Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

High‐throughput DNA sequencing facilitates the analysis of large portions of the genome in nonmodel organisms, ensuring high accuracy of population genetic parameters. However, empirical studies evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double‐digest restriction‐associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a nonmodel plant species for which no reference genome is available. We used resampling techniques to construct simulated populations with a random subset of individuals and SNPs to determine how many individuals and biallelic markers should be sampled for accurate estimates of intra‐ and interpopulation genetic diversity. We identified 3646 and 4900 polymorphic SNPs for the two populations of A. longifolia, respectively. Our simulations show that, overall, a sample size greater than eight individuals has little impact on estimates of genetic diversity within A. longifolia populations, when 1000 SNPs or higher are used. Our results also show that even at a very small sample size (i.e. two individuals), accurate estimates of F_ST can be obtained with a large number of SNPs (≥1500). These results highlight the potential of high‐throughput genomic sequencing approaches to address questions related to evolutionary biology in nonmodel organisms. Furthermore, our findings also provide insights into the optimization of sampling strategies in the era of population genomics.     

Analysis of genetic variability of South American wild rice populations (Oryza glumaepatula) with isozymes and RAPD markers

The knowledge of population structure and genetic diversity of wild relatives of rice is needed to investigate their evolutionary history and potential use in breeding programs. Very little is known about the wild rice species ( Oryza spp.), particularly those that are native to South America. A study using isozyme and RAPD markers was conducted to estimate the level of genetic diversity of four South American wild rice populations ( Oryza glumaepatula ) recently collected in the Amazon forest and western Brazil rivers. F -statistics and genetic diversity parameters calculated from isozyme and RAPD markers indicated high values for inbreeding coefficients and differentiation among the four populations. In agreement with this, a pattern of greater variation between than within populations was observed with both types of markers. These findings were corroborated by an AMOVA analysis, which indicated that a large portion of the total genetic variation was attributed to regional divergence. The partition of the AMOVA analysis among populations showed that most of the genetic diversity was due to differences among populations. This distribution pattern of genetic variation of O. glumaepatula populations is in agreement with the expectation for an autogamous species and provides important baseline data for conservation and collection strategies for this species.     

Is there genetic connectivity among the critically endangered White‐winged Flufftail (Sarothrura ayresi) populations from South Africa and Ethiopia?

The White‐winged Flufftail (Sarothrura ayresi) is known to occur in the highland marshes of Ethiopia, as well as almost 4000 km in South Africa. The White‐winged Flufftail is listed globally as Critically Endangered. In South Africa the population is estimated to be <50 birds. These birds are severely threatened by habitat destruction. Thus far, no genetic studies have been conducted on S. ayresi to confirm genetic connectivity between the South African and Ethiopian populations. In this study, analysis of mitochondrial and nuclear markers was conducted for White‐winged Flufftail samples from South African and Ethiopian birds, as well as Red‐chested Flufftail (Sarothrura rufa) for species comparison. Analyses of the DNA regions identified three variations between the two populations, supporting the hypothesis that these two populations are not different species or subspecies but are rather one migrating population with different seasonal occupied ranges. However, these results do not exclude the possibility of additional breeding and nonbreeding sites. Low genetic diversity in the populations of White‐winged Flufftails was observed, which needs to be further elucidated with fast evolving co‐dominant markers such as microsatellites, as this low diversity may ultimately contribute to the extinction of the species.     

Asymptotic variances of QTL estimators with selective DNA pooling

Investigation on QTL-marker linkage usually requires a great number of observed recombinations, inferred from combined analysis of phenotypes and genotypes. To avoid costly individual genotyping, inferences on QTL position and effects can instead make use of marker allele frequencies. DNA pooling of selected samples makes allele frequency estimation feasible for studies involving large sample sizes. Linkage studies in outbred populations have traditionally exploited half-sib family designs; within the animal production context, half-sibships provide large families that are highly suitable for DNA pooling. Estimators for QTL position and effect have been proposed that make use of information from flanking markers. We present formulas derived by the delta method for the asymptotic variance of these estimators.     

Limited genetic differentiation in Labeo rohita (Hamilton 1822) populations as revealed by microsatellite markers

Labeo rohita, popularly known as rohu is a widely cultured species in the whole Indian subcontinent. Knowledge of the genetic diversity of this species is important to support management and conservation programs which will subsequently help in sustainable production of this species. DNA markers, mostly microsatellite markers are excellent tool to evaluate genetic variation of populations. Genetic variation of three wild and one farm population was assessed using eleven microsatellite loci. In analyzing 192 samples, the number of alleles ranged from 4 to 23; observed heterozygosity 0.500 to 0.870 and expected heterozygosity from 0.389 to 0.878. Exact test for Hardy Weinberg disequilibrium revealed that each riverine sample had at least one locus not in equilibrium except one river. Negative inbreeding coefficients (F_IS) were observed across populations indicating very high level of genetic diversity but little genetic differentiation among populations.     

A genomewide admixture mapping panel for Hispanic/Latino populations

Admixture mapping (AM) is a promising method for the identification of genetic risk factors for complex traits and diseases showing prevalence differences among populations. Efficient application of this method requires the use of a genomewide panel of ancestry-informative markers (AIMs) to infer the population of origin of chromosomal regions in admixed individuals. Genomewide AM panels with markers showing high frequency differences between West African and European populations are already available for disease-gene discovery in African Americans. However, no such a map is yet available for Hispanic/Latino populations, which are the result of two-way admixture between Native American and European populations or of three-way admixture of Native American, European, and West African populations. Here, we report a genomewide AM panel with 2,120 AIMs showing high frequency differences between Native American and European populations. The average intermarker genetic distance is ~1.7 cM. The panel was identified by genotyping, with the Affymetrix GeneChip Human Mapping 500K array, a population sample with European ancestry, a Mesoamerican sample comprising Maya and Nahua from Mexico, and a South American sample comprising Aymara/Quechua from Bolivia and Quechua from Peru. The main criteria for marker selection were both high information content for Native American/European ancestry (measured as the standardized variance of the allele frequencies, also known as "f value") and small frequency differences between the Mesoamerican and South American samples. This genomewide AM panel will make it possible to apply AM approaches in many admixed populations throughout the Americas.     

Ethnic-affiliation estimation by use of population-specific DNA markers.

During the past 10 years, DNA analysis has revolutionized the determination of identity in a forensic context. Statements about the biological identity of two human DNA samples now can be made with complete confidence. Although DNA markers are very powerful for distinguishing among individuals, most offer little power to distinguish ethnicity or to support any statement about the physical characteristics of an individual. Through a search of the literature and of unpublished data on allele frequencies we have identified a panel of population-specific genetic markers that enable robust ethnic-affiliation estimation for major U.S. resident populations. In this report, we identify these loci and present their levels of allele-frequency differential between ethnically defined samples, and we demonstrate, using log-likelihood analysis, that this panel of markers provides significant statistical power for ethnic-affiliation estimation. In addition to their use in forensic ethnic-affiliation estimation, population-specific genetic markers are very useful in both population- and individual-level admixture estimation and in mapping genes by use of the linkage disequilibrium created when populations hybridize.     

ERIC-PCR fingerprinting-based community DNA hybridization to pinpoint genome-specific fragments as molecular markers to identify and track populations common to healthy human guts

Bacterial populations common to healthy human guts may play important roles in human health. A new strategy for discovering genomic sequences as markers for these bacteria was developed using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting. Structural features within microbial communities are compared with ERIC-PCR followed by DNA hybridization to identify genomic fragments shared by samples from healthy human individuals. ERIC-PCR profiles of fecal samples from 12 diseased or healthy human and piglet subjects demonstrated stable, unique banding patterns for each individual tested. Sequence homology of DNA fragments in bands of identical size was examined between samples by hybridization under high stringency conditions with DIG-labeled ERIC-PCR products derived from the fecal sample of one healthy child. Comparative analysis of the hybridization profiles with the original agarose fingerprints identified three predominant bands as signatures for populations associated with healthy human guts with sizes of 500, 800 and 1000 bp. Clone library profiling of the three bands produced 17 genome fragments, three of which showed high similarity only with regions of the Bacteroides thetaiotaomicron genome, while the remainder were orphan sequences. Association of these sequences with healthy guts was validated by sequence-selective PCR experiments, which showed that a single fragment was present in all 32 healthy humans and 13 healthy piglets tested. Two fragments were present in the healthy human group and in 18 children with non-infectious diarrhea but not in eight children with infectious diarrhea. Genome fragments identified with this novel strategy may be used as genome-specific markers for dynamic monitoring and sequence-guided isolation of functionally important bacterial populations in complex communities such as human gut microflora.     

Random Amplified Polymorphic DNA Analysis of Heterodera cruciferae and H. schachtii populations

Heterodera schachtii and H. cruciferae are sympatric in California and frequently occur in the same field upon the same host. We have investigated the use of polymerase chain reaction (PCR) amplification of nematode DNA sequences to differentiate H. schachtii and H. cruciferae and to assess genetic variability within each species. Single, random oligodeoxyribonucleotide primers were used to generate PCR-amplified fragments, termed RAPD (random amplified polymorphic DNA) markers, from genomic DNA of each species. Each of 19 different random primers yielded from 2 to 12 fragments whose size ranged from 200 to 1,500 bp. Reproducible differences in fragment patterns allowed differentiation of the two species with each primer. Similarities and differences among six different geographic populations of H. schachtii were detected. The potential application of RAPD analysis to relationships among nematode populations was assessed through cluster analysis of these six different populations, with 78 scorable markers from 10 different random primers. DNA from single cysts was successfully amplified, and genetic variability was revealed within geographic populations. The use of RAPD markers to assess genetic variability is a simple, reproducible technique that does not require radioisotopes. This powerful new technique can be used as a diagnostic tool and should have broad application in nematology.     

Diversity of Boll Weevil Populations in South America: A Phylogeographic Approach

A phylogeographic approach was conducted to assess the geographic structure and genetic variation in populations of the boll weevil Anthonomus grandis, which is the most harmful insect pest of cotton in the Americas. COI and COII mitochondrial gene sequences were analyzed to test a former hypothesis on the origin of the boll weevil in Argentina, Brazil and Paraguay, using samples from Mexico and USA as putative source populations. The analysis of variability suggests that populations from South American cotton fields and nearby disturbed areas form a phylogroup with a central haplotype herein called A, which is the most common and widespread in USA and South America. The population from Texas has the A haplotype as the most frequent and gathers in the same group as the South American populations associated with cotton. The sample from Tecomán (México) shows high values of within-nucleotide divergence, shares no haplotype in common with the South American samples, and forms a phylogroup separated by several mutational steps. The sample from Iguazú National Park (Misiones Province, Argentina) has similar characteristics, with highly divergent haplotypes forming a phylogroup closer to the samples from cotton fields, than to the Mexican group. We propose that in South America there are: populations with characteristics of recent invaders, which would be remnants of “bottlenecks” that occurred after single or multiple colonization events, probably from the United States, and ancient populations associated with native forests, partially isolated by events of historical fragmentation.     

Identification of six Trypanosoma cruzi phylogenetic lineages by random amplified polymorphic DNA and multilocus enzyme electrophoresis

Genetic characterisation of Trypanosoma cruzi variants is of foremost importance, due to considerable genetic and biological heterogeneity in the parasite populations. Two major phylogenetic lineages, each highly heterogeneous, have been previously described within this species. Here we characterised a geographically and ecologically diverse sample of stocks representative of the breadth of the known clonal diversity of each major lineage, using random amplified polymorphic DNA with 20 primers and multilocus enzyme electrophoresis at 22 loci. Molecular hybridisation experiments were performed to control the homology of randomly amplified DNA markers. Both sets of data were highly consistent and supported the existence of two major lineages. Additionally, we found that lineage 2 appeared further partitioned into five sharply delineated phylogenetic clusters, each comprising one of the following reference strains: CanIII cl1 (Z3 reference), M5631 cl5, Esmeraldo cl3 (Z2 reference), CL Brener, and MN cl2. The two first clusters were found mainly in sylvatic environments, whereas the three latter were restricted to domestic transmission cycles and were only collected South to the Amazon Basin. In contrast, lineage 1, which included Miles' Z1 reference strain X10 cl1, was not further subdivided and was encountered across the entire endemic area, in both domestic and sylvatic cycles. Thus, T. cruzi appeared to be subdivided into six discrete typing units, or DTUs, exhibiting distinct geographic and ecological ranges. Reliable diagnostic markers for the two major lineages and the five smaller DTUs of lineage 2 are described, and correspondence with previous classifications of T. cruzi genotypes is given in order to help communication on T. cruzi phylogenetic diversity.     

Sexual dimorphism and discriminant function sexing in indigenous South African crania

This study aimed to examine sexual dimorphism in, and to produce a practical discriminant function for determining the sex of indigenous, Bantu-speaking, South African crania. The types of data to be used were a small number of traditional, or mathematically transformed three-dimensional, linear measurements, comparable to those in use by most physical and forensic anthropologists. The samples to be examined, separately and pooled, were of the Cape Nguni, Natal Nguni and Sotho subgroups. In addition, three local populations (‘tribes’—Zulu, Xhosa and Southern Sotho) within these subgroups were also studied.

Univariate male/female ratios indicate significant sexual dimorphism in the pooled South African crania. Canonical variates analysis of the pooled sample showed that facial width is the strongest discriminating morphometric variable; cranial length and basi-bregmatic height are the next most significant features. Eight measurements derived from the three-dimensional data were used to produce a series of discriminant functions for sex determination in the pooled sample, for which an accuracy of 77–80% was attained. Analysis of the calvaria and face, separately, has shown that the sex of damaged material can be diagnosed with a reasonable degree of accuracy (75–76%).

The new functions for the pooled indigenous South African sample provide improved sex discrimination accuracy compared to those obtained by employing the commonly utilised statistics of Giles & Elliot (1963), even when a modified sectioning point is used. Functions calculated for the separate local populations gave variable and fairly low improvements in sexing accuracy. As the subdivisions at all levels are at present quite rapidly disappearing in South Africa, for most purposes it is now best to simply apply the pooled data functions for sexing crania.     

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions

The cellular composition of heterogeneous samples can be predicted using an expression deconvolution algorithm to decompose their gene expression profiles based on pre-defined, reference gene expression profiles of the constituent populations in these samples. However, the expression profiles of the actual constituent populations are often perturbed from those of the reference profiles due to gene expression changes in cells associated with microenvironmental or developmental effects. Existing deconvolution algorithms do not account for these changes and give incorrect results when benchmarked against those measured by well-established flow cytometry, even after batch correction was applied. We introduce PERT, a new probabilistic expression deconvolution method that detects and accounts for a shared, multiplicative perturbation in the reference profiles when performing expression deconvolution. We applied PERT and three other state-of-the-art expression deconvolution methods to predict cell frequencies within heterogeneous human blood samples that were collected under several conditions (uncultured mono-nucleated and lineage-depleted cells, and culture-derived lineage-depleted cells). Only PERT''s predicted proportions of the constituent populations matched those assigned by flow cytometry. Genes associated with cell cycle processes were highly enriched among those with the largest predicted expression changes between the cultured and uncultured conditions. We anticipate that PERT will be widely applicable to expression deconvolution strategies that use profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular phenotypic identity.     

Genetic structure in contemporary south Tyrolean isolated populations revealed by analysis of Y-chromosome, mtDNA, and Alu polymorphisms

Most of the inhabitants of South Tyrol in the eastern Italian Alps can be considered isolated populations because of their physical separation by mountain barriers and their sociocultural heritage. We analyzed the genetic structure of South Tyrolean populations using three types of genetic markers: Y-chromosome, mitochondrial DNA (mtDNA), and autosomal Alu markers. Using random samples taken from the populations of Val Venosta, Val Pusteria, Val Isarco, Val Badia, and Val Gardena, we calculated genetic diversity within and among the populations. Microsatellite diversity and unique event polymorphism diversity (on the Y chromosome) were substantially lower in the Ladin-speaking population of Val Badia compared to the neighboring German-speaking populations. In contrast, the genetic diversity of mtDNA haplotypes was lowest for the upper Val Venosta and Val Pusteria. These data suggest a low effective population size, or little admixture, for the gene pool of the Ladin-speaking population from Val Badia. Interestingly, this is more pronounced for Ladin males than for Ladin females. For the pattern of genetic Alu variation, both Ladin samples (Val Gardena and Val Badia) are among the samples with the lowest diversity. An admixture analysis of one German-speaking valley (Val Venosta) indicates a relatively high genetic contribution of Ladin origin. The reduced genetic diversity and a high genetic differentiation in the Rhaetoroman- and German-speaking South Tyrolean populations may constitute an important basis for future medical genetic research and gene mapping studies in South Tyrol.     

Native South American genetic structure and prehistory inferred from hierarchical modeling of mtDNA

Genetic diversity in Native South Americans forms a complexpattern at both the continental and local levels. In comparingthe West to the East, there is more variation within groupsand smaller genetic distances between groups. From this pattern,researchers have proposed that there is more variation in theWest and that a larger, more genetically diverse, founding populationentered the West than the East. Here, we question this characterizationof South American genetic variation and its interpretation.Our concern arises because others have inferred regional variationfrom the mean variation within local populations without takinginto account the variation among local populations within thesame region. This failure produces a biased view of the actualvariation in the East. In this study, we analyze the mitochondrial DNA sequence betweenpositions 16040 and 16322 of the Cambridge reference sequence.Our sample represents a total of 886 people from 27 indigenouspopulations from South (22), Central (3), and North America(2). The basic unit of our analyses is nucleotide identity bydescent, which is easily modeled and proportional to nucleotidediversity. We use a forward modeling strategy to fit a seriesof nested models to identity by descent within and between allpairs of local populations. This method provides estimates ofidentity by descent at different levels of population hierarchywithout assuming homogeneity within populations, regions, orcontinents. Our main discovery is that Eastern South America harbors moregenetic variation than has been recognized. We find no evidencethat there is increased identity by descent in the East relativeto the total for South America. By contrast, we discovered thatpopulations in the Western region, as a group, harbor more identityby descent than has been previously recognized, despite thefact that average identity by descent within groups is lower.In this light, there is no need to postulate separate foundingpopulations for the East and the West because the variabilityin the East could serve as a source for the Western gene pools.     

Phylogeography and population differentiation in terrestrial island populations of Banksia arborea (Proteaceae)

The Banded Iron Formations (BIFs) of south‐western Australia are terrestrial islands characterized by high species richness and endemism. Regional endemics occur across multiple formations without inhabiting the intervening landscape matrix. We investigated whether the occurrence on BIF terrestrial islands has led to genetic differentiation among the eight known populations of the regional endemic, Banksia arborea. Genetic structure was assessed using three chloroplast DNA sequence markers and 11 nuclear microsatellite loci. Phylogenetic relationships were assessed with statistical parsimony and Bayesian methods. Dates of haplotype divergence were estimated using the time to most recent common ancestor of B. arborea and Banksia purdieana, as well as a conservative angiosperm chloroplast (cp)DNA mutation rate. Population genetic diversity and structure was assessed amongst and within populations by genotyping 24 geographically clustered individuals from each BIF and three subpopulations within the Die Hardy Range BIF. Indirect gene flow estimates were determined using a method based on the frequency of private alleles. Banksia arborea showed low genetic diversity in (cp)DNA and a complex structural pattern, with genetic differentiation of some BIF populations and an absence of differentiation amongst others, reflecting either retention of ancestral polymorphism across northern BIF populations or more recent connectivity of these populations. There was little evidence of pollen dispersal both between BIFs and within the large BIF known as Die Hardy Range. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 860–872.     

Population structure of the yellow-footed rock-wallaby Petrogale xanthopus (Gray, 1854) inferred from mtDNA sequences and microsatellite loci

The yellow-footed rock-wallaby Petrogale xanthopus is considered to be potentially vulnerable to extinction. This wallaby inhabits naturally disjunct rocky outcrops which could restrict dispersal between populations, but the extent to which that occurs is unknown. Genetic differences between populations were assessed using mitochondrial DNA (control region) sequencing and analysis of variation at four microsatellite loci among three geographically close sites in south-west Queensland (P. x. celeris) and, for mtDNA only, samples from South Australia (P. x. xanthopus) as well. Populations from South Australia and Queensland had phylogenetically distinct mtDNA, supporting the present classification of these two groups as evolutionarily distinct entities. Within Queensland, populations separated by 70 km of unsuitable habitat differed significantly for mtDNA and at microsatellite loci. Populations separated by 10 km of apparently suitable habitat had statistically homogeneous mtDNA, but a significant difference in allele frequency at one microsatellite locus. Tests for Hardy-Weinberg equilibrium and micro-geographical variation at microsatellite loci did not detect any substructuring between two wallaby aggregations within a colony encircling a single rock outcrop. Although the present study was limited by small sample sizes at two of the three Queensland locations examined, the genetic results suggest that dispersal between colonies is limited, consistent with an ecological study of dispersal at one of the sites. Considering both the genetic and ecological data, we suggest that management of yellow-footed rock-wallabies should treat each colony as an independent unit and that conservation of the Queensland and South Australian populations as separate entities is warranted.     

Cross-sectional changes in anthropometric variables among Wapishana and Patamona Amerindian adults

Although anthropometric information on South American Indian populations has been collected for many years, remarkably little is known about age-related changes in their body size in adulthood. The lack of baseline information on the normal pattern of aging among Amerindian adults hinders investigations into the health consequences of the many economic, environmental and demographic changes that are currently occurring among South American Indian populations. This study presents data on the body size and shape of a convenience sample of 345 Patamona and 186 Wapishana Amerindian adults over 20 years of age living in the remote interior of Guyana. Analysis of the cross-sectional data demonstrated significant declines in stature, sitting height, and biacromial width with age, while there were no changes in subischial leg length or arm length across the age range of the study populations. In contrast, body weight and body mass index (BMI--a measure of body fatness) only declined in those over 50 years of age, after a period of increase. Significant differences in adult linear body dimensions were found between the two Amerindian populations that were proposed to be the result of known differences in childhood growth performance. However, the greater BMI of the Wapishana was shown to be associated with their significantly greater current wealth, thereby highlighting the presence of biological consequences of wealth inequalities even within these subsistence farming populations.     

DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues

Whole-genome copy number analysis platforms, such as array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) arrays, are transformative research discovery tools. In cancer, the identification of genomic aberrations with these approaches has generated important diagnostic and prognostic markers, and critical therapeutic targets. While robust for basic research studies, reliable whole-genome copy number analysis has been unsuccessful in routine clinical practice due to a number of technical limitations. Most important, aCGH results have been suboptimal because of the poor integrity of DNA derived from formalin-fixed paraffin-embedded (FFPE) tissues. Using self-hybridizations of a single DNA sample we observed that aCGH performance is significantly improved by accurate DNA size determination and the matching of test and reference DNA samples so that both possess similar fragment sizes. Based on this observation, we developed a novel DNA fragmentation simulation method (FSM) that allows customized tailoring of the fragment sizes of test and reference samples, thereby lowering array failure rates. To validate our methods, we combined FSM with Universal Linkage System (ULS) labeling to study a cohort of 200 tumor samples using Agilent 1 M feature arrays. Results from FFPE samples were equivalent to results from fresh samples and those available through the glioblastoma Cancer Genome Atlas (TCGA). This study demonstrates that rigorous control of DNA fragment size improves aCGH performance. This methodological advance will permit the routine analysis of FFPE tumor samples for clinical trials and in daily clinical practice.     

Heterologous amplification and characterization of microsatellite markers in the Neotropical fish Leporinus friderici

Leporinus friderici, native to the Amazon Basin and popularly known as "piau-três-pintas", has great ecological and economic importance; it is widely fished and consumed throughout much of tropical South America. Knowledge of the genetic diversity of this native species is important to support management and conservation programs. We evaluated microsatellite loci amplification, using heterologous primers, in 31 individuals of L. friderici. These samples were collected from natural populations of the Araguaia River basin, in central Brazil, and the DNA was extracted from samples of muscle tissue. Eight loci were successfully analyzed. Six of them were polymorphic, and the number of alleles ranged from three to 10. Values of expected heterozygosities for these polymorphic loci ranged from 0.488 to 0.795. Exclusion probability (0.983), the identity probability (0.000073), and the mean genetic diversity values were high, showing that these microsatellite markers are suitable for assessing the genetic variability of L. friderici populations. There is a growing interest in studies that evaluate the genetic variability of natural populations for various purposes, such as conservation. Here, we showed that a viable alternative to the costly development of specific primers for fish populations is simply testing for heterologous amplification of microsatellite markers available from research on other species.