scholarly journals Decline of heterozygosity in a large but isolated population: a 45-year examination of moose genetic diversity on Isle Royale

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3584 ◽  
Author(s):  
Renae L. Sattler ◽  
Janna R. Willoughby ◽  
Bradley J. Swanson
Keyword(s):  
Genetic Diversity ◽  
Wildlife Conservation ◽  
Microsatellite Data ◽  
Isle Royale ◽  
Inbreeding Coefficients ◽  
Large Populations ◽  
Heterozygosity Loss ◽  
Moose Population ◽  
Management Approaches

Wildlife conservation and management approaches typically focus on demographic measurements to assess population viability over both short and long periods. However, genetic diversity is an important predictor of long term population vitality. We investigated the pattern of change in genetic diversity in a large and likely isolated moose (Alces alces) population on Isle Royale (Lake Superior) from 1960–2005. We characterized samples, partitioned into five different 5-year periods, using nine microsatellite loci and a portion of the mtDNA control region. We also simulated the moose population to generate a theoretical backdrop of genetic diversity change. In the empirical data, we found that the number of alleles was consistently low and that observed heterozygosity notably declined from 1960 to 2005 (p = 0.08, R2 = 0.70). Furthermore, inbreeding coefficients approximately doubled from 0.08 in 1960–65 to 0.16 in 2000–05. Finally, we found that the empirical rate of observed heterozygosity decline was faster than the rate of observed heterozygosity loss in our simulations. Combined, these data suggest that genetic drift and inbreeding occurred in the Isle Royale moose populations over the study period, leading to significant losses in heterozygosity. Although inbreeding can be mitigated by migration, we found no evidence to support the occurrence of recent migrants into the population using analysis of our mtDNA haplotypes nor microsatellite data. Therefore, the Isle Royale moose population illustrates that even large populations are subjected to inbreeding in the absence of migration.

scholarly journals Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1972
Author(s):  
Emil Krupa ◽  
Nina Moravčíková ◽  
Zuzana Krupová ◽  
Eliška Žáková
Keyword(s):  
Genetic Diversity ◽  
Correlation Coefficients ◽  
Pedigree Analysis ◽  
Minimum Size ◽  
Snp Analysis ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Snp Data ◽  
Inbreeding Rate

Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, breeding line, and herd for 1971 individuals was considered in the pedigree analysis. The SNP analysis (n = 181) was performed using the Illumina PorcineSNP60 BeadChip kit. The quality of pedigree and SNPs and the inbreeding coefficients (F) and effective population size (Ne) were evaluated. The correlations between inbreeding based on the runs of homozygosity (FROH) and pedigree (FPED) were also calculated. The average FPED for all animals was 3.44%, while the FROH varied from 10.81% for a minimum size of 1 Mbp to 3.98% for a minimum size of 16 Mbp. The average minor allele frequency was 0.28 ± 0.11. The observed and expected within breed heterozygosities were 0.38 ± 0.13 and 0.37 ± 0.12, respectively. The Ne, obtained using both the data sources, reached values around 50 animals. Moderate correlation coefficients (0.49–0.54) were observed between FPED and FROH. It is necessary to make decisions that stabilize the inbreeding rate in the long-term using optimal contribution selection based on the available SNP data.

scholarly journals Genetic Consequences of Fence Confinement in a Population of White-Tailed Deer

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 126
Author(s):  
Emily K. Latch ◽  
Kenneth L. Gee ◽  
Stephen L. Webb ◽  
Rodney L. Honeycutt ◽  
Randy W. DeYoung ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Wildlife Management ◽  
Field Observations ◽  
Adaptive Potential ◽  
Population Isolation ◽  
Potential Benefits ◽  
Wildlife Populations ◽  
Mtdna Diversity

Fencing wildlife populations can aid wildlife management goals, but potential benefits may not always outweigh costs of confinement. Population isolation can erode genetic diversity and lead to the accumulation of inbreeding, reducing viability and limiting adaptive potential. We used microsatellite and mitochondrial DNA data collected from 640 white-tailed deer confined within a 1184 ha fence to quantify changes in genetic diversity and inbreeding over the first 12 years of confinement. Genetic diversity was sustained over the course of the study, remaining comparable to unconfined white-tailed deer populations. Uneroded genetic diversity suggests that genetic drift is mitigated by a low level of gene flow, which supports field observations that the fence is not completely impermeable. In year 9 of the study, we observed an unexpected influx of mtDNA diversity and drop in inbreeding as measured by FIS. A male harvest restriction imposed that year increased male survival, and more diverse mating may have contributed to the inbreeding reduction and temporary genetic diversity boost we observed. These data add to our understanding of the long-term impacts of fences on wildlife, but also highlight the importance of continued monitoring of confined populations.

Soil microbial dynamics and genetic diversity in soil under monoculture wheat grown in different long-term management systems

2007 ◽  
Vol 39 (6) ◽  
pp. 1391-1400 ◽  
Author(s):  
Carmine Crecchio ◽  
Maddalena Curci ◽  
Antonella Pellegrino ◽  
Patrizia Ricciuti ◽  
Nunzia Tursi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Management Systems ◽  
Microbial Dynamics ◽  
Soil Microbial ◽  
Term Management

scholarly journals Statistical analysis in support of maintaining a healthy traditional Siamese cat population

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Arthur M. A. Pistorius ◽  
Ineke Blokker
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Companion Animals ◽  
Hereditary Diseases ◽  
Small Scale ◽  
Genetic Traits ◽  
Inbreeding Coefficients ◽  
A Value ◽  
Siamese Cat ◽  
Line Breeding

Abstract Background For many years, breeders of companion animals have applied inbreeding or line breeding to transfer desirable genetic traits from parents to their offspring. Simultaneously, this resulted in a considerable spread of hereditary diseases and phenomena associated with inbreeding depression. Results Our cluster analysis of kinship and inbreeding coefficients suggests that the Thai or traditional Siamese cat could be considered as a subpopulation of the Siamese cat, which shares common ancestors, although they are considered as separate breeds. In addition, model-based cluster analysis could detect regional differences between Thai subpopulations. We show that by applying optimal contribution selection and simultaneously limiting the contributions by other breeds, the genetic diversity within subpopulations can be improved. Conclusion In principle, the European mainland Thai cat population can achieve a genetic diversity of about 26 founder genome equivalents, a value that could potentially sustain a genetically diverse population. However, reaching such a target will be difficult in the absence of a supervised breeding program. Suboptimal solutions can be obtained by minimisation of kinships within regional subpopulations. Exchanging animals between different regions on a small scale might be already quite useful to reduce the kinship, by achieving a potential diversity of 23 founder genome equivalents. However, contributions by other breeds should be minimised to preserve the original Siamese gene pool.

scholarly journals Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2193
Author(s):  
Angelika Podbielska ◽  
Katarzyna Piórkowska ◽  
Tomasz Szmatoła
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
First Generation ◽  
Expected Heterozygosity ◽  
Hybrid Detection ◽  
Average Coefficient ◽  
Mixed Origin ◽  
Generation Hybrid

This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.

Koala retrovirus genetic diversity and transmission dynamics within captive koala populations

2021 ◽  
Vol 118 (38) ◽  
pp. e2024021118
Author(s):  
Briony A. Joyce ◽  
Michaela D. J. Blyton ◽  
Stephen D. Johnston ◽  
Paul R. Young ◽  
Keith J. Chappell
Keyword(s):  
Genetic Diversity ◽  
Antiretroviral Treatment ◽  
Sexual Transmission ◽  
Transmission Dynamics ◽  
Rapid Decline ◽  
Effective Management ◽  
Additional Challenge ◽  
Management Approaches ◽  
Southeast Queensland ◽  
Koala Retrovirus

Koala populations are currently in rapid decline across Australia, with infectious diseases being a contributing cause. The koala retrovirus (KoRV) is a gammaretrovirus present in both captive and wild koala colonies that presents an additional challenge for koala conservation in addition to habitat loss, climate change, and other factors. Currently, nine different subtypes (A to I) have been identified; however, KoRV genetic diversity analyses have been limited. KoRV is thought to be exogenously transmitted between individuals, with KoRV-A also being endogenous and transmitted through the germline. The mechanisms of exogenous KoRV transmission are yet to be extensively investigated. Here, deep sequencing was employed on 109 captive koalas of known pedigree, housed in two institutions from Southeast Queensland, to provide a detailed analysis of KoRV transmission dynamics and genetic diversity. The final dataset included 421 unique KoRV sequences, along with the finding of an additional subtype (KoRV-K). Our analysis suggests that exogenous transmission of KoRV occurs primarily between dam and joey, with evidence provided for multiple subtypes, including nonendogenized KoRV-A. No evidence of sexual transmission was observed, with mating partners found to share a similar number of sequences as unrelated koala pairs. Importantly, both distinct captive colonies showed similar trends. These findings indicate that breeding strategies or antiretroviral treatment of females could be employed as effective management approaches in combating KoRV transmission.

Captive management and the maintenance of genetic diversity in a vulnerable marsupial, the greater bilby

2015 ◽  
Vol 37 (2) ◽  
pp. 170 ◽  
Author(s):  
Emily J. Miller ◽  
Mark D. B. Eldridge ◽  
Keith Morris ◽  
Neil Thomas ◽  
Catherine A. Herbert
Keyword(s):  
Genetic Diversity ◽  
Captive Breeding ◽  
Natural Habitat ◽  
Species Conservation ◽  
Molecular Data ◽  
Breeding Programs ◽  
Captive Populations ◽  
Genetic Impact ◽  
Captive Breeding Programs

The endemic Australian greater bilby (Macrotis lagotis) is a vulnerable and iconic species. It has declined significantly due to habitat loss, as well as competition and predation from introduced species. Conservation measures include a National Recovery Plan that incorporates several captive breeding programs. Two of these programs were established within 12 months of one another (1997/98), with the same number and sex ratio of founding individuals, but executed different breeding strategies: (1) unmanipulated mating in semi–free range natural habitat versus (2) minimising mean kinship in large enclosures, with the supplementation of new individuals into both populations. This study evaluates the long-term genetic impact of these programs and examines the congruency between the pedigree studbook estimates of diversity and molecular data. Our data demonstrate that genetic diversity was maintained in both populations, with the supplementation of new individuals contributing to the gene pool. The studbook estimates of diversity and inbreeding are not consistent with the microsatellite data and should not solely be relied upon to evaluate the genetic health of captive populations. Our analyses suggest that captive breeding programs may not require costly and intensive management to effectively maintain long-term genetic diversity in a promiscuous species.

scholarly journals Unexpected heterozygosity in an island mouflon population founded by a single pair of individuals

2006 ◽  
Vol 274 (1609) ◽  
pp. 527-533 ◽  
Author(s):  
Renaud Kaeuffer ◽  
David W Coltman ◽  
Jean-Louis Chapuis ◽  
Dominique Pontier ◽  
Denis Réale
Keyword(s):  
Genetic Diversity ◽  
Wild Population ◽  
Ovis Aries ◽  
Stochastic Simulations ◽  
Single Pair ◽  
Small Populations ◽  
Short Period ◽  
Large Populations ◽  
History Of ◽  
Over Time

In population and conservation genetics, there is an overwhelming body of evidence that genetic diversity is lost over time in small populations. This idea has been supported by comparative studies showing that small populations have lower diversity than large populations. However, longitudinal studies reporting a decline in genetic diversity throughout the whole history of a given wild population are much less common. Here, we analysed changes in heterozygosity over time in an insular mouflon ( Ovis aries ) population founded by two individuals in 1957 and located on one of the most isolated locations in the world: the Kerguelen Sub-Antarctic archipelago. Heterozygosity measured using 25 microsatellite markers has actually increased over 46 years since the introduction, and exceeds the range predicted by neutral genetic models and stochastic simulations. Given the complete isolation of the population and the short period of time since the introduction, changes in genetic variation cannot be attributed to mutation or migration. Several lines of evidence suggest that the increase in heterozygosity with time may be attributable to selection. This study shows the importance of longitudinal genetic surveys for understanding the mechanisms that regulate genetic diversity in wild populations.

Ecological Distribution, Agricultural Trade Liberalization, and IN SITU Genetic Diversity

1997 ◽  
Author(s):  
J. Boyce
Keyword(s):  
Genetic Diversity ◽  
Rural Livelihoods ◽  
Agricultural Trade ◽  
Costs And Benefits ◽  
The North ◽  
Agricultural Trade Liberalization ◽  
Agricultural Imports ◽  
World Food Security

Genetic diversity in crop plants is crucial for long-term world food security. This diversity is sustained in the field primarily by poor farmers in developing countries, who receive no compensation for providing this external benefit to humankind. When agricultural imports displace local production in centers of genetic diversity, this threatens both rural livelihoods and the continued provision of this external benefit. The North American Free Trade Agreement’s impact on Mexican maize farming illustrates the problem. The prospects for remedial policies are shaped by the distribution of the costs and benefits of action of inaction.

Irrigation and Rootstocks to Manage Northern Root-Knot Nematode During Wine Grape Vineyard Establishment

2021 ◽  
Author(s):  
Katherine East ◽  
Inga Zasada ◽  
R. Paul Schreiner ◽  
Michelle Marie Moyer
Keyword(s):  
Late Summer ◽  
Field Trials ◽  
Meloidogyne Hapla ◽  
Root Knot Nematode ◽  
Cultural Management ◽  
Host Status ◽  
Management Approaches ◽  
Eastern Washington ◽  
Establishment Phase

Vineyard replanting in Washington state can be negatively impacted by the plant-parasitic nematode Meloidogyne hapla. Chemically-focused nematode management programs do not offer long-term suppression, however, this may be achieved through the adoption of cultural approaches such as rootstocks and irrigation. Nematode-resistant rootstocks are used extensively in other regions, but many have not been tested against M. hapla. Vineyards in eastern Washington are irrigated, so manipulating available soil water may also impact nematode development. In 2017, two field trials were established in eastern Washington to evaluate the effects of: 1) late-summer water limitation on M. hapla population development, and 2) host status of 1103 Paulsen, 3309 Couderc and Matador rootstocks for M. hapla. The efficacy of these cultural management approaches was evaluated under three initial M. hapla densities (0, 50, and 250 M. hapla J2 per 250 g soil) in both trials. Reducing irrigation to manage M. hapla infestation of grape roots was ineffective and may cause harm to the vines by inducing too much water stress. Conversely, rootstocks effectively reduced population densities of M. hapla. Overall, rootstocks show the most promise as a cultural tool to manage M. hapla during the establishment phase in Washington vineyards.

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