| 1. |
- Anderson, Jennifer L, et al.
(author)
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Outcrossing and the maintenance of males within C. elegans populations.
- 2010
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In: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 101 Suppl 1
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Journal article (peer-reviewed)abstract
- Caenorhabditis elegans is an androdioecious nematode with both hermaphrodites and males. Although males can potentially play an important role in avoiding inbreeding and facilitating adaptation, their existence is evolutionarily problematic because they do not directly generate offspring in the way that hermaphrodites do. This review explores how genetic, population genomic, and experimental evolution approaches are being used to address the role of males and outcrossing within C. elegans. Although theory suggests that inbreeding depression and male mating ability should be the primary determinants of male frequency, this has yet to be convincingly confirmed experimentally. Genomic analysis of natural populations finds that outcrossing occurs at low, but not negligible levels, and that observed patterns of linkage disequilibrium consistent with strong selfing may instead be generated by natural selection against outcrossed progeny. Recent experimental evolution studies suggest that males can be maintained at fairly high levels if populations are initiated with sufficient genetic variation and/or subjected to strong natural selection via a change in the environment. For example, as reported here, populations adapting to novel laboratory rearing and temperature regimes maintain males at frequencies from 5% to 40%. Laboratory and field results still await full reconciliation, which may be facilitated by identifying the loci underlying among-strain differences in mating system dynamics.
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| 2. |
- Andersson, Stefan, et al.
(author)
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Quantitative genetic effects of bottlenecks : experimental evidence from a wild plant species, Nigella degenii
- 2010
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In: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 101:3, s. 298-307
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Journal article (peer-reviewed)abstract
- Understanding the genetic consequences of changes in population size is fundamental in a variety of contexts, such as adaptation and conservation biology. In the study presented here, we have performed a replicated experiment with the plant Nigella degenii to explore the quantitative genetic effects of a single-founder bottleneck. In agreement with adetive theory, the bottleneck reduced the mean (co)variance within lines and caused stochastic, line-specific changes in the genetic (co)variance structure. However, a significant portion of the (co)variance structure was conserved, and 2 characters—leaf and flower (sepal) size—turned out to be positively correlated in all data sets, indicating a potential for correlated evolution in these characters, even after a severe bottleneck. The hierarchical partitioning of genetic variance for flower size was in good agreement with predictions from additive theory, whereas the remaining characters showed an excess of within-line variance and a deficiency of among-line variance. The latter discrepancies were most likely a result of selection, given the small proportion of lines (23%) that remained viable until the end of the experiment. Our results suggest that bottlenecked populations of N. degenii generally have a lower adaptive potential than the ancentral population but also highlight the idiosyncratic nature of bottleneck effects.
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| 3. |
- Andersson, Stefan
(author)
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The genetic basis of floral variation in Senecio jacobaea (Asteraceae)
- 2001
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In: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1471-8505. ; 92:5, s. 409-414
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Journal article (peer-reviewed)abstract
- The self-incompatible composite Senecio Jacobaea (ragwort) exhibits geographic variation in the frequency of rayed and discoid (rayless) individuals. Hybrid progenies from within- and between-morph crosses were established in a seminatural (garden) environment to determine whether patterns of segregation conform to single-gene predictions (as found in other Senecio species), whether the direction of dominance is conducive to rapid evolutionary change in ray morphology, and whether geographically distant populations of the discoid morph utilize the same or different genes to suppress ray development. Data from segregating F-2 and BC families were consistent with a genetic model involving one major locus and an unknown number of modifiers. Analysis of F-1 progenies from different intermorph crosses using the same rayed plant as a seed parent revealed a variable and incomplete pattern of dominance, with a trend toward partial dominance in some crosses. Hybridizations between discoid populations produced a few rayed progeny (4%), but there was no tendency for the frequency of rayed progeny to increase with the geographic distance separating the parent populations. Results of this study indicate that major mutations have been important for the evolution of discoid populations of ragwort, that ray-suppressing mutations should be directly available to selection in most populations, and that the suppression of rays is conditioned by the same or similar gene(s) in Atlantic and Baltic populations of the discoid taxon.
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| 4. |
- Andersson, Stefan, et al.
(author)
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The genetic basis of naturally occurring pollen color dimorphisms in Nigella degenii (Ranunculaceae)
- 2005
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In: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 96:5, s. 550-556
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Journal article (peer-reviewed)abstract
- Nigella degenii ssp. barbro and ssp. jenny differ from related taxa in being dimorphic for pollen color, with some plants having dark pollen and others light pollen. In this study we performed experimental crosses to determine whether the difference in pollen color is governed by few or many loci and whether the two subspecies utilize the same gene to control pollen color. Patterns of segregation in crosses between morphs show that dark pollen is dominant over light pollen and that a single major gene is responsible for most of the variation in pollen color. Consequently it should be relatively easy for pollen color dimorphisms to establish and spread in these subspecies. Aberrant segregation ratios were attributed to genetic factors that reduced the expression of the allele conferring dark pollen or processes that sorted between color morphs during seed development. Crosses between dark pollen plants from different subspecies showed signs of complementation in the F-2 generation, but the frequency of the light morph was too low to support a model involving complementary action of recessive alleles at two separate loci. Based on this and other observations, we hypothesize that the pollen color difference is controlled by the same major locus in the two subspecies.
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| 5. |
- Banabazi, Mohammad Hossein
(author)
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Weighted Single-Step GWAS for Body Mass Index and Scans for Recent Signatures of Selection in Yorkshire Pigs
- 2022
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In: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 113, s. 325-335
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Journal article (peer-reviewed)abstract
- Controlling extra fat deposition is economically favorable in modern swine industry. Understanding the genetic architecture of fat deposition traits such as body mass index (BMI) can help in improving genomic selection for such traits. We utilized a weighted single-step genome-wide association study (WssGWAS) to detect genetic regions and candidate genes associated with BMI in a Yorkshire pig population. Three extended haplotype homozygosity (EHH)-related statistics were also incorporated within a de-correlated composite of multiple signals (DCMS) framework to detect recent selection signatures signals. Overall, the full pedigree consisted of 7016 pigs, of which 5561 had BMI records and 598 pigs were genotyped with an 80 K single nucleotide polymorphism (SNP) array. Results showed that the most significant windows (top 15) explained 9.35% of BMI genetic variance. Several genes were detected in regions previously associated with pig fat deposition traits and treated as potential candidate genes for BMI in Yorkshire pigs: FTMT, SRFBP1, KHDRBS3, FOXG1, SOD3, LRRC32, TSKU, ACER3, B3GNT6, CCDC201, ADCY1, RAMP3, TBRG4, CCM2. Signature of selection analysis revealed multiple candidate genes previously associated with various economic traits. However, BMI genetic variance explained by regions under selection pressure was minimal (1.31%). In conclusion, candidate genes associated with Yorkshire pigs' BMI trait were identified using WssGWAS. Gene enrichment analysis indicated that the identified candidate genes were enriched in the insulin secretion pathway. We anticipate that these results further advance our understanding of the genetic architecture of BMI in Yorkshire pigs and provide information for genomic selection for fat deposition in this breed.
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| 6. |
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| 7. |
- Bererhi, Badreddine, et al.
(author)
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Limited effects of inbreeding on breeding coloration
- 2023
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In: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 114:2, s. 143-151
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Journal article (peer-reviewed)abstract
- Animal color signals may function as indicators of fighting ability when males compete for access to females. This allows opponents to settle aggressive interactions before they escalate into physical combat and injury. Thus, there may be strong directional selection on these traits, toward enhanced signal quality. This renders sexually selected traits particularly susceptible to inbreeding depression, due to relatively low ratios of additive genetic variance to dominance variance. We measured the effects of inbreeding on an intrasexually selected color signal (the badge) in a population of Swedish sand lizards (Lacerta agilis) using the Rhh software based on 17 to 21 microsatellites. Males of this sexually dichromatic species use the badge during aggressive interactions to display, and assess, fighting ability. We found negative effects of homozygosity on badge size, saturation, and brightness. However, no such effects were observed on color hue. Pairwise correlations between badge size, hue, and saturation were all statistically significant. Thus, the sand lizard "badge" is a multicomponent signal with variation explained by covariation in badge size, saturation, and color hue. Body mass corrected for skeletal size (body condition) positively predicted badge size and saturation, encouraging future research on the extent that sexual signals may convey information on multigene targets (i.e. "genic capture").
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| 8. |
- Carlborg, Örjan, et al.
(author)
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Parallel computing in interval mapping of quantitative trait loci.
- 2002
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In: Journal of Heredity. - 0022-1503 .- 1465-7333. ; 92:5
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Journal article (peer-reviewed)abstract
- Linear regression analysis is considered the least computationally demanding method for mapping quantitative trait loci (QTL). However, simultaneous search for multiple QTL, the use of permutations to obtain empirical significance thresholds, and larger experimental studies significantly increase the computational demand. This report describes an easily implemented parallel algorithm, which significantly reduces the computing time in both QTL mapping and permutation testing. In the example provided, the analysis time was decreased to less than 15% of a single processor system by the use of 18 processors. We indicate how the efficiency of the analysis could be improved by distributing the computations more evenly to the processors and how other ways of distributing the data facilitate the use of more processors. The use of parallel computing in QTL mapping makes it possible to routinely use permutations to obtain empirical significance thresholds for multiple traits and multiple QTL models. It could also be of use to improve the computational efficiency of the more computationally demanding QTL analysis methods.
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| 9. |
- Catania, Francesco, et al.
(author)
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Endogenous Mechanisms for the Origins of Spliceosomal Introns
- 2009
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In: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 100:5, s. 591-596
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Journal article (peer-reviewed)abstract
- Over 30 years since their discovery, the origin of spliceosomal introns remains uncertain. One nearly universally accepted hypothesis maintains that spliceosomal introns originated from self-splicing group-II introns that invaded the uninterrupted genes of the last eukaryotic common ancestor (LECA) and proliferated by “insertion” events. Although this is a possible explanation for the original presence of introns and splicing machinery, the emphasis on a high number of insertion events in the genome of the LECA neglects a considerable body of empirical evidence showing that spliceosomal introns can simply arise from coding or, more generally, nonintronic sequences within genes. After presenting a concise overview of some of the most common hypotheses and mechanisms for intron origin, we propose two further hypotheses that are broadly based on central cellular processes: 1) internal gene duplication and 2) the response to aberrant and fortuitously spliced transcripts. These two nonmutually exclusive hypotheses provide a powerful way to explain the establishment of spliceosomal introns in eukaryotes without invoking an exogenous source.
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| 10. |
- Chen, Zhiqiang, et al.
(author)
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Increased Prediction Ability in Norway Spruce Trials Using a Marker X Environment Interaction and Non-Additive Genomic Selection Model
- 2019
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In: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 110, s. 830-843
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Journal article (peer-reviewed)abstract
- A genomic selection study of growth and wood quality traits is reported based on control-pollinated Norway spruce families established in 2 Northern Swedish trials at 2 locations using exome capture as a genotyping platform. Nonadditive effects including dominance and first-order epistatic interactions (including additive-by-additive, dominance-by-dominance, and additive-by-dominance) and marker-by-environment interaction (MxE) effects were dissected in genomic and phenotypic selection models. Genomic selection models partitioned additive and nonadditive genetic variances more precisely than pedigree-based models. In addition, predictive ability in GS was substantially increased by including dominance and slightly increased by including MxE effects when these effects are significant. For velocity, response to genomic selection per year increased up to 78.9/80.8%, 86.9/82.9%, and 91.3/88.2% compared with response to phenotypic selection per year when genomic selection was based on 1) main marker effects (M), 2) M + MxE effects (A), and 3) A + dominance effects (AD) for sites 1 and 2, respectively. This indicates that including MxE and dominance effects not only improves genetic parameter estimates but also when they are significant may improve the genetic gain. For tree height, Pilodyn, and modulus of elasticity (MOE), response to genomic selection per year improved up to 68.9%, 91.3%, and 92.6% compared with response to phenotypic selection per year, respectively.
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