Heredity

The use of telomere length in ecology and evolutionary biology.

Publication Date: 2010 Aug 25 PMID: 20736972
Authors: Horn, T. - Robertson, B. C. - Gemmell, N. J.
Journal: Heredity

The measurement of telomere length (TL) is a genetic tool that is beginning to be employed widely in ecological and evolutionary studies as marker of age and fitness. The adoption of this approach has been accelerated by the development of telomere quantitative PCR, which enables the screening of large numbers of samples with little effort. However, the measurement and interpretation of TL change need to be done with a necessary level of rigour that has thus far often been missing where this approach has been employed in an ecological and evolutionary context. In this article, we critically review the literature available on the relationship between TL, age and fitness. We seek to familiarize geneticists, ecologists and evolutionary biologists with the shortcomings of the methods and the most common mistakes made while analysing TL. Prevention of these mistakes will ensure accuracy, reproducibility and comparability of TL studies in different species and allow the identification of ecological and evolutionary principles behind TL dynamics.Heredity advance online publication, 25 August 2010; doi:10.1038/hdy.2010.113.

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The quantitative-genetic and QTL architecture of trait integration and modularity in Brassica rapa across simulated seasonal settings.

Publication Date: 2010 Aug 25 PMID: 20736971
Authors: Edwards, C. E. - Weinig, C.
Journal: Heredity

Within organisms, groups of traits with different functions are frequently modular, such that variation among modules is independent and variation within modules is tightly integrated, or correlated. Here, we investigated patterns of trait integration and modularity in Brassica rapa in response to three simulated seasonal temperature/photoperiod conditions. The goals of this research were to use trait correlations to understand patterns of trait integration and modularity within and among floral, vegetative and phenological traits of B. rapa in each of three treatments, to examine the QTL architecture underlying patterns of trait integration and modularity, and to quantify how variation in temperature and photoperiod affects the correlation structure and QTL architecture of traits. All floral organs of B. rapa were strongly correlated, and contrary to expectations, floral and vegetative traits were also correlated. Extensive QTL co-localization suggests that covariation of these traits is likely due to pleiotropy, although physically linked loci that independently affect individual traits cannot be ruled out. Across treatments, the structure of genotypic and QTL correlations was generally conserved. Any observed variation in genetic architecture arose from genotype x environment interactions (GEIs) and attendant QTL x E in response to temperature but not photoperiod.Heredity advance online publication, 25 August 2010; doi:10.1038/hdy.2010.103.

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Multiple genetic divergences and population expansions of a Mediterranean sandfly, Phlebotomus ariasi, in Europe during the Pleistocene glacial cycles.

Publication Date: 2010 Aug 25 PMID: 20736970
Authors: Mahamdallie, S. S. - Pesson, B. - Ready, P. D.
Journal: Heredity

Phlebotomus ariasi is one of the two sandflies transmitting the causative agent of zoonotic leishmaniasis, Leishmania infantum, in France and Iberia, and provides a rare case study of the postglacial re-colonization of France by a Mediterranean species. Four DNA sequences were analysed-mitochondrial cytochrome b (cyt b), nuclear elongation factor-1alpha (EF-1alpha) and two anonymous nuclear loci-for 14-15 French populations and single populations from northeast Spain, northwest Spain, Portugal and Morocco. The presence of cryptic sibling species was not revealed by phylogenetic analyses and testing for reproductive isolation between sympatric populations defined by the two most divergent cyt b haplogroups. No locus was shown to be under positive directional or balancing selection and, therefore, molecular variation was explained demographically. Each nuclear locus showed shallow isolation by distance from Portugal to the French Pyrenees, but for both cyt b and EF-1alpha there was then a step change to the upland Massif Central, where leading-edge populations showed low diversity at all loci. Multiple genetic divergences and population expansions were detected by analyses of cyt b and dated to the Pleistocene. Endemicity of one cyt b sub-lineage suggested the presence of a refuge north of the Pyrenees during the last glacial period. Monopolization of the Massif Central by genetically differentiated populations of P. ariasi might possibly hinder the northwards spread of leishmaniasis.Heredity advance online publication, 25 August 2010; doi:10.1038/hdy.2010.111.

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The fuel of evolution.

Publication Date: 2010 Aug 25 PMID: 20736969
Authors: Lopez-Fanjul, C. - Garcia-Dorado, A.
Journal: Heredity

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The narrow endemic Norwegian peat moss Sphagnum troendelagicum originated before the last glacial maximum.

Publication Date: 2010 Aug 18 PMID: 20717162
Authors: Stenoien, H. K. - Shaw, A. J. - Stengrundet, K. - Flatberg, K. I.
Journal: Heredity

It is commonly found that individual hybrid, polyploid species originate recurrently and that many polyploid species originated relatively recently. It has been previously hypothesized that the extremely rare allopolyploid peat moss Sphagnum troendelagicum has originated multiple times, possibly after the last glacial maximum in Scandinavia. This conclusion was based on low linkage disequilibrium in anonymous genetic markers within natural populations, in which sexual reproduction has never been observed. Here we employ microsatellite markers and chloroplast DNA (cpDNA)-encoded trnG sequence data to test hypotheses concerning the origin and evolution of this species. We find that S. tenellum is the maternal progenitor and S. balticum is the paternal progenitor of S. troendelagicum. Using various Bayesian approaches, we estimate that S. troendelagicum originated before the Holocene but not before c. 80 000 years ago (median expected time since speciation 40 000 years before present). The observed lack of complete linkage disequilibrium in the genome of this species suggests cryptic sexual reproduction and recombination. Several lines of evidence suggest multiple origins for S. troendelagicum, but a single origin is supported by approximate Bayesian computation analyses. We hypothesize that S. troendelagicum originated in a peat-dominated refugium before last glacial maximum, and subsequently immigrated to central Norway by means of spore flow during the last thousands of years.Heredity advance online publication, 18 August 2010; doi:10.1038/hdy.2010.96.

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Cohort-structured tree populations.

Publication Date: 2010 Aug 18 PMID: 20717161
Authors: Jansson, S. - Ingvarsson, P. K.
Journal: Heredity

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Variability and loss of functionless traits in cave animals. Reply to Jeffery (2010).

Publication Date: 2010 Aug 18 PMID: 20717160
Authors: Wilkens, H.
Journal: Heredity

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Stripes, sex and sparrows: what processes underlie heteromorphic chromosome evolution?

Publication Date: 2010 Aug 18 PMID: 20717159
Authors: Joron, M. - Whibley, A.
Journal: Heredity

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Density-regulated population dynamics and conditional dispersal alter the fate of mutations occurring at the front of an expanding population.

Publication Date: 2010 Aug 18 PMID: 20717158
Authors: Munkemuller, T. - Travis, M. J. - Burton, O. J. - Schiffers, K. - Johst, K.
Journal: Heredity

There is an increasing recognition that the interplay between ecological and evolutionary processes shapes the genetic footprint of populations during and after range expansions. However, more complex ecological processes regularly considered within spatial ecology remain unexplored in models describing the population genetics of range expansion. In this study we integrate flexible descriptions of population growth and competition as well as conditional dispersal into a model that simulates the fate of mutations occurring at the wave front of an expanding population. Our results show that the survival and distribution of a mutation is not only affected by its bias (that is, whether it is deleterious, neutral or beneficial) but also by the mode of local density regulation and conditional dispersal of the simulated populations. It is in particular the chance of a mutation to establish at the front of advance and 'surf' to high frequencies that critically depends on the investigated ecological processes. This is because of the influence of these processes on demographic stochasticity in the system and the differential responses of deleterious, neutral and beneficial mutations to this stochasticity. Generally, deleterious mutations rely more on chance and thus profit the most from ecological processes that enhance demographic stochasticity during the period of establishment. Our study emphasizes the importance of incorporating more ecological realism into evolutionary models to better understand the consequences of shifting geographic ranges for the genetic structure of populations and to find efficient adaptation strategies to mitigate these effects.Heredity advance online publication, 18 August 2010; doi:10.1038/hdy.2010.107.

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Genetic panmixia and demographic dependence across the North Atlantic in the deep-sea fish, blue hake (Antimora rostrata).

Publication Date: 2010 Aug 18 PMID: 20717157
Authors: White, T. A. - Fotherby, H. A. - Stephens, P. A. - Hoelzel, A. R.
Journal: Heredity

The efficient investment of resources and effort into conservation strategies depends on the accurate identification of management units. At the same time, understanding the processes by which population structure evolves requires an understanding of the conditions under which panmixia may exist. Here, we study a species with an unusual, apparently sex-biased pattern of distribution, and test the hypothesis that distribution processes associated with this pattern (for example, congregating at a single dominant spawning site or periodic mixing during reproduction) could lead to panmixia over a large geographic range. Using 13 microsatellite markers, we compared 393 blue hake (Antimora rostrata) from 11 sample sites across a geographic range of over 3000 km, and found no evidence of population structure. We estimated current effective population size and found it to be large ( approximately 15 000) across the sampled area. In addition, we used simulation models to test expectations about demographic correlation among populations and our ability to detect relevant levels of gene flow. All data were consistent with the interpretation of long-range panmixia.Heredity advance online publication, 18 August 2010; doi:10.1038/hdy.2010.108.

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Superinfection of cytoplasmic incompatibility-inducing Wolbachia is not additive in Orius strigicollis (Hemiptera: Anthocoridae).

Publication Date: 2010 Aug 11 PMID: 20700141
Authors: Watanabe, M. - Miura, K. - Hunter, M. S. - Wajnberg, E.
Journal: Heredity

Cytoplasmic incompatibility (CI) allows the intracellular, maternally inherited bacterial symbiont Wolbachia to invade arthropod host populations by inducing infertility in crosses between infected males and uninfected females. The general pattern is consistent with a model of sperm modification, rescued only by egg cytoplasm infected with the same strain of symbiont. The predacious flower bug Orius strigicollis is superinfected with two strains of Wolbachia, wOus1 and wOus2. Typically, superinfections of CI Wolbachia are additive in their effects; superinfected males are incompatible with uninfected and singly infected females. In this study, we created an uninfected line, and lines singly infected with wOus1 and wOus2 by antibiotic treatment. Then, all possible crosses were conducted among the four lines. The results indicated that while wOus2 induces high levels of CI, wOus1 induces very weak or no CI, but can rescue CI caused by wOus2 to a limited extent. Levels of incompatibility in crosses with superinfected males did not show the expected pattern. In particular, superinfected males caused extremely weak CI when mated with either singly infected or uninfected females. An analysis of symbiont densities showed that wOus1 densities were significantly higher than wOus2 densities in superinfected males, and wOus2 densities were lower, but not significantly, in superinfected relative to singly infected males. These data lend qualified support for the hypothesis that wOus1 interferes with the ability of wOus2 to cause CI by suppressing wOus2 densities. To our knowledge, this is the first clear case of non-additive CI in a natural superinfection.Heredity advance online publication, 11 August 2010; doi:10.1038/hdy.2010.100.

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Segregating variation for temperature-dependent sex determination in a lizard.

Publication Date: 2010 Aug 11 PMID: 20700140
Authors: Rhen, T. - Schroeder, A. - Sakata, J. T. - Huang, V. - Crews, D.
Journal: Heredity

Temperature-dependent sex determination (TSD) was first reported in 1966 in an African lizard. It has since been shown that TSD occurs in some fish, several lizards, tuataras, numerous turtles and all crocodilians. Extreme temperatures can also cause sex reversal in several amphibians and lizards with genotypic sex determination. Research in TSD species indicates that estrogen signaling is important for ovary development and that orthologs of mammalian genes have a function in gonad differentiation. Nevertheless, the mechanism that actually transduces temperature into a biological signal for ovary versus testis development is not known in any species. Classical genetics could be used to identify the loci underlying TSD, but only if there is segregating variation for TSD. Here, we use the 'animal model' to analyze inheritance of sexual phenotype in a 13-generation pedigree of captive leopard geckos, Eublepharis macularius, a TSD reptile. We directly show genetic variance and genotype-by-temperature interactions for sex determination. Additive genetic variation was significant at a temperature that produces a female-biased sex ratio (30 degrees C), but not at a temperature that produces a male-biased sex ratio (32.5 degrees C). Conversely, dominance variance was significant at the male-biased temperature (32.5 degrees C), but not at the female-biased temperature (30 degrees C). Non-genetic maternal effects on sex determination were negligible in comparison with additive genetic variance, dominance variance and the primary effect of temperature. These data show for the first time that there is segregating variation for TSD in a reptile and consequently that a quantitative trait locus analysis would be practicable for identifying the genes underlying TSD.Heredity advance online publication, 11 August 2010; doi:10.1038/hdy.2010.102.

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Genetic basis of sexual dimorphism in the threespine stickleback Gasterosteus aculeatus.

Publication Date: 2010 Aug 11 PMID: 20700139
Authors: Leinonen, T. - Cano, J. M. - Merila, J.
Journal: Heredity

Sexual dimorphism (SD) in morphological, behavioural and physiological features is common, but the genetics of SD in the wild has seldom been studied in detail. We investigated the genetic basis of SD in morphological traits of threespine stickleback (Gasterosteus aculeatus) by conducting a large breeding experiment with fish from an ancestral marine population that acts as a source of morphological variation. We also examined the patterns of SD in a set of 38 wild populations from different habitats to investigate the relationship between the genetic architecture of SD of the marine ancestral population in relation to variation within and among natural populations. The results show that genetic architecture in terms of heritabilities, additive genetic variances and covariances (as well as correlations) is very similar in the two sexes in spite of the fact that many of the traits express significant SD. Furthermore, population differences in threespine stickleback body shape and armour SD appear to have evolved despite constraints imposed by genetic architecture. This implies that constraints for the evolution of SD imposed by strong genetic correlations are not as severe and absolute as commonly thought.Heredity advance online publication, 11 August 2010; doi:10.1038/hdy.2010.104.

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Hidden variation mapped.

Publication Date: 2010 Aug 4 PMID: 20683485
Authors: Duveau, F. - Felix, M. A.
Journal: Heredity

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The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure.

Publication Date: 2010 Aug 4 PMID: 20683484
Authors: Kalinowski, S. T.
Journal: Heredity

One of the primary goals of population genetics is to succinctly describe genetic relationships among populations, and the computer program STRUCTURE is one of the most frequently used tools for doing so. The mathematical model used by STRUCTURE was designed to sort individuals into Hardy-Weinberg populations, but the program is also frequently used to group individuals from a large number of populations into a small number of clusters that are supposed to represent the main genetic divisions within species. In this study, I used computer simulations to examine how well STRUCTURE accomplishes this latter task. Simulations of populations that had a simple hierarchical history of fragmentation showed that when there were relatively long divergence times within evolutionary lineages, the clusters created by STRUCTURE were frequently not consistent with the evolutionary history of the populations. These difficulties can be attributed to forcing STRUCTURE to place individuals into too few clusters. Simulations also showed that the clusters produced by STRUCTURE can be strongly influenced by variation in sample size. In some circumstances, STRUCTURE simply put all of the individuals from the largest sample in the same cluster. A reanalysis of human population structure suggests that the problems I identified with STRUCTURE in simulations may have obscured relationships among human populations-particularly genetic similarity between Europeans and some African populations.Heredity advance online publication, 4 August 2010; doi:10.1038/hdy.2010.95.

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Analysis of plant diversity with retrotransposon-based molecular markers.

Publication Date: 2010 Aug 4 PMID: 20683483
Authors: Kalendar, R. - Flavell, A. J. - Ellis, T. H. - Sjakste, T. - Moisy, C. - Schulman, A. H.
Journal: Heredity

Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants.Heredity advance online publication, 4 August 2010; doi:10.1038/hdy.2010.93.

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Power and false-positive rate in QTL detection with near-isogenic line libraries.

Publication Date: 2010 Aug 4 PMID: 20683482
Authors: Falke, K. C. - Frisch, M.
Journal: Heredity

Libraries of near-isogenic lines (NILs) were used for quantitative trait locus (QTL) detection in model species and economically important crops. The experimental design and genetic architecture of the considered traits determine the statistical properties of QTL detection. The objectives of our simulation study were to (i) investigate the population sizes required to develop NIL libraries in barley and maize, (ii) compare NIL libraries with nonoverlapping and overlapping donor segments and (iii) study the number of QTLs and the size of their effects with respect to the power and the false-positive rate of QTL detection. In barley, the development of NIL libraries with target segment lengths of 10 c and marker distances of 5 cM was possible using a BC(3)S(2) backcrossing scheme and population sizes of 140. In maize, population sizes larger than 200 were required. Selection for the recipient parent genome at markers flanking the target segments with distances between 5 and 10 cM was required for an efficient control of the false-positive rate. NIL libraries with nonoverlapping donor chromosome segments had a greater power of QTL detection and a smaller false-positive rate than libraries with overlapping segments. Major genes explaining 30% of the genotypic difference between the donor and recipient were successfully detected even with low heritabilities of 0.5, whereas for minor genes explaining 5 !or 10%, high heritabilities of 0.8 or 0.9 were required. The presented results can assist geneticists and breeders in the efficient development of NIL libraries for QTL detection.Heredity advance online publication, 4 August 2010; doi:10.1038/hdy.2010.87.

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Are dogs genetically special?

Publication Date: 2010 Aug 4 PMID: 20683481
Authors: Hedrick, P. W. - Andersson, L.
Journal: Heredity

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Statistical properties of QTL linkage mapping in biparental genetic populations.

Publication Date: 2010 Sep PMID: 20461101
Authors: Li, H. - Hearne, S. - Banziger, M. - Li, Z. - Wang, J.
Journal: Heredity

Quantitative trait gene or locus (QTL) mapping is routinely used in genetic analysis of complex traits. Especially in practical breeding programs, questions remain such as how large a population and what level of marker density are needed to detect QTLs that are useful to breeders, and how likely it is that the target QTL will be detected with the data set in hand. Some answers can be found in studies on conventional interval mapping (IM). However, it is not clear whether the conclusions obtained from IM are the same as those obtained using other methods. Inclusive composite interval mapping (ICIM) is a useful step forward that highlights the importance of model selection and interval testing in QTL linkage mapping. In this study, we investigate the statistical properties of ICIM compared with IM through simulation. Results indicate that IM is less responsive to marker density and population size (PS). The increase in marker density helps ICIM identify independent QTLs explaining >5% of phenotypic variance. When PS is >200, ICIM achieves unbiased estimations of QTL position and effect. For smaller PS, there is a tendency for the QTL to be located toward the center of the chromosome, with its effect overestimated. The use of dense markers makes linked QTL isolated by empty marker intervals and thus improves mapping efficiency. However, only large-sized populations can take advantage of densely distributed markers. These findings are different from those previously found in IM, indicating great improvements with ICIM.

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Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication.

Publication Date: 2010 Sep PMID: 20179735
Authors: Li, J. - Yang, H. - Li, J. R. - Li, H. P. - Ning, T. - Pan, X. R. - Shi, P. - Zhang, Y. P.
Journal: Heredity

Black coat colour is common in Chinese indigenous domestic pigs, but not among their wild ancestors, and it is thus presumed to be a 'domestication trait.' To determine whether artificial interference contributes to morphological diversification, we examined nucleotide variation from 157 Chinese domestic pigs and 40 wild boars in the melanocortin receptor 1 (MC1R) gene, which has a key role in the coat pigmentation of Sus scrofa. Compared with a pseudogene GPIP, our results showed that the joint effects of demography and selection have resulted in markedly low genetic diversity of MC1R in Chinese domestic pigs. Coalescent simulation and selection tests further suggest that the fixation of two non-synonymous substitutions associated with black colour is the result of artificial selection. In contrast, a much higher genetic diversity and only a single non-synonymous substitution were found among the wild boars, suggesting a strong functional constraint. Moreover, our conclusion is consistent with the preference for black colour in the ancient Chinese sacrificial culture. This case provides an interesting example of a molecular evaluation of artificial livestock selection and its associated cultural impact in ancient China.

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Expression quantitative trait loci analysis of genes in porcine muscle by quantitative real-time RT-PCR compared to microarray data.

Publication Date: 2010 Sep PMID: 20145673
Authors: Ponsuksili, S. - Murani, E. - Phatsara, C. - Schwerin, M. - Schellander, K. - Wimmers, K.
Journal: Heredity

Genetic analysis of transcriptional profiling is a promising approach for identifying biological pathways and dissecting the genetics of complex traits. Here, we report on expression quantitative trait loci (eQTL) that were estimated from the quantitative real-time RT-PCR data of 276 F(2) animals and compared with eQTL identified using 74 microarrays. In total, 13 genes were selected that showed trait-dependent expression in microarray experiments and exhibited 21 eQTL. Real-time RT-PCR and microarray data revealed seven cis eQTL in total, of which one was only detected by real-time RT-PCR, one was only detected by microarray analysis, three were consistently found in overlapping intervals and two were in neighbouring intervals on the same chromosome; whereas no trans eQTL was confirmed. We demonstrate that cis regulation is a stable characteristic of individual transcripts. Consequently, a global microarray eQTL analysis of a limited number of samples can be used for exploring functional and regulatory gene networks and scanning for cis eQTL, whereas the subsequent analysis of a subset of likely cis-regulated genes by real-time RT-PCR in a larger number of samples is relevant to narrow down a QTL region by targeting these positional candidate genes. In fact, when modelling SNPs of six genes as fixed effects in the eQTL analysis, eQTL peaks were shifted downwards, experimentally confirming the impact of the respective polymorphic genes, although these SNPs were not located in the regulatory sequence and these shifts occur as a result of linkage disequilibrium in the F(2) population.

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Genetic basis of incidence and period length of circadian rhythm for locomotor activity in populations of a seed beetle.

Publication Date: 2010 Sep PMID: 20145671
Authors: Harano, T. - Miyatake, T.
Journal: Heredity

Circadian rhythms are ubiquitous in a wide variety of organisms, although their genetic variation has been analyzed in only a few species. We found genetic differences in the circadian rhythm of adult locomotor activity among strains of the adzuki bean beetle, Callosobruchus chinensis, which differed in origin and have been maintained in isolation. All beetles in some strains clearly had free-running rhythms in constant darkness whereas most beetles in other strains were arrhythmic. The period of free-running rhythm varied from approximately 19 to 23 h between the strains. F(1) males from reciprocal crosses among strains with different periods of circadian rhythms had circadian periods that were intermediate between their parental strains. Segregation of the circadian rhythm appeared in the F(2) generation. These findings are consistent with the hypothesis that variation in the period length of circadian rhythm is explained by a major autosomal gene with additive effects and no dominance. This hypothesis was supported by the joint scaling test for the free-running period in the F(1) and F(2) generations. We discuss possible causes for genetic variation in circadian rhythm in the C. chinensis strains in terms of random factors and selection.

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Heritable artificial sex chromosomes in medaka: a leap towards real-time observation of sex chromosome evolution.

Publication Date: 2010 Sep PMID: 20145670
Authors: Lawson Handley, L. J.
Journal: Heredity

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Inbred decorated crickets exhibit higher measures of macroparasitic immunity than outbred individuals.

Publication Date: 2010 Sep PMID: 20125187
Authors: Gershman, S. N. - Barnett, C. A. - Pettinger, A. M. - Weddle, C. B. - Hunt, J. - Sakaluk, S. K.
Journal: Heredity

Inbreeding is assumed to have negative effects on fitness, including the reduced ability to withstand immune challenges. We examined the immunological consequences of inbreeding in decorated crickets, Gryllodes sigillatus, by comparing lytic activity, phenoloxidase (PO) activity, and encapsulation ability of crickets from eight inbred lines with that of crickets from the outbred founder population. Surprisingly, crickets from inbred lines had a greater encapsulation ability compared with crickets from the outbred population. We suggest that because inbred crickets have reduced reproductive effort, they may, therefore, have the option of devoting more resources to this form of immunity than outbred individuals. We also found that both inbred and outbred females had higher immunity than males in PO activity and implant darkness. This result supports the hypothesis that females should devote more effort to somatic maintenance and immunity than males. PO activity and implant darkness were heritable in both males and females, but lytic activity was only heritable in females. Males and females differed in the heritability of, and genetic correlations among, immune traits, suggesting that differences in selective pressures on males and females may have resulted in a sexual conflict over optimal immune trait values.

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Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds.

Publication Date: 2010 Sep PMID: 20104236
Authors: Axelsson, E. - Albrechtsen, A. - van, A. P. - Li, L. - Megens, H. J. - Vereijken, A. L. - Crooijmans, R. P. - Groenen, M. A. - Ellegren, H. - Willerslev, E. - Nielsen, R.
Journal: Heredity

As all four meiotic products give rise to sperm in males, female meiosis result in a single egg in most eukaryotes. Any genetic element with the potential to influence chromosome segregation, so that it is preferentially included in the egg, should therefore gain a transmission advantage; a process termed female meiotic drive. We are aware of two chromosomal components, centromeres and telomeres, which share the potential to influence chromosome movement during meioses and make the following predictions based on the presence of female meiotic drive: (1) centromere-binding proteins should experience rapid evolution as a result of a conflict between driving centromeres and the rest of the genome; and (2) segregation patterns should be skewed near centromeres and telomeres. To test these predictions, we first analyze the molecular evolution of seven centromere-binding proteins in nine divergent bird species. We find strong evidence for positive selection in two genes, lending support to the genomic conflict hypothesis. Then, to directly test for the presence of segregation distortion, we also investigate the transmission of approximately 9000 single-nucleotide polymorphisms in 197 chicken families. By simulating fair Mendelian meioses, we locate chromosomal regions with statistically significant transmission ratio distortion. One region is located near the centromere on chromosome 1 and a second region is located near the telomere on the p-arm of chromosome 1. Although these observations do not provide conclusive evidence in favour of the meiotic drive/genome conflict hypothesis, they do lend support to the hypothesis that centromeres and telomeres drive during female meioses in chicken.

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Heritable artificial sex chromosomes in the medaka, Oryzias latipes.

Publication Date: 2010 Sep PMID: 19997127
Authors: Otake, H. - Masuyama, H. - Mashima, Y. - Shinomiya, A. - Myosho, T. - Nagahama, Y. - Matsuda, M. - Hamaguchi, S. - Sakaizumi, M.
Journal: Heredity

Chromosomal sex determination is widely used by vertebrates, however, only two genes have been identified as master sex-determining genes: SRY/Sry in mammals and DMY in the teleost medaka. Transfer of both genes into genetically female (XX) individuals can induce male development. However, transgenic strains have not been established in both cases because of infertility of the transgenic founders in mammals and low germline transmission rates in medaka. In this study, we used a BAC clone containing DMY in a 117 kb genomic region and two types of fluorescent marker to establish two DMY-transgenic medaka strains. In these strains, exogenous DMY is completely linked to a male phenotype and early gonadal development is not different from that of the wild-type strain. Sex-linkage analysis showed that the exogenous DMY was located on linkage group (LG) 23 in one strain and on LG 5 in the other strain, whereas the sex chromosome in medaka is on LG 1. Real-time PCR analysis indicated that these strains have multiple copies of DMY and higher DMY expression levels than the wild-type strain. These results showed that LGs 23 and 5 function as sex chromosomes in the two strains, respectively. This is not only the first example of the artificial generation of heritable sex chromosomes in vertebrates but also the first evidence showing plasticity of homomorphic sex chromosomes. This plasticity appears to be a characteristic of lower vertebrates and the underlying cause of frequent sex chromosome switching, recently reported in several fish and frog species.

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Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm.

Publication Date: 2010 Sep PMID: 19953121
Authors: Bassene, J. B. - Froelicher, Y. - Dubois, C. - Ferrer, R. M. - Navarro, L. - Ollitrault, P. - Ancillo, G.
Journal: Heredity

Polyploid plants often produce new phenotypes, exceeding the range of variability existing in the diploid gene pool. Several hundred citrus allotetraploid hybrids have been created by somatic hybridization. These genotypes are interesting models to study the immediate effects of allopolyploidization on the regulation of gene expression. Here, we report genome-wide gene expression analysis in fruit pulp of a Citrus interspecific somatic allotetraploid between C. reticulata cv 'Willowleaf mandarin'+C. limon cv 'Eureka lemon', using a Citrus 20K cDNA microarray. Around 4% transcriptome divergence was observed between the two parental species, and 212 and 160 genes were more highly expressed in C. reticulata and C. limon, respectively. Differential expression of certain genes was confirmed by quantitative real-time RT-PCR. A global downregulation of the allotetraploid hybrid transcriptome was observed, as compared with a theoretical mid parent, for the genes displaying interspecific expression divergence between C. reticulata and C. limon. The genes underexpressed in mandarin, as compared with lemon, were also systematically repressed in the allotetraploid. When genes were overexpressed in C. reticulata compared with C. limon, the distribution of allotetraploid gene expression was far more balanced. Cluster analysis on the basis of gene expression clearly indicated the hybrid was much closer to C. reticulata than to C. limon. These results suggest there is a global dominance of the mandarin transcriptome, in consistence with our previous studies on aromatic compounds and proteomics. Interspecific differentiation of gene expression and non-additive gene regulation involved various biological pathways and different cellular components.

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The susceptibility of Atlantic salmon fry to freshwater infectious pancreatic necrosis is largely explained by a major QTL.

Publication Date: 2010 Sep PMID: 19935825
Authors: Houston, R. D. - Haley, C. S. - Hamilton, A. - Guy, D. R. - Mota-Velasco, J. C. - Gheyas, A. A. - Tinch, A. E. - Taggart, J. B. - Bron, J. E. - Starkey, W. G. - McAndrew, B. J. - Verner-Jeffreys, D. W. - Paley, R. K. - Rimmer, G. S. - Tew, I. J. - Bishop, S. C.
Journal: Heredity

Infectious pancreatic necrosis (IPN) is a viral disease with a significant negative impact on the global aquaculture of Atlantic salmon. IPN outbreaks can occur during specific windows of both the freshwater and seawater stages of the salmon life cycle. Previous research has shown that a proportion of the variation seen in resistance to IPN is because of host genetics, and we have shown that major quantitative trait loci (QTL) affect IPN resistance at the seawater stage of production. In the current study, we completed a large freshwater IPN challenge experiment to allow us to undertake a thorough investigation of the genetic basis of resistance to IPN in salmon fry, with a focus on previously identified QTL regions. The heritability of freshwater IPN resistance was estimated to be 0.26 on the observed scale and 0.55 on the underlying scale. Our results suggest that a single QTL on linkage group 21 explains almost all the genetic variation in IPN mortality under our experimental conditions. A striking contrast in mortality is seen between fry classified as homozygous susceptible versus homozygous resistant, with QTL-resistant fish showing virtually complete resistance to IPN mortality. The findings highlight the importance of the major QTL in the genetic regulation of IPN resistance across distinct physiological lifecycle stages, environmental conditions and viral isolates. These results have clear scientific and practical implications for the control of IPN.

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