| 71. |
- Stapley, Jessica, et al.
(författare)
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Adaptation genomics : the next generation
- 2010
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Ingår i: Trends in Ecology & Evolution. - : Elsevier BV. - 0169-5347 .- 1872-8383. ; 25:12, s. 705-712
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Forskningsöversikt (refereegranskat)abstract
- Understanding the genetics of how organisms adapt to changing environments is a fundamental topic in modern evolutionary ecology. The field is currently progressing rapidly because of advances in genomics technologies, especially DNA sequencing. The aim of this review is to first briefly summarise how next generation sequencing (NGS) has transformed our ability to identify the genes underpinning adaptation. We then demonstrate how the application of these genomic tools to ecological model species means that we can start addressing some of the questions that( have puzzled ecological geneticists for decades such as: How many genes are involved in adaptation? What types of genetic: variation are responsible for adaptation? Does adaptation utilise pre-existing genetic variation or does it require new mutations to arise following an environmental change?
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| 72. |
- Thurfjell, Henrik, et al.
(författare)
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Practical application of indicators for genetic diversity in CBD post-2020 global biodiversity framework implementation
- 2022
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Ingår i: Ecological Indicators. - : Elsevier BV. - 1470-160X .- 1872-7034. ; 142
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Tidskriftsartikel (refereegranskat)abstract
- Genetic diversity is a key aspect of biological variation for the adaptability and survival of populations of species and must be monitored to assure maintenance. We used data from the Swedish Red List 2020 and from published reviews to apply three indicators for genetic diversity proposed for the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity (CBD). We studied a wide range of taxonomic groups, and made more detailed indicator assessments for mammals and herptiles.For indicator 1, the proportion of populations with effective population size Ne > 500, 33% of 22,557 investigated species had a population size estimate that could be used as a proxy for Ne. For herptiles and mammals, 70% and 49% of populations of species, respectively, likely had Ne > 500.Data for evaluation of indicator 2, the proportion of remaining populations or historical range, was available for 20% of all species evaluated for the Red List. Meanwhile, 32% of the herptile and 84% of the mammal populations are maintaining their populations and range.For indicator 3, the number of species or populations in which genetic diversity is monitored using DNA-based methods, there are genetic studies on 3% of all species, and 0.3% are beeing monitored genetically. In contrast, 68% of mammals and 29% of herptiles are studied using DNA, and 8% of mammals and 24% of herptiles are genetically monitored.We conclude that the Red List provides data that are suitable for evaluating the genetic indicators, but the data quality can be improved. We also show that the genetic indicators capture conservation issues of genetic erosion that the Red List misses.There is a synergy in estimating the genetic indicators in parallel with the Red Listing process. We propose that indicator values could be included in national Red Listing as a new category - “genetically threatened”, based on the genetic indicators.
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| 73. |
- Wang, Biao, et al.
(författare)
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Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC
- 2012
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 13, s. 553-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The MHC, which is regarded as the most polymorphic region in the genomes of jawed vertebrates, plays a central role in the immune system by encoding various proteins involved in the immune response. The chicken MHC-B genomic region has a highly streamlined gene content compared to mammalian MHCs. Its core region includes genes encoding Class I and Class IIB molecules but is only similar to 92Kb in length. Sequences of other galliform MHCs show varying degrees of similarity as that of chicken. The black grouse (Tetrao tetrix) is a wild galliform bird species which is an important model in conservation genetics and ecology. We sequenced the black grouse core MHC-B region and combined this with available data from related species (chicken, turkey, gold pheasant and quail) to perform a comparative genomics study of the galliform MHC. This kind of analysis has previously been severely hampered by the lack of genomic information on avian MHC regions, and the galliformes is still the only bird lineage where such a comparison is possible. Results: In this study, we present the complete genomic sequence of the MHC-B locus of black grouse, which is 88,390 bp long and contains 19 genes. It shows the same simplicity as, and almost perfect synteny with, the corresponding genomic region of chicken. We also use 454-transcriptome sequencing to verify expression in 17 of the black grouse MHC-B genes. Multiple sequence inversions of the TAPBP gene and TAP1-TAP2 gene block identify the recombination breakpoints near the BF and BLB genes. Some of the genes in the galliform MHC-B region also seem to have been affected by selective forces, as inferred from deviating phylogenetic signals and elevated rates of non-synonymous nucleotide substitutions. Conclusions: We conclude that there is large synteny between the MHC-B region of the black grouse and that of other galliform birds, but that some duplications and rearrangements have occurred within this lineage. The MHC-B sequence reported here will provide a valuable resource for future studies on the evolution of the avian MHC genes and on links between immunogenetics and ecology of black grouse.
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| 74. |
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| 75. |
- Wang, Biao, et al.
(författare)
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Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development
- 2012
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Ingår i: Open Biology. - : The Royal Society. - 2046-2441. ; 2, s. 120054-
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Tidskriftsartikel (refereegranskat)abstract
- The black grouse (Tetrao tetrix) is a galliform bird species that is important forboth ecological studies and conservation genetics. Here, we report the sequencing of the spleen transcriptome of black grouse using 454 GS FLX Titanium sequencing. We performed a large-scale gene discovery analysis with a focus on genes that might be related to fitness in this species and also identified a large set of microsatellites. In total, we obtained 182 179 quality-filtered sequencing reads that we assembled into 9035 contigs. Using these contigs and 15 794 length-filtered (greater than 200 bp) singletons, we identified 7762 transcripts that appear to be homologues of chicken genes. A specific BLAST search with an emphasis on immune genes found 308 homologous chicken genes that have immune function, including ten major histocompatibility complex-related genes located on chicken chromosome 16. We also identified 1300 expressed sequence tag microsatellites and were able to design suitable flanking primers for 526 of these. A preliminary test of the polymorphism of the microsatellites found 10 polymorphic microsatellites of the 102 tested. Genomic resources generated in this study should greatly benefit future ecological, evolutionary and conservation genetic studies on this species.
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| 76. |
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| 77. |
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