Temporal variation of allele frequencies in a natural population of wild Vigna unguiculata

Abstract

Temporal variation in allele frequencies in a natural population of wild Vigna unguiculata was studied by making monthly collections of seeds over a two-year period. Using starch gel electrophoresis, four out of seven loci analysed were shown to be polymorphic (Enp, Fdh, Fle₃ and Pgd₂ ). These four loci showed significant variation in allele frequencies over time. Changes in population structure over time were analysed using F-statistic estimators. Although heterogeneity was evident between loci, the analysis showed significant differentiation among months within a year for all polymorphic loci. Fixation indexes were all positive and statistically different from zero, highlighting a significant departure from random mating. Using analysis of variance (ANOVA), the pattern of inbreeding (f) showed significant changes over time (season); among the polymorphic loci, Enp most strongly contributed to this significance. Significant correlations were found between allele frequencies at different loci. The monthly average gene diversity (He) and allele frequencies at the Enp locus were found to be significantly correlated with weather conditions (temperature and rainfall distribution). These allele frequency deviations over time can be attributed to changes in pollinator behaviour, and frequent genetic bottlenecks that are associated with changes in environmental conditions.     

Study of Eight Blood Protein Polymorphic Systems in Arabian Horses from Turkey

Analysis of the blood protein system was used to study the genetic composition of Arabian horses. Biochemical markers of eight polymorphic loci (Tf, Al, As, AlB, Gc, Hb, PGD, and PGM) were electrophoretically identified in blood samples. A total of 43 phenotypes were identified for these polymorphic systems. The Tf, Hb, and Esloci appeared to be more polymorphic than the other loci studied. Statistically significant differences between the observed and expected genotypic frequencies were found for the PGDandPGMloci (P< 0.05 and P< 0.01, respectively). Individual allele frequencies, observed and expected phenotype frequencies, and the average heterozygosity were estimated for each polymorphic locus.     

New microsatellite loci for the European bushcricket,Ephippiger ephippiger (Orthoptera: Tettigoniidae)

Ephippiger ephippiger is a model organism for studies of sexual selection and phylogeography but little is known about fine‐scale population structure. Available microsatellite loci have null allele problems so we used an enrichment technique to isolate 21 new microsatellite loci for E. ephippiger. We present primer pairs for 10 polymorphic loci (3–11 alleles per locus). Observed heterozygosities at polymorphic loci ranged from 0.118 to 0.787, but several were significantly lower than expected.     

Isolation and characterization of polymorphic microsatellite loci in Wuchang bream (Megalobrama amblycephala)

Wuchang bream (Megalobrama amblycephala) is an economically important fish in China. From a (GT)₁₃‐enriched genomic library, 20 microsatellites were developed. Nine of these 20 loci were polymorphic in a test population with allele numbers ranging from two to four, and the observed and expected heterozygosities ranging from 0.2609 to 0.7826 and from 0.3739 to 0.7546, respectively. In the cross‐species amplifications, six of these nine loci were also polymorphic in white amur bream (Parabramis pekinensis). These polymorphic microsatellite loci are potentially useful for population genetics of Wuchang bream and its closely related species.     

Identification of 15 polymorphic microsatellite loci in the Príncipe seedeater (Serinus rufobrunneus) and assessment of their utility in nine other Serinus species (Fringillidae,Aves)

We tested 74 passerine microsatellite loci for cross‐amplification in the Príncipe seedeater (Serinus rufobrunneus), and identified 15 loci that were both polymorphic and easy to score. In a sample of 113 individuals, the number of alleles ranged between three and 71. Three loci deviated from Hardy–Weinberg equilibrium after correcting for multiple tests, and one locus had high estimated null allele frequency. These 15 loci were highly successful in amplifying polymorphic products also in nine other Serinus species.     

Nine new microsatellite loci for the roundnose grenadier (Coryphaenoides rupestris) with four showing cross-amplification in the shortbeard grenadier (C. brevibarbis)

We isolated nine new microsatellites for the deep-sea fish Coryphaenoides rupestris. These loci are highly polymorphic, with allele number ranging from 14 to 42 and heterozygosity ranging from 0.647 to 0.965. Four of these loci also amplified in C. brevibarbis.     

Isolation and characterization of microsatellites in yellow perch (Perca flavescens)

A total of 45 microsatellite loci from yellow perch, Perca flavescens, were isolated and characterized. Among the 45 microsatellite loci, 32 had more than two alleles. A wild population of P. flavescens (n = 48) was used to examine the allele range of the microsatellite loci. Mendelian inheritance of alleles was confirmed by examining the amplified products in pair‐mated families. The number of alleles for the 32 polymorphic loci varied from two to 16, and observed heterozygosity ranged between 0.024 (YP79) and 0.979 (YP60). Cross‐species polymorphic amplification in four other Percidae species was successful for 22 loci.     

Temporal variation of allele frequencies in populations of Akodon dolores (Rodentia,Cricetidae)

Summary Six population samples of the South American cricetid rodent Akodon dolores were collected at the same site at six-month intervals over a three year period. Changes in density were detected. Seven out of 18 loci analyzed by means of starch gel electrophoresis were polymorphic. Only two of these loci (Est-4 and G6pdh) showed statistically significant variation in allele frequencies following a seasonal pattern. There was no correlation between allele frequencies and population density. When animals were grouped into two classes according to body weight, a clear difference in allele distribution at the Est-4 and G6pdh loci was observed between individuals 39 g or less and those heavier than 39 g. As the first group comprises predominantly younger animals, the data indicate that changes in the age-structure of population, rather than density variations, are responsible for the cyclic pattern of allele frequencies fluctuations.     

Development of microsatellite markers for the dwarf bamboo species Sasa cernua and Sasa kurilensis (Poaceae) in northern Japan

Ten polymorphic microsatellite markers were isolated from the dwarf bamboo species Sasa cernua and Sasa kurilensis. The applicability of these markers was confirmed by genotyping of open‐pollinated seeds and leaf samples from natural populations. Genotypes of seeds from each culm shared at least one allele from the maternal parent without contradiction. All 10 loci were polymorphic in S. cernua with 2–15 alleles (average H_E = 0.532). Eight loci were polymorphic in S. kurilensis with 2–10 alleles (average H_E = 0.532). These markers will be useful in detailing the extent of clonal and sexual reproduction in these species.     

Identification of microsatellite DNA markers for population structure analysis in Indian major carp, Cirrhinus mrigala (Hamilton-Buchanan, 1882)

Forty‐four primer sequences available for four cyprinid fishes were tested to amplify microsatellite loci in Indian major carp, Cirrhinus mrigala. A total of 12 loci were successfully amplified with clear scorable patterns and five thereof were polymorphic. Suitability of the identified polymorphic loci in population structure analysis of C. mrigala was assessed. Genetic variation was examined in 76 specimens collected from five different rivers. The mean observed heterozygosity ranged from 0.247 to 0.333. Significant heterogeneity in allele frequencies was detected, indicating that the samples analysed did not belong to homogenous populations. The identified microsatellite markers are promising for the analysis of intraspecific divergence in C. mrigala across its distribution range.     

Genetic variability in Plantago species in relation to their ecology

Summary A survey of enzyme variability in several populations of Plantago major in the Netherlands has been made. Nine of 36 loci were found to be polymorphic. The most extensively studies population showed 7 polymorphic loci (19%). The average heterozygosity was 0.005, a low value since P. major is predominantly inbreeding; a first estimate of the outcrossing rate is only 10%. All nine variable loci show simple Mendelian inheritance, seven of them could be placed into four different linkage groups. Marked differences in allele frequencies were found between two subspecies: ssp. major and ssp. pleiosperma. Two enzyme loci possess subspecies-specific alleles, Pgm-1 and Got-1. The most likely explanation of this phenomenon is the existence of fitness differences, caused either by the enzyme loci themselves or by linked loci.Grassland Species Research Group Publication no. 14     

Microsatellite DNA markers for the pea aphid Acyrthosiphon pisum

Microsatellite loci were isolated from enriched partial genomic libraries of Acyrthosiphon loti and Acyrthosiphon pisum. Twenty of those loci were characterized in A. pisum. Fifteen of those loci were polymorphic. Genetic diversity varied across loci, allele repeat number ranging from two to 15, and observed heterozygosity from 0.1 and 0.96. An additional eight microsatellite loci originally isolated from other aphids but cross‐priming with A. pisum showed polymorphism as well. Allele size ranged from three to 9 and observed heterozygosity from 0.43 to 0.84. Overall, we present 23 microsatellite loci that can be used to reveal polymorphism in pea aphids.     

Genetic variation in populations of the arctic perennial Pedicularis dasyantha (Scrophulariaceae), on Svalbard,Norway

Isozyme variability was examined in 13 geographically isolated populations of the endemic arctic hairy lousewort (Pedicularis dasyantha) in the Svalbard Archipelago, 80° N latitude, Norway. Of the 23 enzyme systems screened on five buffer systems 18 were interpretable. Of the 31 reliable loci, only 6-phosphogluconate dehydrogenase (6-Pgd), was polymorphic. However, no heterozygotes were detected. Frequencies for allele 1 among the populations varied from 1.00 in the north to 0.00 in the south and 0.53 in the central “overlap” region. At the species level the mean number of alleles per locus (A) was 1.03. Percentage of polymorphic loci (P) was 3%. Expected heterozygosity (H_e) was 0.016. At the population level the mean number of alleles per locus was 1.01, and 1.1% of the loci were polymorphic. H_e was 0.004. These values are low compared to endemic, widespread, selling, and outcrossed species. Flower color morphs were distinct. They varied within and among the 13 populations. The frequency of color morphs coincided with allele frequencies of 6-PGD: allele 1 was found in dark purple morphs, and allele 2 was found in light morphs. This species shows more isozyme genetic variability than the five other species reported in the genus but generally less variation than other species with limited regional distributions. Low-level genetic variation in this diploid species may be a result of colonization events coupled with genetic drift, founder effects, and strong natural selection. Additional factors include the self-compatible reproductive system and the long-lived perennial habit.     

Isolation and characterization of polymorphic microsatellite markers in lesser kestrel (Falco naumanni) and cross-amplification in common kestrel (Falco tinnunculus)

Lesser kestrel, Falco naumanni, is a colonial and migratory species breeding in part of the Mediterranean Basin and part of central Asia and north-east of China and Mongolia. This species is catalogued in IUCN red list category as vulnerable. Twenty microsatellite loci were selected from libraries enriched in AC or AG tandem repeats and specific PCR were devised from their flanking sequences. Most microsatellites (14) were found polymorphic among 30 individuals of F. naumanni representing 20 reproduction areas of the species in the region of Extremadura, Spain. Polymorphisms were detected by size variation of the amplified loci, which allele number and observed heterozygosity ranged from 3 to 20 and from 0.300 to 0.933, respectively. Cross-species amplification showed that 13 of selected loci were also found polymorphic in common kestrel species (Falco tinnunculus). Novel polymorphic microsatellites will serve to conservation studies in lesser kestrel.     

Characterization of 22 microsatellite loci developed from the genome of the Woolly Lemur (Avahi laniger)

Twenty‐two polymorphic microsatellite loci were isolated and characterized from the Avahi laniger genome. All were polymorphic in both the Eastern Woolly Lemur (A. laniger) and the Western Woolly Lemur (A. occidentalis). One locus, WOOL157, harboured allele structures that were species‐specific. This marker suite will be used in future studies to establish the ranges and population structures of the two Avahi species on the island of Madagascar.     

Microsatellite markers isolated from polyploid wood‐sorrel Oxalis alpina (Oxalidaceae)

Twelve polymorphic microsatellite loci were isolated from polyploid alpine wood‐sorrel, Oxalis alpina (Oxalidaceae), and optimized for future studies of its breeding system. The loci were screened for variability among 72 individuals from Pinos Altos, New Mexico. The primers amplified loci with allele number ranging from two to 17 per locus and with estimates of Nei's genetic diversity varying from 0.10 to 0.99. These primers provide an opportunity to use polymorphic DNA markers to study the causes of breeding system variability in this species.     

Characterization of nine microsatellite loci in the sea star Astropecten aranciacus and cross-species amplification for related taxa

So far, only few microsatellite markers have been developed and extensively tested for echinoderms. To study the population genetic structure of the sea star Astropecten aranciacus, we developed primers for nine polymorphic microsatellite loci and tested them on two populations from Faro in Portugal (N = 25) and from La Herradura in Spain (N = 20). Within populations, allele numbers varied from four to 20, while expected and observed heterozygosities ranged from 0.593 to 0.936 and from 0.222 to 0.900, respectively. Additional cross‐species amplifications were polymorphic at some loci, indicating their potential usefulness for related taxa.     

A proposal for standardization in forensic equine DNA typing: allele nomenclature for 17 equine‐specific STR loci

In this study, a proposal is presented for the allele nomenclature of 17 polymorphic STR loci (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, LEX3 and VHL20) for equine genotyping (Equus caballus). The nomenclature is based on sequence data of the polymorphic region of the STR loci as recommended by the DNA commission of the International Society for Forensic Genetics for human DNA typing. For each STR locus, several alleles were selected and animals homozygous for those alleles were subjected to sequence analysis. The alleles of the 17 STR loci consisted either of simple (10), compound (6) or complex repeat patterns (1). Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats, including all variable regions within the amplified fragment.     

Non-random associations between Lap and Pept-1 loci and gene arrangements of chromosome O in D. subobscura — experiments in laboratory populations

In this paper the well-known non-random associations between Lap and Pept-1 loci and gene arrangements of chromosome O are studied in laboratory populations of D. subobscura. An increase of the frequency of the allele Lap ^1.00, towards an equilibrium point (0.70), was found to be associated with an increase of the gene arrangement O₃₊₄. This is an accordance to the associations found in natural populations. On the contrary no such an increase was observed in populations polymorphic for Lap and Pep-1 loci but homokaryotypic for gene arrangement O₃₊₄₊₈ differing in the initial allele frequencies at these loci. Although epistatic selection cannot be completely ruled out, our results are better explained under the assumption of neutrality.     

Microsatellite loci in the house fly,Musca domestica L. (Diptera: Muscidae)

Genomic libraries from house flies enriched for (CA)₁₅ and (CAG)₁₀ repeats were constructed by using biotinylated probes. Twenty‐five loci were isolated and evaluated for polymorphisms in wild flies representing two geographically diverse populations. Fourteen of 19 dinucleotide loci, and one of six trinucleotide loci were polymorphic. One hundred and twenty‐seven alleles were detected, 39 of which were private. Average number of alleles per polymorphic locus was 8.4 ± 2.5 and average heterozygosity was 72 ± 4%. F_ST by the private allele method was 0.73. Three of 15 loci showed significant heterozygote deficiencies, attributed to null alleles. Five of 15 loci were amplified in the face fly, Musca autumnalis.