Average Heterozygosity Research Articles

Microsatellite markers polymorphism in the breeding nutria (Myocastor coypus) population in Poland

The aim of the research was to establish a microsatellite panel to determine the genetic diversity within the breeding nutria population in Poland. In the study, 92 animals representing six color forms were used. Ten fluorescently labeled microsatellite markers were investigated by multicolored capillary electrophoresis. All the microsatellites were polymorphic. The average heterozygosity observed among the population was 41%. The mean number of alleles per locus was 9.2. The average heterozygosity observed in the whole population was lower than expected. This implies that the nutria population deviates from the Hardy–Weinberg equilibrium. Low M values (from 0.078 to 0.545) of the Garza–Williamson index reveal a reduction of genetic variation in the investigated population and suggest that the breeding nutria population is remnant.

Genetic variability and differentiation of rainbow trout strains in Iran

To determine the genetic structure and differences of rainbow trout, variations in 9 microsatellite loci in four stocks of rainbow trout from Mazandran, Iran were examined. Three samples were introduced from Norwegian, French stocks, and one was from Iranian stocks rearing in North of Iran. Most but not all loci were polymorphic in all stocks. There was substantial genetic differentiation among populations, with an average FST value of 0.065. The four stocks averaged 5.2–7.4 alleles per locus, with average heterozygosities of around 0.625 to 0.762. A large variation in observed hetrozygocity, averaged over all samples was observed among loci and ranged from 0.015 in OTSG474 to 0.850 in OTSG249. Nine of 20 tests for Hardy – Weinberg expectations gave significant deviations. The cause(s) of these deviations are unknown. The Norway strain was significant deviations from HWE in all 5 polymorphic loci. The degree of differentiation among strain or Nei Genetic Distance compared pairwise accorded well with their likely genetic connectivity. Two of the strains, Iranian and Norway had the highest Nei Genetic Distance (0.213) and were different in all loci except for OTSG3. The level of genetic variation in the domesticated rainbow trout strains that are farmed in European countries (French, Norway) and Iran did not differ significantly neither within nor between the countries, but the highest pronounced difference was comparable with that of the Norway and Iran strains.

Analysis of ANKKI (rs1800497) and DRD2 (rs1079597, rs1800498) variants in five ethnic groups from Punjab, North-West India

Dopamine D2 receptor (DRD2) is one of the essential neurotransmitters in the brain studied extensively in the field of psychiatric disorders, alcoholic behaviors and Pharmacology. It is also a promising gene for studying the evolutionary and genetic variation among populations. The present study was an attempt to understand the extent of genetic variation among five different ethnic groups (Bania, Brahmin, Jat Sikh, Khatri and Scheduled caste) of Punjab (North West India). A total of 1012 individuals belonging to the above mentioned groups were analyzed for three TaqI Polymorphic loci of DRD2 and ankyrin repeat and kinase domain containing 1 (ANKKI) using the allele frequencies and haplotype frequency distribution pattern. All the three loci were found to be polymorphic among the studied populations. The average heterozygosity for all loci in these ethnic groups was fairly substantial ranging from 0.3936 to 0.4986. The genetic differentiation among the population was observed to be in order of 0.0053.Among of the eight studied haplotypes, only six were shared by all the ethnic groups. TaqID and TaqIB loci were reported to be in significantly higher linkage disequilibrium (LD) in Scheduled Caste only, whereas TaqIA and TaqID showed modest LD in Brahmin, Jat Sikh and Khatri. Multidimensional scaling analysis revealed that the studied ethnic groups formed a close cluster, suggesting similar genetic structure of these populations which are in close proximity with other Indo European speaking North Indian and western Indian population groups. Overall this study highlights the genomic uniformity among the ethnic groups of Punjab (North-West India) owing to their common ancestral history and geographical closeness.

Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers.

We evaluated the genetic variation and population structure in Indian and non-Indian genotypes of finger millet using 87 genomic SSR primers. The 128 finger millet genotypes were collected and genomic DNA was isolated. Eighty-seven genomic SSR primers with 60–70 % GC contents were used for PCR analysis of 128 finger millet genotypes. The PCR products were separated and visualized on a 6 % polyacrylamide gel followed by silver staining. The data were used to estimate major allele frequency using Power Marker v3.0. Dendrograms were constructed based on the Jaccard’s similarity coefficient. Statistical fitness and population structure analyses were performed to find the genetic diversity. The mean major allele frequency was 0.92; the means of polymorphic alleles were 2.13 per primer and 1.45 per genotype; the average polymorphism was 59.94 % per primer and average PIC value was 0.44 per primer. Indian genotypes produced an additional 0.21 allele than non-Indian genotypes. Gene diversity was in the range from 0.02 to 0.35. The average heterozygosity was 0.11, close to 100 % homozygosity. The highest inbreeding coefficient was observed with SSR marker UGEP67. The Jaccard’s similarity coefficient value ranged from 0.011 to 0.836. The highest similarity value was 0.836 between genotypes DPI009-04 and GPU-45. Indian genotypes were placed in Eleusine coracana major cluster (EcMC) 1 along with 6 non-Indian genotypes. AMOVA showed that molecular variance in genotypes from various geographical regions was 4 %; among populations it was 3 % and within populations it was 93 %. PCA scatter plot analysis showed that GPU-28, GPU-45 and DPI009-04 were closely dispersed in first component axis. In structural analysis, the genotypes were divided into three subpopulations (SP1, SP2 and SP3). All the three subpopulations had an admixture of alleles and no pure line was observed. These analyses confirmed that all the genotypes were genetically diverse and had been grouped based on their geographic regions.

Analysis of genetic diversity of four quails by microsatellite markers

Genetic diversity of four quail populations, including Korean quails (maroon quails), Peking white quails, Chinese yellow quails and Chinese black quails, were analyzed by microsatellite markers, aiming to provide scientific basis for new breeds of Chinese black quails for egg production as well as the assessment, protection and utilization of Chinese quail’s genetic resources. The results showed that 48 alleles were detected by nine microsatellite markers in the four quail populations, with the mean of 5.33 alleles in each locus. The average effective number of alleles marked by the nine microsatellite markers in Chinese black quails, Peking white quails, Chinese yellow quails and maroon quails were 3.5338, 3.6135, 4.0312 and 3.6508 respectively. The average heterozygosity of the four quail populations were 0.6952, 0.7046, 0.7353 and 0.7096 respectively. The average polymorphic information content of nine microsatellite loci in four quail populations were 0.6204, 0.6587, 0.6942 and 0.6639, respectively, all of which were greater than 0.5, indicating the four populations’ copious genetic diversity. In this study, the average genetic differentiation coefficient among populations was 0.0349, so the genetic variation among populations accounted for 3.49%, which demonstrated that genetic variation among populations was just a small proportion of the total population genetic variation, and there was little differentiation among the four populations. Cluster analysis indicated that Chinese black quails and Peking white quails were firstly clustered, and then Chinese yellow quails and maroon quails were clustered, and finally the two were clustered together.

Acrocomia emensis (Arecaceae) genetic structure and diversity using SSR molecular markers.

Acrocomia emensis, popularly known as the creeping tucum, belongs to the family Arecaceae, and is an oilseed specie of the Brazilian Savannah. The expansion of agricultural activity has rapidly destroyed its natural habitat, leading to a decrease in its population size. Genetic studies can be used to investigate the genetic variability, and may assist with the charting future conservation strategies. In this study the genetic diversity and structure of 150 individuals sampled in three locations in Minas Gerais were analysed, based on the transferability of six microsatellite markers, previously developed for A. aculeata. The results indicate that the populations studied have low levels of genetic variability (Ho = 0.148) and high, positive and significant inbreeding coefficient, indicating an excess of homozygotes. The average heterozygosity within the population (Hs = 0.700) accounted for 95.03% of the total genetic diversity, indicating that there is greater variability within population than between them, consistent with low genetic differentiation between population (GST = 0.046). Bayesian analysis identified three distinct groups; however, populations shared large numbers of alleles, which can be explained by the reduced distance between populations. These results reveal the need to implement genetic conservation programs for the maintenance of this species and to prioritize population from Bonito and Brasília, which showed the lowest values of genetic diversity.

Genetic variability in three populations of Hypostomus hermanni (Teleostei: Loricariidae) found in the basins of Ivaí River, Tietê River, and Sapucaí-Mirim River of Brazil.

The genetic variability in three populations of Hypostomus hermanni from the tributaries of the rivers Ivaí (Keller), Tietê (Piracicaba), and Sapucaí (Sapucaí-Mirim) was determined using electrophoresis on starch gel. The variability in the genes for eight enzymes, namely, aspartate aminotransferase (EC 2.6.1.1), glucose-6-phosphate isomerase (EC 5.3.1.9), glycerol-3-phosphate dehydrogenase (EC 1.1.1.8), isocitrate dehydrogenase (EC 1.1.1.42), -lactate dehydrogenase (EC 1.1.1.27), malate dehydrogenase (EC 1.1.1.37), malate dehydrogenase NADP+ (EC 1.1.1.40), and phosphoglucomutase (EC 5.4.2.2), was assessed. Three loci with seven alleles were obtained in the population of Keller River whereas eight loci with 20 alleles and six loci with 16 alleles were present in the populations of Piracicaba and Sapucaí-Mirim rivers, respectively. Individuals analyzed in the three watersheds presented all the detected polymorphic loci. The average heterozygosity was 0.0527, 0.1742, and 0.1299 in the Keller, Piracicaba, and Sapucaí-Mirim River populations, respectively. On the basis of identity values and genetic distances, all the three populations were determined to be genetically very similar.

GENETIC DIVERSITY OF THE SIKA DEER CERVUS NIPPON IN LITHUANIA

The sika deer ( Cervus nippon ) are considered to be an invasive species in Europe. The main problem that the European free-living sika deer pose is damage they do to forests as well as hybridisation with the local red deer. The aim of this study was to analyse the genetic diversity of the sika deer and the red deer in Lithuania, and to determine the hybridization, which might be present in red deer population from the past release of sika deer into the nature. Tissue samples were collected from 30 sika deer individuals from enclosures, and 33 wild-living red deer. Samples were genotyped using seven microsatellite (STR) loci; genetic diversity indices were calculated and individuals were classified using Principal Coordinate Analysis (PCoA); the genetic structure of sika deer and red deer was investigated according to Bayesian clustering method using STRUCTURE software. The STR loci were highly polymorphic with up to 17 alleles per locus, and with an average heterozygosity Ho=0.695 and Ho=0.626 for sika deer and red deer respectively. Overall inbreeding coefficient (F IS ) values are 0.004 and 0.127 in sika and red deer respectively. According to the PCoA sika deer samples differ from those of red deer; however, few red deer individuals mix with sika deer. These animals were attributed to red deer according to their phenotype; however according to their genotype they are closer to sika deer. Thus, it can be concluded that wild red deer in Lithuania may hybridise with sika deer.

Diversidad genética de ibias (Oxalis tuberosa Molina) y cubios (Tropaeolum tuberosum Ruíz y Pavón) en Boyacá

La región andina es considerada un área que alberga una gran diversidad de especies entre ellas las raíces y tubérculos andinos como las ibias (Oxalis tuberosa Molina) y los cubios (Tropaeolum tuberosum Ruíz y Pavón), los cuales constituyen un componente básico de la dieta de las comunidades rurales. Sus tubérculos presentan altos contenidos de metabolitos primarios y secundarios que les confiere propiedades antibióticas, antioxidantes insecticidas, nematicidas, anticancerígenas y diuréticas. Teniendo en cuenta su enorme potencial y que en Boyacá no existen estudios de diversidad genética en estas especies se planteó la caracterización molecular de 10 materiales de ibias y 11 de cubios procedentes de los municipios de Soracá, Ventaquemada, Tuta, San Pedro de Iguaque y el Puente de Boyacá. El análisis mediante el coeficiente de NeiLi diferenció a la población en dos grandes grupos de acuerdo a las características morfológicas del tubérculo y a la especie. La heterocigosidad promedio estimada fue de 0,41 y un coeficiente de diferenciación genética de 0,15. Los resultados obtenidos en este estudio mostraron la existencia de una variabilidad genética a nivel intraespecífico y flujo genético entre las dos especies evaluadas lo cual puede ser aprovechado en esquemas de mejoramiento tendientes a la producción de híbridos y la explotación de los efectos heteróticos. Palabras clave:

Genetic variability among cattle breeds of Nigeria using thyroid hormone responsive spot 14 alpha gene (THRSPα) through polymerase chain reaction (PCR)

The genetic variability among three Nigerian indigenous cattle breeds-White Fulani (WF), Red Bororo (RB) and Sokoto Gudali (SG) was carried out using Thyroid Hormone Responsive Spot 14 Alpha Gene (THRSPα) through Polymerase Chain Reaction (PCR). A total of sixty-seven (67) cattle blood samples comprising 30 WF, 25 RB and 12 SG were used. The DNA were extracted from blood samples using Zymobead Genomic DNA extraction kit after which PCR was carried out using 50 ng template DNA, 1.0μM primer (THRSPα), 16μl Nucleasefree water in a BIONEER Accupower premix. Gel electrophoresis was carried out and the gels scored. Statistical analyses were carried out using GENEPOP, PAST, SPSS version 16 and Tools for Population Genetic Analysis (TFPGA) version 1.3. The allelic frequency ranged from 0.3600 to 0.6400 in A and B alleles, average heterozygosity ranged from 0.4608 to 0.4861. Lowest genetic distance of 0.0010 between WF and RB and highest genetic distance of 0.0058 between SG and RB were identified. Lowest genetic identity of 0.9942 between RB and SG and highest genetic identity of 0.9990 between WF and RB was also identified. Two (2) genetic population clusters were identified in the dendogram; WF and RB are in cluster 1 while SG is in cluster 2. Test of Hardy Weinberg equilibrium revealed variation in genotypic frequencies. These results therefore demonstrate variation among these three Nigerian indigenous cattle breeds which is attributed to the response of the breeds to various stimuli which also enhance their survivability and adaptation to their specific environments. Such variation can also be harnessed for conservation and improvement of our indigenous breeds through selection and breeding strategies.

Genetic structure and diversity of the black-throated finch (Poephila cincta) across its current range

Understanding the patterns of population connectivity and level of genetic diversity can facilitate the identification of both ecologically relevant populations and the spatial scales at which conservation management may need to focus. We quantified genetic variation within and among populations of black-throated finches across their current distribution. To quantify genetic structure and diversity, we genotyped 242 individuals from four populations using 14 polymorphic microsatellite markers and sequenced 25 individuals based on a 302-base-pair segment of mitochondrial control region. We found modest levels of genetic diversity (average allelic richness r = 4.37 ± 0.41 (standard error) and average heterozygosity HO = 0.42 ± 0.040 (standard error)) with no bottleneck signature among sampled populations. We identified two genetic groups that represent populations of two subspecies based on Bayesian clustering analysis and low levels of genetic differentiation based on pairwise genetic differentiation statistics (all FST, RST and Nei’s unbiased D values <0.1). Our data suggest that genetic exchange occurs among sampled populations despite recent population declines. Conservation efforts that focus on maintaining habitat connectivity and increasing habitat quality to ensure a high level of gene flow on a larger scale will improve the species’ ability to persist in changing landscapes. Conservation management should also support continuous monitoring of the bird to identify any rapid population declines as land-use intensification occurs throughout the species’ range.

Polymorphism in Exon 17 of Diacylglycerol Acyltransferase-1{DGAT-1)Gene in Indian Sheep Breeds

Polymorphism in exon 17 of DGAT-1 gene was found to have significant effect on carcass weight and mutton. In the present study, 309 bp PCR products were amplified from genomic DNA of native Indian sheep breeds viz. Jaisalmeri, Deccani, Muzaffarnagri, Mandya, Nali, Nellore, Ganjam and Magra. Restriction endonuclease (RE) analysis was done using Alul RE enzyme. Three genotypes (CC, CT and TT) and two allelic variants (C and T) were identified. The frequency of allele C ranged from 0.75 to 0.99. The average heterozygosity of the locus was 0.2188. It was concluded that the native Indian sheep breeds showed variation in DGAT-1 exon 17 locus and it can be used as a marker for within breed selection of mutton type sheep, provided association is established between genotypes and mutton quality traits in native sheep.

ANÁLISIS DE LA DIVERSIDAD GENÉTICA DE LA MORA(Rubus spp.)EN EL DEPARTAMENTO DE BOYACÁ

A simple of 21 Rubus spp genetic ecotypes were characterized using markers Random Microsatellite RAMs. The seven primers produced a total of 160 polymorphic bands with molecular weights between 350 and 1500 Kb. RAMs analysis at a level of 55% similarity distinguished the population into five groups generally agree to the site where the ecotypes were collected. The number of polymorphic loci ranged from 16 (ACA) to 27 (CGA). For the total population the percentage of polymorphic loci and the expected average heterozygosity (He) were 88% and 0,29, respectively, much lower than values found in other genetic diversity studies in the genus Rubus. Therefore, strategies must be found to increase genetic variability. The coefficient of genetic differentiation (Fst) obtained in evaluating ecotypes Rubus, with seven RAMs microsatellite markers was 0,29 with a standard deviation of 0,03, values showing high genetic differentiation, which is associated with the level of population structure it tends to stabilize.

Forensic and population genetic characteristics of 62 X chromosome SNPs revealed by multiplex PCR and MALDI-TOF mass spectrometry genotyping in 4 North Eurasian populations.

X chromosome genetic markers are widely used in basic population genetic research as well as in forensic genetics. In this paper we analyze the genetic diversity of 62 X chromosome SNPs in 4 populations using multiplex genotyping based on multi-locus PCR and MALDI-TOF mass spectrometry, and report forensic and population genetic features of the panel of X-linked SNPs (XSNPid). Studied populations represent Siberian (Buryat and Khakas), North Asian (Khanty) and Central Asian (Kazakh) native people. Khanty, Khakas and Kazakh population demonstrate average gene diversity over 0.45. Only East Siberian Buryat population is characterized by lower average heterozygosity (0.436). AMOVA analysis of genetic structure reveals a relatively low but significant level of genetic differentiation in a group of 4 population studied (FST=0.023, p=0.0000). The XSNPid panel provides a very high discriminating power in each population. The combined probability of discrimination in females (PDf) for XSNPid panel ranged between populations from 0.99999999999999999999999982 in Khakas to 0.9999999999999999999999963 in Buryats. The combined discriminating power in males (PDm) varies from 0.999999999999999792 to 0.9999999999999999819. The developed multiplex set of X chromosome SNPs can be a useful tool for population genetic studies and for forensic identity and kinship testing.

Autosomal indels distribution in Metropolitan Manila, Philippines

The Philippines are a group of islands in the Asia-Pacific region harboring a high diversity of cultures, languages and people due to various migration waves and different degrees of admixture between neighboring groups. In this work we studied the most populous region of the country – Metropolitan Manila – with a set of small autosomal insertion deletion (indel) polymorphisms, to assess their genetic diversity and usefulness in forensic context. Using a single-tube multiplex reaction we characterized 38 indels in 195 individuals born in the National Capital Region, allowing to establish an allele frequency database for future reference in forensic applications. The genetic diversity observed was high (average heterozygosity=0.40890), similar to previous studies in other East Asian populations, and the marker set reached good levels of informativeness, with a combined power of discrimination of 99.999999999997% and combined power of exclusion of 99.50%. In conclusion, our study showed that this simple indel multiplex can be useful for forensic applications in Metropolitan Manila Filipino population.

English

Cowpea [ Vigna unguiculata (L.) Walp.] is cultivated widely by small farmers in the semiarid region of Northeastern Brazil for subsistence purposes, especially to complement the family income. However, owing to the limited availability of water in this region, there is an urgent need for novel highly productive drought-tolerant cultivars. The aim of the present study was to establish the genetic variability of 14 cowpea populations (60 indigenous genotypes from 13 microregions of Rio Grande do Norte and 4 domesticated cultivars produced by Embrapa) using inter-simple sequence repeats (ISSR) markers. The set of 13 selected primers generated a total of 257 loci, 247 (96.11%) of which were polymorphic, with sizes ranging between 200 and 2000 bp. Genetic similarities between accessions were estimated from Jaccard coefficients and genetic relationships were determined from the dendrogram constructed using the unweighted pair group method with arithmetic average (UPGMA) technique. Bayesian statistics coupled with the Markov chain Monte Carlo technique was applied to determine population structure, while the genetic variability was established by analysis of molecular variance. UPGMA analysis allowed the separation of the genotypes into three groups, but no relationship between the genetic and geographical distances was observed. The fixation index was considered intermediary (FST = 0.0818), the average heterozygosity was low (HS = 0.39) and the coefficient of endogamy was high (f = 92.6%). The results show the presence of genetic diversity among the studied populations and revealed that such variability could be attributed mainly to intra-population variability (91.82%). Key words : Vigna unguiculata , genetic diversity, plant improvement, drought stress.

AB048. X-chromosomal SNPs variation in populations of Russia

X-chromosome markers are informative tool for studying a genetic diversity in human populations and have become a useful in DNA identification when certain complex kinship cases need to be unravelled. In this work we present population genetic data on X-chromosome-wide SNPs in North Eurasian populations and report XSNP multiplex system for forensic genetics. A total of 2,867 X-chromosomal SNPs were genotyped in 12 populations using Illumina microarray platform. Twelve populations under study (Komi, Mordva, Russians, Kirghiz, Kazakh, Uzbek, Buryat, Yakut, Evenk, Tuva, Khanty, Ket) represent various language families and geographic regions of North Eurasia (Eastern Europe, Central Asia, Siberia and North Asia). North Eurasian populations are highly genetically differentiated with respect to XSNPs allele frequencies. Average level of genetic differentiation (Gst) for 12 populations is 6.03% and ranged from 1.05% to 30.05% per individual SNP. Principal component analysis of allele frequencies demonstrated geographic pattern of population clustering, as well as longitudinal gradient in genetic diversity. The 66 XSNPs characterized by high expected heterozygosity and linkage equilibrium in populations under study were selected for constructing a panel for forensic genetic applications. Average heterozygosity of selected SNPs varied from 0.4925 to 0.4958. Overall values of power of discrimination for males and females (PDm and PDf) obtained with these XSNPs set are several magnitude higher than those for standard forensic STR panels. Protocol for multiplex amplification of 66 XSNPs in two separate multiplex PCR reactions and MALDI-TOF mass spectrometry genotyping was developed. North Eurasian populations demonstrate high level of genetic diversity and differentiation for X-chromosome-wide SNPs. Based on obtained population genetic data, highly informative multiplex XSNPs panel for forensic genetics was developed.

Parentage determination of yellow catfish (Pelteobagrus Fulvidraco) based on microsatellite DNA markers

The application of microsatellite (SSR) markers for parentage determination is a booming science for selective breeding as it can track the ancestry and lineage of fish and maintain pedigree information. This study was initiated to assess the feasibility of SSR markers for parentage determination in yellow catfish (Pelteobagrus fulvidraco) by using simulation and real data analysis. A panel of nine polymorphic SSR markers was chosen from our 454 pyrosequencing transcriptomes to genotype 180 progenies in eighteen yellow catfish full-sib families. These markers were highly polymorphic with a mean of 16.9 alleles per locus and an expected average heterozygosity value of 0.891 in 180 individuals. The allele frequency date-based simulation indicated that the combined exclusion probability values would be over 99 and 99.9 %, respectively, when six and eight SSRs were used. Based on the simulation, all progenies were unambiguously assigned to their putative parental pairs when six SSRs were used, whereas the rate of assignment success for the real data set was only 98.9 %. Moreover, when the number of SSRs was up to nine, all progenies from the eighteen full-sib families were 100 % allocated to their parents. The double-blind test demonstrated that 96 % of the randomly selected progeny can be clustered into their own families. This study demonstrated that the microsatellite-based approach is effective for parentage assignment in yellow catfish and has a significant application in selective breeding in this species.

<b>Enzyme Polymorphism in <i>Sitophilus oryzae</i> (Linnaeus, 1763) and <i>Sitophilus zeamais</i> (Motschulsky, 1855) (Coleoptera, Curculionidae) in southern Brazil

Beetles of the species Sitophilus oryzae and S. zeamais are pests of great economic importance since they attack not only rice and maize but also several other cereals. In fact, these beetles are one of the most visible threats to sustainable food production. Current study estimated the genetic variability of S. oryzae in two samples, one from the State of Parana (PR), Brazil, and another from the state of Rio Grande do Sul (RS), Brazil, and a sample of S. zeamais from the State of Santa Catarina (SC), Brazil. Isozyme electrophoresis in starch gel technique was employed to analyze eight enzyme systems (AAT, ACP, GDH, GPI, IDH, MDH, PGM and ME). Average heterozygosity rates were 0.0091, 0.0100 and 0.0000 and expected heterozygosity rates were 0.0419, 0.0452 and 0.0000 respectively for the samples of PR, SC and RS samples. The percentage of polymorphic loci was 30% in the PR sample, 0% in the RS sample and 30% in the SC sample. Genetic identity rates were I=0.9983 between samples from PR and RS; I = 0.6892 between PR and SC, and I = 0.6925 between SC and RS. Neis (1978) genetic distance rates were 0.0017, 0.3722 and 0.3675. Samples presented low genetic variability.

The role of climate and out-of-Africa migration in the frequencies of risk alleles for 21 human diseases.

BackgroundDemography and environmental adaptation can affect the global distribution of genetic variants and possibly the distribution of disease. Population heterozygosity of single nucleotide polymorphisms has been shown to decrease strongly with distance from Africa and this has been attributed to the effect of serial founding events during the migration of humans out of Africa. Additionally, population allele frequencies have been shown to change due to environmental adaptation. Here, we investigate the relationship of Out-of-Africa migration and climatic variables to the distribution of risk alleles for 21 diseases.ResultsFor each disease, we computed the regression of average heterozygosity and average allele frequency of the risk alleles with distance from Africa and 9 environmental variables. We compared these regressions to a null distribution created by regressing statistics for SNPs not associated with disease on distance from Africa and these environmental variables. Additionally, we used Bayenv 2.0 to assess the signal of environmental adaptation associated with individual risk SNPs. For those SNPs in HGDP and HapMap that are risk alleles for type 2 diabetes, we cannot reject that their distribution is as expected from Out-of-Africa migration. However, the allelic statistics for many other diseases correlate more closely with environmental variables than would be expected from the serial founder effect and show signals of environmental adaptation. We report strong environmental interactions with several autoimmune diseases, and note a particularly strong interaction between asthma and summer humidity. Additionally, we identified several risk genes with strong environmental associations.ConclusionsFor most diseases, migration does not explain the distribution of risk alleles and the worldwide pattern of allele frequencies for some diseases may be better explained by environmental associations, which suggests that some selection has acted on these diseases.