Evaluation of genetic effects on wild salmon populations from stock enhancement

Abstract Many salmonid populations are of conservation concern, and the release of hatchery-produced juveniles is a frequently used measure to alleviate declines and increase harvest opportunities. While such releases may be of conservation value for some populations, stocking may also decrease the effective population size and subsequently impose additional strain on already threatened populations. In this study, we assessed how the cohort-wise effective number of breeders in five populations of Atlantic salmon (Salmo salar) were affected by supplementation. Altogether, 19 cohorts were studied (2–7 cohorts per population) by estimating the proportion hatchery-released individuals and the effective number of wild and captive breeders in each cohort of the respective populations. We show that the effect of releasing captive-bred individuals varies both between populations and between years within the same population. A Ryman–Laikre effect—where the effective number of breeders has decreased as a consequence of supplementation—was observed for 11 cohorts. We discuss how supplementation can be adapted to optimize the effective population size, demonstrate that evaluation of supplementation can be reliably achieved, and show that supplementation programmes that lead to high proportions of hatchery-origin fish on spawning grounds are more likely to induce a Ryman–Laikre effect.

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On the Potential for Estimating the Effective Number of Breeders From Heterozygote-Excess in Progeny

Genetics ◽

10.1093/genetics/144.1.383 ◽

1996 ◽

Vol 144 (1) ◽

pp. 383-387 ◽

Cited By ~ 11

Author(s):

A I Pudovkin ◽

D V Zaykin ◽

D Hedgecock

Keyword(s):

Population Size ◽

Effective Population Size ◽

Sampling Error ◽

Demographic Data ◽

Rank Correlation ◽

Effective Number ◽

Effective Population ◽

Heterozygote Excess ◽

Effective Number Of Breeders ◽

Age Structured

Abstract The important parameter of effective population size is rarely estimable directly from demographic data. Indirect estimates of effective population size may be made from genetic data such as temporal variation of allelic frequencies or linkage disequilibrium in cohorts. We suggest here that an indirect estimate of the effective number of breeders might be based on the excess of heterozygosity expected in a cohort of progeny produced by a limited number of males and females. In computer simulations, heterozygote excesses for 30 unlinked loci having various numbers of alleles and allele-frequency profiles were obtained for cohorts produced by samples of breeders drawn from an age-structured population and having known variance in reproductive success and effective number. The 95% confidence limits around the estimate contained the true effective population size in 70 of 72 trials and the Spearman rank correlation of estimated and actual values was 0.991. An estimate based on heterozygote excess might have certain advantages over the previous estimates, requiring only single-locus and single-cohort data, but the sampling error among individuals and the effect of departures from random union of gametes still need-to be explored.

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Interannual variation in effective number of breeders and estimation of effective population size in long-lived iteroparous lake sturgeon (Acipenser fulvescens)

Molecular Ecology ◽

10.1111/mec.12167 ◽

2013 ◽

Vol 22 (5) ◽

pp. 1282-1294 ◽

Cited By ~ 40

Author(s):

Thuy Yen Duong ◽

Kim T. Scribner ◽

Patrick S. Forsythe ◽

James A. Crossman ◽

Edward A. Baker

Keyword(s):

Population Size ◽

Effective Population Size ◽

Interannual Variation ◽

Lake Sturgeon ◽

Acipenser Fulvescens ◽

Effective Number ◽

Effective Population ◽

Effective Number Of Breeders

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Significance of Mature Male Parr in a Small Population of Atlantic Salmon (Salmo salar)

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f89-119 ◽

1989 ◽

Vol 46 (6) ◽

pp. 928-931 ◽

Cited By ~ 32

Author(s):

Jan Hennsng L'abée-Lund

Keyword(s):

Atlantic Salmon ◽

Population Size ◽

Effective Population Size ◽

Salmo Salar ◽

Small Population ◽

Mature Male ◽

Effective Population ◽

Atlantic Salmon Salmo Salar ◽

Mature Male Parr

The spawning population of Atlantic salmon, Salmo salar, (mature male parr and adults (anadromous salmon)) were assessed in the River Baevra, central Norway, when the river was treated with rotenone in November 1986. The spawning population of adults consisted of 15 males and 19 females. The spawning population of males consisted of 167 mature male parr per adult male. The effective population size of adults was small; Na = 33.5 individuals. The presence of mature male parr theoretically increased the effective population size to Na = 71.7 individuals. This increase indicated that mature male parr brought the effective population size above a recommended minimum (Na = 50) to ensure long term viability.

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Genetic Diversity, Structure and Effective Population Size of Old-Growth vs. Second-Growth Populations of Keystone and Long-Lived Conifer, Eastern White Pine (Pinus strobus): Conservation Value and Climate Adaptation Potential

Frontiers in Genetics ◽

10.3389/fgene.2021.650299 ◽

2021 ◽

Vol 12 ◽

Author(s):

Om P. Rajora ◽

John W. R. Zinck

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Population Genetic ◽

Conservation Value ◽

Adaptive Potential ◽

Effective Population ◽

White Pine ◽

Old Growth ◽

Second Growth

Whether old-growth (OG) forests have higher genetic diversity and effective population size, consequently higher conservation value and climate adaptive potential than second-growth (SG) forests, remain an unresolved issue. We have tested the hypothesis that old-growth forest tree populations have higher genetic diversity, effective population size (NE), climate adaptive potential and conservation value and lower genetic differentiation than second-growth forest tree populations, employing a keystone and long-lived conifer, eastern white pine (EWP; Pinus strobus). Genetic diversity and population structure of old-growth and second-growth populations of eastern white pine (EWP) were examined using microsatellites of the nuclear and chloroplast genomes and single nucleotide polymorphisms (SNPs) in candidate nuclear genes putatively involved in adaptive responses to climate and underlying multilocus genetic architecture of local adaptation to climate in EWP. Old-growth and second-growth EWP populations had statistically similar genetic diversity, inbreeding coefficient and inter-population genetic differentiation based on nuclear microsatellites (nSSRs) and SNPs. However, old-growth populations had significantly higher chloroplast microsatellites (cpSSRs) haploid diversity than second-growth populations. Old-growth EWP populations had significantly higher coalescence-based historical long-term NE than second-growth EWP populations, but the linkage disequilibrium (LD)-based contemporary NE estimates were statistically similar between the old-growth and second-growth EWP populations. Analyses of population genetic structure and inter-population genetic relationships revealed some genetic constitution differences between the old-growth and second-growth EWP populations. Overall, our results suggest that old-growth and second-growth EWP populations have similar genetic resource conservation value. Because old-growth and second-growth EWP populations have similar levels of genetic diversity in genes putatively involved in adaptive responses to climate, old-growth, and second-growth populations may have similar adaptive potential under climate change. Our results could potentially be generalized across most of the boreal and temperate conifer forest trees. Our study contributes to address a long-standing issue, advances research field and knowledge about conservation and ecological and climate adaptation of forest trees.

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Interrelations between effective population size and other pedigree tools for the management of conserved populations

Genetics Research ◽

10.1017/s0016672399004449 ◽

2000 ◽

Vol 75 (3) ◽

pp. 331-343 ◽

Cited By ~ 240

Author(s):

ARMANDO CABALLERO ◽

MIGUEL A. TORO

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Population Size ◽

Effective Population Size ◽

Genetic Parameters ◽

Effective Number ◽

Effective Population ◽

Clear Cut ◽

Captive Populations ◽

Practical Recommendations

Genetic parameters widely used to monitor genetic variation in conservation programmes, such as effective number of founders, founder genome equivalents and effective population size, are interrelated in terms of coancestries and variances of contributions from ancestors to descendants. A new parameter, the effective number of non-founders, is introduced to describe the relation between effective number of founders and founder genome equivalents. Practical recommendations for the maintenance of genetic variation in small captive populations are discussed. To maintain genetic diversity, minimum coancestry among individuals should be sought. This minimizes the variances of contributions from ancestors to descendants in all previous generations. The method of choice of parents and the system of mating should be independent of each other because a clear-cut recommendation cannot be given on the latter.

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Genetic diversity, viability and conservation value of the global captive population of the Moroccan Royal lions

PLoS ONE ◽

10.1371/journal.pone.0258714 ◽

2021 ◽

Vol 16 (12) ◽

pp. e0258714

Author(s):

Kristina Lehocká ◽

Simon A. Black ◽

Adrian Harland ◽

Ondrej Kadlečík ◽

Radovan Kasarda ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

North Africa ◽

Reference Population ◽

Captive Population ◽

Effective Number ◽

Pedigree Data ◽

Effective Population ◽

Loss Of Diversity

This study evaluates the diversity of the so-called ‘Moroccan Royal lions’ using genealogical information. Lions are no longer extant in North Africa, but the previous wild population was an important element of the now-recognised northern subspecies (Panthera leo leo) that ranged across West Africa, North Africa and the Middle East into India. The remaining captive population of ‘Moroccan Royal lions’ seems to be significantly endangered by the loss of diversity due to the effective population size decrease. The pedigree file of this captive lion population consisted of 454 individuals, while the reference population included 98 animals (47 males and 51 females). The completeness of the pedigree data significantly decreased with an increasing number of generations. The highest percentage of pedigree completeness (over 70%) was achieved in the first generation of the reference population. Pedigree-based parameters derived from the common ancestor and gene origin were used to estimate the state of diversity. In the reference population, the average inbreeding coefficient was 2.14%, while the individual increase in inbreeding over generations was 2.31%. Overall, the reference population showed lower average inbreeding and average relatedness compared with the pedigree file. The number of founders (47), the effective number of founders (24) and the effective number of ancestors (22) were estimated in the reference population. The effective population size of 14.02 individuals confirms the critically endangered status of the population and rapid loss of diversity in the future. Thus, continuous monitoring of the genetic diversity of the ‘Moroccan Royal lion’ group is required, especially for long-term conservation management purposes, as it would be an important captive group should further DNA studies establish an affinity to P. leo leo.

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Runs of homozygosity in killer whale genomes provide a global record of demographic histories

10.22541/au.162496924.41380105/v1 ◽

2021 ◽

Author(s):

Andy Foote ◽

Rebecca Hooper ◽

Alana Alexander ◽

Robin Baird ◽

Charles Baker ◽

...

Keyword(s):

Population Size ◽

Effective Population Size ◽

Killer Whale ◽

Demographic History ◽

Population History ◽

Runs Of Homozygosity ◽

Effective Population ◽

High Background ◽

Genome Wide ◽

Conservation Concern

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically the probability of inbreeding mediated by mating system and/or population demography. Here, we investigate whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global dataset of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstruct demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We find a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations and populations of known conservation concern, including a Scottish population, for which 37.8% of the autosomes comprised of ROH >1.5 Mb in length.

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