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 Temporal patterns of spatial genetic structure and effective population size in European plaice (Pleuronectes platessa) along the west coast of Scotland and in the Irish Sea

2009 ◽  
Vol 67 (4) ◽  
pp. 607-616 ◽  
Author(s):  
Phillip C. Watts ◽  
Suzanne M. Kay ◽  
Drew Wolfenden ◽  
Clive J. Fox ◽  
Audrey J. Geffen ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Size ◽  
Effective Population Size ◽  
West Coast ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Irish Sea ◽  
Effective Population ◽  
The West ◽  
Pleuronectes Platessa

Abstract Watts, P. C., Kay, S. M., Wolfenden, D., Fox, C. J., Geffen, A. J., Kemp, S. J., and Nash, R. D. M. 2010. Temporal patterns of spatial genetic structure and effective population size in European plaice (Pleuronectes platessa) along the west coast of Scotland and in the Irish Sea. – ICES Journal of Marine Science, 67: 607–616. The European plaice (Pleuronectes platessa) is a relatively mobile flatfish species, and previous studies have reported broad-scale genetic homogeneity among samples distributed throughout much of its northern European range, with no evidence for isolation-by-distance (IBD) population structure. Using microsatellite loci, the pattern of spatial genetic structure and effective population size is characterized for >800 plaice collected from locations off the west coast of Great Britain over a 3-year period (2001–2003). The plaice populations are characterized by weak spatial genetic structure, consistent with tagging data, and relatively low effective population sizes. In contrast to previous work, a pattern of isolation by distance is present among pairs of plaice from within each sampling period. However, IBD spatial structure was not observed for comparisons of plaice from different sampling years or using the entire dataset, indicating a patchy temporal genetic structure. Therefore, pooling the data from several years can mask subtle patterns of population structure and potentially confound estimation of other important demographic parameters, such as effective population size.

scholarly journals High genetic diversity and low future habitat suitability: will Cupressus atlantica, endemic to the High Atlas, survive under climate change?

2020 ◽  
Vol 20 (4) ◽  
Author(s):  
Katarzyna Sękiewicz ◽  
Łukasz Walas ◽  
Berika Beridze ◽  
Mohamed Fennane ◽  
Monika Dering
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Endemic Species ◽  
Spatial Genetic Structure ◽  
Species Range ◽  
Ex Situ ◽  
Genetic Connectivity ◽  
Effective Population ◽  
High Atlas ◽  
Cupressus Atlantica

AbstractCupressus atlantica is a narrow endemic species of semi-arid and sub-humid habitats in the western High Atlas, Morocco. We explored the possible dynamics of the species’ range under climatic changes using species distribution modelling (SDM) to identify populations vulnerable to range changes. Additionally, we investigated the spatial genetic structure (SGS), the effective population size and genetic connectivity in natural populations, which may provide important data on demo-genetic processes and support the conservation management of this critically endangered species. The SDM results showed that the current species range constitutes only 49% of the potential distribution. Under the most pessimistic scenarios (RCP6.0 and RCP8.5), a significant reduction in the species range was predicted. However, the projection based on RPC4.5 revealed possible extensions of the habitats suitable for C. atlantica. Potentially, these areas could serve as new habitats that could be used with the assisted migration approach aiming to mitigate the current fragmentation. In terms of the SGS, significant and positive aggregation of relatives was detected up to ca. 100 m. In comparison to other fragmented and endemic species, the detected SGS was weak (Sp = 0.0112). The estimated level of recent gene flow was considerable, which likely prevented a strong SGS and allowed diversity to accumulate (HE = 0.894). The most alarming results concern the effective population size, which was very low in the studied populations (< 53), suggesting a possible increase in inbreeding and loss of diversity in the near future. More effective conservation actions integrating in situ and ex situ measures should be undertaken to prevent extirpation of the species.

scholarly journals Low genetic diversity in the endangered Taxus yunnanensis following a population bottleneck, a low effective population size and increased inbreeding

2016 ◽  
Vol 65 (1) ◽  
pp. 59-66 ◽  
Author(s):  
Y. C. Miao ◽  
Z. J. Zhang ◽  
J. R. Su
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Population Bottleneck ◽  
Effective Population ◽  
Taxus Yunnanensis ◽  
Low Genetic Diversity ◽  
Two Populations

Abstract Taxus yunnanensis, which is an endangered tree that is considered valuable because it contains the effective natural anticancer metabolite taxol and heteropolysaccharides, has long suffered from severe habitat fragmentation. In this study, the levels of genetic diversity in two populations of 136 individuals were analyzed based on eleven polymorphic microsatellite loci. Our results suggested that these two populations were characterized by low genetic diversity (NE = 2.303/2.557; HO = 0.168/0.142; HE = 0.453/0.517), a population bottleneck, a low effective population size (Ne = 7/9), a high level of inbreeding (FIS = 0.596/0.702), and a weak, but significant spatial genetic structure (Sp = 0.001, b = −0.001*). Habitat fragmentation, seed shadow overlap and limited seed and pollen dispersal and potential selfing may have contributed to the observed gene tic structure. The results of the present study will enable development of practical conservation measures to effectively conserve the valuable genetic resources of this endangered plant.

Effective population size and genetic structure of a Piute ground squirrel (Spermophilus mollis) population

2001 ◽  
Vol 79 (1) ◽  
pp. 26-34 ◽  
Author(s):  
Michael F. Antolin ◽  
Beatrice Van Horne ◽  
Michael D. Berger, Jr. ◽  
Alisha K. Holloway ◽  
Jennifer L. Roach ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Ground Squirrel ◽  
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.

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.

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