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9 - Implications of landscape alteration for the conservation of genetic diversity of endangered species
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- By Paul L. Leberg, University of Louisiana, Giridhar N. R. Athrey, University of Louisiana, Kelly R. Barr, University of Louisiana, Denise L. Lindsay, U.S. Army Engineer Research and Development Center, Richard F. Lance, U.S. Army Engineer Research and Development Center
- Edited by J. Andrew DeWoody, Purdue University, Indiana, John W. Bickham, Purdue University, Indiana, Charles H. Michler, Purdue University, Indiana, Krista M. Nichols, Purdue University, Indiana, Gene E. Rhodes, Purdue University, Indiana, Keith E. Woeste, Purdue University, Indiana
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- Book:
- Molecular Approaches in Natural Resource Conservation and Management
- Published online:
- 05 July 2014
- Print publication:
- 14 June 2010, pp 212-238
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- Chapter
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Summary
Humans have dramatically altered biotic communities around the world. During the process of converting forests, grasslands, and wetlands for agriculture, urban development, and transportation, the remnants of natural habitat have become increasingly fragmented. This fragmentation of habitat has many biological consequences. Foremost is the reduction of available habitat resulting in a reduced size of populations of species dependent on natural land covers (Andren 1994; Fahrig 1997, 2003). Fragmentation, though, is more than just habitat loss; it is also the division of remaining habitat into patches that experience at least partial isolation from other such fragments (Fahrig 2003). Fragmentation increases habitat edges and, consequently, the exposure of populations to the resulting alterations in microclimate and biota associated with edge environments (Suarez et al. 1998; Fagan et al. 1999). As fragments become more isolated, the frequency of movements between fragments is reduced. Furthermore, when localized extinctions in isolated fragments occur, immigration from neighboring fragments can be insufficient to allow recolonization (Tilman et al. 1994; Fahrig 2003). Extinctions associated with demographic stochasticity are expected to be more common in small fragments than in more continuous habitat tracts (Griffen & Drake 2008).
The consequences of fragmentation have the potential to influence genetic diversity in species requiring continuous tracts of habitat (see Chapter 8 by J. Hamrick). Localized population declines cause allele frequencies to drift; moreover, widespread population declines due to fragmentation across the range of a species may reduce its effective population size (Pannell & Charlesworth 2000; Alo & Turner 2005). With declines of census and effective population size, inhabitants of isolated fragments begin to resemble independent populations, become more vulnerable to stochastic processes, lose genetic diversity, and increase in relatedness (Barrowclough 1980; Leberg 2005).
Biases associated with population estimation using molecular tagging
- Juliann L. Waits, Paul L. Leberg
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- Journal:
- Animal Conservation forum / Volume 3 / Issue 3 / August 2000
- Published online by Cambridge University Press:
- 08 November 2000, pp. 191-199
- Print publication:
- August 2000
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- Article
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Although capture–recapture techniques are often used to estimate population size, these approaches are difficult to implement for a wide variety of species. Highly polymorphic microsatellite markers are useful in individual identification, and these ‘molecular tags’ can be collected without having to capture or trap the individual. However, several sources of error associated with molecular identification techniques, including failure to identify individuals with the same genotype for these markers as being different, and incorrect assignment of individual genotypes, could bias population estimates. Simulations of populations sampled for the purpose of estimating population size were used to assess the extent of these potential biases. Population estimates tended to be biased downward as the likelihood of individuals sharing the same genotype increased (as measured by the probability of identity (PI) of the multi-locus genotype); this bias increased with population size. Populations of 1000 individuals were underestimated by ≥5% when the PI was as small as 1.4 × 10−7. A similar-sized bias did not occur for populations of 50 individuals until the PI had increased to approximately 2.5 × 10−5. Errors in genotype assignment resulted in overestimates of population size; this problem increased with the number of samples and loci that were genotyped. Population estimates were often >200% the size of the simulated populations when the probability of making a genotyping error was 0.05/locus and 7–10 loci were used to identify individuals. This bias was substantially reduced by decreasing genotyping error rate to 0.005. If possible, only highly polymorphic loci that are critical for the identification of the individual should be used in molecular tagging, and considerable efforts should be made to minimize errors in genotype determination.