Defining population boundaries: use of three Bayesian approaches with microsatellite data from British natterjack toads (Bufo calamita)

Defining boundaries between populations is often difficult in the absence of information about current levels of gene flow. Such definitions can be important, however, both for the understanding of population dynamics and for conservation planning. Recently developed Bayesian methods for analysing genetic data now provide a powerful approach to this problem. Natterjack toads Bufo calamita are endangered in Britain, where their distribution is restricted to four geographically discrete regions. In three of these regions the boundaries between populations are often uncertain. We therefore used Bayesian approaches with microsatellite data to try and define British natterjack population structure, and thus inform conservation management. A large sample of natterjack toads from all 38 locations in Britain where the species is native was genotyped at eight microsatellite loci. The genetic diversity of natterjack populations declined as a function of increasing latitude, echoing postglacial colonization dynamics. Comparisons of three assignment methods (structure, baps and geneland) generated some broad similarities but also some inconsistencies in the definitions of population structure, especially in the most complex region (south Cumbria). Implications of the analyses for the future conservation of Bufo calamita in Britain are discussed.     

Absence of the trade-off between the size and number of offspring in the natterjack toad (Bufo calamita)

Summary A trade-off between size and number of offspring was not found for females of similar sizes of the natterjack toad (Bufo calamita). Moreover, for large females, clutches with higher number of eggs had larger eggs as well. This suggests that larger females produce more numerous and larger eggs because they potentially have more energy available for reproduction. Egg size diminished allometrically with clutch size. Egg size, however, did not increase offspring fitness. Therefore, this allometric decrease may be considered a consequence of phylogenetic constraints rather than a result of optimizing selection.     

The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus)

This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long-term population size for an abundant and commercially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and temporal allelic variation was measured at eight polymorphic microsatellite loci. Moments-based and maximum-likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long-term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non-infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology.     

Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches

The effective population size (N(e) ) could be the ideal parameter for monitoring populations of conservation concern as it conveniently summarizes both the evolutionary potential of the population and its sensitivity to genetic stochasticity. However, tracing its change through time is difficult in natural populations. We applied four new methods for estimating N(e) from a single sample of genotypes to trace temporal change in N(e) for bears in the Northern Dinaric Mountains. We genotyped 510 bears using 20 microsatellite loci and determined their age. The samples were organized into cohorts with regard to the year when the animals were born and yearly samples with age categories for every year when they were alive. We used the Estimator by Parentage Assignment (EPA) to directly estimate both N(e) and generation interval for each yearly sample. For cohorts, we estimated the effective number of breeders (N(b) ) using linkage disequilibrium, sibship assignment and approximate Bayesian computation methods and extrapolated these estimates to N(e) using the generation interval. The N(e) estimate by EPA is 276 (183-350 95% CI), meeting the inbreeding-avoidance criterion of N(e) > 50 but short of the long-term minimum viable population goal of N(e) > 500. The results obtained by the other methods are highly consistent with this result, and all indicate a rapid increase in N(e) probably in the late 1990s and early 2000s. The new single-sample approaches to the estimation of N(e) provide efficient means for including N(e) in monitoring frameworks and will be of great importance for future management and conservation.     

Exploring the structure of genetic variation and the influences of demography on effective population size in the gag grouper Mycteroperca microlepi (Goode & Bean)

Using 11 microsatellite markers, genetic analyses of three successive year-classes of gag Mycteroperca microlepis juveniles across the north-eastern Gulf of Mexico revealed a lack of spatial structure and very little temporal variation between year-classes. These results are consistent with long-term effective population sizes on the order of 30 000 adults. The importance of reproductive-style and sex-ratio variation is discussed as an important influence on long-term effective sizes.     

Short-term genetic changes: evaluating effective population size estimates in a comprehensively described brown trout (Salmo trutta) population

The effective population size (N(e)) is notoriously difficult to accurately estimate in wild populations as it is influenced by a number of parameters that are difficult to delineate in natural systems. The different methods that are used to estimate N(e) are affected variously by different processes at the population level, such as the life-history characteristics of the organism, gene flow, and population substructure, as well as by the frequency patterns of genetic markers used and the sampling design. Here, we compare N(e) estimates obtained by different genetic methods and from demographic data and elucidate how the estimates are affected by various factors in an exhaustively sampled and comprehensively described natural brown trout (Salmo trutta) system. In general, the methods yielded rather congruent estimates, and we ascribe that to the adequate genotyping and exhaustive sampling. Effects of violating the assumptions of the different methods were nevertheless apparent. In accordance with theoretical studies, skewed allele frequencies would underestimate temporal allele frequency changes and thereby upwardly bias N(e) if not accounted for. Overlapping generations and iteroparity would also upwardly bias N(e) when applied to temporal samples taken over short time spans. Gene flow from a genetically not very dissimilar source population decreases temporal allele frequency changes and thereby acts to increase estimates of N(e). Our study reiterates the importance of adequate sampling, quantification of life-history parameters and gene flow, and incorporating these data into the N(e) estimation.     

Genetic variation, genetic structure and effective population size in the tropical holoparasitic endophyteBdallophyton bambusarum (Rafflesiaceae)

The genetic population structure inBdallophyton bambusarum, an endoparasite, was studied in ten subpopulations from a subdeciduous tropical forest in Veracruz Mexico. The sample was analyzed using seven polymorphic loci in cellulose acetate electrophoresis. Isozyme data indicated that the subpopulations ofB. bambusarum contained high genetic variability (H_ep = 0.452 ± 0.045, S.E.). Our analysis suggests that almost each inflorescence ofB. bambusarum is an individual. The subpopulations studied were genetically similar (average Nei's genetic identity 0.941 ± 0.051 and F _st values 0.097 ± 0.026), suggesting that genetic differentiation among subpopulations was small. Direct estimates of effective population size was derived from observations of three fluorescent dyes, and from the genetic neighborhood area derived from these data. The neighborhood area, multiplied by the total density of individuals, gave an N_e = 124.84 plants, and when corrected to consider the proportion of males and females gave an N_e = 118.59 individuals. An indirect estimate of Nm was obtained from the F _st values (mean Nm=2.037), giving an indirect estimate of the effective population size N_b = 12.8 individuals. Both values are relatively high when compared to other plant studies. The gene flow and/or effective populations size of the studied subpopulations ofB. bambusarum are believed to be large enough to prevent differentiation among subpopulations due to genetic drift.     

Relative contribution of contemporary pollen and seed dispersal to the effective parental size of seedling population of California valley oak (Quercus lobata, Née)

For plant populations, gene movement through pollen and seed dispersal governs the size of local genetic neighbourhoods and shapes the opportunities for natural selection and genetic drift. A critical question is how together these two processes influence the evolutionary dynamics of local populations. To assess the respective contributions of pollen and seed flow, we propose a novel indirect assessment of the separate male and female gametic contributions to total effective parental size ( N _e), based on parental correlations estimated via kinship coefficients, that can be applied to data sets that include unambiguous genotypes for male and female gametic contributions. Using the endemic Californian valley oak ( Quercus lobata ) as our study species, we apply this method to a set of microsatellite genotypes for two distinct ecological sets of naturally recruiting seedlings with acorns attached. We found that the effective numbers of contributing male parents ( N _ep) exceed effective numbers of female parents ( N _em) for seedlings established beneath adult trees ( N _ep = 8.1 and N _em = 1.1), as well as for seedlings established away from adult trees ( N _ep = 15.4 and N _em = 2.7), illustrating that seed dispersal enhances pollen dispersal and increases the effective number of seed sources in open seedling patches. The resulting effective parental size of seedling populations translates into smaller effective numbers of parents for undispersed vs. dispersed seedlings ( N _e = 3.6 and N _e = 6.7, respectively). This study introduces a novel statistic method and provides important new evidence that, on a short-term temporal scale, seed dispersal shapes the local neighbourhood size of new recruits.     

Spatial and temporal genetic differentiation and effective population size of brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>, L.) in small Danish rivers

The spatial and temporal genetic structure of brown trout populations from three small tributaries of Lake Hald, Denmark, was studied using analysis of variation at eight microsatellite loci. From two of the populations temporal samples were available, separated by up to 13 years (3.7 generations). Significant genetic differentiation was observed among all samples, however, hierarchical analysis of molecular variance (AMOVA) showed that differentiation among populations accounted for a non-significant amount of the genetic differentiation, whereas differentiation among temporal samples within populations was highly significant (0.0244, P<0.001). Estimates of effective population size (N _e) using a maximum-likelihood based implementation of the temporal method, yielded small values (N _e ranging from 33 to 79). When a model was applied that allows for migration among populations, N _e estimates were even lower (24–54), and migration rates were suggested to be high (0.13–0.36). All samples displayed a clear signal of a recent bottleneck, probably stemming from a period of unfavourable conditions due to organic pollution in the 1970–1980’s. By comparison to other estimates of N _e in brown trout, Lake Hald trout represent a system of small populations linked by extensive gene flow, whereas other populations in larger rivers exhibit much higher N _e values and experience lower levels of immigration. We suggest that management considerations for systems like Lake Hald brown trout should focus both on a regional scale and at the level of individual populations, as the future persistence of populations depends both on maintaining individual populations and ensuring sufficient migration links among these populations.     

Mangabey (Cercocebus albigena) population density,group size,and ranging: A twenty-year comparison

Mangabey groups studied in the Kibale Forest Reserve, Uganda, in 1971 were studied again in 1991 using similar data collection protocols. The results were used to assess the effect of group size on activity budgets and travel costs, and to document the effects of habitat changes on mangabey density and demography. Larger mangabey groups traveled longer distances per day than smaller groups. Time budgets were less clearly influenced by group size. Mangabey population density increased over the 20 year period. This increase in population density paralleled habitat changes, particularly an increase in tree density, and was accompanied by increased use of regenerating forest. © 1994 Wiley-Liss, Inc.     

Total phenolic,size‐fractionated phenolics and fucoxanthin content of tropical Sargassaceae (Fucales,Phaeophyceae) from the South Pacific Ocean: Spatial and specific variability

This innovative study investigates 18 Turbinaria and Sargassum brown seaweed samples from three archipelagos of the South West Pacific Ocean. The phenolic content of crude and size‐fractionated extracts was determined by the Folin‐Ciocalteu method; fucoxanthin was measured using high performance liquid chromatography. Although the phenolic content proved to be low for the species of both genera tested, the levels in the species of Turbinaria were higher than those of Sargassum tested, except in the Fiji islands where both species produced similar contents. These investigations also highlighted variations of total phenolic content with spatial, reef morphology and depth. A large number of small phenolic compounds (<2000 Da) were observed irrespective of the genus analyzed. Nevertheless, the composition of the phenolic pool varied in relation with the genus, the archipelago from which the material was collected, geomorphological features and the depth of each collection field site. A similar observation was for fucoxanthin content and in general, the measured constituents of the Turbinaria were less than those of the Sargassum species. The results are discussed in terms of inter‐ and intra‐specific variability. Variations in both phenolic and fucoxanthin content were noted in tropical members of the Sargassaceae; such differences could be a result of specific chemical defense mechanisms adopted by members of each genus.     

Spatial and temporal variation of genetic diversity and estimation of effective population sizes in Atlantic salmon (Salmo salar, L.) populations from Asturias (Northern Spain) using microsatellites

Rivers in Asturias (northern Spain) constitute the southern limit of the distribution of Atlantic salmon (Salmo salar L.) in Europe, a biological resource facing one of the more serious challenges for conservation today. In this work, eight microsatellite loci have been used to analyse samples collected in 1993 and 1999 from four Asturian rivers (Esva, Narcea, Sella, and Cares), obtaining information about the temporal and the spatial genetic variation in these populations and, in addition, estimations of their effective population sizes. The temporal analysis revealed a general decrease in all the estimated genetic variability parameters when samples from 1993 (mean A ₍₁₉₉₃₎ = 6.47, mean H _O(1993) = 0.472, mean H _E(1993) = 0.530) were compared with those obtained in 1999 (mean A ₍₁₉₉₉₎ = 6.16, mean H _O(1999) = 0.460, mean H _E(1999) = 0.490). This reduction was particularly notable for the case of the Esva river. Our results pointed to a pattern of spatial genetic differentiation inside the Asturian region (F _{ST (1993)} = 0.016 P < 0.01; F _{ST (1999)} = 0.023 P < 0.01). Using the standard Temporal Method we found estimates of N _e^{^} _(Esva) = 75.1 (33.2–267.2); N _e^{^} _(Cares) = 96.6 (40.0–507.5), N _e^{^} _(Sella) = 106.5 (39.1–9396.4) and N _e^{^} _(Narcea) = 113.9 (42.0–3693.3). The use of likelihood-based methods for the N _e^{^} estimations improved the results (smaller CIs) for the Esva and Cares rivers (N _e^{^} _(Esva) = 63.9 (32.3–165.3); N _e^{^} _(Cares) = 76.4 (38.8–202.0) using a Maximum likelihood approach) and suggested the presence of larger populations for the Sella and Narcea rivers (N _e^{^}≈200). These results showed that the Asturian Atlantic salmon populations (in particular Esva and Cares river populations) could be close to the conservation genetic borderline for avoiding inbreeding depression although we discuss some implications of the analysis of temporal genetic change in populations with overlapping generations.     

Population genetic analysis of microsatellite variation of guppies (Poecilia reticulata) in Trinidad and Tobago: evidence for a dynamic source–sink metapopulation structure,founder events and population bottlenecks

Riverine fish populations are traditionally considered to be highly structured and subject to strong genetic drift. Here, we use microsatellites to analyse the population structure of the guppy (Poecilia reticulata), focussing on the headwater floodplain area of the Caroni drainage in Trinidad. We also analyse the population genetics of guppies in the Northern Drainage in Trinidad, a habitat characterized by rivers flowing directly into the sea, and a small isolated population in Tobago. Upland Caroni populations are highly differentiated and display low levels of genetic diversity. However, we found no evidence to suggest that these upland populations experienced recent population crashes and the populations appear to approach mutation–drift equilibrium. Dominant downstream migration over both short‐ and long‐time frames has a strong impact on the population genetics of lowland Caroni populations. This drainage system could be considered a source–sink metapopulation, with the tributary furthest downstream representing a ‘super sink’, receiving immigrants from rivers upstream in the drainage. Moreover, the effective population size in the lowlands is surprisingly low in comparison with the apparently large census population sizes.     

Single‐nucleotide polymorphism (A118G) in exon 1 of OPRM1 gene causes alteration in downstream signaling by mu‐opioid receptor and may contribute to the genetic risk for addiction

The opioid receptor mu1 (OPRM1) mediates the action of morphine. Although genetic background plays an important role in the susceptibility toward abuse of drugs as evident from familial, adoption and twin studies, association of specific single‐nucleotide polymorphisms of OPRM1 gene with narcotic addiction is to be established. Here, we demonstrate the involvement of A118G polymorphism of exon1 of human OPRM1 gene (hOPRM1), with heroin and alcohol addiction, in a population in eastern India. Statistical analysis exhibited a significant association of G allele with both heroin and alcohol addiction with a risk factor of P_trend < 0.05. The functional significance of G allele in A118G single‐nucleotide polymorphisms was evaluated by studying the regulation of protein kinase A (PKA), pCREB, and pERK1/2 by morphine in Neuro 2A cells, stably transfected with either wild type or A118G mutant hOPRM1. Unlike acute morphine treatment, both chronic morphine exposure and withdrawal precipitated by naloxone were differentially regulated by A118 and G118 receptor isoforms when both PKA and pERK1/2 activities were compared. Results suggest that the association of A118G polymorphism to heroin and alcohol addiction may be because of the altered regulation of PKA and pERK1/2 during opioid and alcohol exposures.     

Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long‐lived tree endemic to Hainan Island,China

Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long‐lived trees. Dracaena cambodiana is an endangered, long‐lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter‐simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat‐private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments.