Heredity

Association genetics in Pinus taeda L. II. Carbon isotope discrimination.

Publication Date: 2008 May 14 PMID: 18478029
Authors: Gonzalez-Martinez, S. C. - Huber, D. - Ersoz, E. - Davis, J. M. - Neale, D. B.
Journal: Heredity

Dissection of complex traits that influence fitness is not only a central topic in evolutionary research but can also assist breeding practices for economically important plant species, such as loblolly pine (Pinus taeda L). In this study, 46 single nucleotide polymorphisms (SNPs) from 41 disease and abiotic stress-inducible genes were tested for their genetic association with carbon isotope discrimination (CID), a time-integrated trait measure of stomatal conductance. A family-based approach to detect genotype/phenotype genetic association was developed for the first time in plants by applying the quantitative transmission disequilibrium test on an association population of 961 clones from 61 families (adopted from previous breeding programs) evaluated for phenotypic expression of CID at two sites. Two particularly promising candidates for their genetic effects on CID are: dhn-1, involved in stabilization of cell structures, and lp5-like, a glycine rich protein putatively related to cell wall reinforcement proteins, both of which were shown in previous studies to be water-deficit inducible. Moreover, association in lp5-like involves a nonsynonymous mutation in linkage disequilibrium with two other nonsynonymous polymorphisms that could, by acting together, enhance overall phenotypic effects. This study highlights the complexity of dissecting CID traits and provides insights for designing second-generation association studies based on candidate gene approaches in forest trees.Heredity advance online publication, 14 May 2008; doi:10.1038/hdy.2008.21.

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Molecular genetics: Trees' genes and traits link up.

Publication Date: 2008 May 14 PMID: 18478028
Authors: Heinze, B.
Journal: Heredity

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An integrated approach to the characterization of two autochthonous lentil (Lens culinaris) landraces of Molise (south-central Italy).

Publication Date: 2008 May 14 PMID: 18478027
Authors: Scippa, G. S. - Trupiano, D. - Rocco, M. - Viscosi, V. - Di Michele, M. - D'Andrea, A. - Chiatante, D.
Journal: Heredity

Plant biodiversity must be safeguarded because it constitutes a resource of genes that may be used, for instance, in breeding programs. Lentil (Lens culinaris Medik.) is one of the most ancient crops of the Mediterranean region. Extensive differentiation of L. culinaris over millennia has resulted in a myriad of different landraces. However, in more recent times many landraces have disappeared consequent to environmental and socioeconomic changes. To promote the survival of endangered lentil landraces, we have investigated the genetic relationship between two ancient landrace cultivated in Capracotta and Conca Casale (Molise, south-central Italy) and widely spread commercial varieties using an integrated approach consisting of studies at morphological, DNA and protein level. Seeds of these two landraces were collected from local farmers and conserved in the Molise germoplasm bank. The two local landraces were well differentiated from each other, and the Conca Casale landrace was separated from the commercial varieties at morphological, protein and DNA level. The Capracotta landrace, was well separated from the commercial varieties, except Castelluccio di Norcia, at DNA level showing a more complex and heterogeneous segregation at morphological and biochemical level. The correlation between morphological, DNA and protein data, illustrates that proteomics is a powerful tool with which to complement the analysis of biodiversity in ecotypes of a single plant species and to identify physiological and/or environmental markers.Heredity advance online publication, 14 May 2008; doi:10.1038/hdy.2008.39.

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Detecting recent speciation events: the case of the finless porpoise (genus Neophocaena).

Publication Date: 2008 May 14 PMID: 18478026
Authors: Wang, J. Y. - Frasier, T. R. - Yang, S. C. - White, B. N.
Journal: Heredity

Recent speciation events provide important insights into the understanding and conservation of Earth's biodiversity, representing recent adaptations to a changing environment and an important source of future evolutionary potential. However, the most frequently applied criterion for molecular-based speciation investigations, that of reciprocal monophyly of mitochondrial sequences, overlooks recent speciation events where insufficient time has passed for fixed molecular differences to develop between putative species. Two morphologically distinguishable forms of finless porpoise (genus Neophocaena) exist in sympatry in the strait of Taiwan, however the taxonomic relationship of these different forms is controversial. To test the hypothesis that the two forms represent different species, a study was conducted based on morphological characters and microsatellite and mitochondrial markers. The data suggest that the two forms are highly differentiated in terms of both morphology and genetic characteristics, despite being sympatric, and therefore represent different species as defined by the biological species concept. Moreover, the two forms appear to have been reproductively isolated since sharing a common ancestor prior to the last major glaciation event approximately 18 000 years ago. However, this represents an insufficient amount of time for reciprocal monophyly to have developed, and thus previous studies based on this criterion have overlooked this speciation event and resulted in incorrect taxonomic classification of these forms.Heredity advance online publication, 14 May 2008; doi:10.1038/hdy.2008.40.

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Population structure of flounder (Platichthys flesus) in the Baltic Sea: differences among demersal and pelagic spawners.

Publication Date: 2008 May 7 PMID: 18461089
Authors: Florin, A. B. - Hoglund, J.
Journal: Heredity

We found significant population structure and isolation by distance among samples of flounder (Platichthys flesus) in the Baltic, Kattegat and Skagerrak seas using microsatellite genetic markers. This pattern was almost entirely due to a difference between flounder that have demersal spawning in the northern Baltic, as compared to pelagic spawners in the southern Baltic and on the west coast of Sweden. Among demersal spawners we found neither genetic differentiation nor any isolation by distance among sampling sites. We speculate that demersal flounder are descendants of a population that colonized the Baltic previous to pelagic spawners. The demersal flounder may thus have had longer time to adapt to the low salinity in the Baltic, and accordingly display egg characteristics that make it possible to reproduce at the low salinity levels in the northern Baltic. Among pelagic spawners significant isolation by distance was detected. Pelagic spawners have previously been shown to display clinal variation in egg size, which allows them to float also at the moderate salinity levels up to the region north of the island Bornholm. Management units for harvesting should ideally be based on true biological populations, and for the commercially important flounder up to 15 different management stocks in the Baltic have been suggested. We could not find a population genetic foundation for such a high number of management units, and our data suggest three management units: the northern Baltic (demersal populations), southern Baltic with the Oresund straits and the most northwestern sampling sites (Skagerrak, Kattegat and North Sea).Heredity advance online publication, 7 May 2008; doi:10.1038/hdy.2008.22.

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Mapping epistatic quantitative trait loci underlying endosperm traits using all markers on the entire genome in a random hybridization design.

Publication Date: 2008 May 7 PMID: 18461088
Authors: He, X. H. - Zhang, Y. M.
Journal: Heredity

Triploid endosperm is of great economic importance owing to its nutritious quality. Mapping endosperm trait loci (ETL) can provide an efficient way to genetically improve grain quality. However, most triploid ETL mapping methods do not produce unbiased estimates of the two dominant effects of ETL. A random hybridization design is an alternative method that may be used to overcome this problem. However, epistasis has an important role in the dissection of genetic architecture for complex traits. In this study, therefore, an attempt was made to map epistatic ETL (eETL) under a triploid genetic model of endosperm traits in a random hybridization design. The endosperm trait means of random hybrid lines, together with known marker genotype information from their corresponding parental F(2) plants, were used to estimate, efficiently and without bias, the positions and all of the effects of eETL using a penalized maximum likelihood method. The method proposed in this article was verified by a series of Monte Carlo simulation experiments. Results from the simulated studies show that the proposed method provides accurate estimates of eETL parameters with a low false-positive rate and a relatively short running time. This new method enables us to map triploid eETL in the same way as diploid quantitative traits.Heredity advance online publication, 7 May 2008; doi:10.1038/hdy.2008.23.

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The mariner transposable element in natural populations of Drosophila simulans.

Publication Date: 2008 May 7 PMID: 18461087
Authors: Picot, S. - Wallau, G. L. - Loreto, E. L. - Heredia, F. O. - Hua-Van, A. - Capy, P.
Journal: Heredity

In cosmopolitan species, geographical variations in copy number and/or level of transposition activity have been observed for several transposable elements (TEs). Environment, history and population structure can contribute to such variation in ways that are difficult to tease apart. For the mariner element, previous studies of the geographic variation of its somatic activity in natural populations of Drosophila simulans have shown contradictory results (latitudinal clines of divergent orientations or no apparent structure). To try and resolve these inconsistencies, we gathered all available data on the mariner somatic activity of worldwide natural populations. This includes previously published results by different groups and also new data. The correlations between the level of activity and several geoclimatic factors were tested. Although no general effect of temperature was found, a relationship with the invasion history was detected. It was also shown that recent invasive populations have a higher level of activity than the putative ancestral ones. Our results strongly suggest that variability of the mariner somatic activity among natural populations of D. simulans is mainly due to populational and historical factors probably related to the recent world colonization of this species. Indeed, this activity is correlated to the main route out of Africa (the Nile route) and the recent colonization of continents such as Australia and South America.Heredity advance online publication, 7 May 2008; doi:10.1038/hdy.2008.27.

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The effects of contemporary processes in maintaining the genetic structure of western song sparrows (Melospiza melodia).

Publication Date: 2008 May 7 PMID: 18461086
Authors: Pruett, C. L. - Arcese, P. - Chan, Y. L. - Wilson, A. G. - Patten, M. A. - Keller, L. F. - Winker, K.
Journal: Heredity

Historic events and contemporary processes work in concert to create and maintain geographically partitioned variation and are instrumental in the generation of biodiversity. We sought to gain a better understanding of how contemporary processes such as movement and isolation influence the genetic structure of widely distributed vagile species such as birds. Song sparrows (Melospiza melodia) in western North America provide a natural system for examining the genetics of populations that have different patterns of geographic isolation and migratory behavior. We examined the population genetics of 576 song sparrows from 23 populations using seven microsatellite loci to assess genetic differentiation among populations and to estimate the effects of drift and immigration (gene flow) on each population. Sedentary, isolated populations were characterized by low levels of immigration and high levels of genetic drift, whereas those populations less isolated displayed signals of high gene flow and little differentiation from other populations. Contemporary dispersal rates from migratory populations, estimated by assignment test, were higher and occurred over larger distances than dispersal from sedentary populations but were also probably too low to counter the effects of drift in most populations. We suggest that geographic isolation and limited gene flow facilitated by migratory behavior are responsible for maintaining observed levels of differentiation among Pacific coastal song sparrow populations.Heredity advance online publication, 7 May 2008; doi:10.1038/hdy.2008.31.

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Quantitative trait loci determining autogeny and body size in the Asian tiger mosquito (Aedes albopictus).

Publication Date: 2008 May 7 PMID: 18461085
Authors: Mori, A. - Romero-Severson, J. - Black, W. C. 4th - Severson, D. W.
Journal: Heredity

The majority of mosquito species require a blood meal to stimulate vitellogenesis and subsequent oviposition (anautogeny), but some autogenous individuals complete their first ovarian cycle without a blood meal. Autogeny may be facultative or obligatory. In this study, we selected for an autogenous strain in the Asian tiger mosquito Aedes albopictus and examined an F(1) intercross population for quantitative trait loci (QTL) determining the autogeny trait as well as wing length as a proxy for body size. Using composite interval mapping, we identified four QTL for each trait and observed considerable overlap in genome positions between each QTL for autogeny (follicle size) and wing length. Most QTL were minor in magnitude, individually explaining <10% of the phenotypic variation. Alleles from the autogenous parent generally showed a dominance or overdominance effect on both phenotypes. Strong genetic and phenotypic correlations indicate that autogeny and wing length are determined by up to four clusters of tightly linked genes or the potential pleiotropic effects of single genes. Although females from the autogenous strain produced approximately fivefold more eggs following a blood meal than through autogeny, we suggest that the maintenance of alleles for autogeny in natural populations is likely due to balancing selection. Autogeny should be favored under conditions of limited host availability for blood feeding or increased defensive behavior by the host and adequate larval nutrition. Correlation between autogeny and body size may reflect an increased ability for larger females to accumulate sufficient nutrient reserves to support oogenesis without the requirement for a blood meal.Heredity advance online publication, 7 May 2008; doi:10.1038/hdy.2008.32.

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Adaptive responses of independent traits to the same environmental gradient in the intertidal snail Bembicium vittatum.

Publication Date: 2008 May 7 PMID: 18461084
Authors: Johnson, M. S. - Black, R.
Journal: Heredity

The snail Bembicium vittatum occupies a wide range of intertidal habitats in the Houtman Abrolhos Islands, Western Australia. Allozyme variation reflects patterns of connectivity, which are independent of local habitat. In contrast, heritable differences in shell shape among 83 shore sites vary with habitat, indicating local adaptation. Here we examine dimorphisms of colour and spotting of the shell in the same populations, as a test of consistency and complexity of patterns of local adaptation. Within populations, the frequency of spotted shells is higher in dark shells. Despite this association, spatial variations of colour and spotting are only weakly correlated. As predicted for traits associated with local adaptation, subdivision is greater for colour, spotting and shape than for allozymes. Colour and shape are associated with local habitat, such that populations on vertical shores have higher frequencies of dark and relatively flatter shells than those on gently sloping shores. These associations are repeatable between three separate groups of islands. Spotting shows a weaker, but significant association with the same gradient. Although shape does not differ between colour morphs within populations, the proportion of dark shells is strongly associated with shape. Thus, the independent shell traits are apparently adapted to a common, biologically significant gradient, even though the adaptive mechanisms probably differ for colour and shape. The parallel variations of independent traits highlight both the complexity of local adaptation and the potential to reveal evolutionarily significant environmental contrasts by examining adaptively relevant traits.Heredity advance online publication, 7 May 2008; doi:10.1038/hdy.2008.33.

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Array-based high-throughput DNA markers for crop improvement.

Publication Date: 2008 May 7 PMID: 18461083
Authors: Gupta, P. K. - Rustgi, S. - Mir, R. R.
Journal: Heredity

The last two decades have witnessed a remarkable activity in the development and use of molecular markers both in animal and plant systems. This activity started with low-throughput restriction fragment length polymorphisms and culminated in recent years with single nucleotide polymorphisms (SNPs), which are abundant and uniformly distributed. Although the latter became the markers of choice for many, their discovery needed previous sequence information. However, with the availability of microarrays, SNP platforms have been developed, which allow genotyping of thousands of markers in parallel. Besides SNPs, some other novel marker systems, including single feature polymorphisms, diversity array technology and restriction site-associated DNA markers, have also been developed, where array-based assays have been utilized to provide for the desired ultra-high throughput and low cost. These microarray-based markers are the markers of choice for the future and are already being used for construction of high-density maps, quantitative trait loci (QTL) mapping (including expression QTLs) and genetic diversity analysis with a limited expense in terms of time and money. In this study, we briefly describe the characteristics of these array-based marker systems and review the work that has already been done involving development and use of these markers, not only in simple eukaryotes like yeast, but also in a variety of seed plants with simple or complex genomes.Heredity advance online publication, 7 May 2008; doi:10.1038/hdy.2008.35.

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Temporal changes in allele frequencies but stable genetic diversity over the past 40 years in the Irish Sea population of thornback ray, Raja clavata.

Publication Date: 2008 May 7 PMID: 18461082
Authors: Chevolot, M. - Ellis, J. R. - Rijnsdorp, A. D. - Stam, W. T. - Olsen, J. L.
Journal: Heredity

Rays and skates are an unavoidable part of the by-catch in demersal fisheries. Over the past 40 years, the thornback ray (Raja clavata) has decreased in numbers and even disappeared in some areas, leading to concerns about genetic risk. For this reason, the effective population size (N(e)), the migration rate (m) and temporal changes in the genetic diversity were estimated for the population of thornback rays in the Irish Sea and Bristol Channel. Using genotyped, archived and contemporary samples (1965 and 2003-2004), N(e) was estimated at 283 individuals (95% CI=145-857), m at 0.1 (95% CI=0.03-0.25) and the N(e)/N ratio between 9 x 10(-5) and 6 x 10(-4). Although these results must be treated with caution, due to the small sample sizes, this is the first attempt to estimate N(e) in an elasmobranch species. The low N(e)/N ratio suggests that relatively few individuals contribute to the next generation. The combined effect of sex bias, inbreeding, fluctuations in population size and, perhaps most important, the variance in reproductive success may explain the low N(e)/N ratio. In addition, the relatively high gene flow between Irish Sea population and other source populations is likely to have had an impact on our estimate, which may be more relevant at the metapopulation scale. No significant loss of genetic diversity was found over the 40-year timeframe and long-term maintenance of the genetic diversity could be due to gene flow.Heredity advance online publication, 7 May 2008; doi:10.1038/hdy.2008.36.

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Are lice good proxies for host history? A comparative analysis of the Australian magpie, Gymnorhina tibicen, and two species of feather louse.

Publication Date: 2008 May 7 PMID: 18461081
Authors: Toon, A. - Hughes, J. M.
Journal: Heredity

Parasites have been recently advocated as useful proxies for unravelling a complex evolutionary history of a host. In the present study, two species of feather lice, Brueelia semiannulata and Philopterus sp. were analysed for mitochondrial variation and compared to mitochondrial and nuclear variation in their host, the Australian magpie Gymnorhina tibicen. Phylogenies constructed using maximum likelihood methods revealed geographic structuring for both species of feather lice and host. Our genetic analysis shows concordance of east-west structure between host and Philopterus sp. indicating that it is an informative proxy for host history. Analysis of the Philopterus sp. phylogeny also suggested cryptic structuring within the eastern magpie population that had not been previously realized through genetic analysis of the host. B. semiannulata however, did not show congruent phylogeographic structuring with the host. Rather than showing an east-west split between lineages, the phylogeny of B. semiannulata showed north-south geographic structuring. It is postulated that this incongruence may be due to ecological habitat differences and/or the dispersal ability of B. semiannulata.Heredity advance online publication, 7 May 2008; doi:10.1038/hdy.2008.37.

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The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies.

Publication Date: 2008 May PMID: 18449959
Authors: MacLean, R. C.
Journal: Heredity

First principles of thermodynamics imply that metabolic pathways are faced with a trade-off between the rate and yield of ATP production. Simple evolutionary models argue that this trade-off generates a fundamental social conflict in microbial populations: average fitness in a population is highest if all individuals exploit common resources efficiently, but individual reproductive rate is maximized by consuming common resources at the highest possible rate, a scenario known as the tragedy of the commons. In this paper, I review studies that have addressed two key questions: What is the evidence that the rate-yield trade-off is an evolutionary constraint on metabolic pathways? And, if so, what determines evolutionary outcome of the conflicts generated by this trade-off? Comparative studies and microbial experiments provide evidence that the rate-yield trade-off is an evolutionary constraint that is driven by thermodynamic constraints that are common to all metabolic pathways and pathway-specific constraints that reflect the evolutionary history of populations. Microbial selection experiments show that the evolutionary consequences of this trade-off depend on both kin selection and biochemical constraints. In well-mixed populations with low relatedness, genotypes with rapid and efficient metabolism can coexist as a result of negative frequency-dependent selection generated by density-dependent biochemical costs of rapid metabolism. Kin selection can promote the maintenance of efficient metabolism in structured populations with high relatedness by ensuring that genotypes with efficient metabolic pathways gain an indirect fitness benefit from their competitive restraint. I conclude by suggesting avenues for future research and by discussing the broader implications of this work for microbial social evolution.

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A simple method for calculating the statistical power for detecting a QTL located in a marker interval.

Publication Date: 2008 Apr 30 PMID: 18446184
Authors: Hu, Z. - Xu, S.
Journal: Heredity

We developed a simple method for calculating the statistical power for detecting a QTL located in an interval flanked by two markers. The statistical method for QTL detection is assumed to be the Haley and Knott's simple regression method of interval mapping. This method allows us to answer one of the fundamental questions in designing a QTL mapping experiment: What is the minimum marker density required to detect a QTL explaining a certain heritable proportion of the phenotypic variance (denoted by h(2)) with a power gamma under a Type I error alpha in an F(2) or other mating designs with a sample size n? Computing the statistical power only requires the ability to evaluate a non-central F-distribution function and the inverse function of this distribution.Heredity advance online publication, 30 April 2008; doi:10.1038/hdy.2008.25.

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Cross-species replication of a resistin mRNA QTL, but not QTLs for circulating levels of resistin, in human and baboon.

Publication Date: 2008 Apr 30 PMID: 18446183
Authors: Tejero, M. E. - Voruganti, V. S. - Proffitt, J. M. - Curran, J. E. - Goring, H. H. - Johnson, M. P. - Dyer, T. D. - Jowett, J. B. - Collier, G. R. - Moses, E. K. - Maccluer, J. W. - Mahaney, M. C. - Blangero, J. - Comuzzie, A. G. - Cole, S. A.
Journal: Heredity

Resistin has been associated with inflammation and risk for cardiovascular disease. We previously reported evidence of a QTL on chromosome 19p13 affecting the abundance of resistin (RETN) mRNA in the omental adipose tissue of baboons (L0D score 3.8). In this study, whole genome transcription levels were assessed in human lymphocyte samples from 1240 adults participating in the San Antonio Family Heart Study, using the Sentrix Human-6 Expression Beadchip. Lymphocytes were surveyed, as it has been proposed that their expression levels may reflect those in harder to ascertain tissues, such as adipose tissue, that are thought to be more directly relevant to disease procesn was conducted to detect loci affecting RETN mRNA levels. We obtained significant evidence for a QTL influencing the RETN expression (LOD score 10.7) on chromosome 19p. This region is orthologous/homologous to the region previously localized on baboon chromosome 19. The strongest positional candidate gene in this region is the structural gene for resistin, itself. We also found evidence for a QTL influencing resistin protein levels (LOD score 5.3) on chromosome 14q. This differs from our previously reported QTL on chromosome 18 in baboons. The different QTLs for circulating protein suggests that post-translational processing and turnover may be influenced by different or multiple genes in baboons and humans. The parallel findings of a cis-eQTL for RETN mRNA in baboon omental tissue and human lymphocytes lends support to the strategy of using lymphocyte gene expression levels as a surrogate for gene expression levels in other tissues.Heredity advance online publication, 30 April 2008; doi:10.1038/hdy.2008.28.

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Revealing cryptic spatial patterns in genetic variability by a new multivariate method.

Publication Date: 2008 Apr 30 PMID: 18446182
Authors: Jombart, T. - Devillard, S. - Dufour, A. B. - Pontier, D.
Journal: Heredity

Increasing attention is being devoted to taking landscape information into account in genetic studies. Among landscape variables, space is often considered as one of the most important. To reveal spatial patterns, a statistical method should be spatially explicit, that is, it should directly take spatial information into account as a component of the adjusted model or of the optimized criterion. In this paper we propose a new spatially explicit multivariate method, spatial principal component analysis (sPCA), to investigate the spatial pattern of genetic variability using allelic frequency data of individuals or populations. This analysis does not require data to meet Hardy-Weinberg expectations or linkage equilibrium to exist between loci. The sPCA yields scores summarizing both the genetic variability and the spatial structure among individuals (or populations). Global structures (patches, clines and intermediates) are disentangled from local ones (strong genetic differences between neighbors) and from random noise. Two statistical tests are proposed to detect the existence of both types of patterns. As an illustration, the results of principal component analysis (PCA) and sPCA are compared using simulated datasets and real georeferenced microsatellite data of Scandinavian brown bear individuals (Ursus arctos). sPCA performed better than PCA to reveal spatial genetic patterns. The proposed methodology is implemented in the adegenet package of the free software R.Heredity advance online publication, 30 April 2008; doi:10.1038/hdy.2008.34.

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Experimental evolution.

Publication Date: 2008 May PMID: 18431410
Authors: Bell, G.
Journal: Heredity

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Revisiting horizontal transfer of transposable elements in Drosophila.

Publication Date: 2008 Apr 23 PMID: 18431403
Authors: Loreto, E. L. - Carareto, C. M. - Capy, P.
Journal: Heredity

Horizontal transfer (HT), defined as the transfer of genetic material between species, is considered to be an essential step in the 'life cycle' of transposable elements. We present a broad overview of suspected cases of HT of transposable elements in Drosophila. Hundred-one putative events of HT have been proposed in Drosophila for 21 different elements (5.0% refer to non-long terminal repeat (LTR) retrotransposons, 42.6% to LTR retrotransposons and 52.4% to DNA transposons). We discuss the methods used to infer HT, their limits and the putative vectors of transposable elements. We outline all the alternative hypotheses and ask how we can be almost certain that phylogenetic inconsistencies are due to HT.Heredity advance online publication, 23 April 2008; doi:10.1038/sj.hdy.6801094.

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Variation in mate preference across a house mouse hybrid zone.

Publication Date: 2008 Apr 16 PMID: 18414506
Authors: Ganem, G. - Litel, C. - Lenormand, T.
Journal: Heredity

Reproductive character displacement is known to occur at the borders of a secondary contact zone between the two European subspecies of the house mouse (in Jutland, Denmark), where selection against hybridization occurs. This study assessed patterns of mate preference in naturally occurring hybrids of the two subspecies. Mate odour choice was investigated in male and female mice sampled across the hybrid zone. Odour samples comprised urine (from the opposite sex to the test animal) obtained from populations geographically distant from the hybrid zone. Urine is known to carry subspecies recognition signals. The behavioural results changed across the hybrid zone, and were analysed by a model of clinal variation. This behavioural cline was compared with the allozyme cline across the same hybrid zone. Males on both sides of the hybrid zone showed an assortative preference, which shifted significantly and abruptly approximately 10 km from the genetic centre of the hybrid zone on the Mus musculus musculus side. Directional preference was not detected in females, which could relate to variation in sexual receptivity. Our model indicates that the peculiar pattern of male preference could involve several genes and be characterized by mild to strong epistasis favouring the expression of M. m. domesticus-like preference over a large portion of the hybrid zone. This study may provide the first picture of the genetic determination of mate preference in a mammal.Heredity advance online publication, 16 April 2008; doi:10.1038/hdy.2008.20.

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Satellite DNA in insects: a review.

Publication Date: 2008 Apr 16 PMID: 18414505
Authors: Palomeque, T. - Lorite, P.
Journal: Heredity

The study of insect satellite DNAs (satDNAs) indicates the evolutionary conservation of certain features despite their sequence heterogeneity. Such features can include total length, monomer length, motifs, particular regions and/or secondary and tertiary structures. satDNAs may act as protein-binding sites, structural domains or sites for epigenetic modifications. The selective constraints in the evolution of satDNAs may be due to the satDNA sequence interaction with specific proteins important in heterochromatin formation and possible a role in controlling gene expression. The transcription of satDNA has been described in vertebrates, invertebrates and plants. In insects, differential satDNA expression has been observed in different cells, developmental stages, sex and caste of the individuals. These transcription differences may suggest their involvement in gene-regulation processes. In addition, the satDNA or its transcripts appear to be involved in heterochromatin formation and in chromatin-elimination processes. The importance of transposable elements to insect satDNA is shown by their presence as a constituent of satDNA in several species of insects (including possible active elements). In addition, they may be involved in the formation of centromeres and telomeres and in the homogenization and expansion of satDNA.Heredity advance online publication, 16 April 2008; doi:10.1038/hdy.2008.24.

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Fine mapping of E(kp)-1, a locus associated with silkworm (Bombyx mori) proleg development.

Publication Date: 2008 May PMID: 18364737
Authors: Xiang, H. - Li, M. - Yang, F. - Guo, Q. - Zhan, S. - Lin, H. - Miao, X. - Huang, Y.
Journal: Heredity

The silkworm homeotic mutant E(kp) has a pair of rudimentary abdominal legs, called prolegs, in its A2 segment. This phenotype is caused by a single dominant mutation at the E(kp)-1 locus, which was previously mapped to chromosome 6. To explore the possible association of Hox genes with proleg development in the silkworm, a map-based cloning strategy was used to isolate the E(kp)-1 locus. Five E(kp)-1-linked simple sequence repeat markers on chromosome 6 were used to generate a low-resolution map with a total genetic distance of 39.5 cM. Four additional cleaved amplified polymorphic sequence markers were developed based on the initial map. The closest marker to E(kp)-1 was at a genetic distance of 2.7 cM. A high-resolution genetic map was constructed using nine BC1 segregating populations consisting of 2396 individuals. Recombination suppression was observed in the vicinity of E(kp)-1. Four molecular markers were tightly linked to E(kp)-1, and three were clustered with it. These markers were used to screen a BAC library. A single bacterial artificial chromosome (BAC) clone spanning the E(kp)-1 locus was identified, and E(kp)-1 was delimited to a region less than 220 kb long that included the Hox gene abdominal-A and a non-coding locus, iab-4. These results provide essential information for the isolation of this locus, which may shed light on the mechanism of proleg development in the silkworm and possibly in Lepidoptera.

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Sex-specific crossover patterns in Zebrafish (Danio rerio).

Publication Date: 2008 May PMID: 18322458
Authors: Kochakpour, N. - Moens, P. B.
Journal: Heredity

Some species display intersex variation in their rate of meiotic recombination, where recombination is usually suppressed in the heterogametic sex. Although no heteromorphic sex chromosomes have been detected in zebrafish (Danio rerio), genetic analysis has indicated a lower frequency of recombination in males relative to females. Our study of the meiotic recombination pattern in female zebrafish indicates that adult females have only a few meiotic oocytes that are found in groups in the ventral zone of the ovarian surface. We used antibody staining of human mutL homolog 1 (MLH1) protein to mark the sites of putative chiasmata to seek a physical basis for the pattern of recombination and its relative frequency in both sexes. We report that MLH1 foci are found mostly in distal regions of the synaptonemal complexes (SCs) in males, but tend to be more evenly distributed in females. Our cytological analysis yields a ratio of MLH1 foci per chromosome in males versus females of 1:1.55. This lower level of recombination in males is in general agreement with previously published results from linkage map analysis. However, the similar ratio of MLH1 foci per unit length of SCs in both sexes demonstrates a correlation between SC length and the frequency of recombination rather than a mechanism that suppresses recombination in males. Thus, chiasma interference seems to provide similar expression in males and females in agreement with the situation in humans, where oocytes with longer SCs display a higher level of recombination that is not a consequence of more closely spaced crossovers along the SCs.

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Mitochondrial and nuclear DNA variability in the living fossil Triops cancriformis (Bosc, 1801) (Crustacea, Branchiopoda, Notostraca).

Publication Date: 2008 May PMID: 18285812
Authors: Mantovani, B. - Cesari, M. - Luchetti, A. - Scanabissi, F.
Journal: Heredity

The living fossil Triops cancriformis comprises bisexual (either gonochoric or hermaphroditic) and unisexual populations. Genetic surveys have recently revealed a general trend of low differentiation of 12S and 16S mitochondrial genes. We, therefore, surveyed further mitochondrial (COI gene and control region) and nuclear markers (dinucleotide microsatellites) to assess the genetic variability and to establish any relationship with the different reproductive modes found in European populations. The mitochondrial analyses confirmed the pattern of low variability. Hence, the low mitochondrial genetic variability appears as a common feature of the genus Triops. The microsatellite analysis found that Italian populations are monomorphic or exhibit little polymorphism, while other European samples display a higher degree of polymorphism and private alleles. Spanish, Austrian and Italian populations show patterns of Hardy-Weinberg disequilibrium that could be explained by the mode of reproduction, or by a higher frequency of null alleles in these populations. The low diversity and differentiation among Italian populations lead us to question the Monopolization Hypothesis. One microsatellite locus appears to be sex-linked, with heterozygotes detected only in males and hermaphrodites.

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How multilocus genotypic pattern helps to understand the history of selfing populations: a case study in Medicago truncatula.

Publication Date: 2008 May PMID: 18285811
Authors: Siol, M. - Prosperi, J. M. - Bonnin, I. - Ronfort, J.
Journal: Heredity

The occurrence of populations exhibiting high genetic diversity in predominantly selfing species remains a puzzling question, since under regular selfing genetic diversity is expected to be depleted at a faster rate than under outcrossing. Fine-scale population genetics approaches may help to answer this question. Here we study a natural population of the legume Medicago truncatula in which both the fine-scale spatial structure and the selfing rate are characterized using three different methods. Selfing rate estimates were very high ( approximately 99%) irrespective of the method used. A clear pattern of isolation by distance reflecting small seed dispersal distances was detected. Combining genotypic data over loci, we could define 34 multilocus genotypes. Among those, six highly inbred genotypes (lines) represented more than 75% of the individuals studied and harboured all the allelic variation present in the population. We also detected a large set of multilocus genotypes resembling recombinant inbred lines between the most frequent lines occurring in the population. This finding illustrates the importance of rare recombination in redistributing available allelic diversity into new genotypic combinations. This study shows how multilocus and fine-scale spatial analyses may help to understand the population history of self-fertilizing species, especially to make inferences about the relative role of foundation/migration and recombination events in such populations.

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Gene interactions constrain the course of evolution of phosphine resistance in the lesser grain borer, Rhyzopertha dominica.

Publication Date: 2008 May PMID: 18270533
Authors: Schlipalius, D. I. - Chen, W. - Collins, P. J. - Nguyen, T. - Reilly, P. E. - Ebert, P. R.
Journal: Heredity

Phosphine, a widely used fumigant for the protection of stored grain from insect pests, kills organisms indirectly by inducing oxidative stress. High levels of heritable resistance to phosphine in the insect pest of stored grain, Rhyzopertha dominica have been detected in Asia, Australia and South America. In order to understand the evolution of phosphine resistance and to isolate the responsible genes, we have undertaken genetic linkage analysis of fully sensitive (QRD14), moderately resistant (QRD369) and highly resistant (QRD569) strains of R. dominica collected in Australia. We previously determined that two loci, rph1 and rph2, confer high-level resistance on strain QRD569, which was collected in 1997. We have now confirmed that rph1 is responsible for the moderate resistance of strain QRD369, which was collected in 1990, and is shared with a highly resistant strain from the same geographical region, QRD569. In contrast, rph2 by itself confers only very weak resistance, either as a heterozygote or as a homozygote and was not discovered in the field until weak resistance (probably due to rph1) had become ubiquitous. Thus, high-level resistance against phosphine has evolved via stepwise acquisition of resistance alleles, first at rph1 and thereafter at rph2. The semi-dominance of rph2 together with the synergistic interaction between rph1 and rph2 would have led to rapid selection for homozygosity. A lack of visible fitness cost associated with alleles at either locus suggests that the resistance phenotype will persist in the field.

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Avian mtDNA diversity?: An alternate explanation for low mtDNA diversity in birds: an age-old solution?

Publication Date: 2008 May PMID: 18270532
Authors: Hickey, A. J.
Journal: Heredity

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Patterns in genetic diversity of Trifolium pallescens populations do not reflect chronosequence on alpine glacier forelands.

Publication Date: 2008 May PMID: 18270530
Authors: Raffl, C. - Holderegger, R. - Parson, W. - Erschbamer, B.
Journal: Heredity

How does genetic diversity within populations of plants develop during primary succession on alpine glacier forelands? Theory predicts that pioneer populations are characterized by low genetic diversity due to founder effects and that genetic diversity increases within populations as they mature and recurrent gene flow occurs. However, few genetic studies have so far been carried out on plants on glacier forelands. In this study, we analysed the development of genetic diversity with time for populations of Trifolium pallescens along successional series (chronosequences) on three parallel glacier forelands in the European Alps, using neutral amplified fragment length polymorphism. No general trend in the development of genetic diversity was observed with increasing population age: even pioneer populations harboured substantial genetic diversity. Assignment tests showed that the latter consist of a genetic sub-sample from several source areas, and not just from other populations on the glacier forelands. We also detected some long distances-that is, inter-valley gene flow events. However, gene flow was not spatially unrestricted, as shown by a weak isolation by distance pattern within glacier valleys. The actual patterns of genetic diversity along the chronosequences are a result of the combination of factors, such as gene flow and growth rate, influenced by site- and species-specific attributes.

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Mitochondria and the W chromosome: low variability on the W chromosome in birds is more likely to indicate selection on mitochondrial genes.

Publication Date: 2008 May PMID: 18270529
Authors: Lane, N.
Journal: Heredity

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Experimental evolution of plant RNA viruses.

Publication Date: 2008 May PMID: 18253158
Authors: Elena, S. F. - Agudelo-Romero, P. - Carrasco, P. - Codoner, F. M. - Martin, S. - Torres-Barcelo, C. - Sanjuan, R.
Journal: Heredity

Undoubtedly, viruses represent a major threat faced by human and veterinary medicines and by agronomy. The rapid evolution of viruses enables them to escape from natural immunities and from state-of-the-art antiviral treatments, with new viruses periodically emerging with deadly consequences. Viruses have also become powerful and are increasingly used tools in the field of experimental evolution. A growing body of evidence points that the evolution of viruses is mainly determined by key features such as their compacted genomes, enormous population sizes, and short generation times. In addition, RNA viruses also present large selection coefficients, antagonistic epistasis, and high mutation rates. Most of this knowledge comes from studies that have used either bacteriophages or animal viruses in cell cultures as experimental systems. However, plant viruses provide almost identical advantages for evolutionary studies and, in addition, offer an invaluable tool for studying the interplay between viruses and pluricellular hosts. Without seeking to be exhaustive, here we summarize some peculiarities of plant viruses and review recent experiments that have explored important questions on evolution, such as the role of deleterious mutation and neutrality, the effect of different transmission modes in the evolution of virulence, and the heterogeneous selective constraints imposed by multiple hosts.

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Predicting evolution from genomics: experimental evolution of bacteriophage T7.

Publication Date: 2008 May PMID: 18212807
Authors: Bull, J. J. - Molineux, I. J.
Journal: Heredity

A wealth of molecular biology has been exploited in designing and interpreting experimental evolution studies with bacteriophage T7. The modest size of its genome (40 kb dsDNA) and the ease of making genetic constructs, combined with the many genetic resources for its host (Escherichia coli), have enabled comprehensive and detailed studies of experimental adaptations. In several studies, the genome was specifically altered (gene knockouts, gene replacements, reordering of genetic elements) such that a priori knowledge of genetics and biochemistry of the phage could be used to predict the pathways of compensatory evolution when the modified phage is adapted to recover fitness. In other work, the phage has been adapted to specific environmental conditions chosen to select phenotypic outcomes with a quantitative basis, and the molecular bases of that evolution have been explored. Predicting the outcomes of these adaptations has been challenging. In hindsight, one-third to one-half of the compensatory nucleotide changes observed during the adaptation can be rationalized based on T7 biology. This rationalization usually only applies at the genetic level-a gene product may be known to be involved in the affected pathway, but it usually remains unknown how the observed change affects activity. The progress is encouraging, but the prediction of experimental evolution pathways remains far from complete, and is still sometimes confounded by observation when an adaptation yields a completely unexpected outcome.

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Kin selection and the evolution of virulence.

Publication Date: 2008 May PMID: 18212805
Authors: Buckling, A. - Brockhurst, M. A.
Journal: Heredity

Social interactions between conspecific parasites are partly dependent on the relatedness of interacting parasites (kin selection), which, in turn, is predicted to affect the extent of damage they cause their hosts (virulence). High relatedness is generally assumed to favour less competitive interactions, but the relationship between relatedness and virulence is crucially dependent on the social behaviour in question. Here, we discuss the rather limited body of experimental work that addresses how kin-selected social behaviours affect virulence. First, if prudent use of host resources (a form of cooperation) maximizes the transmission success of the parasite population, decreased relatedness is predicted to result in increased host exploitation and virulence. Experimental support for this well-established theoretical result is surprisingly limited. Second, if parasite within-host growth rate is a positive function of cooperation (that is, when individuals need to donate public goods, such as extracellular enzymes), virulence is predicted to increase with increasing relatedness. The limited studies testing this hypothesis are broadly consistent with this prediction. Finally, there is some empirical evidence supporting theory that suggests that spiteful behaviours are maximized at intermediate degrees of relatedness, which, in turn, leads to minimal virulence because of the reduced growth rate of the infecting population. We highlight the need for further thorough experimentation on the role of kin selection in the evolution of virulence and identify additional biological complexities to these simple frameworks.

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Experimental evolution: experimental evolution and evolvability.

Publication Date: 2008 May PMID: 18212804
Authors: Colegrave, N. - Collins, S.
Journal: Heredity

The suggestion that there are characteristics of living organisms that have evolved because they increase the rate of evolution is controversial and difficult to study. In this review, we examine the role that experimental evolution might play in resolving this issue. We focus on three areas in which experimental evolution has been used previously to examine questions of evolvability; the evolution of mutational supply, the evolution of genetic exchange and the evolution of genetic architecture. In each case, we summarize what studies of experimental evolution have told us so far and speculate on where progress might be made in the future. We show that, while experimental evolution has helped us to begin to understand the evolutionary dynamics of traits that affect evolvability, many interesting questions remain to be answered.

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The spread of a beneficial mutation in experimental bacterial populations: the influence of the environment and genotype on the fixation of rpoS mutations.

Publication Date: 2008 May PMID: 18073783
Authors: Ferenci, T.
Journal: Heredity

The spread of beneficial mutations through populations is at the core of evolutionary change. A long-standing hindrance to understanding mutational sweeps was that beneficial mutations have been slow to be identified, even in commonly studied experimental populations. The lack of information on what constitutes a beneficial mutation has led to many uncertainties about the frequency, fitness benefit and fixation of beneficial mutations. A more complete picture is currently emerging for a limited set of identified mutations in bacterial populations. In turn, this will allow quantitation of several features of mutational sweeps. Most importantly, the 'benefit' of beneficial mutations can now be explained in terms of physiological function and how variations in the environment change the selectability of mutations. Here, the sweep of rpoS mutations in Escherichia coli, in both experimental and natural populations, is described in detail. These studies reveal the subtleties of physiology and regulation that strongly influence the benefit of a mutation and explain differences in sweeps between strains and between various environments.

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