scholarly journals Temporal trends in genetic data and effective population size support efficacy of management practices in critically endangered dusky gopher frogs ( Lithobates sevosus )

2016 ◽  
Vol 6 (9) ◽  
pp. 2667-2678 ◽  
Author(s):  
Kristin M. Hinkson ◽  
Stephen C. Richter
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Management Practices ◽  
Temporal Trends ◽  
Genetic Data ◽  
Critically Endangered ◽  
Effective Population

scholarly journals Conservation Assessment of the State Goat Farms by Using SNP Genotyping Data

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 652
Author(s):  
Rabiul Islam ◽  
Zhangfa Liu ◽  
Yefang Li ◽  
Lin Jiang ◽  
Yuehui Ma
Keyword(s):  
Genetic Resources ◽  
Population Size ◽  
Effective Population Size ◽  
Management Practices ◽  
Genetic Erosion ◽  
The State ◽  
Genomic Relationship ◽  
Effective Population ◽  
Conservation Assessment ◽  
Goat Farm

Conservation of genetic resources is of great concern globally to maintain genetic diversity for sustainable food security. Comprehensive identification of the breed composition, estimation of inbreeding and effective population size are essential for the effective management of farm animal genetic resources and to prevent the animals from genetic erosion. The Zhongwei male (ZWM), Arbas Cashmere male (ACM) and Jining Grey male (JGM) goats are conserved in three different state goat farms in China but their family information, level of inbreeding and effective population size are unknown. We investigated the genomic relationship, inbreeding coefficient and effective population size in these three breeds from three state goat farms using the Illumina goat SNP50 BeadChip. Genomic relationships and phylogenetic analysis revealed that the breeds are clearly separated and formed separate clusters based on their genetic relationship. We obtained a high proportion of informative SNPs, ranging from 91.8% in the Arbas Cashmere male to 96.2% in the Jining Grey male goat breeds with an average mean of 96.8%. Inbreeding, as measured by FROH, ranged from 1.79% in ZWM to 8.62% in ACM goat populations. High FROH values, elevated genomic coverage of very long ROH (>30 Mb) and severe decline in effective population size were recorded in ACM goat farm. The existence of a high correlation between FHOM and FROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. The Ne estimates 13 generations ago were 166, 69 and 79 for ZWM, ACM and JGM goat farm, respectively indicating that these goat breeds were strongly affected by selection pressure or genetic drift. This study provides insight into the genomic relationship, levels of inbreeding and effective population size in the studied goat populations conserved in the state goat farms which will be valuable in prioritizing populations for conservation and for developing suitable management practices for further genetic improvement of these Chinese male goats.

Microsatellite loci over a thirty-three year period for a malaria parasite (Plasmodium mexicanum): bottleneck in effective population size and effect on allele frequencies

Parasitology ◽  
2012 ◽  
Vol 140 (1) ◽  
pp. 21-28 ◽  
Author(s):  
J. J. SCHALL ◽  
K. M. ST. DENIS
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Malaria Parasite ◽  
Genetic Data ◽  
Parasite Prevalence ◽  
Allele Frequencies ◽  
The Other ◽  
Effective Population ◽  
Blood Smears ◽  
Parasite Plasmodium

SUMMARYChanges in population allele frequencies may be driven by several forces, including selection and drift, and are revealed only by sampling over many generations. Such studies, however, are rare for protist parasites. Microsatellite allele frequencies for 4 loci were followed in a population of Plasmodium mexicanum, a malaria parasite of lizards in California USA at 1 site from 1978 to 2010. Rapid turnover of the lizards indicates the parasite was studied for a minimum of 33 transmission cycles and possibly twice that number. Sample sizes ranged from 841 to 956 scored parasite clones per locus. DNA was extracted from frozen dried blood and blood removed from stained blood smears from the earliest years, and a verification study demonstrated DNA from the blood smears provided valid genetic data. Parasite prevalence and effective population size (Ne) dropped after 2000, remaining lower for the next decade. For 2 loci, allele frequencies appeared stable for the first 2 decades of the study, but changed more rapidly after the decline in prevalence. Allele frequencies changed more gradually for the other 2 loci. Genetic drift could account for changes in allele frequencies, especially after the drop in prevalence and Ne, but the force of selection could also have driven the observed patterns.

NeEstimatorv2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data

2013 ◽  
Vol 14 (1) ◽  
pp. 209-214 ◽  
Author(s):  
C. Do ◽  
R. S. Waples ◽  
D. Peel ◽  
G. M. Macbeth ◽  
B. J. Tillett ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genetic Data ◽  
Effective Population

scholarly journals Maximum likelihood inference of pathogen population size history from a phylogeny

2021 ◽  
Author(s):  
Xavier Didelot ◽  
Erik M Volz
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Sequence Data ◽  
Demographic History ◽  
Genetic Data ◽  
Parametric Models ◽  
Process Models ◽  
Effective Population ◽  
Latent Process ◽  
Non Parametric

ABSTRACTInference of effective population size from genomic data can provide unique information about demographic history, and when applied to pathogen genetic data can also provide insights into epidemiological dynamics. Non-parametric models for population dynamics combined with molecular clock models which relate genetic data to time have enabled phylodynamic inference based on large sets of time-stamped genetic sequence data. The theory for non-parametric inference of effective population size is well-developed in the Bayesian setting, but here we develop a frequentist approach based on non-parametric latent process models of population size dynamics. We appeal to statistical principles based on out-of-sample prediction accuracy in order to optimize parameters that control shape and smoothness of the population size over time. We demonstrate the flexibility and speed of this approach in a series of simulation experiments and apply the models to genetic data from several pathogen data sets.

Sign in / Sign up

Export Citation Format

Share Document