Showing papers in "Journal of Genetics in 2004"

Studies in quantitative inheritance. XI. Genetic and environmental correlation between body size and egg production in Drosophila melanogaster. 1957.

Abstract: 1. The variation of body size and egg production between individuals of a laboratory population ofDrosophila melanogaster has been examined. Estimates of genetic and environmental contributions to the phenotypic variation have been derivedby comparing the variability of the flies of the wild population with that of genetically uniform flies from crosses between inbred lines reared under similar favourable conditions. Apparently about 50 % of the variance of body size and about 60 % of the variance of egg production is attributable to genetic segregation. 2. From the results of two-way selection for body size and also egg production, the heritability of the two characters is estimated as respectively 0.43 and 0.18, suggesting that most of the genetic variation in body size behaves as additive in the statistical sense, while non-additive effects predominate in the variability of egg production. 3. There is a clear-cut phenotypic correlation between size and egg production among the individuals of the wild population and this is mostly genetic in origin. Selection for large and small size leads to comparatively little change in egg production. A series of different genotypes, each represented by a number of genetically identical individuals; were prepared by combining haploid sets of chromosomes from the wild population with a haploid set from an inbred line—and these provided no evidence of genetic correlation between size and egg production. Hence the genetic correlation in the wild stock is essentially non-additive in behaviour. 4. Gene-environment interaction has been demonstrated for both egg production and body size by comparing estimates of variance and heritability on the live medium with those found on a synthetic medium which permits normal growth. It is suggested that gene-environment interaction will be particularly important under the suboptimal condition in which the population usually lives. 5. Reduction of the body size of genetically uniform flies by varying the nutrition of the larvae leads to a proportional reduction in the rate at which eggs are laid. 6. The variability of development time has also been examined in preliminary experiments which indicate that about half the variance is genetic in origin. Under favourable conditions there is a high correlation between length of development and body size, while egg production tends to be negatively correlated, suggesting that egg production and growth rate are genetically associated. 7. The results are discussed in relation to the stability of average body size in. the population and the ease with which selection either way leads to striking change. There are strong indications that the apparently continuous variation of attributes such as size or egg production are heterogeneous with respect to the effects on physiology and development which contribute to the final variation, while the relative contribution of different sorts of effect may vary according to environmental conditions.

Structural and functional analysis of rice genome.

Abstract: Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (> 10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macroand micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.

Mitochondrial DNA sequence variation in the Anatolian Peninsula (Turkey).

Abstract: Throughout human history, the region known today as the Anatolian peninsula (Turkey) has served as a junction connecting the Middle East, Europe and Central Asia, and, thus, has been subject to major population movements. The present study is undertaken to obtain information about the distribution of the existing mitochondrial D-loop sequence variations in the Turkish population of Anatolia. A few studies have previously reported mtDNA sequences in Turks. We attempted to extend these results by analysing a cohort that is not only larger, but also more representative of the Turkish population living in Anatolia. In order to obtain a descriptive picture for the phylogenetic distribution of the mitochondrial genome within Turkey, we analysed mitochondrial D-loop region sequence variations in 75 individuals from different parts of Anatolia by direct sequencing. Analysis of the two hypervariable segments within the noncoding region of the mitochondrial genome revealed the existence of 81 nucleotide mutations at 79 sites. The neighbourjoining tree of Kimura’s distance matrix has revealed the presence of six main clusters, of which H and U are the most common. The data obtained are also compared with several European and Turkic Central Asian populations.

Excess of counterclockwise scalp hair-whorl rotation in homosexual men.

Abstract: While most men prefer women as their sexual partners, some are bisexual and others are homosexuals. It has been debated for a long time whether a person's sexual preference is innate, learned, or due to a combination of both causes. It was recently discovered that the human right-versus-left-hand use preference and the direction of scalp hair-whorl rotation develop from a common genetic mechanism. Such a mechanism controls functional specialization of brain hemispheres. Whether the same mechanism specifying mental makeup influences sexual preference was determined here by comparing hair-whorl rotation in groups enriched with homosexual men with that in males at large. Only a minority of 8.2% (n = 207) unselected 'control' group of males had counterclockwise rotation. In contrast, all three samples enriched with homosexual men exhibited highly significant (P < 0.0001), 3.6-fold excess (29.8%, n = 272) counterclockwise rotation. These results suggest that sexual preference may be influenced in a significant proportion of homosexual men by a biological/genetic factor that also controls direction of hair-whorl rotation.

Haldane and the first estimates of the human mutation rate

Abstract: Mutation is the ultimate source of genetic no velty. As such, the rate at which new mutations arise is a central i ssue in gene tics, with profound implications for both ev olution and human health. Haldane’s 1935 paper (reprinted in this issue, pages 235–244) was the first to provide a careful estimate of the mutation rate in h umans. In fact, previous studies had already provided est imates of mutation rates in other organism s (Muller 1928; Stadler 1932). The chief difficulty confronting exper imentalists was the fact that mutations occur at a very low rate. Muller (1928) was able to measure mutation rates in Drosophila melanogaster using a scheme of balanced lethals. By workin g with flies, he was also able to breed many individuals and score large numbers of progeny easily. Stadler (1932), working with maize, was able to count millions of seeds to arrive at mutation rates mostly between 10 –4 and 10 –6 for eight different genes. These approaches were clearly not available in humans, and it was recognized that measures of the mutation rate had to come from other methods. Haldane (1927) was the first to develop the fo rmal theory for equilibrium frequencies of alleles in mut ation– selection balance, and these calculations later formed the basis for the indirect estimates of mutation rate in his 1935 paper. Haldane suggested that if selection acts against deleterious alleles it must be balanced by mut ation pressure to generate observ ed allele frequencies in a population. This provided a straightforwar d way to est imate the mutation rate for deleterious alleles: if the fr equency of an allele could be measured and if the strength of selection could be estimated, it should be po ssible to calculate the mutation rate. Since most mutations in genes are harmful, the mutation rate for deleterious a lleles will be only a slight underestimate of the total mut ation rate. For autosomal dominant mutations, the equilibrium allele frequency, q, is simply µ/s, where µ is the mutation rate and s is the selection coefficient associated with the del eterious mutant. This well-known result can now be found in any population genetics textbook (e.g. Crow and K imura

PCR-based detection of allergenic mackerel ingredients in seafood.

Abstract: Fish is one of the most common causes of food allergy, especially in coastal countries such as Japan. An investigation conducted by the Japanese Government in 1997 reported that fish was ranked second among various causes of food allergy for adults and that approximately 20% of food allergic adults in Japan were sensitive to fish. Several fish species and seafood products are known to cause allergy, and were classified into four groups consisting of (i) salmon, sardine and mackerel, (ii) cod and tuna, (iii) octopus and squid, and (iv) crab and shrimp, by a cluster analysis of immunoglobulin reactivities of children (Tanaka et al. 2000). Scomber mackerel belonging to the family Scombridae are one of the most commercially important seafoods in Japan, where the annual consumption of Scomber mackerel is much larger than that of salmon, sardine, cod and tuna, all of which are also allergenic fish. Three species – Japanese mackerel (Scomber japonicus), Pacific mackerel (Scomber australasicus) and Atlantic mackerel (Scomber scombrus) – constitute a significant part of the absolute mackerel consumption, and are considered to be most frequently involved in incidents of fish allergy in Japan. Since Scomber mackerel possess unique characteristics in the skin, they are easily differentiated from other whole fish, but processed foods containing Scomber mackerel with the skin removed are difficult to identify. In addition, foods containing even a trace of Scomber mackerel sometimes cause serious allergenic episodes (Sackesen and Adalioglu 2003). In this study, we report a rapid and reliable method to detect and differentiate Scomber mackerel fish from other Perciformes marine fish by a simple PCR technique using new Scomber genus specific primers. Nucleotide sequences of the nuclear 5S ribosomal RNA gene (5S rDNA) were compared among 15 marine fish species belonging to 13 genera in 6 families of Perciformes. Alignment of their sequences allowed the selection of a pair of oligonucleotide primers specific for Scomber mackerel. These primers enabled PCR amplification of the flanking nontranscribed spacer region of the 5S rDNA from S. japonicus, S. australasicus and S. scombrus, but no amplification from other fish including closely related Scombridae fish. This simple and robust method can serve in routine detection and authentication of allergenic Scomber mackerel ingredients in seafood in food inspection laboratories.

Cytochrome P450c17α 5'-untranslated region *T/C polymorphism in endometriosis

Abstract: Estrogen plays a role in the pathogenesis of endometriosis. The CYP17 gene codes for the cytochrome P450c17α enzyme that is involved in the estrogen biosynthesis. We aimed to investigate if CYP17 polymorphism could be used as marker to predict the susceptibility of endometriosis. Women were divided into two groups: (1) severe endometriosis (n=119); (2) non-endometriosis groups (n=128). A 169-bp fragment encompassing the T/C polymorphic site in 5′-untranslated promoter region (5′-UTR) of the CYP17 was amplified by the polymerase chain reaction, treated with restriction enzyme MspA1I, and electrophoresis. The polymorphism was divided into restriction-enzyme indigestible (T homozygote), T/C heterozygote, and digestible (C homozygote). Genotypes and allelic frequencies for this polymorphism in both groups were compared. We observed a higher but non-significant percentage of T homozygote in the endometriosis women compared with the non-endometriosis women. Proportions of T homozygote/heterozygote/C homozygote for CYP17 in both groups were: (1) 26.1/46.2/27.7% and (2) 17.2/45.3/37.5% (p-value=0.131). T allele was related with higher susceptibility of endometriosis. T and C allele frequencies in both groups were: (1) 49.2/50.8%; (2) 39.8/60.2% (p-value=0.046). Despite the CYP17* T allele appearing to be asscoiatd with a trend of increased risk of endometriosis, CYP17 5′-UTR gene polymorphism might not be a useful marker for prediction of endometriosis susceptibility.

Quantitative genetics of functional characters in Drosophila melanogaster populations subjected to laboratory selection.

Abstract: What are the genetics of phenotypes other than fitness, in outbred populations? To answer this question, the quantit ative-genetic basis of divergence was characterized for outbred Drosophila melanogaster populations that had previously undergone selection to enhance characters related to fitness. Line -cross analysis using first -generation and second-generation hybrids from reciprocal crosses was co nducted for two types of cross, each replicated fivefold. One type of cross was between representatives of the ancestral population, a set of five populations maintained for several hundred generations on a two-week discrete-generation life cycle and a set of five populations adapted to sta rvation stress. The other type of cross was between the same set of ancestral -representative populations and another set of five populations selected for accelerated development from egg to egg. Developmental time from egg to eclosion, starvation resistance, dry body weight and fecundity at day 14 from egg were fit to regression models estimating si ngle-locus additive and dominant effects, maternal and paternal effects, and digenic additive and dominance epistatic effects. Additive genetic variation explained most of the differences between populations, with additive maternal and cytoplasmic effects also commonly found. Both within-locus and between-locus dominance effects were inferred in some cases, as well as one instance of additive epistasis. Some of these effects may have been caused by linkage disequilibrium. We conclude with a brief discussion concerning the relationship of the genetics of population differenti ation to adaptation.

Deciphering diversity in populations of various linguistic and ethnic affiliations of different geographical regions of India: analysis based on 15 microsatellite markers.

Abstract: The extent of genetic polymorphism at fifteen autosomal microsatellite markers in 54 ethnically, linguistically and geographically diverse human populations of India was studied to decipher intrapopulation diversity. The parameters used to quantify intrapopulation diversity were average allele diversity, average heterozygosity, allele range (base pairs), and number of alleles. Multilocus genotype frequencies calculated for selected populations were utilized for testing conformity with the assumption of Hardy-Weinberg equilibrium. The exact test values, after Bonferroni correction, showed significant deviation amongst Gowda (vWA, Penta E); Dhangar, Satnami and Gounder (D8S1179); Hmar (FGA); Kuki and Balti (vWA) groups. Relatively low number of alleles and allelic diversity (base-pairs size) had been observed in populations of central India as compared with southern and northern regions of the country. The communities of Indo-Caucasoid ethnic origin and Indo-European linguistic family (Kshatriya of Uttar Pradesh) showed highest allelic diversity, as well as rare alleles, not reported in any other Indian populations. Analysis based on average heterozygosity was also found to be lowest among the populations of central India (0.729) and highest among the populations from north (0.777) and west (0.784) regions of the country, having Indo-Caucasoid ethnic origin and Austro-Asiatic linguistic affiliation. The maximum power of discrimination (85%-89%) had been observed at loci FGA, Penta E, D18S51 and D21S11, suggested high intrapopulation diversity in India. Genetic diversity revealed by STR markers was consistent with the known demographic histories of populations. Thus, the present study clearly demonstrated that the intrapopulation diversity is not only present at the national level, but also within smaller geographical regions of the country. This is the first attempt to understand the extent of diversity within populations of India at such a large scale at genomic level.

Abnormal pollen mitoses (PM I and PM II) in an interspecific hybrid ofBrachiaria ruziziensis andBrachiaria decumbens (Gramineae)

Abstract: Microgametogenesis was analysed in an interspecific hybrid resulting from a cross between an artificially tetraploidized sexual accession of Brachiaria ruziziensis (2n = 4x = 36) and the apomictic cultivar (cv. Basilisk) of B. decumbens (2n = 4x = 36). Although each microspore initiated its differentiation by pollen mitosis, polarization of the nucleus was not observed in 28.85% of the microspores, and the typical hemispherical cell plate was not detected as well. The usual asymmetry was not seen at first pollen mitosis (PM I), and microspores therefore lacked differentiation between the vegetative and the generative cell. After telophase, each cell entered PM II, but this was not always followed by cytokinesis. Tripolar spindle and restitutional nuclei were observed among microspores that lacked the first cytokinesis. Pollen from such abnormal divisions were sterile and larger than those resulting from the normal ones. Male gametogenesis in flowering plants depends on a determinative asymmetry in the cell division at pollen mitosis I (PM I), which gives rise to a larger vegetative cell and a smaller generative cell. To achieve this asymmetry, the microspore undergoes several unique cellular events, including the establishment of cell polarity through nuclear migration, development of an asymmetric mitotic spindle, and an expected process of cytokinesis to form a hemispherical cell plate. Control of gametophytic cytokinesis is, therefore, a critical process in pollen cell fate determination which results in the asymmetric distribution of cellular components that presumably include cell fate determinants (Twell et al. 1998; Park and Twell 2001). During cell division in somatic cells, a pre-prophase band of microtubules marks the future division plane and the exact site of cytokinesis, and the cell plate arises from the phragmoplast and grows toward the cell wall (Sylvester 2000). On the other hand, in gametophytic cytokinesis at PM I the pre-prophase band is absent and a unique hemispherical cell plate is formed and surrounds the generative nucleus (Terasaka and Niitsu 1990). Asymmetric cytoplasm cleavage is ensured by a curved profile of phragmoplast microtubules that appear to guide the centrifugal growth of the cell plate from its margin (Brown and Lemmon 1991). Mutations altering cell division asymmetry during pollen mitosis have been reported in Arabidopsis thaliana (Park et al. 1998) and B. decumbens (Junqueira Filho et al. 2003). This paper reports a new occurrence of symmetry in pollen mitoses (PM I and PM II) in a hybrid involving B. decumbens as the male genitor. Absence of cytokinesis following PM I and PM II was also observed.

Short tandem repeat (STR) polymorphisms in Turkish population

Abstract: In recent years, short tandem repeat (STR) systems have gained importance in forensic analysis of biological specimens as well as in paternity testing, as an alternative to the use of restriction fragment length polymorphism (RFLP) analysis (Edwards et al. 1991; Hammond et al. 1994; Nakamura et al. 1987). The analysis of STR polymorphisms by PCR-based method offers certain advantages over RFLP typing: (1) STR loci can be typed with a high degree of specificity and sensitivity in a short time period, (2) these loci can be succesfully amplified from a limited amount of DNA even if it is degraded, and (3) typing of multiple loci can be accomplished in a single multiplex reaction (Hochmeister et al. 1991; Lins et al. 1996). In this study, allele frequencies for the nine STR loci―D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820―were analyzed in 200 unrelated Turkish individuals. All loci, except for the FGA locus, were in HardyWeinberg equilibrium. The observed heterozygosity (Ho), expected heterozygosity (He), power of discrimination (PD), probability of exclusion (PE) and polymorphism information content (PIC) were calculated for the nine loci. The combined power of discrimination and combined probability of exclusion were 0.999999 and 0.999909 over the nine STR loci, respectively. These results suggest that these nine STR loci are a useful marker for forensic identification and paternity analysis.

REML estimates of genetic parameters of sexual dimorphism for wing and thorax length in Drosophila melanogaster

Abstract: Restricted maximum likelihood was used to estimate genetic parameters of male and female wing and thorax length in isofemale lines of Drosophila melanogaster, and results compared to estimates obtained earlier with the classical analysis of variance approach. As parents within an isofemale line were unknown, a total of 500 parental pedigrees were simulated and mean estimates computed. Full and half sibs were distinguished, in contrast to usual isofemale studies in which animals were all treated as half sibs and hence heritability was overestimated. Heritability was thus estimated at 0.33, 0.38, 0.30 and 0.33 for male and female wing length and male and female thorax length, respectively, whereas corresponding estimates obtained using analysis of variance were 0.46, 0.54, 0.35 and 0.38. Genetic correlations between male and female traits were 0.85 and 0.62 for wing and thorax length, respectively. Sexual dimorphism and the ratio of female to male traits were moderately heritable (0.30 and 0.23 for wing length, 0.38 and 0.23 for thorax length). Both were moderately and positively correlated with female traits, and weakly and negatively correlated with male traits. Such heritabilities confirmed that sexual dimorphism might be a fast evolving trait in Drosophila.

Engineered XcmI cassette-containing vector for PCR-based phylogenetic analyses.

Abstract: A simple and general method is described to construct a new vector bearing a synthetic XcmI cassette for direct cloning of PCR-amplified genes of interest. Cleavage of the vector with XcmI generates a linearized molecule with a single thymidine (T) overhang at the 3′ ends (T-vector) that facilitates TA cloning of PCR products carrying complementary 3′ adenosine (A) residue, without modification. Once constructed, this newly designed circularized vector (pEMX) is reproducible in any molecular biology laboratory, and is a high performance and cost effective alternative to commercially available T-vectors. PCR-based DNA analysis has become a widely used tool in investigating genetic relationships in naturally occurring and aquaculture populations of marine organisms. In general, genes of interest are amplified by PCR using thermostable DNA polymerase, and subsequently cloned into adequate vectors for sequencing and other manipulations. Taq polymerase, the most widely used PCR enzyme, adds a single adenosine at the 3′ ends of PCR products due to the terminal transferase activity (Clark 1988). PCR products derived using such polymerases can be directly cloned into vectors with complementary 3′ thymidine overhangs (T-vectors). T-vectors are routinely utilized for sequence analysis of 5S ribosomal RNA genes (5S rDNA) as a genetic marker to assess phylogenetic relationships in marine organisms (Martins and Galetti 2001). Multiple products encoding various sizes of multilocus 5S rDNA are amplified from a single fish species by PCR, and each product is separately cloned into a T-vector. This requires large numbers of T-vectors for constructing 5S rDNA library of even a single species. Moreover, commercially available T-vectors, such as pGEM-T (Promega) and pT7Blue (Novagen), are expensive and cannot be regenerated in the laboratory for further use. We describe here the development of a simple and general method for constructing T-vectors bearing an oligonucleotide cassette that produces complementary 3′ thymidine overhangs by restriction enzyme digestion.

From fruit flies to fallout: Ed Lewis and his science.

Abstract: This article is based on a talk presented in honor of Ed Lewis at the Cali-fornia Institute of Technology on February 4, 2004 to coincide with thepublication of “Genes, Development and Cancer: The Life and Work ofEdward B. Lewis”. The present tense has been retained despite Lewis’recent death on July 21, 2004.

Genetic and genotype x environment interaction effects for the content of seven essential amino acids in indica rice.

Abstract: It is necessary for rice breeders to understand the genetic basis of nutrient quality traits of rice. Essential amino acids are most important in determining the nutrient quality of rice grain and can affect the health of people who depend on rice as a staple food. In view of the paucity of genetic information available on essential amino acids inindica rice, we estimated the genetic main effects and genotype × environment (G × E) interaction effects on the content of essential amino acids. Nine cytoplasmic male sterile lines as females and five restorer lines as males were introduced in a North Carolina II design across environments. Estimates of the content of the essential amino acids valine, methionine, leucine and phenylalanine showed that they were mainly controlled by genetic main effects, while the contents of threonine, cysteine and isoleucine were mainly affected by G × E effects. In the case of genetic main effects, both cytoplasmic and maternal genetic effects were predominant for all essential amino acids, indicating that selection for improving essential amino acid content based on maternal performance would be more effective than that based on seeds. The total narrow-sense heritabilities were high and ranged from 0.72 to 0.83. Since general heritabilities for these essential amino acids (except for cysteine) were found to be much larger than G × E interaction heritability, the improvement of content of most essential amino acids under selection would be expected under various environments. Rice varieties such as Zhenan 3, Yinchao 1, T49, 26715, 102 and 1391 should be selected as optimal parents for increasing the content of most essential amino acids, while the total genetic effects from Zhexie 2, Xieqingzao, Gangchao 1, V20, Zuo 5 and Zhenshan 97 were mainly negative and these parents could decrease the contents of most essential amino acids.

Refinement of the locus for non-syndromic sensorineural deafness (DFN2).

Abstract: Non-syndromic X-linked deafness is a rare form of genetic deafness in humans accounting for a small proportion of all hereditary hearing loss. Different clinical forms of non-syndromic X-linked deafness have been described, and most of these have been mapped. Here, we report a Chinese family affected by a congenital profound sensorineural hearing loss. All phenotypes of this family are clinically compatible with non-syndromic sensorineural deafness (DFN2). A maximum two-point Lod score of 2.32 was obtained at markerDXS6797 (θ = 0.00). Recombinants define a region of 4.3 cm flanked by markersDXS6799 andGATA172D05. This region overlaps the previously reported DFN2 region by 2.0 cm.

Circadian clocks and life-history related traits: is pupation height affected by circadian organization in Drosophila melanogaster?

Abstract: In D. melanogaster, the observation of greater pupation height under constant darkness than under constant light has been explained by the hypothesis that light has an inhibitory effect on larval wandering behaviour, preventing larvae from crawling higher up the walls of culture vials prior to pupation. If this is the only role of light in affecting pupation height, then various light : dark regimes would be predicted to yield pupation heights intermediate between those seen in constant light and constant darkness. We tested this hypothesis by measuring pupation height under various light : dark regimes in four laboratory populations of Drosophila melanogaster. Pupation height was the greatest in constant darkness, intermediate in constant light, and the least in a light/dark regime of LD 14:14 h. The results clearly suggest that there is more to light regime effects on pupation height than mere behavioural inhibition of wandering larvae, and that circadian organization may play some role in determining pupation height, although the details of this role are not yet clear. We briefly discuss these results in the context of the possible involvement of circadian clocks in life-history evolution.

Allelic structure and distribution of 103 STR loci in a Southern Tunisian population.

Abstract: Genotypes of 103 short tandem repeat (STR) markers distributed at an average of 40 cM intervals throughout the genome were determined for 40 individuals from the village of BirEl Hfai (BEH). This village of approximately 31,000 individuals is localized in the south-west of Tunisia. The allele frequency distributions in BEH were compared with those obtained for individuals in the CEPH (Centre d'Etude du Polymorphisme Humain) data using a Kolmogorov-Smirnov two-sample test. Fourteen out of the 103 markers (13.2%) showed significant differences (P<0.05) in distribution between the two populations. Population heterogeneity in BEH was indicated by an excess of observed homozygosity deviations from Hardy-Weinberg equilibrium at three loci (P<0.0005). No evidence for genotypic disequilibrium was found for any of the marker pairs. This demonstrated that in spite of a high inbreeding level in the population, few markers showed evidence for a different pattern of allelic distribution compared to CEPH.

DNA marker mining of ILSTS035 microsatellite locus on chromosome 6 of Hanwoo cattle.

Abstract: We describe tests for detecting and locating quantitative trait loci (QTL) for traits in Hanwoo cattle. From results of a permutation test to detect QTL for marbling, we selected the microsatellite locus ILSTS035 on chromosome 6 for further analysis. K-means clustering analysis applied to five traits and nine DNA markers in ILSTS035 resulted in three cluster groups. Finally we employed the bootstrap test method to calculate confidence intervals using the resampling method to find major DNA markers. We conclude that the major markers of ILSTS035 locus on chromosome 6 of Hanwoo cattle are markers 235 bp and 266 bp.

Genetic characterization of Indian Spiti horses.

Abstract: India has a rich biodiversity of equines in the form of six distinct indigenous horse (Equus caballus) breeds, namely Kathiawari, Marwari, Spiti, Zanskari, Bhutia and Manipuri, in addition to indigenous donkeys and wild asses (Yadav et al. 2001). These horse breeds are well adapted to different agroclimatic regions and possess certain unique characteristics. Spiti horses are slow moving, sure-footed, and are found mainly in the hilly areas of the Himalayan range, mostly in the districts of Lahaul-Spiti and Kinnaur in the state of Himachal Pradesh, India. Spiti horses not only thrive under such harsh conditions but are also used as pack animals. Unfortunately, the population numbers of this breed are decreasing at an alarming rate and it is thought to be close to extinction. Consequently, there is an urgent need to characterize this valuable breed to set priorities for its conservation. Molecular characterization is an essential prerequisite to developing an effective and meaningful conservation programme for Spiti horses. Several DNA-based technologies have been developed in the last decade to type polymorphic loci, including random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), variable number of tandem repeats (VNTRs), single-strand conformational polymorphism (SSCP), and methods that make use of polymorphisms of short tandem repeats called microsatellites. Among the array of molecular markers, microsatellites are considered especially suitable for biodiversity evaluation, owing to their codominant inheritance, high heterozygosity, ease and reliability of scoring, ubiquitous presence throughout the genome, and high degree of polymorphism (Takezaki and Nei 1996). The aim of the present work was to assess genetic variation in the Spiti breed of Indian horses, using 25 microsatellite markers that had been observed in earlier studies to be polymorphic in exotic breeds of horses (Ellegren et al. 1992; van Haeringen et al. 1994, 1998; Ewen and Matthews 1995; Eggleston-Stott et al. 1996, 1997; Meyer et al. 1997; Swinburne et al. 1997, 2000; Coogle and Bailey 1998; Lindgren et al. 1999; Kakoi et al. 1999).

Variation in the relative magnitude of intraspecific and interspecific competitive effects in novel versus familiar environments in two Drosophila species.

Abstract: Models of competitor coevolution, especially the genetic feedback hypothesis, suggest that a negative correlation between intraspecific and interspecific competitive effects may be important in sustaining competitor coexistence, and can give rise to oscillatory dynamics with repeated reversals of competitive superiority. I reanalyzed previously published census data from an experiment in which populations of Drosophila melanogaster and D. simulans underwent competitive coevolution in one familiar and two novel environments, to specifically look for any evidence of a negative relationship between intraspecific and interspecific competitive effects on population growth rates, and for any indication of short period cycling in the relative magnitude of intraspecific and interspecific competitive effects. While there was considerable variation in the relative magnitude of intraspecific and interspecific competitive effects over generations, among both populations and environments, there was no clear evidence supporting the genetic feedback hypothesis. Intraspecific and interspecific competitive effects on population growth rates were strongly positively correlated in novel environments, and uncorrelated in the familiar environment. Data from the familiar environment indicated that indices of competition of populations of the initially superior competitor, D. melanogaster, might be showing some cyclic behaviour, but I argue that this is likely to be transient, and not suggestive of sustained oscillatory dynamics predicted by the genetic feedback model. I discuss the results in the context of the importance of the genetic architecture of intraspecific and interspecific competitive abilities in determining the coevolutionary trajectory of competitive interactions.

Benefits of being biased

Abstract: The genetic code is degenerate: most amino acids are coded by multiple codons. However, it is known that certain codons for a given amino acid are preferred over other synonymous codons. Theoretical studies have predicted and experiments have shown that this kind of a bias can lead to higher efficiency of translation, presumably accompanied by benefits in terms of the Darwinian fitness of the organism. However, population genetics models based on gene sequence data predict that, at least for certain organisms like the fruit fly, Drosophila melanogaster, the fitness effects might be too small to be observed. Two recent studies (Carlini and Stephan 2003; Carlini 2004) show that even in such systems, under certain conditions, it is possible to empirically demonstrate the effects of codon bias at the phenotypic level, and the corresponding effect on at least one major component of the fitness of the organism. The neutral theory of molecular evolution assumes that synonymous mutations do not affect fitness (King and Jukes 1969). This implies that all the different codons that code for the same amino acid are expected to be equally abundant in a large sample of genes (Powell and Moriyama 1997). However, it is known that, in most genes, certain codons are found more frequently than their synonymous counterparts: a phenomenon often termed as codon bias. This naturally leads to the question as to whether codon bias actually has any selective advantage, and several lines of evidence suggest that this is indeed the case. Among all the synonymous codons, the most often used codons are generally the ones whose matching tRNAs are the most abundant in the tRNA pool (Moriyama and Powell 1997). Moreover, the level of bias is generally found to be higher in genes that have high levels of expression (Duret and Muchiroud 1999), suggesting that the presence of codon bias is probably related to translation efficiency (Bulmer 1991). This might be possible in two ways that are not mutually exclusive: (i) Presence of optimal codons might increase the speed of translation, by decreasing the time taken for attachment of the correct aminoacyl tRNA, which in turn would increase the availability of free ribosomes in the cytoplasm. This would lead to an increase in the level of proteins in a cell, particularly for genes that are expressed at very high rates (Kurland 1987). (ii) It has been shown that unpreferred codons can increase the frequency of incorporation of incorrect amino acids to the nascent polypeptide (Precup and Parker 1987). This reduces the fidelity of protein synthesis, thus enhancing the metabolic costs incurred in terms of nonfunctional/ misfunctional proteins. Hence, codon bias leading to translational accuracy is expected to be under positive selection, particularly in highly expressed genes (Akashi 1994). It has been shown empirically that the usage of optimal codons can increase the rate of translation and hence presumably affect the fitness of an organism. For example, Sörensen et al. (1989) introduced small DNA fragments containing infrequent codons into the lacZ gene of E. coli, and measured the translation rate of the mRNA transcripts. They found that usage of the biased codons actually increased the translation rate up to six times. However, owing to the multitude of tissue types that can vary in their gene expression and codon usage patterns, extending such works in vivo for multicellular organisms was a difficult proposition (Powell and Moriyama 1997). Since synonymous mutations do not change the final protein product, selection for optimal codons is thought to be fairly weak. Using different methodologies, Akashi (1995, 1996) and McVean and Viera (2001) came to the conclusion that the strength of selection (given as the product of the effective population size, Ne and the selection coefficient, s) for any synonymous codon substitution in D. melanogaster would be almost negligible, implying that the difference in fitness arising out of preferential usage of optimal codons was likely to be very low. Thus, empirical measurements of the effects of codon bias on the fitness of an organism appeared to be difficult, if not impossible. However, Carlini and Stephan (2003) point out that these estimates are actually averaged over many codon families across a large subset of genes. They argue that since selection coefficients are not the same for all codon families, it might be possible to empirically observe the effects of codon bias by manipulating codon families that have a high level

Cloning of a novel gene, Cymg1, related to family 2 cystatins and expressed at specific stages of mouse testis development.

Abstract: We have cloned a novel gene,Cymg1 (GenBank accession number AY600990), from a mouse testis cDNA library.Cymg1 is located in 2G3 of mouse chromosome 2. The cDNA includes an open reading frame that encodes 141 amino acid residues. The encoded polypeptide has a cysteine protease inhibitor domain found in the family 2 cystatins but lacks critical consensus sites important for cysteine protease inhibition. These characteristics are seen in the proteins of the CRES subfamily of the family 2 cystatins which are expressed specifically in the reproductive tract. CYMG1 protein shows 44% identity with mouse CRES and 30% identity with mouse cystatin C. Northern blot analysis showed that theCymg1 gene was specifically expressed in adult mouse testis. RT-PCR also showed thatCymg1 was expressed in testis and spermatogonial cells.Cymg1 expression level varied in the different developmental stages of mouse testis, and were coincidental with spermatogenesis and sex maturation. These results indicate thatCymg1 may play important roles in mouse spermatogenesis and sex maturation

Are bigger flies always better: the role of genes and environment.

Abstract: Body size, especially in invertebrates, is often positively correlated with major fitness components such as female fecundity and male mating success, and it is believed that the evolution of larval growth rate and adult body size in insects is largely shaped by a tradeoff between the fitness benefits of being large versus those of developing to adulthood fast (Santos et al. 1988; Partridge and Fowler 1993). Understanding the phenotypic inter-relationships between development time, body size and adult fitness components in insects, and how these relationships are affected by genotype and environment, is therefore directly relevant to two contentious and central issues in evolutionary genetics: (1) the nature of genetic constraints on the attainment of an optimal life-history, and (2) the relative role of genotypic and environmental variation and covariation in determining the magnitude and sign of phenotypic correlations between fitness related traits (Prasad and Joshi 2003). Almost half a century ago, in a characteristically rigorous and detailed study, Robertson (1957) examined the nature of genetic variation and covariation between body size (thorax length) and egg production (total fecundity between days 4–8 post-eclosion), under benign and uniform rearing conditions, in a large, genetically variable laboratory population of Drosophila melanogaster. The major findings of Robertson’s (1957) study were that (a) there was a significant positive phenotypic correlation between body size and egg production, (b) about 50% of the phenotypic variance in body size was due to genetic variation, mostly additive, (c) about 60% of the phenotypic variance in egg production was due to genetic variation, with a large non-additive component, (d) body size and egg production appeared to be independently genetically correlated with development time, the latter negatively and the former positively, and (e) the genetic correlation underlying the positive phenotypic correlation between body size and egg production was largely non-additive. Quite apart from the significance of the results, there are several appreciable methodological features of Robertson’s (1957) study, features that are important to experimental design and execution in evolutionary genetics but, unfortunately, often overlooked, although practitioners of experimental evolution have recently been repeatedly calling attention to them (e.g. Rose et al. 1996; Ackermann et al. 2001; Chippindale et al. 2003). For example, Robertson (1957) worked with a large, genetically variable, and reasonably well laboratory-adapted population that was close to genetic equilibrium for the traits being studied, explicitly controlled larval density during assays, recognized that trait relationships could be environmentand age-specific and tried to incorporate this knowledge in the choice of measures for size and egg production, and was sensitive to the fact that phenotypic measures of fitness related traits often vary from day to day, and assay to assay, and, consequently, tried to account for that variation in the experimental design and analysis. Except for the lack of population level replication, these precautions, and the caveats one finds throughout Robertson’s (1957) discussion of the results, make for a very ‘modern’ paper in experimental evolutionary genetics, in stark and somewhat unfortunate contrast to many contemporary papers that often seem to be imbued with a combination of an abiding faith in selection as an inexorable optimizing force and an overly simplistic view of the evolutionary process.

C. C. Li (1912-2003): his science and his spirit.

Abstract: Ching Chun Li passed away on 20 October 2003, in Pittsburgh. He was an outstanding population geneticist, a wonderful teacher, and above all, a great human being. Devotion to work and humility were the hallmarks of C. C. Li, who was known as C.C. to his contemporaries and colleagues, and as Dr Li to his students. In the United States, he stayed with the same University (the University of Pittsburgh) from 1951 until his death. He formally retired in 1982, but continued to come to work regularly for two decades after his retirement. “I go to my office because there is nothing else better to do.” He published over 25 papers after his “retirement;” he wrote his last scientific paper when he was 88 years of age. In 2002, Dr Li and his wife, Clara, established an Endowed Research and Education Fund in Human Genetics through a generous gift of $ 1 million to ensure that human genetics education and research play an important role at the University of Pittsburgh. “This is not about what I’m giving to the University; it’s about what the University has given me.” Dr Li was a very courageous, kind, and relaxed person, with a strong sense of humor. If you walked into his office, he was always reading, writing, or calculating something. However, he always had time for you. If you gave him a manuscript, you could be sure of receiving his thoughtful comments in a short time. His style of work was amusing to many of us. Even if he had derived an equation algebraically, he had to work out some numerical examples to verify that the equation was correct. Sometimes, of course, such numerical exercises provided further insights for him. Thus, he would spend hours in his office working on his desk calculator that had a large red LED display—his eyesight was poor. And, of course, he always used the white backsides of discarded pages for such purposes. You could also discuss your personal problems with him; you could be sure of receiving his wise counsel. He was very affectionate to everyone. C. C. Li supervised the work of 12 Ph.D. students. He was elected a Fellow of the American Statistical Association and of the American Association for the Advancement of Science, President (1960) of the American Society of Human Genetics (ASHG), and Member of the International Statistical Institute and the Academia Sinica (Chinese Academy). In 1970, he was elected “Pittsburgh Statistician of the Year” by the American Statistical Association. In 1998, the ASHG honored him with their “Award for Excellence in Education.” Throughout his life, C. C. Li steadfastly strove to uphold the autonomy of science and the freedom of scientists. In his speech delivered during the ASHG award ceremony in 1998, Dr Li said, “If one insists that science itself has also its own ideology, then I shall say: let that ideology be the autonomy of science, although I personally feel that autonomy is an essential property of science, not its guiding ideology. If there were no autonomy, there would be no science to speak of.” He was also acutely aware of the social responsibility of scientists. “They must look after the social consequences” of their science, he said. C. C. Li wrote 10 books. These were on population genetics, human genetics, the design of experiments, and path analysis. Two of these books were his Chinese translations of books by T. D. Lysenko (Heredity and its Variability) and Julian Huxley (Soviet Genetics and World Science). He published over 100 papers in peer-reviewed journals; he was the sole author on about 60% of these.

Genetically engineered monogamy in voles lends credence to the modus operandi of behavioural ecology.

Abstract: Behavioural ecologists investigate the evolutionary forces that select for one behavioural pattern over another (Krebs and Davies 1991, 1993. ) Why do lions hunt in prides while the tiger stalks its prey alone? Why are honey bee workers so industrious while the drones are so lazy? Why do koels lay their eggs in the nests of crows while the latter go through the trouble of building nests and caring for chicks, their own as well those of the koel? Why do Siberian cranes fly some 6400 kilometres from their breeding grounds in Siberia to over winter in Bharatpur in Rajasthan, India, only to return to Siberia in summer? Why are males in many species of birds monogamous, pairing for life and providing paternal care to the chicks, while the males of many mammals are polygynous, mating with many females and contributing little more than a sperm-full of genes to their offspring? Behavioural ecologists estimate, and wherever possible calculate, the relative costs and benefits of alternative behavioural strategies under the given ecological circumstances and attempt to predict the winning strategy. What are the relative advantages of cooperative hunting versus stalking in stealth, for the lion that lives in open savannas and the tiger that lives in dense jungle? What are the inclusive fitness benefits to the worker bee who rears sisters related to her by 0.75 instead of daughters related to her by 0.5, as compared to similar benefits for drones, of rearing sisters related to them by 0.5 instead of daughters related to them by 1.0? What are the benefits to the koel of saving the cost of nest building and brood care and to the crow of attempting to selectively destroy the koels' eggs without destroying her own? What are the costs for the Siberian crane of attempting to survive, let alone breed, in the severe winters of Siberia compared to the cost of risky and energy-consuming flights to Bharatpur and back? What are the costs to males of denying paternal care to their offspring when the mothers are up to the task by themselves and what are the costs to the females of abandoning their offspring? Difficult as it is to do, these costs and benefits are often measurable. The more risky gambit of the behavioural ecologists appears to be the assumption that alternative behavioural strategies are readily available or easily created by mutation so that natural selection can choose from among them (Grafen 1991). The source of uncertainty is our profound ignorance of the proximate physiological, genetic or epigenetic, neurobiological and developmental mechanisms that orchestrate these behaviours. This ignorance has to do, in part but only in part, with the formidable difficulty of unraveling the proximate mechanisms of complex behaviour patterns. The remaining part has undoubtedly to be attributed to the behavioural ecologists' obsession with ultimate factors and habitual neglect of proximate causation (Gadagkar 1997). But of course there are exceptions, and a particularly spectacular exception concerns our present understanding of the proximate factors involved in the presence and absence of affiliation, pair-bonding and paternal behaviour in voles. Voles are small mouse like rodents that can sometimes be serious pests. Of particular interest for this tale are two North American species, the prairie vole, Microtus ochrogaster, and the meadow vole, Microtus pennsylvanicus. These two species have contrasting mating systems. The prairie vole is very social, forms lasting pair bonds, males prefer the company of their mates and are aggressive to other individuals, and both parents provide extended parental care to offspring. In contrast, the meadow vole is rather asocial, mating is polygynous or promiscuous, mated pairs do not pair-bond and males do not provide parental care to offspring. There are also two other similarly contrasting species, the monogamous pine vole (Microtus pinetorum) and the promiscuous montane vole (Microtus montanus) which have been substituted for prairie voles and meadow voles, respectively, in some of the studies. Despite such contrasting social behaviour, prairie/pine voles and meadow/montane voles share more than 99% genome homology and look very similar. The obvious advantage of these vole species as model systems to investigate the evolution of social behaviour in general, and mat

On the genetic basis of temperature compensation of circadian clocks

Abstract: Circadian (about a day) rhythms recur at various levels of organisation, in organisms ranging from bacteria to humans, and researchers in the field believe that these rhythms are adaptive (Sharma 2003a). Although the adaptive significance of circadian rhythms is yet to be unequivocally demonstrated empirically, their functional importance is well recognized in a variety of organisms, and some circumstantial evidence suggests that circadian clocks enhance survival of organisms living in periodic environments (Sharma 2003b). Circadian rhythms were first demonstrated in 1729, but it was only after 1950 that they caught the attention of several renowned biologists, especially after it was demonstrated that these rhythms are temperature compensated, i.e. their periodicities do not change drastically with increase or decrease of temperature within the physiological range. After the discovery of the period (per) gene in Drosophila melanogaster (Konopka and Benzer 1971), and the frequency (frq) gene in Neurospora crassa (Feldman and Hoyle 1973), the molecular mechanisms regulating circadian rhythms began to become clear. The consensus view is that the molecular mechanism underlying circadian rhythms involves two interlocked feedback loops based on transcription-translation controls (Sharma 2003a). Since the identification of various mutant alleles at the per and frq loci (short period mutants, per or frq, frq; and long period mutants per or frq, frq), several key components of the circadian molecular loops have been discovered (Dunlap et al. 2003). An interesting aspect of these mutants is that unlike the wild type organisms, which display robust temperature compensation, they show partial or complete loss of temperature compensation (Mattern et al. 1982; Loros and Feldman 1986; Huang et al. 1995). Further, both per and frq genes include within their coding regions an internally repetitive array of threonine-glycine codons, and in D. melanogaster this region is polymorphic in length, both in natural and laboratory populations (Costa et al. 1992). These repeat sequences show a direct relationship with the ability of flies to maintain a temperature compensated circadian rhythm at different temperatures (Sawyer et al. 1997), and deleting the threonine-glycine repeat region produces flies that have temperature sensitive circadian clocks (Costa et al. 1992), which suggests that the ability of temperature compensation involves the clock genes. Given that most biochemical process are normally temperature dependent, i.e. their rates become faster or slower with increase or decrease of temperature, it is intriguing that circadian rhythms are temperature compensated. In this write-up I will try to put together ideas that are based on experiments on temperature compensation in clock mutants, and attempt to provide a framework for understanding temperature compensation of circadian rhythms, and designing future experiments to study this interesting and important phenomenon. Unless the biochemical processes that constitute the molecular feedback loops of circadian clocks are themselves temperature compensated, which seems to be quite unlikely, temperature compensation of circadian rhythms can stem from either of the following two mechanisms:

Genetic correlations: transient truths of adaptive evolution.

Abstract: The concept of ‘truth’, arguably, exists only in the discourse of poets and mathematicians. The rest of us have to make do by replacing the sublime ‘truth’ by the more mundane ‘consistency’. Much thinking in evolution is based on the implicit notion of consistency in the relationship among fitness traits, relationships that can either facilitate or constrain certain evolutionary trajectories being taken by a population. Such thinking is exemplified by the notion of tradeoffs that is ubiquitous in the study of life-history evolution (Prasad and Joshi 2003). Formal theory, on the other hand, clearly suggests that genetic correlations can change in the process of adaptive evolution, being partly a function of allele frequencies (Falconer 1981). Thus, the question remains as to whether, genetic correlations among traits are really consistent across populations and evolutionary time, at least in the short to medium term? Though several studies have previously addressed the issue of consistency of trait correlations within and across environments (e.g. Wilkinson et al. 1990; Joshi and Thompson 1995, 1997; Bell 1997), three recently published studies (Archer et al. 2003; Chippindale et al. 2003 and Phelan et al. 2003) deserve mention for their magnitude and scope, experimental design and rigour, and the consequent ability to determine the causes for change in trait correlation with greater confidence by controlling for various confounding factors. All three studies from the same laboratory, were done on populations of Drosophila melanogaster descended from a common ancestral population, and under similar maintenance and assay conditions. These studies show that (a) trait correlations can change over few tens of generations even in a controlled laboratory environment, (b) selection – rather than linkage disequilibrium, inbreeding or genotype × environment (G × E) interaction – is the major factor that changes trait correlations, at least in these studies, and (c) long-term laboratory selection experiments, though technically and logistically daunting, offer breathtaking insights into the subtleties of the process of adaptive evolution, which would be difficult by following other experimental approaches. The relevance and importance of these studies to experimental evolution in particular, and evolutionary thought in general, becomes clear if we consider the process of adaptive evolution. The evolutionary trajectory of a population depends, to a large extent, on the interplay between selective forces acting on the population and the genetic architecture of fitness components, where the genetic architecture can be defined as the pattern of genetic correlations among traits relevant to fitness. The evolutionary trajectories are further affected by chance. Therefore, it follows that, given the long time scale and, hence, the number of contingent events expected to occur, it is highly improbable that one can predict macro-evolutionary trends with