Heredity

Local adaptation within a hybrid species.

Publication Date: 2013 May 22 PMID: 23695379
Authors: Eroukhmanoff, F. - Hermansen, J. S. - Bailey, R. I. - Saether, S. A. - Saetre, G. P.
Journal: Heredity (Edinb)

Ecological divergence among populations may be strongly influenced by their genetic background. For instance, genetic admixture through introgressive hybridization or hybrid speciation is likely to affect the genetic variation and evolvability of phenotypic traits. We studied geographic variation in two beak dimensions and three other phenotypic traits of the Italian sparrow (Passer italiae), a young hybrid species formed through interbreeding between house sparrows (P. domesticus) and Spanish sparrows (P. hispaniolensis). We found that beak morphology was strongly influenced by precipitation regimes and that it appeared to be the target of divergent selection within Italian sparrows. Interestingly, however, the degree of parental genetic contribution in the hybrid species had no effect on phenotypic beak variation. Moreover, beak height divergence may mediate genetic differentiation between populations, consistent with isolation-by-adaptation within this hybrid species. The study illustrates how hybrid species may be relatively unconstrained by their admixed genetic background, allowing them to adapt rapidly to environmental variation.Heredity advance online publication, 22 May 2013; doi:10.1038/hdy.2013.47.

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Mapping of two suppressors of OVATE (sov) loci in tomato.

Publication Date: 2013 May 15 PMID: 23673388
Authors: Rodriguez, G. R. - Kim, H. J. - van der Knaap, E.
Journal: Heredity (Edinb)

Tomato fruit shape varies significantly in the cultivated germplasm. To a large extent, this variation can be explained by four genes including OVATE. While most varieties with the OVATE mutation bear elongated fruits, some accessions carry round fruit, suggesting the existence of suppressors of OVATE in the germplasm. We developed three intraspecific F2 populations with parents that carried the OVATE mutation but differed in fruit shape. We used a bulk segregant analysis approach and genotyped the extreme classes using a high-throughput genotyping platform, the SolCAP Infinium Assay. The analyses revealed segregation at two quantitative trait loci (QTLs), sov1 and sov2. These loci were confirmed by genotyping and QTL analyses of the entire population. More precise location of those loci using progeny testing confirmed that sov1 on chromosome 10 controlled obovoid and elongated shape, whereas sov2 on chromosome 11 controlled mainly elongated fruit shape. Both loci were located in intervals of <2.4 Mb on their respective chromosomes.Heredity advance online publication, 15 May 2013; doi:10.1038/hdy.2013.45.

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The genetic basis of speciation in the Giliopsis lineage of Ipomopsis (Polemoniaceae).

Publication Date: 2013 May 8 PMID: 23652565
Authors: Nakazato, T. - Rieseberg, L. H. - Wood, T. E.
Journal: Heredity (Edinb)

One of the most powerful drivers of speciation in plants is pollinator-mediated disruptive selection, which leads to the divergence of floral traits adapted to the morphology and behavior of different pollinators. Despite the widespread importance of this speciation mechanism, its genetic basis has been explored in only a few groups. Here, we characterize the genetic basis of pollinator-mediated divergence of two species in genus Ipomopsis, I. guttata and I. tenuifolia, using quantitative trait locus (QTL) analyses of floral traits and other variable phenotypes. We detected one to six QTLs per trait, with each QTL generally explaining small to modest amounts of the phenotypic variance of a backcross hybrid population. In contrast, flowering time and anthocyanin abundance (a metric of color variation) were controlled by a few QTLs of relatively large effect. QTLs were strongly clustered within linkage groups, with 26 of 37 QTLs localized to six marker-interval 'hotspots,' all of which harbored pleiotropic QTLs. In contrast to other studies that have examined the genetic basis of pollinator shifts, our results indicate that, in general, mutations of small to modest effect on phenotype were involved. Thus, the evolutionary transition between the distinct pollination modes of I. guttata and I. tenuifolia likely proceeded incrementally, rather than saltationally.Heredity advance online publication, 8 May 2013; doi:10.1038/hdy.2013.41.

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Multigenerational hybridisation and its consequences for maternal effects in Atlantic salmon.

Publication Date: 2013 May 8 PMID: 23652564
Authors: Debes, P. V. - Fraser, D. J. - McBride, M. C. - Hutchings, J. A.
Journal: Heredity (Edinb)

Outbreeding between segregating populations can be important from an evolutionary, conservation and economical-agricultural perspective. Whether and how outbreeding influences maternal effects in wild populations has rarely been studied, despite both the prominent maternal influence on early offspring survival and the known presence of fitness effects resulting from outbreeding in many taxa. We studied several traits during the yolk-feeding stage in multigenerational crosses between a wild and a domesticated Atlantic salmon (Salmo salar) population up to their third-generation hybrid in a common laboratory environment. Using cross-means analysis, we inferred that maternal additive outbreeding effects underlie most offspring traits but that yolk mass also underlies maternal dominant effects. As a consequence of the interplay between additive and dominant maternally controlled traits, offspring from first-generation hybrid mothers expressed an excessive proportion of residual yolk mass, relative to total mass, at the time of first feeding. Their residual yolk mass was 23-97% greater than those of other crosses and 31% more than that predicted by a purely additive model. Offspring additive, epistatic and epistatic offspring-by-maternal outbreeding effects appeared to further modify this largely maternally controlled cross-means pattern, resulting in an increase in offspring size with the percentage of domesticated alleles. Fitness implications remain elusive because of unknown phenotype-by-environment interactions. However, these results suggest how mechanistically co-adapted genetic maternal control on early offspring development can be disrupted by the effects of combining alleles from divergent populations. Complex outbreeding effects at both the maternal and offspring levels make the prediction of hybrid phenotypes difficult.Heredity advance online publication, 8 May 2013; doi:10.1038/hdy.2013.43.

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Antennapedia is involved in the development of thoracic legs and segmentation in the silkworm, Bombyx mori.

Publication Date: 2013 May 8 PMID: 23652563
Authors: Chen, P. - Tong, X. L. - Li, D. D. - Fu, M. Y. - He, S. Z. - Hu, H. - Xiang, Z. H. - Lu, C. - Dai, F. Y.
Journal: Heredity (Edinb)

Homeotic genes, which are associated closely with body patterning of various species, specify segment identity. The Wedge eye-spot (Wes) is a new homeotic mutant located on the sixth linkage group. Homozygous Wes/Wes embryos are lethal and display a pair of antenna-like appendages under the mouthparts as well as fused thoracic segments. These mutants also exhibit a narrower eye-spot at the larval stage compared with the wild type. By positional cloning, we identified the candidate gene of the Wes locus, Bombyx mori Antennapedia (BmAntp). Two BmAntp transcripts were identified in the homozygote of the Wes mutant, including a normal form and an abnormal form with a 1570-bp insertion. Our data showed that the insertion element was a long interspersed nuclear element (LINE)-like transposon that destroyed the original open reading frame of BmAntp. Quantitative RT-PCR analysis showed that the expression levels of normal BmAntp transcripts were increased markedly in the Wes heterozygous larvae compared with the wild type. Furthermore, we performed RNAi of BmAntp and observed fused thoracic segments and defective thoracic legs in the developing embryos. Our results indicated that BmAntp is responsible for the Wes mutant and has an important role in determining the proper development of the thoracic segments. Our identification of a homeotic mutation in the silkworm is an important contribution to our understanding of the regulation of Hox genes at different levels of expression.Heredity advance online publication, 8 May 2013; doi:10.1038/hdy.2013.36.

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Mediation of seed provisioning in the transmission of environmental maternal effects in Maritime pine (Pinus pinaster Aiton).

Publication Date: 2013 May 8 PMID: 23652562
Authors: Zas, R. - Cendan, C. - Sampedro, L.
Journal: Heredity (Edinb)

Although maternal environmental effects are increasingly recognized as an important source of phenotypic variation with relevant impacts in evolutionary processes, their relevance in long-lived plants such as pine trees is largely unknown. Here, we used a powerful sample size and a strong quantitative genetic approach to analyse the sources of variation of early seedling performance and to identify seed mass (SM)-dependent and -independent maternal environmental effects in Maritime pine. We measured SM of 8924 individual seeds collected from 10 genotypes clonally replicated in two environments of contrasting quality (favourable and stressful), and we measured seedling growth rate and biomass allocation to roots and shoots. SM was extremely variable (up to 14-fold) and strongly determined by the maternal environment and the genotype of the mother tree. The favourable maternal environment led to larger cones, larger seeds and reduced SM variability. The maternal environment also determined the offspring phenotype, with seedlings coming from the favourable environment being 35% larger and with greater root/shoot ratio. Transgenerational plasticity appears, thus, to be a relevant source of phenotypic variation in the early performance of this pine species. Seed provisioning explained most of the effect of the maternal environment on seedling total biomass. Environmental maternal effects on seedling biomass allocation were, however, determined through SM-independent mechanisms, suggesting that other epigenetic regulation channels may be involved.Heredity advance online publication, 8 May 2013; doi:10.1038/hdy.2013.44.

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Estimation of effective population size in continuously distributed populations: there goes the neighborhood.

Publication Date: 2013 May 8 PMID: 23652561
Authors: Neel, M. C. - McKelvey, K. - Ryman, N. - Lloyd, M. W. - Short Bull, R. - Allendorf, F. W. - Schwartz, M. K. - Waples, R. S.
Journal: Heredity (Edinb)

Use of genetic methods to estimate effective population size (Ne) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating structure, as envisioned by Wright's concept of neighborhood size (NS), and evaluated performance of a single-sample estimator based on linkage disequilibrium (LD), which provides an estimate of the effective number of parents that produced the sample (Nb). Results illustrate the interacting effects of two phenomena, drift and mixture, that contribute to LD. Samples from areas equal to or smaller than a breeding window produced estimates close to the NS. As the sampling window increased in size to encompass multiple genetic neighborhoods, mixture LD from a two-locus Wahlund effect overwhelmed the reduction in drift LD from incorporating offspring from more parents. As a consequence, never approached the global Ne, even when the geographic scale of sampling was large. Results indicate that caution is needed in applying standard methods for estimating effective size to continuously distributed populations.Heredity advance online publication, 8 May 2013; doi:10.1038/hdy.2013.37.

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Basal metabolic rate can evolve independently of morphological and behavioural traits.

Publication Date: 2013 May 1 PMID: 23632896
Authors: Mathot, K. J. - Martin, K. - Kempenaers, B. - Forstmeier, W.
Journal: Heredity (Edinb)

Quantitative genetic analyses of basal metabolic rate (BMR) can inform us about the evolvability of the trait by providing estimates of heritability, and also of genetic correlations with other traits that may constrain the ability of BMR to respond to selection. Here, we studied a captive population of zebra finches (Taeniopygia guttata) in which selection lines for male courtship rate have been established. We measure BMR in these lines to see whether selection on male sexual activity would change BMR as a potentially correlated trait. We find that the genetic correlation between courtship rate and BMR is practically zero, indicating that the two traits can evolve independently of each other. Interestingly, we find that the heritability of BMR in our population (h2=0.45) is markedly higher than was previously reported for a captive zebra finch population from Norway. A comparison of the two studies shows that additive genetic variance in BMR has been largely depleted in the Norwegian population, especially the genetic variance in BMR that is independent of body mass. In our population, the slope of BMR increase with body mass differs not only between the sexes but also between the six selection lines, which we tentatively attribute to genetic drift and/or founder effects being strong in small populations. Our study therefore highlights two things. First, the evolvability of BMR may be less constrained by genetic correlations and lack of independent genetic variation than previously described. Second, genetic drift in small populations can rapidly lead to different evolvabilities across populations.Heredity advance online publication, 1 May 2013; doi:10.1038/hdy.2013.35.

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Global spread and genetic variants of the two CYP9M10 haplotype forms associated with insecticide resistance in Culex quinquefasciatus Say.

Publication Date: 2013 May 1 PMID: 23632895
Authors: Itokawa, K. - Komagata, O. - Kasai, S. - Kawada, H. - Mwatele, C. - Dida, G. O. - Njenga, S. M. - Mwandawiro, C. - Tomita, T.
Journal: Heredity (Edinb)

Insecticide resistance develops as a genetic factor (allele) conferring lower susceptibility to insecticides proliferates within a target insect population under strong positive selection. Intriguingly, a resistance allele pre-existing in a population often bears a series of further adaptive allelic variants through new mutations. This phenomenon occasionally results in replacement of the predominating resistance allele by fitter new derivatives, and consequently, development of greater resistance at the population level. The overexpression of the cytochrome P450 gene CYP9M10 is associated with pyrethroid resistance in the southern house mosquito Culex quinquefasciatus. Previously, we have found two genealogically related overexpressing CYP9M10 haplotypes, which differ in gene copy number (duplicated and non-duplicated). The duplicated haplotype was derived from the non-duplicated overproducer probably recently. In the present study, we investigated allelic series of CYP9M10 involved in three C. quinquefasciatus laboratory colonies recently collected from three different localities. Duplicated and non-duplicated overproducing haplotypes coexisted in African and Asian colonies indicating a global distribution of both haplotype lineages. The duplicated haplotypes both in the Asian and African colonies were associated with higher expression levels and stronger resistance than non-duplicated overproducing haplotypes. There were slight variation in expression level among the non-duplicated overproducing haplotypes. The nucleotide sequences in coding and upstream regions among members of this group also showed a little diversity. Non-duplicated overproducing haplotypes with relatively higher expression were genealogically closer to the duplicated haplotypes than the other non-duplicated overproducing haplotypes, suggesting multiple cis-acting mutations before duplication.Heredity advance online publication, 1 May 2013; doi:10.1038/hdy.2013.40.

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A sequential coalescent algorithm for chromosomal inversions.

Publication Date: 2013 May 1 PMID: 23632894
Authors: Peischl, S. - Koch, E. - Guerrero, R. F. - Kirkpatrick, M.
Journal: Heredity (Edinb)

Chromosomal inversions are common in natural populations and are believed to be involved in many important evolutionary phenomena, including speciation, the evolution of sex chromosomes and local adaptation. While recent advances in sequencing and genotyping methods are leading to rapidly increasing amounts of genome-wide sequence data that reveal interesting patterns of genetic variation within inverted regions, efficient simulation methods to study these patterns are largely missing. In this work, we extend the sequential Markovian coalescent, an approximation to the coalescent with recombination, to include the effects of polymorphic inversions on patterns of recombination. Results show that our algorithm is fast, memory-efficient and accurate, making it feasible to simulate large inversions in large populations for the first time. The SMC algorithm enables studies of patterns of genetic variation (for example, linkage disequilibria) and tests of hypotheses (using simulation-based approaches) that were previously intractable.Heredity advance online publication, 1 May 2013; doi:10.1038/hdy.2013.38.

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Genetic and host-associated differentiation within Thrips tabaci Lindeman (Thysanoptera: Thripidae) and its links to Tomato spotted wilt virus-vector competence.

Publication Date: 2013 May 1 PMID: 23632893
Authors: Westmore, G. C. - Poke, F. S. - Allen, G. R. - Wilson, C. R.
Journal: Heredity (Edinb)

Of eight thelytokous populations of onion thrips (Thrips tabaci) collected from potato (three populations), onion (four) or Chrysanthemum (one) hosts from various regions of Australia, only those from potato were capable of transmitting Tomato spotted wilt virus (TSWV) in controlled transmission experiments. Genetic differentiation of seven of these eight populations, and nine others not tested for TSWV vector competence, was examined by comparison of the DNA sequences of mitochondrial cytochrome oxidase subunit 1 (COI) gene. All Australian populations of T. tabaci grouped within the European 'L2' clade of Brunner et al. (2004). Within this clade the seven populations from potato, the three from onion, and the four from other hosts (Chrysanthemum, Impatiens, lucerne, blackberry nightshade) clustered as three distinct sub-groupings characterised by source host. Geographical source of thrips populations had no influence on genetic diversity. These results link genetic differentiation of thelytokous T. tabaci to source host and to TSWV vector capacity for the first time.Heredity advance online publication, 1 May 2013; doi:10.1038/hdy.2013.39.

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Genetic architecture underlying morning and evening circadian phenotypes in fruit flies Drosophila melanogaster.

Publication Date: 2013 Apr 24 PMID: 23612693
Authors: Vaze, K. M. - Nikhil, K. L. - Sharma, V. K.
Journal: Heredity (Edinb)

Circadian rhythms are perhaps among the genetically best characterized behaviours. Several mutations with drastic effects on circadian processes have been identified and models developed to explain how clock genes and their products generate self-sustained oscillations. Although natural variations in circadian phenotypes have been studied extensively, the genetic basis of such adaptive variations remains largely unknown. Here we report the results of a preliminary genetic analysis of adaptive divergence of circadian phenotypes in populations of fruit flies Drosophila melanogaster. Two sets of populations, 'early' and 'late', were created in a long-term laboratory selection for morning and evening emergence, with four independent replicates each. Over the course of approximately 55 generations, the early flies evolved increased morning emergence and a shorter circadian period, whereas late flies evolved increased evening emergence and longer period. To examine the genetic basis of circadian phenotypes, we set up crosses between early and late flies, and monitored emergence and activity/rest rhythms in the F1, backcrossed and F2 progeny. Our analysis suggests that the genetic basis of divergent circadian phenotypes in early and late stocks is primarily autosomal. Line-cross analysis revealed that additive and non-additive genetic effects contribute to the divergence of circadian phenotypes in early and late flies.Heredity advance online publication, 24 April 2013; doi:10.1038/hdy.2013.28.

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An improvement on the maximum likelihood reconstruction of pedigrees from marker data.

Publication Date: 2013 Apr 24 PMID: 23612692
Authors: Wang, J.
Journal: Heredity (Edinb)

Many methods have been proposed to reconstruct the pedigree of a sample of individuals from their multilocus marker genotypes. These methods, like those in other fields of statistical inferences, may suffer from both type I (falsely related) and type II (falsely unrelated) errors. In sibship reconstruction, type I errors come from the spurious fusion of two or more small sibships into a single sibship, and type II errors originate from the spurious splitting of a large sibship into two or more small sibships. In this study I investigate the tendencies of both types of errors made by the likelihood methods in sibship reconstruction, using both analytical and simulation approaches. I propose an improvement on the likelihood methods to reduce sibship splitting, and thus type II errors by downscaling the number of inferred siblings sharing the same genotype at a locus. Simulations are then conducted to compare the accuracy of the original and improved likelihood methods in sibship reconstruction of a large sample of individuals in full-sib families of the same small size, the same large size and highly variable sizes, using a variable number of loci with a variable number of alleles per locus. The methods were also applied to the analysis of a salmon data set. I show that my scaling scheme prevents effectively the splitting of large sibships, and reduces type II errors greatly with little increase in type I errors. As a result, it improves the overall accuracy of sibship assignments, except when sibships are expected to be uniformly small or marker information is unrealistically scarce.Heredity advance online publication, 24 April 2013; doi:10.1038/hdy.2013.34.

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The evolution of quantitative traits in complex environments.

Publication Date: 2013 Apr 24 PMID: 23612691
Authors: Anderson, J. T. - Wagner, M. R. - Rushworth, C. A. - Prasad, K. V. - Mitchell-Olds, T.
Journal: Heredity (Edinb)

Species inhabit complex environments and respond to selection imposed by numerous abiotic and biotic conditions that vary in both space and time. Environmental heterogeneity strongly influences trait evolution and patterns of adaptive population differentiation. For example, heterogeneity can favor local adaptation, or can promote the evolution of plastic genotypes that alter their phenotypes based on the conditions they encounter. Different abiotic and biotic agents of selection can act synergistically to either accelerate or constrain trait evolution. The environmental context has profound effects on quantitative genetic parameters. For instance, heritabilities measured in controlled conditions often exceed those measured in the field; thus, laboratory experiments could overestimate the potential for a population to respond to selection. Nevertheless, most studies of the genetic basis of ecologically relevant traits are conducted in simplified laboratory environments, which do not reflect the complexity of nature. Here, we advocate for manipulative field experiments in the native ranges of plant species that differ in mating system, life-history strategy and growth form. Field studies are vital to evaluate the roles of disparate agents of selection, to elucidate the targets of selection and to develop a nuanced perspective on the evolution of quantitative traits. Quantitative genetics field studies will also shed light on the potential for natural populations to adapt to novel climates in highly fragmented landscapes. Drawing from our experience with the ecological model system Boechera (Brassicaceae), we discuss advancements possible through dedicated field studies, highlight future research directions and examine the challenges associated with field studies.Heredity advance online publication, 24 April 2013; doi:10.1038/hdy.2013.33.

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Lineage-specific mapping of quantitative trait loci.

Publication Date: 2013 Apr 24 PMID: 23612690
Authors: Chen, C. - Ritland, K.
Journal: Heredity (Edinb)

We present an approach for quantitative trait locus (QTL) mapping, termed as 'lineage-specific QTL mapping', for inferring allelic changes of QTL evolution along with branches in a phylogeny. We describe and analyze the simplest case: by adding a third taxon into the normal procedure of QTL mapping between pairs of taxa, such inferences can be made along lineages to a presumed common ancestor. Although comparisons of QTL maps among species can identify homology of QTLs by apparent co-location, lineage-specific mapping of QTL can classify homology into (1) orthology (shared origin of QTL) versus (2) paralogy (independent origin of QTL within resolution of map distance). In this light, we present a graphical method that identifies six modes of QTL evolution in a three taxon comparison. We then apply our model to map lineage-specific QTLs for inbreeding among three taxa of yellow monkey-flower: Mimulus guttatus and two inbreeders M. platycalyx and M. micranthus, but critically assuming outcrossing was the ancestral state. The two most common modes of homology across traits were orthologous (shared ancestry of mutation for QTL alleles). The outbreeder M. guttatus had the fewest lineage-specific QTL, in accordance with the presumed ancestry of outbreeding. Extensions of lineage-specific QTL mapping to other types of data and crosses, and to inference of ancestral QTL state, are discussed.Heredity advance online publication, 24 April 2013; doi:10.1038/hdy.2013.24.

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Godfrey M Hewitt (1940-2013): highlights in Heredity from a career in evolutionary genetics.

Publication Date: 2013 May PMID: 23591550
Authors: Nichols, R. A. - Butlin, R. K. - Bruford, M. W.
Journal: Heredity (Edinb)

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Mapping shape quantitative trait loci using a radius-centroid-contour model.

Publication Date: 2013 Jun PMID: 23572125
Authors: Fu, G. - Bo, W. - Pang, X. - Wang, Z. - Chen, L. - Song, Y. - Zhang, Z. - Li, J. - Wu, R.
Journal: Heredity (Edinb)

As the consequence of complex interactions between different parts of an organ, shape can be used as a predictor of structural-functional relationships implicated in changing environments. Despite such importance, however, it is no surprise that little is known about the genetic detail involved in shape variation, because no approach is currently available for mapping quantitative trait loci (QTLs) that control shape. Here, we address this problem by developing a statistical model that integrates the principle of shape analysis into a mixture-model-based likelihood formulated for QTL mapping. One state-of-the-art approach for shape analysis is to identify and analyze the polar coordinates of anatomical landmarks on a shape measured in terms of radii from the centroid to the contour at regular intervals. A procrustes analysis is used to align shapes to filter out position, scale and rotation effects on shape variation. To the end, the accurate and quantitative representation of a shape is produced with aligned radius-centroid-contour (RCC) curves, that is, a function of radial angle at the centroid. The high dimensionality of the RCC data, crucial for a comprehensive description of the geometric feature of a shape, is reduced by principal component (PC) analysis, and the resulting PC axes are treated as phenotypic traits, allowing specific QTLs for global and local shape variability to be mapped, respectively. The usefulness and utilization of the new model for shape mapping in practice are validated by analyzing a mapping data collected from a natural population of poplar, Populus szechuanica var tibetica, and identifying several QTLs for leaf shape in this species. The model provides a powerful tool to compute which genes determine biological shape in plants, animals and humans.

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On the origin of sweet potato (Ipomoea batatas (L.) Lam.) genetic diversity in New Guinea, a secondary centre of diversity.

Publication Date: 2013 Jun PMID: 23531982
Authors: Roullier, C. - Kambouo, R. - Paofa, J. - McKey, D. - Lebot, V.
Journal: Heredity (Edinb)

New Guinea is considered the most important secondary centre of diversity for sweet potato (Ipomoea batatas). We analysed nuclear and chloroplast genetic diversity of 417 New Guinea sweet potato landraces, representing agro-morphological diversity collected throughout the island, and compared this diversity with that in tropical America. The molecular data reveal moderate diversity across all accessions analysed, lower than that found in tropical America. Nuclear data confirm previous results, suggesting that New Guinea landraces are principally derived from the Northern neotropical genepool (Camote and Batata lines, from the Caribbean and Central America). However, chloroplast data suggest that South American clones (early Kumara line clones or, more probably, later reintroductions) were also introduced into New Guinea and then recombined with existing genotypes. The frequency distribution of pairwise distances between New Guinea landraces suggests that sexual reproduction, rather than somaclonal variation, has played a predominant role in the diversification of sweet potato. The frequent incorporation of plants issued from true seed by farmers, and the geographical and cultural barriers constraining crop diffusion in this topographically and linguistically heterogeneous island, has led to the accumulation of an impressive number of variants. As the diversification of sweet potato in New Guinea is primarily the result of farmers' management of the reproductive biology of their crop, we argue that on-farm conservation programmes that implement distribution of core samples (clones representing the useful diversity of the species) and promote on-farm selection of locally adapted variants may allow local communities to fashion relatively autonomous strategies for coping with ongoing global change.

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Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes.

Publication Date: 2013 Jun PMID: 23531981
Authors: Hvilsom, C. - Frandsen, P. - Borsting, C. - Carlsen, F. - Salle, B. - Simonsen, B. T. - Siegismund, H. R.
Journal: Heredity (Edinb)

Despite ample focus on this endangered species, conservation planning for chimpanzees residing outside Africa has proven a challenge because of the lack of ancestry information. Here, we analysed the largest number of chimpanzee samples to date, examining microsatellites in >100 chimpanzees from the range of the species in Africa, and 20% of the European zoo population. We applied the knowledge about subspecies differentiation throughout equatorial Africa to assign origin to chimpanzees in the largest conservation management programme globally. A total of 63% of the genotyped chimpanzees from the European zoos could be assigned to one of the recognized subspecies. The majority being of West African origin (40%) will help consolidate the current breeding programme for this subspecies and the identification of individuals belonging to the two other subspecies so far found in European zoos can form the basis for breeding programmes for these. Individuals of various degree of mixed ancestry made up 37% of the genotyped European zoo population and thus highlight the need for appropriate management programmes guided by genetic analysis to preserve maximum genetic diversity and reduce hybridization among subspecies.

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Genome-wide association and regional heritability mapping to identify loci underlying variation in nematode resistance and body weight in Scottish Blackface lambs.

Publication Date: 2013 May PMID: 23512009
Authors: Riggio, V. - Matika, O. - Pong-Wong, R. - Stear, M. J. - Bishop, S. C.
Journal: Heredity (Edinb)

The genetic architecture underlying nematode resistance and body weight in Blackface lambs was evaluated comparing genome-wide association (GWA) and regional heritability mapping (RHM) approaches. The traits analysed were faecal egg count (FEC) and immunoglobulin A activity against third-stage larvae from Teladorsagia circumcincta, as indicators of nematode resistance, and body weight in a population of 752 Scottish Blackface lambs, genotyped with the 50k single-nucleotide polymorphism (SNP) chip. FEC for both Nematodirus and Strongyles nematodes (excluding Nematodirus), as well as body weight were collected at approximately 16, 20 and 24 weeks of age. In addition, a weighted average animal effect was estimated for both FEC and body weight traits. After quality control, 44 388 SNPs were available for the GWA analysis and 42 841 for the RHM, which utilises only mapped SNPs. The same fixed effects were used in both analyses: sex, year, management group, litter size and age of dam, with day of birth as covariate. Some genomic regions of interest for both nematode resistance and body weight traits were identified, using both GWA and RHM approaches. For both methods, strong evidence for association was found on chromosome 14 for Nematodirus average animal effect, chromosome 6 for Strongyles FEC at 16 weeks and chromosome 6 for body weight at 16 weeks. Across the entire data set, RHM identified more regions reaching the suggestive level than GWA, suggesting that RHM is capable of capturing some of the variation not detected by GWA analyses.

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Molecular evolution and the latitudinal biodiversity gradient.

Publication Date: 2013 Jun PMID: 23486082
Authors: Dowle, E. J. - Morgan-Richards, M. - Trewick, S. A.
Journal: Heredity (Edinb)

Species density is higher in the tropics (low latitude) than in temperate regions (high latitude) resulting in a latitudinal biodiversity gradient (LBG). The LBG must be generated by differential rates of speciation and/or extinction and/or immigration among regions, but the role of each of these processes is still unclear. Recent studies examining differences in rates of molecular evolution have inferred a direct link between rate of molecular evolution and rate of speciation, and postulated these as important drivers of the LBG. Here we review the molecular genetic evidence and examine the factors that might be responsible for differences in rates of molecular evolution. Critical to this is the directionality of the relationship between speciation rates and rates of molecular evolution.

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Edge effects enhance selfing and seed harvesting efforts in the insect-pollinated Neotropical tree Copaifera langsdorffii (Fabaceae).

Publication Date: 2013 Jun PMID: 23486081
Authors: Tarazi, R. - Sebbenn, A. M. - Kageyama, P. Y. - Vencovsky, R.
Journal: Heredity (Edinb)

Edge effects may affect the mating system of tropical tree species and reduce the genetic diversity and variance effective size of collected seeds at the boundaries of forest fragments because of a reduction in the density of reproductive trees, neighbour size and changes in the behaviour of pollinators. Here, edge effects on the genetic diversity, mating system and pollen pool of the insect-pollinated Neotropical tree Copaifera langsdorffii were investigated using eight microsatellite loci. Open-pollinated seeds were collected from 17 seed trees within continuous savannah woodland (SW) and were compared with seeds from 11 seed trees at the edge of the savannah remnant. Seeds collected from the SW had significantly higher heterozygosity levels (Ho=0.780; He=0.831) than seeds from the edge (Ho=0.702; He=0.800). The multilocus outcrossing rate was significantly higher in the SW (tm=0.859) than in the edge (tm=0.759). Pollen pool differentiation was significant, however, it did not differ between the SW (=0.105) and the edge (=0.135). The variance effective size within the progenies was significantly higher in the SW (Ne=2.65) than at the edge (Ne=2.30). The number of seed trees to retain the reference variance effective size of 500 was 189 at the SW and 217 at the edge. Therefore, it is preferable that seed harvesting for conservation and environmental restoration strategies be conducted in the SW, where genetic diversity and variance effective size within progenies are higher.

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Diversity and abundance of the abnormal chromosome 10 meiotic drive complex in Zea mays.

Publication Date: 2013 Jun PMID: 23443059
Authors: Kanizay, L. B. - Pyhajarvi, T. - Lowry, E. G. - Hufford, M. B. - Peterson, D. G. - Ross-Ibarra, J. - Dawe, R. K.
Journal: Heredity (Edinb)

Maize Abnormal chromosome 10 (Ab10) contains a classic meiotic drive system that exploits the asymmetry of meiosis to preferentially transmit itself and other chromosomes containing specialized heterochromatic regions called knobs. The structure and diversity of the Ab10 meiotic drive haplotype is poorly understood. We developed a bacterial artificial chromosome (BAC) library from an Ab10 line and used the data to develop sequence-based markers, focusing on the proximal portion of the haplotype that shows partial homology to normal chromosome 10. These molecular and additional cytological data demonstrate that two previously identified Ab10 variants (Ab10-I and Ab10-II) share a common origin. Dominant PCR markers were used with fluorescence in situ hybridization to assay 160 diverse teosinte and maize landrace populations from across the Americas, resulting in the identification of a previously unknown but prevalent form of Ab10 (Ab10-III). We find that Ab10 occurs in at least 75% of teosinte populations at a mean frequency of 15%. Ab10 was also found in 13% of the maize landraces, but does not appear to be fixed in any wild or cultivated population. Quantitative analyses suggest that the abundance and distribution of Ab10 is governed by a complex combination of intrinsic fitness effects as well as extrinsic environmental variability.

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SYMPHONY, an information-theoretic method for gene-gene and gene-environment interaction analysis of disease syndromes.

Publication Date: 2013 Jun PMID: 23423149
Authors: Knights, J. - Yang, J. - Chanda, P. - Zhang, A. - Ramanathan, M.
Journal: Heredity (Edinb)

We develop an information-theoretic method for gene-gene (GGI) and gene-environmental interactions (GEI) analysis of syndromes, defined as a phenotype vector comprising multiple quantitative traits (QTs). The K-way interaction information (KWII), an information-theoretic metric, was derived for multivariate normal distributed phenotype vectors. The utility of the method was challenged with three simulated data sets, the Genetic Association Workshop-15 (GAW15) rheumatoid arthritis data set, a high-density lipoprotein (HDL) and atherosclerosis data set from a mouse QT locus study, and the 1000 Genomes data. The dependence of the KWII on effect size, minor allele frequency, linkage disequilibrium, population stratification/admixture, as well as the power and computational time requirements of the novel method was systematically assessed in simulation studies. In these studies, phenotype vectors containing two and three constituent multivariate normally distributed QTs were used and the KWII was found to be effective at detecting GEI associated with the phenotype. High KWII values were observed for variables and variable combinations associated with the syndrome phenotype compared with uninformative variables not associated with the phenotype. The KWII values for the phenotype-associated combinations increased monotonically with increasing effect size values. The KWII also exhibited utility in simulations with non-linear dependence between the constituent QTs. Analysis of the HDL and atherosclerosis data set indicated that the simultaneous analysis of both phenotypes identified interactions not detected in the analysis of the individual traits. The information-theoretic approach may be useful for non-parametric analysis of GGI and GEI of complex syndromes.

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Inferring population size changes with sequence and SNP data: lessons from human bottlenecks.

Publication Date: 2013 May PMID: 23423148
Authors: Gattepaille, L. M. - Jakobsson, M. - Blum, M. G.
Journal: Heredity (Edinb)

Reconstructing historical variation of population size from sequence and single-nucleotide polymorphism (SNP) data is valuable for understanding the evolutionary history of species. Changes in the population size of humans have been thoroughly investigated, and we review different methodologies of demographic reconstruction, specifically focusing on human bottlenecks. In addition to the classical approaches based on the site-frequency spectrum (SFS) or based on linkage disequilibrium, we also review more recent approaches that utilize atypical shared genomic fragments, such as identical by descent or homozygous segments between or within individuals. Compared with methods based on the SFS, these methods are well suited for detecting recent bottlenecks. In general, all these various methods suffer from bias and dependencies on confounding factors such as population structure or poor specification of the mutational and recombination processes, which can affect the demographic reconstruction. With the exception of SFS-based methods, the effects of confounding factors on the inference methods remain poorly investigated. We conclude that an important step when investigating population size changes rests on validating the demographic model by investigating to what extent the fitted demographic model can reproduce the main features of the polymorphism data.

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Comparative genomics of chemosensory protein genes reveals rapid evolution and positive selection in ant-specific duplicates.

Publication Date: 2013 Jun PMID: 23403962
Authors: Kulmuni, J. - Wurm, Y. - Pamilo, P.
Journal: Heredity (Edinb)

Gene duplications can have a major role in adaptation, and gene families underlying chemosensation are particularly interesting due to their essential role in chemical recognition of mates, predators and food resources. Social insects add yet another dimension to the study of chemosensory genomics, as the key components of their social life rely on chemical communication. Still, chemosensory gene families are little studied in social insects. Here we annotated chemosensory protein (CSP) genes from seven ant genomes and studied their evolution. The number of functional CSP genes ranges from 11 to 21 depending on species, and the estimated rates of gene birth and death indicate high turnover of genes. Ant CSP genes include seven conservative orthologous groups present in all the ants, and a group of genes that has expanded independently in different ant lineages. Interestingly, the expanded group of genes has a differing mode of evolution from the orthologous groups. The expanded group shows rapid evolution as indicated by a high dN/dS (nonsynonymous to synonymous changes) ratio, several sites under positive selection and many pseudogenes, whereas the genes in the seven orthologous groups evolve slowly under purifying selection and include only one pseudogene. These results show that adaptive changes have played a role in ant CSP evolution. The expanded group of ant-specific genes is phylogenetically close to a conservative orthologous group CSP7, which includes genes known to be involved in ant nestmate recognition, raising an interesting possibility that the expanded CSPs function in ant chemical communication.

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Geographical parthenogenesis and population genetic structure in the alpine species Ranunculus kuepferi (Ranunculaceae).

Publication Date: 2013 Jun PMID: 23403961
Authors: Cosendai, A. C. - Wagner, J. - Ladinig, U. - Rosche, C. - Horandl, E.
Journal: Heredity (Edinb)

Geographical parthenogenesis describes the enigmatic phenomenon that asexual organisms have larger distribution areas than their sexual relatives, especially in previously glaciated areas. Classical models suggest temporary advantages to asexuality in colonization scenarios because of uniparental reproduction and clonality. We analyzed population genetic structure and self-fertility of the plant species Ranunculus kuepferi on 59 populations from the whole distribution area (European Alps, Apennines and Corsica). Amplified fragment length polymorphisms (AFLPs) and five microsatellite loci revealed individual genotypes for all populations and mostly insignificant differences between diploid sexuals and tetraploid apomicts in all measures of genetic diversity. Low frequencies of private AFLP fragments/simple sequence repeat alleles, and character incompatibility analyses suggest that facultative recombination explains best the unexpectedly high genotypic diversity of apomicts. STRUCTURE analyses using AFLPs revealed a higher number of partitions and a stronger geographical subdivision for diploids than for tetraploids, which contradicts expectations of standard gene flow models, but indicates a reduction of genetic structure in asexuals. Apomictic populations exhibited high admixture near the sexual area, but appeared rather uniform in remote areas. Bagging experiments and analyses of pollen tube growth confirmed self-fertility for pollen-dependent apomicts, but self-sterility for diploid sexuals. Facultative apomixis combines advantages of both modes of reproduction: uniparental reproduction allows for rapid colonization of remote areas, whereas facultative sexuality and polyploidy maintains genetic diversity within apomictic populations. The density dependence of outcrossing limits range expansions of sexual populations.

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Gene flow and gene flux shape evolutionary patterns of variation in Drosophila subobscura.

Publication Date: 2013 Jun PMID: 23321709
Authors: Pegueroles, C. - Aquadro, C. F. - Mestres, F. - Pascual, M.
Journal: Heredity (Edinb)

Gene flow (defined as allele exchange between populations) and gene flux (defined as allele exchange during meiosis in heterokaryotypic females) are important factors decreasing genetic differentiation between populations and inversions. Many chromosomal inversions are under strong selection and their role in recombination reduction enhances the maintenance of their genetic distinctness. Here we analyze levels and patterns of nucleotide diversity, selection and demographic history, using 37 individuals of Drosophila subobscura from Mount Parnes (Greece) and Barcelona (Spain). Our sampling focused on two frequent O-chromosome arrangements that differ by two overlapping inversions (OST and O3+4), which are differentially adapted to the environment as observed by their opposing latitudinal clines in inversion frequencies. The six analyzed genes (Pif1A, Abi, Sqd, Yrt, Atpalpha and Fmr1) were selected for their location across the O-chromosome and their implication in thermal adaptation. Despite the extensive gene flux detected outside the inverted region, significant genetic differentiation between both arrangements was found inside it. However, high levels of gene flow were detected for all six genes when comparing the same arrangement among populations. These results suggest that the adaptive value of inversions is maintained, regardless of the lack of genetic differentiation within arrangements from different populations, and thus favors the Local Adaptation hypothesis over the Coadapted Genome hypothesis as the basis of the selection acting on inversions in these populations.

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Contrasting the distribution of phenotypic and molecular variation in the freshwater snail Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni.

Publication Date: 2013 May PMID: 23321708
Authors: Tian-Bi, Y. N. - Jarne, P. - Konan, J. N. - Utzinger, J. - N'goran, E. K.
Journal: Heredity (Edinb)

Population differentiation was investigated by confronting phenotypic and molecular variation in the highly selfing freshwater snail Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni. We sampled seven natural populations separated by a few kilometers, and characterized by different habitat regimes (permanent/temporary) and openness (open/closed). A genetic analysis based on five microsatellite markers confirms that B. pfeifferi is a selfer (s approximately 0.9) and exhibits limited variation within populations. Most pairwise FST were significant indicating marked population structure, though no isolation by distance was detected. Families from the seven populations were monitored under laboratory conditions over two generations (G1 and G2), allowing to record several life-history traits, including growth, fecundity and survival, over 25 weeks. Marked differences were detected among populations for traits expressed early in the life cycle (up to sexual maturity). Age and size at first reproduction had high heritability values, but such a trend was not found for early reproductive traits. In most populations, G1 snails matured later and at a larger size than G2 individuals. Individuals from permanent habitats matured at a smaller size and were more fecund than those from temporary habitats. The mean phenotypic differentiation over all populations (QST) was lower than the mean genetic differentiation (FST), suggesting stabilizing selection. However, no difference was detected between QST and FST for both habitat regime and habitat openness.

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Linking transcriptomic and genomic variation to growth in brook charr hybrids (Salvelinus fontinalis, Mitchill).

Publication Date: 2013 May PMID: 23321707
Authors: Bougas, B. - Normandeau, E. - Audet, C. - Bernatchez, L.
Journal: Heredity (Edinb)

Hybridization can lead to phenotypic differences arising from changes in gene expression patterns or new allele combinations. Variation in gene expression is thought to be controlled by differences in transcription regulation of parental alleles, either through cis- or trans-regulatory elements. A previous study among brook charr hybrids from different populations (Rupert, Laval, and domestic) showing distinct length at age during early life stages also revealed different patterns in transcription regulation inheritance of transcript abundance. In the present study, transcript abundance using RNA-sequencing and quantitative real-time PCR, single-nucleotide polymorphism (SNP) genotypes and allelic imbalance were assessed in order to understand the molecular mechanisms underlying the observed transcriptomic and differences in length at age among domestic x Rupert hybrids and Laval x domestic hybrids. We found 198 differentially expressed genes between the two hybrid crosses, and allelic imbalance could be analyzed for 69 of them. Among these 69 genes, 36 genes exhibited cis-acting regulatory effects in both of the two crosses, thus confirming the prevalent role of cis-acting regulatory elements in the regulation of differentially expressed genes among intraspecific hybrids. In addition, we detected a significant association between SNP genotypes of three genes and length at age. Our study is thus one of the few that have highlighted some of the molecular mechanisms potentially involved in the differential phenotypic expression in intraspecific hybrids for nonmodel species.

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Purging deleterious mutations in conservation programmes: combining optimal contributions with inbred matings.

Publication Date: 2013 Jun PMID: 23321706
Authors: de Cara, M. A. - Villanueva, B. - Toro, M. A. - Fernandez, J.
Journal: Heredity (Edinb)

Conservation programmes aim at minimising the loss of genetic diversity, which allows populations to adapt to potential environmental changes. This can be achieved by calculating how many offspring every individual should contribute to the next generation to minimise global coancestry. However, an undesired consequence of this strategy is that it maintains deleterious mutations, compromising the viability of the population. In order to avoid this, optimal contributions could be combined with inbred matings, to expose and eliminate recessive deleterious mutations by natural selection in a process known as purging. Although some populations that have undergone purging experienced reduced inbreeding depression, this effect is not consistent across species. Whether purging by inbred matings is efficient in conservation programmes depends on the balance between the loss of diversity, the initial decrease in fitness and the reduction in mutational load. Here we perform computer simulations to determine whether managing a population by combining optimal contributions with inbred matings improves its long-term viability while keeping reasonable levels of diversity. We compare the management based on genealogical information with management based on molecular data to calculate coancestries. In the scenarios analysed, inbred matings never led to higher fitness and usually maintained lower diversity than random or minimum coancestry matings. Replacing genealogical with molecular coancestry can maintain a larger genetic diversity but can also lead to a lower fitness. Our results are strongly dependent on the mutational model assumed for the trait under selection, the population size during management and the reproductive rate.

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Exploitation of interspecific diversity for monocot crop improvement.

Publication Date: 2013 May PMID: 23321705
Authors: King, J. - Armstead, I. - Harper, J. - Ramsey, L. - Snape, J. - Waugh, R. - James, C. - Thomas, A. - Gasior, D. - Kelly, R. - Roberts, L. - Gustafson, P. - King, I.
Journal: Heredity (Edinb)

In many cultivated crop species there is limited genetic variation available for the development of new higher yielding varieties adapted to climate change and sustainable farming practises. The distant relatives of crop species provide a vast and largely untapped reservoir of genetic variation for a wide range of agronomically important traits that can be exploited by breeders for crop improvement. In this paper, in what we believe to be the largest introgression programme undertaken in the monocots, we describe the transfer of the entire genome of Festuca pratensis into Lolium perenne in overlapping chromosome segments. The L. perenne/F. pratensis introgressions were identified and characterised via 131 simple sequence repeats and 1612 SNPs anchored to the rice genome. Comparative analyses were undertaken to determine the syntenic relationship between L. perenne/F. pratensis and rice, wheat, barley, sorghum and Brachypodium distachyon. Analyses comparing recombination frequency and gene distribution indicated that a large proportion of the genes within the genome are located in the proximal regions of chromosomes which undergo low/very low frequencies of recombination. Thus, it is proposed that past breeding efforts to produce improved varieties have centred on the subset of genes located in the distal regions of chromosomes where recombination is highest. The use of alien introgression for crop improvement is important for meeting the challenges of global food supply and the monocots such as the forage grasses and cereals, together with recent technological advances in molecular biology, can help meet these challenges.

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The influence of parental effects on transcriptomic landscape during early development in brook charr (Salvelinus fontinalis, Mitchill).

Publication Date: 2013 May PMID: 23299101
Authors: Bougas, B. - Audet, C. - Bernatchez, L.
Journal: Heredity (Edinb)

Parental effects represent an important source of variation in offspring phenotypes. Depending on the specific mechanisms involved, parental effects may be caused to different degrees by either the maternal or the paternal parent, and these effects may in turn act at different stages of development. To detect parental effects acting on gene transcription regulation and length phenotype during ontogeny, the transcriptomic profiles of two reciprocal hybrids from Laval x Rupert and Laval x Domestic populations of brook charr were compared at hatching, yolk sac resorption and 15 weeks after exogenous feeding. Using a salmonid cDNA microarray, our results show that parental effects modulated gene expression among reciprocal hybrids only at the yolk sac resorption stage. In addition, Laval x Domestic and Laval x Rupert reciprocal hybrids differed in the magnitude of theses parental effects, with 199 and 630 differentially expressed transcripts, respectively. This corresponds to a maximum of 18.5% of the analyzed transcripts. These transcripts are functionally related to cell cycle, nucleic acid metabolism and intracellular protein traffic, which is consistent with observed differences associated with embryonic development and growth differences in other fish species. Our results thus illustrate how parental effects on patterns of gene transcription seem dependent on the genetic architecture of the parents. In addition, in absence of transcriptional differences, non-transcript deposits in the yolk sac could contribute to the observed length differences among the reciprocal hybrids before yolk sac resorption.

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Multilocus phylogeography (mitochondrial, autosomal and Z-chromosomal loci) and genetic consequence of long-distance male dispersal in Black-throated tits (Aegithalos concinnus).

Publication Date: 2013 May PMID: 23299099
Authors: Dai, C. - Wang, W. - Lei, F.
Journal: Heredity (Edinb)

Multilocus data from the different genomes are essential to understand the phylogeographic history of species, particularly when a species has the male-biased dispersal pattern. Although Black-throated tits (Aegithalos concinnus) are socially monogamous and cooperatively breeding birds, limited observational data suggested that males may have the ability of long-distance dispersal. We have previously detected three highly supported mitochondrial populations within two subspecies of Black-throated tits (A. c. concinnus and A. c. talifuensis). Here, we used several genetic markers with different inheritance patterns to gain insights about their phylogeographic history. Phylogenetic and individual-based Bayesian analysis showed weak geographical structure amongst nuclear sequences (autosomal and Z-chromosomal loci). Coalescent analysis revealed high levels of gene flow among mitochondrial populations, even between allopatric populations. These results strongly suggested that male-biased gene flow was responsible for the discordant cytonuclear phylogeographic patterns. Consistent with expectation on the genetic consequence of long-distance male dispersal, mantel tests revealed a significant pattern of isolation by distance for mitochondrial sequences, but failed to provide a similar pattern for nuclear genes within a continuous population; female Black-throated tits showed a stronger but not significantly different relationship of isolation by distance than males when using mitochondrial DNA alone. We discussed the contribution of male juveniles with delayed dispersal to the non-significantly different IBD patterns between sexes. Our results using multilocus genetic data revealed aspects of the complex evolutionary history of Black-throated tits and the important role of long-distance male dispersal in the population structuring.

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Speciation genetics.

Publication Date: 2013 May PMID: 23232834
Authors: Hansson, B.
Journal: Heredity (Edinb)

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Additive genetic variation in resistance traits of an exotic pine species: little evidence for constraints on evolution of resistance against native herbivores.

Publication Date: 2013 May PMID: 23232833
Authors: Moreira, X. - Zas, R. - Sampedro, L.
Journal: Heredity (Edinb)

The apparent failure of invasions by alien pines in Europe has been explained by the co-occurrence of native pine congeners supporting herbivores that might easily recognize the new plants as hosts. Previous studies have reported that exotic pines show reduced tolerance and capacity to induce resistance to those native herbivores. We hypothesize that limited genetic variation in resistance to native herbivores and the existence of evolutionary trade-offs between growth and resistance could represent additional potential constraints on the evolution of invasiveness of exotic pines outside their natural range. In this paper, we examined genetic variation for constitutive and induced chemical defences (measured as non-volatile resin in the stem and total phenolics in the needles) and resistance to two major native generalist herbivores of pines in cafeteria bioassays (the phloem-feeder Hylobius abietis and the defoliator Thaumetopoea pityocampa) using half-sib families drawn from a sample of the population of Pinus radiata introduced to Spain in the mid-19th century. We found (i) significant genetic variation, with moderate-to-high narrow-sense heritabilities for both the production of constitutive non-volatile resin and induced total phenolics, and for constitutive resistance against T. pityocampa in bioassays, (ii) no evolutionary trade-offs between plant resistance and growth traits or between the production of different quantitative chemical defences and (iii) a positive genetic correlation between constitutive resistance to the two studied herbivores. Overall, results of our study indicate that the exotic pine P. radiata has limited genetic constraints on the evolution of resistance against herbivores in its introduced range, suggesting that, at least in terms of interactions with these enemies, this pine species has potential to become invasive in the future.

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Molecular and quantitative signatures of biparental inbreeding depression in the self-incompatible tree species Prunus avium.

Publication Date: 2013 May PMID: 23211795
Authors: Jolivet, C. - Rogge, M. - Degen, B.
Journal: Heredity (Edinb)

Genetic diversity strongly influences populations' adaptability to changing environments and therefore survival. Sustainable forest management practices have multiple roles including conservation of genetic resources and timber production. In this study, we aimed at better understanding the variation in genetic diversity among adult and offspring individuals, and the effects of mating system on offspring survival and growth in wild cherry, Prunus avium. We analysed adult trees and open pollinated seed-families from three stands in Germany at eight microsatellite loci and one incompatibility system locus and conducted paternity analyses. Seed viability testing and seed sowing in a nursery allowed further testing for the effects of pollen donor diversity and genetic similarity between mates on the offspring performance at the seed and seedling stages. Our results were contrasting across stands. Loss of genetic diversity from adult to seedling stages and positive effect of mate diversity on offspring performance occurred in one stand only, whereas biparental inbreeding depression and significant decrease in fixation index from adults to seedlings was detected in two stands. We discussed the effects of stand genetic diversity on the magnitude of biparental inbreeding depression at several life-stages and its consequences on the management of genetic resources in P. avium.

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Sex-determining chromosomes and sexual dimorphism: insights from genetic mapping of sex expression in a natural hybrid Fragaria x ananassa subsp. cuneifolia.

Publication Date: 2013 May PMID: 23169558
Authors: Govindarajulu, R. - Liston, A. - Ashman, T. L.
Journal: Heredity (Edinb)

We studied the natural hybrid (Fragaria x ananassa subsp. cuneifolia) between two sexually dimorphic octoploid strawberry species (Fragaria virginiana and Fragaria chiloensis) to gain insight into the dynamics of sex chromosomes and the genesis of sexual dimorphism. Male sterility is dominant in both the parental species and thus will be inherited maternally, but the chromosome that houses the sex-determining region differs. Thus, we asked whether (1) the cytotypic composition of hybrid populations represents one or both maternal species, (2) the sex-determining chromosome of the hybrid reflects the location of male sterility within the maternal donor species and (3) crosses from the hybrid species show less sexual dimorphism than the parental species. We found that F. x ananassa subsp. cuneifolia populations consisted of both parental cytotypes but one predominated within each population. Genetic linkage mapping of two crosses showed dominance of male sterility similar to the parental species, however, the map location of male sterility reflected the maternal donor in one cross, but not the other. Moreover, female function mapped to a single region in the first cross, but to two regions in the second cross. Aside from components of female function (fruit set and seed set), other traits that have been found to be significantly sexually dimorphic in the pure species were either not dimorphic or were dimorphic in the opposite direction to the parental species. These results suggest that hybrids experience some disruption of dimorphism in secondary sexual traits, as well as novel location and number of quantitative trait locus (QTL) affecting sex function.

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