Repeatable Territorial Aggression in a Neotropical Poison Frog

Intra-specific aggressive interactions play a prominent role in the life of many animals. While studies have found evidence for repeatability in boldness, activity, and exploration in amphibians, we know relatively little about consistent among-individual variation in aggressiveness, despite its importance for male-male competition and territoriality. Amphibians, and Neotropical poison frogs (Dendrobatidae) in particular, are highly suitable for investigating among-individual variation in aggressiveness, as most species exhibit strong territoriality in at least one of the sexes. In the present study, we aimed to fill this gap in knowledge, by investigating within- and between-individual variation in territorial aggression in a semi-natural population of the Neotropical poison frog Allobates femoralis (Dendrobatidae) in French Guiana. We conducted repeated, standardized behavioral tests to assess if the level of territorial aggression is consistent within and different between individuals. Further, we tested a possible link between body size and level of territorial aggression. We found moderate repeatability in territorial aggressiveness, but no link to age and/or body size. In conclusion, our study represents the first documentation of repeatable aggressive behavior in a territorial context in amphibians.

Space use and parental care behaviour in Andinobates claudiae (Dendrobatidae)

The selection of habitats with potential reproductive resources may maximize individual reproductive success and overall fitness. Dendrobatid frogs display remarkable parental care which is associated with water bodies (phytotelmata) contained in plants with characteristics that are important to offspring survival. It has been shown that the size of phytotelmata is a key factor that drove the divergence in parental care patterns in poison frogs and that the distribution of reproductive resources can influence space use in these species. Here, we investigated parental care strategies and the influence of reproductive resource distribution on space use patterns in a wild population of Andinobates claudiae in Bocas del Toro, Panama. We identified the phytotelmata characteristics that predict tadpole deposition and analysed the association between the spatial distribution of phytotelmata and spatial use of males and females. Our observations showed that this species mates polygamously and exhibits male parental care. We found that male frogs have smaller kernel density home ranges and core areas compared to females, and that space use is related to the density of Heliconia plants whose axil cavities are used for tadpole rearing. Furthermore, we found that tadpoles were more frequently found in phytotelmata that were at lower heights and contained larger water volumes. Fathers invested time inspecting multiple cavities and travelled further than predicted from their territories to find suitable deposition sites. Our observations suggest a selective choice of phytotelmata regarding tadpole deposition, where distribution and quality of cavities might influence parental care decisions.

Genetic evidence for polyandry in the threatened green and golden bell frog

Identifying which species exhibit polyandry may lead to further insights into evolutionary biology and social behaviour. However, confirming polyandry can be difficult. High-resolution genetics provides a useful means to gain evidence. Although the threatened Pelodryadid frog, the green and golden bell frog Litoria aurea, has been subject to numerous ecological studies, there is uncertainty surrounding its reproductive ecology. Polyandry has not been formally identified in L. aurea or any species within the Pelodryadidae family. We aimed to identify if there was genetic evidence of polyandry in a population occurring in a wetland complex on Kooragang Island, New South Wales. To accomplish this, we collected genetic samples of tadpoles within the same size cohort about 20-30 days after explosive breeding events. Genotypes of 14 females, nine males and 70 tadpoles were analysed with COLONY (1988 single nucleotide polymorphisms after filtering) to identify parentage, full-siblings and half-siblings. We found support for the hypothesis that L. aurea is polyandrous. Based on previous observations of multi-male matings and the narrow time periods that breeding occurred in, it is likely this species exhibits simultaneous polyandry. We discuss these results in regards to behavioural adaptive processes and avenues for further research.

Aposematism facilitates the diversification of parental care strategies in poison frogs

Many organisms have evolved adaptations to increase the odds of survival of their offspring. Parental care has evolved several times in animals including ectotherms. In amphibians, ~ 10% of species exhibit parental care. Among these, poison frogs (Dendrobatidae) are well-known for their extensive care, which includes egg guarding, larval transport, and specialized tadpole provisioning with trophic eggs. At least one third of dendrobatids displaying aposematism by exhibiting warning coloration that informs potential predators about the presence of defensive skin toxins. Aposematism has a central role in poison frog diversification, including diet specialization, and visual and acoustic communication; and it is thought to have impacted their reproductive biology as well. We tested the latter association using multivariate phylogenetic methods at the family level. Our results show complex relationships between aposematism and certain aspects of the reproductive biology in dendrobatids. In particular, aposematic species tend to use more specialized tadpole-deposition sites, such as phytotelmata, and ferry fewer tadpoles than non-aposematic species. We propose that aposematism may have facilitated the diversification of microhabitat use in dendrobatids in the context of reproduction. Furthermore, the use of resource-limited tadpole-deposition environments may have evolved in tandem with an optimal reproductive strategy characterized by few offspring, biparental care, and female provisioning of food in the form of unfertilized eggs. We also found that in phytotelm-breeders, the rate of transition from cryptic to aposematic phenotype is 17 to 19 times higher than vice versa. Therefore, we infer that the aposematism in dendrobatids might serve as an umbrella trait for the evolution and maintenance of their complex offspring-caring activities.

Genetic connectivity between Atlantic bluefin tuna larvae spawned in the Gulf of Mexico and in the Mediterranean Sea

The highly migratory Atlantic bluefin tuna (ABFT) is currently managed as two distinct stocks, in accordance with natal homing behavior and population structuring despite the absence of barriers to gene flow. Larval fish are valuable biological material for tuna molecular ecology. However, they have hardly been used to decipher the ABFT population structure, although providing the genetic signal from successful breeders. For the first time, cooperative field collection of tuna larvae during 2014 in the main spawning area for each stock, the Gulf of Mexico (GOM) and the Mediterranean Sea (MED), enabled us to assess the ABFT genetic structure in a precise temporal and spatial frame exclusively through larvae. Partitioning of genetic diversity at nuclear microsatellite loci and in the mitochondrial control region in larvae spawned contemporarily resulted in low significant fixation indices supporting connectivity between spawners in the main reproduction area for each population. No structuring was detected within the GOM after segregating nuclear diversity in larvae spawned in two hydrographically distinct regions, the eastern GOM (eGOM) and the western GOM (wGOM), with the larvae from eGOM being more similar to those collected in the MED than the larvae from wGOM. We performed clustering of genetically characterized ABFT larvae through Bayesian analysis and by Discriminant Analysis of Principal Components (DAPC) supporting the existence of favorable areas for mixing of ABFT spawners from Western and Eastern stocks, leading to gene flow and apparent connectivity between weakly structured populations. Our findings suggest that the eastern GOM is more prone for the mixing of breeders from the two ABFT populations. Conservation of this valuable resource exploited for centuries calls for intensification of tuna ichthyoplankton research and standardization of genetic tools for monitoring population dynamics.

The paradox of retained genetic diversity of Hippocampus guttulatus in the face of demographic decline

Genetic diversity is the raw foundation for evolutionary potential. When genetic diversity is significantly reduced, the risk of extinction is heightened considerably. The long-snouted seahorse (Hippocampus guttulatus) is one of two seahorse species occurring in the North-East Atlantic. The population living in the Ria Formosa (South Portugal) declined dramatically between 2001 and 2008, prompting fears of greatly reduced genetic diversity and reduced effective population size, hallmarks of a genetic bottleneck. This study tests these hypotheses using samples from eight microsatellite loci taken from 2001 and 2013, on either side of the 2008 decline. The data suggest that the population has not lost its genetic diversity, and a genetic bottleneck was not detectable. However, overall relatedness increased between 2001 to 2013, leading to questions of future inbreeding. The effective population size has seemingly increased close to the threshold necessary for the population to retain its evolutionary potential, but whether these results have been affected by sample size is not clear. Several explanations are discussed for these unexpected results, such as gene flow, local decline due to dispersal to other areas of the Ria Formosa, and the potential that the duration of the demographic decline too short to record changes in the genetic diversity. Given the results presented here and recent evidence of a second population decline, the precise estimation of both gene flow and effective population size via more extensive genetic screening will be critical to effective population management.

Reproductive Strategies Change With Time in a Newly Founded Colony of Spotless Starlings (Sturnus unicolor)

Variation in avian reproductive strategies is often studied from a comparative perspective, since even closely-related taxa differ greatly in the degree of polygyny, extra-pair paternity (EPP) or intra-specific brood-parasitism. However, substantial variation at the species level suggests that ecological factors are important in shaping these patterns. In this study, we examined the temporal plasticity of these strategies, following a population from the year of colony formation to 2 years after this. Parentage data from these years shows that polygyny decreased with time, likely as a consequence of increased competition for nesting sites and mates by new recruits, and immigrants of higher quality arriving to the colony as time passed. In parallel to this temporal change, we found an increase in intra-specific brood-parasitism and quasi-parasitism (QP). We interpret these patterns as a consequence of an increase of floaters with time; these birds pursue a mixture of alternative mating strategies to succeed in the population. We also found evidence of conspecific brood parasitism (CBP), by nesting females that laid part of the clutch in another nest or that after losing a partially laid clutch resorted to lay the last eggs in another nest. Analyses of the distance between the main nest and nests containing the secondary polygynous brood or extra-pair or parasitic young showed an avoidance of contiguous nests for conducting these alternative reproductive tactics. At the same time, these secondary nests were closer to the main nest than random distances within the colony, suggesting that access to public information was restricted to a narrow area around the main nest. Our study emphasizes how behavioral patterns are plastic traits that vary not only with individual circumstances, but also with time, tracking changes in density and social structure.

Genetic structure and molecular diversity of Brazilian grapevine germplasm: Management and use in breeding programs

The management of germplasm banks is complex, especially when many accessions are involved. Microsatellite markers are an efficient tool for assessing the genetic diversity of germplasm collections, optimizing their use in breeding programs. This study genetically characterizes a large collection of 410 grapevine accessions maintained at the Agronomic Institute of Campinas (IAC) (Brazil). The accessions were genotyped with 17 highly polymorphic microsatellite markers. Genetic data were analyzed to determine the genetic structure of the germplasm, quantify its allelic diversity, suggest the composition of a core collection, and discover cases of synonymy, duplication, and misnaming. A total of 304 alleles were obtained, and 334 unique genotypes were identified. The molecular profiles of 145 accessions were confirmed according to the literature and databases, and the molecular profiles of more than 100 genotypes were reported for the first time. The analysis of the genetic structure revealed different levels of stratification. The primary division was between accessions related to Vitis vinifera and V. labrusca, followed by their separation from wild grapevine. A core collection of 120 genotypes captured 100% of all detected alleles. The accessions selected for the core collection may be used in future phenotyping efforts, in genome association studies, and for conservation purposes. Genetic divergence among accessions has practical applications in grape breeding programs, as the choice of relatively divergent parents will maximize the frequency of progeny with superior characteristics. Together, our results can enhance the management of grapevine germplasm and guide the efficient exploitation of genetic diversity to facilitate the development of new grape cultivars for fresh fruits, wine, and rootstock.

Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm

Croatian viticulture was most extensive at the beginning of the 20th century, when about 400 varieties were in use. Autochthonous varieties are the result of spontaneous hybridization from the pre-phylloxera era and are still cultivated today on about 35 % of vineyard area, while some exist only in repositories. We present what is the most comprehensive genetic analysis of all major Croatian national repositories, with a large number of microsatellite, or simple sequence repeat (SSR) markers, and it is also the first study to apply single nucleotide polymorphism (SNP) markers. After 212 accessions were fingerprinted, 95 were classified as unique to Croatian germplasm. Genetic diversity of Croatian germplasm is rather high considering its size. SNP markers proved useful for fingerprinting but less informative and practical than SSRs. Analysis of the genetic structure showed that Croatian germplasm is predominantly part of the Balkan grape gene pool. A high number of admixed varieties and synonyms is a consequence of complex pedigrees and migrations. Parentage analysis confirmed 24 full parentages, as well as 113 half-kinships. Unexpectedly, several key genitors could not be detected within the present Croatian germplasm. The low number of reconstructed parentages (19%) points to severe genetic erosion and stresses the importance of germplasm repositories.

Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa

Savannah elephant populations have been severely reduced and fragmented throughout its remaining range. In general, however, there is limited information regarding their genetic status, which is essential knowledge for conservation. We investigated patterns of genetic variation in savannah elephants from the Greater Kruger Biosphere, with a focus on those in previously unstudied nature reserves adjacent to Kruger National Park, using dung samples from 294 individuals and 18 microsatellites. The results of genetic structure analyses using several different methods of ordination and Bayesian clustering strongly suggest that elephants throughout the Greater Kruger National Park (GKNP) constitute a single population. No evidence of a recent genetic bottleneck was detected using three moment-based approaches and two coalescent likelihood methods. The apparent absence of a recent genetic bottleneck associated with the known early 1900s demographic bottleneck may result from a combination of rapid post-bottleneck population growth, immigration and long generation time. Point estimates of contemporary effective population size (Ne) for the GKNP were ~ 500-700, that is, at the low end of the range of Ne values that have been proposed for maintaining evolutionary potential and the current ratio of Ne to census population size (Nc) may be quite low (<0.1). This study illustrates the difficulties in assessing the impacts on Ne in populations that have suffered demographic crashes but have recovered rapidly and received gene flow, particularly in species with long generation times in which genetic time lags are longer. This work provides a starting point and baseline information for genetic monitoring of the GKNP elephants.

Performing Parentage Analysis in the Presence of Inbreeding and Null Alleles

Parentage analysis is an important method that is used widely in zoological and ecological studies. Current mathematical models of parentage analyses usually assume that a population has a uniform genetic structure and that mating is panmictic. In a natural population, the geographic or social structure of a population, and/or nonrandom mating, usually leads to a genetic structure and results in genotypic frequencies deviating from those expected under the Hardy-Weinberg equilibrium (HWE). In addition, in the presence of null alleles, an observed genotype represents one of several possible true genotypes. The true father of a given offspring may thus be erroneously excluded in parentage analyses, or may have a low or negative LOD score. Here, we present a new mathematical model to estimate parentage that includes simultaneously the effects of inbreeding, null alleles, and negative amplification. The influences of these three factors on previous model are evaluated by Monte-Carlo simulations and empirical data, and the performance of our new model is compared under controlled conditions. We found that, for both simulated and empirical data, our new model outperformed other methods in many situations. We make available our methods in a new, free software package entitled parentage. This can be downloaded via http://github.com/huangkang1987/parentage.

Diversity in warning coloration: selective paradox or the norm?

Aposematic theory has historically predicted that predators should select for warning signals to converge on a single form, as a result of frequency‐dependent learning. However, widespread variation in warning signals is observed across closely related species, populations and, most problematically for evolutionary biologists, among individuals in the same population. Recent research has yielded an increased awareness of this diversity, challenging the paradigm of signal monomorphy in aposematic animals. Here we provide a comprehensive synthesis of these disparate lines of investigation, identifying within them three broad classes of explanation for variation in aposematic warning signals: genetic mechanisms, differences among predators and predator behaviour, and alternative selection pressures upon the signal. The mechanisms producing warning coloration are also important. Detailed studies of the genetic basis of warning signals in some species, most notably Heliconius butterflies, are beginning to shed light on the genetic architecture facilitating or limiting key processes such as the evolution and maintenance of polymorphisms, hybridisation, and speciation. Work on predator behaviour is changing our perception of the predator community as a single homogenous selective agent, emphasising the dynamic nature of predator–prey interactions. Predator variability in a range of factors (e.g. perceptual abilities, tolerance to chemical defences, and individual motivation), suggests that the role of predators is more complicated than previously appreciated. With complex selection regimes at work, polytypisms and polymorphisms may even occur in Müllerian mimicry systems. Meanwhile, phenotypes are often multifunctional, and thus subject to additional biotic and abiotic selection pressures. Some of these selective pressures, primarily sexual selection and thermoregulation, have received considerable attention, while others, such as disease risk and parental effects, offer promising avenues to explore. As well as reviewing the existing evidence from both empirical studies and theoretical modelling, we highlight hypotheses that could benefit from further investigation in aposematic species. Finally by collating known instances of variation in warning signals, we provide a valuable resource for understanding the taxonomic spread of diversity in aposematic signalling and with which to direct future research. A greater appreciation of the extent of variation in aposematic species, and of the selective pressures and constraints which contribute to this once‐paradoxical phenomenon, yields a new perspective for the field of aposematic signalling.

Mating patterns and pollen dispersal in a Japanese larch (Larix kaempferi) clonal seed orchard: a case study

Pollination dynamics highly determines the genetic quality of seed orchard crops. However, there is less research about the effect of mating patterns on seed productivity of orchard crops. So far, clonal seed orchards have been producing genetically improved seedlings used for most Japanese larch (Larix kaempferi (Lamb.) Carr.) plantations in China. In the present study, a total of 17 highly variable simple sequence repeat (SSR) markers were used for genotyping a progeny trial population consisting of 647 open-pollinated progenies germinated from seeds which were collected from 63 maternal clones with 140 potential paternal clones in a Japanese larch clonal seed orchard in China. Paternity analysis was used in the present case study in order to evaluate the level of paternal gametic contribution, estimate pollen contamination and selfing rates, and investigate pollination patterns, pollen dispersal patterns and the impact of mating patterns on seed productivity of orchard crops. We observed 93.7% of the success rate of the parental assignment, unequal paternal gametic contribution (0-12.4%) with 6.3% of the progenies derived from pollen contamination or unsampled pollen donors, and absence of evidence for selfing. We also found that pollination rate highly depended on the distance between pollen donors and maternal parents, the majority of the identified crossing (65.7%) occurred between clones within a 150-m radius, and large variations in growth performance existed among the paternal half-siblings. Progeny growth performance (diameter at breast (DBH) and height (HGT)) was measured at Age-20 in order to investigate the impact of mating patterns on timber production of orchard crops. As either the paternal or maternal, two clones (i. e., clones Z38 and Z62) were identified to have produced progenies with higher average stem volume breeding values than that of all of the progenies. Specifically, the genetic gains for volume were 3.53% for the two clones as paternal parents, and 8.26% as the maternal parents at Age-20. Thus, both elite clones were ideal candidates for the construction of next-generation clonal seed orchards due to their synchronous reproductive phenology with greater crossing rate and higher genetic gain. These results improved the pedigree information to provide solid evidence of mating patterns for future design and effective management of seed orchards and for the development of viable long-term breeding strategies for other coniferous species.

Evaluation of efficiency of controlled pollination based parentage analysis in a Larix gmelinii var. principis-rupprechtii Mayr. seed orchard

Controlled pollination (CP) is an important tool for breeding programs to improve seed quality, as it rapidly generates desirable genotypes and maximizes genetic gains. However, few studies have evaluated the success rate of CP, especially in Larix gmelinii var. principis-rupprechtii Mayr. seed orchards. In this study, we estimated the rate of correct parentage in 257 CP progeny in an L. gmelinii var. principis-rupprechtii seed orchard from ten candidate parents using 13 microsatellites. The parentage exclusion probabilities of all combined loci in the single parent and parent pair tests were > 0.99, which was sufficient to distinguish the relatedness of the sampled individuals. Comparing the maximum likelihood-based parentage analysis results with breeding records revealed that the percentages of correctly identified maternal and paternal parents were 22.6% and 35.0% at 95% CL, respectively, suggestive of parent mislabeling and pollen contamination in the CP population. We conducted a pedigree reconstruction by identifying the expected parents and assigned maternity, paternity, and parent pairs to 176 (68.5%), 199 (77.4%), and 132 (51.4%) progeny, respectively. This study provides a reference for future selection of elite genotypes for commercial production. To increase the efficiency of CP, molecular markers should be used to correctly identify individuals in seed orchards before conducting CP.

Brood-partitioning behaviour in unpredictable environments: hedging the bets?

Spreading reproduction across time or space can optimize fitness by minimizing the risks for offspring survival in varying and unpredictable environments. Poison frogs (Dendrobatidae) are characterized by complex spatial and reproductive behaviour, such as territoriality, prolonged courtship and parental care. The partitioning of larvae from terrestrial clutches across several water bodies is mainly known from species with carnivorous tadpoles that allocate their tadpoles in very small pools, where limited food availability is accompanied by an increased risk of cannibalism. However, little is known about the deposition behaviour of non-carnivorous species that use medium-sized to large pools. In the present study, we investigated whether the Neotropical poison frog Allobates femoralis exhibits brood-partitioning behaviour when males transport tadpoles 3 weeks after oviposition. We sampled 30 artificial water bodies for tadpoles, which we genotyped at seven highly polymorphic microsatellite loci. Based on the reconstructed pedigree, we show that A. femoralis males distribute larvae of single and of successive clutches across several water bodies. The number of pools used was significantly associated with the number of clutches per male. Ninety-three percent of the males that were assigned to more than one clutch spread their tadpoles across several water bodies. Given the highly variable and unpredictable biotic and abiotic conditions in tropical rainforest, at the spatial scale of the study species’ behaviour, we interpret this behaviour as bet-hedging to improve offspring survival.

'True' null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties and survey of possible improvements

Null alleles are alleles that for various reasons fail to amplify in a PCR assay. The presence of null alleles in microsatellite data is known to bias the genetic parameter estimates. Thus, efficient detection of null alleles is crucial, but the methods available for indirect null allele detection return inconsistent results. Here, our aim was to compare different methods for null allele detection, to explain their respective performance and to provide improvements. We applied several approaches to identify the 'true' null alleles based on the predictions made by five different methods, used either individually or in combination. First, we introduced simulated 'true' null alleles into 240 population data sets and applied the methods to measure their success in detecting the simulated null alleles. The single best-performing method was ML-NullFreq_frequency. Furthermore, we applied different noise reduction approaches to improve the results. For instance, by combining the results of several methods, we obtained more reliable results than using a single one. Rule-based classification was applied to identify population properties linked to the false discovery rate. Rules obtained from the classifier described which population genetic estimates and loci characteristics were linked to the success of each method. We have shown that by simulating 'true' null alleles into a population data set, we may define a null allele frequency threshold, related to a desired true or false discovery rate. Moreover, using such simulated data sets, the expected null allele homozygote frequency may be estimated independently of the equilibrium state of the population.

Fractional parentage analysis and a scale-free reproductive network of brown trout

In this study, we developed a method of fractional parentage analysis using microsatellite markers. We propose a method for calculating parentage probability, which considers missing data and genotyping errors due to null alleles and other causes, by regarding observed alleles as realizations of random variables which take values in the set of alleles at the locus and developing a method for simultaneously estimating the true and null allele frequencies of all alleles at each locus. We then applied our proposed method to a large sample collected from a wild population of brown trout (Salmo trutta). On analyzing the data using our method, we found that the reproductive success of brown trout obeyed a power law, indicating that when the parent-offspring relationship is regarded as a link, the reproductive system of brown trout is a scale-free network. Characteristics of the reproductive network of brown trout include individuals with large bodies as hubs in the network and different power exponents of degree distributions between males and females.

Reliability assessment of null allele detection: inconsistencies between and within different methods

Microsatellite loci are widely used in population genetic studies, but the presence of null alleles may lead to biased results. Here, we assessed five methods that indirectly detect null alleles and found large inconsistencies among them. Our analysis was based on 20 microsatellite loci genotyped in a natural population of Microtus oeconomus sampled during 8 years, together with 1200 simulated populations without null alleles, but experiencing bottlenecks of varying duration and intensity, and 120 simulated populations with known null alleles. In the natural population, 29% of positive results were consistent between the methods in pairwise comparisons, and in the simulated data set, this proportion was 14%. The positive results were also inconsistent between different years in the natural population. In the null-allele-free simulated data set, the number of false positives increased with increased bottleneck intensity and duration. We also found a low concordance in null allele detection between the original simulated populations and their 20% random subsets. In the populations simulated to include null alleles, between 22% and 42% of true null alleles remained undetected, which highlighted that detection errors are not restricted to false positives. None of the evaluated methods clearly outperformed the others when both false-positive and false-negative rates were considered. Accepting only the positive results consistent between at least two methods should considerably reduce the false-positive rate, but this approach may increase the false-negative rate. Our study demonstrates the need for novel null allele detection methods that could be reliably applied to natural populations.

The impact of past introductions on an iconic and economically important species, the red deer of Scotland

The red deer (Cervus elaphus) is an iconic species in Scotland and, due to its value as a game species, an important element of the Scottish rural economy. The native status of this species is sometimes questioned because of many recorded introductions of nonnative deer in the past that were an attempt to improve trophy size. In this study, we assessed the impact of past introductions on the genetic makeup of Scottish red deer by genotyping at 15 microsatellite loci a large number of samples (n = 1152), including mainland and island Scottish red deer and individuals from several putative external source populations used in introductions to improve trophy size. Population structure and introgression assessment analyses revealed that the impact of introductions was weak in Highland red deer populations but more prominent on the islands, especially on those where current red deer populations are mostly or entirely derived from introductions (Harris & Lewis, Arran, and Rum). Frequent imports of Central-Eastern European red deer into English deer parks were reflected in the higher genetic introgression values found in some of the individuals collected in parks.

The female perspective of mating in A. femoralis, a territorial frog with paternal care--a spatial and genetic analysis

The adaptive significance of sequential polyandry is a challenging question in evolutionary and behavioral biology. Costs and benefits of different mating patterns are shaped by the spatial distribution of individuals and by genetic parameters such as the pairwise relatedness between potential mating partners. Thus, females should become less choosy as costs of mating and searching for mates increase. We used parentage assignments to investigate spatial and genetic patterns of mating across a natural population of the Neotropical frog Allobates femoralis, a species characterized by male territoriality and care and female iteroparity. There was no correlation between genetic and spatial distances between adult individuals across the population. In 72% of cases, females mated with males available within a radius of 20 m. Mean pairwise relatedness coefficients of successful reproducers did not differ from random mating but had a lower variance than expected by chance, suggesting maximal reproductive output at intermediate genetic divergence. We also found evidence for selection in favor of more heterozygous individuals between the embryo and adult stage. The level of sequential polyandry significantly increased with the number of spatially available males. Females that had more candidate males also produced more adult progeny. We hypothesize that the benefits associated with female multiple mating outweigh the costs of in- and outbreeding depression, and consequently precluded the evolution of 'choosy' mate selection in this species.

Reproductive success of male Atlantic spotted dolphins (Stenella frontalis) revealed by noninvasive genetic analysis of paternity

Cetaceans are known to frequently engage in sexual behavior; however, the lack of male parental investment in offspring makes assessment of male reproductive success difficult. We assessed paternity in a small population (mean individuals sighted per year = 93) of Atlantic spotted dolphins ( Stenella frontalis (G. Cuvier, 1829)) utilizing noninvasively collected fecal material. Samples (n = 88) were collected from dolphins from four social clusters. Of the 29 offspring tested, 34.5% were assigned paternity, resulting in 10 paternities assigned to seven males. Our study indicates that achieving a certain age is a potential precursor for males to mate successfully, as 18 years was the youngest estimated age of a male at the time of calf conception. In all pairings but one, the males were older than the female (mean age difference = 7.7+ years). Successful males were from two of the four social clusters and males most often mated within their social group or with females from the next geographically closest group. The study combines genetic data with known maternal pedigree information and reveals patterns in the overall mating system in a cetacean species where reproductive success of males was previously unknown.

The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin

A collection of 1005 grapevine accessions was genotyped at 34 microsatellite loci (SSR) with the aim of analysing genetic diversity and exploring parentages. The comparison of molecular profiles revealed 200 groups of synonymy. The removal of perfect synonyms reduced the database to 745 unique genotypes, on which population genetic parameters were calculated. The analysis of kinship uncovered 74 complete pedigrees, with both parents identified. Many of these parentages were not previously known and are of considerable historical interest, e.g. Chenin blanc (Sauvignon × Traminer rot), Covè (Harslevelu selfed), Incrocio Manzoni 2-14 and 2-15 (Cabernet franc × Prosecco), Lagrein (Schiava gentile × Teroldego), Malvasia nera of Bolzano (Perera × Schiava gentile), Manzoni moscato (Raboso veronese × Moscato d'Amburgo), Moscato violetto (Moscato bianco × Duraguzza), Muscat of Alexandria (Muscat blanc à petit grain × Axina de tres bias) and others. Statistical robustness of unexpected pedigrees was reinforced with the analysis of an additional 7-30 SSRs. Grouping the accessions by profile resulted in a weak correlation with their geographical origin and/or current area of cultivation, revealing a large admixture of local varieties with those most widely cultivated, as a result of ancient commerce and population flow. The SSRs with tri- to penta-nucleotide repeats adopted for the present study showed a great capacity for discriminating amongst accessions, with probabilities of identity by chance as low as 1.45 × 10(-27) and 9.35 × 10(-12) for unrelated and full sib individuals, respectively. A database of allele frequencies and SSR profiles of 32 reference cultivars are provided.

Genetic structuring in the freshwater mussel Anodonta corresponds with major hydrologic basins in the western United States

Freshwater mussels (unionids) are increasingly recognized as important providers of ecosystem services, yet are among the most endangered fauna in the world. Because unionids are generally sessile and require specific fish hosts for development and dispersal, they are particularly vulnerable to habitat degradation. Surprisingly, little is known about the distribution of genetic diversity in freshwater mussels and this gap has a negative impact on taxonomy, monitoring, conservation and ecological research in these species. Here, we focus on western North American Anodonta, one of only three genera known to exist in this broad landscape and which contains three highly divergent lineages. We describe phylogeographical subdivision in the most widespread and diverse of these lineages, which includes Anodonta californiensis and Anodonta nuttalliana and occurs from Canada to Mexico. Using mitochondrial and nuclear data, we found that genetic structuring within this clade is inconsistent with morphologically based species designations, but instead follows patterns of vicariance among major hydrogeologic basins. Furthermore, there was a strong tendency for population diversity within drainage systems to increase downstream, implying greater habitat or host fish availability in this direction. Microsatellite results indicated that sampling locations were all genetically distinct, even at short distances. Many of our sample populations showed evidence of a recent demographic bottleneck, although this effect seemed to be very local and not drainage or basin-specific. This study provides a foundation for the establishment of appropriate management units and future research on adaptive differentiation and host fish relationships.

Population genetics and social organization of the sperm whale (Physeter macrocephalus) in the Azores inferred by microsatellite analyses

In the northeast Atlantic Ocean, the archipelago of the Azores is frequented by female–offspring groups of sperm whales ( Physeter macrocephalus L., 1758), as well as large males. The Azores apparently constitute both a feeding ground and a reproduction site. Little is known about the population and group structure of sperm whales in the area. We analysed 151 sloughed skin and biopsy samples collected from 2002 to 2004. Molecular analyses involved genetic tagging using 11 microsatellite loci and molecular sexing. Our objectives were to determine the population genetic structure, compare relatedness within and between social groups, infer kinship, and estimate the age of males at dispersal. Results suggest that individuals visiting the archipelago of the Azores belong to a single population. High genetic diversity and absence of inbreeding suggest that the population is recovering from whaling. Individuals sampled in close association are highly related, as well as those observed in the same area on the same day, suggesting that secondary social groups (i.e., the union of primary social units) are largely but not exclusively composed of relatives. Probable mother–offspring and full-sibling pairs were identified. Age of males at dispersal was estimated at 16.6 years, which was well above previous estimates for this species.