scholarly journals Estimates of effective population size and inbreeding in South African indigenous chicken populations: implications for the conservation of unique genetic resources

2016 ◽  
Vol 48 (5) ◽  
pp. 943-950 ◽  
Author(s):  
Bohani Mtileni ◽  
Kennedy Dzama ◽  
Khathutshelo Nephawe ◽  
Clint Rhode
Keyword(s):  
Genetic Resources ◽  
Population Size ◽  
Effective Population Size ◽  
South African ◽  
Effective Population ◽  
Indigenous Chicken

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 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.

Genetic analyses reveal declining trends and low effective population size in an overfished South African sciaenid species, the dusky kob (Argyrosomus japonicus)

2016 ◽  
Vol 67 (2) ◽  
pp. 266 ◽  
Author(s):  
Luca Mirimin ◽  
Brett Macey ◽  
Sven Kerwath ◽  
Stephen Lamberth ◽  
Aletta Bester-van der Merwe ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
South African ◽  
Fish Farming ◽  
The South ◽  
Effective Population ◽  
Farmed Fish ◽  
Essential Information ◽  
Key Species ◽  
African Coast

Overfishing has led to the collapse of many marine fish stocks along the South African coast, particularly species characterised by predictable distribution patterns and vulnerable life-history traits. Dusky kob (Argyrosomus japonicus) is an estuarine-dependent sciaenid fish that has been severely depleted by overfishing and is currently managed by suboptimal management measures aggravated by poor enforcement and compliance to regulations. The present study utilised microsatellite markers to evaluate levels of genetic diversity and population structuring of dusky kob along the South African coast, including five estuarine areas. Results showed signatures of bottlenecking, low and declining trends of effective population size and weak differentiation among samples collected along 2000km of coastline, indicating that dusky kob continues to be subject to the detrimental influence of fishing pressure. Additionally, because dusky kob is a key species in the emerging South African aquaculture sector, parentage analyses were used to successfully identify the origin of first-generation (F1) individuals from a commercial hatchery, hence allowing traceability of farmed products and discrimination between wild and farmed fish. Findings from the present study provided essential information to aid future management of wild populations, as well as to establish sustainable fish farming.

scholarly journals Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

2015 ◽  
Vol 6 ◽  
Author(s):  
Sithembile O. Makina ◽  
Jeremy F. Taylor ◽  
Este van Marle-Köster ◽  
Farai C. Muchadeyi ◽  
Mahlako L. Makgahlela ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
South African ◽  
Effective Population ◽  
Cattle Breeds ◽  
Sanga Cattle

scholarly journals The Analysis of Czech Genetic Resources of Nutrias (Myocastor coypus)

2018 ◽  
Vol 49 (2) ◽  
pp. 93-97
Author(s):  
T. Němeček ◽  
E. Tůmová
Keyword(s):  
Genetic Resources ◽  
Population Size ◽  
Effective Population Size ◽  
Litter Size ◽  
Biodiversity Loss ◽  
Effective Population ◽  
Myocastor Coypus ◽  
Colour Type

Abstract The aim of this study is to evaluate the effective population size and fertility in the Czech Genetic Resources of nutrias during the last ten years. This study includes three Czech colour types of nutrias: Czech Type of Standard (ST), Moravian Silver (MS), and Prestice Multicolour (PM). The effective population size of ST shows that this colour type is endangered, while MS and PM are critical. The average number of pregnancy was the highest (P ≤ 0.004) in ST (1.7 pregnancy) and the lowest in PM (1.3 pregnancy). ST and MS nutrias had the significantly biggest litter size (P ≤ 0.004). For the number of kits born per female in a year (P < 0.001) the significantly lowest value was in PM (5.1 kits). For weaned kits the highest value (P ≤ 0.006) was in ST (4.8 kits). The results showed that the population size of MS and PM is low and there is a risk of biodiversity loss in these colour types.

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