Markers For Population Genetic Studies Research Articles

Unbiased Interpretation of Haplotypes at Duplicated Microsatellites

The Y-chromosome is a powerful tool for population geneticists to study human evolutionary history. Haploid and largely non-recombining, it should contain a simple record of past mutational events. However, this apparent simplicity is compromised by Y-linked duplicons, which make up approximately 35% of this chromosome; 25% of these duplicons are large inverted repeats (palindromes). For microsatellites lying in these palindromes, two loci cannot be easily distinguished due to PCR co-amplification, and this order misspecification of alleles generates an additional variance component. Due to this ambiguity, population geneticists have traditionally used an arbitrary method to assign the alleles (shorter allele to locus 1, larger allele to locus 2). Here, we simulate these posterior estimate distributions under three different novel allele assignment priors and compare this with the original method. We use a sample of 33 human populations, typed for duplicated microsatellites lying within palindrome P8, to illustrate our approach. We show that both intra- and inter-population statistics can be dramatically affected by order misspecification. Surprisingly, matrices of pairwise F-statistics or distance estimates appear far less sensitive to order misspecification and remain relatively unchanged under the priors considered, suggesting that these microsatellites can be considered as useful markers for population genetic studies using an appropriate data treatment. Duplicated microsatellites represent an attractive source of information to investigate the extensive structural polymorphism observed among human Y chromosomes, as well as processes of intra-chromosomal gene conversion acting between duplicons.

Chloroplast microsatellites reveal colonization and metapopulation dynamics in the Canary Island pine

Chloroplast microsatellites are becoming increasingly popular markers for population genetic studies in plants, but there has been little focus on their potential for demographic inference. In this work the utility of chloroplast microsatellites for the study of population expansions was explored. First, we investigated the power of mismatch distribution analysis and the F(S) test with coalescent simulations of different demographic scenarios. We then applied these methods to empirical data obtained for the Canary Island pine (Pinus canariensis). The results of the simulations showed that chloroplast microsatellites are sensitive to sudden population growth. The power of the F(S) test and accuracy of demographic parameter estimates, such as the time of expansion, were reduced proportionally to the level of homoplasy within the data. The analysis of Canary Island pine chloroplast microsatellite data indicated population expansions for almost all sample localities. Demographic expansions at the island level can be explained by the colonization of the archipelago by the pine, while population expansions of different ages in different localities within an island could be the result of local extinctions and recolonization dynamics. Comparable mitochondrial DNA sequence data from a parasite of P. canariensis, the weevil Brachyderes rugatus, supports this scenario, suggesting a key role for volcanism in the evolution of pine forest communities in the Canary Islands.

Surnames as genetic markers in population studies

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Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

Alu elements are the most active and predominant type of short interspersed elements (SINEs) in the human genome. Recently inserted polymorphic (for presence/absence) Alu elements contribute to genome diversity among different human populations, and they are useful genetic markers for population genetic studies. The objective of this study is to identify polymorphic Alu insertions through an in silico comparative genomics approach and to analyze their distribution pattern throughout the human genome. By computationally comparing the public and Celera sequence assemblies of the human genome, we identified a total of 800 polymorphic Alu elements. We used polymerase chain reaction-based assays to screen a randomly selected set of 16 of these 800 Alu insertion polymorphisms using a human diversity panel to demonstrate the efficiency of our approach. Based on sequence analysis of the 800 Alu polymorphisms, we report three new Alu subfamilies, Ya3, Ya4b, and Yb11, with Yb11 being the smallest known Alu subfamily. Analysis of retrotransposition activity revealed Yb11, Ya8, Ya5, Yb9, and Yb8 as the most active Alu subfamilies and the maintenance of a very low level of retrotransposition activity or recent gene conversion events involving S subfamilies. The 800 polymorphic Alu insertions are characterized by the presence of target site duplications (TSDs) and longer than average polyA-tail length. Their pre-integration sites largely follow an extended “NT-AARA” motif. Among chromosomes, the density of Alu insertion polymorphisms is positively correlated with the Alu-site availability and is inversely correlated with the densities of older Alu elements and genes.

Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure

Single-nucleotide polymorphisms (SNPs) are a class of attractive genetic markers for population genetic studies and for identifying genetic variations underlying complex traits. However, the usefulness and efficiency of SNPs in comparison to microsatellites in different scientific contexts, e.g., population structure inference or association analysis, still must be systematically evaluated through large empirical studies. In this article, we use the Collaborative Studies on Genetics of Alcoholism (COGA) data from Genetic Analysis Workshop 14 (GAW14) to compare the performance of microsatellites and SNPs in the whole human genome in the context of population structure inference. A total of 328 microsatellites and 15,840 SNPs are used to infer population structure in 236 unrelated individuals. We find that, on average, the informativeness of random microsatellites is four to twelve times that of random SNPs for various population comparisons, which is consistent with previous studies. Our results also indicate that for the combined set of microsatellites and SNPs, SNPs constitute the majority among the most informative markers and the use of these SNPs leads to better inference of population structure than the use of microsatellites. We also find that the inclusion of less informative markers may add noise and worsen the results.

Application of bovine microsatellite markers for genetic diversity analysis of Swiss yak (Poephagus grunniens)

In order to assess the applicability of bovine microsatellite markers for population genetic studies in Swiss yak, 131 bovine microsatellite markers were tested on a panel of 10 animals. Efficient amplification was observed for 124 markers (94.6%) with a total of 476 alleles, of which 117 markers (94.3%) were polymorphic. The number of alleles per locus among the polymorphic markers ranged from two to nine. Seven loci (ILSTS005, BMS424B, BMS1825, BMS672, BM1314, ETH123 and BM6017) failed to amplify yak genomic DNA. Two cattle Y-chromosome specific microsatellite markers (INRA126 and BM861) amplified genomic DNA from both male and female yaks. However, two additional markers on cattle Y-chromosome (INRA124 and INRA189) amplified DNA from only males. Of the polymorphic markers, 24 microsatellites proposed by CaDBase for within- and cross-species comparisons and two additional highly polymorphic markers (MHCII and TGLA73) were used to investigate the genetic variability and the population structure of a Swiss yak herd that included 51 additional animals. The polymorphic information content ranged from 0.355 to 0.752, while observed heterozygosity (HO) ranged from 0.348 to 0.823. Furthermore, a set of 13 markers, organized into three multiplex polymerase chain reactions, was evaluated for routine parentage testing. This set provided an exclusion probability in a family of four yaks (both parents and two offspring) of 0.995. These microsatellites serve as useful tools for genetic characterization of the yak, which continues to be an important domestic livestock species.

Eleven new highly polymorphic microsatellite loci in the yellow croaker,Pseudosciaena crocea

AbstractWe developed 11 new microsatellite markers inPseudosciaena croceaby screening an enriched genomic library using nonradioactive polymerase chain reaction (PCR) techniques. All loci were found to be polymorphic with an average of 14.9 alleles per locus (range four to 30). The mean observed and expected heterozygosities were 0.86 (range 0.57–1.00) and 0.90 (range 0.62–0.98), respectively. Four loci showed significant Hardy–Weinberg disequilibrium. The high variabilities revealed in this study suggest that these microsatellite loci should provide useful markers for population genetic studies ofP. crocea.

Development and characterization of microsatellite markers for the poplar rust fungi Melampsora medusae and Melampsora larici‐populina

Abstract Melampsora species and their hybrids are obligate parasites of Populus and Salix species worldwide. The increasing interest in Populus and Salix for biomass and fibre production necessitates genetic markers for population studies of Melampsora spp. Libraries enriched for simple sequence repeats were used to develop five microsatellite markers for Melampsora medusae and Melampsora larici‐populina. The variation detected by these markers will be valuable for phylogenetic and population genetic studies, substantiate putative hybrids, and deployment of resistant poplar clones.

Genetic markers in blue crabs ( Callinectes sapidus) I: Isolation and characterization of microsatellite markers

Given the commercial and ecological importance of the dwindling Chesapeake Bay blue crab ( Callinectes sapidus) fishery, there is a surprising scarcity of information concerning the molecular ecology of this species. The few studies published to date are based on allozyme data and indicate a single, panmictic population along the Atlantic coast. To address this shortcoming, we have initiated the development of genetic markers from both the nuclear and mitochondrial genomes of the blue crab. To this end, we performed two separate screenings of the blue crab nuclear genome using both dinucleotide and tetranucleotide repeat oligonucleotide probes and the highly efficient “FIASCO” (Fast Isolation by AFLP of Sequences COntaining repeats) methodology. Our screenings produced 34 microsatellite loci. Genotyping of a captive-mated pair of blue crabs and 30 of their offspring at 10 of our isolated loci shows that eight loci are inherited in true Mendelian fashion, with two loci being monomorphic. Additionally, we genotyped 102 blue crab DNA samples collected from different parts of the Chesapeake Bay with the same 10 loci. The results of these screenings, including heterozygosities ranging between 0.26 and 0.97, indicate that a majority of the loci isolated in our screen will ultimately be useful markers for population genetic studies. The molecular tools described in this paper will be used, in tandem with differences in the blue crab mitochondrial genome [Place, A.R., Feng, X., Steven, C.R., Fourcade, H.M., Boore, J.L., 2005. Genetic markers in blue crabs ( Callinectes sapidus) II: Complete mitochondrial DNA sequence and characterization of variation. J. Exp. Mar. Biol. Ecol. 319, 15–27], to investigate potential genetic substructure within the Chesapeake Bay and across the entire Atlantic Coast/Gulf Coast range of the blue crab, as well as monitor the results of restocking hatchery-reared crabs into the Bay.

Cross‐species amplification of zebrafish and central stoneroller microsatellite loci in six other cyprinids

One hundred and twenty Danio rerio and Campostoma anomalum microsatellite loci were tested for amplification in the cyprinids Phoxinus phoxinus, Scardinius erythrophthalmus, Rutilus rutilus, Abramis brama, Carassius carassius and Gobio gobio. The PCR amplification products were recorded in 35 to 50 loci, depending on focal species. Eight to 28 of the amplifying loci were also polymorphic, establishing potential sets of genetic markers for population genetics studies.

Microsatellite DNA markers for population genetic studies and parentage assignment in cobia, Rachycentron canadum

AbstractTwenty nuclear‐encoded microsatellites from a genomic DNA library of cobia, Rachycentron canadum, were isolated and characterized. The microsatellites include two tetranucleotide, one trinucleotide, three combination tetranucleotide/dinucleotide, nine dinucleotide, and five imperfect (dinucleotide) repeat motifs. Gene diversity ranged between zero to 0.910; the number of alleles among a sample of 24 fish ranged from one to 15. Cobia support an important recreational fishery in the southeastern United States and recently have become of interest to aquaculture. The microsatellites developed will be useful tools for studying both population genetics (e.g. stock structure, effective population size) and inheritance of traits important to aquaculture.

Efficiency of microsatellite enrichment inProsopis chilensis using magnetic capture

Microsatellites (i.e., simple sequence repeats [SSRs]) are highly variable genetic markers that are widely used at an intraspecific level in population genetic studies. Here we employed an enrichment strategy for microsatellite isolation by using microsatellite oligoprobes and magnetic capture of the fragments (Fischer and Bachmann, 1998) inProsopis chilensis (Mol.) Stuntz (Fabaceae). We analyzed the obtained level of enrichment by sequencing 120 enriched genomic fragments. A total of 521 SSR motives were detected. According to specific search criteria (SSR motifs ≥3 repeat units and ≥6 bp length), 95.8% of the clones contained SSR motifs. Of these, 7.8% showed homology to chloroplast sequences and 92.2% to nuclear sequences. When regarding only nuclear SSRs with 5 or more repeat units and a minimum length of 10 bp, the level of enrichment was 30.8%. A FASTA search against the European Molecular Biology Laboratory (EMBL) database univocally revealed 4 clones in transcribed regions, 102 clones in genomic regions with unknown function, and 9 clones in chloroplast regions. Among the loci with longer repeat units (≥10 bp, ≥5 repeat units), 3 were in transcribed regions and 65 were in other genomic regions. We discuss the applicability of these markers for population genetic studies.

Genetic variability at the D1S80 minisatellite: predominance of allele 18 among some Indian populations

Background: Hypervariable minisatellites are considered as useful genetic markers in population studies because they are highly polymorphic, multiallelic and co-dominant in nature. The D1S80 minisatellite is one of the well studied markers, and has been used for differentiating population groups of various geographic, linguistic, cultural and genetic origins.Objective: The present study reports the genetic variation observed at the D1S80 minisatellite among seven anthropologically distinct ethnic groups from Kerala state in south India and is compared with other reported Indian and world populations.Subjects and methods: DNA was isolated from the peripheral blood samples of 282 random, normal and healthy volunteers, PCR amplified and electrophoresed on 4% PAGE followed by silver staining.Results: A total of 22 alleles (14–39 repeats) were detected with high heterozygosity (0.63–0.84) and Polymorphic Information Content (PIC) values (0.63–0.83). Allele 18 was the predominant allele, except in Ezhavas. The comparison of allele frequency data with world populations including other studied Indian ethnic groups has revealed that the majority of Indian populations possessed allele 18 as the predominant allele. In contrast, allele 24 was reported to be the predominant allele worldwide with a few exceptions.Conclusions: This study at the D1S80 minisatellite on seven ethnic groups will provide useful information for the Indian population genetic database. However, the most important observation was the predominance of allele 18 among the majority of Indian ethnic groups. The reason is not clear yet and thus further studies on Indian ethnic groups from different regions are necessary to find out the importance of allele 18 as the predominant allele in Indian population.

Genetic data on 15 STRs in a population sample of religious minority of Old Believers residing in the northeastern Poland

This study provides a 15 STRs database for a population sample of Old Believers ( n=136) living in the northeastern Poland for the use as a highly discriminatory system of genetic markers in population studies and in personal identification. Significant differences revealed between the Old Believers and the autochthonous Poles by using RxC test as well as F ST and F IS estimates suggest a certain degree of genetic isolation of this religious minority.

Isolation of Microsatellite Loci in Sceloporus grammicus (Squamata, Phrynosomatidae)

The mesquite lizard (Sceloporus grammicus) exhibits multiple Robertsonian chromosomal rearrangements (mainly centric fissions) resulting in several cytotypes. In a transitional environment from oak-pine forests to a drier xeric habitat in central Mexico, two cytotypes (F5: 2n = 34 and FM2: 2n = 46) are known to hybridize. A partial genomic library was constructed from S. grammicus genomic DNA and then screened for microsatellites. Microsatellites are short tandem nucleotide repeats that have near universal occurrence in all eukaryotic genomes. Microsatellites exhibit variable length polymorphisms that can be characterized and utilized as genetic markers for population studies. Thirteen microsatellite arrays were isolated from the S. grammicus genomic library and PCR primers were designed in the flanking regions for the amplification of these alleles. These microsatellite loci would be the primary tool used to answer behavioral, ecological, chromosomal and evolutionary questions that influence the maintenance of this hybrid zone.

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

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

Avaliação do polimorfismo de grupos sanguíneos e fenótipo de hemoglobinas em um grupo de universitários de São José do Rio Preto, SP

The studies of the phenotypes of the blood groups are important for blood transfusions, for obstetrics, neonatology and law medicine, apart from its application in anthropology where it can be used as genetic markers in population studies. Works with hemoglobin polymor-phisms as a genetic marker of populations has been increased over the last few years, particularly for different population groups of Brazil. In the investigation the hemoglobin polymorphisms of 200 university students from Sao Jose do Rio Preto, Brazil were studied to establish a possible relation between the different phenotypes. Statistical analysis of the phenotypes showed that the differences observed were not significant, without a relationship among the polymorphisms of blood groups and hemoglobins.

Polymorphic microsatellite loci for tiger salamanders,Ambystoma tigrinum

AbstractMicrosatellites have been developed for few amphibian species. However, developing genetic markers for population genetic studies in amphibians is critical because amphibians are declining globally. The tiger salamander,Ambystoma tigrinum, is widespread throughout the United States and includes the endangered subspecies,A. t. stebbinsi. We present primers and amplification conditions for 10 polymorphic microsatellite loci that have produced successful results in three subspecies ofA. tigrinum. Number of alleles per locus ranged from one to 11 and heterozygosity ranged from 0 to 0.815 depending on the subspecies and locus analysed. These markers should prove useful for future studies of genetic diversity and population subdivision.

Development of Contamination-Free Restriction Fragment Length Polymorphism Probes for the Obligate Biotroph Peronospora tabacina, an Oomycete Causing Blue Mold of Tobacco

ABSTRACT Peronospora tabacina is an obligately parasitic oomycete that causes blue mold, a devastating disease of tobacco. Genetic studies of this pathogen have been hampered by the lack of molecular markers. We generated a set of molecular markers for P. tabacina by collecting sporangiospores from infected tobacco leaves, extracting spore DNA, and cloning it in a plasmid vector. The resulting clones were then used to probe DNA from a collection of P. tabacina isolates to survey for polymorphisms. Most probes gave unexpected hybridization patterns with signal intensities that varied significantly from one DNA sample to another or between different DNA preparations of the same isolate. These results indicated that certain DNA preparations contained DNA from a source other than P. tabacina, which in turn suggested that some probes might have been derived from contaminating organisms present in the spore suspensions. Therefore, we characterized the inserts of several recombinant plasmids to determine their origins. Sequence analysis revealed that several of the inserts encoded peptides with similarity to bacterial proteins, suggesting that they were derived from bacterial contaminants. Of the remaining clones, five exhibited similarity to retroelements, one resembled eukaryotic helicase genes, and nine had no similarity to sequences in the databases. These were postulated to be true P. tabacina DNA clones. Verification of the origin of each probe was achieved by filtering a spore suspension, extracting DNA from the retentate and filtrate, and probing Southern blots of these DNA samples. These experiments confirmed the probe origins predicted by sequence analysis, resulting in the generation of 20 different restriction fragment length polymorphism probes that are specific for P. tabacina DNA. These probes should enable identification of reliable genetic markers for population studies of the blue mold organism.

Applications of PCR-based tools for detection and identification of animal trypanosomes: a review and perspectives.

This paper aims to review the applications of the polymerase chain reaction (PCR) for the detection and identification of trypanosomes in animals. The diagnosis of trypanosomes, initially based on microscopic observations and the host range of the parasites, has been improved, since the 1980s, by DNA-based identification. These diagnostic techniques evolved successively through DNA probing, PCR associated to DNA probing, and currently to PCR alone. Several DNA sequences have been investigated as possible targets for diagnosis, especially multi-copy genes such as mini-exon, kinetoplastid mini-circles, etc., but the most favoured target is the nuclear satellite DNA of mini-chromosomes, which presents the advantages, and the drawbacks, of highly repetitive short sequences (120-600 bp). Several levels of specificity have been achieved from sub-genus to species, sub-species and even types. Random priming of trypanosome DNA has even allowed "isolate specific" identification. Other work based on microsatellite sequences has provided markers for population genetic studies. For regular diagnosis, the sensitivity of PCR has increased with the advancement of technologies for sample preparation, to reach a level of 1 trypanosome/ml of blood, which has brought to field samples a sensitivity two to three times higher than microscopic observation of the buffy coat. Similarly, PCR has allowed an increase in the specificity and sensitivity of diagnosis in vectors such as tsetse flies. However, because of the diversity of Trypanosoma species potentially present in a single host, PCR diagnosis carried out on host material requires several PCR reactions; for example, in cattle, up to five reactions per sample may be required. Research is now focusing on a diagnosis based on the amplification of the internal transcribed spacer-1 (ITS-1) of ribosomal DNA which presents the advantages of being a multi-copy locus (100-200), having a small size (300-800 bp), which varies from one taxon to another but is conserved in size in a given taxon. This may lead to the development of a multi-species-specific diagnostic protocol using a single PCR. By reducing the cost of the PCR diagnosis, this technique would allow a greater number of field samples to be tested in epidemiological studies and/or would increase the variety of Trypanosoma species that could be detected. Further investigations are required to develop and optimise multi-species-specific diagnostic tools for trypanosomes, which could also serve as a model for such tools in other pathogens.