| 1. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 2. |
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| 3. |
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| 4. |
- Lindblad-Toh, Kerstin, et al.
(författare)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Tidskriftsartikel (refereegranskat)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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| 5. |
- Saastamoinen, Marjo, et al.
(författare)
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Genetics of dispersal
- 2018
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Ingår i: Biological Reviews. - : Wiley. - 1464-7931 .- 1469-185X. ; 93:1, s. 574-599
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Forskningsöversikt (refereegranskat)abstract
- Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal-related phenotypes or evidence for the micro-evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment-dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non-additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non-equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context-dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits.
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| 6. |
- Hoppe, Camilla, et al.
(författare)
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Intake and sources of gluten in 20- to 75-year-old Danish adults: a national dietary survey
- 2017
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Ingår i: European Journal of Nutrition. - : Springer Science and Business Media LLC. - 1436-6207 .- 1436-6215 .- 1435-1293. ; 56:1, s. 107-117
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Celiac disease, an immunological response triggered by gluten, affects ~1 % of the Western population. Information concerning gluten intake in the general population is scarce. We determined intake of gluten from wheat, barley, rye and oat in the Danish National Survey of Diet and Physical Activity 2005–2008. The study population comprised a random cross-sectional sample of 1494 adults 20–75 years, selected from the Danish Civil Registration System. Methods: Protein content in wheat, rye, barley and oat was determined from the National Danish Food Composition Table and multiplied with the amount of cereal used in recipes. Amount of gluten was calculated as amount of cereal protein ×0.80 for wheat and oat, ×0.65 for rye and ×0.50 for barley. Dietary intake was recorded daily during seven consecutive days in pre-coded food diaries with open-answer possibilities. Results: Mean total gluten intake was 10.4 ± 4.4 g/day (10th–90th percentiles; 5.4–16.2 g/day), in men 12.0 ± 4.6 g/day and 9.0 ± 3.4 g/day in women. It was higher among men than among women in all age groups (20–75 years; P
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| 7. |
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| 8. |
- Mason, Lucy R., et al.
(författare)
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Population responses of bird populations to climate change on two continents vary with species’ ecological traits but not with direction of change in climate suitability
- 2019
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Ingår i: Climatic Change. - : Springer Science and Business Media LLC. - 0165-0009 .- 1573-1480. ; 157:3-4, s. 337-354
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Tidskriftsartikel (refereegranskat)abstract
- Climate change is a major global threat to biodiversity with widespread impacts on ecological communities. Evidence for beneficial impacts on populations is perceived to be stronger and more plentiful than that for negative impacts, but few studies have investigated this apparent disparity, or how ecological factors affect population responses to climatic change. We examined the strength of the relationship between species-specific regional population changes and climate suitability trends (CST), using 30-year datasets of population change for 525 breeding bird species in Europe and the USA. These data indicate a consistent positive relationship between population trend and CST across the two continents. Importantly, we found no evidence that this positive relationship differs between species expected to be negatively and positively impacted across the entire taxonomic group, suggesting that climate change is causing equally strong, quantifiable population increases and declines. Species’ responses to changing climatic suitability varied with ecological traits, however, particularly breeding habitat preference and body mass. Species associated with inland wetlands responded most strongly and consistently to recent climatic change. In Europe, smaller species also appeared to respond more strongly, whilst the relationship with body mass was less clear-cut for North American birds. Overall, our results identify the role of certain traits in modulating responses to climate change and emphasise the importance of long-term data on abundance for detecting large-scale species’ responses to environmental changes.
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| 9. |
- Stephens, Philip A., et al.
(författare)
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Consistent response of bird populations to climate change on two continents
- 2016
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 352:6281, s. 84-87
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Tidskriftsartikel (refereegranskat)abstract
- Global climate change is a major threat to biodiversity. Large-scale analyses have generally focused on the impacts of climate change on the geographic ranges of species and on phenology, the timing of ecological phenomena. We used long-term monitoring of the abundance of breeding birds across Europe and the United States to produce, for both regions, composite population indices for two groups of species: those for which climate suitability has been either improving or declining since 1980. The ratio of these composite indices, the climate impact indicator (CII), reflects the divergent fates of species favored or disadvantaged by climate change. The trend in CII is positive and similar in the two regions. On both continents, interspecific and spatial variation in population abundance trends are well predicted by climate suitability trends.
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| 10. |
- Bebbington, Natalie A., et al.
(författare)
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A Nordic survey of CT doses in hybrid PET/CT and SPECT/CT examinations
- 2019
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Ingår i: EJNMMI Physics. - : Springer Science and Business Media LLC. - 2197-7364. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Computed tomography (CT) scans are routinely performed in positron emission tomography (PET) and single photon emission computed tomography (SPECT) examinations globally, yet few surveys have been conducted to gather national diagnostic reference level (NDRL) data for CT radiation doses in positron emission tomography/computed tomography (PET/CT) and single photon emission computed tomography/computed tomography (SPECT/CT). In this first Nordic-wide study of CT doses in hybrid imaging, Nordic NDRL CT doses are suggested for PET/CT and SPECT/CT examinations specific to the clinical purpose of CT, and the scope for optimisation is evaluated. Data on hybrid imaging CT exposures and clinical purpose of CT were gathered for 5 PET/CT and 8 SPECT/CT examinations via designed booklet. For each included dataset for a given facility and scanner type, the computed tomography dose index by volume (CTDIvol) and dose length product (DLP) was interpolated for a 75-kg person (referred to as CTDIvol,75kg and DLP75kg). Suggested NDRL (75th percentile) and achievable doses (50th percentile) were determined for CTDIvol,75kg and DLP75kg according to clinical purpose of CT. Differences in maximum and minimum doses (derived for a 75-kg patient) between facilities were also calculated for each examination and clinical purpose. Results: Data were processed from 83 scanners from 43 facilities. Data were sufficient to suggest Nordic NDRL CT doses for the following: PET/CT oncology (localisation/characterisation, 15 systems); infection/inflammation (localisation/characterisation, 13 systems); brain (attenuation correction (AC) only, 11 systems); cardiac PET/CT and SPECT/CT (AC only, 30 systems); SPECT/CT lung (localisation/characterisation, 12 systems); bone (localisation/characterisation, 30 systems); and parathyroid (localisation/characterisation, 13 systems). Great variations in dose were seen for all aforementioned examinations. Greatest differences in DLP75kg for each examination, specific to clinical purpose, were as follows: SPECT/CT lung AC only (27.4); PET/CT and SPECT/CT cardiac AC only (19.6); infection/inflammation AC only (18.1); PET/CT brain localisation/characterisation (16.8); SPECT/CT bone localisation/characterisation (10.0); PET/CT oncology AC only (9.0); and SPECT/CT parathyroid localisation/characterisation (7.8). Conclusions: Suggested Nordic NDRL CT doses are presented according to clinical purpose of CT for PET/CT oncology, infection/inflammation, brain, PET/CT and SPECT/CT cardiac, and SPECT/CT lung, bone, and parathyroid. The large variation in doses suggests great scope for optimisation in all 8 examinations.
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| 11. |
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| 12. |
- Husby, Arild, et al.
(författare)
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Testing Mechanisms of Bergmann's Rule : Phenotypic Decline but No Genetic Change in Body Size in Three Passerine Bird Populations
- 2011
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Ingår i: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 178:2, s. 202-213
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Tidskriftsartikel (refereegranskat)abstract
- Bergmann's rule predicts a decrease in body size with increasing temperature and has much empirical support. Surprisingly, we know very little about whether "Bergmann size clines" are due to a genetic response or are a consequence of phenotypic plasticity. Here, we use data on body size (mass and tarsus length) from three long-term (1979-2008) study populations of great tits (Parus major) that experienced a temperature increase to examine mechanisms behind Bergmann's rule. We show that adult body mass decreased over the study period in all populations and that tarsus length increased in one population. Both body mass and tarsus length were heritable and under weak positive directional selection, predicting an increase, rather than a decrease, in body mass. There was no support for microevolutionary change, and thus the observed declines in body mass were likely a result of phenotypic plasticity. Interestingly, this plasticity was not in direct response to temperature changes but seemed to be due to changes in prey dynamics. Our results caution against interpreting recent phenotypic body size declines as adaptive evolutionary responses to temperature changes and highlight the importance of considering alternative environmental factors when testing size clines.
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| 13. |
- Jensen, Tina Kold, et al.
(författare)
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Prenatal Exposure to Phthalates and Anogenital Distance in Male Infants from a Low-Exposed Danish Cohort (2010-2012)
- 2016
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Ingår i: Journal of Environmental Health Perspectives. - : National Institute of Environmental Health Sciences (NIEHS). - 0091-6765 .- 1552-9924. ; 124:7, s. 1107-1113
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Phthalates comprise a large class of chemicals used in a variety of consumer products. Several have anti-androgenic properties, and in rodents prenatal exposure has been associated with reduced anogenital distance (AGD)-the distance from the anus to the genitals in male offspring. Few human studies have been conducted, but associations between the anti-androgenic phthalates and male AGD have been reported. OBJECTIVE: We aimed to study the association between phthalate exposure in late pregnancy in Danish women pregnant in 2010-2012 and AGD in their male infants at 3 months of age (n = 273). METHODS: In the Odense child cohort study, urinary concentrations of 12 phthalate metabolites of diethyl, di-n-butyl, diisobutyl, di(2-ethylhexyl), butylbenzyl, and diisononyl phthalate (DEP, DnBP, DiBP, DEHP, BBzP, and DiNP, respectively) were measured among 245 mothers of boys at approximately gestational week 28 (range, 20.4-30.4) and adjusted for osmolality. AGD, penile width, and weight were measured 3 months after the expected date of birth. Associations between prenatal phthalate and AGD and penile width were estimated using multivariable linear regression adjusting for age and weight-for-age standard deviation score. RESULTS: Phthalate levels were lower in this population than in a recent Swedish study in which phthalates were measured in the first trimester. No consistent associations were seen between any prenatal phthalate and AGD or penile width. Most associations were negative for exposures above the first quartile, and for ln-transformed exposures modeled as continuous variables, but there were no consistent dose-response patterns, and associations were not statistically significant (p > 0.05). CONCLUSION: We found no significant trends towards shorter AGD in boys with higher phthalates exposures in this low exposed Danish population.
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| 14. |
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| 15. |
- Kawakami, Takeshi, et al.
(författare)
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Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array
- 2014
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 14:6, s. 1248-1260
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Tidskriftsartikel (refereegranskat)abstract
- With the access to draft genome sequence assemblies and whole-genome resequencing data from population samples, molecular ecology studies will be able to take truly genome-wide approaches. This now applies to an avian model system in ecological and evolutionary research: Old World flycatchers of the genus Ficedula, for which we recently obtained a 1.1Gb collared flycatcher genome assembly and identified 13 million single-nucleotide polymorphism (SNP)s in population resequencing of this species and its sister species, pied flycatcher. Here, we developed a custom 50K Illumina iSelect flycatcher SNP array with markers covering 30 autosomes and the Z chromosome. Using a number of selection criteria for inclusion in the array, both genotyping success rate and polymorphism information content (mean marker heterozygosity=0.41) were high. We used the array to assess linkage disequilibrium (LD) and hybridization in flycatchers. Linkage disequilibrium declined quickly to the background level at an average distance of 17kb, but the extent of LD varied markedly within the genome and was more than 10-fold higher in genomic islands' of differentiation than in the rest of the genome. Genetic ancestry analysis identified 33 F-1 hybrids but no later-generation hybrids from sympatric populations of collared flycatchers and pied flycatchers, contradicting earlier reports of backcrosses identified from much fewer number of markers. With an estimated divergence time as recently as <1Ma, this suggests strong selection against F-1 hybrids and unusually rapid evolution of reproductive incompatibility in an avian system.
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| 16. |
- Kragh, Kristin, et al.
(författare)
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Convergent and divergent validity of the schedule for affective disorders and schizophrenia for school-age children - present and lifetime version diagnoses in a sample of children and adolescents with obsessive-compulsive disorder.
- 2019
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Ingår i: Nordic journal of psychiatry. - : Informa UK Limited. - 1502-4725 .- 0803-9488. ; 73:2, s. 111-117
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Tidskriftsartikel (refereegranskat)abstract
- The presence of comorbid conditions associated with paediatric obsessive-compulsive disorder (OCD) is reported to range from 50 to 80% and to have an impact on treatment outcome. Accurate identification of comorbid psychiatric disorders is necessary in order to provide personalised care. Reliable and valid diagnostic interviews are essential in the process of establishing the correct diagnoses. The objective of this study was to evaluate the convergent and divergent validity of four diagnose categories generated by the Schedule for Affective Disorders and Schizophrenia for School-Age Children - Present and Lifetime Version (K-SADS-PL). The diagnose categories were: anxiety, depression, attention deficit hyperactivity disorder (ADHD), and oppositional defiant disorder (ODD). The K-SADS-PL was applied in a clinical sample of youth aged 7-17 years (N=269), who were participants in the Nordic long-term OCD-treatment study (NordLOTS). Youth and parents completed measures to evaluate symptoms of anxiety, depression, ADHD, and ODD. Convergent and divergent validity of K-SADS-PL anxiety diagnosis was supported based on both anxiety self- and parent-reports. Similarly, support was found for convergent and divergent validity of ADHD and ODD diagnoses. For depressive disorder, support for convergent validity was found based on the depression self-report. Support for divergent validity of depression was found based on both the depression self- and parent-reports. Results of the present study suggest that the K-SADS-PL generates valid diagnoses of comorbid anxiety disorders, depression disorders, ODD, and ADHD in children and adolescents with OCD.
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| 17. |
- Lehikoinen, Aleksi, et al.
(författare)
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Declining population trends of European mountain birds
- 2019
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 25:2, s. 577-588
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Tidskriftsartikel (refereegranskat)abstract
- Mountain areas often hold special species communities, and they are high on the list of conservation concern. Global warming and changes in human land use, such as grazing pressure and afforestation, have been suggested to be major threats for biodiversity in the mountain areas, affecting species abundance and causing distribution shifts towards mountaintops. Population shifts towards poles and mountaintops have been documented in several areas, indicating that climate change is one of the key drivers of species’ distribution changes. Despite the high conservation concern, relatively little is known about the population trends of species in mountain areas due to low accessibility and difficult working conditions. Thanks to the recent improvement of bird monitoring schemes around Europe, we can here report a first account of population trends of 44 bird species from four major European mountain regions: Fennoscandia, UK upland, south-western (Iberia) and south-central mountains (Alps), covering 12 countries. Overall, the mountain bird species declined significantly (−7%) during 2002–2014, which is similar to the declining rate in common birds in Europe during the same period. Mountain specialists showed a significant −10% decline in population numbers. The slope for mountain generalists was also negative, but not significantly so. The slopes of specialists and generalists did not differ from each other. Fennoscandian and Iberian populations were on average declining, while in United Kingdom and Alps, trends were nonsignificant. Temperature change or migratory behaviour was not significantly associated with regional population trends of species. Alpine habitats are highly vulnerable to climate change, and this is certainly one of the main drivers of mountain bird population trends. However, observed declines can also be partly linked with local land use practices. More efforts should be undertaken to identify the causes of decline and to increase conservation efforts for these populations.
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| 18. |
- Lindner, Melanie, et al.
(författare)
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Rapid changes in DNA methylation associated with the initiation of reproduction in a small songbird
- 2021
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 30:15, s. 3645-3659
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Tidskriftsartikel (refereegranskat)abstract
- Species with a circannual life cycle need to match the timing of their life history events to the environment to maximize fitness. However, our understanding of how circannual traits such as timing of reproduction are regulated on a molecular level remains limited. Recent studies have implicated that epigenetic mechanisms can be an important part in the processes that regulate circannual traits. Here, we explore the role of DNA methylation in mediating reproductive timing in a seasonally breeding bird species, the great tit (Parus major), using genome-wide DNA methylation data from individual females that were blood sampled repeatedly throughout the breeding season. We demonstrate rapid and directional changes in DNA methylation within the promoter region of several genes, including a key transcription factor (NR5A1) known from earlier studies to be involved in the initiation of timing of reproduction. Interestingly, the observed changes in DNA methylation at NR5A1 identified here are in line with earlier gene expression studies of reproduction in chicken, indicating that the observed shifts in DNA methylation at this gene can have a regulatory role. Our findings provide an important step towards elucidating the genomic mechanism that mediates seasonal timing of a key life history traits and provide support for the idea that epigenetic mechanisms may play an important role in circannual traits.
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| 19. |
- Lindner, Melanie, et al.
(författare)
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Temporal changes in DNA methylation and RNA expression in a small song bird : within- and between-tissue comparisons
- 2021
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Ingår i: BMC Genomics. - : BioMed Central (BMC). - 1471-2164. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of DNA methylation we need simultaneous within-individual assessment of methylation changes and gene expression changes over time. Within-individual repeated sampling of tissues, which are essential for trait expression is, however, unfeasible (e.g. specific brain regions, liver and ovary for reproductive timing). Here, we explore to what extend between-individual changes in DNA methylation in a tissue accessible for repeated sampling (red blood cells (RBCs)) reflect such patterns in a tissue unavailable for repeated sampling (liver) and how these DNA methylation patterns are associated with gene expression in such inaccessible tissues (hypothalamus, ovary and liver). For this, 18 great tit (Parus major) females were sacrificed at three time points (n=6 per time point) throughout the pre-laying and egg-laying period and their blood, hypothalamus, ovary and liver were sampled.Results: We simultaneously assessed DNA methylation changes (via reduced representation bisulfite sequencing) and changes in gene expression (via RNA-seq and qPCR) over time. In general, we found a positive correlation between changes in CpG site methylation in RBCs and liver across timepoints. For CpG sites in close proximity to the transcription start site, an increase in RBC methylation over time was associated with a decrease in the expression of the associated gene in the ovary. In contrast, no such association with gene expression was found for CpG site methylation within the gene body or the 10kb up- and downstream regions adjacent to the gene body.Conclusion: Temporal changes in DNA methylation are largely tissue-general, indicating that changes in RBC methylation can reflect changes in DNA methylation in other, often less accessible, tissues such as the liver in our case. However, associations between temporal changes in DNA methylation with changes in gene expression are mostly tissue- and genomic location-dependent. The observation that temporal changes in DNA methylation within RBCs can relate to changes in gene expression in less accessible tissues is important for a better understanding of how environmental conditions shape traits that temporally change in expression in wild populations.
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| 20. |
- Morrison, Catriona A., et al.
(författare)
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Covariation in population trends and demography reveals targets for conservation action
- 2021
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Ingår i: Royal Society of London. Proceedings B. Biological Sciences. - : The Royal Society. - 1471-2954. ; 288:1946, s. 20202955-20202955
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Tidskriftsartikel (refereegranskat)abstract
- Wildlife conservation policies directed at common and widespread, but declining, species are difficult to design and implement effectively, as multiple environmental changes are likely to contribute to population declines. Conservation actions ultimately aim to influence demographic rates, but targeting actions towards feasible improvements in these is challenging in widespread species with ranges that encompass a wide range of environmental conditions. Across Europe, sharp declines in the abundance of migratory landbirds have driven international calls for action, but actions that could feasibly contribute to population recovery have yet to be identified. Targeted actions to improve conditions on poor-quality sites could be an effective approach, but only if local conditions consistently influence local demography and hence population trends. Using long-term measures of abundance and demography of breeding birds at survey sites across Europe, we show that co-occurring species with differing migration behaviours have similar directions of local population trends and magnitudes of productivity, but not survival rates. Targeted actions to boost local productivity within Europe, alongside large-scale (non-targeted) environmental protection across non-breeding ranges, could therefore help address the urgent need to halt migrant landbird declines. Such demographic routes to recovery are likely to be increasingly needed to address global wildlife declines.
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| 21. |
- Mäkinen, Hannu, et al.
(författare)
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Temporally replicated DNA methylation patterns in great tit using reduced representation bisulfite sequencing
- 2019
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Ingår i: Scientific Data. - : NATURE PUBLISHING GROUP. - 2052-4463. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Seasonal timing of reproduction is an important fitness trait in many plants and animals but the underlying molecular mechanism for this trait is poorly known. DNA methylation is known to affect timing of reproduction in various organisms and is therefore a potential mechanism also in birds. Here we describe genome wide data aiming to detect temporal changes in methylation in relation to timing of breeding using artificial selection lines of great tits (Parus major) exposed to contrasting temperature treatments. Methylation levels of DNA extracted from erythrocytes were examined using reduced representation bisulfite sequencing (RRBS). In total, we obtained sequencing data from 63 libraries over four different time points from 16 birds with on average 20 million quality filtered reads per library. These data describe individual level temporal variation in DNA methylation throughout the breeding season under experimental temperature regimes and provides a resource for future studies investigating the role of temporal changes in DNA methylation in timing of reproduction.
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| 22. |
- Niskanen, Alina K., et al.
(författare)
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Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation
- 2020
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:25, s. 14584-14592
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Tidskriftsartikel (refereegranskat)abstract
- Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environmental conditions and differ in demographic history and genetic composition, characteristics that can affect the severity of inbreeding depression. We utilized extensive long-term data on more than 3,100 individuals from eight islands in an insular house sparrow metapopulation to examine the generality of inbreeding effects. Using genomic estimates of realized inbreeding, we discovered that inbred individuals had lower survival probabilities and produced fewer recruiting offspring than noninbred individuals. Inbreeding depression, measured as the decline in fitness-related traits per unit inbreeding, did not vary appreciably among populations or with time. As a consequence, populations with more resident inbreeding (due to their demographic history) paid a higher total fitness cost, evidenced by a larger variance in fitness explained by inbreeding within these populations. Our results are in contrast to the idea that effects of inbreeding generally depend on ecological factors and genetic differences among populations, and expand the understanding of inbreeding depression in natural subdivided populations.
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| 23. |
- Rice, Amber M., et al.
(författare)
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Optimizing the trade-off between offspring number and quality in unpredictable environments: Testing the role of differential androgen transfer to collared flycatcher eggs
- 2013
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Ingår i: Hormones and Behavior. - : Elsevier BV. - 1095-6867 .- 0018-506X. ; 63:5, s. 813-822
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Tidskriftsartikel (refereegranskat)abstract
- According to the brood reduction hypothesis, parents adjust their brood size in response to current environmental conditions. When resources are abundant, parents can successfully raise all hatched offspring, but when resources are scarce, brood reduction, i.e., the sacrifice of some siblings to secure the quality of a subset of offspring, may maximize fitness. Differential transfer of maternal androgens is one potential proximate mechanism through which female birds may facilitate brood reduction because it may alter the relative competitive ability of sibling nestlings. We tested the hypothesis that female collared flycatchers (Ficedula albicollis) manipulate sibling competition by transferring less androgens to eggs late in the laying sequence. We experimentally elevated androgen levels in i) whole clutches and ii) only the two last laid eggs, and compared growth and begging behavior of offspring from these treatments with a control treatment. By using three treatments and video assessment of begging, we examined the effects of within-clutch patterns of yolk androgen transfer on levels of sibling competition in situ. When androgens were elevated in only the two last laid eggs, begging was more even among siblings compared to control nests. We also found that female nestlings receiving additional yolk androgens showed higher mass gain later in the breeding season, while their male counterparts did not. Our results suggest that females may improve reproductive success in unpredictable environments by altering within-clutch patterns of yolk androgen transfer. We discuss the possibility that life-history divergence between the co-occurring collared and pied flycatcher (Ficedula hypoleuca) is amplified by patterns of yolk androgen transfer. (C) 2013 Elsevier Inc. All rights reserved.
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| 24. |
- Silva, C. N. S., et al.
(författare)
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Insights into the genetic architecture of morphological traits in two passerine bird species
- 2017
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 119:3, s. 197-205
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict evolutionary dynamics. The number of causal loci, magnitude of the effects and location in the genome are, however, still largely unknown. Here, we use genome-wide single-nucleotide polymorphism (SNP) data from two large-scale data sets on house sparrows and collared flycatchers to examine the genetic architecture of different morphological traits (tarsus length, wing length, body mass, bill depth, bill length, total and visible badge size and white wing patches). Genomic heritabilities were estimated using relatedness calculated from SNPs. The proportion of variance captured by the SNPs (SNP-based heritability) was lower in house sparrows compared with collared flycatchers, as expected given marker density (6348 SNPs in house sparrows versus 38 689 SNPs in collared flycatchers). Indeed, after downsampling to similar SNP density and sample size, this estimate was no longer markedly different between species. Chromosome-partitioning analyses demonstrated that the proportion of variance explained by each chromosome was significantly positively related to the chromosome size for some traits and, generally, that larger chromosomes tended to explain proportionally more variation than smaller chromosomes. Finally, we found two genome-wide significant associations with very small-effect sizes. One SNP on chromosome 20 was associated with bill length in house sparrows and explained 1.2% of phenotypic variation (V-P), and one SNP on chromosome 4 was associated with tarsus length in collared flycatchers (3% of V-P). Although we cannot exclude the possibility of undetected large-effect loci, our results indicate a polygenic basis for morphological traits.
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| 25. |
- Thompson, Keith M, et al.
(författare)
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Articular, monoclonal gamma3 heavy-chain deposition disease: characterization of a partially deleted heavy-chain gene and its protein product synthesized in vivo and in vitro.
- 2003
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Ingår i: Arthritis and Rheumatism. - : Wiley. - 1529-0131 .- 0004-3591. ; 48:11, s. 3266-3271
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Tidskriftsartikel (refereegranskat)abstract
- Objective A patient presented with heavy-chain deposition disease (HCDD), exhibiting severe erosive polyarthropathy caused by synovial deposits of abnormal monoclonal, heavily deleted free 3 heavy chains lacking the VH and CH1 domains. The absence of VH was surprising, since it is considered important for pathogenic tissue deposition. This study was undertaken to analyze the genetic structure of the heavy chain, the protein product synthesized in vitro, and that deposited in the synovium in comparison with the serum and urinary proteins. Methods Hybridomas were made by fusion of blood and bone marrow mononuclear cells with mouse myeloma cells. Cloned B cell hybridomas secreting 3 were selected and analyzed by polymerase chain reaction. Purified hybridoma Ig was sequenced by Edman degradation. Antiserum raised to a peptide corresponding to residues 2-15 of the truncated VH was used in Western blots of synovial tissue. Results The hybridomas secreted free 3 chains consisting of a VH4 gene truncated 21 nucleotides into the first complementarity-determining region and then reading straight into the hinge region. The amino acid sequence confirmed the presence of residues 1-32 of the VH4 gene. Immunoblotting of synovial tissue showed the presence of Ig with truncated VH. Conclusion The 3 heavy chain had a deletion of VH from codon 33 and of the entire CH1. In vivo, the 32 VH amino acids were proteolytically degraded. In the joint, however, the 32 residues of VH remained intact, consistent with a pathogenic role of VH for tissue deposition. To our knowledge, this is the first reported case of HCDD causing an erosive, polyarticular arthropathy as the dominating clinical feature.
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