Dataset Information

Harvest-induced evolution and effective population size.

ABSTRACT: Much has been written about fishery-induced evolution (FIE) in exploited species, but relatively little attention has been paid to the consequences for one of the most important parameters in evolutionary biology-effective population size (N e). We use a combination of simulations of Atlantic cod populations experiencing harvest, artificial manipulation of cod life tables, and analytical methods to explore how adding harvest to natural mortality affects N e, census size (N), and the ratio N e/N. We show that harvest-mediated reductions in N e are due entirely to reductions in recruitment, because increasing adult mortality actually increases the N e/N ratio. This means that proportional reductions in abundance caused by harvest represent an upper limit to the proportional reductions in N e, and that in some cases N e can even increase with increased harvest. This result is a quite general consequence of increased adult mortality and does not depend on harvest selectivity or FIE, although both of these influence the results in a quantitative way. In scenarios that allowed evolution, N e recovered quickly after harvest ended and remained higher than in the preharvest population for well over a century, which indicates that evolution can help provide a long-term buffer against loss of genetic variability.

SUBMITTER: Kuparinen A

PROVIDER: S-EPMC4869408 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Harvest-induced evolution and effective population size.

Kuparinen Anna A Hutchings Jeffrey A JA Waples Robin S RS

Evolutionary applications 20160408 5

Much has been written about fishery-induced evolution (FIE) in exploited species, but relatively little attention has been paid to the consequences for one of the most important parameters in evolutionary biology-effective population size (N e). We use a combination of simulations of Atlantic cod populations experiencing harvest, artificial manipulation of cod life tables, and analytical methods to explore how adding harvest to natural mortality affects N e, census size (N), and the ratio N e/N. ...[more]

PMID: 27247617

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Project description:The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (Ne) and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r2=0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of Ne was noted in the very recent generations with a peak value of 19 for Ne at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for FROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (FPed=0.10) was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively. The objectives of the present study were to genotype 28 Lundehund using the canine Illumina high density beadchip (Illumina, San Diego, CA, USA) to estimate the effective population size (Ne) from data on linkage disequilibria (LD). We identified runs of homozygosity (ROH) as regions with a local loss of genetic variation. Inbreeding coefficients were calculated on the basis of pedigree data (FPed) and genotype information (FROH, FIS) to compare the results of these different methods for this population. We applied the long-range haplotype test to search for potential selective sweeps.

Dataset Information

Harvest-induced evolution and effective population size.

Publications

Harvest-induced evolution and effective population size.

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