Genomic toolboxes for conservation biologists
Article first published online: 17 NOV 2011
© 2011 Blackwell Publishing Ltd. This is an open access article under the terms of the Creative Commons Attribution Non Commercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
Special Issue: The evolutionary basis of biodiversity and its potential for adaptation to global change
Volume 5, Issue 2, pages 130–143, February 2012
How to Cite
Angeloni, F., Wagemaker, N., Vergeer, P. and Ouborg, J. (2012), Genomic toolboxes for conservation biologists. Evolutionary Applications, 5: 130–143. doi: 10.1111/j.1752-4571.2011.00217.x
- Issue published online: 29 FEB 2012
- Article first published online: 17 NOV 2011
- Received: 12 October 2011 Accepted: 18 October 2011 First published online: 17 November 2011
- 2010. Genomics and the future of conservation genetics. Nature Reviews Genetics11:697–709. , , and .
- 2011. De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next generation sequencing techniques. Molecular Ecology Resources11:662–674. , , , , , , et al.
- 2005. Inbreeding depression in benign and stressful environments. Heredity95:235–242. , and .
- 2010. Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana in-bred lines. Nature465:627–631. , , , , , , et al.
- 1997. The significance of digital gene expression profiles. Genome Research7:986–995. , and .
- 2010. Statistical design and analysis of RNA sequencing data. Genetics185:405–416. , and .
- 2010. Perspective: conservation genetics enters the genomic era. Conservation Genetics11:665–669.
- 2009. A genomewide assessment of inbreeding depression: gene number, function, and mode of action. Conservation Biology23:920–930. , , , , , , et al.
- 2011. Fine-scale spatial genetic structure and gene dispersal in Silene latifolia. Heredity106:13–24. , , , , , and .
- 2011. The coupling hypothesis: why genome scans may fail to map local adaptation genes. Molecular Ecology20:2044–2072. , , , , and .
- 2005. Molecular characterization of major histocompatibility complex class II alleles in wild tiger salamanders (Ambystoma tigrinum). Immunogenetics57:775–781. , and .
- 2009. The genetics of inbreeding depression. Nature Reviews10:783–796. , and .
- 2010. How to do successful gene expression analysis using real-time PCR. Methods50:227–230. , , and .
- 2010. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity107:1–15. , and .
- 2010. Digital gene expression analysis of the zebra finch genome. BMC Genomics11:219. , , , and .
- 2010. Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. Molecular Ecology19(Suppl. 1):197–211. , , , , , , and .
- 2006. Computer programs for population genetics data analysis: a survival guide. Nature Reviews. Genetics7:745–758. , and .
- 2008. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources8:92–94.
- 1935. The logic of inductive inference. Journal of the Royal Statistical Society98:39–82.
- 2010. Challenges and opportunities of genetic approaches to biological conservation. Biological Conservation143:1919–1927.
- 2010. An EST-based genome scan using 454 sequencing in the marine snail Littorina saxatilis. Journal of Evolutionary Biology23:2004–2016. , , and .
- 2001. Population genomics: linkage disequilibrium holds the key. Current Biology11:R576–R579. , and .
- 2000. The metapopulation capacity of a fragmented landscape. Nature (London)404:755–758. , and .
- 2008. Whole-genome sequencing and variant discovery in C. elegans. Nature Methods5:183–188. , , , , , , et al.
- 2005. Genome-wide association studies for common diseases and complex traits. Nature Reviews. Genetics6:95–108. , and .
- 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genetics6:1–23. , , , , , and .
- 2011. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources11:117–122. , , , , and .
- 1999. Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources. Molecular Biology of the Cell10:1859–1872. , , , , , , et al.
- 2007. Microarray challenges in ecology. Trends in Ecology and Evolution22:273–279. , , , , and .
- 2002. Inbreeding effects in wild populations. Trends in Ecology and Evolution17:230–241. , and .
- 2009. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics25:2283–2285. , , , , , , et al.
- 2007. SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics23:1683–1685. , , and .
- 2006. Genomics and conservation genetics. Trends in Ecology and Evolution21:629–637. , , , and .
- 2005. Inbreeding: lessons from animal breeding, evolutionary biology, and conservation genetics. Animal Science80:121–133. , and .
- 2002. Inbreeding affects Hsp70 expression in two species of Drosophila even at benign temperatures. Evolutionary Ecology Research4:1209–1216. , , and .
- 2006. Inbreeding by environmental interactions affect gene expression in Drosophila melanogaster. Genetics173:1329–1336. , , , , and .
- 2010. Research on inbreeding in the ‘omic’ era. Trends in Ecology and Evolution25:44–52. , , , and .
- 2009. Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. BMC Genomics10:345. , , , and .
- 2010. Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Molecular Ecology19(Suppl. 1):266–276. , , , , , , et al.
- 2007. Linkage disequilibrium in wild mice. PLoS Genetics3:e144. , , , , , , et al.
- 2006. How general are positive relationship between plant population size, fitness and genetic variation?Journal of Ecology94:942–952. , , , and .
- 2008. Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis. Journal of Evolutionary Biology21:1–17. , , , and .
- 2007. Heterosis: revisiting the magic. Trends in Genetics23:60–66. , and .
- 2003. The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics4:981–994. , , , , and .
- 2009. Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions. Ageing Research Reviews9:315–323. , , and
- 2000. POWER_SAGE: comparing statistical tests for SAGE experiments. Bioinformatics16:953–959. , , and .
- 2010. RNA-seq: from technology to biology. Cellular and Molecular Life Sciences97:569–579. , and .
- 2010. Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing. BMC Genomics11:560. , , , , , , et al.
- 2007. The structure of linkage disequilibrium around a selective sweep. Genetics175:1395–1406.
- 2010. QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics26:403–404. , , , , , , and .
- 2010. Sequencing technologies – the next generation. Nature Reviews11:31–46.
- 2009. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics10:219. , , , , , , et al.
- 2007. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research17:240–248. , , , , and .
- 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods5:621–628. , , , , and .
- 2008. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics9:312. , , , , , , and .
- 2008. Interpreting principal component analyses of spatial population genetic variation. Nature Genetics40:646–649. , and .
- 2010. Genome-wide scans for footprints of natural selection. Philosophical Transactions of the Royal Society B365:185–205. , , and .
- 2010. Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon. BMC Genomics11:310. , , , , , and .
- 1999. Population genetics, molecular markers and the study of dispersal in plants. Journal of Ecology87:551–568. , , and .
- 2006. The rough edges of the conservation genetics paradigm for plants. Journal of Ecology94:1233–1248. , , and .
- 2010a. Conservation genetics in transition to conservation genomics. Trends in Genetics26:177–187. , , , , and .
- 2010b. An essay on the necessity and feasibility of conservation genomics. Conservation Genetics11:643–653. , , and .
- 2010. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics11:180. , , , , and .
- 2011. The hrpZ gene of Pseudomonas syringae pv. phaseolicola enhances resistance to rhizomania disease in transgenic Nicotiana benthamiana and sugar beet. PLoS ONE6:e17306. , , , and .
- 2005. Effects of inbreeding and rate of inbreeding in Drosophila melanogaster– Hsp70 expression and fitness. Journal of Evolutionary Biology18:756–762. , , and .
- 2008. Metabolomic signatures of inbreeding at benign and stressful temperatures in Drosophila melanogaster. Genetics180:1233–1243. , , , , , , and .
- 2009. From conservation genetics to conservation genomics. Annals of the New York Academy of Sciences1162:357–368.
- 2011. Acclimation to high CO(2) in maize is related to water status and dependent on leaf rank. Plant Cell and Environment34:314–331. , , , , , , et al.
- 2004. Genetic status and management of California condors. The Condor106:215–228. , and .
- 2000. Genetic management of chondrodystrophy in California condors. Animal Conservation3:145–153. , , , and .
- 2006. Construction of a California condor BAC library and first-generation chicken-condor comparative physical map as an endangered species conservation genomics resource. Genomics88:711–718. , , , , and .
- 2001. Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests. Human Molecular Genetics10:2133–2141. , , and .
- 2011. RAD in the realm of next-generation sequencing technologies. Molecular Ecology20:3499–3502. , , and .
- 2002. Statistical evaluation of SAGE libraries: consequences for experimental design. Physiological Genomics11:37–44. , , and .
- 2009. Single nucleotidrs polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics10:559. , , , , , , and .
- 2010. On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs. Molecular Ecology19:1439–1451. , , , , , and .
- 2009. Gene mapping in the wild with SNPs: guidelines and future directions. Genetica136:97–107. , , , , , and .
- 2010. Adaptation genomics: the next generation. Trends in Ecology & Evolution25:705–712. , , , , , , et al.
- 2005. Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa. Molecular Biology and Evolution21:1800–1811. , , and .
- 2006. Msatfinder: Detection and Characterization of Microsatellites. Oxford. http://www.genomics.ceh.ac.uk/msatfinder/ (accessed on 15 October 2011). , and
- 2011. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nature Genetics43:159–162. , , , , , , et al.
- 2009. Characterization of microsatellite loci in the fungus, Grosmannia clavigera, a pine pathogen associated with the mountain pine beetle. Molecular Ecology Resources9:1500–1503. , , , , , , and .
- 2010. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nature Genetics42:260–263. , , , , and .
- 2010. Conservation genomics of Atlantic salmon: variation in gene expression between and within regions of the Bay of Fundy. Molecular Ecology19:1842–1859. , , , , and .
- 2008. Rapid transcriptome characterization for a non model organism using 454 pyrosequencing. Molecular Ecology17:1636–1647. , , , , , , and .
- 2008. Heritability in the genomic era – concepts and misconceptions. Nature9:255–266. , , and .
- 2003. Haplotype blocks and linkage disequilibrium in the human genome. Nature Reviews. Genetics4:587–597. , and .
- 2008. RNA-seq: a revolutionary tool for transcriptomics. Nature Reviews. Genetics10:57–63. , , and .
- 2011. Functional genomics of life history variation in a butterfly metapopulation. Molecular Ecology20:1813–1828. , , , , , , et al.
- 2009. Testing for spatially divergent selection: comparing QST to FST. Genetics183:1055–1063. , and .
- 2009. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods48:249–257. , and .
- 1984. Evolution and the Genetics of Populations. University of Chicago Press, Chicago, IL.
- 2011. The impact of next-generation sequencing on genomics. Journal of Genetics and Genomics38:95–109. , , , and .