlantic Ridge between 37 degrees 50' N and 14 degrees 45' N latitude. Mitochondrial DNA (mtDNA), allozymes and multivariate-morphometric evidence discriminated between individuals of a northern species, Bathymodiolus azoricus, and a southern species, B. puteoserpentis, that were separated by an intermediate ridge segment almost devoid of mussels. A small sample of mussels from Broken Spur, a vent locality along this intermediate zone, revealed a mixed population with gene frequencies and morphology that were broadly intermediate to those of the northern and southern species. Multilocus clines in mtDNA and allozyme frequencies were centred over the intermediate zone. We consider intrinsic and extrinsic processes that might limit genetic exchange across this hybrid zone.

Extraordinary multilocus genetic organization in mole crickets, Gryllotalpidae

Allozymic diversity at 21 loci was analyzed in 470 individuals of three species of mole cricket superspecies, Gryllotalpa gryllotalpa (two new chromosomal species, G. tali and G. marismortui) and G. africana in Israel, which are distributed along a southward transect of increasing aridity. Two outstanding findings emerged in G. tali and G. marismortui: (1) genetic polymorphism was high but heterozygosity very low, indicating significant deviations from Hardy-Weinberg expectations; and (2) significant linkage disequilibria at an unprecedented level for outbreeders and remarkable intersite differences. The results may characterize subterranean gryllotalpids worldwide because a single sample of Neocurtilla hexadactyla from Tefé, Amazonia, shows the same features. Significant variation of heterozygote paucity among loci, combined with the biology of the species, rejects the simple explanation of inbreeding or any other single explanatory model. Likewise, direct selection against heterozygotes or specific multilocus associations can explain, but is not necessary nor likely to explain, the observed results in mole crickets. To explain these results, we developed a multiple-factor mathematical model combining niche viability selection, niche choice, and positive assortative mating. This model involves a special case of Wahlund effect and inbreeding. Simulations based on this model showed that a combination of these three mechanisms may produce the observed distribution of alleles, via selection on a few loci, to affect the entire genome organization.

Physiological components of growth differences between individual oysters (Crassostrea gigas) and a comparison with Saccostrea commercialis

Pacific oysters (Crassostrea gigas) of identical age from two genetically distinct lines, one fast growing and the other slow growing, were held at three levels of ration and analysed for physiological traits to explain differences in their rates of growth. The data supported three hypotheses; faster growth was associated with faster rates of consumption of food, reduced metabolic rate at maintenance (i.e., at zero growth), and reduced metabolic costs of growth. A comparison with the Sydney rock oyster, Saccostrea commercialis, based on similar experiments on the two species, indicated that faster growth of Pacific oysters depended on similar physiological differences; the mean metabolic costs of growth, however, were similar in the two species. It is suggested that a general model for genetically linked differences in the growth rate of bivalve molluscs will need to include the processes of metabolic control rather than relying solely on an analysis of the individual components of the energetics of growth.

Heterozygosity-fitness correlations: new perspectives on old problems

Heterozygosity-fitness correlations (HFC) have been studied in various organisms for more than two decades, but they are not universal. Although their detectability is limited by several factors (null alleles, inaccuracy of the phenotypic description of fitness, small sample sizes) the correlations appear intrinsically weak and often inconsistent across samples. Determining the origins of HFC is therefore a complex task. However, this issue might soon be resolved provided clear hypotheses and definitions are used (especially, if the problem of the neutrality of allozyme variation is not identified with the related issue of HFC), as well as new empirical (molecular markers) & theoretical (statistical models) tools.

Early effect of inbreeding as revealed by microsatellite analyses on Ostrea edulis larvae

This paper reports new experimental evidence on the effect of inbreeding on growth and survival in the early developmental phase of a marine bivalve, the flat oyster Ostrea edulis. Two crosses between full sibs were analyzed using four microsatellite markers. Samples of 96 individuals were taken just after spawning (day 1), at the end of the larval stage before metamorphosis (day 10) and at the postlarval stage (day 70). Significant departure from Mendelian expectation was observed at two loci in the first cross and two loci in the second. Departure from 1:1 segregation occurred in one parent of the first cross at three loci and genotypic selection, which resulted in highly significant heterozygote excesses, was recorded at three out of four loci in cross C1 and at two out of three loci in cross C2. Across the four markers, there were similar significant excesses of multilocus heterozygosity, and significant multilocus heterozygosity-growth correlations were recorded for both crosses at all stages. These results suggest that microsatellite markers, often assumed to be neutral, cosegregated with fitness-associated genes, the number of which is estimated to be between 15 and 38 in the whole genome, and that there is a potentially high genetic load in Ostrea edulis genome. This load provides a genetic basis for heterosis in marine bivalves.

Conditions for positive and negative correlations between fitness and heterozygosity in equilibrium populations

The past decades have witnessed extensive efforts to correlate fitness traits with genomic heterozygosity. While positive correlations are revealed in most of the organisms studied, results of no/negative correlations are not uncommon. There has been little effort to reveal the genetic causes of these negative correlations. The positive correlations are regarded either as evidence for functional overdominance in large, randomly mating populations at equilibrium, or the results of populations at disequilibrium under dominance. More often, the positive correlations are viewed as a phenomenon of heterosis, so that it cannot possibly occur under within-locus additive allelic effects. Here we give exact genetic conditions that give rise to positive and negative correlations in populations at Hardy-Weinberg and linkage equilibria, thus offering a genetic explanation for the observed negative correlations. Our results demonstrate that the above interpretations concerning the positive correlations are not complete or even necessary. Such a positive correlation can result under dominance and potentially under additivity, even in populations where associated overdominance due to linked alleles at different loci is not significant. Additionally, negative correlations and heterosis can co-occur in a single population. Although our emphasis is on equilibrium populations and for biallelic genetic systems, the basic conclusions are generalized to non-equilibrium populations and for multi-allelic situations.

Heterozygosity and fitness: no association in Scots pine

The association of six quantitative traits related to fitness with heterozygosity at 12 allozyme loci has been examined in three populations of Scots pine, Pinus sylvestris. Because of several characteristics of this organism and of this extensive data set, it appeared that this study would show a positive association between heterozygosity and these traits if indeed heterozygotes had higher values for these quantitative traits. Using several different statistical techniques including analysis of variance, regression with the scaling recommended from the adaptive distance model, and multiple regression, no evidence of an association was found. For example, only between 7 and 8% of the regression tests were significant at the 5% level and half of these showed a positive association and half showed a negative association. Further, the multiple regression analysis explained on average only 5.8% of the variation observed in the six different traits and only 1.5% of this variation was explained by a positive association. Power analysis was carried out (for the first time on these type of data), both for the single locus heterozygous advantage and the association of individual multiple locus heterozygosity and the quantitative traits. For diameter and height, two traits often used in similar studies, the average power to detect a single locus heterozygous advantage of 0.10 was 0.737 and the average power to detect a mean heterozygote advantage of 0.05 per locus for multiple loci was 0.797. As a result of this study and an examination of the published results from other studies, it appears that what positive associations have been observed are probably not, in large part, due to the presence of intrinsic heterozygote advantage.

The evolutionary history of Drosophila buzzatii. XXXII. Linkage disequilibrium between allozymes and chromosome inversions in two colonizing populations

Chromosome polymorphism in Drosophila buzzatii is under selection but the genes responsible for the effect of the inversions of fitness are unknown. On the other hand, there is evidence for selection on several allozyme loci but the presence of paracentric inversions on the second chromosome, where most of the polymorphic loci are located, complicates the interpretation. Studies of the associations between allozymes and inversions are thus necessary to help understand the effect of selection at both the chromosomal and allozymic level. Until now this kind of information has only been available in D. buzzatii for two loci, Est-1 and Est-2, in Australian populations. Here we describe the genetic constitution of two Old World populations, Carboneras and Colera. Emphasis has been placed on the analysis of the linkage disequilibria between the second chromosome arrangements and three allozyme loci, Est-2, Pept-2 and Aldox, located on this chromosome. In addition, the recombination frequencies between the loci, and between the loci and the inversion breakpoints, have been estimated and a genetic map of the three loci has been produced. The two populations differ in allele and arrangement frequencies, as well as in the pattern of one-locus disequilibria. Est-2 and Aldox are associated with the second chromosome arrangements in both populations. On the other hand, Pept-2 is associated with the inversions in Colera but not in Carboneras. The gametic associations among the three loci are discussed taking into account the position of these loci on the chromosome map and the lack of recombination in the heterokaryotypes.

Distinct genetic subdivision in sympatric and sibling species of the genus Littorina (Gastropoda: Littorinidae)

The genetic structure of two sibling and sympatric species of the genus Littorina was compared using allozymic loci. The two species are biologically and ecologically well-known and mostly show similar life history characteristics. Three populations of L. mariae Sacchi & Rastelli and L. obstusata (L.) were studied in the Muros-Noya Ria (Galicia, NW Spain). In addition, four microgeographical subsamples taken from one of the populations were analysed for each species. Age, sex and genotypes for nine polymorphic loci were studied in 1250 snails of both species. L. mariae showed larger genetic population subdivision and lower heterozygosity levels for the loci studied than did L. obtusata. Heterozygote deficiencies were found in only a few cases in natural populations of both species, usually affecting the Lap-1 locus. No significant genetic differences among age or sex classes were found. These results may be explained by the lower effective population size in L. mariae than in L. obtusata. Known differences between these species in generation interval and population density during the winter can cause the different effective population sizes suggested. These life history characteristics appear to provide the most likely explanations for the differences in genetic differentiation and heterozygosity between the two species. A previously unknown L. mariae morph from exposed shores is tentatively suggested to be conspecific.