Adenosine deaminase polymorphism (EC: 3.5.4.4): Formal genetics and linkage relations

Summary The formal genetics of the ADA polymorphism had been investigated in a series of 156 German families with 319 children. The results correspond to the formal model of two alleles at an autosomal locus. There is no evidence for close linkage between the loci of ADA and ABO, MNS, Kell, P, Duffy, Rhesus, Haptoglobin, Gc, ac. Phosphatase, AK, PGM₁, 6-PGD.Supported by the Deutsche Forschungsgemeinschaft.     

Patterns of genetic variation in Native America.

Allele frequencies from seven polymorphic red cell antigen loci (ABO, Rh, MN, S, P, Duffy, and Diego) were examined in 144 Native American populations. Mean genetic distances (Nei's D) and the fixation index FST are approximately equal for the North and South American samples but are reduced in the Central American geographic area. The relationship between genetic distance and geographic distance differs markedly across geographic areas. The correlation between geographic distance and genetic distance for the North and Central American data is twice as large as that observed for the South American samples. This geographic difference is confirmed in spatial autocorrelation analyses; no geographic structure is apparent in the South American data but geographic structure is prominent in North and Central American samples. These results confirm earlier observations regarding differences between North and South American gene frequency patterns.     

Genetic variability in natural populations of Arabidopsis thaliana in northern Europe

Ten populations of the model plant Arabidopsis thaliana were collected along a north-south gradient in Norway and screened for microsatellite polymorphisms in 25 loci and variability in quantitative traits. Overall, the average levels of genetic diversity were found to be relatively high in these populations, compared to previously published surveys of within population variability. Six of the populations were polymorphic at microsatellite loci, resulting in an overall proportion of polymorphic loci of 18%, and a relatively high gene diversity for a selfing species (HE = 0.06). Of the overall variability, 12% was found within populations. Two of six polymorphic populations contained heterozygous individuals. Both FST and phylogenetic analyses showed no correlation between geographical and genetic distances. Haplotypic diversity patterns suggested postglacial colonization of Scandinavia from a number of different sources. Heritable variation was observed for many of the studied quantitative traits, with all populations showing variability in at least some traits, even populations with no microsatellite variability. There was a positive association between variability in quantitative traits and microsatellites within populations. Several quantitative traits exhibited QST values significantly less than FST, suggesting that selection may be acting to retard differentiation for these traits.     

Hierarchical gene diversity and genetic structure of tribal populations of Andhra Pradesh,India

Gene diversity and genetic structure of tribal populations of Andhra Pradesh, India, have been analyzed under a hierarchical model consisting of five regions of the state, tribes within the regions, and local subpopulations within the tribes. Average gene diversity has been estimated from gene frequency data for 15 polymorphic loci by using nested gene diversity analysis of G_ST. The intralocation coefficient of gene diversity was estimated at 96% of the total, whereas the intertribal, within—and between—regional gene diversities were found to be only 1.90, 0.95, and 1.43%, respectively. The estimate of gene diversity was higher for loci with higher degrees of polymorphism such as ABO, MN, ESD, and PTC and lower for loci with low-level polymorphism and extreme gene frequencies such as Hb, Tf, PHI, 6PGD, and Hp. The nature of selective preference or neutrality at the loci seems to be important in this respect. Tribes of the plains exhibit the least gene diversity, apparently because of higher gene flow among them. The contribution of loci with intermediate gene frequencies in intertribal and regional gene diversity was found to be higher than for loci with extreme allelic frequencies. These results suggest that the most significant component of variation is between individuals within locations and that variation between local subpopulations is negligible in the genetic structure of a population. Forces like selection, gene flow and drift also influence the diversity depending upon the nature of the locus. © 1993 Wiley-Liss, Inc.     

Frequencies of ABO, MNSs, and Duffy phenotypes among blood donors and malaria patients from four Brazilian Amazon areas

We compared the serological phenotypic frequencies of ABO, MNSs, and Duffy in 417 blood donors and 309 malaria patients from four Brazilian Amazon areas. Our results suggest no correlation between ABO phenotype and malaria infection in all areas studied. We observed significant correlation between the S +s +, S +s -, and S -s + phenotypes and malaria infection in three areas. Some of the Duffy phenotypes showed significant correlation between donors and malaria patients in different areas. These data are an additional contribution to the establishment of differential host susceptibility to malaria.     

Natural selection influences AFLP intraspecific genetic variability and introgression patterns in Atlantic eels

Investigating patterns of genetic variation in hybridizing species provides an opportunity to understand the impact of natural selection on intraspecific genetic variability and interspecific gene exchange. The Atlantic eels Anguilla rostrata and A. anguilla each occupy a large heterogeneous habitat upon which natural selection could differentially shape genetic variation. They also produce viable hybrids only found in Iceland. However, the possible footprint of natural selection on patterns of genetic variation within species and introgressive hybridization in Icelandic eels has never been assessed. We revisited amplified fragment length polymorphism data collected previously using population genomics and admixture analyses to test if (i) genetic variation could be influenced by non-neutral mechanisms at both the intra- and interspecific levels, and if (ii) selection could shape the spatio-temporal distribution of Icelandic hybrids. We first found candidate loci for directional selection within both species. Spatial distributions of allelic frequencies displayed by some of these loci were possibly related with the geographical patterns of life-history traits in A. rostrata , and could have been shaped by natural selection associated with an environmental gradient along European coasts in A. anguilla . Second, we identified outlier loci at the interspecific level. Non-neutral introgression was strongly suggested for some of these loci. We detected a locus at which typical A. rostrata allele hardly crossed the species genetic barrier, whereas three other loci showed accelerated patterns of introgression into A. anguilla in Iceland. Moreover, the level of introgression at these three loci increased from the glass eel to the yellow eel stage, supporting the hypothesis that differential survival of admixed genotypes partly explains the spatio-temporal pattern of hybrid abundance previously documented in Iceland.     

Contribution to study of Asmat genetic variability

During an anthropological survey in the South-West of Irian Jaya (Indonesian New Guinea), 145 blood samples were collected from the coastal Asmat population. ABO, MNSs, Rh, Kell, Duffy and Kidd red cell antigen systems were investigated and the results are presented here. ABO, MNSs, Rh gene frequencies of the Asmat, together with those of 21 other New Guinea populations, were examined by principal component analysis. The topological representation of the distribution of the selected New Guinea populations confirms high variability in the interior of the island, and possible causes are discussed. A hypothesis is advanced, concordant with language evidence which would explain the resemblance among populations from opposite coasts of New Guinea and between some mountain and coastal groups. When the comparison includes 32 other world populations, the New Guinea groups constitute one assemblage distinct from the others.     

Microsatellite variation and recombination rate in the human genome

Background (purifying) selection on deleterious mutations is expected to remove linked neutral mutations from a population, resulting in a positive correlation between recombination rate and levels of neutral genetic variation, even for markers with high mutation rates. We tested this prediction of the background selection model by comparing recombination rate and levels of microsatellite polymorphism in humans. Published data for 28 unrelated Europeans were used to estimate microsatellite polymorphism (number of alleles, heterozygosity, and variance in allele size) for loci throughout the genome. Recombination rates were estimated from comparisons of genetic and physical maps. First, we analyzed 61 loci from chromosome 22, using the complete sequence of this chromosome to provide exact physical locations. These 61 microsatellites showed no correlation between levels of variation and recombination rate. We then used radiation-hybrid and cytogenetic maps to calculate recombination rates throughout the genome. Recombination rates varied by more than one order of magnitude, and most chromosomes showed significant suppression of recombination near the centromere. Genome-wide analyses provided no evidence for a strong positive correlation between recombination rate and polymorphism, although analyses of loci with at least 20 repeats suggested a weak positive correlation. Comparisons of microsatellites in lowest-recombination and highest-recombination regions also revealed no difference in levels of polymorphism. Together, these results indicate that background selection is not a major determinant of microsatellite variation in humans.     

Erythrocyte and HLA antigens of Atacameño Indians

The present study reports the results of erythrocyte antigen typing for the following systems: ABO, MN, Rh, Kell, Duffy, and Diego in roughly 180 Atacameño Indians from the oasis of Toconao, northern Chile. A subsample was tested for variation at the histocompatibility loci A, B, and C. Results agree with previous findings based on smaller samples. Caucasian admixture of the Atacameños from Toconao was estimated to be 0.056 ± 0.022.     

Genome-wide effects of postglacial colonization in Arabidopsis lyrata

The perennial outcrossing Arabidopsis lyrata is becoming a plant model species for molecular ecology and evolution. However, its evolutionary history, and especially the impact of the climatic oscillations of the Pleistocene on its genetic diversity and population structure, is not well known. We analyzed the broad-scale population structure of the species based on microsatellite variation at 22 loci. A wide sample in Europe revealed that glaciations and postglacial colonization have caused high divergence and high variation in variability between populations. Colonization from Central Europe to Iceland and Scandinavia was associated with a strong decrease of genetic diversity from South to North. On the other hand, the Russian population included in our data set may originate from a different refugium probably located more to the East. These genome-wide patterns must be taken into account in studies aiming at elucidating the genetic basis of local adaptation. As shown by sequence data, most of the loci used in this study do not evolve like typical microsatellite loci and show variable levels of homoplasy: this mode of evolution makes these markers less suitable to investigate the between-continent divergence and more generally the worldwide evolution of the species. Finally, a strong negative correlation was detected between levels of within-population diversity and indices of differentiation such as F(ST). We discuss the causes of this correlation as well as the potential bias it induces on the quantification and interpretation of population structure.     

Analysing environments for plant breeding purposes as exemplified by multivariate analyses of long term wheat yields

Summary A previous attempt to relate long term yields from the Western Australian wheat belt to climatic factors proved only partially successful. Here, principal component analysis has been used to examine the patterns of variability created by those socio-economic factors which may have obscured any underlying relationship which existed between yield and climate. In fact, these analyses revealed the existence of variation peculiar to particular groups of years, a result which could explain why many attempts to relate crop yields directly to climatic factors have proved unsuccessful. The plant breeding implications of these genotype x environment interactions are considered.     

Genetic diversity and bottleneck analysis of Indian bellary sheep by microsatellite markers

Bellary sheep population variability and structure was investigated genetically utilizing FAO recommended microsatellite markers. Genetic variation at 20 microsatellite loci, population structure, and genetic bottleneck hypothesis were examined. Estimates of genetic variability such as effective number of alleles and gene diversities revealed substantial genetic variation frequently displayed by microsatellite markers. A total of 133 alleles were detected. Average polymorphism across the studied loci and expected gene diversity in the population were 1.419 +/- 0.405 and 0.684 +/- 0.140, respectively. No significant genotypic linkage disequilibrium was detected across population, suggesting no evidence of linkage between loci. The population was observed to be significantly differentiated into different groups, showed fairly high level of inbreeding (f = 0.253 +/- 0.050) and global heterozygote deficit. Population structure analysis indicated the intermixing/introduction of unique/rare alleles in these migrating flocks. A normal L-shaped distribution of mode-shift test, non-significant heterozygosity excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests suggested that there was no recent bottleneck. The study revealed that even breed with increasing population trend needs genetic management for the conservation and improvement.     

Biochemical heterozygosity and morphological variability: interpopulational versus intrapopulational analyses

The literature is replete with articles suggesting the existence of a relationship between variability at biochemical loci and morphological variation in various animal populations, including humans. With few exceptions these previous studies have utilized an interpopulational approach by examining levels of heterozygosity between modal and extreme phenotypes, typically by use of analysis of variance. Here we consider these purported relationships in a midwestern Mennonite population (n = 890) by correlating individual biochemical heterozygosity and deviation from the mean for anthropometric traits. The results of this intrapopulational correlation indicate that (1) with protection for multiple tests, there are few significant correlations and these have low R2 values, and (2) males and females show different patterns of correlation (males negative, females positive). Based on these findings, the results of earlier studies are in question because nonprotected alpha values are used for multiple tests and heterozygosity is calculated on the basis of a few highly heterozygous blood group systems and is assumed to be representative of the heterozygosity for the entire genome. In general, no evidence is found to support the concept of a direct relationship between biochemical heterozygosity and morphological variability.     

Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain)

Legionella pneumophila is associated to recurrent outbreaks in several Comunidad Valenciana (Spain) localities, especially in Alcoi, where social and climatic conditions seem to provide an excellent environment for bacterial growth. We have analysed the nucleotide sequences of three loci from 25 environmental isolates from Alcoi and nearby locations sampled over 3 years. The analysis of these isolates has revealed a substantial level of genetic variation, with consistent patterns of variability across loci, and comparable to that found in a large, European-wide sampling of clinical isolates. Among the tree loci studied, fliC showed the highest level of nucleotide diversity. The analysis of isolates sampled in different years revealed a clear differentiation, with samples from 2001 being significantly distinct from those obtained in 2002 and 2003. Furthermore, although linkage disequilibrium measures indicate a clonal nature for population structure in this sample, the presence of some recombination events cannot be ruled out.     

The importance of temporal climate variability for spatial patterns in plant diversity

Spatial variation in absolute climatic conditions (means, maxima or minima) is widely acknowledged to play a fundamental role in controlling species diversity patterns. In contrast, while evidence is accumulating that variability around mean climatic conditions may also influence species coexistence and persistence, the importance of spatial variation in temporal climatic variability for species diversity is still largely unknown. We used a unique dataset capturing fine‐scale spatial heterogeneity in temperature variability across 2490 plots in southeast Australia to examine the comparative strength of absolute temperature and temperature variability in explaining spatial variation in plant diversity. Across all plots combined and in three of five forest types, temperature variability emerged as the better predictor of diversity. In all but one forest type, diversity also exhibited either a significant unimodal or positive linear correlation with temperature variability. This relationship is consistent with theory that predicts diversity will initially increase along a climate variability gradient due to temporal niche partitioning, but at an intermediary point, may decline as the risk of stochastic extinction exceeds competitive stabilization. These findings provide critical empirical evidence of a linkage between spatial variation in temporal climate variability and plant species diversity, and in light of changing climate variability regimes, highlight the need for ecologists to expand their purview beyond absolutes and averages.     

Comparative Genetics of Functional Trinucleotide Tandem Repeats in Humans and Apes

Several human neurodegenerative disorders are caused by the expansion of polymorphic trinucleotide repeat regions. Many of these loci are functional short tandem repeats (STRs) located in brain-expressed genes, and their study is thus relevant from both a medical and an evolutionary point of view. The aims of our study are to infer the comparative pattern of variation and evolution of this set of loci in order to show species-specific features in this group of STRs and on their potential for expansion (therefore, an insight into evolutionary medicine) and to unravel whether any human-specific feature may be identified in brain-expressed genes involved in human disease. We analyzed the variability of the normal range of seven expanding STR CAG/CTG loci (SCA1, SCA2, SCA3-MJD, SCA6, SCA8, SCA12, and DRPLA) and two nonexpanding polymorphic CAG loci (KCNN3 and NCOA3) in humans, chimpanzees, gorillas, and orangutans. The study showed a general conservation of the repetitive tract and of the polymorphism in the four species and high heterogeneity among loci distributions. Humans present slightly larger alleles than the rest of species but a more relevant difference appears in variability levels: Humans are the species with the largest variance, although only for the expanding loci, suggesting a relationship between variability levels and expansion potential. The sequence analysis shows high levels of sequence conservation among species, a lack of correspondence between interruption patterns and variability levels, and signs of conservative selective pressure for some of the STR loci. Only two loci (SCA1 and SCA8) show a human specific distribution, with larger alleles than the rest of species. This could account, at the same time, for a human-specific trait and a predisposition to disease through expansion.This article contains online supplementary material.     

Quantitative expression of maize HSPs: genetic dissection and association with thermotolerance

Summary In higher plants, within-species qualitative polymorphism for heat shock proteins (HSPs) is extremely rare, even between genotypes showing different heritable levels of thermotolerance. Here we have explored the amount of quantitative variability in HSP synthesis in maize. We have analyzed the quantitative expression of the typical HSPs in a set of recombinant inbreds (RIs) derived from the f₁ hybrid between a thermotolerant (T232)- and a thermosensitive (CM37)-genotype, characterized for about 200 mapped RFLP loci. Significant differences were detected in the level of expression of five HSPs, and their frequency distribution in the RI population is that of a quantitative trait. Subsequent mapping of loci controlling the characters, based on RFLP analysis, confirmed the multigenic control of HSP expression: the regression analysis of the band intensities of each variant HSP on RFLPs revealed, for the different HSPs, a minimum number of three to eight quantitative trait loci (QTLs) accounting for a high proportion (0.35–0.60) of the genetic variability of these bands. An analysis of the correlation between the variability of HSPs and that of cellular membrane stability, a cellular component of thermotolerance, did not reveal any significant association of the two parameters.     

Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans

Surveys of molecular variation in Drosophila melanogaster and Drosophila simulans have suggested that diversity outside of Africa is a subset of that within Africa. It has been argued that reduced levels of diversity in non-African populations reflect a population bottleneck, adaptation to temperate climates, or both. Here, I summarize the available single-nucleotide polymorphism data for both species. A simple "out of Africa" bottleneck scenario is consistent with geographic patterns for loci on the X chromosome but not with loci on the autosomes. Interestingly, there is a trend toward lower nucleotide diversity on the X chromosome relative to autosomes in non-African populations of D. melanogaster, but the opposite trend is seen in African populations. In African populations, autosomal inversion polymorphisms in D. melanogaster may contribute to reduced autosome diversity relative to the X chromosome. To elucidate the role that selection might play in shaping patterns of variability, I present a summary of within- and between-species patterns of synonymous and replacement variation in both species. Overall, D. melanogaster autosomes harbor an excess of amino acid replacement polymorphisms relative to D. simulans. Interestingly, range expansion from Africa appears to have had little effect on synonymous-to-replacement polymorphism ratios.     

RAPD variation and population genetic structure of Physalaemus cuvieri (Anura: Leptodactylidae) in Central Brazil

Studies about the organization of the genetic variability and population structure in natural populations are used either to understand microevolutionary processes or the effects of isolation by human-inducted landscape modifications. In this paper, we analyzed patterns of genetic population structure using 126 RAPD loci scored for 214 individuals of Physalaemus cuvieri, sampled from 18 local populations. Around 97% of these loci were polymorphic. The among-population variation component (Φ_ST) obtained by AMOVA was equal to 0.101 and θ ^B obtained using a Bayesian approach for dominant markers was 0.103. Genetic divergence, analyzed by Mantel spatial correlogram, revealed only a short-distance significant correlation between genetic and geographic distances. This is expected if low levels of population differentiation, due to high abundance buffering the effect of stochastic processes, are combined with low spatially restricted gene flow. Although this may be consistent with the current knowledge of species’ biology, the spatial distribution of local populations observed in this study also suggest that, at least in part, recent human occupation and habitat fragmentation may also explain part of the interpopulational component of the genetic variation.     

Population genetics of polymorphisms in Cardiff newborn. Relationship between blood group and allozyme heterozygosity and birth weight

A newborn population of Cardiff, Wales, was screened for variation at three blood group loci (ABO, Rhesus and MN) and four enzyme loci (ACP-1, PGM-1, ADA and EST-D). Birth weights were measured. There were no significant differences between mean birth weights or birth weight variances for individuals homozygous or heterozygous at the MN and the four enzyme loci. (ABO and Rhesus loci cannot be used in these tests.) There was no significant heterogeneity in contingency tables relating phenotypes at the seven loci to birth weight. There were no significant differences in mean heterozygosity per locus between babies placed in different birth weight categories, ranging from 2.5 to 4.2 kg. The genetic variation screened appears therefore to be neutral with respect to this character.