Population Genetic Tools Research Articles

Testing theoretical metapopulation conditions with genotypic data from Boreal Chorus Frogs (Pseudacris maculata)

The metapopulation concept has far-reaching implications in ecology and conservation biology. Hanski’s criteria operationally define metapopulations, yet testing them is hindered by logistical and financial constraints inherent to the collection of long-term demographic data. Hence, ecologists and conservationists often assume metapopulation existence for dispersal-limited species that occupy patchy habitats. To advance understanding of metapopulation theory and improve conservation of metapopulations, we used population and landscape genetic tools to develop a methodological framework for evaluating Hanski’s criteria. We used genotypic data (11 microsatellite loci) from a purported metapopulation of Boreal Chorus Frogs (Pseudacris maculata (Agassiz, 1850)) in Colorado, U.S.A., to test Hanski’s four criteria. We found support for each criterion: (1) significant genetic differentiation between wetlands, suggesting distinct breeding populations; (2) wetlands had small effective population sizes and recent bottlenecks, suggesting populations do not experience long-term persistence; (3) population graphs provided evidence of gene flow between patches, indicating potential for recolonization; and (4) multiscale bottleneck analyses suggest asynchrony, indicating that simultaneous extinction of all populations was unlikely. Our methodological framework provides a logistically and financially feasible alternative to long-term demographic data for identifying amphibian metapopulations.

Microsatellite loci development and population genetics in Neotropical fish Curimata mivartii (Characiformes: Curimatidae).

The Curimatidae family plays an ecological role in the recycling and distribution of nutrients and constitutes a major food source for several commercially important fishes. Curimata mivartii, a member of this family, is considered a short-distance migratory species (≤100 km), categorized by the International Union for Conservation of Nature as a near threatened species, based on its declining population densities and habitat disturbance and fragmentation. Since population genetics and species-specific molecular tools remain unknown for all members of the Curimatidae family, this study developed a set of microsatellite loci and studied the population genetics of C. mivartii in the lower section of the Colombian Magdalena-Cauca basin. The results showed high levels of genetic diversity and evidence of gene flow even between locations separated over 350 km. This information provides a baseline for designing conservation and management programs for C.mivartii and constitutes the first study of population genetics in Curimatidae.

Phylogenetics of Mycoplasma hominis clinical strains associated with gynecological infections or infertility as disclosed by an expanded multilocus sequence typing scheme

To our knowledge, the phylodistribution of M. hominis clinical strains associated with various pathological conditions of the urogenital tract has not been explored hitherto. Here we analyzed the genetic diversity and phylogenetic relationships among 59 M. hominis Tunisian clinical isolates, categorized as gynecological infections- or infertility-associated pathotypes. For this purpose, we developed an expanded multilocus sequence typing (eMLST) scheme, combining the previously reported multilocus sequence typing (MLST) loci (gyrB, tuf, ftsY, uvrA, gap) with a new selected set of putative virulence genes (p120’, vaa, lmp1, lmp3, p60), referred herein to as multi-virulence-locus sequence typing (MVLST) loci. In doing so, M. hominis population was segregated into two distinct genetic lineages, which were differentially associated with each pathotype. Such a clear dichotomy was supported by several phylogenetic and population genetic analysis tools. Recombination was found to take place, but not sufficient enough to break down the overall clonal population structure of M. hominis, most likely as a result of purifying selection, which accommodated the most fit clones. In sum, and owing to the eMLST scheme described herein, we provide insightful data on the phylogenetics of M. hominis, arguing for the existence of genetically differentiable urogenital pathotypes.

Complex Haplotypes of GSTM1 Gene Deletions Harbor Signatures of a Selective Sweep in East Asian Populations.

The deletion of the metabolizing Glutathione S-transferase Mu 1 (GSTM1) gene has been associated with multiple cancers, metabolic and autoimmune disorders, as well as drug response. It is unusually common, with allele frequency reaching up to 75% in some human populations. Such high allele frequency of a derived allele with apparent impact on an otherwise conserved gene is a rare phenomenon. To investigate the evolutionary history of this locus, we analyzed 310 genomes using population genetics tools. Our analysis revealed a surprising lack of linkage disequilibrium between the deletion and the flanking single nucleotide variants in this locus. Tests that measure extended homozygosity and rapid change in allele frequency revealed signatures of an incomplete sweep in the locus. Using empirical approaches, we identified the Tanuki haplogroup, which carries the GSTM1 deletion and is found in approximately 70% of East Asian chromosomes. This haplogroup has rapidly increased in frequency in East Asian populations, contributing to a high population differentiation among continental human groups. We showed that extended homozygosity and population differentiation for this haplogroup is incompatible with simulated neutral expectations in East Asian populations. In parallel, we found that the Tanuki haplogroup is significantly associated with the expression levels of other GSTM genes. Collectively, our results suggest that standing variation in this locus has likely undergone an incomplete sweep in East Asia with regulatory impact on multiple GSTM genes. Our study provides the necessary framework for further studies to elucidate the evolutionary reasons that maintain disease-susceptibility variants in the GSTM1 locus.

Amplificación cruzada de microsatélites en dos especies de haemúlidos (Haemulon aurolineatum y Haemulon steindachneri)

Genetic-population studies in marine fish have allowed to study patterns of dispersal and connectivity between habitats. Oneimportant tool in population genetics is the use of microsatellite molecular markers. Cross-amplification of microsatellite is amethod that consists in using primers designed for one species in a different one but phylogenetically related. Because of theimportance of genetic studies of populations in artisanal fisheries species, primers were evaluated and designed for the species Haemulon aurolineatum and Haemulon steindachneri. Samples were collected from the artisanal fisheries in Barú-Colombia. Amplification was standardized for 12 microsatellites which ten were polymorphic for H. aurolineatum and nine for H. steindachneri. It is considered that the primers implemented in this study are useful for future studies of gene flow in these species.

MLSTar: automatic multilocus sequence typing of bacterial genomes in R

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci which allows us to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has allowed us to apply and extend MLST schemes by automatic extraction of allele information from the genomes. The PubMLST database is the most comprehensive resource of described schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows us to (i) connect with the PubMLST database to select a target scheme, (ii) screen a desired set of genomes to assign alleles and sequence types, and (iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze more than 2,500 bacterial genomes from different species, showing great accuracy, and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.

The Rocky Mountains as a dispersal barrier between barn owl (Tyto alba) populations in North America

AbstractAimGeological barriers within a species range play a key role in shaping patterns of genetic variation by restricting gene flow. Mountain ranges are particularly imposing barriers responsible for creating genetic differentiation across multiple taxa, from small amphibians to large mammals and birds. Here, we examined the population structure of North American barn owls (Tyto alba) and investigated whether the Rocky Mountains influence gene flow and dispersal at the continental scale.LocationContinental North America.MethodsWe collected 292 museum samples covering the species range, genotyped them at 20 microsatellite markers and sequenced 410 bp of the mitochondrial gene ND6. Population and landscape genetics tools were used to study range‐wide patterns of structure and identify gene flow barriers. Ring recapture data were also analysed to investigate individual movement patterns and frequency of exchanges between both sides of the Rocky Mountains.ResultsWe found faint overall genetic structure, which is consistent with barn owl's high mobility across its continuous range. Nonetheless, we identified two distinct genetic groups on the western and eastern regions of the Rocky Mountains with a likely contact point through the narrow southern pass between them and the Sierra Madre Occidental in Mexico. Accordingly, most recaptured barn owls remain on the same side of the mountains. The Rockies appear to significantly isolate the populations in the west, which, as a consequence, display lower genetic diversity than their counterparts to the east.Main conclusionsThe Rocky Mountains appear to constrain barn owl dispersal and gene flow. Our study supports the hypothesis that regional landscape barriers can shape gene flow and population structure even in highly mobile organisms.

Adding injury to infection: The relationship between injury status and genetic diversity of Theileria infecting plains zebra, Equus quagga

Asymptomatic tick-borne infections are a common feature in wild herbivores. In human-dominated habitats, snare injuries to wild herbivores are common and are likely to co-occur with enzootic infections. The influence of injury on pattern, course and outcome of enzootic infection in wild herbivores is unknown. We identified Theileria species infecting zebra and assessed the relationship between host injury-status and parasitaemia, parasite diversity and selection regimes. We also determined host leucocyte differential as this can reveal mechanisms by which injuries influence infections. Theileria infecting zebra was identified using PCR and sequencing of the V4 region of the 18 s rRNA gene and confirmed with phylogenetic analyses. The influence of injury status on parasite infection patterns, genetic diversity and selection were assessed using population genetic tools. Parasitaemia estimated from prevalence and leucocyte differential were determined from microscopic examination of Giemsa stained thin blood smears. Phylogenetic and sequence analyses revealed that the zebra population studied was infected with three Theileria equi haplotypes. Parasitaemia was lower among injured compared to non-injured animals and lower during dry than wet season. Mean (±SD) genetic diversity was 0.386 (±0.128) in injured and 0.513 (±0.144) in non-injured zebra (P = .549). Neutrality tests indicated that T. equi is under strong purifying selection in injured females (Li & Fu's D* = −2.037) and demographic expansion in all zebra during the wet season (Tajima D = −1.904). Injured zebras had a higher median per cent of neutrophils (64% vs 37%) a lower median per cent of basophils (0% vs 1%) and eosinophils (2% vs 4.5%) than non-injured animals, suggesting a heightened immune response and a shift from a Th2 to Th1 T-Cell response favoring the elimination of intracellular parasites in injured animals. This study demonstrates the utility of population genetics in revealing factors influencing parasite diversity and infection patterns.

High Mitochondrial Genome Diversity and Intricate Population Structure of Bursaphelenchus xylophilus in Kyushu, Japan.

Mitogenomic diversity and genetic population structure of the pinewood nematode (PWN) Bursaphelenchus xylophilus inhabiting Kyushu, Japan were analyzed. A method for performing long PCR using single nematodes and sequencing nematode mitochondrial genomes individually is presented here. About 8 kb (∼55%) of the complete mitochondrial genome was successfully obtained from 285 individuals collected from 12 populations. The 158 single nucleotide polymorphisms detected corresponded to 30 haplotypes, clearly classified into two clades. Haplotype diversity was 0.83, evidencing a remarkable high diversity within Kyushu. The high genetic differentiation among the 12 populations (0.331) might be due to past invasion and expansion routes of PWN in northeastern and southeastern Kyushu. The distinct genetic composition of populations within the northwestern, central western, and southwestern Kyushu seems to be mostly related to the extinction of pine forests and long-range migration of PWN due to human activity. Overall, direct long PCR and sequencing of single nematode individuals are effective methods for investigating mitochondrial polymorphisms, and these are effective tools for PWN population genetics and other intraspecific studies.

Harnessing Population Genetics for Pest Management: Theory and Application for Urban Rats (Abstract)

Effective management of rodent pests requires an ecological understanding of how they move through their environment, and how those movements influence the invasion, persistence, or reinvasion of problematic colonies. Traditional methodologies used to describe rodent movement patterns, such as mark-recapture, are hindered by their time-consuming nature and limited geographic scope. As such, our understanding of how rodents interact with urban environments remains limited. Population genetic principles and tools have the capacity to greatly increase our understanding of rodent population dynamics, ecological relationships, and movements across space but this field is often unapproachable to non-scientist pest management professionals. In this paper we aim to promote collaborative and integrative rodent pest management by introducing relevant population genetic principles, providing examples of their applications in studies of urban brown rats, and proposing future initiatives that link scientific, private, and government entities. Using a densely-sampled brown rat population in the city of Vancouver, BC we show how genetic relationships among individual brown rats can be leveraged to understand the geographic distribution of genetic clusters (i.e., colonies), natural barriers to migration, and the spatial scale of dispersal. We describe how these results can be exploited by PMPs to directly inform the creation of management units and decrease the likelihood of rapid post-treatment reinvasion. Further, we discuss the difficulties inherent in population genetic studies and the potential for high-quality model sites to develop generalizable strategies. Overall, we hope to expand the toolbox of pest management professionals, foster collaboration, and move towards more informed and sustainable management strategies.

How Do Young Bats Find Suitable Swarming and Hibernation Sites? Assessing the Plausibility of the Maternal Guidance Hypothesis Using Genetic Maternity Assignment for two European Bat Species

In many temperate zone bat species, large numbers of individuals aggregate in autumn at potential hibernacula such as caves, mines, and cellars, for a behaviour known as swarming. This autumn swarming probably serves two functions, the achievement of matings and the assessment of potential hibernation sites. Even though this remarkable behaviour has attracted a lot of research during the last decades, several central questions regarding the autumn swarming of temperate zone bats remain unanswered. One of them is how juvenile bats (defined here as young of the year) are able to find swarming sites, which are typically dozens of kilometres away from the maternity colonies where they had been born. In this study, we used a combination of field data and population genetic tools to assess whether the juveniles are likely to learn the location of swarming sites from their mothers. To obtain non-destructive wing-tissue samples for DNA-based maternity assignments, 170 Myotis daubentonii and 195 Myotis nattereri were captured during the swarming seasons in two subsequent years, at a large hibernaculum in Germany. Based on 14, respectively 13, highly polymorphic microsatellite loci, maternity assignment tests were conducted for all captured adult females and juveniles that had been born in the two respective years. For M. daubentonii we found four assigned mother-offspring pairs, whereas in M. nattereri, eight mother-offspring pairs could be assigned with high certainty. Moreover, among the latter species, in seven pairs the mothers and the assigned offspring were caught within ten minutes of one another on the same night. Using a simulation, we show that for M. nattereri, significantly more juveniles than expected are caught together with their mothers at the hibernacula. We discuss the implications of our findings with regard to understanding autumn swarming behaviour in temperate zone bats, as well as for the conservation of bats that depend on swarming sites for mating and hibernation.

Seasonal Food Scarcity Prompts Long-Distance Foraging by a Wild Social Bee.

Foraging is an essential process for mobile animals, and its optimization serves as a foundational theory in ecology and evolution; however, drivers of foraging are rarely investigated across landscapes and seasons. Using a common bumblebee species from the western United States (Bombus vosnesenskii), we ask whether seasonal decreases in food resources prompt changes in foraging behavior and space use. We employ a unique integration of population genetic tools and spatially explicit foraging models to estimate foraging distances and rates of patch visitation for wild bumblebee colonies across three study regions and two seasons. By mapping the locations of 669 wild-caught individual foragers, we find substantial variation in colony-level foraging distances, often exhibiting a 60-fold difference within a study region. Our analysis of visitation rates indicates that foragers display a preference for destination patches with high floral cover and forage significantly farther for these patches, but only in the summer, when landscape-level resources are low. Overall, these results indicate that an increasing proportion of long-distance foraging bouts take place in the summer. Because wild bees are pollinators, their foraging dynamics are of urgent concern, given the potential impacts of global change on their movement and services. The behavioral shift toward long-distance foraging with seasonal declines in food resources suggests a novel, phenologically directed approach to landscape-level pollinator conservation and greater consideration of late-season floral resources in pollinator habitat management.

Population genetics and distribution data reveal conservation concerns to the sky island endemic Pithecopus megacephalus (Anura, Phyllomedusidae)

Pithecopus megacephalus is a reticulated monkey–frog species endemic to the highlands of the Espinhaco Mountain Range in southeastern Brazil, an important centre of endemism in South America. This species has a discontinuous distribution and is considered “data-deficient” by the IUCN Red List, raising concerns about its conservation. Understanding the historical dynamics and connectivity of P. megacephalus populations can provide guidelines for preservation of this species in the wild. To investigate the population dynamics of P. megacephalus, we obtained multilocus DNA data for 55 individuals from different locations along the species’ known distribution. Spatial population structure, genetic diversity and demographic parameters were evaluated using population genetic and phylogeographical tools. We also evaluated its extent of occurrence and area of occupancy to investigate extinction risk of this species. We found genetic structure along P. megacephalus’ spatial distribution in the South Espinhaco Mountain Range corresponding to three population groups: northern, central and southern. Our results could provide important data on geographic distribution and population dynamics for a Data Deficient species. Therefore, we suggest these population data, together with the species’ limited occurrence in sky island environments could be used for a more accurate classification of P. megacephalus in the IUCN list, and conservation strategies for the species should be planned accordingly.

Turtle soup, Prohibition, and the population genetic structure of Diamondback Terrapins (Malaclemys terrapin).

Diamondback terrapins (Malaclemys terrapin) were a popular food item in early twentieth century America, and were consumed in soup with sherry. Intense market demand for terrapin meat resulted in population declines, notably along the Atlantic seaboard. Efforts to supply terrapins to markets resulted in translocation events, as individuals were moved about to stock terrapin farms. However, in 1920 the market for turtle soup buckled with the enactment of the eighteenth amendment to the United States’ Constitution—which initiated the prohibition of alcoholic drinks—and many terrapin fisheries dumped their stocks into local waters. We used microsatellite data to show that patterns of genetic diversity along the terrapin’s coastal range are consistent with historical accounts of translocation and cultivation activities. We identified possible instances of human-mediated dispersal by estimating gene flow over historical and contemporary timescales, Bayesian model testing, and bottleneck tests. We recovered six genotypic clusters along the Gulf and Atlantic coasts with varying degrees of admixture, including increased contemporary gene flow from Texas to South Carolina, from North Carolina to Maryland, and from North Carolina to New York. In addition, Bayesian models incorporating translocation events outperformed stepping-stone models. Finally, we were unable to detect population bottlenecks, possibly due to translocation reintroducing genetic diversity into bottlenecked populations. Our data suggest that current patterns of genetic diversity in the terrapin were altered by the demand for turtle soup followed by the enactment of alcohol prohibition. In addition, our study shows that population genetic tools can elucidate metapopulation dynamics in taxa with complex genetic histories impacted by anthropogenic activities.

Development of novel genic microsatellite markers from transcriptome sequencing in sugar maple (Acer saccharum Marsh.)

BackgroundSugar maple (Acer saccharum Marsh.) is a hardwood tree species native to northeastern North America and economically valued for its wood and sap. Yet, few molecular genetic resources have been developed for this species to date. Microsatellite markers have been a useful tool in population genetics, e.g., to monitor genetic variation and to analyze gene flow patterns. The objective of this study is to develop a reference transcriptome and microsatellite markers in sugar maple.FindingsA set of 117,861 putative unique transcripts were assembled using 29.2 Gb of RNA sequencing data derived from different tissues and stress treatments. From this set of sequences a total of 1068 microsatellite motifs were identified. Out of 58 genic microsatellite markers tested on a population of 47 sugar maple trees in upper Michigan, 22 amplified well, of which 16 were polymorphic and 6 were monomorphic. Values for expected heterozygosity varied from 0.224 to 0.726 for individual loci. Of the 16 polymorphic markers, 15 exhibited transferability to other Acer L. species.ConclusionsGenic microsatellite markers can be applied to analyze genetic variation in potentially adaptive genes relative to genomic reference markers as a basis for the management of sugar maple genetic resources in the face of climate change.

Exploiting natural variation for accelerating discoveries in plant specialized metabolism

Plants have the capacity to produce a staggering array of chemically diverse low molecular weight compounds called specialized metabolites. Though they are non-essential for basic cell activities, these molecules are characterized by their role as integral enhancers of plant fitness, and have distinct biological functions including defense against herbivory, immunity, pollinator attraction, molecular signaling, and abiotic stress tolerance. The chemicals are of particular interest because of their pharmacological, industrial, and agricultural usefulness. The inter- or intraspecies variation in the production of specialized metabolites has been widely observed and found to be largely genetically controlled. The natural genetic variation can be used to help identify biosynthetic and regulatory genes, elucidate mechanistic properties of gene function and gene regulation, and explore evolutionary and ecological questions. Recent advances in sequencing and data mining technologies have facilitated the integration of population genetics tools such as quantitative trait loci (QTL) mapping and genome wide association (GWA) with metabolite and/or gene expression profiling to exploit the natural variation for making new discoveries in the model plant Arabidopsis thaliana, as well as in more agriculturally relevant species. Here we highlight key discoveries that were catalyzed by taking advantage of naturally occurring variation, and comment on technologies and resources employed by this approach, in hopes of providing phytochemists an archetype for harnessing the power of natural variation to accelerate discoveries in plant specialized metabolism.

Effect of compensatory immigration on the genetic structure of coyotes

ABSTRACTDespite efforts to reduce their effects on livestock and native ungulates within the southeastern United States, coyotes (Canis latrans) can recover from control programs. It is unknown how coyotes compensate for high mortality following trapping, so there is great interest to identify methods that can provide insight into coyote response to intensive trapping. To investigate if population genetic tools can decipher how coyotes recover from intensive trapping, we combined an empirical test of how genetic differentiation, diversity, and familial structure changed following trapping on the Savannah River Site (SRS), South Carolina, USA, with spatially explicit genetic simulations. The pre‐ and post‐trapping periods had similar genetic diversities and were not genetically differentiated as expected by either compensatory reproduction or immigration from a single genetic source. The post‐trapping coyote populations exhibited weaker signatures of philopatry with little evidence for increased dispersal distances of young coyotes, which suggests immigration caused a decrease in familial structure. Our simulations indicated that spatial autocorrelation coefficients and observed heterozygosities change as immigration increases, whereas population differentiation, allelic richness, and displacement distances do not. Collectively, our results suggest that coyotes recover from intensive trapping via reproduction and immigration, which likely makes preventing compensation difficult. Monitoring post‐trapping populations may offer more insight into maximizing the effectiveness of control efforts, and based on our simulations, population genetics can provide critical information about the amount of compensatory immigration following trapping. © 2017 The Wildlife Society.

Development of 36 SNP markers in Ophiocephalus argus Cantor based on high-throughput sequencing

The Channa argus (Ophicephalus argus Cantor) is an endemic freshwater species which is widely distributed in the lower Yellow and Yangtze river systems in eastern China. The Ophicephalus argus is a high commercially valuable aquaculture fish in China. Due to river fragmentation, over-fishing, and water pollution, the wild population of Ophiocephalus argus suffered a dramatic decline. In the present study, 38 novel single nucleotide polymorphism (SNP) markers were developed based on high-throughput sequencing. Genetic diversity analysis revealed that the values of observed heterozygosity and expected heterozygosity varied from 0.1024 to 0.7033 and from 0.3638 to 0.8266, respectively, and the minor allele frequency ranged from 0.1911 to 0.6422. Only three loci showed significant deviation from Hardy–Weinberg equilibrium. These SNP markers will serve as a valuable tool for further population genetics, genetic breeding, and resource conservation in this species.

Isolation and Characterisation of Novel Polymorphic Microsatellite Markers for the Wedge-Billed Woodcreeper Glyphorynchus Spirurus

In order to study the population genetic structure of the Amazonian understorey bird Glyphorynchus spirurus, we have isolated eight polymorphic microsatellite loci using next-generation sequencing. All loci were screened using 40 samples from central Amazonia. The number of alleles varied from five to 22. The observed heterozygosities ranged from 0.475 to 0.875. No linkage disequilibrium was found among the loci. None of the loci showed significant deviation from Hardy–Weinberg equilibrium. These novel microsatellite markers will be a useful tool for future population genetics and ecological studies of the Wedge-billed Woodcreeper.

New Microsatellite Markers for the Common Tern (Sterna hirundo) Developed with 454 Shot-Gun Pyrosequencing

Long term studies, focusing on population- and socio-biology research, require the unequivocal identification of individuals. DNA studies with Short Tandem Repeats (STR loci) became a widespread tool in population genetics. We used the next-generation sequencing (NGS) approach with 454 shot-gun pyrosequencing to identify 13 new polymorphic STR loci for the Common Tern,Sterna hirundo. To enlarge the marker set we added two more loci originally developed for Black-legged Kittiwake (Rissa tridactyla) and Red-billed Gull (Chroicocephalus scopulinus) and arranged these 15 loci into three multiplex PCR panels for high throughput genotyping. Loci characterization demonstrated that our marker set is of high quality. A PIC value of about 0.67 and a power of exclusion value of 0.99 were reached. Deviation from Hardy-Weinberg expectations of some loci and low frequencies for null alleles are interpreted as a result of inbreeding and founder effect in the investigated tern colony. We used a test data set of this well-studied breeding colony of Common Tern at Banter Lake, Wilhelmshaven, Germany, to perform a parentage test. Parent-chick relationships, known from the social pedigree of that colony, were compared with genetically calculated ones. In order to test our markers and the used parentage program COLONY, we conducted six competing data sets with varying completeness of included parental genotypes. By including fully sampled parent pairs of known family assignment, results were correct for nest mates, single parents and parent pairs. Our marker set provides a powerful tool to investigate life-time reproductive success and other issues of population and socio-biology for Common Terns,e.g. in the aforementioned colony monitored for decades.