| 1. |
- Backström, Niclas, et al.
(författare)
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The recombination landscape of the zebra finch Taeniopygia guttata genome
- 2010
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 20:4, s. 485-495
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the causes and consequences of variation in the rate of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variation. We genotyped 1920 single nucleotide polymorphisms in a multigeneration pedigree of more than 1000 zebra finches (Taeniopygia guttata) to develop a genetic linkage map, and then we used these map data together with the recently available draft genome sequence of the zebra finch to estimate recombination rates in 1 Mb intervals across the genome. The average zebra finch recombination rate (1.5 cM/Mb) is higher than in humans, but significantly lower than in chicken. The local rates of recombination in chicken and zebra finch were only weakly correlated, demonstrating evolutionary turnover of the recombination landscape in birds. The distribution of recombination events was heavily biased toward ends of chromosomes, with a stronger telomere effect than so far seen in any organism. In fact, the recombination rate was as low as 0.1 cM/Mb in intervals up to 100 Mb long in the middle of the larger chromosomes. We found a positive correlation between recombination rate and GC content, as well as GC-rich sequence motifs. Levels of linkage disequilibrium (LD) were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations.
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| 2. |
- Bolund, Elisabeth, et al.
(författare)
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Correlates of male fitness in captive zebra finches : a comparison of methods to disentangle genetic and environmental effects
- 2011
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 327-
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Tidskriftsartikel (refereegranskat)abstract
- Backgound: It is a common observation in evolutionary studies that larger, more ornamented or earlier breeding individuals have higher fitness, but that body size, ornamentation or breeding time does not change despite of sometimes substantial heritability for these traits. A possible explanation for this is that these traits do not causally affect fitness, but rather happen to be indirectly correlated with fitness via unmeasured non-heritable aspects of condition (e. g. undernourished offspring grow small and have low fitness as adults due to poor health). Whether this explanation applies to a specific case can be examined by decomposing the covariance between trait and fitness into its genetic and environmental components using pedigree-based animal models. We here examine different methods of doing this for a captive zebra finch population where male fitness was measured in communal aviaries in relation to three phenotypic traits (tarsus length, beak colour and song rate). Results: Our case study illustrates how methods that regress fitness over breeding values for phenotypic traits yield biased estimates as well as anti-conservative standard errors. Hence, it is necessary to estimate the genetic and environmental covariances between trait and fitness directly from a bivariate model. This method, however, is very demanding in terms of sample sizes. In our study parameter estimates of selection gradients for tarsus were consistent with the hypothesis of environmentally induced bias (beta(A) = 0.035 +/- 0.25 (SE), beta(E) = 0.57 +/- 0.28 (SE)), yet this differences between genetic and environmental selection gradients falls short of statistical significance. Conclusions: To examine the generality of the idea that phenotypic selection gradients for certain traits (like size) are consistently upwardly biased by environmental covariance a meta-analysis across study systems will be needed.
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| 3. |
- Evans, Simon R., et al.
(författare)
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Nonautosomal Genetic Variation in Carotenoid Coloration
- 2014
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Ingår i: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 184:3, s. 374-383
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Tidskriftsartikel (refereegranskat)abstract
- Carotenoid-based coloration plays an important role in signaling, is often sexually dimorphic, and is potentially subject to directional and/or sex-specific selection. To understand the evolutionary dynamics of such color traits, it is essential to quantify patterns of inheritance, yet nonautosomal sources of genetic variation are easily overlooked by classical heritability analyses. Carotenoid metabolism has recently been linked to mitochondria, highlighting the potential for color variation to be explained by cytoplasmically inherited factors. In this study, we used quantitative genetic animal models to estimate the importance of mitochondrial and sex chromosome-linked sources of genetic variation in coloration in two songbird populations in which dietary carotenoids are either unmodified (great tit plumage) or metabolized into alternative color forms (zebra finch beak). We found no significant Z-linked genetic variance in great tit plumage coloration, while zebra finch beak coloration exhibited significant W linkage and cytoplasmic inheritance. Our results support cytoplasmic inheritance of color in the zebra finch, a trait based on endogenously metabolized carotenoids, and demonstrate the potential for nonautosomal sources to account for a considerable share of genetic variation in coloration. Although often overlooked, such nonautosomal genetic variation exhibits sex-dependent patterns of inheritance and potentially influences the evolution of sexual dichromatism.
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| 4. |
- Forstmeier, Wolfgang, et al.
(författare)
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Heterozygosity-fitness correlations in zebra finches : microsatellite markers can be better than their reputation
- 2012
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 21:13, s. 3237-3249
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Tidskriftsartikel (refereegranskat)abstract
- Numerous studies have reported associations between heterozygosity in microsatellite markers and fitness-related traits (heterozygosityfitness correlations, HFCs). However, it has often been questioned whether HFCs reflect general inbreeding depression, because a small panel of microsatellite markers does not reflect very well an individuals inbreeding coefficient (F) as calculated from a pedigree. Here, we challenge this prevailing view. Because of chance events during Mendelian segregation, an individuals realized proportion of the genome that is identical by descent (IBD) may substantially deviate from the pedigree-based expectation (i.e. F). This Mendelian noise may result in a weak correlation between F and multi-locus heterozygosity, but this does not imply that multi-locus heterozygosity is a bad estimator of realized IBD. We examined correlations between 11 fitness-related traits measured in up to 1192 captive zebra finches and three measures of inbreeding: (i) heterozygosity across 11 microsatellite markers, (ii) heterozygosity across 1359 single-nucleotide polymorphism (SNP) markers and (iii) F, based on a 5th-generation pedigree. All 11 phenotypic traits showed positive relationships with measures of heterozygosity, especially traits that are most closely related to fitness. Remarkably, the small panel of microsatellite markers produced equally strong HFCs as the large panel of SNP markers. Both marker-based approaches produced stronger correlations with phenotypes than the pedigree-based F, and this did not seem to result from the shortness of our pedigree. We argue that a small panel of microsatellites with high allelic richness may better reflect an individuals realized IBD than previously appreciated, especially in species like the zebra finch, where much of the genome is inherited in large blocks that rarely experience cross-over during meiosis.
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| 5. |
- Forstmeier, Wolfgang, et al.
(författare)
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Trisomy and triploidy are sources of embryo mortality in the zebra finch
- 2010
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 277:1694, s. 2655-2660
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Tidskriftsartikel (refereegranskat)abstract
- Hatching failure is a surprisingly common phenomenon given that natural selection constantly works against it. In birds, an average of about 10 per cent of eggs across species fail to hatch, often owing to the death of embryos. While embryo mortality owing to inbreeding is both well-documented and evolutionarily plausible, this is not true for other sources of mortality. In fact, the basis for hatching failure in natural populations remains largely unexplained. Here, we demonstrate that embryo mortality in captive zebra finches (Taeniopygia guttata) follows from chromosomal aneuploidy or polyploidy. As part of microsatellite genotyping of a captive breeding population, we found 12 individuals ( 3.6%) with three alleles among 331 embryos that had died during development, while there were no such cases observed among 1210 adult birds. Subsequent genotyping of 1920 single nucleotide polymorphism markers distributed across the genome in birds with three alleles at microsatellite loci, and in greater than 1000 normal birds, revealed that the aberrant karyotypes involved cases of both trisomies and triploidy. Cases of both maternally and paternally inherited trisomies resulted from non-disjunction during meiosis. Maternally inherited cases of triploidy were attributable to failure of meiosis leading to diploid eggs, while paternally inherited triploidy could have arisen either from diploid sperm or from dispermy. Our initial microsatellite screening set only had the power to detect less than 10 per cent of trisomies and by extrapolation, our data therefore tentatively suggest that trisomy might be a major cause of embryo mortality in zebra finches.
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| 6. |
- Husby, Arild, et al.
(författare)
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Sex chromosome linked genetic variance and the evolution of sexual dimorphism of quantitative traits
- 2013
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 67:3, s. 609-619
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Tidskriftsartikel (refereegranskat)abstract
- Theory predicts that sex chromsome linkage should reduce intersexual genetic correlations thereby allowing the evolution of sexual dimorphism. Empirical evidence for sex linkage has come largely from crosses and few studies have examined how sexual dimorphism and sex linkage are related within outbred populations. Here, we use data on an array of different traits measured on over 10,000 individuals from two pedigreed populations of birds (collared flycatcher and zebra finch) to estimate the amount of sex-linked genetic variance (h2z). Of 17 traits examined, eight showed a nonzero h2Z estimate but only four were significantly different from zero (wing patch size and tarsus length in collared flycatchers, wing length and beak color in zebra finches). We further tested how sexual dimorphism and the mode of selection operating on the trait relate to the proportion of sex-linked genetic variance. Sexually selected traits did not show higher h2Z than morphological traits and there was only a weak positive relationship between h2Z and sexual dimorphism. However, given the relative scarcity of empirical studies, it is premature to make conclusions about the role of sex chromosome linkage in the evolution of sexual dimorphism.
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| 7. |
- Knief, Ulrich, et al.
(författare)
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QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch
- 2012
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 21:15, s. 3704-3717
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Tidskriftsartikel (refereegranskat)abstract
- The intra- and interspecific diversity of avian beak morphologies is one of the most compelling examples for the power of natural selection acting on a morphological trait. The development and diversification of the beak have also become a textbook example for evolutionary developmental biology, and variation in expression levels of several genes is known to causally affect beak shape. However, until now, no genomic polymorphisms have been identified, which are related to beak morphology in birds. QTL mapping does reveal the location of causal polymorphisms, albeit with poor spatial resolution. Here, we estimate heritability and genetic correlations for beak length, depth and width and perform a QTL linkage analysis for these traits based on 1404 informative single-nucleotide polymorphisms genotyped in a four-generation pedigree of 992 captive zebra finches (Taeniopygia guttata). Beak size, relative to body size, was sexually dimorphic (larger in males). Heritability estimates ranged from 0.47 for beak length to 0.74 for beak width. QTL mapping revealed four to five regions of significant or suggestive genome-wide linkage for each of the three beak dimensions (nine different regions in total). Eight out of 11 genes known to influence beak morphology are located in these nine peak regions. Five QTL do not cover known candidates demonstrating that yet unknown genes or regulatory elements may influence beak morphology in the zebra finch.
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| 8. |
- Schielzeth, Holger, et al.
(författare)
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QTL linkage mapping of wing length in zebra finch using genome-wide single nucleotide polymorphisms markers
- 2012
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 21:2, s. 329-339
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Tidskriftsartikel (refereegranskat)abstract
- Avian wing length is an important trait that covaries with the ecology and migratory behaviour of a species and tends to change rapidly when the conditions are altered. Long-distance migrants typically have longer wings than short-distance migrants and sedentary species, and long-winged species also tend to be more dispersive. Although the substantial heritability of avian wing length is well established, the identification of causal genes has remained elusive. Based on large-scale genotyping of 1404 informative single nucleotide polymorphisms (SNP) in a captive population of 1067 zebra finches, we here show that the within-population variation of relative wing length (h(2) = 0.74 +/- 0.05) is associated with standing genetic variation in at least six genomic regions (one genome-wide significant and five suggestive). The variance explained by these six quantitative trait loci (QTL) sums to 36.8% of the phenotypic variance (half of the additive genetic variance), although this likely is an overestimate attributable to the Beavis effect. As avian wing length is primarily determined by the length of the primary feathers, we then searched for candidate genes that are related to feather growth. Interestingly, all of the QTL signals co-locate with Wnt growth factors and closely interacting genes (Wnt3a, Wnt5a, Wnt6, Wnt7a, Wnt9a, RhoU and RhoV). Our findings therefore suggest that standing genetic variation in the Wnt genes might be linked to avian wing morphology, although there are many other genes that also fall within the confidence regions.
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| 9. |
- Schielzeth, Holger, et al.
(författare)
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QTL linkage mapping of Zebra finch beak color shows an oligogenic control of a sexually selected trait
- 2012
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 66:1, s. 18-30
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Tidskriftsartikel (refereegranskat)abstract
- Mate choice based on sexual ornaments can impose strong selection, which raises the question of how genetic variation in ornaments is maintained. One mechanism that has been proposed is genic capture. If ornament expression is influenced by general condition and condition is under polygenic control, selection will be inefficient in removing genetic variation. Here we analyze whether the genetic architecture of beak color in a population of zebra finches supports this hypothesis. Zebra finch beak color is commonly assumed to be under strong selection by mate choice, although some of the evidence is ambiguous. We show that beak redness has a heritability of 34% in our population and that it is strongly genetically correlated between the sexes, suggesting that it is largely controlled by the same genes in males and females. We mapped variation in beak redness based on 1404 single-nucleotide polymorphism (SNP) markers genotyped in a large pedigree. We find evidence for linkage on four chromosomes (Tgu1, Tgu5, Tgu13, Tgu21), which together explain a large part of the additive genetic variance. Our finding of genomic regions with major additive effects is not consistent with directional selection and genic capture, but rather suggests a role of antagonistic pleiotropy in maintaining genetic variation.
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| 10. |
- Schielzeth, Holger, et al.
(författare)
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Quantitative genetics and fitness consequences of neophilia in zebra finches
- 2011
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Ingår i: Behavioral Ecology. - : Oxford University Press (OUP). - 1045-2249 .- 1465-7279. ; 22:1, s. 126-134
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Tidskriftsartikel (refereegranskat)abstract
- Consistent between-individual differences in context-general behavioral traits (often called personality traits) are particularly interesting for behavioral ecologists because they might show unexpected cross-context correlations and explain maladaptive behavior. In order to understand their evolutionary significance, it is relevant to know the heritability of these traits and how they relate to reproductive success. This might give insights into selective processes that maintain variation as well as into potential trade-offs. We scored approach to novel objects of 530 captive zebra finches in a familiar environment. Scores were highly repeatable and showed substantial additive genetic variation. We measured reproductive success, promiscuity, and extrapair paternity rates under aviary conditions and calculated linear and nonlinear selection differentials based on fertilization success as well as effects on chick-rearing success of pairs. Approach to novel objects had little influence on these components of reproductive success. However, we found that the social environment ( manipulated operational sex ratios) influenced the correlation between approach to a novel object and the proportion of extrapair paternity. We also found that the sex ratio manipulation affected measures of the intensity of sexual selection. Both effects were stronger in males than in females. We conclude that despite the lack of differences in overall reproductive success, approach to novel objects reflects variation in reproductive strategies.
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