Inbreeding coefficients for stochastically varying small population sizes—bias of calculation based on effective numbers

2004 ◽  
Vol 226 (4) ◽  
pp. 467-475 ◽  
Author(s):  
Manfred Hühn ◽  
Hans-Peter Piepho
Botany ◽  
2013 ◽  
Vol 91 (5) ◽  
pp. 301-308 ◽  
Author(s):  
Jeremie B. Fant ◽  
Andrea Kramer ◽  
Eileen Sirkin ◽  
Kayri Havens

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.


Author(s):  
Matthew C. Fitzpatrick ◽  
Aaron M. Ellison

Climatic change likely will exacerbate current threats to carnivorous plants. However, estimating the severity of climatic change is challenged by the unique ecology of carnivorous plants, including habitat specialization, dispersal limitation, small ranges, and small population sizes. We discuss and apply methods for modeling species distributions to overcome these challenges and quantify the vulnerability of carnivorous plants to rapid climatic change. Results suggest that climatic change will reduce habitat suitability for most carnivorous plants. Models also project increases in habitat suitability for many species, but the extent to which these increases may offset habitat losses will depend on whether individuals can disperse to and establish in newly suitable habitats outside of their current distribution. Reducing existing stressors and protecting habitats where numerous carnivorous plant species occur may ameliorate impacts of climatic change on this unique group of plants.


The Condor ◽  
2002 ◽  
Vol 104 (4) ◽  
pp. 877-881
Author(s):  
Eben H. Paxton ◽  
Mark K. Sogge ◽  
Tracy D. McCarthey ◽  
Paul Keim

AbstractUsing molecular-genetic techniques, we determined the gender of 202 Southwestern Willow Flycatcher (Empidonax traillii extimus) nestlings from 95 nests sampled over a five-year period. Overall nestling sex ratio did not vary significantly from 50:50 among years, by clutch order, or by mating strategy (monogamous vs. polygamous pairings). However, we did observe significant differences among the four sites sampled, with sex ratios biased either toward males or females at the different sites. Given the small population sizes and geographic isolation of many of the endangered subspecies' breeding populations, sex-ratio differences may have localized negative impacts.Cociente de Sexos en Polluelos de Empidonax traillii extimusResumen. Utilizando técnicas moleculares determinamos el sexo de 202 polluelos de Empidonax traillii extimus pertenecientes a 95 nidos que fueron muestreados durante un período de cinco años. En general, el cociente de sexos no varió significativamente de 50:50 entre años, ya sea por orden de la nidada o por estrategia de apareamiento (monogamia vs. poligamia). Sin embargo, observamos diferencias significativas entre los cuatro sitios muestreados, en los cuales la razón de sexos estuvo sesgada hacia los machos o las hembras dependiendo del sitio. Dados los pequeños tamaños poblacionales y el aislamiento geográfico de muchas de las poblaciones reproductivas de esta subespecie en peligro, las diferencias en el cociente de sexos pueden tener un impacto negativo a nivel local.


Author(s):  
Morten Hertz ◽  
Iben Ravnborg Jensen ◽  
Laura Østergaard Jensen ◽  
Iben Vejrum Nielsen ◽  
Jacob Winde ◽  
...  

SummaryMany domestic breeds face challenges concerning genetic variability, because of their small population sizes along with a high risk of inbreeding. Therefore, it is important to obtain knowledge on their extinction risk, along with the possible benefits of certain breeding strategies. Since many domestic breeds face the same problems, results from such studies can be applied across breeds and species. Here a Population Viability Analysis (PVA) was implemented to simulate the future probability of extinction for a population of the endangered Danish Jutland cattle (Bos taurus), based on the software Vortex. A PVA evaluates the extinction risk of a population by including threats and demographic values. According to the results from the PVA the population will go extinct after 122 years with the current management. Four scenarios were created to investigate which changes in the breeding scheme would have the largest effect on the survival probabilities, including Scenario 1: More females in the breeding pool, scenario 2: More males in the breeding pool, scenario 3: Increased carrying capacity, and scenario 4: Supplementing males to the population through artificial insemination using semen from bulls used in the populations in past generations. All scenarios showed a positive effect on the population's probability of survival, and with a combination of the different scenarios, the population size seems to be stabilized.


1998 ◽  
Vol 25 (3) ◽  
pp. 262-272 ◽  
Author(s):  
M. K. PANDIT ◽  
C. R. BABU

Medicinal plants are a valuable resource for regional economic development in the tropics, and the Eastern Himalaya in particular harbours many such species. Extensive deforestation and over-exploitation in this region have brought several species to the brink of extinction, and Coptis teeta is such an endangered species; yet scientific information for its conservation is lacking. Investigations on the distribution range, demography, ecology, cytology, reproductive biology and population genetic structure of C. teeta were carried out; it was found to be endemic to a small area, to occupy a very narrow habitat and to be highly dispersed with very small population sizes. Edaphic factors were found to have played a vital role in ecological preference, natural distribution and evolutionary divergence of the species. The species exhibits a ‘K’ strategy, high male sterility, low reproductive success and efficiency, inadequate seed dispersal, and little genetic variability. A combination of these genetic hurdles and external threats in the form of habitat disturbance and over-exploitation for commercial purposes could result in its extinction. The species was found to have highly specific microsite requirements that cannot be met in other habitats. It is argued that in situ conservation measures would be the best strategy for the continued survival of this species. For effective management of the species it is recommended that its habitat be declared a protected area with the active cooperation of local inhabitants including the sharing of benefits of conservation.


2016 ◽  
Vol 283 (1829) ◽  
pp. 20152411 ◽  
Author(s):  
Bernt-Erik Sæther ◽  
Marcel E. Visser ◽  
Vidar Grøtan ◽  
Steinar Engen

Understanding the variation in selection pressure on key life-history traits is crucial in our rapidly changing world. Density is rarely considered as a selective agent. To study its importance, we partition phenotypic selection in fluctuating environments into components representing the population growth rate at low densities and the strength of density dependence, using a new stochastic modelling framework. We analysed the number of eggs laid per season in a small song-bird, the great tit, and found balancing selection favouring large clutch sizes at small population densities and smaller clutches in years with large populations. A significant interaction between clutch size and population size in the regression for the Malthusian fitness reveals that those females producing large clutch sizes at small population sizes also are those that show the strongest reduction in fitness when population size is increased. This provides empirical support for ongoing r - and K -selection in this population, favouring phenotypes with large growth rates r at small population sizes and phenotypes with high competitive skills when populations are close to the carrying capacity K . This selection causes long-term fluctuations around a stable mean clutch size caused by variation in population size, implying that r - and K -selection is an important mechanism influencing phenotypic evolution in fluctuating environments. This provides a general link between ecological dynamics and evolutionary processes, operating through a joint influence of density dependence and environmental stochasticity on fluctuations in population size.


2014 ◽  
Author(s):  
Molly Schumer ◽  
Rongfeng Cui ◽  
Gil G Rosenthal ◽  
Peter Andolfatto

Despite its role in homogenizing populations, hybridization has also been proposed as a means to generate new species. The conceptual basis for this idea is that hybridization can result in novel phenotypes through recombination between the parental genomes, allowing a hybrid population to occupy ecological niches unavailable to parental species. A key feature of these models is that these novel phenotypes ecologically isolate hybrid populations from parental populations, precipitating speciation. Here we present an alternative model of the evolution of reproductive isolation in hybrid populations that occurs as a simple consequence of selection against incompatibilities. Unlike previous models, our model does not require small population sizes, the availability of new niches for hybrids or ecological or sexual selection on hybrid traits. We show that reproductive isolation between hybrids and parents evolves frequently and rapidly under this model, even in the presence of ongoing migration with parental species and strong selection against hybrids. Our model predicts that multiple distinct hybrid species can emerge from replicate hybrid populations formed from the same parental species, potentially generating patterns of species diversity and relatedness that mimic adaptive radiations.


2016 ◽  
Author(s):  
Thomas LaBar ◽  
Christoph Adami

AbstractMost mutations are deleterious and cause a reduction in population fitness known as the mutational load. In small populations, weakened selection against slightly-deleterious mutations results in an additional fitness reduction. Many studies have established that populations can evolve a reduced mutational load by evolving mutational robustness, but it is uncertain whether small populations can evolve a reduced susceptibility to drift-related fitness declines. Here, using mathematical modeling and digital experimental evolution, we show that small populations do evolve a reduced vulnerability to drift, or “drift robustness”. We find that, compared to genotypes from large populations, genotypes from small populations have a decreased likelihood of small-effect deleterious mutations, thus causing small-population genotypes to be drift-robust. We further show that drift robustness is not adaptive, but instead arises because small populations preferentially adapt to drift-robust fitness peaks. These results have implications for genome evolution in organisms with small population sizes.


2019 ◽  
Author(s):  
Ellie E. Armstrong ◽  
Ryan W. Taylor ◽  
Danny E. Miller ◽  
Christopher Kaelin ◽  
Gregory Barsh ◽  
...  

AbstractThe lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly for the captive African lion from the Exotic Feline Rescue Center as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length and levels of homozygosity across the genomes of the lion sequenced here and other previous published resequence data, indicating contrasting histories of recent and ancient small population sizes and/or inbreeding. Demographic analyses reveal similar histories across all individuals except the Asiatic lion, which shows a more rapid decline in population size. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion.


2021 ◽  
Author(s):  
George Shirreff ◽  
Jean-Ralph Zahar ◽  
Simon Cauchemez ◽  
Laura Temime ◽  
Lulla Opatowski ◽  
...  

AbstractCovid-19 poses significant risk of nosocomial transmission, and preventing this requires good estimates of the basic reproduction number R0 in hospitals and care facilities, but these are currently lacking. Such estimates are challenging due to small population sizes in these facilities and inconsistent testing practices.We estimate the patient-to-patient R0 and daily transmission rate of SARS-CoV-2 using data from a closely monitored hospital outbreak in Paris 2020 during the first wave. We use a realistic epidemic model which accounts for progressive stages of infection, stochastic effects and a large proportion of asymptomatic infections. Innovatively, we explicitly include changes in testing capacity over time, as well as the evolving sensitivity of PCR testing at different stages of infection. We conduct rigorous statistical inference using iterative particle filtering to fit the model to the observed patient data and validate this methodology using simulation.We provide estimates for R0 across the entire hospital (2.6) and in individual wards (from 3 to 15), possibly reflecting heterogeneity in contact patterns or control measures. An obligatory mask-wearing policy introduced during the outbreak is likely to have changed the R0, and we estimate values before (8.7) and after (1.3) its introduction, corresponding to a policy efficacy of 85%.


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