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Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion.

Hoban S, Arntzen JA, Bruford MW, Godoy JA, Rus Hoelzel A, Segelbacher G, Vilà C, Bertorelle G - Evol Appl (2014)

Bottom Line: The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect.Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest.Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.

View Article: PubMed Central - PubMed

Affiliation: National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee Knoxville, TN, USA ; Department of Life Science, Università di Ferrara Ferrara, Italy.

ABSTRACT
Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of temporal samples) for monitoring genetic erosion following demographic decline. To do so, we utilized individual-based simulations featuring an array of different initial population sizes, types and severity of demographic decline, and DNA markers [single nucleotide polymorphisms (SNPs) and microsatellites] as well as decline followed by recovery. Number of alleles markedly outperformed other indicators across all situations. The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect. Sampling 50 individuals at as few as two time points with 20 microsatellites performed well (good power), and could detect genetic erosion while 80-90% of diversity remained. This sampling and genotyping effort should often be affordable. Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest. Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.

No MeSH data available.


Related in: MedlinePlus

Number of alleles and heterozygosity, through time, under a scenario in which near-instantaneous population recovery takes places either 10 or two generations after a period of a small size due to instant decline. Indicator values before the decline and after the recovery are shown by gray solid and red dashed lines, respectively.
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fig06: Number of alleles and heterozygosity, through time, under a scenario in which near-instantaneous population recovery takes places either 10 or two generations after a period of a small size due to instant decline. Indicator values before the decline and after the recovery are shown by gray solid and red dashed lines, respectively.

Mentions: In spite of a slight upward response in indicators following full demographic recovery, there was essentially no power to detect genetic diversity increase, for all three recovery situations, for any indicator (Figure S5). Nonetheless, we observed that recovery after two generations resulted in a population that lost approximately one-third of the heterozygosity and number of alleles that would be lost in a more delayed recovery (5% heterozygosity loss and 10% allelic loss for a two generation decline, vs 15% and 30% loss after 20 generations, Fig.6). Thus, genetic erosion can be halted quickly via demographic recovery, although the genetic erosion that has occurred is essentially irreversible on small time-scales (tens of generations) and genetic indicators will not substantially increase (noted also in Nei 1975).


Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion.

Hoban S, Arntzen JA, Bruford MW, Godoy JA, Rus Hoelzel A, Segelbacher G, Vilà C, Bertorelle G - Evol Appl (2014)

Number of alleles and heterozygosity, through time, under a scenario in which near-instantaneous population recovery takes places either 10 or two generations after a period of a small size due to instant decline. Indicator values before the decline and after the recovery are shown by gray solid and red dashed lines, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231590&req=5

fig06: Number of alleles and heterozygosity, through time, under a scenario in which near-instantaneous population recovery takes places either 10 or two generations after a period of a small size due to instant decline. Indicator values before the decline and after the recovery are shown by gray solid and red dashed lines, respectively.
Mentions: In spite of a slight upward response in indicators following full demographic recovery, there was essentially no power to detect genetic diversity increase, for all three recovery situations, for any indicator (Figure S5). Nonetheless, we observed that recovery after two generations resulted in a population that lost approximately one-third of the heterozygosity and number of alleles that would be lost in a more delayed recovery (5% heterozygosity loss and 10% allelic loss for a two generation decline, vs 15% and 30% loss after 20 generations, Fig.6). Thus, genetic erosion can be halted quickly via demographic recovery, although the genetic erosion that has occurred is essentially irreversible on small time-scales (tens of generations) and genetic indicators will not substantially increase (noted also in Nei 1975).

Bottom Line: The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect.Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest.Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.

View Article: PubMed Central - PubMed

Affiliation: National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee Knoxville, TN, USA ; Department of Life Science, Università di Ferrara Ferrara, Italy.

ABSTRACT
Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of temporal samples) for monitoring genetic erosion following demographic decline. To do so, we utilized individual-based simulations featuring an array of different initial population sizes, types and severity of demographic decline, and DNA markers [single nucleotide polymorphisms (SNPs) and microsatellites] as well as decline followed by recovery. Number of alleles markedly outperformed other indicators across all situations. The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect. Sampling 50 individuals at as few as two time points with 20 microsatellites performed well (good power), and could detect genetic erosion while 80-90% of diversity remained. This sampling and genotyping effort should often be affordable. Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest. Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.

No MeSH data available.


Related in: MedlinePlus