Parentage in natural populations: novel methods to detect parent-offspring pairs in large data sets

Close-kin mark-recapture methods to estimate demographic parameters of mosquitoes

Close-kin mark-recapture (CKMR) methods have recently been used to infer demographic parameters such as census population size and survival for fish of interest to fisheries and conservation. These methods have advantages over traditional mark-recapture methods as the mark is genetic, removing the need for physical marking and recapturing that may interfere with parameter estimation. For mosquitoes, the spatial distribution of close-kin pairs has been used to estimate mean dispersal distance, of relevance to vector-borne disease transmission and novel biocontrol strategies. Here, we extend CKMR methods to the life history of mosquitoes and comparable insects. We derive kinship probabilities for mother-offspring, father-offspring, full-sibling and half-sibling pairs, where an individual in each pair may be a larva, pupa or adult. A pseudo-likelihood approach is used to combine the marginal probabilities of all kinship pairs. To test the effectiveness of this approach at estimating mosquito demographic parameters, we develop an individual-based model of mosquito life history incorporating egg, larva, pupa and adult life stages. The simulation labels each individual with a unique identification number, enabling close-kin relationships to be inferred for sampled individuals. Using the dengue vector Aedes aegypti as a case study, we find the CKMR approach provides unbiased estimates of adult census population size, adult and larval mortality rates, and larval life stage duration for logistically feasible sampling schemes. Considering a simulated population of 3,000 adult mosquitoes, estimation of adult parameters is accurate when ca. 40 adult females are sampled biweekly over a three month period. Estimation of larval parameters is accurate when adult sampling is supplemented with ca. 120 larvae sampled biweekly over the same period. The methods are also effective at detecting intervention-induced increases in adult mortality and decreases in population size. As the cost of genome sequencing declines, CKMR holds great promise for characterizing the demography of mosquitoes and comparable insects of epidemiological and agricultural significance.

Population size estimates based on the frequency of genetically assigned parent-offspring pairs within a subsample

Estimating population density as precise as possible is a key premise for managing wild animal species. This can be a challenging task if the species in question is elusive or, due to high quantities, hard to count. We present a new, mathematically derived estimator for population size, where the estimation is based solely on the frequency of genetically assigned parent-offspring pairs within a subsample of an ungulate population. By use of molecular markers like microsatellites, the number of these parent-offspring pairs can be determined. The study's aim was to clarify whether a classical capture-mark-recapture (CMR) method can be adapted or extended by this genetic element to a genetic-based capture-mark-recapture (g-CMR). We numerically validate the presented estimator (and corresponding variance estimates) and provide the R-code for the computation of estimates of population size including confidence intervals. The presented method provides a new framework to precisely estimate population size based on the genetic analysis of a one-time subsample. This is especially of value where traditional CMR methods or other DNA-based (fecal or hair) capture-recapture methods fail or are too difficult to apply. The DNA source used is basically irrelevant, but in the present case the sampling of an annual hunting bag is to serve as data basis. In addition to the high quality of muscle tissue samples, hunting bags provide additional and essential information for wildlife management practices, such as age, weight, or sex. In cases where a g-CMR method is ecologically and hunting-wise appropriate, it enables a wide applicability, also through its species-independent use.

Cultivated Olive Diversification at Local and Regional Scales: Evidence From the Genetic Characterization of French Genetic Resources

Molecular characterization of crop genetic resources is a powerful approach to elucidate the origin of varieties and facilitate local cultivar management. Here we aimed to decipher the origin and diversification of French local olive germplasm. The 113 olive accessions of the ex situ collection of Porquerolles were characterized with 20 nuclear microsatellites plus their plastid haplotype. We then compared this collection to Mediterranean olive varieties from the Worldwide Olive Germplasm Bank of Marrakech, Morocco. High genetic diversity was observed within local French varieties, indicating a high admixture level, with an almost equal contribution from the three main Mediterranean gene pools. Nearly identical and closely related genotypes were observed among French and Italian/Spanish varieties. A high number of parent-offspring relationships were also detected among French varieties and between French and two Italian varieties ('Frantoio' and 'Moraiolo') and the Spanish variety ('Gordal Sevillana'). Our investigations indicated that French olive germplasm resulted from the diffusion of material from multiple origins followed by diversification based on parentage relationships between varieties. We strongly suggest that farmers have been actively selecting olives based on local French varieties. French olive agroecosystems more affected by unexpected frosts than southernmost regions could also be seen as incubators and as a bridge between Italy and Spain that has enhanced varietal olive diversification.

Long-Distance Benefits of Marine Reserves: Myth or Reality?

Long-distance (>40-km) dispersal from marine reserves is poorly documented; yet, it can provide essential benefits such as seeding fished areas or connecting marine reserves into networks. From a meta-analysis, we suggest that the spatial scale of marine connectivity is underestimated due to the limited geographic extent of sampling designs. We also found that the largest marine reserves (>1000km²) are the most isolated. These findings have important implications for the assessment of evolutionary, ecological, and socio-economic long-distance benefits of marine reserves. We conclude that existing methods to infer dispersal should consider the up-to-date genomic advances and also expand the spatial scale of sampling designs. Incorporating long-distance connectivity in conservation planning will contribute to increase the benefits of marine reserve networks.

Genetic diversity in fishes is influenced by habitat type and life-history variation

Populations of fishes are increasingly threatened by over-exploitation, pollution, habitat destruction, and climate change. In order to better understand the factors that can explain the amount of genetic diversity in wild populations of fishes, we collected estimates of genetic diversity (mean heterozygosity and mean rarefied number of alleles per locus) along with habitat associations, conservation status, and life-history information for 463 fish species. We ran a series of phylogenetic generalized least squares models to determine which factors influence genetic diversity in fishes after accounting for shared evolutionary history among related taxa. We found that marine fishes had significantly higher genetic diversity than freshwater fishes with marine fishes averaging 11.3 more alleles per locus than their freshwater counterparts. However, contrary to our expectations, genetic diversity was not found to be lower in threatened versus not-threatened fishes. Finally, we found that both age at maturity and fecundity were negatively related to genetic variation in both marine and freshwater fishes. Our results demonstrate that both life-history characteristics and habitat play a role in shaping patterns of genetic diversity in fishes and should be considered when prioritizing species for conservation.

Life history variation is maintained by fitness trade-offs and negative frequency-dependent selection

The maintenance of diverse life history strategies within and among species remains a fundamental question in ecology and evolutionary biology. By using a near-complete 16-year pedigree of 12,579 winter-run steelhead (Oncorhynchus mykiss) from the Hood River, Oregon, we examined the continued maintenance of two life history traits: the number of lifetime spawning events (semelparous vs. iteroparous) and age at first spawning (2-5 years). We found that repeat-spawning fish had more than 2.5 times the lifetime reproductive success of single-spawning fish. However, first-time repeat-spawning fish had significantly lower reproductive success than single-spawning fish of the same age, suggesting that repeat-spawning fish forego early reproduction to devote additional energy to continued survival. For single-spawning fish, we also found evidence for a fitness trade-off for age at spawning: older, larger males had higher reproductive success than younger, smaller males. For females, in contrast, we found that 3-year-old fish had the highest mean lifetime reproductive success despite the observation that 4- and 5-year-old fish were both longer and heavier. This phenomenon was explained by negative frequency-dependent selection: as 4- and 5-year-old fish decreased in frequency on the spawning grounds, their lifetime reproductive success became greater than that of the 3-year-old fish. Using a combination of mathematical and individual-based models parameterized with our empirical estimates, we demonstrate that both fitness trade-offs and negative frequency-dependent selection observed in the empirical data can theoretically maintain the diverse life history strategies found in this population.

Dispersal influences genetic and acoustic spatial structure for both males and females in a tropical songbird

Animals exhibit diverse dispersal strategies, including sex‐biased dispersal, a phenomenon common in vertebrates. Dispersal influences the genetic structure of populations as well as geographic variation in phenotypic traits. Patterns of spatial genetic structure and geographic variation may vary between the sexes whenever males and females exhibit different dispersal behaviors. Here, we examine dispersal, spatial genetic structure, and spatial acoustic structure in Rufous‐and‐white Wrens, a year‐round resident tropical bird. Both sexes sing in this species, allowing us to compare acoustic variation between males and females and examine the relationship between dispersal and song sharing for both sexes. Using a long‐term dataset collected over an 11‐year period, we used banding data and molecular genetic analyses to quantify natal and breeding dispersal distance in Rufous‐and‐white Wrens. We quantified song sharing and examined whether sharing varied with dispersal distance, for both males and females. Observational data and molecular genetic analyses indicate that dispersal is female‐biased. Females dispersed farther from natal territories than males, and more often between breeding territories than males. Furthermore, females showed no significant spatial genetic structure, consistent with expectations, whereas males showed significant spatial genetic structure. Overall, natal dispersal appears to have more influence than breeding dispersal on spatial genetic structure and spatial acoustic structure, given that the majority of breeding dispersal events resulted in individuals moving only short distances. Song sharing between pairs of same‐sex animals decreases with the distance between their territories for both males and females, although males exhibited significantly greater song sharing than females. Lastly, we measured the relationship between natal dispersal distance and song sharing. We found that sons shared fewer songs with their fathers the farther they dispersed from their natal territories, but that song sharing between daughters and mothers was not significantly correlated with natal dispersal distance. Our results reveal cultural differences between the sexes, suggesting a relationship between culture and sex‐biased dispersal.

Absolute abundance of southern bluefin tuna estimated by close-kin mark-recapture

Southern bluefin tuna is a highly valuable, severely depleted species, whose abundance and productivity have been difficult to assess with conventional fishery data. Here we use large-scale genotyping to look for parent-offspring pairs among 14,000 tissue samples of juvenile and adult tuna collected from the fisheries, finding 45 pairs in total. Using a modified mark-recapture framework where 'recaptures' are kin rather than individuals, we can estimate adult abundance and other demographic parameters such as survival, without needing to use contentious fishery catch or effort data. Our abundance estimates are substantially higher and more precise than previously thought, indicating a somewhat less-depleted and more productive stock. More broadly, this technique of 'close-kin mark-recapture' has widespread utility in fisheries and wildlife conservation. It estimates a key parameter for management-the absolute abundance of adults-while avoiding the expense of independent surveys or tag-release programmes, and the interpretational problems of fishery catch rates.

Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations

Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half-siblings or cousins) is strongly suggested.

Parentage assignment with genomic markers: a major advance for understanding and exploiting genetic variation of quantitative traits in farmed aquatic animals

Since the middle of the 1990s, parentage assignment using microsatellite markers has been introduced as a tool in aquaculture breeding. It now allows close to 100% assignment success, and offered new ways to develop aquaculture breeding using mixed family designs in commercial conditions. Its main achievements are the knowledge and control of family representation and inbreeding, especially in mass spawning species, above all the capacity to estimate reliable genetic parameters in any species and rearing system with no prior investment in structures, and the development of new breeding programs in many species. Parentage assignment should not be seen as a way to replace physical tagging, but as a new way to conceive breeding programs, which have to be optimized with its specific constraints, one of the most important being to well define the number of individuals to genotype to limit costs, maximize genetic gain while minimizing inbreeding. The recent possible shift to (for the moment) more costly single nucleotide polymorphism markers should benefit from future developments in genomics and marker-assisted selection to combine parentage assignment and indirect prediction of breeding values.

Beyond connectivity: how empirical methods can quantify population persistence to improve marine protected-area design

Demographic connectivity is a fundamental process influencing the dynamics and persistence of spatially structured populations. Consequently, quantifying connectivity is essential for properly designing networks of protected areas so that they achieve their core ecological objective of maintaining population persistence. Recently, many empirical studies in marine systems have provided essential, and historically challenging to obtain, data on patterns of larval dispersal and export from marine protected areas (MPAs). Here, we review the empirical studies that have directly quantified the origins and destinations of individual larvae and assess those studies' relevance to the theory of population persistence and MPA design objectives. We found that empirical studies often do not measure or present quantities that are relevant to assessing population persistence, even though most studies were motivated or contextualized by MPA applications. Persistence of spatial populations, like nonspatial populations, depends on replacement, whether individuals reproduce enough in their lifetime to replace themselves. In spatial populations, one needs to account for the effect of larval dispersal on future recruitment back to the local population through local retention and other connectivity pathways. The most commonly reported descriptor of larval dispersal was the fraction of recruitment from local origin (self-recruitment). Self-recruitment does not inform persistence-based MPA design because it is a fraction of those arriving, not a fraction of those leaving (local retention), so contains no information on replacement. Some studies presented connectivity matrices, which can inform assessments of persistence with additional knowledge of survival and fecundity after recruitment. Some studies collected data in addition to larval dispersal that could inform assessments of population persistence but which were not presented in that way. We describe how three pieces of empirical information are needed to fully describe population persistence in a network of MPAs: (1) lifetime fecundity, (2) the proportion of larvae that are locally retained (or the full connectivity matrix), and (3) survival rate after recruitment. We conclude by linking theory and data to provide detailed guidance to empiricists and practitioners on field sampling design and data presentation that better informs the MPA objective of population persistence.

How much does inbreeding contribute to the reduced fitness of hatchery-born steelhead (Oncorhynchus mykiss) in the wild?

Many declining populations are supplemented with captive-born individuals that are released directly into the wild. Because captive-born individuals can have lower fitness in the wild than their wild-born counterparts, a comprehensive understanding of the mechanisms responsible for the reduced fitness of these individuals is required for appropriate conservation and management decisions. Inbreeding among captive-born individuals is one plausible mechanism because captive breeding programs frequently use small numbers of breeders to create large numbers of siblings that are subsequently released together into the wild. We tested this hypothesis in a supplementation program for steelhead (Oncorhynchus mykiss) from the Hood River, Oregon, for which first-generation hatchery fish were demonstrated to have lower fitness in the wild than their wild-born counterparts. To determine the contribution of inbreeding to this fitness decline, we first assigned 11 run-years of hatchery steelhead (3005 fish) back to their broodstock parents (462 fish) using 8 polymorphic microsatellite loci. By combining pedigree analyses with species-specific estimates of genetic load, we found that inbreeding could at most account for a 1-4% reduction in the fitness of hatchery fish relative to wild fish. Thus, inbreeding alone cannot adequately explain the 15% average fitness decline observed in first-generation hatchery fish from this population.

On minimizing assignment errors and the trade-off between false positives and negatives in parentage analysis

Genetic parentage analyses provide a practical means with which to identify parent-offspring relationships in the wild. In Harrison et al.'s study (2013a), we compare three methods of parentage analysis and showed that the number and diversity of microsatellite loci were the most important factors defining the accuracy of assignments. Our simulations revealed that an exclusion-Bayes theorem method was more susceptible to false-positive and false-negative assignments than other methods tested. Here, we analyse and discuss the trade-off between type I and type II errors in parentage analyses. We show that controlling for false-positive assignments, without reporting type II errors, can be misleading. Our findings illustrate the need to estimate and report both the rate of false-positive and false-negative assignments in parentage analyses.

Bayesian parentage analysis with systematic accountability of genotyping error, missing data and false matching

MOTIVATION

The goal of any parentage analysis is to identify as many parent-offspring relationships as possible, while minimizing incorrect assignments. Existing methods can achieve these ends, but they require additional information in the form of demographic data, thousands of markers and/or estimates of genotyping error rates. For many non-model systems, it is simply not practical, cost-effective or logistically feasible to obtain this information. Here, we develop a Bayesian parentage method that only requires the sampled genotypes to account for genotyping error, missing data and false matches.

RESULTS

Extensive testing with microsatellite and SNP datasets reveals that our Bayesian parentage method reliably controls for the number of false assignments, irrespective of the genotyping error rate. When the number of loci is limiting, our approach maximizes the number of correct assignments by accounting for the frequencies of shared alleles. Comparisons with exclusion and likelihood-based methods on an empirical salmon dataset revealed that our Bayesian method had the highest ratio of correct to incorrect assignments.

Evidence of stable genetic structure across a remote island archipelago through self-recruitment in a widely dispersed coral reef fish

We used microsatellite markers to assess the population genetic structure of the scribbled rabbitfish Siganus spinus in the western Pacific. This species is a culturally important food fish in the Mariana Archipelago and subject to high fishing pressure. Our primary hypothesis was to test whether the individuals resident in the southern Mariana Island chain were genetically distinct and hence should be managed as discrete stocks. In addition to spatial sampling of adults, newly-settled individuals were sampled on Guam over four recruitment events to assess the temporal stability of the observed spatial patterns, and evidence of self-recruitment. We found significant genetic structure in S. spinus across the western Pacific, with Bayesian analyses revealing three genetically distinct clusters: the southern Mariana Islands, east Micronesia, and the west Pacific; with the southern Mariana Islands being more strongly differentiated from the rest of the region. Analyses of temporal samples from Guam indicated the southern Mariana cluster was stable over time, with no genetic differentiation between adults versus recruits, or between samples collected across four separate recruitment events spanning 11 months. Subsequent assignment tests indicated seven recruits had self-recruited from within the Southern Mariana Islands population. Our results confirm the relative isolation of the southern Mariana Islands population and highlight how local processes can act to isolate populations that, by virtue of their broad-scale distribution, have been subject to traditionally high gene flows. Our results add to a growing consensus that self-recruitment is a highly significant influence on the population dynamics of tropical reef fish.

Effective size of a wild salmonid population is greatly reduced by hatchery supplementation

Many declining and commercially important populations are supplemented with captive-born individuals that are intentionally released into the wild. These supplementation programs often create large numbers of offspring from relatively few breeding adults, which can have substantial population-level effects. We examined the genetic effects of supplementation on a wild population of steelhead (Oncorhynchus mykiss) from the Hood River, Oregon, by matching 12 run-years of hatchery steelhead back to their broodstock parents. We show that the effective number of breeders producing the hatchery fish (broodstock parents; N(b)) was quite small (harmonic mean N(b)=25 fish per brood-year vs 373 for wild fish), and was exacerbated by a high variance in broodstock reproductive success among individuals within years. The low N(b) caused hatchery fish to have decreased allelic richness, increased average relatedness, more loci in linkage disequilibrium and substantial levels of genetic drift in comparison with their wild-born counterparts. We also documented a substantial Ryman-Laikre effect whereby the additional hatchery fish doubled the total number of adult fish on the spawning grounds each year, but cut the effective population size of the total population (wild and hatchery fish combined) by nearly two-thirds. We further demonstrate that the Ryman-Laikre effect is most severe in this population when (1) >10% of fish allowed onto spawning grounds are from hatcheries and (2) the hatchery fish have high reproductive success in the wild. These results emphasize the trade-offs that arise when supplementation programs attempt to balance disparate goals (increasing production while maintaining genetic diversity and fitness).

Genetic adaptation to captivity can occur in a single generation

Captive breeding programs are widely used for the conservation and restoration of threatened and endangered species. Nevertheless, captive-born individuals frequently have reduced fitness when reintroduced into the wild. The mechanism for these fitness declines has remained elusive, but hypotheses include environmental effects of captive rearing, inbreeding among close relatives, relaxed natural selection, and unintentional domestication selection (adaptation to captivity). We used a multigenerational pedigree analysis to demonstrate that domestication selection can explain the precipitous decline in fitness observed in hatchery steelhead released into the Hood River in Oregon. After returning from the ocean, wild-born and first-generation hatchery fish were used as broodstock in the hatchery, and their offspring were released into the wild as smolts. First-generation hatchery fish had nearly double the lifetime reproductive success (measured as the number of returning adult offspring) when spawned in captivity compared with wild fish spawned under identical conditions, which is a clear demonstration of adaptation to captivity. We also documented a tradeoff among the wild-born broodstock: Those with the greatest fitness in a captive environment produced offspring that performed the worst in the wild. Specifically, captive-born individuals with five (the median) or more returning siblings (i.e., offspring of successful broodstock) averaged 0.62 returning offspring in the wild, whereas captive-born individuals with less than five siblings averaged 2.05 returning offspring in the wild. These results demonstrate that a single generation in captivity can result in a substantial response to selection on traits that are beneficial in captivity but severely maladaptive in the wild.

Strength, diversity and plasticity of postmating reproductive barriers between two hybridizing oak species (Quercus robur L. and Quercus petraea (Matt) Liebl.)

Very little is known about the nature and strength of reproductive isolation (RI) in Quercus species, despite extensive research on the estimation and evolutionary significance of hybridization rates. We characterized postmating pre- and postzygotic RI between two hybridizing oak species, Quercus robur and Quercus petraea, using a large set of controlled crosses between different genotypes. Various traits potentially associated with reproductive barriers were quantified at several life history stages, from pollen-pistil interactions to seed set and progeny fitness-related traits. Results indicate strong intrinsic postmating prezygotic barriers, with significant barriers also at the postzygotic level, but relatively weaker extrinsic barriers on early hybrid fitness measures assessed in controlled conditions. Using general linear modelling of common garden data with clonal replicates, we showed that most traits exhibited important genotypic differences, as well as different levels of sensitivity to micro-environmental heterogeneity. These new findings suggest a large potential genetic diversity and plasticity of reproductive barriers and are confronted with hybridization evidence in these oak species.

Genetic correlations between adults and larvae in a marine fish: potential effects of fishery selection on population replenishment

Correlated genetic responses have been hypothesized as important components of fishery-induced evolution, although predictive data from wild populations have been difficult to obtain. Here, we demonstrate substantial genetic correlations between a trait often subjected to fishery selection (adult body length) and traits that affect survival of larvae (length and swimming performance) in a wild population of a marine fish (bicolor damselfish, Stegastes partitus). Through both genetic covariance and size-dependent maternal effects, selection on adult size may cause a considerable, correlated response in larval traits. To quantify how variation in larval traits may affect survival, we introduce a flexible method that uses information from selection measurements to account for frequency dependence and estimate the relationship between phenotype and relative survival across a broad range of phenotypic values. Using this method, we synthesize studies of selective mortality on larval size for eight species of fish and show that variation in larval size may result in considerable variation in larval survival. We predict that observed rates of fishery selection on adult marine fishes may substantially reduce larval size and survival. The evolution of smaller larvae in response to fishery selection may therefore have substantial consequences for the viability of fished populations.

Individual-based analysis opens new insights into understanding population structure and animal behaviour

Studying the movement of individuals in the wild has always been a challenge in ecology. However, estimating such movement is essential in life sciences as it is the base-line for evaluating connectivity, a major component in developing management and conservation plans. Furthermore, movement, or migration, is an essential parameter in population genetics, as it directly affects genetic differentiation. The development of highly variable markers has allowed genetic discrimination between individuals within populations and at larger scales, and the availability of high-throughput technologies means that many samples and hence many individuals can be screened. These advances mean that we can now use genetic identification for tracking individuals, and hence follow both survival and reproductive output through the life cycle. The paper by Morrissey & Ferguson (2011, this issue) is a demonstration of this new capability, as authors were able to infer the movement of salmonid fish initially captured as juveniles, and later as reproductively mature adults.

Grandfathering in a new era of parentage analysis

The advent of DNA fingerprinting and microsatellite techniques has revolutionized the way in which we investigate genetic pedigrees in the wild (Pemberton 2008). With large and often incomplete data sets consisting of hundreds to thousands of individuals over multiple generations becoming commonplace, new methods in parentage analysis are being developed to rise to the next generation of questions and challenges. In this issue, Christie et al. (2011) provide a simple yet elegant solution to the problem of identifying missing parents and assessing hybrid fitness in a mixed population of wild and hatchery steelhead trout (Oncorhynchus mykiss) where not all individuals can be sampled effectively. They develop a new method of grandparent analysis where parental genotypes can be reconstructed using data from candidate grandparent crosses and F2 offspring genotypes, allowing for new explorations of hybridization, migration and gene flow in wild populations.

Genotyping errors in a calibrated DNA register: implications for identification of individuals

BACKGROUND

The use of DNA methods for the identification and management of natural resources is gaining importance. In the future, it is likely that DNA registers will play an increasing role in this development. Microsatellite markers have been the primary tool in ecological, medical and forensic genetics for the past two decades. However, these markers are characterized by genotyping errors, and display challenges with calibration between laboratories and genotyping platforms. The Norwegian minke whale DNA register (NMDR) contains individual genetic profiles at ten microsatellite loci for 6737 individuals captured in the period 1997-2008. These analyses have been conducted in four separate laboratories for nearly a decade, and offer a unique opportunity to examine genotyping errors and their consequences in an individual based DNA register. We re-genotyped 240 samples, and, for the first time, applied a mixed regression model to look at potentially confounding effects on genotyping errors.

RESULTS

The average genotyping error rate for the whole dataset was 0.013 per locus and 0.008 per allele. Errors were, however, not evenly distributed. A decreasing trend across time was apparent, along with a strong within-sample correlation, suggesting that error rates heavily depend on sample quality. In addition, some loci were more error prone than others. False allele size constituted 18 of 31 observed errors, and the remaining errors were ten false homozygotes (i.e., the true genotype was a heterozygote) and three false heterozygotes (i.e., the true genotype was a homozygote).

CONCLUSIONS

To our knowledge, this study represents the first investigation of genotyping error rates in a wildlife DNA register, and the first application of mixed models to examine multiple effects of different factors influencing the genotyping quality. It was demonstrated that DNA registers accumulating data over time have the ability to maintain calibration and genotyping consistency, despite analyses being conducted on different genotyping platforms and in different laboratories. Although errors were detected, it is demonstrated that if the re-genotyping of individual samples is possible, these will have a minimal effect on the database's primary purpose, i.e., to perform individual identification.

Larval connectivity in an effective network of marine protected areas

Acceptance of marine protected areas (MPAs) as fishery and conservation tools has been hampered by lack of direct evidence that MPAs successfully seed unprotected areas with larvae of targeted species. For the first time, we present direct evidence of large-scale population connectivity within an existing and effective network of MPAs. A new parentage analysis identified four parent-offspring pairs from a large, exploited population of the coral-reef fish Zebrasoma flavescens in Hawai'i, revealing larval dispersal distances ranging from 15 to 184 km. In two cases, successful dispersal was from an MPA to unprotected sites. Given high adult abundances, the documentation of any parent-offspring pairs demonstrates that ecologically-relevant larval connectivity between reefs is substantial. All offspring settled at sites to the north of where they were spawned. Satellite altimetry and oceanographic models from relevant time periods indicated a cyclonic eddy that created prevailing northward currents between sites where parents and offspring were found. These findings empirically demonstrate the effectiveness of MPAs as useful conservation and management tools and further highlight the importance of coupling oceanographic, genetic, and ecological data to predict, validate and quantify larval connectivity among marine populations.

Reproductive patterns shape introgression dynamics and species succession within the European white oak species complex

The reproductive system of hybrids is an important factor shaping introgression dynamics within species complexes. We combined paternity and parentage analyses with previous species characterization by genetic assignment, to directly identify reproductive events that occurred within a stand comprising four European white oak species. Comparing species status of parent pairs provided a precise quantification of hybridization rate, backcrosses, and intraspecific matings in two life stages. The detailed mating system analysis revealed new findings on the dynamics of interspecific gene flow. First, hybrids acted successfully as both male and female during reproduction. They produced acorns and seedlings that were as viable as those sired by purebreds. Second, species maintenance could be due to a relatively low level of interspecific mating contrasting with a large proportion of intraspecific crosses and backcrosses. Despite a high proportion of hybrids and extensive interspecific gene flow, partial species integrity is maintained by genetically controlled pollen discrimination, ensuring preferential matings within purebreds and high parental species fidelity in hybrid reproduction, which impedes complete collapse into a continuous hybrid swarm. Finally, we showed that pollen from the different species had unequal contributions to reproduction suggesting that introgression processes could ultimately lead to extirpation or expansion of some species.