Sibship Reconstruction Research Articles

Evaluating factors that affect full- and half-sibling inferences via genetic pedigree reconstruction without parental genotypes

Close-kin mark-recapture (CKMR) is a challenging but exciting new approach to study dispersal because sampled and genotyped individuals can be used to “tag” full- and half-sibling family members without using parental genotypes via sibship reconstruction. CKMR increases sampling efficiency and, as a result, has enabled abundance estimation of migratory species and improved understanding of dispersal for species that are difficult to sample using traditional methods. Accordingly, there is interest in using CKMR to study dispersal ecology for the invasive sea lamprey in the Great Lakes, yet much is unknown about this new approach. We investigated the performance of a Rapture panel for sea lamprey reconstruction pedigrees without parental genotypes using two programs, Colony and Sequoia. Initially, datasets were created in the simulation module of Colony, where the number of parents (250, 500, 1000), number of offspring (250 or 500), and the number of loci (400, 600, 800) varied totaling 50 datasets for each of the 18 parameter combinations. Colony and Sequoia were then used to reconstruct the pedigrees without parental genotypes. Performance metrics were compared across parameter space and between sibship reconstruction programs. Colony and Sequoia inferred full-sibling and unrelated individuals with low assignment error. Sequoia was much faster at reconstructing pedigrees (<5 min compared to ∼ 1 week); however, the program nearly always (>0.99) misassigned known half-siblings as unrelated, which is an issue because sea lamprey likely produce many half-siblings. Accordingly, Colony should be used to reconstruct sea lamprey pedigrees when only offspring genotypes are provided.

Direct and Molecular Observation of Movement and Reproduction by Candy Darter, Etheostoma osburni, an Endangered Benthic Stream Fish in Virginia, USA

Direct and indirect measures of individual movement provide valuable knowledge regarding a species’ resiliency to environmental change. Information on patterns of movement can inform species management and conservation but is lacking for many imperiled fishes. The Candy Darter, Etheostoma osburni, is an endangered stream fish with a dramatically reduced distribution in Virginia in the eastern United States, now known from only four isolated populations. We used visual implant elastomer tags and microsatellite DNA markers to directly describe movement patterns in two populations. Parentage analysis based on parent-offspring pairs was used to infer movement patterns of young-of-year and age-1 individuals, as well as the reproductive contribution of certain adults. Direct measurements of movement distances were generally similar between methods, but microsatellite markers revealed greater distances moved, commensurate with greater spatial frames sampled. Parent-offspring pairs were found throughout the species’ 18.8-km distribution in Stony Creek, while most parent-offspring pairs were in 2 km of the 4.25-km distribution in Laurel Creek. Sibship reconstruction allowed us to characterize the mating system and number of spawning years for adults. Our results provide the first measures of movement patterns of Candy Darter as well as the spatial distribution of parent-offspring pairs, which may be useful for selecting collection sites in source populations to be used for translocation or reintroductions. Our results highlight the importance of documenting species movement patterns and spatial distributions of related individuals as steps toward understanding population dynamics and informing translocation strategies. We also demonstrate that the reproductive longevity of this species is greater than previously described, which may be the case for other small stream fishes.

Long-term monitoring of a brown trout (Salmo trutta) population reveals kin-associated migration patterns and contributions by resident trout to the anadromous run

BackgroundIn species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006–2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts.ResultsCensus counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000–2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents.ConclusionsThe results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.

Molecular approaches reveal weak sibship aggregation and a high dispersal propensity in a non-native fish parasite.

Inferring parameters related to the aggregation pattern of parasites and to their dispersal propensity are important for predicting their ecological consequences and evolutionary potential. Nonetheless, it is notoriously difficult to infer these parameters from wildlife parasites given the difficulty in tracking these organisms. Molecular‐based inferences constitute a promising approach that has yet rarely been applied in the wild. Here, we combined several population genetic analyses including sibship reconstruction to document the genetic structure, patterns of sibship aggregation, and the dispersal dynamics of a non‐native parasite of fish, the freshwater copepod ectoparasite Tracheliastes polycolpus. We collected parasites according to a hierarchical sampling design, with the sampling of all parasites from all host individuals captured in eight sites spread along an upstream–downstream river gradient. Individual multilocus genotypes were obtained from 14 microsatellite markers, and used to assign parasites to full‐sib families and to investigate the genetic structure of T. polycolpus among both hosts and sampling sites. The distribution of full‐sibs obtained among the sampling sites was used to estimate individual dispersal distances within families. Our results showed that T. polycolpus sibs tend to be aggregated within sites but not within host individuals. We detected important upstream‐to‐downstream dispersal events of T. polycolpus between sites (modal distance: 25.4 km; 95% CI [22.9, 27.7]), becoming scarcer as the geographic distance from their family core location increases. Such a dispersal pattern likely contributes to the strong isolation‐by‐distance observed at the river scale. We also detected some downstream‐to‐upstream dispersal events (modal distance: 2.6 km; 95% CI [2.2–23.3]) that likely result from movements of infected hosts. Within each site, the dispersal of free‐living infective larvae among hosts likely contributes to increasing genetic diversity on hosts, possibly fostering the evolutionary potential of T. polycolpus.

Sibship reconstruction with SNPs illuminates the scope of a cryptic invasion of Asian Swamp Eels (Monopterus albus) in Georgia, USA

Cryptic invasive species are particularly problematic to study, manage, and control because of the difficulty detecting these species within their invaded habitats. Such is the case of the Asian Swamp Eel (Monopterus albus; ASE) where it is established in vegetated marshes along the Chattahoochee River, Georgia. Adult eels have been nearly impossible to detect or quantify with traditional sampling, although leaf-litter trapping of juvenile ASEs has been somewhat successful. In this study, we leveraged a collection of juveniles from the 2015 cohort and used single-nucleotide polymorphisms to reconstruct sibship among these juveniles in COLONY. Sibship reconstruction allowed us to learn about adult breeding behaviors and provided the first quantified estimates of breeder abundance. Pedigree reconstruction revealed that adults of both sexes were polygamous and likely traveled up to 0.5 km among marsh habitats during a single breeding season. Estimates of the number of breeding adults contributing to offspring (Ns) and the effective number of breeders (Nb) indicated an approximate minimum bound of 100 breeding adults in the marshes in 2015. Our study updated the invasion status of a cryptic population formerly riddled with uncertainty, highlighting that low captures of adult eels in the study area have been the result of low detectability, not low abundance. Given that low detectability would likely hinder removal efforts, our results suggest that future efforts could focus on suppression of ASE abundance when they are most vulnerable to capture and containing the spatial extent of the invasion.

Patterns of genetic variation in leading-edge populations of Quercus robur: genetic patchiness due to family clusters

The genetic structure of populations at the edge of species distribution is important for species adaptation to environmental changes. Small populations may experience non-random mating and differentiation due to genetic drift but larger populations, too, may have low effective size, e.g., due to the within-population structure. We studied spatial population structure of pedunculate oak, Quercus robur, at the northern edge of the species’ global distribution, where oak populations are experiencing rapid climatic and anthropogenic changes. Using 12 microsatellite markers, we analyzed genetic differentiation of seven small to medium size populations (census sizes 57–305 reproducing trees) and four populations for within-population genetic structures. Genetic differentiation among seven populations was low (Fst = 0.07). We found a strong spatial genetic structure in each of the four populations. Spatial autocorrelation was significant in all populations and its intensity (Sp) was higher than those reported in more southern oak populations. Significant genetic patchiness was revealed by Bayesian structuring and a high amount of spatially aggregated full and half sibs was detected by sibship reconstruction. Meta-analysis of isoenzyme and SSR data extracted from the (GD)2 database suggested northwards decreasing trend in the expected heterozygosity and an effective number of alleles, thus supporting the central-marginal hypothesis in oak populations. We suggest that the fragmented distribution and location of Finnish pedunculate oak populations at the species’ northern margin facilitate the formation of within-population genetic structures. Information on the existence of spatial genetic structures can help conservation managers to design gene conservation activities and to avoid too strong family structures in the sampling of seeds and cuttings for afforestation and tree improvement purposes.

Multiple Paternity in a Reintroduced Rookery of Kemp's Ridley Sea Turtles on South Padre Island, Texas

Multiple mating is common in Sea Turtles, and previous studies have suggested that levels of multiple paternity are higher in larger rookeries compared with smaller rookeries. As a result, smaller rookeries may be more vulnerable to the loss of genetic variation than would larger rookeries. The critically endangered Kemp's Ridley Sea Turtle (Lepidochelys kempii) has a single high-density rookery (∼5,000 females) in Rancho Nuevo, Mexico, where high levels of multiple paternity were reported (81% of nests). A secondary nesting colony was re-established on Padre Island National Seashore, Texas, USA, in the early 1980s and, by 2010, 140 nests were found along the entire Texas coast. The relatively small size of the Texas rookery led us to predict low levels of multiple paternity compared with Rancho Nuevo, and we tested our hypothesis by genotyping 158 hatchling tissue samples from 25 nests on South Padre Island (SPI) at 14 microsatellite loci. Full sibship reconstruction indicated that multiple paternity occurred in 47.6% of nests, a value that is significantly lower than the 81% of nests in Rancho Nuevo. Genetic diversity on SPI was high (HO = 0.80) and similar to Rancho Nuevo, although there was a genetic signal of a population bottleneck at SPI. Multiple paternity, small geographic range, and extensive movements by individuals probably act to maintain high genetic variation in this species, despite severe population declines.

Genetic evidence supports polygamous mating system in a wild population of Prochilodus lineatus (Characiformes: Prochilodontidae), a Neotropical shoal spawner fish

ABSTRACT Behavioral observations made on fish have revealed remarkably diverse reproductive strategies, including polygamy by both sexes. Still, to date, most Neotropical species remain unstudied as to whether the observed reproductive behavior in natural populations correlates with their genetic mating systems. Here, we investigated the genetic mating system of a wild population of Prochilodus lineatus settled in the Middle Uruguay River basin. By using sibship reconstruction and parental inference methods based on microsatellites’ genotypes, we inferred 45 females and 47 males as potential parents of the 87 larvae analyzed. We found evidence supporting polygamous mating in both sexes: while a high percentage of males (44.7%) fertilized the eggs of one female, 55.3% of the inferred males fertilized eggs of up to four females. Likewise, while 44.5% of the inferred females had their eggs fertilized by one only male, 55.5% of females were fertilized by multiple males. The estimated proxy of the effective population size (Nb) was 126, exhibiting moderate to high levels of genetic diversity. The genetic evidence contributed in this study complements earlier behavioral observations of formation of spawning nuclei of aggregating breeders, which may be promoting a polygamous mating strategy in this long-distance migratory fish.

Reduced genetic diversity and low effective size in peripheral northern European catfish Silurus glanis populations.

Using 10 polymorphic microsatellites and 1251 individual samples (some dating back to the early 1980s), genetic structure and effective population size in all native and introduced Swedish populations of the European wels catfish or Silurus glanis were studied. Levels of genetic variability and phylogeographic relationships were compared with data from a previous study of populations in other parts of Europe. The genetically distinct Swedish populations displayed comparably low levels of genetic variability and according to one-sample estimates based on linkage disequilibrium and sib ship-reconstruction, current local effective population sizes were lower than minimum levels recommended for short-term genetic conservation. In line with a previous suggestion of postglacial colonisation from a single refugium, all Swedish populations were assembled on a common branch in a star-shaped dendrogram together with other European populations. Two distinct subpopulations were detected in upper and lower habitats of River Emån, indicating that even minor dispersal barriers may restrict gene flow for wels in running waters. Genetic assignment of specimens encountered in the brackish Baltic Sea and in lakes where the species does not occur naturally indicated presence of long-distance sea dispersal and confirmed unauthorised translocations, respectively.

Evaluating the Effects of Barriers on Slimy Sculpin Movement and Population Connectivity Using Novel Sibship‐based and Traditional Genetic Metrics

AbstractPopulation genetics‐based approaches can provide robust and cost‐effective ways to assess the effects of potential barriers, including dams and road‐stream crossings, on the passage and population connectivity of aquatic organisms. Determining the best way to apply and modify genetic tools for different species and situations is essential for making these genetics‐based approaches broadly applicable to fisheries and aquatic habitat management. Here, we used multiple genetic approaches to assess the movement and population structure of Slimy Sculpin Cottus cognatus at two road‐stream crossings in Michigan and one dam in Massachusetts, USA. We captured and genotyped individual sculpin and assessed movement and population connectivity by using (1) a sibship‐based approach, where the presence and proportional distribution of siblings on either side of a barrier indicates population connectivity and the possible direction of movement (i.e., presumed movement from higher to lower proportions), and (2) two Bayesian genetic assignment approaches (STRUCTURE and BayesAss) to identify migrants across potential barriers based on individual population assignment probabilities. We also used traditional genetic metrics to assess within‐population genetic variation and among‐population genetic divergence. At all three locations, we found evidence for sculpin movement across the potential barrier based on sibship reconstruction, but small family sizes limited the ability of this approach to provide robust estimates of the rate and direction of movement. At two sites, a lack of genetic differentiation between above‐ and below‐barrier populations limited the effectiveness of the genetic assignment methods for identifying possible migrants. At the third site, reduced upstream allelic diversity and effective number of breeders resulted in high genetic differentiation (FST) between above‐ and below‐barrier populations, and both sibship and genetic assignment methods provided strong evidence of limited connectivity and bias against upstream movement. Overall, combining approaches and metrics may help overcome the limitations of any one method and maximize the value of datasets for genetics‐based monitoring and assessment.

Estimating helminth burdens using sibship reconstruction

BackgroundSibship reconstruction is a form of parentage analysis that can be used to identify the number of helminth parental genotypes infecting individual hosts using genetic data on only their offspring. This has the potential to be used for estimating individual worm burdens when adult parasites are otherwise inaccessible, the case for many of the most globally important human helminthiases and neglected tropical diseases. Yet methods of inferring worm burdens from sibship reconstruction data on numbers of unique parental genotypes are lacking, limiting the method’s scope of application.ResultsWe developed a novel statistical method for estimating female worm burdens from data on the number of unique female parental genotypes derived from sibship reconstruction. We illustrate the approach using genotypic data on Schistosoma mansoni (miracidial) offspring collected from schoolchildren in Tanzania. We show how the bias and precision of worm burden estimates critically depends on the number of sampled offspring and we discuss strategies for obtaining sufficient sample sizes and for incorporating judiciously formulated prior information to improve the accuracy of estimates.ConclusionsThis work provides a novel approach for estimating individual-level worm burdens using genetic data on helminth offspring. This represents a step towards a wider scope of application of parentage analysis techniques. We discuss how the method could be used to assist in the interpretation of monitoring and evaluation data collected during mass drug administration programmes targeting human helminthiases and to help resolve outstanding questions on key population biological processes that govern the transmission dynamics of these neglected tropical diseases.

Assessing multiple mating and reproductive skew in three species of clinid fishes (Blenniiformes: Clinidae: Clinini), in reference to multiple mating in viviparous teleosts

This study investigated multiple mating in three species of intertidal klipfishes (family Clinidae): super klipfish Clinus superciliosus, bluntnose klipfish Clinus cottoides, and nosestripe klipfish Muraenoclinus dorsalis. These species display the rare reproductive mode of female vivipary with superfetation, a phenomenon where offspring at various stages of development are found within the female. Three or four microsatellite loci were used to genotype 25–30 adults of each species, as well as embryos of 131 C. superciliosus from six broods, 103 C. cottoides from six broods, and 63 M. dorsalis from five broods. The presence of multiple mating by females was assessed by maximum-likelihood sibship reconstruction implemented in the program COLONY, and the non-random distribution of reproductive success among individuals (reproductive skew) within broods was tested using the binomial skew index. Multiple mating by females was pervasive and observed in 83%, 100% and 80% of the broods of C. superciliosus, C. cottoides and M. dorsalis, respectively. The mean number of sires per brood was 4.3, 3.0 and 3.2, and, correspondingly, 5/5, 5/6 and 1/4 of multiply-sired broods showed significant reproductive skew in C. superciliosus, C. cottoides and M. dorsalis, respectively. The presence of pronounced reproductive skew may indicate post-copulatory processes taking place that bias paternity. We compared our results on multiple mating within the klipfish family, and with four other fish families that have vivipary with superfetation, and found the klipfish patterns were among those of live-bearing vertebrate groups with the highest average numbers of sires per brood.

Effect of Hidden Relatedness on Single-Step Genetic Evaluation in an Advanced Open-Pollinated Breeding Program.

Open-pollinated (OP) mating is frequently used in forest tree breeding due to the relative temporal and financial efficiency of the approach. The trade-off is the lower precision of the estimated genetic parameters. Pedigree/sib-ship reconstruction has been proven as a tool to correct and complete pedigree information and to improve the precision of genetic parameter estimates. Our study analyzed an advanced generation Eucalyptus population from an OP breeding program using single-step genetic evaluation. The relationship matrix inferred from sib-ship reconstruction was used to rescale the marker-based relationship matrix (G matrix). This was compared with a second scenario that used rescaling based on the documented pedigree. The proposed single-step model performed better with respect to both model fit and the theoretical accuracy of breeding values. We found that the prediction accuracy was superior when using the pedigree information only when compared with using a combination of the pedigree and genomic information. This pattern appeared to be mainly a result of accumulated unrecognized relatedness over several breeding cycles, resulting in breeding values being shrunk toward the population mean. Using biased, pedigree-based breeding values as the base with which to correlate predicted GEBVs, resulted in the underestimation of prediction accuracies. Using breeding values estimated on the basis of sib-ship reconstruction resulted in increased prediction accuracies of the genotyped individuals. Therefore, selection of the correct base for estimation of prediction accuracy is critical. The beneficial impact of sib-ship reconstruction using G matrix rescaling was profound, especially in traits with inbreeding depression, such as stem diameter.

Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering.

Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems.

Estimating the effective number of breeders from single parr samples for conservation monitoring of wild populations of Atlantic salmon Salmo salar.

This study assesses whether the effective number of breeders (Nb ) can be estimated using a time and cost-effective protocol using genetic sibship reconstruction from a single sample of young-of-the-year (YOY) for the purposes of Atlantic salmon Salmo salar population monitoring. Nb was estimated for 10 consecutive reproductive seasons for S. salar in the River Nivelle, a small population located at the rear-edge of the species distribution area in France, chronically under its conservation limit and subjected to anthropogenic and environmental changes. Subsampling of real and simulated data showed that accurate estimates of Nb can be obtained from YOY genotypes, collected at moderate random sampling intensity, achievable using routine juvenile electrofishing protocols. Spatial bias and time elapsed since spawning were found to affect estimates, which must be accounted for in sampling designs. Nb estimated in autumn for S. salar in the River Nivelle was low and variable across years from 23 (95% C.I. 14-41) to 75 (53-101) and was not statistically correlated with the estimated number of returning adults, but it was positively correlated with the estimated number of YOY at age 9months. Nb was found to be lower for intermediate levels of redd aggregation, suggesting that the strength of the competition between males to access females affects reproductive success variance depending on redd spatial configuration. Thus, environmental factors such as habitat availability and quality for spawning and YOY development predominate over demographic ones (number of returning adults) in driving long-term population viability for S. salar in the River Nivelle. This study showcases Nb as an integrated parameter, encompassing demographic and ecological information about a reproductive event, relevant to the assessment of both short-term effects of management practices and long-term population conservation status.

Exploration of genetic architecture through sib-ship reconstruction in advanced breeding population of Eucalyptus nitens.

Accurate inference of relatedness between individuals in breeding population contributes to the precision of genetic parameter estimates, effectiveness of inbreeding management and the amount of genetic progress delivered from breeding programs. Pedigree reconstruction has been proven to be an efficient tool to correct pedigree errors and recover hidden relatedness in open pollinated progeny tests but the method can be limited by the lack of parental genotypes and the high proportion of alien pollen from outside the breeding population. Our study investigates the efficiency of sib-ship reconstruction in an advanced breeding population of Eucalyptus nitens with only partially tracked pedigree. The sib-ship reconstruction allowed the identification of selfs (4% of the sample) and the exploration of their potential effect on inbreeding depression in the traits studied. We detected signs of inbreeding depression in diameter at breast height and growth strain while no indications were observed in wood density, wood stiffness and tangential air-dry shrinkage. After the application of a corrected sib-ship relationship matrix, additive genetic variance and heritability were observed to increase where signs of inbreeding depression were initially detected. Conversely, the same genetic parameters for traits that appeared to be free of inbreeding depression decreased in size. It therefore appeared that greater genetic variance may be due, at least in part, to contributions from inbreeding in these studied populations rather than a removal of inbreeding as is traditionally thought.

Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead.

Effective population size (N e) is among the most important metrics in evolutionary biology. In natural populations, it is often difficult to collect adequate demographic data to calculate N e directly. Consequently, genetic methods to estimate N e have been developed. Two N e estimators based on sibship reconstruction using multilocus genotype data have been developed in recent years: sibship assignment and parentage analysis without parents. In this study, we evaluated the accuracy of sibship reconstruction using a large empirical dataset from five hatchery steelhead populations with known pedigrees and using 95 single nucleotide polymorphism (SNP) markers. We challenged the software COLONY with 2,599,961 known relationships and demonstrated that reconstruction of full‐sib and unrelated pairs was greater than 95% and 99% accurate, respectively. However, reconstruction of half‐sib pairs was poor (<5% accurate). Despite poor half‐sib reconstruction, both estimators provided accurate estimates of the effective number of breeders (N b) when sample sizes were near or greater than the true N b and when assuming a monogamous mating system. We further demonstrated that both methods provide roughly equivalent estimates of N b. Our results indicate that sibship reconstruction and current SNP panels provide promise for estimating N b in steelhead populations in the region.

The ART of mating: alternative reproductive tactics and mating success in a nest-guarding fish.

Behavioural observations in the field of male Mediterranean damselfish Chromis chromis were combined with molecular analyses, using bi-parentally and maternally inherited markers, to investigate reproductive success patterns of alternative reproductive tactics (ARTs) in terms of number of eggs sired and number of females contributing to each nest. Cuckoldry was observed in every nest sampled, with at least two and up to seven sneaker males per nest. The nesting male, however, always significantly fertilized the greater number of eggs (on average 49%) in each clutch, whereas each sneaker fertilized around 7% of the clutch. The average number of females whose eggs were fertilized by nesting males was 6·76 (range 2-13), while each sneaker on average fertilized the eggs of 1·74 (range 1-8) females. Using this sibship reconstruction, some of the factors involved in the regulation of the dynamic equilibrium of reproductive success were investigated between the two ARTs shown by C. chromis males. Results show that the sneakers' reproductive success was positively linked to egg clutch size; the density of individuals in the nesting area negatively affected the size of egg clutches; the rate of defence behaviours performed by nesting males negatively influenced the number of females contributing to each nest.

Managed European-Derived Honey Bee, Apis mellifera sspp, Colonies Reduce African-Matriline Honey Bee, A. m. scutellata, Drones at Regional Mating Congregations.

African honey bees (Apis mellifera scutellata) dramatically changed the South American beekeeping industry as they rapidly spread through the Americas following their introduction into Brazil. In the present study, we aimed to determine if the management of European-derived honey bees (A. mellifera sspp.) could reduce the relative abundance of African-matriline drones at regional mating sites known as drone congregation areas (DCAs). We collected 2,400 drones at six DCAs either 0.25 km or >2.8 km from managed European-derived honey bee apiaries. The maternal ancestry of each drone was determined by Bgl II enzyme digestion of an amplified portion of the mitochondrial Cytochrome b gene. Furthermore, sibship reconstruction via nuclear microsatellites was conducted for a subset of 1,200 drones to estimate the number of colonies contributing drones to each DCA. Results indicate that DCAs distant to managed European apiaries (>2.8 km) had significantly more African−matriline drones (34.33% of the collected drones had African mitochondrial DNA) than did DCAs close (0.25 km) to managed European apiaries (1.83% of the collected drones had African mitochondrial DNA). Furthermore, nuclear sibship reconstruction demonstrated that the reduction in the proportion of African matriline drones at DCAs near apiaries was not simply an increase in the number of European matriline drones at the DCAs but also the result of fewer African matriline colonies contributing drones to the DCAs. Our data demonstrate that the management of European honey bee colonies can dramatically influence the proportion of drones with African matrilines at nearby drone congregation areas, and would likely decreasing the probability that virgin European queens will mate with African drones at those drone congregation areas.

Strategies for determining kinship in wild populations using genetic data.

Knowledge of kin relationships between members of wild animal populations has broad application in ecology and evolution research by allowing the investigation of dispersal dynamics, mating systems, inbreeding avoidance, kin recognition, and kin selection as well as aiding the management of endangered populations. However, the assessment of kinship among members of wild animal populations is difficult in the absence of detailed multigenerational pedigrees. Here, we first review the distinction between genetic relatedness and kinship derived from pedigrees and how this makes the identification of kin using genetic data inherently challenging. We then describe useful approaches to kinship classification, such as parentage analysis and sibship reconstruction, and explain how the combined use of marker systems with biparental and uniparental inheritance, demographic information, likelihood analyses, relatedness coefficients, and estimation of misclassification rates can yield reliable classifications of kinship in groups with complex kin structures. We outline alternative approaches for cases in which explicit knowledge of dyadic kinship is not necessary, but indirect inferences about kinship on a group‐ or population‐wide scale suffice, such as whether more highly related dyads are in closer spatial proximity. Although analysis of highly variable microsatellite loci is still the dominant approach for studies on wild populations, we describe how the long‐awaited use of large‐scale single‐nucleotide polymorphism and sequencing data derived from noninvasive low‐quality samples may eventually lead to highly accurate assessments of varying degrees of kinship in wild populations.