Genetic rescue, the greater prairie chicken and the problem of conservation reliance in the Anthropocene

A central question in conservation is how best to manage biodiversity, despite human domination of global processes (= Anthropocene). Common responses (i.e. translocations, genetic rescue) forestall potential extirpations, yet have an uncertain duration. A textbook example is the greater prairie chicken (GRPC: Tympanuchus cupido pinnatus ), where translocations (1992–1998) seemingly rescued genetically depauperate Illinois populations. We re-evaluated this situation after two decades by genotyping 21 microsatellite loci from 1831 shed feathers across six leks in two counties over 4 years (2010–2013). Low migration rates (less than 1%) established each county as demographically independent, but with declining-population estimates (4 year average N = 79). Leks were genetically similar and significantly bottlenecked, with low effective population sizes (average N e = 13.1; 4 year N e / N = 0.166). Genetic structure was defined by 12 significantly different family groups, with relatedness r = 0.31 > half-sib r = 0.25. Average heterozygosity, indicating short-term survival, did not differ among contemporary, pre- and post-translocated populations, whereas allelic diversity did. Our results, the natural history of GRPC (i.e. few leks, male dominance hierarchies) and its controlled immigration suggest demographic expansion rather than genetic rescue. Legal protection under the endangered species act (ESA) may enhance recovery, but could exacerbate political–economic concerns on how best to manage ‘conservation-reliant’ species, for which GRPC is now an exemplar.

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Genetics of reintroduced populations of the narrowly endemic thistle, Cirsium pitcheri (Asteraceae)

Botany ◽

10.1139/cjb-2012-0232 ◽

2013 ◽

Vol 91 (5) ◽

pp. 301-308 ◽

Cited By ~ 12

Author(s):

Jeremie B. Fant ◽

Andrea Kramer ◽

Eileen Sirkin ◽

Kayri Havens

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Empirical Studies ◽

Small Population ◽

Native Plant ◽

Effective Population ◽

Term Survival ◽

Inbreeding Coefficients ◽

Native Populations ◽

Population Sizes

The aim of any reintroduction is to provide sufficient genetic variability to buffer against changing selection pressures and ensure long-term survival. To date, few empirical studies have compared levels of genetic diversity in reintroduced and native plant populations. Using microsatellite markers, we measured the genetic diversity within reintroduced and native populations of the threatened Cirsium pitcher (Eaton) Torrey and Gray. We found that the use of local mixed source was successful in establishing populations with significantly higher genetic diversity (P < 0.005) than the native populations (allelic richness is 3.39 in reintroduced and 1.84 in native populations). However, the reintroduced populations had significantly higher inbreeding coefficients (P < 0.002) (FIS is 0.405 and 0.213 in reintroduced and in native populations, respectively), despite having multiple genetic founders, population sizes equivalent to native populations and a positive growth rate. These results may be due to inbreeding or the Wahlund effect, driven by genetic substructuring. This suggests that the small population size of these reintroduced populations may lead to genetic issues in the future, given the low number of flowering individuals each year. This highlights the importance of considering not only the number of source individuals but the effective population size of the reintroduction.

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Retriever and Pointer: Software to Evaluate Inbreeding and Genetic Management in Captive Populations

Animals ◽

10.3390/ani11051332 ◽

2021 ◽

Vol 11 (5) ◽

pp. 1332

Author(s):

Jack J. Windig ◽

Ina Hulsegge

Keyword(s):

Population Structure ◽

Allelic Diversity ◽

Captive Population ◽

Pedigree Data ◽

Effective Population ◽

Genetic Management ◽

Captive Populations ◽

Population Structures ◽

Population Sizes ◽

Well Data

The Retriever and Pointer software has been developed for genetic management of (small) captive populations The Retriever program uses as input pedigree data and extracts data on population structure that determine inbreeding rates such as skewness of sire contributions. Levels and rates of inbreeding and kinship and effective population sizes are determined as well. Data on population structure can be used as input for the Pointer program. This program uses stochastic simulation to evaluate a population and provides expected levels and rates of inbreeding and kinship, and optionally allelic diversity. The user can simulate different options for genetic management such as sire restrictions, restrictions on inbreeding levels, mean kinships and breeding circles. Both Retriever and Pointer can analyze populations with subpopulations and different rates of exchange between them. Although originally devised for dogs, the software can be, and has been, used for any captive population including livestock and zoo populations, and a number of examples are provided. The pointer software is also suitable in education where students may generate their own populations and evaluate effects of different population structures and genetic management on genetic diversity. Input is provided via a graphical user interface. The software can be downloaded for free.

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Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation

10.1101/2021.07.02.450939 ◽

2021 ◽

Author(s):

Lionel N Di Santo ◽

Sean Hoban ◽

Thomas L Parchman ◽

Jessica W Wright ◽

Jill A Hamilton

Keyword(s):

Genetic Diversity ◽

Rare Species ◽

Population Genetic ◽

Genetic Connectivity ◽

Genetic Rescue ◽

Effective Population ◽

Reduced Representation ◽

Population Sizes ◽

Pinus Torreyana ◽

Reduced Representation Sequencing

Understanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world's rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species' evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to assess loci possibly under selection, and evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation reflecting consistently low effective population sizes across time and limited genetic differentiation suggesting maintenance of gene flow following divergence. However, genome scans identified more than 2000 SNPs candidates for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates that natural selection has likely contributed to population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effect of rarity, divergent selection between populations indicates that genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.

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Faculty Opinions recommendation of Fitness decline in spontaneous mutation accumulation lines of Caenorhabditis elegans with varying effective population sizes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.723874420.793504625 ◽

2015 ◽

Author(s):

Charles Baer

Keyword(s):

Caenorhabditis Elegans ◽

Spontaneous Mutation ◽

Mutation Accumulation ◽

Effective Population ◽

Population Sizes

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Greater Prairie-Chicken (Tympanuchus cupido)

10.2173/bna.grpchi.02 ◽

2011 ◽

Cited By ~ 1

Author(s):

Jeff A. Johnson ◽

Michael A. Schroeder ◽

Leslie A. Robb

Keyword(s):

Tympanuchus Cupido ◽

Prairie Chicken ◽

Greater Prairie Chicken

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EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON SHORT-TERM RESPONSE TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽

10.1093/genetics/73.3.513 ◽

1973 ◽

Vol 73 (3) ◽

pp. 513-530

Author(s):

J P Hanrahan ◽

E J Eisen ◽

J E Legates

Keyword(s):

Population Size ◽

Selection Response ◽

Selection Intensity ◽

Realized Heritability ◽

Family Selection ◽

Effective Population ◽

Population Sizes ◽

Selection For ◽

Selection Intensities ◽

Term Response

ABSTRACT The effects of population size and selection intensity on the mean response was examined after 14 generations of within full-sib family selection for postweaning gain in mice. Population sizes of 1, 2, 4, 8 and 16 pair matings were each evaluated at selection intensities of 100% (control), 50% and 25% in a replicated experiment. Selection response per generation increased as selection intensity increased. Selection response and realized heritability tended to increase with increasing population size. Replicate variability in realized heritability was large at population sizes of 1, 2 and 4 pairs. Genetic drift was implicated as the primary factor causing the reduced response and lowered repeatability at the smaller population sizes. Lines with intended effective population sizes of 62 yielded larger selection responses per unit selection differential than lines with effective population sizes of 30 or less.

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Greater prairie-chicken nest success and habitat selection in southeastern Nebraska

Journal of Wildlife Management ◽

10.1002/jwmg.564 ◽

2013 ◽

Vol 77 (6) ◽

pp. 1202-1212 ◽

Cited By ~ 19

Author(s):

Ty W. Matthews ◽

Andrew J. Tyre ◽

J. Scott Taylor ◽

Jeffrey J. Lusk ◽

Larkin A. Powell

Keyword(s):

Habitat Selection ◽

Nest Success ◽

Prairie Chicken ◽

Greater Prairie Chicken

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Temperature, wind, vegetation, and roads influence incubation patterns of Greater Prairie-Chickens (Tympanuchus cupido pinnatus) in the Nebraska Sandhills, USA

Canadian Journal of Zoology ◽

10.1139/cjz-2018-0130 ◽

2019 ◽

Vol 97 (2) ◽

pp. 91-99

Author(s):

Ian R. Hoppe ◽

Jocelyn O. Harrison ◽

Edward J. Raynor IV ◽

Mary Bomberger Brown ◽

Larkin A. Powell ◽

...

Keyword(s):

Adult Survival ◽

Tympanuchus Cupido ◽

Ambient Temperatures ◽

Wind Speeds ◽

Trade Offs ◽

Nebraska Sandhills ◽

Avian Incubation ◽

Prairie Chicken ◽

Greater Prairie Chicken ◽

Tympanuchus Cupido Pinnatus

Avian incubation involves behavioral decisions that must balance trade-offs between the incubating bird’s survival and current and future reproductive success. We evaluated variation in incubation off-bout duration and frequency among Greater Prairie-Chickens (Tympanuchus cupido pinnatus (Brewster, 1885)) in the Nebraska Sandhills, USA. Greater Prairie-Chicken life history favors incubation behaviors that prioritize success of the current breeding attempt over adult survival. Previous observations suggest incubating females make these behavioral decisions based on ambient temperature conditions, their own body condition, and predation risk. We monitored nest attendance by females at 30 Greater Prairie-Chicken nests to identify proximate cues used to make behavioral decisions regarding incubation. We recorded 930 incubation off-bouts. Females took 1.9 ± 0.7 off-bouts/day (mean ± SD), each with a mean (±SD) duration of 43.3 ± 24.1 min. Off-bouts were shorter in duration at higher wind speeds, at lower ambient temperatures, at nests with less cover, and at nests closer to roads. Females were most likely to leave the nest during mid-morning and evening, as are most gallinaceous birds, and incubation off-bouts became less frequent later in the season. We did not observe differences in incubation behavior between nests that failed and those that successfully hatched one or more chicks.

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The effect of life-history and mode of inheritance on neutral genetic variability

Genetics Research ◽

10.1017/s0016672301004979 ◽

2001 ◽

Vol 77 (2) ◽

pp. 153-166 ◽

Cited By ~ 114

Author(s):

BRIAN CHARLESWORTH

Keyword(s):

Sequence Variation ◽

Adult Mortality ◽

Structured Populations ◽

Human Populations ◽

Effective Population ◽

Transmission Modes ◽

Population Sizes ◽

Age Structured ◽

Infinite Sites Model ◽

Site Diversity

Formulae for the effective population sizes of autosomal, X-linked, Y-linked and maternally transmitted loci in age-structured populations are developed. The approximations used here predict both asymptotic rates of increase in probabilities of identity, and equilibrium levels of neutral nucleotide site diversity under the infinite-sites model. The applications of the results to the interpretation of data on DNA sequence variation in Drosophila, plant, and human populations are discussed. It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X-linked loci relative to autosomal or Y-linked loci. These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes.

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