Allele Size Differences Research Articles

Development of a reference panel as a way to harmonize data of genotyped Sclerotinia sclerotiorum

Several population studies of S. sclerotiorum have been conducted and resulted in important publications furthering our knowledge of this pathogen. Genotype data from those studies has been published with the notion that this data could be re‐used by other scientists. However, amplicon sizes were known to vary across labs due to primer modifications for fluorophore labeling and the instrument used to perform fragment analysis. Thus, it is necessary to create a reference panel of DNA that represents allele sizes known to be present within the population, which is a technique used in human DNA forensics for the same type of genetic marker. Given recent completion of genotyping of more than 366 S. sclerotiorum isolates from across the U.S., development of a DNA Reference Panel that represents most alleles within S. sclerotiorum loci isis now possible. Here, we identified 22 S. sclerotiorum isolates that were collected and genotyped previously and represented all known possible alleles among the 366 S. sclerotiorum. Then, DNA was isolated from those 22 S. sclerotiorum strains and genotyping was performed using 11 previously developed SSR markers. PCR used a 3‐primer indirect fluorescent labeling system that was slightly different from the system used to genotype the 366 isolates, which used direct primer labeling. Amplicons were sized using capillary electrophoresis and raw chromatograms imported into R for sizing and analysis. This data was used to determine differences in allele sizes and create an R function to automatically re‐classify observed data so that it could be seamlessly integrated into our 366 genotype database. Using results of 22 isolates, harmonization of data from two previous studies that genotyped 95 isolates mainly from Brazil and 366 isolates from U.S. took place. From this data, estimation of population genetic statistics, such as genetic/genotypic diversity, evenness, and richness, and test for evidence of sexual recombination was done. Taken together, the DNA reference panel represents most alleles within S. sclerotiorum and allows for integration of previously published population genetic data of this plant pathogen.Support or Funding InformationSupported by Margarita Marroquin‐Guzman and Sydney E. Everhart. Funded by Undergraduate Creative Activities and Research Experience at UNLThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Dissimilarity of individual microsatellite profiles under different mutation models: Empirical approach.

Microsatellites (simple sequence repeats, SSRs) still remain popular molecular markers for studying neutral genetic variation. Two alternative models outline how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that all possible alleles are equally likely to result from a mutation, while stepwise mutation model (SMM) describes microsatellite evolution as stepwise adding or subtracting single repeat units. Genetic relationships between individuals can be analyzed in higher precision when assuming the SMM scenario with allele size differences as a proxy of genetic distance. If population structure is not predetermined in advance, an empirical data analysis usually includes (a) estimating proximity between individual SSR profiles with a selected dissimilarity measure and (b) determining putative genetic structure of a given set of individuals using methods of clustering and/or ordination for the obtained dissimilarity matrix. We developed new dissimilarity indices between SSR profiles of haploid, diploid, or polyploid organisms assuming different mutation models and compared the performance of these indices for determining genetic structure with population data and with simulations. More specifically, we compared SMM with a constant or variable mutation rate at different SSR loci to IAM using data from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria graminis (monokaryon). We show that inferences about population genetic structure are sensitive to the assumed mutation model. With simulations, we found that Bruvo's distance performs generally poorly, while the new metrics are capturing the differences in the genetic structure of the populations.

P185 Next generation sequencing of HLA class II in an argentinian registry population reveals the complexity of these loci

Aim This study used next generation sequencing (NGS) in 1472 healthy volunteers from an Argentinian registry to characterize class II gene diversity. Complications of using NGS for these regions arise from large introns, different length alleles, regions with few polymorphisms, and incomplete sequences in the IPD-IMGT/HLA database. Methods Amplicons were generated to include exons 2–6 of HLA-DQB1, and exons 2–3 of -DRB1 and -DPB1 using DNA extracted from blood. Samples were combined and sequenced on an Illumina MiSeq with an in-house library construction protocol. Conexio Assign was used to identify alleles based on the IPD-IMGT/HLA database from October 2016. Full length gene sequencing of select samples was performed with two overlapping amplicons for HLA-DPB1 and -DRB1. Results The majority of the alleles identified at each locus were common with ⩽1% of alleles per gene designated as well-documented or with frequency not defined. With only exons 2–3 sequenced, 6% of HLA-DRB1 assignments and 11% of -DPB1 were ambiguous. When additional exons were sequenced, most showed the common allele; however, DPB1∗104:01 was seen in 16% of samples typed as DPB1∗03:FNVX. For HLA-DRB1, preferential amplification due to differences in allele size and presence of pseudogenes led to certain alleles with low read depth and poor sequence quality, in particular DRB1∗04. Analysis of HLA-DQB1 introns proved difficult due to insertions and deletions that poorly aligned to the reference. Intron 2 of HLA-DPB1 is large and has few variations between certain combinations of alleles that were not phased in 14% of samples. These were not resolved with full length sequencing. Conclusions Although conditions still need to be optimized, NGS of HLA class II is a powerful tool in determining genetic diversity. HLA-DRB1 ambiguities would be reduced by 82% with the initial sequencing of exons 2–4; however, longer amplicons reduce read depth. Addition of primers to maximize amplification of low amplifying alleles may be necessary to increase read depth. Alternate methodology such as sequencing of single DNA molecules is necessary to solve the ambiguities for alleles that are not phased. These proposed changes will lead to more successful sequencing of HLA class II. Even so, these complications make NGS challenging when applied to high volume typing.

Massively parallel sequencing of 68 insertion/deletion markers identifies novel microhaplotypes for utility in human identity testing

Short tandem repeat (STR) loci are the traditional markers used for kinship, missing persons, and direct comparison human identity testing. These markers hold considerable value due to their highly polymorphic nature, amplicon size, and ability to be multiplexed. However, many STRs are still too large for use in analysis of highly degraded DNA. Small bi-allelic polymorphisms, such as insertions/deletions (INDELs), may be better suited for analyzing compromised samples, and their allele size differences are amenable to analysis by capillary electrophoresis. The INDEL marker allelic states range in size from 2 to 6 base pairs, enabling small amplicon size. In addition, heterozygote balance may be increased by minimizing preferential amplification of the smaller allele, as is more common with STR markers. Multiplexing a large number of INDELs allows for generating panels with high discrimination power. The Nextera™ Rapid Capture Custom Enrichment Kit (Illumina, Inc., San Diego, CA) and massively parallel sequencing (MPS) on the Illumina MiSeq were used to sequence 68 well-characterized INDELs in four major US population groups. In addition, the STR Allele Identification Tool: Razor (STRait Razor) was used in a novel way to analyze INDEL sequences and detect adjacent single nucleotide polymorphisms (SNPs) and other polymorphisms. This application enabled the discovery of unique allelic variants, which increased the discrimination power and decreased the single-locus random match probabilities (RMPs) of 22 of these well-characterized INDELs which can be considered as microhaplotypes. These findings suggest that additional microhaplotypes containing human identification (HID) INDELs may exist elsewhere in the genome.

Development and characterization of microsatellite markers in two agarophyte species, Gracilaria birdiae and Gracilaria caudata (Gracilariaceae, Rhodophyta), using next-generation sequencing

The two red algal species, Gracilaria birdiae Plastino and E.C. Oliveira and Gracilaria caudata J. Agardh, are the most important natural sources of agar in Brazil. Using the 454 sequencing system, we identified 464 and 487 perfect microsatellite loci in 6908 and 9602 sequences/contigs from G. birdiae and G. caudata, respectively. After a conservative removal of potentially problematic loci, 144 loci were tested (72 from each species). A total of 25 polymorphic microsatellite loci were defined (13 loci for G. birdiae and 17 loci for G. caudata, including 5 loci common to both species). The five microsatellite loci that cross-amplified in both species showed species-specific differences in allele size. Polymorphic microsatellite loci were used to assess the genetic diversity of both species in their main harvest and cultivation areas on the Brazilian coast. Gene diversity was similar in G. birdiae and G. caudata. However, significant heterozygote deficiency was observed in G. birdiae, whereas heterozygote excess occurred in G. caudata, suggesting that these two related species differ in their mating system. These results also raised new questions on their biology in the field and on their patterns of genetic structure across their geographical ranges. In addition, the 20 loci developed in this study proved successful in identifying each individual in the field as a unique multilocus genotype, and will be useful for studying lineage sorting, breeding programs, or conservation issues.

Always Look on Both Sides: Phylogenetic Information Conveyed by Simple Sequence Repeat Allele Sequences

Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker’s sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within-locus polymorphism is not known.

The distribution of coalescence times and distances between microsatellite alleles with changing effective population size

We investigate the effects of past changes of the effective population size on the present allelic diversity at a microsatellite marker locus. We first derive the analytical expression of the generating function of the joint probabilities of the time to the Most Recent Common Ancestor for a pair of alleles and of their distance (the difference in allele size). We give analytical solutions in the case of constant population size and the geometrical mutation model. Otherwise, numerical inversion allows the distributions to be calculated in general cases. The effects of population expansion or decrease and the possibility to detect an ancient bottleneck are discussed. The method is extended to samples of three and four alleles, which allows investigating the covariance structure of the frequencies f ( k ) of pairs of alleles with a size difference of k motifs, and suggesting some approaches to the estimation of past demography.

Adult survival and microsatellite diversity in possums: effects of major histocompatibility complex-linked microsatellite diversity but not multilocus inbreeding estimators

Adult survival is perhaps the fitness parameter most important to population growth in long-lived species. Intrinsic and extrinsic covariates of survival are therefore likely to be important drivers of population dynamics. We used long-term mark-recapture data to identify genetic, individual and environmental covariates of local survival in a natural population of mountain brushtail possums (Trichosurus cunninghami). Rainfall and intra-individual diversity at microsatellite DNA markers were associated with increased local survival of adults and juveniles. We contrasted the performance of several microsatellite heterozygosity measures, including internal relatedness (IR), homozygosity by loci (HL) and the mean multilocus estimate of the squared difference in microsatellite allele sizes within an individual (mean d (2)). However, the strongest effect on survival was not associated with multilocus microsatellite diversity (which would indicate a genome-wide inbreeding effect), but a subset of two loci. This included a major histocompatibility complex (MHC)-linked marker and a putatively neutral microsatellite locus. For both loci, diversity measures incorporating allele size information had stronger associations with survival than measures based on heterozygosity, whether or not allele frequency information was included (such as IR). Increased survival was apparent among heterozygotes at the MHC-linked locus, but the benefits of heterozygosity to survival were reduced in heterozygotes with larger differences in allele size. The effect of heterozygosity on fitness-related traits was supported by data on endoparasites in a subset of the individuals studied in this population. There was no apparent density dependence in survival, nor an effect of sex, age or immigrant status. Our findings suggest that in the apparent absence of inbreeding, variation at specific loci can generate strong associations between fitness and diversity at linked markers.

Characterization of Deletions in the DYS385 Flanking Region and Null Alleles Associated with AZFc Microdeletions in Koreans

Eight DYS385 allele size discrepancies and six DYS448 null types were detected among 708 Korean men when results of three in-house multiplex short tandem repeat (STR) systems were compared. The systems included both ordinary and reduced size amplicons. Sequence analysis revealed deletion mutations at two sites upstream of the DYS385 core repeats and deletion of the entire DYS448 locus. At DYS385, allele size differences were one or two repeats and were dependent on the primer set used for polymerase chain reaction (PCR) amplification. Location of the primer target sequence in a flanking region of the STR, distal or proximal to the deletion, determined allele size. Two widely used commercial kits amplify DYS385 so as to include the mutable sites. Arrangement analysis of sequence tagged sites demonstrated that the deletion patterns at DYS448 (and DYS464) were associated with arrangements of the azoospermia factor c gene (AZFc). The DYS448 deletion appears relatively frequent in Asians.

Microsatellite variation and evolution in the Peromyscus maniculatus species group

Variation at 12 pure-repeat dinucleotide microsatellites from Peromyscus maniculatus was analyzed for samples of all species in the P. maniculatus species group and P. leucopus. Except for one locus ( Pml08) that amplified a product only for P. maniculatus, these microsatellites yielded reliable estimates of variation across these species; per-locus polymorphism and allele-size distribution were not significantly different among or between any of the species sampled from mainland populations. Significantly lower levels of variation and the distribution of alleles in the two populations of the insular-endemic P. sejugis were consistent with the expectation of substantial founder effect and suggest a lack of recent gene flow between these populations. Phenetic analyses of genetic distances based on shared allele frequencies uniformly produced well-supported trees that were entirely concordant with the a priori corroborated relationships within the P. maniculatus species group; this result was not obtained with analyses of a genetic distance computed from differences in allele sizes. The microsatellite data do not support the hypothesis that P. sejugis should be considered conspecific with P. maniculatus but yield a strongly supported sister-group association between P. sejugis and P. keeni.

Microsatellite markers in avocado ( Persea americana Mill.): development of dinucleotide and trinucleotide markers

This paper compares the development of microsatellite markers from two genomic DNA libraries of avocado cultivar Hass enriched for dinucleotide and trinucleotide repeats. Sequencing showed 86 and 31% of clones from the respective libraries to contain microsatellites. However, banding profiles of trinucleotide loci were easier to interpret than those of dinucleotide loci. Of 376 dinucleotide-containing clones, 81% harbored AG repeats and 19% contained AC repeats. A subset of 104 trinucleotide-containing clones consisted of ATG repeats (44%), AGT repeats (30%), and AAG repeats (16%). Array lengths of up to 34 were attained in the dinucleotide repeat microsatellites, whereas trinucleotide arrays never exceeded 11 elements. Typing 37 genotypes at 25 loci (11 dinucleotide and 14 trinucleotide loci) revealed a total of 204 alleles, of which 60% originated from the dinucleotide loci. Average heterozygosity of the di- and trinucleotide loci was 73.4 and 52.6%, respectively. Many loci, especially dinucleotide loci, exhibited allele size differences that were not multiples of the repeat unit, suggesting nonstepwise mutational mechanisms. Several loci were additionally characterized by large gaps in the allele size distribution.

Association study of CAG repeats in the KCNN3 gene in Israeli patients with major psychosis.

Several studies reported contradictory findings regarding the association of major psychosis with CAG repeats in the KCNN3 gene. We investigated the contribution of the CAG repeat at the KCNN3 gene, localized to chromosome 1q21.3, to the genetic susceptibility for schizophrenia, schizoaffective and bipolar disorders. Analysis of the number of CAG repeats and the differences in allele length were performed for Israeli Ashkenazi Jews, non-Ashkenazi Jews, and Arabs diagnosed with major psychosis (n=181) versus matched ethnic controls (n=207). We found no significant difference in the number of CAG repeats between the entire sample of patients and controls. However, an analysis of the differences of allele length revealed a significantly greater number of patients with identical allele length (43.1%) when compared with normal controls (30.4%). Furthermore, an earlier age of non-paranoid schizophrenia onset was found associated with differences in allele sizes. There were no significant differences in the number of CAG repeats and the differences in allele length when subjects were grouped according to gender, ethnic origins of their parents, family history, and diagnostic groups. Our results support the hypothesis that a contribution of the KCNN3 gene to genetic susceptibility to major psychosis and their phenotypic polymorphism may be related to the difference of allele length rather than to the number of CAG repeats.

Deriving evolutionary relationships among populations using microsatellites and (deltamu)(2): all loci are equal, but some are more equal than others...

Numerous studies have relied on microsatellite DNA data to assess the relationships among populations in a phylogenetic framework, converting microsatellite allelic composition of populations into evolutionary distances. Among other coefficients, (deltamu)(2) and R(st) are often employed because they make use of the differences in allele sizes on the basis of the stepwise mutation model. While it has been recognized that some microsatellites can yield disproportionate interpopulation distance estimates, no formal investigation has been conducted to evaluate to what extent such loci could affect the topology of the corresponding dendrograms. Here we show that single loci, displaying extremely large among-population variance, can greatly bias the topology of the phylogenetic tree, using data from European grayling (Thymallus thymallus, Salmonidae) populations. Importantly, we also demonstrate that the inclusion of a single disproportionate locus will lead to an overestimation of the stability of trees assessed using bootstrapping. To avoid this bias, we introduce a simple statistical test for detecting loci with significantly disproportionate variance prior to phylogenetic analyses and further show that exclusion of offending loci eliminates the false increase in phylogram stability.

An association of CAG repeats at the KCNN3 locus with symptom dimensions of schizophrenia

Background: In 1999 Cardno et al reported that long CAG repeats in the calcium-activated potassium channel gene hSKCa3/KCNN3 are associated with higher negative symptom dimension scores in schizophrenia patients. There has been no attempt to replicate the results. In this study, we investigated whether a symptom polymorphism of schizophrenia is associated with both the CAG repeat numbers and the difference in allele sizes. Methods: We tested the association of CAG repeats with symptom models of schizophrenia in 117 unrelated Jewish patients. A multivariate analysis (MANOVA) of two models of schizophrenia with the repeat distribution and the difference in allele sizes was performed. Results: We found a significant positive association of the number of CAG repeats with negative syndrome, anergia, activation, and paranoid symptoms. In addition, nonparanoid schizophrenia patients who had differences in allele sizes were characterized by earlier onset of illness. Conclusions: The study supports the hypothesis that the combined effect of long CAG repeats and the differences in allele sizes contribute to symptom expression of schizophrenia, particularly on the anergia-activation-paranoid axis.

Fitness and microsatellite diversity estimates were not correlated in two outbred anuran populations.

Larval fitness traits were investigated in two anuran species (Bufo calamita and Rana temporaria) under controlled laboratory conditions, and allelic diversity measured in the same individuals at five and seven microsatellite loci, respectively. For both species there were significant differences among sibships in larval growth and development rates, and in some cases also in microsatellite heterozygosity and mean d2 (a measure of diversity based on differences in allele sizes). However, there were no significant correlations between any of the fitness and genetic measures either among all individuals, among sibships or among individuals within sibships. Under the conditions and within the statistical power of the study there was no relationship between fitness-related quantitative trait variation and that seen at presumed-neutral microsatellite loci in these outbred populations.

Microsatellite instability in tumors as a model to study the process of microsatellite mutations.

We screened 42 sporadic gastric tumors and found that seven of them had significant microsatellite instability. These were then studied at 26 microsatellite loci, comprising di-, tri- and tetranucleotide repeats. The instability level of individual microsatellites in the tumors was found to be positively correlated with the population average heterozygosity and variance of repeat number of the microsatellite loci, as predicted by the stepwise mutation model. Moreover, as is known to occur in human populations, instability was strongly correlated with the number of repeats at each microsatellite locus and with the perfection of the reiterated sequence. These results demonstrate that microsatellite mutations in unstable tumors show similarities to germline mutations and suggest that their study may be useful in understanding the mechanisms that generate microsatellite variability in human populations. We used this model to test the claims that the microsatellite mutation process is biased towards increased size and heterozygosity with wide differences in allele sizes. These assertions were not confirmed.

Comparative allele sizing can produce inaccurate allele size differences for microsatellites.

Molecular EcologyVolume 8, Issue 8 p. 1347-1349 Comparative allele sizing can produce inaccurate allele size differences for microsatellites M. Haberl, Corresponding Author M. Haberl Zoologisches Institut, Universität München, Luisenstr. 14, 80333 München, Germany M. Haberl. Fax: + 49-6422-9406-33; E-mail:haberl@mailer.uni-marburg.de Present addresses:*Hessische Landesanstalt für Tierzucht, Abteilung für Bienenzucht, Erlenstr. 9, 35274 Kirchhain, Germany.†Institut für Genetik, Universität zu Köln, Weyertal 121, 50931 Köln, Germany.Search for more papers by this authorD. Tautz, D. TautzSearch for more papers by this author M. Haberl, Corresponding Author M. Haberl Zoologisches Institut, Universität München, Luisenstr. 14, 80333 München, Germany M. Haberl. Fax: + 49-6422-9406-33; E-mail:haberl@mailer.uni-marburg.de Present addresses:*Hessische Landesanstalt für Tierzucht, Abteilung für Bienenzucht, Erlenstr. 9, 35274 Kirchhain, Germany.†Institut für Genetik, Universität zu Köln, Weyertal 121, 50931 Köln, Germany.Search for more papers by this authorD. Tautz, D. TautzSearch for more papers by this author First published: 02 July 2002 https://doi.org/10.1046/j.1365-294X.1999.00692_1.xCitations: 31Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Citing Literature Volume8, Issue8August 1999Pages 1347-1349 RelatedInformation

Comparative allele sizing can produce inaccurate allele size differences for microsatellites

Comparative allele sizing can produce inaccurate allele size differences for microsatellites

Do assemblages of Coregonus (Teleostei: Salmoniformes) in the Central Alpine region of Europe represent species flocks?

To examine models of evolution for Coregonus from the Central Alpine region of Europe, 20 populations from nine lakes were assessed for variation at six microsatellite DNA loci. Patterns of variation were tested against three evolutionary models: phenotypic plasticity, multiple invasions of lakes by divergent forms, and within‐lake radiation of species flocks. All sympatric and all but one allopatric pairs of populations were significantly divergent in allele frequencies. Pairwise F‐statistics indicated reduced gene flow among phenotypically divergent sympatric populations. These results reject the hypothesis that within‐lake morphological and ecological diversity reflects phenotypic plasticity within a single gene pool. Genetic similarity was higher among forms within lakes than between populations of the same form in different lakes. Among‐lake divergence was primarily a product of allele size differences. Mantel tests contrasting patterns of genetic divergence against patterns predicted from the multiple invasions and species flocks models indicated that the latter is the best explanation of the observed genetic variation. Thus, reproductively isolated species diverged within lakes, with similar patterns repeatedly emerging among lakes. While this study argues for a particular mode of evolution in Central Alpine Coregonus, the taxonomy of these forms remains unresolved.

The influence of mutation, selection and reproductive systems on microsatellite variability: a simulation approach

The influence of mutation, selection and reproductive systems on within-population size variation at microsatellite loci was analysed using simulations. Mutation occurred through either (biased or unbiased) replication slippage, or unequal recombination between homologous chromosomes. Selection acted either on large allele size, or on the difference in size between the two homologous alleles of an individual. Reproduction was either sexual (panmictic) or clonal. Classical population genetics parameters, such as gene diversity or variance of allele size, were followed over (generally) 5000 generations for various sets of values of the mutation rate and strength of selection, in either clonally or sexually reproducing populations. The reproduction system had little influence on genetic parameters, either under neutral conditions or when selection acted on large allele size. Selection against difference in allele size strongly constrained variability in panmictic populations, whereas a limited influence was observed in clonal populations. Selection against the difference in allele size between the two alleles of an individual is an alternative explanation for the long life expectancy of microsatellite loci in sexual species. Whether this selection process actually occurs can therefore be tested by comparing the allele size distribution of microsatellite loci between regions/genomes exhibiting markedly different recombination rates.