Heredity

Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters.

Publication Date: 2012 Jan 25 PMID: 22274647
Authors: Zhang, H. - Hare, M. P.
Journal: Heredity (Edinb)

Phylogeographic inferences about gene flow are strengthened through comparison of co-distributed taxa, but also depend on adequate genomic sampling. Amplified fragment length polymorphisms (AFLPs) provide a rapid and inexpensive source of multilocus allele frequency data for making genomically robust inferences. Every AFLP study initially generates markers with a range of locus-specific genotyping error rates and applies criteria to select a subset for analysis. However, there has been very little empirical evaluation of the best tradeoff between culling all but the lowest-error loci to minimize overall genotyping error versus the potential for increasing population genetic signal by retaining more loci. Here, we used AFLPs to compare population structure in co-distributed broadcast spawning (Crassostrea virginica) and brooding (Ostrea equestris) oyster species. Using existing methods for almost entirely automated marker selection and scoring, genotyping error tradeoffs were evaluated by comparing results across a nested series of data sets with mean mismatch errors of 0, 1, 2, 3, 4 and >4%. Artifactual population structure was diagnosed in high-error data sets and we assessed the low-error point at which expected population substructure signal was lost. In both species, we identified substructure patterns deemed to be inaccurate at average mismatch error rates 4%. In the species comparison, the optimum data sets showed higher gene flow for the brooding oyster with more oceanic salinity tolerances. AFLP tradeoffs may differ among studies, but our results suggest that important signal may be lost in the pursuit of 'acceptable' error levels and our procedures provide a general method for empirically exploring these tradeoffs.Heredity advance online publication, 25 January 2012; doi:10.1038/hdy.2011.132.

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A brief note on the resemblance between relatives in the presence of population stratification.

Publication Date: 2012 Jan 11 PMID: 22234249
Authors: Sebro, R. - Risch, N. J.
Journal: Heredity (Edinb)

Population stratification occurs when a study population is comprised of several sub-populations, and can result in increased false positive findings in genomewide-association studies. Recently published work shows that sub-population-specific positive assortative mating at the genotypic level results in population stratification. We show that if the allele frequency of a single nucleotide polymorphism responsible for a trait varies between sub-populations and there is no dominance variance, then the heritability of the trait increases, primarily due to an increase in the additive genetic variance of the trait.Heredity advance online publication, 11 January 2012; doi:10.1038/hdy.2011.124.

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AFLPs do not support deep phylogenetic relationships among darters (Teleostei: Percidae: Etheostomatinae).

Publication Date: 2012 Jan 11 PMID: 22234248
Authors: Near, T. J. - Keck, B. P.
Journal: Heredity (Edinb)

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Two distinct genomic regions, harbouring the period and fruitless genes, affect male courtship song in Drosophila montana.

Publication Date: 2012 Jan 11 PMID: 22234247
Authors: Lagisz, M. - Wen, S. Y. - Routtu, J. - Klappert, K. - Mazzi, D. - Morales-Hojas, R. - Schafer, M. A. - Vieira, J. - Hoikkala, A. - Ritchie, M. G. - Butlin, R. K.
Journal: Heredity (Edinb)

Acoustic signals often have a significant role in pair formation and in species recognition. Determining the genetic basis of signal divergence will help to understand signal evolution by sexual selection and its role in the speciation process. An earlier study investigated quantitative trait locus for male courtship song carrier frequency (FRE) in Drosophila montana using microsatellite markers. We refined this study by adding to the linkage map markers for 10 candidate genes known to affect song production in Drosophila melanogaster. We also extended the analyses to additional song characters (pulse train length (PTL), pulse number (PN), interpulse interval, pulse length (PL) and cycle number (CN)). Our results indicate that loci in two different regions of the genome control distinct features of the courtship song. Pulse train traits (PTL and PN) mapped to the X chromosome, showing significant linkage with the period gene. In contrast, characters related to song pulse properties (PL, CN and carrier FRE) mapped to the region of chromosome 2 near the candidate gene fruitless, identifying these genes as suitable loci for further investigations. In previous studies, the pulse train traits have been found to vary substantially between Drosophila species, and so are potential species recognition signals, while the pulse traits may be more important in intra-specific mate choice.Heredity advance online publication, 11 January 2012; doi:10.1038/hdy.2011.129.

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Genetic uniqueness of the Waorani tribe from the Ecuadorian Amazon.

Publication Date: 2012 Jan 11 PMID: 22234246
Authors: Cardoso, S. - Alfonso-Sanchez, M. A. - Valverde, L. - Sanchez, D. - Zarrabeitia, M. T. - Odriozola, A. - Martinez-Jarreta, B. - de Pancorbo, M. M.
Journal: Heredity (Edinb)

South America and especially the Amazon basin is known to be home to some of the most isolated human groups in the world. Here, we report on a study of mitochondrial DNA (mtDNA) in the Waorani from Ecuador, probably the most warlike human population known to date. Seeking to look in more depth at the characterization of the genetic diversity of this Native American tribe, molecular markers from the X and Y chromosomes were also analyzed. Only three different mtDNA haplotypes were detected among the Waorani sample. One of them, assigned to Native American haplogroup A2, accounted for more than 94% of the total diversity of the maternal gene pool. Our results for sex chromosome molecular markers failed to find close genetic kinship between individuals, further emphasizing the low genetic diversity of the mtDNA. Bearing in mind the results obtained for both the analysis of the mtDNA control region and complete mitochondrial genomes, we suggest the existence of a 'Waorani-specific' mtDNA lineage. According to current knowledge on the phylogeny of haplogroup A2, we propose that this lineage could be designated as subhaplogroup A2s. Its wide predominance among the Waorani people might have been conditioned by severe genetic drift episodes resulting from founding events, long-term isolation and a traditionally small population size most likely associated with the striking ethnography of this Amazonian community. In all, the Waorani constitute a fine example of how genetic imprint may mirror ethnopsychology and sociocultural features in human populations.Heredity advance online publication, 11 January 2012; doi:10.1038/hdy.2011.131.

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Genetic basis of stage-specific melanism: a putative role for a cysteine sulfinic acid decarboxylase in insect pigmentation.

Publication Date: 2012 Jan 11 PMID: 22234245
Authors: Saenko, S. V. - Jeronimo, M. A. - Beldade, P.
Journal: Heredity (Edinb)

Melanism, the overall darkening of the body, is a widespread form of animal adaptation to particular environments, and includes bookcase examples of evolution by natural selection, such as industrial melanism in the peppered moth. The major components of the melanin biosynthesis pathway have been characterized in model insects, but little is known about the genetic basis of life-stage specific melanism such as cases described in some lepidopteran species. Here, we investigate two melanic mutations of Bicyclus anynana butterflies, called Chocolate and melanine, that exclusively affect pigmentation of the larval and adult stages, respectively. Our analysis of Mendelian segregation patterns reveals that the larval and adult melanic phenotypes are due to alleles at different, independently segregating loci. Our linkage mapping analysis excludes the pigmentation candidate gene black as the melanine locus, and implicates a gene encoding a putative pyridoxal phosphate-dependant cysteine sulfinic acid decarboxylase as the Chocolate locus. We show variation in coding sequence and in expression levels for this candidate larval melanism locus. This is the first study that suggests a biological function for this gene in insects. Our findings open up exciting opportunities to study the role of this locus in the evolution of adaptive variation in pigmentation, and the uncoupling of regulation of pigment biosynthesis across developmental stages with different ecologies and pressures on body coloration.Heredity advance online publication, 11 January 2012; doi:10.1038/hdy.2011.127.

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Molecular genetic and quantitative trait divergence associated with recent homoploid hybrid speciation: a study of Senecio squalidus (Asteraceae).

Publication Date: 2012 Feb PMID: 21829224
Authors: Brennan, A. C. - Barker, D. - Hiscock, S. J. - Abbott, R. J.
Journal: Heredity (Edinb)

Hybridization is increasingly seen as a trigger for rapid evolution and speciation. To quantify and qualify divergence associated with recent homoploid hybrid speciation, we compared quantitative trait (QT) and molecular genetic variation between the homoploid hybrid species Senecio squalidus and its parental species, S. aethnensis and S. chrysanthemifolius, and also their naturally occurring Sicilian hybrids. S. squalidus originated and became invasive in the United Kingdom following the introduction of hybrid plants from Mount Etna, Sicily, about 300 years ago. We recorded considerable molecular genetic differentiation between S. squalidus and its parents and their Sicilian hybrids in terms of both reduced genetic diversity and altered allele frequencies, potentially due to the genetic bottleneck associated with introduction to the United Kingdom. S. squalidus is also distinct from its parents and Sicilian hybrids for QTs, but less so than for molecular genetic markers. We suggest that this is due to resilience of polygenic QTs to changes in allele frequency or lack of selection for hybrid niche divergence in geographic isolation. While S. squalidus is intermediate or parental-like for most QTs, some trangressively distinct traits were observed, which might indicate emerging local adaptation in its invasive range. This study emphasizes the important contribution of founder events and geographic isolation to successful homoploid hybrid speciation.

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Simultaneous estimation of multiple quantitative trait loci and growth curve parameters through hierarchical Bayesian modeling.

Publication Date: 2012 Feb PMID: 21792229
Authors: Sillanpaa, M. J. - Pikkuhookana, P. - Abrahamsson, S. - Knurr, T. - Fries, A. - Lerceteau, E. - Waldmann, P. - Garcia-Gil, M. R.
Journal: Heredity (Edinb)

A novel hierarchical quantitative trait locus (QTL) mapping method using a polynomial growth function and a multiple-QTL model (with no dependence in time) in a multitrait framework is presented. The method considers a population-based sample where individuals have been phenotyped (over time) with respect to some dynamic trait and genotyped at a given set of loci. A specific feature of the proposed approach is that, instead of an average functional curve, each individual has its own functional curve. Moreover, each QTL can modify the dynamic characteristics of the trait value of an individual through its influence on one or more growth curve parameters. Apparent advantages of the approach include: (1) assumption of time-independent QTL and environmental effects, (2) alleviating the necessity for an autoregressive covariance structure for residuals and (3) the flexibility to use variable selection methods. As a by-product of the method, heritabilities and genetic correlations can also be estimated for individual growth curve parameters, which are considered as latent traits. For selecting trait-associated loci in the model, we use a modified version of the well-known Bayesian adaptive shrinkage technique. We illustrate our approach by analysing a sub sample of 500 individuals from the simulated QTLMAS 2009 data set, as well as simulation replicates and a real Scots pine (Pinus sylvestris) data set, using temporal measurements of height as dynamic trait of interest.

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Host genotype changes bidirectional to unidirectional cytoplasmic incompatibility in Nasonia longicornis.

Publication Date: 2012 Feb PMID: 21792226
Authors: Raychoudhury, R. - Werren, J. H.
Journal: Heredity (Edinb)

Wolbachia are the most abundant maternally inherited endosymbionts of insects and cause various reproductive alterations in their hosts. One such manipulation is cytoplasmic incompatibility (CI), which is a sperm-egg incompatibility typically resulting in zygotic death. Nasonia longicornis (Hymenoptera: Pteromalidae) has an A supergroup and two closely related B supergroup Wolbachia infections. The B supergroup bacteria co-diverged in this host genus. Both triple (wNlonAwNlonB1wNlonB2) and double infections (wNlonAwNlonB1, wNlonAwNlonB2) have been obtained from the field. In the present study, CI was determined among the three Wolbachia types in different host genetic backgrounds. Results show that host genetic background determines whether bidirectional CI or unidirectional CI occurs between the two closely related B group Wolbachia. Results show that the wNlonB1-infected males are bidirectionally incompatible with wNlonB2 in their 'native' nuclear genetic background, whereas wNlonB1 males are compatible with wNlonB2 in two other N. longicornis genetic backgrounds, resulting in unidirectional CI. In contrast, wNlonB2-infected males are incompatible with wNlonB1 females in all three host genetic backgrounds. These changes in incompatibility are not due to the loss of the bacteria. We hypothesize that a repressor gene for sperm modification by wNlonB1 is segregating in N. longicornis populations. The relevance of these findings to the potential role of Wolbachia in host-reproductive divergence and speciation is discussed.

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From Russia with lobe: genetic differentiation in trilobed uncus Ostrinia spp. follows food plant, not hairy legs.

Publication Date: 2012 Feb PMID: 21772289
Authors: Frolov, A. N. - Audiot, P. - Bourguet, D. - Kononchuk, A. G. - Malysh, J. M. - Ponsard, S. - Streiff, R. - Tokarev, Y. S.
Journal: Heredity (Edinb)

Trilobed uncus taxa of the genus Ostrinia (Lepidoptera, Crambidae) illustrate the complex relationship, at early stages of speciation, between reproductive isolation and differentiation in morphology, resource use and genetic variation. On the basis of behaviour and ecology, we recently hypothesized that individuals with small mid-tibiae belong to two distinct species depending on host plant-O. nubilalis and O. scapulalis sensu Frolov et al. (2007) feeding on maize and on a number of dicotyledons, respectively. Individuals with small, medium or massive mid-tibiae would all belong to O. scapulalis as long as they feed on these dicotyledons. This contrasts with previous taxonomy, which distinguished three species by male mid-tibia morphology, regardless of host plant. Here, we test our hypothesis by examining the genetic structure of Ostrinia populations from regions with mid-tibia polymorphism-Western Russia and Kazakhstan-and comparing it with that of French populations where only small mid-tibiae occur. Results support two predictions: (1) maize- and dicotyledon-collected populations are genetically differentiated from each other like in France, and (2) dicotyledon-collected populations show no genetic evidence of consisting of more than one species. Between-species differentiation was unrelated to geographic distance, despite significant isolation by distance within species. The distinction between two and only two species differing by host plant thus holds at continental scale. Interestingly, one microsatellite locus contributed approximately 10 times more than the others to differentiation between both taxa. This deserves further investigation, as it might reveal a linkage between this outlier and loci involved in host-plant adaptation and/or reproductive isolation.

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Worldwide genetic structure in 37 genes important in telomere biology.

Publication Date: 2012 Feb PMID: 21731055
Authors: Mirabello, L. - Yeager, M. - Chowdhury, S. - Qi, L. - Deng, X. - Wang, Z. - Hutchinson, A. - Savage, S. A.
Journal: Heredity (Edinb)

Telomeres form the ends of eukaryotic chromosomes and are vital in maintaining genetic integrity. Telomere dysfunction is associated with cancer and several chronic diseases. Patterns of genetic variation across individuals can provide keys to further understanding the evolutionary history of genes. We investigated patterns of differentiation and population structure of 37 telomere maintenance genes among 53 worldwide populations. Data from 898 unrelated individuals were obtained from the genome-wide scan of the Human Genome Diversity Panel (HGDP) and from 270 unrelated individuals from the International HapMap Project at 716 single-nucleotide polymorphism (SNP) loci. We additionally compared this gene set to HGDP data at 1396 SNPs in 174 innate immunity genes. The majority of the telomere biology genes had low to moderate haplotype diversity (45-85%), high ancestral allele frequencies (>60%) and low differentiation (F(ST) <0.10). Heterozygosity and differentiation were significantly lower in telomere biology genes compared with the innate immunity genes. There was evidence of evolutionary selection in ACD, TERF2IP, NOLA2, POT1 and TNKS in this data set, which was consistent in HapMap 3. TERT had higher than expected levels of haplotype diversity, likely attributable to a lack of linkage disequilibrium, and a potential cancer-associated SNP in this gene, rs2736100, varied substantially in genotype frequency across major continental regions. It is possible that the genes under selection could influence telomere biology diseases. As a group, there appears to be less diversity and differentiation in telomere biology genes than in genes with different functions, possibly due to their critical role in telomere maintenance and chromosomal stability.

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Variation for host range within and among populations of the parasitic plant Striga hermonthica.

Publication Date: 2012 Feb PMID: 21731054
Authors: Huang, K. - Whitlock, R. - Press, M. C. - Scholes, J. D.
Journal: Heredity (Edinb)

Striga hermonthica is an angiosperm parasite that causes substantial damage to a wide variety of cereal crop species, and to the livelihoods of subsistence farmers in sub-Saharan Africa. The broad host range of this parasite makes it a fascinating model for the study of host-parasite interactions, and suggests that effective long-term control strategies for the parasite will require an understanding of the potential for host range adaptation in parasite populations. We used a controlled experiment to test the extent to which the success or failure of S. hermonthica parasites to develop on a particular host cultivar (host resistance/compatibility) depends upon the identity of interacting host genotypes and parasite populations. We also tested the hypothesis that there is a genetic component to host range within individual S. hermonthica populations, using three rice cultivars with known, contrasting abilities to resist infection. The developmental success of S. hermonthica parasites growing on different rice-host cultivars (genotypes) depended significantly on a parasite population by host-genotype interaction. Genetic analysis using amplified fragment length polymorphism (AFLP) markers revealed that a small subset of AFLP markers showed 'outlier' genetic differentiation among sub-populations of S. hermonthica attached to different host cultivars. We suggest that, this indicates a genetic component to host range within populations of S. hermonthica, and that a detailed understanding of the genomic loci involved will be crucial in understanding host-parasite specificity and in breeding crop cultivars with broad spectrum resistance to S. hermonthica.

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Towards the genetic architecture of seed lipid biosynthesis and accumulation in Arabidopsis thaliana.

Publication Date: 2012 Feb PMID: 21731053
Authors: O'Neill, C. M. - Morgan, C. - Hattori, C. - Brennan, M. - Rosas, U. - Tschoep, H. - Deng, P. X. - Baker, D. - Wells, R. - Bancroft, I.
Journal: Heredity (Edinb)

We report the quantitative genetic analysis of seed oil quality and quantity in six Arabidopsis thaliana recombinant inbred populations, in which the parent accessions were from diverse geographical origins, and were selected on the basis of variation for seed oil content and lipid composition. Although most of the biochemical steps involved in lipid biosynthesis are known and the key genes have been identified, the regulation of the processes that results in the final oil composition and total amount is not understood. By using physically anchored markers it was possible to compare results across populations. A total of 219 quantitative trait loci (QTLs) were identified, of which 81 were significant at P<0.001. Some of these colocalise with QTLs identified previously, but many novel QTLs were also identified. The results highlight the importance of studying traits in multiple populations, which will lead to a better understanding of the contribution that natural variation makes to the genetic architecture of a phenotype.

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