Dominant (AFLP) and co‐dominant (microsatellite) markers for the kelp Postelsia palmaeformis (Laminariales)

To aid in understanding the structure, dispersal and genetic dynamics of their populations, we developed microsatellite and amplified fragment length polymorphism (AFLP) markers for the sea palm, Postelsia palmaeformis (Laminariales) for samples taken from nine sites in the area of Cape Flattery, Washington State, USA. We identified two AFLP primers that yielded 798 variable fragments and five microsatellite markers with three to seven alleles each. We also report patterns of allelic variation for four previously identified microsatellite markers in this species and several new alleles.     

GENETIC VARIABILITY AND SPATIAL SEPARATION IN THE SEA PALM KELP POSTELSIA PALMAEFORMIS (PHAEOPHYCEAE) AS ASSESSED WITH M13 FINGERPRINTS AND RAPDS1

Postelsia palmaeformis Ruprecht is an annual species, occuring from southern California to Vancouver Island, Canada, in upper intertidal sites exposed to extreme wave shock. Because of its limited spore dispersal, discrete and inbred populations are likely on the local scale, yet dispersal of drifting and fertile thalli raises the possibility of outbred populations on a regional scale. M13 minisatellite DNA fingerprinting and random amplified polymorphic DNA (RAPD) marks were used in a complementary fashion to investigate genetic variability among 24 individuals on scales of clusters (= coalesced holdfasts). < 1 m, 10 m, 25 m, 16 km, and 250 km. Based on M13 fingerprinting, genetic relatedness within clusters was extremely high. Three of six clusters had at hast two identical individuals, and similarity values within five clusters were ≧0.90. Similarities between two of three clusters separated by < 1 m were significantly higher than between cluster pairs separated by 25 m and 250 km: however, the similarity between two clusters separated by 25 m was equivalent to the similarity between two clusters separated by 250 km. Thus, genetic relatedness as determined by M13 fingerprinting generally decreased as distance increased to 25 m. Conversely, RAPD data easily discriminated populations separated by 16 and 250 km but were not useful in discriminating individuals from < 1 to 25 m. Results from the complementary data sets suggest that most dispersal occurs over distances of 1–5 m, individuals within a cluster are siblings, and distinguishable biogeographic populations are present along the coast.     

Increased inbreeding and strong kinship structure in Taxus baccata estimated from both AFLP and SSR data

Habitat fragmentation can have severe genetic consequences for trees, such as increased inbreeding and decreased effective population size. In effect, local populations suffer from reduction of genetic variation, and thus loss of adaptive capacity, which consequently increases their risk of extinction. In Europe, Taxus baccata is among a number of tree species experiencing strong habitat fragmentation. However, there is little empirical data on the population genetic consequences of fragmentation for this species. This study aimed to characterize local genetic structure in two natural remnants of English yew in Poland based on both amplified fragment length polymorphism (AFLP) and microsatellite (SSR) markers. We introduced a Bayesian approach that estimates the average inbreeding coefficient using AFLP (dominant) markers. Results showed that, in spite of high dispersal potential (bird-mediated seed dispersal and wind-mediated pollen dispersal), English yew populations show strong kinship structure, with a spatial extent of 50–100 m, depending on the population. The estimated inbreeding levels ranged from 0.016 to 0.063, depending on the population and marker used. Several patterns were evident: (1) AFLP markers showed stronger kinship structure than SSRs; (2) AFLP markers provided higher inbreeding estimates than SSRs; and (3) kinship structure and inbreeding were more pronounced in denser populations regardless of the marker used. Our results suggest that, because both kinship structure and (bi-parental) inbreeding exist in populations of English yew, gene dispersal can be fairly limited in this species. Furthermore, at a local scale, gene dispersal intensity can be more limited in a dense population.     

The mixed mating system of the sea palm kelp Postelsia palmaeformis: few costs to selfing

Naturally isolated populations have conflicting selection pressures for successful reproduction and inbreeding avoidance. These species with limited seasonal reproductive opportunities may use selfing as a means of reproductive assurance. We quantified the frequency of selfing and the fitness consequences for inbred versus outcrossed progeny of an annual kelp, the sea palm (Postelsia palmaeformis). Using experimentally established populations and microsatellite markers to assess the extent of selfing in progeny from six founding parents, we found the frequency of selfing was higher than expected in every population, and few fitness costs were detected in selfed offspring. Despite a decline in heterozygosity of 30 per cent in the first generation of selfing, self-fertilization did not affect individual size or reproduction, and correlated only with a marginally significant decline in survival. Our results suggest both that purging of deleterious recessive alleles may have already occurred and that selfing may be key to reproductive assurance in this species with limited dispersal. Postelsia has an alteration of a free-living diploid and haploid stage, where the haploid stage may provide increased efficiency for purging the genetic load. This life history is shared by many seaweeds and may thus be an important component of mating system evolution in the sea.     

Conservation genetics of endangeredBrasenia schreberi based on RAPD and AFLP markers

Brasenia schreberi J.F. Gmelin is a declared endangered species found in the lakes and ponds of South Korea. For planning its conservation strategy, we examined the genetic diversity within and among six populations, using randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP). Polymorphisms were more frequently detected per loci with AFLP (69.3%) than RAPD (36.8%). High genetic diversity was recognized within populations: polymorphic loci (PPL) values ranged from 36.3% in the CJM population to 74.5% in the GGT population, with a mean value of 47.8% based on AFLP markers. Great genetic differentiation (θ^B) was detected among the six populations (0.670 on RAPD and 0.196 on AFLP), and we calculated a low rate of gene flow (N_em), i.e., 0.116 on RAPD and 0.977 on AFLP. Furthermore, a Mantel test revealed that no correlation existed between genetic distances and geographical distances among the six local populations, based on RAPD or AFLP markers. These results are attributed to a number of factors, including an insufficient length of time for genetic diversity to be reduced following a natural decline in population size and isolation, adaptation of the genetic system to small population conditions, and a restricted gene flow rate. Based on both its genetic diversity and population structure, we suggest that a strategy for conserving and restoringB. schreberi must focus on maintaining historical processes, such as high levels of outbreeding, while monitoring increased gene flow among populations. This is because a reduction in genetic diversity as a result of genetic drift is undesirable.     

Patterns of genetic diversity in colonizing plant species: Nassauvia lagascae var. lanata (Asteraceae: Mutisieae) on Volcan Lonquimay, Chile

The effect of colonization on the distribution of genetic diversity within and among populations in relation to species characteristics remains an open empirical question. The objective of this study was to contrast genetic diversity within and among established and colonizing populations of Nassauvia lagascae var. lanata on Volcán Lonquimay (Araucanía Region, Chile), which erupted on 25 December 1988, and relate genetic diversity to biological characteristics of the populations. We analyzed a total of 240 individuals from 15 populations distributed along the Andes Cordillera using AFLP and obtained a total of 307 AFLP bands, of which 97.7% are polymorphic. Values of population differentiation (F(ST)) did not differ significantly among established and colonizing populations, but colonizing populations did have reduced levels of genetic divergence (as indicated by private and rare bands) and genetic variation (e.g., Shannon index). We conclude that a founder effect through limited numbers of founding propagules derived from nearby source populations has not yet been compensated for by subsequent population growth and migration. Low rates of secondary dispersal via running water, kin-structure within populations, and slow population growth seem to contribute to the slow recovery of genetic diversity.     

Genetic analysis reveals human-mediated long-distance dispersal among war cemeteries in Trifolium micranthum

Many grassland plant species have limited capacity to disperse their seeds beyond local boundaries by natural means. Meanwhile, various forms of human transportation are observed to provide long-distance dispersal. However, the contribution of human-mediated dispersal to the spatial dynamics of established (meta)populations on the regional scale has only scarcely been addressed. Trifolium micranthum is a very small legume that is rare in western Belgium. It is found (i) inland, as a lawn weed on war cemeteries that are managed by the Commonwealth War Graves Commission, and (ii) in coastal grasslands that are managed for conservation. These stations lie over 30?km apart, though interestingly, a number of satellite war cemeteries are found within the vicinity of the coastal reserves, and these also harbor T. micranthum. We have sampled plants from these populations to study their affinities through genetic analysis (AFLP). Results indicated that the coastal cemetery populations were closely related to the inland cemeteries and not to the coastal reserves. This most likely is the result of exchange of seeds with composted lawn material among regions, whereas mowing machinery and livestock may effectuate frequent dispersal within regions. Assignment tests nonetheless indicated limited genetic admixture to have taken place at the coastal cemeteries. Thus, human management is responsible for the realization of gene flow among these remote gene pools. Human-mediated long-distance dispersal is likely to play a role in the local or regional dynamics of many other native plants, including more common and well-dispersing species.     

Fine‐scale hierarchical genetic structure and kinship analysis of the ascidian Pyura chilensis in the southeastern Pacific

Studying population structure and genetic diversity at fine spatial scales is key for a better understanding of demographic processes that influence population connectivity. This is particularly important in marine benthic organisms that rely on larval dispersal to maintain connectivity among populations. Here, we report the results of a genetic survey of the ascidian Pyura chilensis from three localities along the southeastern Pacific. This study follows up on a previous report that described a genetic break in this region among localities only 20 km apart. By implementing a hierarchical sampling design at four spatial levels and using ten polymorphic microsatellite markers, we test whether differences in fine‐scale population structure explain the previously reported genetic break. We compared genetic spatial autocorrelations, as well as kinship and relatedness distributions within and among localities adjacent to the genetic break. We found no evidence of significant autocorrelation at the scale up to 50 m despite the low dispersal potential of P. chilensis that has been reported in the literature. We also found that the proportion of related individuals in close proximity (<1 km) was higher than the proportion of related individuals further apart. These results were consistent in the three localities. Our results suggest that the spatial distribution of related individuals can be nonrandom at small spatial scales and suggests that dispersal might be occasionally limited in this species or that larval cohorts can disperse in the plankton as clustered groups. Overall, this study sheds light on new aspects of the life of this ascidian as well as confirms the presence of a genetic break at 39°S latitude. Also, our data indicate there is not enough evidence to confirm that this genetic break can be explained by differences in fine‐scale genetic patterns among localities.     

Clonal diversity and genetic differentiation of <Emphasis Type="Italic">Maianthemum bifolium</Emphasis> among forest fragments of different age

Maianthemum bifolium Schmidt (May Lily) is a woodland species with low colonisation ability and high demands for seedling establishment conditions. To study the colonisation process, we analysed the clonal organisation and population structure of Maianthemum bifolium populations in a number of forest fragments using AFLP. A total of 129 genets were identified. Most (41/53) patches of M. bifolium in recent (less than 80 years old) and old (at least 175 years of age) parts of the woodlands contained single genets. Only one of the 12 patches with multiple genotypes showed intermingled growth. Besides seed dispersal also dispersal of vegetative material contributed to colonisation since five genotypes were found in more than one patch, with patches up to 51 m apart. Population differentiation between populations in different forests was significant (F_ST = 0.10) and indicated low gene flow. This level of differentiation was already found between populations in different parts of the same forest, just over 200 m apart. In fact, only two adjacent populations were not significantly differentiated, one population located in old forest whereas the other was established next to it on a former pasture re-forested after 1916. Limited gene flow is also consistent with the decrease of genetic similarities with physical distance, which relationship is highly significant but only for distances up to 400 m.     

An unusual case of seed dispersal in an invasive aquatic; yellow flag iris (<Emphasis Type="Italic">Iris pseudacorus</Emphasis>)

Invasive aquatic plants typically reproduce vegetatively, but there have been conflicting hypotheses of invasive aquatic yellow flag iris dispersing primarily by seed versus rhizome fragmentation. We performed genetic analysis of 20 aquatic yellow flag iris populations across the Pacific Northwest, USA, with leaf tissue taken from plants between 2 and 5 m apart. We found 167 unique genotypes in 171 plants, and we never found genetically identical plants from different populations. We found that 99.1 % of seed is viable. Our results support that this obligately outcrossing invasive disperses almost entirely by seed, not rhizome fragmentation. We found no significant relationship between genetic and geographic distance across the Pacific Northwest, suggesting recent long distance dispersal and/or multiple founding events. Bayesian analysis shows the presence of two major genotypic clusters within our collections which also suggests more than one distinct genetic source for the invasion. These processes have led to genetically distinct populations that can be geographically close. Our findings are unusual for an aquatic invasive, and inform yellow flag iris managers of two things: (1) to limit dispersal, development of mature seed in the field should be prevented; and (2) if classical biological control is proposed, an agent guild that limits seed production would be effective for managing most dispersal.     

Genetic structure of Rhododendron ferrugineum at a wide range of spatial scales

Rhododendron ferrugineum L. (Ericaceae) is a subalpine shrub found throughout the Pyrenees and Alps at elevations of 1600-2200 m. We examined relationships between genetic and geographic distance, using 115 dominant amplified fragment length polymorphism (AFLP) markers to assess genetic structure over a wide range of spatial scales. We sampled 17 sites with distances of 4 km to more than 1000 km between them. At these scales we detected no association between geographic distance and genetic distance between populations. This suggests that genetic drift and gene flow are not in equilibrium for these populations. This pattern could have resulted from recent and rapid postglacial colonization, from more recent human disturbance, or as a function of frequent and random "natural" long-distance colonization. At two of our sites we used transects (two horizontal and two vertical with respect to slope at each site) to sample at distances ranging from 10 m to more than 5000 m. At this scale we observed a positive relationship between genetic and spatial distance along two vertical transects, one at each site. We hypothesize that isolation-by-distance at this smaller scale is a function of restricted gene flow via seed dispersal.     

Spatial genetic structure in wild cherry (Prunus avium L.): I. variation among natural populations of different density

Conservation of forest genetic resources requires intensive knowledge of the spatial arrangement of genetic diversity. In this study, we used four natural Prunus avium stands in Germany with contrasting for densities to understand patterns of spatial genetic structure. To this end, we genotyped adults and saplings at eight microsatellite markers, 54 AFLP loci and at the gametophytic incompatibility locus. We estimated levels of clonal propagation, spatial genetic structure and gene dispersal. High mortality occurred among young clonal individuals, as depicted by the lower clonal diversity in saplings. Contrasting levels of spatial genetic structure were observed among markers, ontogenic stages and populations. AFLP were more efficient for detecting spatial autocorrelation but did not allow us to differentiate low and high density populations, while high density populations showed substantially stronger spatial genetic structure at microsatellite loci. Furthermore, kinship decreased with tree age only in low density stands. We discuss the present results in terms of population history, pollen and seed dispersal and population density. Although conspecific density seems to be an interesting indicator of genetic diversity for conservation programmes, we still need to disentangle the relative influence of clonal propagation and density on the strength of spatial genetic structure. Simulation studies are needed to further address this question.     

Fine-scale genetic structure and gene dispersal inferences in 10 neotropical tree species

The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift-dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies.     

Tug of war between continental gene flow and rearing site philopatry in a migratory bird: the sex-biased dispersal paradigm reconsidered

Nonrandom dispersal has been recently advanced as a mechanism promoting fine-scale genetic differentiation in resident populations, yet how this applies to species with high rates of dispersal is still unclear. Using a migratory species considered a classical example of male-biased dispersal (the greater snow goose, Chen caerulescens atlantica ), we documented a temporally stable fine-scale genetic clustering between spatially distinct rearing sites (5–30 km apart), where family aggregates shortly after hatching. Such genetic differentiation can only arise if, in both sexes, dispersal is restricted and nonrandom, a surprising result considering that pairing occurs among mixed flocks of birds more than 3000 km away from the breeding grounds. Fine-scale genetic structure may thus occur even in migratory species with high gene flow. We further show that looking for genetic structure based on nesting sites only may be misleading. Genetically distinct individuals that segregated into different rearing sites were in fact spatially mixed during nesting. These findings provide new, scale-dependent links between genetic structure, pairing, and dispersal and show the importance of sampling different stages of the breeding cycle in order to detect a spatial genetic structure.     

The impact of mating systems and dispersal on fine‐scale genetic structure at maternally,paternally and biparentally inherited markers

For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens—hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual‐level simulations to investigate the effects of dispersal and mating system on fine‐scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine‐scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex‐biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine‐scale genetic structure.     

Genetic diversity and phylogenetic relationships in alder,Alnus firma, revealed by AFLP

Molecular markers for alder,Alnus firma Sieb. et Zucc, have not been studied extensively. Here, we used amplified fragment length polymorphism (AFLP) to investigate genetic relationships among 15 natural populations. EcoRI-ACG + Msel-CTG combinations revealed the highest polymorphism (62.2%). A total of 171 DNA fragments were identified. On average, 58.1% of the AFLP markers that were generated using four primer pairs were polymorphic. Diversity was insignificant among the populations. The combination of a wind-pollinated, outcrossing breeding system along with large population sizes, and the ability to regenerate by stump sprouting may explain the high level of genetic diversity within this species. The majority (98%) of the genetic variance resided within populations. The average number of individuals that were exchanged between populations per generation was very high (N _em = 12.3). Gene dispersal in alder is apparently by seed dispersalvia water and human activity as well as through pollen. Five individuals per population were claded in the same cluster.     

Genetic Variation among <Emphasis Type="Italic">Ambystoma</Emphasis> Breeding Populations on the Savannah River Site

We surveyed 16 Carolina bay breeding ponds for Ambystoma salamanders. Tail tissue samples were collected from adult and juvenile mole salamanders (A. talpoideum), marbled salamanders (A. opacum), and spotted salamanders (A. maculatum) captured leaving the Carolina bays. We used amplified fragment length polymorphisms (AFLP) to determine the genetic variation associated with the breeding populations. The Carolina bays could be considered as individual populations, metapopulation groups, or as one big metapopulation depending on gene flow between these bays. Bays range from less than 100 m apart to more than 24 km apart, much further than any reported movement for these species. Animals were marked in the field. We documented little movement of salamanders between breeding locations. Using 392 polymorphic bands produced with the AFLP technique, we were able to separate the samples into the correct species from which the tissues were collected. However, within species analyses failed to find structure associated with populations of salamanders. We failed to document a correlation between geographic and genetic distance (Mantel r = 0.05235, P=0.6800 for mole salamanders; r = 0.46077, P=0.9547 for marbled salamanders). Only 27.8% of mole salamanders and 60.9% of marbled salamanders were assigned back to the population of capture. The majority of the genetic variation was attributable to the individual as opposed to the population. The results of this study suggest that while the majority of these salamanders may be philopatric, some mixing maybe occurring or alternatively, that these populations have not been genetically isolated for sufficient time to develop unique genotypes through drift.     

‘Good-genes’ and ‘compatible-genes’ effects in an Alpine whitefish and the information content of breeding tubercles over the course of the spawning season

Abies ziyuanensis is a highly endangered fir species endemic to South China. Unlike other Abies species that are distributed in areas with cold climates, A. ziyuanensis is restricted to several isolated island-like localities at subtropical mountains. In this study, we used dominant amplified fragment length polymorphism (AFLP) and co-dominant simple sequence repeats (SSR) markers to infer the genetic structure of A. ziyuanensis. Seven populations consisting of 139 individuals were sampled across their whole distribution. A. ziyuanenesis has a relatively low level of genetic variation, with a mean genetic diversity per population (He) of 0.136 (AFLP) and 0.337 (SSR), which is lower than that of other reported endemic species based on the same kind of marker. We observed high population differentiation, with Gst = 0.482 (AFLP) and Fst = 0.250 (SSR), among the seven populations. AMOVA also detected significant differentiation among populations (Φst (AFLP) = 0.550 and Φst (SSR) = 0.289) and among regions (Φct (AFLP) = 0.139 and Φct (SSR) = 0.135) in both marker types. Both ongoing evolutionary forces (e.g., genetic drift resulting from small population size) and historical events (e.g., population contraction and fragmentation during and after the Quaternary glacial cycles) may have contributed to the genetic structure in A. ziyuanensis.     

Landscape genetics of the widespread ground-beetle Carabus auratus in an agricultural region

The brachypterous carabid beetle Carabus auratus was chosen as an indicator organism for analysing the relationship between landscape composition and population genetic structure (AFLP) in an agricultural region. We selected eight landscape sections with different landscape composition. The landscapes were analysed in 7 radii ranging from 500 to 2000 m (step size: 250 m). It is shown that the population as a whole exhibits a moderate genetic differentiation with geographically restricted genetic exchange. Genetic diversity of local populations is high. It is positively associated with increasing numbers of migrants estimated from the molecular data. This indicates that even widespread species with a presumed low dispersal capacity may exhibit high levels of genetic exchange at larger spatial scales. The availability of grassland within the landscape sections enhanced genetic diversity of local populations at larger spatial scales and explained over 50% of the observed genetic diversity. Thus, the unexpectedly high genetic exchange of C. auratus critically depends on the availability of suitable landscape features. Our results emphasise the need to take into account the adverse effects of ongoing changes in landscape composition on the genetic diversity even of widespread species when aiming at conserving genetic and functional diversity in agricultural landscapes.     

Genetic structure in populations of an ancient woodland sedge, Carex sylvatica Hudson, at a regional and local scale

Wood sedge (Carex sylvatica) is a well-known ancient woodland species with a long-term persistent seed bank and a caespitose growth habit. All thirteen isolated Carex sylvatica populations in the Dutch Rhine floodplain (including the river branches Waal and IJssel) were mapped in detail and analysed for genetic variation at a large number of AFLP loci and one microsatellite locus. Across all populations, only 40 % of the sampled individuals (n=216) represented a unique genotype. A high number of the studied patches (spatial clusters of tussocks, 2-10 m in diameter) within populations contained only one or a few genotypes. Identical plants (tussocks) were also found 20-500 m apart and in one case even 1000 m apart. Observed heterozygosity levels (H(O)=0.029) were low, indicating low levels of gene flow, which is in agreement with the selfing nature of other caespitose sedges. Although the number of genotypes in populations is low, these genotypes are genetically very distinct and variation within populations accounted for 55% of the total variation. The absence of a correlation between genetic and geographic distances among populations, and the scattered distribution of genotypes among patches within woodlands, support our hypothesis of rare establishments and subsequent local dispersal within woodlands in this forest floor species, which may benefit from and partly depend on human land use and forest management activities.