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| 2. |
- Karlsson, Maria, et al.
(författare)
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House sparrow Passer domesticus survival is not associated with MHC-I diversity, but possibly with specific MHC-I alleles
- 2015
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Ingår i: Journal of Avian Biology. - : Wiley. - 0908-8857 .- 1600-048X. ; 46:2, s. 167-174
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Tidskriftsartikel (refereegranskat)abstract
- The MHC (Major Histocompatibility Complex) plays an important role in the immune system of vertebrates. MHC genes are extremely polymorphic and this variation is considered to be maintained by selection from pathogens. We investigate whether MHC diversity (number of different alleles per individual) affects the survival and recruitment of nestling house sparrows. We hypothesize that individuals with higher MHC diversity can recognize and combat a wider range of pathogens, and therefore are more likely to survive and recruit into the breeding population. Additionally, we hypothesize that specific MHC class I alleles (MHC-I) could be associated with survival and recruitment. We screened MHC-I genotypes in 518 house sparrow chicks hatched on Lundy Island but we found no evidence for a relationship between nestling survival, post-fledging survival or recruitment success with MHC diversity. Then we investigated effects of specific MHC-I alleles in 195 individuals from a single cohort. Twenty-one MHC-I alleles were tested for relationships with nestling survival, post-fledging survival and recruitment, and we detected associations with survival for three different alleles. This pattern was, however, not different to what would be expected from random, so we could not conclude that particular MHC-I alleles are associated with survival in house sparrows on Lundy Island. Nonetheless, one of these alleles (1105) showed both a tendency for a higher probability of surviving in nestlings, and a significant association with survival in fledglings. We envision that allele 1105 could be an interesting candidate gene for testing associations with survival in house sparrows in the future.
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| 3. |
- Küpper, Clemens, et al.
(författare)
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Kentish versus Snowy Plover: Phenotypic and Genetic Analyses of Charadrius alexandrinus Reveal Divergence of Eurasian and American Subspecies
- 2009
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Ingår i: Auk. - 0004-8038. ; 126:4, s. 839-852
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Tidskriftsartikel (refereegranskat)abstract
- Abstract.—Many shorebird species have widespread geographic distributions comprising several continents. Because shorebirds are excellent flyers and can migrate large distances, it is often unclear whether reproductive barriers between subspecies and populations from different continents exist. Kentish–Snowy Plovers (Charadrius alexandrinus) are cosmopolitan shorebirds. Whether the American and Eurasian subspecies—Snowy Plover and Kentish Plover, respectively—constitute a single species is the subject of a longstanding debate. We examined the divergence between American and Eurasian populations to reassess the current taxonomy by comparing genetic and phenotypic characters of the American subspecies C. a. nivosus and the Eurasian subspecies C. a. alexandrinus from seven populations. Genetic analyses revealed that American and Eurasian populations have strongly diverged, the Kentish Plover being more closely related to the White-fronted Plover (C. marginatus) than to the Snowy Plover. These results were consistent across all assessed nuclear markers (26 microsatellites and a partial CHD sequence) and two mitochondrial markers (ND3 and ATPase 6/8). Within subspecies, populations sampled across large geographic distances were not genetically differentiated (all Fst ≤ 0.01 and all Φst ≤ 0.06), which suggests panmixia. Snowy Plovers differed morphologically from Kentish Plovers, having significantly shorter tarsi and wings. Chick plumage and calls also may serve as diagnostic characters to distinguish Snowy and Kentish plovers, although more data are needed to quantify these differences. Our combined results suggest that the taxonomic status of C. alexandrinus needs to be revised, and we propose that Kentish Plover and Snowy Plover be recognized as separate species: C. alexandrinus and C. nivosus, respectively.
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| 5. |
- Küpper, Clemens, et al.
(författare)
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Heterozygosity-fitness correlations of conserved microsatellite markers in Kentish plovers Charadrius alexandrinus
- 2010
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Ingår i: Molecular Ecology. - 1365-294X. ; 19:23, s. 5172-5185
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Tidskriftsartikel (refereegranskat)abstract
- Abstract Heterozygosity-fitness correlations (HFCs) are frequently used to examine the relationship between genetic diversity and fitness. Most studies have reported positive HFCs, although there is a strong bias towards investigating HFCs in genetically impoverished populations. We investigated HFCs in a large genetically diverse breeding population of Kentish plovers Charadrius alexandrinus in southern Turkey. This small shorebird exhibits highly variable mating and care systems, and it is becoming an ecological model species to understand breeding system evolution. Using 11 conserved and six anonymous microsatellite markers, we tested whether and how heterozygosity was associated with chick survival, tarsus and body mass growth controlling for nongenetic effects (chick sex, hatching date, length of biparental care and site quality) that influence survival and growth. There was no genome-wide effect of heterozygosity on fitness, and we did not find any significant effects of heterozygosity on growth rates. However, two of the 11 conserved markers displayed an association with offspring survival: one marker showed a positive HFC, whereas the other marker showed a negative HFC. Heterozygosity at three further conserved loci showed significant interaction with nongenetic variables. In contrast, heterozygosity based on anonymous microsatellite loci was not associated with fitness or growth. Markers that were correlated with chick survival were not more likely to be located in exons or introns than other markers that lacked this association.
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| 6. |
- Culina, Antica, et al.
(författare)
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Connecting the data landscape of long-term ecological studies : The SPI-Birds data hub
- 2021
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Ingår i: Journal of Animal Ecology. - : John Wiley & Sons. - 0021-8790 .- 1365-2656. ; 90:9, s. 2147-2160
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Tidskriftsartikel (refereegranskat)abstract
- The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database ()-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.
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| 7. |
- Dawson, Deborah A., et al.
(författare)
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Gene order and recombination rate in homologous chromosome regions of the chicken and a passerine bird
- 2007
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 24:7, s. 1537-1552
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Tidskriftsartikel (refereegranskat)abstract
- Genome structure has been found to be highly conserved between distantly related birds and recent data for a limited part of the genome suggest that this is true also for the gene order (synteny) within chromosomes. Here, we confirm that synteny is maintained for large chromosomal regions in chicken and a passerine bird, the great reed warbler Acrocephalus arundinaceus, with few rearrangements, but in contrast show that the recombination-based linkage map distances differ substantially between these species. We assigned a chromosomal location based on sequence similarity to the chicken genome sequence to a set of inicrosatellite loci mapped in a pedigree of great reed warblers. We detected homologous loci on 14 different chromosomes corresponding to chicken chromosomes Gga1-5, 7-9, 13, 19, 20, 24, 25, and Z. It is known that 2 passerine macrochromosomes correspond to the chicken chromosome Gga1. Homology of 2 different great reed warbler linkage groups (LG13 and LG5) to Gga1 allowed us to locate the split to a position between 20.8 and 84.8 Mb on Gga1. Data from the 5 chromosomal regions (on Gga1, 2, 3, 5, and Z) with 3 or more homologous loci showed that synteny was conserved with the exception of 2 large previously unreported inversions on Gga1/LG5 and Gga2/LG3, respectively. Recombination data from the 9 chromosomal regions in which we identified 2 or more homologous loci (accounting for the inversions) showed that the linkage map distances in great reed warblers were only 6.3% and 13.3% of those in chickens for males and females, respectively. This is likely to reflect the true interspecific difference in recombination rate because our markers were not located in potentially low-recombining regions: several linkage groups covered a substantial part of their corresponding chicken chromosomes and were not restricted to centromeres. We conclude that recombination rates may differ strongly between bird species with highly conserved genome structure and synteny and that the chicken linkage map may not be suitable, in terms of genetic distances, as a model for all bird species.
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| 8. |
- Dawson, Deborah A., et al.
(författare)
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New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility - as demonstrated for birds
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:3, s. 475-494
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a new approach to create microsatellite primer sets that have high utility across a wide range of species. The success of this method was demonstrated using birds. We selected 35 avian EST microsatellite loci that had a high degree of sequence homology between the zebra finch Taeniopygia guttata and the chicken Gallus gallus and designed primer sets in which the primer bind sites were identical in both species. For 33 conserved primer sets, on average, 100% of loci amplified in each of 17 passerine species and 99% of loci in five non-passerine species. The genotyping of four individuals per species revealed that 24-76% (mean 48%) of loci were polymorphic in the passerines and 18-26% (mean 21%) in the non-passerines. When at least 17 individuals were genotyped per species for four Fringillidae finch species, 71-85% of loci were polymorphic, observed heterozygosity was above 0.50 for most loci and no locus deviated significantly from Hardy-Weinberg proportions. This new set of microsatellite markers is of higher cross-species utility than any set previously designed. The loci described are suitable for a range of applications that require polymorphic avian markers, including paternity and population studies. They will facilitate comparisons of bird genome organization, including genome mapping and studies of recombination, and allow comparisons of genetic variability between species whilst avoiding ascertainment bias. The costs and time to develop new loci can now be avoided for many applications in numerous species. Furthermore, our method can be readily used to develop microsatellite markers of high utility across other taxa.
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| 9. |
- Deans, Andrew R, et al.
(författare)
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Finding Our Way through Phenotypes.
- 2015
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Ingår i: PLoS Biology. - : Public Library of Science (PLoS). - 1545-7885. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.
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| 10. |
- Ekblom, Robert, et al.
(författare)
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Digital gene expression analysis of the zebra finch genome
- 2010
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11, s. 219-
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Tidskriftsartikel (refereegranskat)abstract
- Background: In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results: Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions: Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates.
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