Assessing genetic diversity of protected coho salmon (Oncorhynchus kisutch) populations in California

2007 ◽  
Vol 64 (1) ◽  
pp. 30-42 ◽  
Author(s):  
Katherine A Bucklin ◽  
Michael A Banks ◽  
Dennis Hedgecock
Keyword(s):  
Genetic Diversity ◽  
Coho Salmon ◽  
Random Mating ◽  
Oncorhynchus Kisutch ◽  
Legal Protection ◽  
Population Level ◽  
Population Subdivision ◽  
Minimal Impact ◽  
Low Genetic Diversity ◽  
Microsatellite Dna Markers

California coho salmon (Oncorhynchus kisutch) are under legal protection owing to significant declines in abundance over the last decades. Previously, California coho salmon were characterized as having low genetic diversity and weak population subdivision, attributable potentially to homogenization by out-of-basin hatchery releases. Here, diversity at seven highly polymorphic microsatellite DNA markers is assessed within and among 32 collections of coho salmon from 16 California watersheds. In 71% of local populations, genotypic composition deviates significantly from that expected under the assumption of random mating. We develop and apply methods to adjust for two potential causes of deviation from random mating expectations: (i) Wahlund effects, owing to heterogeneous collections of individuals, and (ii) the "Allendorf–Phelp's effect", owing to closely related juveniles in samples. Such population-level "adjustments" reduce within-region and increase among-region variance; after adjustment, we find strong concordance of genetic and geographic distances. We conclude that stock transfers have had minimal impact on population structure and that California coho salmon populations likely comprise small numbers of endemic breeders, potentially experiencing high levels of genetic drift and inbreeding.

scholarly journals Assessment of genetic diversity in Coho salmon (Oncorhynchus kisutch) populations with no family records using ddRAD-seq

2018 ◽  
Vol 11 (1) ◽  
Author(s):  
Sho Hosoya ◽  
Kiyoshi Kikuchi ◽  
Hiroshi Nagashima ◽  
Junichi Onodera ◽  
Kouichi Sugimoto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Coho Salmon ◽  
Oncorhynchus Kisutch

scholarly journals Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tika B. Adhikari ◽  
Norman Muzhinji ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Genetic Diversity ◽  
North Carolina ◽  
Population Structure ◽  
Genetic Variation ◽  
Dna Sequences ◽  
Random Mating ◽  
Population Expansion ◽  
The United States ◽  
Population Subdivision ◽  
The Impact

AbstractEarly blight (EB) caused by Alternaria linariae or Alternaria solani and leaf blight (LB) caused by A. alternata are economically important diseases of tomato and potato. Little is known about the genetic diversity and population structure of these pathogens in the United States. A total of 214 isolates of A. alternata (n = 61), A. linariae (n = 96), and A. solani (n = 57) were collected from tomato and potato in North Carolina and Wisconsin and grouped into populations based on geographic locations and tomato varieties. We exploited 220 single nucleotide polymorphisms derived from DNA sequences of 10 microsatellite loci to analyse the population genetic structure between species and between populations within species and infer the mode of reproduction. High genetic variation and genotypic diversity were observed in all the populations analysed. The null hypothesis of the clonality test based on the index of association $$\left( {\overline{r}_{d} } \right)$$ r ¯ d was rejected, and equal frequencies of mating types under random mating were detected in some studied populations of Alternaria spp., suggesting that recombination can play an important role in the evolution of these pathogens. Most genetic differences were found between species, and the results showed three distinct genetic clusters corresponding to the three Alternaria spp. We found no evidence for clustering of geographic location populations or tomato variety populations. Analyses of molecular variance revealed high (> 85%) genetic variation within individuals in a population, confirming a lack of population subdivision within species. Alternaria linariae populations harboured more multilocus genotypes (MLGs) than A. alternata and A. solani populations and shared the same MLG between populations within a species, which was suggestive of gene flow and population expansion. Although both A. linariae and A. solani can cause EB on tomatoes and potatoes, these two species are genetically differentiated. Our results provide new insights into the evolution and structure of Alternaria spp. and can lead to new directions in optimizing management strategies to mitigate the impact of these pathogens on tomato and potato production in North Carolina and Wisconsin.

scholarly journals Population Analysis of Fusarium graminearum from Wheat Fields in Eastern China

2002 ◽  
Vol 92 (12) ◽  
pp. 1315-1322 ◽  
Author(s):  
L. Rosewich Gale ◽  
L.-F. Chen ◽  
C. A. Hernick ◽  
K. Takamura ◽  
H. C. Kistler
Keyword(s):  
Fusarium Graminearum ◽  
Gene Diversity ◽  
Population Analysis ◽  
Eastern China ◽  
Random Mating ◽  
Population Level ◽  
Population Subdivision ◽  
Rflp Markers ◽  
Head Blight ◽  
Pairwise Linkage Disequilibrium

Wheat heads showing symptoms of Fusarium head blight were collected from four commercial fields in Zhejiang Province, China, an area where epidemics occur regularly. A total of 225 isolates were subjected to population-level analyses using restriction fragment length polymorphism (RFLP) as markers. Diagnostic RFLP markers established that all isolates belonged to Fusarium graminearum lineage 6. Nine polymorphic probes were hybridized to all isolates, resulting in 65 multilocus RFLP haplotypes (MRH). Probing with the telomeric clone pNla17, which reveals differences among isolates in the hypervariable subtelomeric region, differentiated the 65 MRH further into 144 clones. Mean gene diversity for the four field populations was similar, ranging from H = 0.306 - 0.364 over the nine RFLP loci for clone-corrected data. High levels of gene flow were inferred from a low level of population subdivision among all field populations, indicating that they were part of the same population. Pairwise linkage disequilibrium measures did not unequivocally support a random mating population, because one-third of locus pairs were significantly different from the null hypothesis of no-association between alleles. We speculate therefore that sexual recombination may not be frequent and that high levels of genotypic diversity may be maintained by relatively low selection pressure acting on a highly diverse population.

Effects of nonrandom mating schemes to delay the inbreeding accumulation in cultured populations of coho salmon (Oncorhynchus kisutch)

2004 ◽  
Vol 61 (4) ◽  
pp. 547-553 ◽  
Author(s):  
José A Gallardo ◽  
Jean Paul Lhorente ◽  
Ximena García ◽  
Roberto Neira
Keyword(s):  
Coho Salmon ◽  
Random Mating ◽  
Oncorhynchus Kisutch ◽  
Linear Unbiased Prediction ◽  
Breeding Values ◽  
Nonrandom Mating ◽  
The Family ◽  
Best Linear Unbiased ◽  
The Mean ◽  
High Degree

Chilean salmon culture is based on a high degree of artificial selection, which has had the tendency to increase the inbreeding (F). Three types of nonrandom mating were evaluated to control the inbreeding in two best linear unbiased prediction selected coho salmon (Oncorhynchus kisutch) populations (even and odd). These included compensatory mating on the basis of breeding values (C), modified compensatory mating (C1) based on the family mean of breeding values, and mating that minimized the mean co-ancestry of the group selected (MC scheme). In the odd population, the MC scheme (F = 2.0%) reduced the increase in inbreeding of the next generation by 50% and 46% when compared with random mating of selected individuals with sib mating restricted (F = 3.9%) and with C (F = 3.7%), respectively. In the even population, the MC scheme reduced the increase in inbreeding by 14% compared with C1 (9.7 versus 11.2). In both populations, the MC scheme also reduced variance in inbreeding (even, 59%; odd, 39%). Thus, the MC scheme was more efficient in reducing the increase and variance of inbreeding, thus limiting the expression of inbreeding depression. Although the MC scheme was more time consuming, we recommend this scheme to carry out crosses in each generation.

scholarly journals Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations

2020 ◽  
Author(s):  
Aaron J. Sams ◽  
Brett Ford ◽  
Adam Gardner ◽  
Adam R. Boyko
Keyword(s):  
Genetic Diversity ◽  
Random Mating ◽  
Companion Animals ◽  
Genetic Erosion ◽  
Population Level ◽  
Domestic Dog ◽  
Animal Populations ◽  
Genome Wide ◽  
Long Term Impact ◽  
The Impact

ABSTRACTIn many ways dogs are an ideal model for the study of genetic erosion and population recovery, problems of major concern in the field of conservation genetics. Genetic diversity in many dog breeds has been declining systematically since the beginning of the 1800’s, when modern breeding practices came into fashion. As such, inbreeding in domestic dog breeds is substantial and widespread and has led to an increase in recessive deleterious mutations of high effect as well as general inbreeding depression. Pedigrees can in theory be used to guide breeding decisions, though are often incomplete and do not reflect the full history of inbreeding. Small microsatellite panels are also used in some cases to choose mating pairs to produce litters with low levels of inbreeding. However, the long-term impact of such practices have not been thoroughly evaluated. Here, we use forward simulation on a model of the dog genome to examine the impact of using limited markers panels to guide pairwise mating decisions on genome-wide population level genetic diversity. Our results suggest that in unsupervised mating schemes, where breeding decisions are made at the pairwise-rather than population-level, such panels can lead to accelerated loss of genetic diversity compared to random mating at regions of the genome unlinked to panel markers and demonstrate the importance of genome-wide genetic panels for managing and conserving genetic diversity in dogs and other companion animals.

Conservation genomics reveals low genetic diversity and multiple parentage in the threatened freshwater mussel, Margaritifera hembeli

2020 ◽  
Author(s):  
Nicole L. Garrison ◽  
Paul D. Johnson ◽  
Nathan V. Whelan
Keyword(s):  
Genetic Diversity ◽  
Multiple Paternity ◽  
Freshwater Mussel ◽  
Population Level ◽  
Conservation Genomics ◽  
The North ◽  
Low Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Genetic Patterns ◽  
Genomic Approach

AbstractMargaritifera hembeli is a federally threatened freshwater mussel species restricted to three central Louisiana drainages. Currently, management efforts are being formulated without an understanding of population-level genetic patterns, which could result in sub-optimal conservation outcomes. In particular, information about riverscape genetic patterns is needed to design effective propagation and reintroduction plans. We apply a genomic approach (RADseq) to assess genetic diversity and structure among four wild populations sampled from across the species range. We also assess the genetic diversity of a captively reared cohort produced from a single female. We recovered population differentiation between individuals sampled to the north and south of the Red River. All sites had similarly low levels of heterogeneity and other measures of genetic diversity. The captive cohort displayed higher levels of genetic diversity than expected and likely represents a case of multiple paternity. Future propagation efforts will likely be able to produce genetically diverse cohorts from a small number of wild-caught females, and we recommend future reintroduction efforts utilize brooders within the sub-drainage closest to the reintroduction effort.

Variation in Agonistic Behavior between Newly Emerged Juveniles from Hatchery and Wild Populations of Coho Salmon, Oncorhynchus kisutch

1990 ◽  
Vol 47 (3) ◽  
pp. 566-571 ◽  
Author(s):  
D. P. Swain ◽  
B. E. Riddell
Keyword(s):  
Agonistic Behavior ◽  
Coho Salmon ◽  
Oncorhynchus Kisutch ◽  
Its Region ◽  
Population Level ◽  
Mirror Image ◽  
Aggressive Display ◽  
Wild Populations ◽  
Breeding Programs ◽  
Stimulation Tests

We compared agonistic behavior of newly emerged coho salmon (Oncorhynchus kisutch) between hatchery and wild populations using mirror image stimulation tests. We used hatchery populations from two different regions of Vancouver Island B.C., each matched with a wild population from its region. In both comparisons, hatchery juveniles were more aggressive than wild juveniles. Rates of aggressive display increased with time since emergence for both hatchery and wild fish, as did the differences in behavior between the two types. By the sixth day of observation (13 d postemergence), the overall effect of fish type was highly significant for all aggressive behaviours. Since the individuals compared were reared from eggs under identical conditions, these differences are presumably genetic. Comparisons involved relatively few families from each population. However, because heritability was moderate to low within populations, and variance between population types exceeded variance among families within populations, these results indicate real differences at the population level. These results may have important implications for programs to rebuild wild populations using hatchery transplants and for selective breeding programs to develop domestic stocks of coho.

scholarly journals Genetic variation characterization of the boreal tree Acer ginnala population in response to environmental change of Northern China

2019 ◽  
Author(s):  
Yiling Wang ◽  
Jiahui Wu ◽  
Zhi Wang ◽  
Hang Ye ◽  
Huimin Hou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Population Level ◽  
Northeastern China ◽  
Last Interglacial ◽  
Economic Resource ◽  
Low Genetic Diversity ◽  
Local Selection ◽  
Acer Ginnala

Abstract Background: Acer ginnala is a deciduous shrub/small tree that primarily distributed across the northern regions of China. It comprises a foundation species in many terrestrial ecosystems and has significant ornamental and economic value. Owing to its increased use as an economic resource, overexploitation and environmental destruction have resulted in the vulnerability of this species. Thus, the elucidation of the genetic differentiation and influence of environmental factors on A. ginnala is very critical for its management and future utilization strategies. Results: Our results revealed that high genetic variation occurred in A. ginnala species while low genetic diversity was observed at the population level. Most differentiation has found among populations. A significant correlation existed between genetic and environmental distances. Seven climate variables (bio1, bio2, bio3, bio4, bio13, bio15 and bio18) might explain the substantial levels of genetic variation (> 40%) in populations. The most suitable areas of this species appeared in Shaanxi, Shanxi, Anhui Provinces, and Northeastern China based on ENM results. Compared to the last interglacial (LIG) period, A. ginnala migrated toward Northern and Northeastern China, and extended to the most suitable areas during the last glacial maximum (LGM) period. Shanxi and Anhui Provinces might have served as refugium owing to their relatively high genetic variation. Conclusions: Low genetic diversity at the population level that may be the source of its vulnerability. Climate heterogeneity would play an important role in the pattern of genetic differentiation in A. ginnala populations. The A. ginnala population was isolated by a heterogeneous climate and subsequently began to adapt to local selection processes resulted in high genetic divergence.

scholarly journals Population Structure and Genetic Diversity of the Medicinal and Aromatic Plant Cunila spicata Benth. (Lamiaceae) Based on Inter-Simple Sequence Repeat (ISSR) Markers

2015 ◽  
Vol 5 (2) ◽  
pp. 652-658
Author(s):  
Ana Paula Longaray Delamare ◽  
Sergio Echeverrigaray ◽  
Marcos Albuquerque ◽  
Jucimar Zacaria
Keyword(s):  
Genetic Diversity ◽  
Population Level ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Genetic Distances ◽  
Aromatic Plant ◽  
Low Genetic Diversity ◽  
Main Factors ◽  
Simple Sequence ◽  
South Brazil

Cunila spicata is an endangered aromatic and medicinal plant of South Brazil. In the present paper, the ISSR technique was employed to study the intra- and inter-population genetic diversity of this species. Nine primers generated a total of 109 amplification products, most of which were polymorphics. Low genetic diversity at population level (HE= 0.053) and species level (HT=0.196), and high differentiation among populations (GST= 0.727) were detected in C. spicata. The genetic diversity, low estimated genetic flow and absence of correlation between genetic distances, geographic distances and chemical composition, indicates that genetic drift and inbreeding may be the main factors involved in the genetic structure of C. spicata. Based on these findings, strategies are proposed for the genetic conservation and management of this species. 

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