scholarly journals Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions

2018 ◽  
Author(s):  
Melak Weldenegodguad ◽  
Ruslan Popov ◽  
Kisun Pokharel ◽  
Innokentyi Ammosov ◽  
Ming Yao ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Artificial Selection ◽  
Demographic History ◽  
Population Variation ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Taurine Cattle ◽  
Cattle Farming

AbstractNorthern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome resequencing to genetically characterize three rare native breeds Eastern Finncattle, Western Finncattle and Yakutian cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian taurine cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European taurine breeds. This result is in contrast to the results of marker-based cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic taurine cattle may have been higher than that of the European cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on cattle genomes and on the value of the adapted breeds for the conservation of cattle genetic resources.

scholarly journals Low effective population size and high spatial genetic structure of black poplar populations from the Oder valley in Poland

2021 ◽  
Vol 78 (2) ◽  
Author(s):  
Błażej Wójkiewicz ◽  
Andrzewj Lewandowski ◽  
Weronika B. Żukowska ◽  
Monika Litkowiec ◽  
Witold Wachowiak
Keyword(s):  
Genetic Structure ◽  
Genetic Resources ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Demographic History ◽  
River Valley ◽  
Ex Situ ◽  
Effective Population ◽  
Black Poplar

Abstract Context Black poplar (Populus nigra L.) is a keystone species of European riparian ecosystems that has been negatively impacted by riverside urbanization for centuries. Consequently, it has become an endangered tree species in many European countries. The establishment of a suitable rescue plan of the remaining black poplar forest stands requires a preliminary knowledge about the distribution of genetic variation among species populations. However, for some parts of the P. nigra distribution in Europe, the genetic resources and demographic history remain poorly recognized. Aims Here, we present the first study on identifying and characterizing the genetic resources of black poplar from the Oder valley in Poland. This study (1) assessed the genetic variability and effective population size of populations and (2) examined whether gene flow is limited by distance or there is a single migrant pool along the studied river system. Methods A total of 582 poplar trees derived from nine black poplar populations were investigated with nuclear microsatellite markers. Results (1) The allelic richness and heterozygosity level were high and comparable between populations. (2) The genetic structure of the studied poplar stands was not homogenous. (3) The signatures of past bottlenecks were detected. Conclusion Our study (1) provides evidence for genetic substructuring of natural black poplar populations from the studied river catchment, which is not a frequent phenomenon reported for this species in Europe, and (2) indicates which poplar stands may serve as new genetic conservation units (GCUs) of this species in Europe. Key message The genetic resources of black poplar in the Oder River valley are still substantial compared to those reported for rivers in Western Europe. On the other hand, clear signals of isolation by distance and genetic erosion reflected in small effective population sizes and high spatial genetic structure of the analyzed populations were detected. Based on these findings, we recommend the in situ and ex situ conservation strategies for conserving and restoring the genetic resources of black poplar populations in this strongly transformed by human river valley ecosystem.

scholarly journals Inbreeding in artificial selection programmes

1961 ◽  
Vol 2 (2) ◽  
pp. 189-194 ◽  
Author(s):  
Alan Robertson
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Artificial Selection ◽  
Actual Number ◽  
Effective Population

In a population under artificial selection, the effective population size may be less than the actual number of parents selected because there will be variation between families in the character under selection and consequently in the probability of selection. Expressions are developed for the magnitude of the effect, which will be greater the more intense the selection and the higher the heritability of the selected character. The inbreeding due to outstanding individuals may rise for several generations after their use.

scholarly journals The effects of X-rays on quantitative characters

1964 ◽  
Vol 5 (3) ◽  
pp. 410-422 ◽  
Author(s):  
G. A. Clayton ◽  
Alan Robertson
Keyword(s):  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Artificial Selection ◽  
Inbred Lines ◽  
X Rays ◽  
Effective Population ◽  
Outbred Population ◽  
Culture Bottle ◽  
Quantitative Characters

1. The rate of production by X-rays of new genetic variation in two quantitative characters in Drosophila melanogaster (sternital and sternopleural bristles) has been investigated, using ‘plateaued’ populations which had reached the limit under artificial selection and, for sternital bristles only, populations which had been made genetically invariant by inbreeding. The genetic variation was always measured by the response of the population to selection. The X-rays dose given in any generation was always 1800 r. to adults.2. Seven plateaued lines had eight cycles of alternate irradiation and selection, each with its non-irradiated control. All the responses were small but in three lines they were significantly greater after irradiation.3. Selection was applied to three different inbred lines, genetically marked to detect contamination, after varying periods of irradiation. At the same time, the inbred lines and lines derived from them which had been mass mated in bottles were selected. The irradiated populations showed a greater response. The new genetic variance produced by the irradiation was approximately 10−5 units/r. The estimate of the dose required to introduce new variation equal to that in a standard outbred population was 500,000 r.4. The effective population size was an important factor in the interpretation of some of these results on the long-term effects of radiation. By observing the variation between replicate lines in the frequency of a gene with a visible effect under these culture conditions (i.e. in a single culture bottle) the effective population size was estimated at sixty. Outbred populations kept under these conditions for many generations showed a reduction of genetic variability in agreement with this value.5. To investigate the possibility that the deleterious genes produced by irradiation would interfere with the response to artificial selection, a standard outbred population was irradiated and selected. In spite of the observed high frequency of recessive lethals produced, the response to selection was very similar to that of the standard population.

scholarly journals Genetic Diversity in the Italian Holstein Dairy Cattle Based on Pedigree and SNP Data Prior and After Genomic Selection

2022 ◽  
Vol 8 ◽  
Author(s):  
Michela Ablondi ◽  
Alberto Sabbioni ◽  
Giorgia Stocco ◽  
Claudio Cipolat-Gotet ◽  
Christos Dadousis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dairy Cattle ◽  
Population Size ◽  
Genomic Selection ◽  
Effective Population Size ◽  
Genomic Data ◽  
Future Market ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Snp Data

Genetic diversity has become an urgent matter not only in small local breeds but also in more specialized ones. While the use of genomic data in livestock breeding programs increased genetic gain, there is increasing evidence that this benefit may be counterbalanced by the potential loss of genetic variability. Thus, in this study, we aimed to investigate the genetic diversity in the Italian Holstein dairy cattle using pedigree and genomic data from cows born between 2002 and 2020. We estimated variation in inbreeding, effective population size, and generation interval and compared those aspects prior to and after the introduction of genomic selection in the breed. The dataset contained 84,443 single-nucleotide polymorphisms (SNPs), and 74,485 cows were analyzed. Pedigree depth based on complete generation equivalent was equal to 10.67. A run of homozygosity (ROH) analysis was adopted to estimate SNP-based inbreeding (FROH). The average pedigree inbreeding was 0.07, while the average FROH was more than double, being equal to 0.17. The pattern of the effective population size based on pedigree and SNP data was similar although different in scale, with a constant decrease within the last five generations. The overall inbreeding rate (ΔF) per year was equal to +0.27% and +0.44% for Fped and FROH throughout the studied period, which corresponded to about +1.35% and +2.2% per generation, respectively. A significant increase in the ΔF was found since the introduction of genomic selection in the breed. This study in the Italian Holstein dairy cattle showed the importance of controlling the loss of genetic diversity to ensure the long-term sustainability of this breed, as well as to guarantee future market demands.

scholarly journals Whole genome linkage disequilibrium and effective population size in a coho salmon (Oncorhynchus kisutch) breeding population

2018 ◽  
Author(s):  
Agustín Barría ◽  
Kris A. Christensen ◽  
Grazyella Yoshida ◽  
Ana Jedlicki ◽  
Jean P. Lhorente ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Coho Salmon ◽  
Association Studies ◽  
Breeding Population ◽  
Physical Distance ◽  
Average Density ◽  
Whole Genome ◽  
Effective Population

AbstractThe estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection and for inferring historical events influencing different populations. This work aimed to evaluate the extent and decay of linkage disequilibrium in a coho salmon breeding population using ddRAD genomic markers.Linkage disequilibrium was estimated between a total of 7,505 SNPs found in 62 individuals (33 dams and 29 sires) from the breeding population. The makers encompass all 30 coho salmon chromosomes and comprise 1,655.19 Mb of the genome. The average density of markers per chromosome ranged from 3.45 to 6.11 per 1 Mbp. The minor allele frequency averaged 0.20 (with a range from 0.08 to 0.50). The overall average linkage disequilibrium among SNPs pairs measured as r2 was 0.054. The Average r2 value decreased with increasing physical distance, with values ranging from 0.37 to 0.054 at distances lower than 1 kb and up to 10 Mb, respectively. An r2 threshold of 0.1 was reached at distance of approximately 1.3 Mb. Chromosomes Okis05, Okis15 and Okis28 showed high levels of linkage disequilibrium (> 0.20 at distances lower than 1 Mb). Average r2 values were lower than 0.1 for all chromosomes at distances greater than 4 Mb. Linkage disequilibrium values suggest that whole genome association and selection studies could be performed using about 75,000 SNPs in aquaculture populations (depending on the trait under investigation). From the identified SNPs, an effective population size of 100 was estimated for the population 10 generation ago, and 1,000, for 139 generations ago.Based on the extent of r2 decay, we suggest that at least 75,000 SNPs would be necessary for an association mapping study. Over 100,000 SNPs would be necessary for a high power study, in the current coho salmon population.

scholarly journals Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

2017 ◽  
Author(s):  
Erik M. Volz ◽  
Xavier Didelot
Keyword(s):  
Growth Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Growth Rates ◽  
Sequence Data ◽  
Demographic History ◽  
Parametric Models ◽  
Effective Population ◽  
Epidemic Dynamics ◽  
Non Parametric

AbstractNon-parametric population genetic modeling provides a simple and flexible approach for studying demographic history and epidemic dynamics using pathogen sequence data. Existing Bayesian approaches are premised on stationary stochastic processes which may provide an unrealistic prior for epidemic histories which feature extended period of exponential growth or decline. We show that non-parametric models defined in terms of the growth rate of the effective population size can provide a more realistic prior for epidemic history. We propose a non-parametric autoregressive model on the growth rate as a prior for effective population size, which corresponds to the dynamics expected under many epidemic situations. We demonstrate the use of this model within a Bayesian phylodynamic inference framework. Our method correctly reconstructs trends of epidemic growth and decline from pathogen genealogies even when genealogical data is sparse and conventional skyline estimators erroneously predict stable population size. We also propose a regression approach for relating growth rates of pathogen effective population size and time-varying variables that may impact the replicative fitness of a pathogen. The model is applied to real data from rabies virus and Staphylococcus aureus epidemics. We find a close correspondence between the estimated growth rates of a lineage of methicillin-resistant S. aureus and population-level prescription rates of β-lactam antibiotics. The new models are implemented in an open source R package called skygrowth which is available at https://mrc-ide.github.io/skygrowth/.

scholarly journals Demographic history and divergence of sibling grouse species inferred from whole genome sequencing reveal past effects of climate change

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kai Song ◽  
Bin Gao ◽  
Peter Halvarsson ◽  
Yun Fang ◽  
Siegfried Klaus ◽  
...  
Keyword(s):  
Climate Change ◽  
Boreal Forest ◽  
Population Size ◽  
Effective Population Size ◽  
Demographic History ◽  
Bird Species ◽  
Future Climate Change ◽  
Effective Population ◽  
Hazel Grouse ◽  
Chinese Grouse

Abstract Background The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To understand the possible effects of on-going and future climate change it would be useful to reconstruct past population size changes and relate such to climatic events in the past. We sequenced the genomes of 32 individuals from two forest inhabiting bird species, Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of two outgroup species from Europe and China. Results We estimated the divergence time of Chinese Grouse and Hazel Grouse to 1.76 (0.46–3.37) MYA. The demographic history of different populations in these two sibling species was reconstructed, and showed that peaks and bottlenecks of effective population size occurred at different times for the two species. The northern Qilian population of Chinese Grouse became separated from the rest of the species residing in the south approximately 250,000 years ago and have since then showed consistently lower effective population size than the southern population. The Chinese Hazel Grouse population had a higher effective population size at the peak of the Last Glacial Period (approx. 300,000 years ago) than the European population. Both species have decreased recently and now have low effective population sizes. Conclusions Combined with the uplift history and reconstructed climate change during the Quaternary, our results support that cold-adapted grouse species diverged in response to changes in the distribution of palaeo-boreal forest and the formation of the Loess Plateau. The combined effects of climate change and an increased human pressure impose major threats to the survival and conservation of both species.

scholarly journals Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)

2019 ◽  
Author(s):  
Xi Wang ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Picea Abies ◽  
Population Size ◽  
Effective Population Size ◽  
Norway Spruce ◽  
Demographic History ◽  
Sequencing Data ◽  
Effective Population ◽  
Genome Wide

AbstractUnder the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity of P.abies is low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

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