Multiple Microsatellite Loci Research Articles

Population Genetic Structure of a Rare Butterfly in a Fragmented South Florida Ecosystem.

We investigated the genetic structure and diversity between populations of a rare butterfly, the Florida duskywing (Ephyriades brunnea floridensis E. Bell and W. Comstock, 1948) (Lepidoptera: Hesperiidae) across a network of South Florida pine rockland habitat fragments. Based on 81 individuals from seven populations and using multiple polymorphic microsatellite loci, our analyses support the presence of mainland Florida (peninsular) and Florida Keys (island) population groupings, with a moderate, asymmetrical gene flow connecting them, and the presence of private alleles providing unique identities to each. We additionally found that despite a prevalence in many Lepidoptera, the presence of Wolbachia was not identified in any of the samples screened. Our findings can be used to inform conservation and recovery decisions, including population monitoring, organism translocation, and priority areas for management, restoration or stepping-stone creation to help maintain the complex genetic structure of separate populations.

Genotyping confirms significant cannibalism in northern Gulf of Mexico invasive red lionfish, Pterois volitans

DNA barcoding is used in a variety of ecological applications to identify organisms, including partially digested prey items from diet samples. That particular application can enhance the ability to characterize diet and predator–prey dynamics but is problematic when genetic sequences of prey match those of consumer species (i.e., self-DNA). Such a result may indicate cannibalism, but false positives can result from contamination of degraded prey samples with consumer DNA. Here, nuclear-encoded microsatellite markers were used to genotype invasive lionfish, Pterois volitans, consumers and their prey (n = 80 pairs) previously barcoded as lionfish. Cannibalism was confirmed when samples exhibited two or more different alleles between lionfish and prey DNA across multiple microsatellite loci. This occurred in 26.2% of all samples and in 42% of samples for which the data were considered conclusive. These estimates should be considered conservative given rigorous assignment criteria and low allelic diversity in invasive lionfish populations. The highest incidence of cannibalism corresponded to larger sized consumers from areas with high lionfish densities, suggesting cannibalism in northern Gulf of Mexico lionfish is size- and density-dependent. Cannibalism has the potential to influence population dynamics of lionfish which lack native western Atlantic predators. These results also have important implications for interpreting DNA barcoding analysis of diet in other predatory species where cannibalism may be underreported.

High-Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model.

Genetic diversity and population studies are essential for conservation and wildlife management programs. However, monitoring requires the analysis of multiple loci from many samples. These processes can be laborious and expensive. The choice of microsatellites and PCR calibration for genotyping are particularly daunting. Here we optimized a low-cost genotyping method using multiple microsatellite loci for simultaneous genotyping of up to 384 samples using next-generation sequencing (NGS). We designed primers with adapters to the combinatorial barcoding amplicon library and sequenced samples by MiSeq. Next, we adapted a bioinformatics pipeline for genotyping microsatellites based on read-length and sequence content. Using primer pairs for eight microsatellite loci from the fish Prochilodus costatus, we amplified, sequenced, and analyzed the DNA of 96, 288, or 384 individuals for allele detection. The most cost-effective methodology was a pseudo-multiplex reaction using a low-throughput kit of 1 M reads (Nano) for 384 DNA samples. We observed an average of 325 reads per individual per locus when genotyping eight loci. Assuming a minimum requirement of 10 reads per loci, two to four times more loci could be tested in each run, depending on the quality of the PCR reaction of each locus. In conclusion, we present a novel method for microsatellite genotyping using Illumina combinatorial barcoding that dispenses exhaustive PCR calibrations, since non-specific amplicons can be eliminated by bioinformatics analyses. This methodology rapidly provides genotyping data and is therefore a promising development for large-scale conservation-genetics studies.

Rapid increase in genetic diversity in an endemic Patagonian tuco-tuco following a recent volcanic eruption

Catastrophic natural events can have profound impacts on patterns of genetic diversity. Due to the typically unpredictable nature of such phenomena, however, few studies have been able to directly compare patterns of diversity before and after natural catastrophic events. Here, we examine the impacts of a recent volcanic eruption in southern Chile on genetic variation in the colonial tuco-tuco (Ctenomys sociabilis), a subterranean species of rodent endemic to the area most affected by the June 2011 eruption of the Puyehue-Cordon Caulle volcanic complex. To provide a comparative context for interpreting changes in genetic variation in this species, we also analyze the effects of this eruption on genetic variation in the geographically proximate but more widely distributed Patagonian tuco-tuco (C. haigi). Our analyses indicate that while both C. sociabilis and C. haigi displayed significant post-eruption decreases in population density, the apparent impacts of the eruption on genetic diversity differed between species. In particular, genetic diversity at multiple microsatellite loci increased in C. sociabilis after the eruption while no comparable post-eruption increase in C. haigi was observed at these loci. No changes in post-eruption diversity at the mitochondrial cytochrome b locus were detected for either species. To place these findings in a larger spatiotemporal context, we compared our results for C. sociabilis to genetic data from additional modern and ancient populations of this species. These comparisons, combined with Bayesian serial coalescent modeling, suggest that post-eruption gene flow from nearby populations represents the most probable explanation for the apparent increase in post-eruption microsatellite diversity in C. sociabilis. Thus, detailed comparisons of pre- and post-eruption populations provide important insights into not only the genetic consequences of a natural catastrophic event, but also the demographic processes by which these changes in genetic diversity likely occurred.

Varver: a database of microsatellite variation in vertebrates.

Understanding how genetic variation is maintained within a species is important in ecology, evolution, conservation and population genetics. Tremendous efforts have been made to evaluate the patterns of genetic variation in natural populations of various species. For this purpose, microsatellites have played a major role since the 1990s. Here we describe a comprehensive database, varver (Variation in Vertebrates) that provides complete information regarding microsatellite variation in natural populations of vertebrates. For each species, varver includes basic information of the species, a list of publications reporting the microsatellite variation, and tables of genetic variation within and between populations (heterozygosity and FST ). The geographic location and rough sampling range are also shown for each sampled population. The database should be useful for researchers interested in not only specific species but also comparing multiple species. We discuss the utility of microsatellite data, particularly for meta-analyses that involve multiple microsatellite loci from various species. We show that in such analyses, it is extremely important to correct for biases caused by differences in mutation rate, mainly due to repeat unit and number.

Exceptionally long-range haplotypes in Plasmodium falciparum chromosome 6 maintained in an endemic African population.

BackgroundPrevious genome-wide analyses of single nucleotide variation in Plasmodium falciparum identified evidence of an extended haplotype region on chromosome 6 in West Africa, suggesting recent positive selection. Such a pattern is not seen in samples from East Africa or South East Asia, so it could be marking a selective process specific to West Africa. Analyses of the haplotype structure in samples taken at different times could give clues to possible causes of selection.MethodsThis study investigates chromosome 6 extended haplotypes in The Gambia by analysing alleles at multiple microsatellite loci using genome sequence data previously obtained from clinical isolates collected in 2008, followed by genotyping of 13 loci in 439 isolates from 1984, 1991, 2008 and 2014. Temporal changes in haplotype structure and frequencies were determined.ResultsA region of high linkage disequilibrium spanning over 170 kilobases (kb) was identified with both NGS and laboratory determined microsatellite alleles. Multiple long haplotypes were found in all temporal populations from The Gambia. Two of the haplotypes were detected in samples from 1984 and 1991. The frequency of long-range haplotypes increased in 2008 and 2014 populations. There was higher Fst between older and more recent populations at loci in proximity to genes involved in drug metabolism pathways.ConclusionsThe occurrence of several long haplotypes at intermediate frequencies suggests an unusual mode of selection in chromosome 6, possibly combined with recombination suppression on specific haplotypes. Such selection apparently occurred before the emergence of known anti-malarial drug resistance alleles, and could be due to effects of other drugs or unknown processes that have long been operating in this endemic region.Electronic supplementary materialThe online version of this article (doi:10.1186/s12936-016-1560-7) contains supplementary material, which is available to authorized users.

Hierarchical behaviour, habitat use and species size differences shape evolutionary outcomes of hybridization in a coral reef fish.

Hybridization is an important evolutionary process, with ecological and behavioural factors influencing gene exchange between hybrids and parent species. Patterns of hybridization in anemonefishes may result from living in highly specialized habitats and breeding status regulated by size-based hierarchal social groups. Here, morphological, ecological and genetic analyses in Kimbe Bay, Papua New Guinea, examine the hybrid status of Amphiprion leucokranos, a nominal species and presumed hybrid between Amphiprion sandaracinos and Amphiprion chrysopterus. We test the hypothesis that habitat use and relative size differences of the parent species and hybrids determine the patterns of gene exchange. There is strong evidence that A.leucokranos is a hybrid of smaller A.sandaracinos and larger A.chrysopterus, where A.chrysopterus is exclusively the mother to each hybrid, based on mtDNA cytochrome b and multiple nDNA microsatellite loci. Overlap in habitat, depth and host anemone use was found, with hybrids intermediate to parents and cohabitation in over 25% of anemones sampled. Hybrids, intermediate in body size, colour and pattern, were classified 55% of the time as morphologically first-generation hybrids relative to parents, whereas 45% of hybrids were more A.sandaracinos-like, suggesting backcrossing. Unidirectional introgression of A.chrysopterus mtDNA into A.sandaracinos via hybrid backcrosses was found, with larger female hybrids and small male A.sandaracinos mating. Potential nDNA introgression was also evident through distinct intermediate hybrid genotypes penetrating both parent species. Findings support the hypothesis that anemonefish hierarchical behaviour, habitat use and species-specific size differences determine how hybrids form and the evolutionary consequences of hybridization.

Microsatellite Instability Confounds Engraftment Analysis of Hematopoietic Stem-cell Transplantation

Polymorphic short tandem-repeat, or microsatellite, loci have been widely used to analyze chimerism status after allogeneic hematopoietic stem-cell transplantation. In molecular diagnostic laboratories, it is recommended to calculate mixed chimerism for at least 2 informative loci and to avoid microsatellite loci on chromosomes with copy number changes. In this report, we show that microsatellite instability observed in 2 patients with acute leukemia may confound chimerism analysis. Interpretation errors may occur even if 2 to 3 loci are analyzed because of length variation in multiple microsatellite loci. Although microsatellite loci with length variation should not be selected for chimerism analysis, the presence of microsatellite instability, like copy number alteration because of aberrant chromosomes, provides evidence of recurrent or residual cancer cells after hematopoietic stem-cell transplantation.

GENETIC DIVERGENCE IS DECOUPLED FROM ECOLOGICAL DIVERSIFICATION IN THE HAWAIIAN NESOSYDNE PLANTHOPPERS

Adaptive radiation involves ecological shifts coupled with isolation of gene pools. However, we know little about what drives the initial stages of divergence. We study a system in which ecological diversification is found within a chronologically well-defined geological matrix to provide insight into this enigmatic phase of radiation. We tested the hypothesis that a period of geographic isolation precedes ecological specialization in an adaptive radiation of host-specialized Hawaiian planthoppers. We examined population structure and history using mitochondrial and multiple independent microsatellite loci in a species whose geographic distribution on the island of Hawaii enabled us to observe the chronology of divergence in its very earliest stages. We found that genetic divergence is associated with geographic features but not different plant hosts and that divergence times are very recent and on the same timescales as the dynamic geology of the island. Our results suggest an important role for geography in the dynamics of the early stages of divergence.

Detecting and investigating the significance of high-frequency LOH chromosome regions for endometriosis-related candidate genes

To detect the high-frequency loss of heterozygosity (LOH) chromosome regions for ectopic endometrium of ovarian endometriosis (EMs) and to investigate the significance of high-frequency LOH chromosome regions in EMs, we obtained ectopic endometrium by laser capture microdissection (LCM (22 samples)), manual capture microdissection (MCM (18 samples)), and routine dissection (14 samples), respectively. After restriction and circularization-aided rolling circle amplification (RCA-RCA), LOH was detected at 12 microsatellite (MS) loci. The frequency of LOH was 59.09% (13/22) in LCM group, 61.11% (11/18) in the MCM group and 21.43% (3/14) in the routine dissection group. The latter was significantly lower when compared with the former two (p < 0.05). In the LCM group, candidate chromosome regions 17q21.31 and 9p21.3 had LOH frequencies of 23.8 and 13.6%, respectively. The highest LOH frequency was detected at the locus AAAT2 on chromosome 17q21.31 (40%). The chromosome region with the highest frequency of LOH for ectopic endometrium was 17q21.31, especially at the AAAT2 locus, which prompted that down regulation of the candidate genes nearby the locus might be one of the mechanisms of EMs pathogenesis. LCM combined with RCA-RCA is a reliable technique for analyzing endometrial LOH at multiple MS loci. MCM combined with RCA-RCA, which provided similar results, was more cost-effective.

Molecular diversity and association mapping of quantitative traits in Tibetan wild and worldwide originated barley (Hordeum vulgare L.) germplasm

Molecular diversity of 40 accessions of Tibetan wild barley (TB), 10 Syrian (SY), 72 North American (NA), 36 European (EU), 9 South American (SA) and 8 Australian (AU) varieties were characterized using multiple microsatellite loci. The 42 SSR primers amplified 278 alleles across the 175 barley accessions tested in the present study. The average gene diversity for the whole sample was 0.3387 whereas the mean value for the each population was as follows: TB = 0.3286, SY = 0.2474, EU = 0.299, AU = 0.2867, NA = 0.3138, SA = 0.2536. Clustering analysis based on Nei’s original genetic distance showed that the EU and NA barley populations were grouped together. The TB population was well separated from the other 5 barley populations. Associations between microsatellite markers and 14 quantitative traits were also investigated. Significant associations were found for 18 microsatellite marker loci. The number of marker loci associated with each trait ranged from one (stem diameter, filled grains per plant, grain weight per plant, length of main spike and awn length) to seven (plant height). The percentage of the total variation explained by each marker ranged from 4.59% (HVM2 associated with plant height) to 17.48% (Bmac90 associated with density of main spike). This study provides candidate markers for further QTL mapping of these traits and for marker-assisted selection.

787 An evaluation of prostate cancer gene 3 (PCA3) in patients with suspected prostate cancer

Instability in the repeat size of microsatellite sequences has been described in both hereditary nonpolyposis and sporadic colorectal cancers. Tumors expressing microsatellite instability are identified through the comparison of the repeat sizes at multiple microsatellite loci between tumor and matched normal tissue DNA. The use of a five-marker panel including two mononucleotide repeat microsatellites, BAT-25 and BAT-26, has recently been suggested for the clinical determination of tumor microsatellite instability. The BAT-25 and BAT-26 loci included in this panel have both demonstrated sensitivity to microsatellite instability and normal quasimonomorphic allelic patterns, which has simplified the distinction between normal and unstable alleles. However, in this study, we identified allelic variations in the size of the poly(A) tract at BAT-26 in 12.6% of 103 healthy African-Americans screened. In addition, 18.4% exhibited allelic size variations in the poly(T) tract at BAT-25. Finally, 2.9% showed variant alleles at both BAT-25 and BAT-26 loci. Screening a small population of Nigerians confirmed the polymorphic nature of both loci and the ethnic origin of alleles not identified in other populations studied thus far. Our results dispute the quasimonomorphic nature of both BAT-25 and BAT-26 in all populations and support the need for thorough population studies to define the different allelic profiles and frequencies at microsatellite loci.

Outbreeding and possibly inbreeding depression in a pollinating fig wasp with a mixed mating system

Mixed mating systems are somewhat of an enigma as most models predict that organisms should either inbreed when inbreeding depression is low, or outbreed when inbreeding depression is high. Many wasps mix routine inbreeding with a little random mating. This random mating is most common when all local sibmating opportunities are exhausted and dispersal is the only way males can further increase their fitness. The males of the pollinating fig wasp, Platyscapa awekei, are slightly different in that they disperse before all sibmating opportunities have been exhausted. To see if this is a response to inbreeding depression we quantify inbreeding depression by comparing females' life time reproductive success to their heterozygosity at multiple microsatellite loci. We find that a female wasp's heterozygosity is an accurate predictor of her inbreeding coefficient and that P. awekei females actually seem to suffer from outbreeding depression and possibly from a little inbreeding depression. Male dispersal is thus not a means to effect the optimal mating system, but more likely a mechanism to reduce competition among brothers. The number of mature offspring a female produces depends on her own heterozygosity and not on that of the offspring, and may be determined by egg and gall quality.

Spatio‐temporal variation in the strength and mode of selection acting on major histocompatibility complex diversity in water vole (Arvicola terrestris) metapopulations

Patterns of spatio-temporal genetic variation at a class II major histocompatibility complex (MHC) locus and multiple microsatellite loci were analysed within and between three water vole metapopulations in Scotland, UK. Comparisons of MHC and microsatellite spatial genetic differentiation, based on standardised tests between two demographically asynchronous zones within a metapopulation, suggested that spatial MHC variation was affected by balancing selection, directional selection and random genetic drift, but that the relative effects of these microevolutionary forces vary temporally. At the metapopulation level, between-year differentiation for MHC loci was significantly correlated with that of microsatellites, signifying that neutral factors such as migration and drift were primarily responsible for overall temporal genetic change at the metapopulation scale. Between metapopulations, patterns of genetic differentiation implied that, at large spatial scales, MHC variation was primarily affected by directional selection and drift. Levels of MHC heterozygosity in excess of Hardy-Weinberg expectations were consistent with overdominant balancing selection operating on MHC variation within metapopulations. However, this effect was not constant among all samples, indicating temporal variation in the strength of selection relative to other factors. The results highlight the benefit of contrasting variation at MHC with neutral markers to separate the effects of stochastic and deterministic microevolutionary forces, and add to a growing body of evidence showing that the mode and relative strength of selection acting on MHC diversity varies both spatially and temporally.

Microsatellite-based molecular diversity of bread wheat germplasm and association mapping of wheat resistance to the Russian wheat aphid

Genetic diversity of a set of 71 wheat accessions, including 53 biotype 2 Russian wheat aphid (RWA2)-resistant landraces and 18 RWA2 susceptible accessions, was assessed by examining molecular variation at multiple microsatellite (SSR) loci. Fifty-one wheat SSR primer pairs were used, 81 SSR loci were determined, and 545 SSR alleles were detected. These SSR loci covered all the three genomes, 21 chromosomes, and at least 41 of the 42 chromosome arms. Diversity values averaged over SSR loci were high with mean number of SSR alleles/locus = 6.7, mean Shannon's index (H) = 1.291, and mean Nei's gene diversity (He) = 0.609. The three wheat genomes ranked as A > D > B and the homoeologous groups ranked as 7 > 3 > 1 > 2 > 6 > 5 > 4 based on the number of alleles per locus. Xgwm136 on chromosome arm 1AS is the most polymorphic SSR locus with the largest number of observed and effective alleles and the highest H and He. Among all 2485 pairs of wheat accessions, genetic distance (GD) ranged from 0.054 to 1.933 and averaged 0.9832. A dendrogram based on GD matrix showed that all the wheat accessions could be grouped into distinct clusters. Most of the susceptible cultivars (13/18) were clustered into groups that contains all or mostly susceptible accessions. Most of the U.S. cultivars belong to a group that is distinguishable from all the different RWA2 resistant groups. Diversity analysis was also conducted separately for subgroups containing 53 RWA2-resistant accessions and 18 RWA2-susceptible accessions. Association mapping revealed 28 SSR loci significantly associated with leaf chlorosis, and 8 with leaf rolling. New chromosome regions associated with RWA2 resistance were detected, and indicated existence of new RWA resistance genes located on chromosomes of all other homoeologous groups in addition to the groups 1 and 7 in bread wheat. This information is helpful for development of mapping populations for RWA2 resistance genes from different phylogenetic groups, and for wise utilization of the RWA-resistant germplasm in wheat breeding programs.

Genetic discrimination of middle Mississippi River Scaphirhynchus sturgeon into pallid, shovelnose, and putative hybrids with multiple microsatellite loci

The pallid sturgeon (Scaphirhynchus albus), which is protected under the US endangered species act, and shovelnose sturgeon (S. platorhynchus), which is legally harvested in some locations, are sympatric throughout the range of pallid sturgeon. There is considerable morphological overlap between the species making discrimination problematic. The inability to reliably differentiate between species across all life stages has hampered pallid sturgeon recovery efforts. Furthermore, the two species are believed to hybridize. This study used allele frequency data at multiple microsatellite loci to perform Bayesian and likelihood-based assignment testing and morphological measures and meristics to discriminate pallid, shovelnose, and putative hybrid sturgeons from the middle Mississippi River. Bayesian model-based clustering of the genetic data indicated that two natural genetic units occur in the region. These units correspond to morphologically identified pallid and shovelnose sturgeon. Some individuals were morphologically intermediate and many of these failed to strongly assign genetically as either pallid or shovelnose sturgeon, suggesting they may be hybrids. These data indicate that pallid sturgeon and shovelnose sturgeon are genetically distinct in the middle Mississippi River (F ST = 0.036, P < 0.0001) and suggest that hybridization between pallid sturgeon and shovelnose sturgeon has occurred in this region with genetic distance estimates indicating the greatest distance is between pallid and shovelnose sturgeon, while hybrid sturgeon are intermediate but closer to shovelnose. This study demonstrates that assignment testing with multiple microsatellite markers can be successful at discriminating pallid sturgeon and shovelnose sturgeon, providing a valuable resource for pallid sturgeon recovery and conservation.

Identification of microsatellite loci in Collinsia verna (Veronicaceae)

AbstractWe developed eight polymorphic microsatellite loci for Collinsia verna (Veronicaceae). In a sample of 18–35 individuals from a single population, we found two to 15 alleles per locus (mean 8.3). We also tested these loci for cross‐amplification in all 22 species in the tribe Collinseae. Overall, more than half the species in the tribe amplified one microsatellite while three species most closely related to C. verna (Collinsia violacea, Collinsia parviflora and Collinsia grandiflora) amplified multiple microsatellite loci. These microsatellite loci will be used in future studies of mating system in this tribe and other quantitative genetic and population genetic studies.

Origins and evolution of the Europeans' genome: evidence from multiple microsatellite loci

There is general agreement that the current European gene pool is mainly derived from Palaeolithic hunting-gathering and Neolithic farming ancestors, but different studies disagree on the relative weight of these contributions. We estimated admixture rates in European populations from data on 377 autosomal microsatellite loci in 235 individuals, using five different numerical methods. On average, the Near Eastern (and presumably Neolithic) contribution was between 46 and 66%, and admixture estimates showed, with all methods, a strong and significant negative correlation with distance from the Near East. If the assumptions of the model are approximately correct, i.e. if the Basques' and Near Easterners' genomes represent a good approximation to the Palaeolithic and Neolithic settlers of Europe, respectively, these results imply that half or more of the Europeans' genes are descended from Near Eastern ancestors who immigrated in Europe 10000 years ago. If these assumptions are incorrect, our results show anyway that clinal variation is the rule in the Europeans' genomes and that lower estimates of Near Eastern admixture obtained from the analysis of single markers do not reflect the patterns observed at the genomic level.

Major histocompatibility complex and microsatellite variation in two populations of wild gorillas

In comparison to their close relatives the chimpanzees and humans, very little is known concerning the amount and structure of genetic variation in gorillas. Two species of gorillas are recognized and while the western gorillas number in the tens of thousands, only several hundred representatives of the mountain gorilla subspecies of eastern gorillas survive. To analyse the possible effects of these different population sizes, this study compares the variation observed at microsatellite and major histocompatibility complex (MHC) loci in samples of wild western and mountain gorillas, collected using a sampling scheme that targeted multiple social groups within defined geographical areas. Noninvasive samples proved a viable source of DNA for sequence analysis of the second exon of the DRB loci of the MHC. Observed levels of variation at the MHC locus were similar between the two gorilla species and were comparable to those in other primates. Comparison of results from analysis of variation at multiple microsatellite loci found only a slight reduction in heterozygosity for the mountain gorillas despite the relatively smaller population size.

Technical challenges in the microsatellite genotyping of a wild chimpanzee population using feces

Noninvasive collection of samples from wild mammal populations presents an extraordinary opportunity to conduct genetic analysis without necessarily capturing or even directly observing the subjects of interest. Unfortunately, the hair or feces samples typically collected present formidable challenges in the laboratory. The investment of time and expense required makes careful experimental design a necessity. Researchers who want to examine the genetics of wild mammal populations have great interest in the use of noninvasively collected sample materials. Questions that can potentially be answered range from population-level inquiries into such topics as population size, sex composition, individual relationship, and dispersal, to comparisons between populations providing information on geographic differentiation, comparative levels of genetic diversity, and phylogenetic relationships.1 Effective investigation of these matters relies on an ability to examine genetic variation from the nuclear genome as well as the maternally transmitted mitochondrial DNA (mtDNA). A typical approach to examining the genetic structure of a population involves the assessment of variation at multiple nuclear microsatellite loci. Alleles of these microsatellite loci vary in the length of simple repeat elements, hence allowing for the potential assemblage, when enough loci are examined, of individually distinctive genotypes.2 I will therefore focus here on microsatellite analyses. Numerous studies have employed microsatellite analysis of noninvasive samples in the form of feces or shed hair.3–8 But, as Taberlet et al.9 recently noted, to date there have been relatively few “comprehensive” studies using nuclear DNA from noninvasive samples. This is surprising in view of the existence of the large body of literature on the topic, and the subjective impression that many field researchers are equipped with collection materials and a plan or at least a hope of arranging for later genetic analysis. The indication is thus that, years after it was heralded as representing a revolution in field studies of primates,10 noninvasive sampling for genetic analysis either has not yet reached its potential or has proved disappointing. Ironically, the simplicity and low costs of the polymerase chain reaction (PCR) that have led to its ubiquitous use in molecular analysis laboratories may have led to an underestimation by laboratory and field researchers alike of the difficulties inherent in the use of noninvasive samples. Such analyses in fact present considerable technical challenges that can only be overcome by investing a great deal of time, expense, and laboratory expertise. Most technical considerations involved in the production of accurate genotypes from noninvasive samples have been thoroughly addressed elsewhere.9,11 In this contribution, I will present some preliminary results from a study of habituated communities of chimpanzees (Pan troglodytes verus) in the Tai National Forest, Ivory Coast. The necessary investment, particularly in terms of time and expense, of generating reliable genotypes from a large number of individuals will be described.