Microsatellites, from molecules to populations and back

Genetic structure of the deep-sea coral Lophelia pertusa in the northeast Atlantic revealed by microsatellites and internal transcribed spacer sequences

The azooxanthellate scleractinian coral Lophelia pertusa has a near-cosmopolitan distribution, with a main depth distribution between 200 and 1000 m. In the northeast Atlantic it is the main framework-building species, forming deep-sea reefs in the bathyal zone on the continental margin, offshore banks and in Scandinavian fjords. Recent studies have shown that deep-sea reefs are associated with a highly diverse fauna. Such deep-sea communities are subject to increasing impact from deep-water fisheries, against a background of poor knowledge concerning these ecosystems, including the biology and population structure of L. pertusa. To resolve the population structure and to assess the dispersal potential of this deep-sea coral, specific microsatellites markers and ribosomal internal transcribed spacer (ITS) sequences ITS1 and ITS2 were used to investigate 10 different sampling sites, distributed along the European margin and in Scandinavian fjords. Both microsatellite and gene sequence data showed that L. pertusa should not be considered as one panmictic population in the northeast Atlantic but instead forms distinct, offshore and fjord populations. Results also suggest that, if some gene flow is occurring along the continental slope, the recruitment of sexually produced larvae is likely to be strongly local. The microsatellites showed significant levels of inbreeding and revealed that the level of genetic diversity and the contribution of asexual reproduction to the maintenance of the subpopulations were highly variable from site to site. These results are of major importance in the generation of a sustainable management strategy for these diversity-rich deep-sea ecosystems.

Stabilizing selection on genomic divergence in a wild fish population

Conservation programs use breeding protocols to increase genomic divergence (by mating genetically dissimilar individuals) in an attempt to circumvent population declines resulting from inbreeding depression. However, disruption of either beneficial gene complexes or local genetic adaptations can lead to outbreeding depression, and thus, there should be a reduction in fitness of individuals at either end of the genomic divergence continuum. Although such simultaneous inbreeding and outbreeding depression has been observed in plant populations, it rarely has been demonstrated in animal populations. Here, I use both genetic and phenotypic measures to show that there is stabilizing selection on genomic divergence in a wild population of bluegill sunfish (Lepomis macrochirus). I also show that breeding individuals that exercise mate choice produce offspring that are closer to the optimal level of genomic divergence than random mating alone would predict.

Genome and genomics of schistosomes

Schistosomes infect over 200 million people and 600 million are at risk. Genomics and post-genomic studies of schistosomes will contribute greatly to developing new reagents for diagnostic purposes and new vaccines that are of interest to the biotechnology industry. In this review, the most recent advances in these fields as well as new projects and future perspectives will de described. A vast quantity of data is publicly available, including short cDNA and genomic sequences, complete large genomic fragments, and the mitochondrial genomes of three species of the genus Schistosoma. The physical structure of the genome is being studied by physically mapping large genomic fragments and characterizing the highly abundant repetitive DNA elements. Bioinformatic manipulations of the data have already been carried out, mostly dealing with the functional analysis of the genes described. Specific search tools have also been developed. Sequence variability has been used to better understand the phylogeny of the species and for population studies, and new polymorphic genomic markers are currently being developed. The information generated has been used for the development of post-genomic projects. A small microarray detected genes that were differentially expressed between male and female worms. The identification of two-dimensional spots by mass spectrometry has also been demonstrated.

A morphological cline in Eucalyptus: a genetic perspective

The putative hybrid zone between Eucalyptus populnea and E. brownii is examined using morphological and molecular techniques. This species complex displays continuous morphological variation across the study area, which has been previously interpreted as the product of hybridization between allopatric species. A microsatellite analysis indicates that there was little genetic structuring across the morphological cline and only low levels of population differentiation. The nested clade analysis of the JLA+ region of the chloroplast DNA (cpDNA) indicates that the geographical distribution of cpDNA haplotypes is unlikely to be the result of historical hybridization events, and that restricted seed-mediated gene flow with isolation by distance is responsible for the phylogeographical distribution. A more plausible explanation for the origin and persistence of the morphological cline is that the process of continuous morphological diversification has been promoted by a directional selection gradient. This study addresses species status within Eucalyptus and the belief that hybridization is widespread and is an important process in the group's evolution.

Population genetic structure of mahogany (Swietenia macrophylla King, Meliaceae) across the Brazilian Amazon, based on variation at microsatellite loci: implications for conservation

Mahogany (Swietenia macrophylla, Meliaceae) is the most valuable and intensively exploited Neotropical tree. No information is available regarding the genetic structure of mahogany in South America, yet the region harbours most of the unlogged populations of this prized hardwood. Here we report on the genetic diversity within and the differentiation among seven natural populations separated by up to 2100 km along the southern arc of the Brazilian Amazon basin. We analysed the variation at eight microsatellite loci for 194 adult individuals. All loci were highly variable, with the number of alleles per locus ranging from 13 to 27 (mean = 18.4). High levels of genetic diversity were found for all populations at the eight loci (mean HE = 0.781, range 0.754-0.812). We found moderate but statistically significant genetic differentiation among populations considering both estimators of FST and RST, theta = 0.097 and rho = 0.147, respectively. Estimates of theta and rho were significantly greater than zero for all pairwise population comparisons. Pairwise rho-values were positively and significantly correlated with geographical distance under the isolation-by-distance model. Furthermore, four of the populations exhibited a significant inbreeding coefficient. The finding of local differentiation among Amazonian mahogany populations underscores the need for in situ conservation of multiple populations of S. macrophylla across its distribution in the Brazilian Amazon. In addition, the occurrence of microgeographical genetic differentiation at a local scale indicates the importance of maintaining populations in their diverse habitats, especially in areas with mosaics of topography and soil.

Factors affecting polymorphism at microsatellite loci in bread wheat [ Triticum aestivum (L.) Thell]: effects of mutation processes and physical distance from the centromere

The effects of factors known to influence the level of polymorphism at microsatellite loci were studied using 99 markers and seven lines of bread wheat. Mutational factors as well as indirect selective events shape diversity at these loci. Theory predicts that the selection of favorable alleles should reduce polymorphism at neutral neighboring loci in genomic areas with low recombination rates. In wheat, local recombination rate is positively correlated with physical distance from the centromere. Seventy four loci among the 99 used could be physically located on the chromosome. We studied how the following affected the diversity among a set of inbred lines: the length of the alleles, the motif (CA versus CT), the structure of the loci (perfect versus imperfect) and the chromosomal position of the loci. For each locus, we determined whether the polymorphism observed at a locus was compatible with the Stepwise Mutation Model (SMM) or the Two-Phase Model (TPM). Both the mutation rate and the compatibility with the SMM or the TPM were shown to be variable between loci. Wheat microsatellite loci were found to be more variable when segregating alleles were perfect and had long motifs (composed of many repetitions). Diversity observed at 19 loci was not compatible with the SMM. Loci located in distal regions, with presumably high recombination rates, had longer allele sizes and were more polymorphic than loci located in proximal regions. We conclude that both mutation factors and indirect selective events vary according to the local recombination rate and therefore jointly influence the level of polymorphism at microsatellite loci in wheat.

Timing of first feeding and life-history strategies in salmon: genetic data

To investigate the relationship between genetic composition and some physiological traits of interest (age at smoltification, precocious maturation in male parr) in early and late first feeding Atlantic salmon, genetic variation at 6 isozyme and 8 microsatellite loci was examined. Early and late first feeding salmon showed different allelic and genotypic distributions at both isozyme and microsatellite loci. A positive relation between enzymatic loci heterozygosity and precocious active alimentation and earlier smoltification (S1 cf. S2) were also found.

Identification of Atlantic hake species by a simple PCR-based methodology employing microsatellite loci

Three Atlantic hake species (Merluccius merluccius, M. bilinearis, and M. hubbsi) were PCR typed for two microsatellite loci. A blind survey of the markers in samples of the three species determined the suitability of microsatellite loci for identification of hake product. All the analyzed samples were correctly assigned to the corresponding species. Typing of processed products (fish fingers, preprocessed frozen pieces) employing an automated sequencer was successful. This simple (PCR + fragment size) automated determination method is faster than any other method yet described for identification of hake commercial products.

Development of single-copy RFLP markers for population genetic studies of Phialocephala fortinii and closely related taxa

Single-copy RFLP markers were developed for the root endophytic fungus Phialocephala fortinii. After an initial screening of 40 probes with four restriction enzymes, EcoRV and HindIII were chosen to analyse 31 strains of P. fortinii and nine strains of a closely related morphotype (Type 1) which have known ISSR-PCR or allozyme phenotypes. Type 1 isolates and a single genetically different isolate with Type 1 like morphology, a representative of a possible third taxon, showed unique alleles with several probes and both restriction enzymes. Consequently, both taxa were easily distinguishable from P. fortinii isolates. Whereas EcoRV in combination with seven probes revealed only eight multi-locus haplotypes among 17 ISSR phenotypes, HindIII in combination with 12 probes was able to distinguish all ISSR and/or allozyme phenotypes except two pairs of strains. Strains of P. fortinii showed a high gene diversity, and up to 15 alleles per locus were observed among the 31 strains of P. fortinii. The 12 probes used in combination with HindIII were (partially) sequenced and BLAST searches showed no similarities with known sequences indicating that they probably are non-coding regions of the genome. Enzyme-probe combinations suitable to indicate the genetic structure of P. fortinii and Type 1 populations were easily identified in the present study. This opens up avenues to study communities of the P. fortinii complex exposed to various environments and management intensities, and will help to promote the understanding of these extremely successful organisms.

Genetic variation among interconnected populations of Catostomus occidentalis: implications for distinguishing impacts of contaminants from biogeographical structuring

Exposure to contaminants can affect survivorship, recruitment, reproductive success, mutation rates and migration, and may play a significant role in the partitioning of genetic variation among exposed and nonexposed populations. However, the application of molecular population genetic data to evaluate such influences has been uncommon and often flawed. We tested whether patterns of genetic variation among native fish populations (Sacramento sucker, Catostomus occidentalis) in the Central Valley of California were consistent with long-term pesticide exposure history, or primarily with expectations based on biogeography. Field sampling was designed to rigorously test for both geographical and contamination influences. Fine-scale structure of these interconnected populations was detected with both amplified fragment length polymorphisms (AFLP) and microsatellite markers, and patterns of variation elucidated by the two marker systems were highly concordant. Analyses indicated that biogeographical hypotheses described the data set better than hypotheses relating to common historical pesticide exposure. Downstream populations had higher genetic diversity than upstream populations, regardless of exposure history, and genetic distances showed that populations from the same river system tended to cluster together. Relatedness among populations reflected primarily directions of gene flow, rather than convergence among contaminant-exposed populations. Watershed geography accounted for significant partitioning of genetic variation among populations, whereas contaminant exposure history did not. Genetic patterns indicating contaminant-induced selection, increased mutation rates or recent bottlenecks were weak or absent. We stress the importance of testing contaminant-induced genetic change hypotheses within a biogeographical context. Strategic application of molecular markers for analysis of fine-scale structure, and for evaluating contaminant impacts on gene pools, is discussed.

Patterns of population subdivision and gene flow in the ant Nothomyrmecia macrops reflected in microsatellite and mitochondrial DNA markers

The Australian endemic ant Nothomyrmecia macrops is renowned for having retained a large proportion of 'primitive' morphological and behavioural characters. Another less studied peculiarity of this species is the production of short-winged (brachypterous) female sexuals, which presumably are poor dispersers. The males, in contrast, bear a full set of normally developed wings and thus may disperse widely. We investigated patterns of genetic differentiation within and among three distantly separated populations in South Australia using nine polymorphic microsatellite loci and four regions of mitochondrial DNA (COI, COII, Cytb, lrRNA). We sampled eight subpopulations, one in the Lake Gilles CP, two near Penong and five around Poochera where distances ranged from 360 km to sites separated by 2-10 km. Only little differentiation was found at the local scale (within the assumed dispersal distance of males) using nuclear markers, whereas the three distant locations were moderately differentiated (FST = 0.06). Mitochondrial DNA genetic structure was much more pronounced on all scales (phiST = 0.98), with regular differences in both haplotype composition and frequency even occurring among closely located sites. This lack of congruence between nuclear and mitochondrial markers strongly suggests limited female dispersal and male-biased gene flow among populations. As to the conservation status of the species there is no evidence for severe population reductions in the recent past, which would have left populations genetically depauperate.

Comparative genetic study confirms exceptionally low genetic variation in the ancient and endangered relictual conifer, Wollemia nobilis (Araucariaceae)

The Wollemi pine, Wollemia nobilis (Araucariaceae), was discovered in 1994 as the only extant member of the genus, previously known only from the fossil record. With fewer than 100 trees known from an inaccessible canyon in southeastern Australia, it is one of the most endangered tree species in the world. We conducted a comparative population genetic survey at allozyme, amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) loci in W. nobilis, Araucaria cunninghamii and Agathis robusta - representatives of the two sister genera. No polymorphism was detected at 13 allozyme loci, more than 800 AFLP loci or the 20 SSR loci screened in W. nobilis. In Ag. robusta only one of 12 allozyme loci, five of 800 AFLP loci and none of the 15 SSR loci were variable. For A. cunninghamii, 10 of > 800 AFLP loci and five of 20 SSR loci were variable. Thus low genetic diversity characterizes all three species. While not ruling out the existence of genetic variation, we conclude that genetic diversity is exceptionally low in the Wollemi pine. To our knowledge this is the most extreme case known in plants. We conclude that the combination of small population effects, clonality and below-average genetic variation in the family are probable contributing factors to the low diversity. The exceptionally low genetic diversity of the Wollemi pine, combined with its known susceptibility to exotic fungal pathogens, reinforces current management policies of strict control of access to the pines and secrecy of the pine locations.

Host-based divergence in populations of the pea aphid: insights from nuclear markers and the prevalence of facultative symbionts

In North America, the pea aphid Acyrthosiphon pisum encompasses ecologically and genetically distinct host races that offer an ideal biological system for studies on sympatric speciation. In addition to its obligate symbiont Buchnera, pea aphids harbour several facultative and phylogenetically distant symbionts. We explored the relationships between host races of A. pisum and their symbiotic microbiota to gain insights into the historical process of ecological specialization and symbiotic acquisition in this aphid. We used allozyme and microsatellite markers to analyse the extent of genetic differentiation between populations of A. pisum on pea, alfalfa and clover in France. In parallel, we examined: (i) the distribution of four facultative symbionts; and (ii) the genetic variation in the Buchnera genome across host-associated populations of A. pisum. Our study clearly demonstrates that populations of A. pisum on pea, clover and alfalfa in France are genetically divergent, which indicates that they constitute distinct host races. We also found a very strong association between host races of A. pisum and their symbiotic microbiota. We stress the need for phylogeographic studies to shed light on the process of host-race formation and acquisition of facultative symbionts in A. pisum. We also question the effects of these symbionts on aphid host fitness, including their role in adaptation to a host plant.

Long-distance colonization, isolation by distance, and historical demography in a relictual Mexican pinyon pine (Pinus nelsonii Shaw) as revealed by paternally inherited genetic markers (cpSSRs)

Pinus nelsonii is a relictual pinyon pine distributed across a wide altitudinal range in semiarid zones in Mexico near the border between the States of Nuevo León and Tamaulipas. It also occurs in small patches in the State of San Luis Potosí. Pinus nelsonii is classified in the monotypic subsection Nelsoniae, separated from other pinyon pines (subsection Cembroides), because it possesses several distinctive characters including persistent fascicle sheaths, connate needles, and a distinctive wood anatomy. In the present study, chloroplast simple sequence repeats (cpSSRs) were used to estimate genetic variation in most known populations (nine) of P. nelsonii. The genetic variation (HT = 0.73; 27 haplotypes in 256 individuals) is moderate when compared to other pine species. Population differentiation ranged between low and moderate (FST = 0.13 and RST = 0.05), as did the Nei and Goldstein genetic distances between populations. However, this pattern varied depending on whether the infinite alleles or stepwise mutation model was used. In the former case a significant isolation by distance was found, but not in the latter. A significant association between geographical and genetic structure in one clade, through a nested clade analysis, was found, which suggested long-distance colonization between 125000 and 309000 years ago. We found weak evidence for a population expansion. A mismatch distribution suggests that P. nelsonii populations underwent an expansion 4.25 times their size between 59000 and 146000 years ago. On the other hand, the populations' star-like phylogeny and a slight parabolic relationship between coalescence times and lineage number also suggest weak population expansion. Overall, this species appears to have been in demographic stasis for a large proportion of the time detected by the markers used.

Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane

The use of maize microsatellite markers as a potential cost-effective method for molecular analysis of sugarcane was evaluated. Of the 34 primer pairs obtained from maize genomic libraries, 14 showed repeatable amplifications in Saccharum species clones, commercial hybrids, and the related genera Erianthus, accounting for 41.17% cross transferability. Complex banding patterns were encountered in sugarcane with the number of amplified fragments ranging from 7 to 14 with an average of 10 per primer, indicating the high polyploidy and heterozygosity existing in sugarcane. Phenetic analysis of the SSR polymorphisms produced by nine primers could clearly differentiate the different species of Saccharum and Erianthus and revealed the relationships that existed between them. Genetic similarity co-efficient indicated low diversity existing among the S. officinarum clones (82%) and a relatively higher level of diversity in the S. spontaneum clones (69.7%). Higher level of divergence of Erianthus from Saccharum was also clearly estabilished. Five primers produced genus- and species-specific fragments for Erianthus, S. spontaneum, S. officinarum, and S. barberi. The polymorphic primers, when tested on a panel of 30 commercial sugarcane cultivars, revealed a broad range (32.4-83.3%) of pair-wise similarity values, indicating their ability to detect high levels of polymorphism. A combination of two primers could differentiate all the varieties, further emphasizing their potential in fingerprinting and varietal identification.

Cross-species amplification from crop soybean Glycine max provides informative microsatellite markers for the study of inbreeding wild relatives

The development of microsatellite markers through transfer of primers from related species (cross-species amplification) remains a little-explored alternative to the de novo method in plants. In this study of 100 microsatellite loci from Glycine max, we examined two aspects of primer transfer. First, we tested if source locus properties can predict primer transfer and polymorphism in Glycine cyrtoloba and Glycine clandestina. We transferred 23 primers to G. cyrtoloba and 42 to G. clandestina, with 19 loci polymorphic within G. clandestina. However, we could not predict transfer or polymorphism from the source locus properties. Second, we evaluated the subset of 11 polymorphic loci for study in G. clandestina populations representing two local morphotypes. All loci were informative within populations (population mean He +/- SE = 0.58 +/- 0.04). We directly sequenced 28 alleles at 4 representative loci. The allelic patterns and sequencing results established that 8 of 11 loci were typical microsatellites, confirming the utility of primer transfer as an alternative to de novo development. Additionally, we found that morphotypic differentiation between populations was paralleled by changes in polymorphism level at six loci and size homoplasy at one locus. We interpret these patterns as being a product of selfing in G. clandestina. Our results demonstrate the value of allele sequence knowledge for the most effective use of microsatellites.

Molecular genetic variability of Australian isolates of five cereal rust pathogens

Rust fungi cause economically important diseases of cereals, and their ability to rapidly evolve new virulent races has hindered attempts to control them by genetic resistance. PCR-based molecular tools may assist in understanding the genetic structure of pathogen populations. The high multiplex DNA fingerprinting techniques, amplified fragment length polymorphisms (AFLP), selectively amplified microsatellites (SAM) and sequence-specific amplification polymorphisms (S-SAP) were assessed for their potential in investigations of the genetic relationships among isolates of the wheat rust pathogens, Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and P. striiformis f. sp. tritici (Pst), the oat stem rust pathogen P. graminis f. sp. avenae (Pga), and a putative new P. striiformis special form tentatively designated Barley grass yellow rust (Bgyr). Marker information content, as indicated by the number of species-specific fragments, polymorphic fragments among pathotypes, percentage of polymorphic loci, and the marker index, was highest for the SAM assay, followed by the AFLP and S-SAP assays. UPGMA analysis revealed that all marker types efficiently discriminated the five different taxa and Mantel tests revealed significant correlations between the marker types. Within pathogen groups, the marker types differed in the amount of variation detected among isolates; however, the major differences were consistent and polymorphism was generally low. This was reflected by the AMOVA analysis that significantly partitioned 90% of the genetic variation between taxa. Of the three marker types, SAMS were the most informative, and have the potential for the development of locus-specific microsatellites.

Effect of habitat fragmentation on levels and patterns of genetic diversity in natural populations of the peat moss Polytrichum commune

Peat bogs represent unique ecosystems that are under particular threat from fragmentation due to peat harvesting, with only 38% of the original peatland in Europe remaining intact and unaffected by peat cutting, drainage and silviculture. In this study, we have used microsatellite markers to determine levels and patterns of genetic diversity in both cut and uncut natural populations of the peat moss Polytrichum commune. Overall diversity levels suggest that there is more genetic variation present than had previously been assumed for bryophytes. Despite this, diversity values from completely cut bogs were found to be lower than those from uncut peatlands (average 0.729 versus 0.880). In addition, the genetic diversity was more highly structured in the cut populations, further suggesting that genetic drift is already affecting genetic diversity in peat bogs subjected to fragmentation.

Population differentiation of Phlebotomus perniciosus in Spain following postglacial dispersal

Comparative sequencing of mitochondrial cytochrome b (Cyt b) and isoenzyme analyses have not resolved the population structure of the Iberian lineage of the sandfly Phlebotomus perniciosus, the most widespread vector of Leishmania infantum (Protozoa, Trypanosomatidae) to humans and dogs in the western Mediterranean subregion. Allelic variation at trinucleotide microsatellite loci was investigated in 13 Spanish populations of P. perniciosus. Four out of five loci showed significant differentiation between (pairwise F(ST)>0.23), but not within (pairwise F(ST)&<0.05), two regional groups of populations (southern and northeastern). All Cyt b sequences belonged to the Iberian lineage, which differs by six fixed nucleotide differences from the typical lineage found in northwest Africa, Malta and Italy. The northeastern group of Spanish populations had a reduced number of microsatellite alleles (16 out of the 29 present in the southern populations), indicating its derivation as a peripheral isolate following the species' dispersal from a southern Ice Age refuge 8000-12 000 years ago. Pairwise F(ST) values did not increase with geographical distance between populations, over distances of 246-850 km (between regions) and 16-491 km (within regions). This suggests that the two regional groups of populations remain isolated, but that within each region there are no significant permanent barriers to gene flow between contiguous populations. These findings will help to predict the capacity of this sandfly to disperse, and originate new foci of leishmaniasis, in response to climate warming.

Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation

The mutation process at microsatellite loci typically occurs at high rates and with stepwise changes in allele sizes, features that may introduce bias when using classical measures of population differentiation based on allele identity (e.g., F(ST), Nei's Ds genetic distance). Allele size-based measures of differentiation, assuming a stepwise mutation process [e.g., Slatkin's R(ST), Goldstein et al.'s (deltamu)(2)], may better reflect differentiation at microsatellite loci, but they suffer high sampling variance. The relative efficiency of allele size- vs. allele identity-based statistics depends on the relative contributions of mutations vs. drift to population differentiation. We present a simple test based on a randomization procedure of allele sizes to determine whether stepwise-like mutations contributed to genetic differentiation. This test can be applied to any microsatellite data set designed to assess population differentiation and can be interpreted as testing whether F(ST) = R(ST). Computer simulations show that the test efficiently identifies which of F(ST) or R(ST) estimates has the lowest mean square error. A significant test, implying that R(ST) performs better than F(ST), is obtained when the mutation rate, mu, for a stepwise mutation process is (a) >/= m in an island model (m being the migration rate among populations) or (b) >/= 1/t in the case of isolated populations (t being the number of generations since population divergence). The test also informs on the efficiency of other statistics used in phylogenetical reconstruction [e.g., Ds and (deltamu)(2)], a nonsignificant test meaning that allele identity-based statistics perform better than allele size-based ones. This test can also provide insights into the evolutionary history of populations, revealing, for example, phylogeographic patterns, as illustrated by applying it on three published data sets.

Fine-scale genetic structure and gene flow within Costa Rican populations of mahogany (Swietenia macrophylla)

Fine-scale structure of genetic diversity and gene flow were analysed in three Costa Rican populations of mahogany, Swietenia macrophylla. Population differentiation estimated using AFLPs and SSRs was low (38.3 and 24%) and only slightly higher than previous estimates for Central American populations based on RAPD variation (20%). Significant fine-scale spatial structure was found in all of the surveyed mahogany populations and is probably strongly influenced by the limited seed dispersal range of the species. Furthermore, a survey of progeny arrays from selected mother trees in two of the plots indicated that most pollinations involved proximate trees. These data indicate that very little gene flow, via either pollen or seed, is occurring between blocks of mahogany within a continuous or disturbed forest landscape. Thus, once diversity is removed from a forest population of mahogany, these data suggest that recovery would be difficult via seed or pollen dispersal, and provides an explanation for mahogany's apparent susceptibility to the pressures of logging. Evidence is reviewed from other studies of gene flow and seedling regeneration to discuss alternative extraction strategies that may maintain diversity or allow recovery of genetic resources.

Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects

Population-genetic studies have been remarkably productive and successful in the last decade following the invention of PCR technology and the introduction of mitochondrial and microsatellite DNA markers. While mitochondrial DNA has proven powerful for genealogical and evolutionary studies of animal populations, and microsatellite sequences are the most revealing DNA markers available so far for inferring population structure and dynamics, they both have important and unavoidable limitations. To obtain a fuller picture of the history and evolutionary potential of populations, genealogical data from nuclear loci are essential, and the inclusion of other nuclear markers, i.e. single copy nuclear polymorphic (scnp) sequences, is clearly needed. Four major uncertainties for nuclear DNA analyses of populations have been facing us, i.e. the availability of scnp markers for carrying out such analysis, technical laboratory hurdles for resolving haplotypes, difficulty in data analysis because of recombination, low divergence levels and intraspecific multifurcation evolution, and the utility of scnp markers for addressing population-genetic questions. In this review, we discuss the availability of highly polymorphic single copy DNA in the nuclear genome, describe patterns and rate of evolution of nuclear sequences, summarize past empirical and theoretical efforts to recover and analyse data from scnp markers, and examine the difficulties, challenges and opportunities faced in such studies. We show that although challenges still exist, the above-mentioned obstacles are now being removed. Recent advances in technology and increases in statistical power provide the prospect of nuclear DNA analyses becoming routine practice, allowing allele-discriminating characterization of scnp loci and microsatellite loci. This certainly will increase our ability to address more complex questions, and thereby the sophistication of genetic analyses of populations.

Short tandem repeat (STR) DNA markers are hypervariable and informative in Cannabis sativa: implications for forensic investigations

Short tandem repeat (STR) markers are the DNA marker of choice in forensic analysis of human DNA. Here we extend the application of STR markers to Cannabis sativa and demonstrate their potential for forensic investigations. Ninety-three individual cannabis plants, representing drug and fibre accessions of widespread origin were profiled with five STR makers. A total of 79 alleles were detected across the five loci. All but four individuals from a single drug-type accession had a unique multilocus genotype. An analysis of molecular variance (AMOVA) revealed significant genetic variation among accessions, with an average of 25% genetic differentiation. By contrast, only 6% genetic difference was detected between drug and fibre crop accessions and it was not possible to unequivocally assign plants as either drug or fibre type. However, our results suggest that drug strains may typically possess lower genetic diversity than fibre strains, which may ultimately provide a means of genetic delineation. Our findings demonstrate the promise of cannabis STR markers to provide information on: (1) agronomic type, (2) the geographical origin of drug seizures, and (3) evidence of conspiracy in production of clonally propagated drug crops.

Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout

Estimates of effective population size (Ne) are required to predict the impacts of genetic drift and inbreeding on the evolutionary dynamics of populations. How the ratio of Ne to the number of sexually mature adults (N) varies in natural vertebrate populations has not been addressed. We examined the sensitivity of Ne/N to fluctuations of N and determined the major variables responsible for changing the ratio over a period of 17 years in a population of steelhead trout (Oncorhynchus mykiss) from Washington State. Demographic and genetic methods were used to estimate Ne. Genetic estimates of Ne were gained via temporal and linkage disequilibrium methods using data from eight microsatellite loci. DNA for genetic analysis was amplified from archived smolt scales. The Ne/N from 1977 to 1994, estimated using the temporal method, was 0.73 and the comprehensive demographic estimate of Ne/N over the same time period was 0.53. Demographic estimates of Ne indicated that variance in reproductive success had the most substantial impact on reducing Ne in this population, followed by fluctuations in population size. We found increased Ne/N ratios at low N, which we identified as genetic compensation. Combining the information from the demographic and genetic methods of estimating Ne allowed us to determine that a reduction in variance in reproductive success must be responsible for this compensation effect. Understanding genetic compensation in natural populations will be valuable for predicting the effects of changes in N (i.e. periods of high population density and bottlenecks) on the fitness and genetic variation of natural populations.

Landscape scale genetic effects of habitat fragmentation on a high gene flow species: Speyeria idalia (Nymphalidae)

Detection of the genetic effects of recent habitat fragmentation in natural populations can be a difficult task, especially for high gene flow species. Previous analyses of mitochondrial DNA data from across the current range of Speyeria idalia indicated that the species exhibited high levels of gene flow among populations, with the exception of an isolated population in the eastern portion of its range. However, some populations are found on isolated habitat patches, which were recently separated from one another by large expanses of uninhabitable terrain, in the form of row crop agriculture. The goal of this study was to compare levels of genetic differentiation and diversity among populations found in relatively continuous habitat to populations in both recently and historically isolated habitat. Four microsatellite loci were used to genotype over 300 individuals from five populations in continuous habitat, five populations in recently fragmented habitat, and one historically isolated population. Results from the historically isolated population were concordant with previous analyses and suggest significant differentiation. Also, microsatellite data were consistent with the genetic effects of habitat fragmentation for the recently isolated populations, in the form of increased differentiation and decreased genetic diversity when compared to nonfragmented populations. These results suggest that given the appropriate control populations, microsatellite markers can be used to detect the effects of recent habitat fragmentation in natural populations, even at a large geographical scale in high gene flow species.

On the correlation between heterozygosity and fitness in natural populations

Three primary hypotheses currently prevail for correlations between heterozygosity at a set of molecular markers and fitness in natural populations. First, multilocus heterozygosity-fitness correlations might result from selection acting directly on the scored loci, such as at particular allozyme loci. Second, significant levels of linkage disequilibrium, as in recently bottlenecked-and-expanded populations, might cause associations between the markers and fitness loci in the local chromosomal vicinity. Third, in partially inbred populations, heterozygosity at the markers might reflect variation in the inbreeding coefficient and might associate with fitness as a result of effects of homozygosity at genome-wide distributed loci. Despite years of research, the relative importance of these hypotheses remains unclear. The screening of heterozygosity at polymorphic DNA markers offers an opportunity to resolve this issue, and relevant empirical studies have now emerged. We provide an account of the recent progress on the subject, and give suggestions on how to distinguish between the three hypotheses in future studies.

Microsatellite analysis of multiple paternity and male reproductive success in the promiscuous snowshoe hare

Few genetic studies have addressed patterns of paternity in promiscuous mammals. I used microsatellite DNA primers developed in the European rabbit to analyze paternity in the promiscuous snowshoe hare (Lepus americanus). Sixty-five offspring, their 12 mothers, and their 24 putative fathers were genotyped at seven polymorphic loci (3–22 alleles/locus). Paternal allele counts and likelihood-based paternity assignments confirmed that multiple paternity occurs in snowshoe hare litters. However, the estimated frequency of multiple paternity was lower than expected in an unstructured promiscuous mating system. A relatively low variance in male reproductive success indicated that no males dominated paternity. A few males did achieve significantly more paternities than average, largely by fathering one or two complete litters rather than a few offspring in many litters. The results suggest that successful multiple mating is limited among both male and female snowshoe hares. An important role for pre- and (or) post-copulatory competition is implied.

Genetic effective size is three orders of magnitude smaller than adult census size in an abundant, Estuarine-dependent marine fish (Sciaenops ocellatus)

Using eight microsatellite loci and a variety of analytical methods, we estimated genetic effective size (N(e)) of an abundant and long-lived marine fish species, the red drum (Sciaenops ocellatus), in the northern Gulf of Mexico (Gulf). The ratio N(e)/N, where short-term variance N(e) was estimated via the temporal method from shifts in allele-frequency data over four cohorts and where N reflected a current estimate of adult census size in the northern Gulf, was approximately 0.001. In an idealized population, this ratio should approximate unity. The extraordinarily low value of N(e)/N appears to arise from high variance in individual reproductive success and perhaps more importantly from variance in productivity of critical spawning and nursery habitats located in spatially discrete bays and estuaries throughout the northern Gulf. An estimate of N(e) based on a coalescent approach, which measures long-term, inbreeding effective size, was four orders of magnitude lower than the estimate of current census size, suggesting that factors presently driving N(e)/N to low values among red drum in the northern Gulf may have operated similarly in the past. Models that predict N(e)/N exclusively from demographic and life-history features will seriously overestimate N(e) if variance in reproductive success and variance in productivity among spatially discrete demes is underestimated. Our results indicate that these variances, especially variance in productivity among demes, must be large for red drum. Moreover, our study indicates that vertebrate populations with enormous adult census numbers may still be at risk relative to decline and extinction from genetic factors.

Evolution of a perfect simple sequence repeat locus in the context of its flanking sequence

Microsatellites, which have rapidly become the preferred markers in population genetics, reliably assign individual chinook salmon to the winter, fall, late-fall, or spring chinook runs in the Sacramento River in California's Central Valley (Banks et al. 2000. Can. J. Fish. Aquat. Sci. 57:915-927). A substantial proportion of this discriminatory power comes from Ots-2, a simple CA repeat, which is expected to evolve rapidly under the stepwise mutation model. We have sequenced a 300-bp region around this locus and typed 668 microsatellite-flanking sequence haplotypes to explore further the basis of this microsatellite divergence. Three sites of nucleotide polymorphism in the Ots-2 flanking sequence define five haplotypes that are shared by the Californian and Canadian populations. The Ots-2 microsatellite alleles are nonrandomly distributed among these five haplotypes in a pattern of gametic disequilibrium that is also shared among populations. Divergence between the winter run and other Central Valley stocks appears to be caused by a combination of surprisingly static evolution at Ots-2 within a context of more rapidly changing haplotype frequencies.

Population genetic structure and male-biased dispersal in the queenless ant Diacamma cyaneiventre

In this study we investigated the population genetic structure of the queenless ant Diacamma cyaneiventre. This species, lacking winged queens, is likely to have a restricted female dispersal. We used both mitochondrial and microsatellite markers to assess the consequence of such restricted female dispersal at three geographical scales: within a given locality (< 1 km), between localities within a given region (< 10 km) and between regions (> 36 km). Within a locality, a strong population structure was observed for mitochondrial DNA (mtDNA) whereas weak or nonexistent population genetic structure was observed for the microsatellites (around 5% of the value for mtDNA). Male gene flow was estimated to be about 20-30 times higher than female gene flow at this scale. At a larger spatial scale, very strong genetic differentiation for both markers was observed between localities - even within a single region. Female dispersal is nonexistent at these scales and male dispersal is very restricted, especially between regions. The phylogeographical structure of the mtDNA haplotypes as well as the very low genetic diversity of mtDNA within localities indicate that new sites are colonized by a single migration event from adjacent localities, followed by successive colony fissions. These patterns of genetic variability and differentiation agree with what is theoretically expected when colonization events are kin-structured and when, following colonization, dispersion is mainly performed by males.

Efficiency of semi-automated fluorescent multiplex PCRs with 11 microsatellite markers for genetic studies of deer populations

Thirty bovine and eight ovine microsatellite primer pairs were tested on four tropical deer species: Eld's and Swamp deer (highly threatened) and Rusa and Vietnamese Sika deer (economically important). Thirty markers gave an amplified product in all four species (78.9%). The number of polymorphic microsatellite markers varied among the species from 14 in Eld's deer (47%) to 20 in Swamp deer (67%). Among them, 11 microsatellite loci were multiplexed in three polymerase chain reactions (PCRs) and labelled with three different fluorochromes that can be loaded in one gel-lane. To test the efficiency of the multiplex, primary genetic studies (mean number of alleles, expected heterozygosities and Fis values) were carried out on four deer populations. Parentage exclusion probability and probability of identity were computed and discussed on a Swamp deer population. These multiplexes PCRs were also tested on several other deer species and subspecies. The aim of this study is to establish a tool useful for genetic studies of population structure and diversity in four tropical deer species which with few modifications can be applied to other species of the genus Cervus.

Late glacial history of the cold-adapted freshwater fish Cottus gobio, revealed by microsatellites

The distribution of genetic diversity at 10 highly polymorphic microsatellite loci within the European freshwater fish, Cottus gobio, L. was examined. The sampling range comprised a large geographical scale including lineages known to be highly divergent at both mitochondrial DNA (mtDNA) and allozymes. An analysis of genetic variability within populations showed that expected heterozygosity and allelic richness could be explained largely by current effective population sizes. Evidence was found, however, that historical processes predating the last major glaciation affected allelic richness. In addition to confirming the large-scale patterns from earlier studies, the microsatellite data revealed new insights into recent processes by analysing genetic structure within ancient lineages defined by mtDNA data. Stepwise mutation model (SMM) and nonSMM-based methods demonstrated a clear genetic structuring within the Northwestern European lineage comprising populations from Britain and Belgium, and within the Central European lineage populations from the rivers Danube, Elbe and Main. Supported by an analysis of genetic variability within populations these results showed that the bullhead populations most probably persisted throughout the last major glaciation within the British Isles and within the drainages of the rivers Elbe and Main. Such observations provide the first genetic evidence for a glacial refugium in such close proximity to the European glacial margins.

Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis

Homoplasy has recently attracted the attention of population geneticists, as a consequence of the popularity of highly variable stepwise mutating markers such as microsatellites. Microsatellite alleles generally refer to DNA fragments of different size (electromorphs). Electromorphs are identical in state (i.e. have identical size), but are not necessarily identical by descent due to convergent mutation(s). Homoplasy occurring at microsatellites is thus referred to as size homoplasy. Using new analytical developments and computer simulations, we first evaluate the effect of the mutation rate, the mutation model, the effective population size and the time of divergence between populations on size homoplasy at the within and between population levels. We then review the few experimental studies that used various molecular techniques to detect size homoplasious events at some microsatellite loci. The relationship between this molecularly accessible size homoplasy size and the actual amount of size homoplasy is not trivial, the former being considerably influenced by the molecular structure of microsatellite core sequences. In a third section, we show that homoplasy at microsatellite electromorphs does not represent a significant problem for many types of population genetics analyses realized by molecular ecologists, the large amount of variability at microsatellite loci often compensating for their homoplasious evolution. The situations where size homoplasy may be more problematic involve high mutation rates and large population sizes together with strong allele size constraints.

Extreme sex-biased dispersal in the communally breeding, nonmigratory Bechstein's bat (Myotis bechsteinii)

Maternity colonies of the communally breeding, nonmigratory Bechstein's bat consist of closely related females that live together with unrelated females, and average colony relatedness is low despite the absence of immigration. We compared the genetic structure of both nuclear and mitochondrial microsatellites in order to quantify sex-specific dispersal rates. More specifically, we aimed at testing whether male dispersal is able to balance the genetic effect of strong (absolute) female philopatry. Absolute female philopatry, indicated by an extreme mitochondrial DNA population differentiation of 96%, was indeed opposed by strong (possibly complete) male dispersal. Based on our knowledge of the biology of Myotis bechsteinii, we conclude that inbreeding avoidance is likely to be the crucial factor driving male dispersal in this species.

Genetic differentiation within and between populations of a hermaphroditic freshwater planarian

Dispersal of individuals is an important factor that can influence genetic differentiation between populations. The hermaphroditic freshwater planarian Schmidtea polychroainhabits shallow regions of lakes and streams, in which they appear to be continuously distributed. In the present study we used three highly polymorphic markers for analysing small-scale and large-scale genetic structure within one, and between four natural lake populations. Genetic differentiation could already be observed between samples collected at least 13 m apart, but not between neighbouring samples, and was most pronounced between samples from different lakes. Probably due to the high variance in F(ST)values, a significant correlation between genetic differentiation and geographic distance could not be observed. These results show that individual dispersal of S. polychroa is limited, but that there is gene flow between subpopulations from the same lake. They further suggest that long-distance dispersal and gene flow between lakes, if present, is not a common process in S. polychroa.

Population structure of plaice (Pleuronectes platessa L.) in northern Europe: microsatellites revealed large-scale spatial and temporal homogeneity

Philopatry to spawning grounds combined with well-known migratory patterns in the flatfish Pleuronectes platessa (plaice) has led to the hypothesis that regional populations may reflect relatively discrete, genetic stocks. Using six microsatellite loci we genotyped 240 adult individuals collected from locations in Norway, the Faeroe plateau, the Irish Sea, the Femer Baelt, Denmark, and the southern North Sea, and 240 0-class juveniles collected from five nursery-ground locations in Iceland, northwest Scotland, two sites in the Wadden Sea, and the Bay of Vilaine in Southern Brittany. The mean number of alleles/locus ranged from 5.3 to 20.4, with a mean of 13.9. Expected heterozygosity was uniformly high across all locations (multilocus H(exp)= 0.744 +/- 0.02). Pairwise comparisons of theta; among all 11 locations revealed significant differentiation between Iceland and all other locations (theta = 0.0290*** to 0.0456***), which is consistent with the deep-water barrier to dispersal in plaice. In contrast, no significant differentiation was found among any of the remaining continental-shelf sampling locations. This suggests that regional stocks are themselves composed of several genetic stocks under a model of panmixia which persists even to the spawning grounds. The presence of significant heterozygote deficiencies at all locations (not due to null alleles) suggests a temporal Wahlund effect yet the absence of significant population differentiation among continental shelf localities makes this explanation alone, difficult to reconcile. Sampling of eggs at the spawning grounds will be required to resolve this issue. Causes of the mismatch between genetic and geographical stocks is discussed in the context of high gene flow.

High male reproductive success of hermaphrodites in the androdioecious Phillyrea angustifolia

Androdioecy, the coexistence of males and hermaphrodites within a population, is a rare breeding system, often considered as unlikely to evolve because of restrictive conditions for its maintenance. Phillyrea angustifolia, a wind-pollinated shrub, is one of the handful species reported to be androdioecious. Our previous studies have shown that natural populations of this species in southern France exhibit higher male frequencies (approximately 50%) than predicted on theoretical grounds. Thus, the male functionality of hermaphrodites is still debated. To assess the functional breeding system of this species in the wild, a paternity analysis was performed with two highly polymorphic microsatellite loci on 729 seeds collected on 10 maternal shrubs in a natural population of 24 mature individuals of P. angustifolia. A large proportion of seeds were found to have been sired by pollen from outside the population. Analysis of seeds sired by individuals within the study population revealed a high male fertility of hermaphrodites resulting in a low male advantage in fertility for male plants. Intermate distances were found to have a strong impact on male reproductive success, whereas sexual morph had no effect, with males and hermaphrodites performing equivalently. This study is the first to unequivocally document the occurrence of a male function of hermaphrodites in a natural population of an androdioecious species.

Characterization of the (GAAA) microsatellite region in the plant parasitic nematode Meloidogyne artiellia

Microsatellites have become one of the most powerful genetic markers in biology. We have used DNA sequencing to characterize a highly variable microsatellite (GAAA) locus in the root-knot nematode Meloidogyne artiellia. The use of microsatellite flanking primers produced four amplification products that are defined as electromorphs, based on conventional length criteria. The sequencing of these four amplification products revealed the presence of new variants in the population due to sequence variability. The sum of electromorphs and sequence polymorphisms resulted in a total of six variants. The high degree of variability in the microsatellite containing region is due not only to variation in the number of tetranucleotide repeats but also to variation (length and site variation) in the flanking regions of the microsatellite. These investigations show that, in spite of the size homoplasy, the variability of the microsatellite flanking sequences of M. artiellia could be used as informative markers for phylogenetic reconstructions.

Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments

Most studies of microsatellite evolution utilize long, highly mutable loci, which are unrepresentative of the majority of simple repeats in the human genome. Here we use an unbiased sample of 2,467 microsatellite loci derived from alignments of 5.1 Mb of genomic sequence from human and chimpanzee to investigate the mutation process of tandemly repetitive DNA. The results indicate that the process of microsatellite evolution is highly heterogeneous, exhibiting differences between loci of different lengths and motif sizes and between species. We find a highly significant tendency for human dinucleotide repeats to be longer than their orthologues in chimpanzees, whereas the opposite trend is observed in mononucleotide repeat arrays. Furthermore, the rate of divergence between orthologues is significantly higher at longer loci, which also show significantly greater mutability per repeat number. These observations have important consequences for understanding the molecular mechanisms of microsatellite mutation and for the development of improved measures of genetic distance.