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. 2016 Oct 18;10(2):146-160.
doi: 10.1111/eva.12433. eCollection 2017 Feb.

Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead

Michael W Ackerman  1 , Brian K Hand  2 , Ryan K Waples  3 , Gordon Luikart  2 , Robin S Waples  4 , Craig A Steele  5 , Brittany A Garner  2 , Jesse McCane  5 , Matthew R Campbell  6
Affiliations

Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead

Michael W Ackerman et al. Evol Appl. .

Abstract

Effective population size (Ne ) is among the most important metrics in evolutionary biology. In natural populations, it is often difficult to collect adequate demographic data to calculate Ne directly. Consequently, genetic methods to estimate Ne have been developed. Two Ne estimators based on sibship reconstruction using multilocus genotype data have been developed in recent years: sibship assignment and parentage analysis without parents. In this study, we evaluated the accuracy of sibship reconstruction using a large empirical dataset from five hatchery steelhead populations with known pedigrees and using 95 single nucleotide polymorphism (SNP) markers. We challenged the software COLONY with 2,599,961 known relationships and demonstrated that reconstruction of full-sib and unrelated pairs was greater than 95% and 99% accurate, respectively. However, reconstruction of half-sib pairs was poor (<5% accurate). Despite poor half-sib reconstruction, both estimators provided accurate estimates of the effective number of breeders (Nb ) when sample sizes were near or greater than the true Nb and when assuming a monogamous mating system. We further demonstrated that both methods provide roughly equivalent estimates of Nb . Our results indicate that sibship reconstruction and current SNP panels provide promise for estimating Nb in steelhead populations in the region.

Keywords: COLONY; Oncorhynchus mykiss; PwoP; conservation genetics; effective population size; genetic monitoring; sibship assignment; sibship reconstruction.

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Figures

Figure 1
Figure 1
The number (panel a) and proportion (panel b) of successful parents that produced offspring and the number of offspring produced by each for five Snake River hatchery populations
Figure 2
Figure 2
N b estimates for five Snake River hatcheries assuming polygamous (open symbols), male polygamy/female monogamy (gray symbols), and monogamous (filled symbols) mating systems in COLONY. Analyses were repeated using three assumed genotyping error rates: 0.0001 (diamonds), 0.001 (circles), and 0.01 (squares). Dashed lines represent the true N b for each hatchery
Figure 3
Figure 3
Estimates of N b for five Snake River hatcheries using subsets of 10%, 20%, 30%,…100% of the total number of offspring sampled (via bootstrap resampling). Ten random draws of offspring were made at each interval for 10% to 90%. Each point represents one run of COLONY. Dashed lines represent the true N b. The solid line is the root‐mean‐squared bias (RMSB) among the 10 runs (secondary axis) at each sample interval
Figure 4
Figure 4
Histogram showing ratio of SA and PwoP N b estimates when each are calculated using the same sets of sibship reconstruction results from COLONY. Results are shown for 180 COLONY runs of offspring from Dworshak hatchery including 90 runs assuming a monogamous mating system and 90 runs assuming polygamy
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References

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