genetic management
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Author(s):  
Kimberley G. Barrett ◽  
Geneviève Amaral ◽  
Melanie Elphinstone ◽  
Malcolm L. McAdie ◽  
Corey S. Davis ◽  
...  

AbstractCaptive breeding is often a last resort management option in the conservation of endangered species which can in turn lead to increased risk of inbreeding depression and loss of genetic diversity. Thus, recording breeding events via studbook for the purpose of estimating relatedness, and facilitating mating pair selection to minimize inbreeding, is common practice. However, as founder relatedness is often unknown, loss of genetic variation and inbreeding cannot be entirely avoided. Molecular genotyping is slowly being adopted in captive breeding programs, however achieving sufficient resolution can be challenging in small, low diversity, populations. Here, we evaluate the success of the Vancouver Island marmot (Marmota vancouverensis; VIM; among the worlds most endangered mammals) captive breeding program in preventing inbreeding and maintaining genetic diversity. We explored the use of high-throughput amplicon sequencing of microsatellite regions to assay greater genetic variation in both captive and wild populations than traditional length-based fragment analysis. Contrary to other studies, this method did not considerably increase diversity estimates, suggesting: (1) that the technique does not universally improve resolution, and (2) VIM have exceedingly low diversity. Studbook estimates of pairwise relatedness and inbreeding in the current population were weakly, but positively, correlated to molecular estimates. Thus, current studbooks are moderately effective at predicting genetic similarity when founder relatedness is known. Finally, we found that captive and wild populations did not differ in allelic frequencies, and conservation efforts to maintain diversity have been successful with no significant decrease in diversity over the last three generations.


Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3574
Author(s):  
Roel Meyermans ◽  
Wim Gorssen ◽  
Nadine Buys ◽  
Steven Janssens

Genetic diversity is increasingly important for researchers and society. Small and local populations deserve more attention especially, as they may harbor important characteristics. Moreover, small populations are at greater risk and their genetic management is often more challenging. Likewise, European red cattle populations are threatened, as they are outcompeted by more specialized cattle breeds. In this study, we investigate the genetic diversity of two local Belgian red cattle breeds: Belgian Red and Belgian White Red cattle. A total of 270 animals were genotyped via medium density SNP arrays. Genetic diversity was assessed using runs of homozygosity screening, effective population size estimation and Fst analyses. Genomic inbreeding coefficients based on runs of homozygosity were estimated at 7.0% for Belgian Red and 6.1% for Belgian White Red cattle, and both populations had a low effective population size (68 and 86, respectively). PCA, Fst and admixture analyses revealed the relationship to 52 other international breeds, where they were closest related to some Belgian, French, Scandinavian and Dutch breeds. Moreover, Fst analyses revealed for Belgian Red cattle a signature of selection on BTA6, adjacent to the KIT gene. This study gains important knowledge on the genetic diversity of these two small local red cattle breeds, and will aid in their (genetic) management.


2021 ◽  
Author(s):  
◽  
Rosalynn Marie Anderson-Lederer

<p>The African black rhinoceros (Diceros bicornis) is critically endangered. Like other megafauna, the species is managed in parks and is often translocated to expand their range into reserves where they have been extirpated. Management of genetic variation has been identified as an important consideration in long-term management plans for many wild and captive endangered species including black rhino. In this thesis I examined the contemporary levels of genetic variation within the black rhinoceros (D. b. minor) in KwaZulu-Natal (KZN), South Africa, and specifically the relict source population at Hluhluwe-iMfolozi Game Reserve (HiP), and how this information can be incorporated into management decisions to improve the long-term viability and persistence of the population. Previous studies have examined levels of genetic variation and differentiation among the three black rhino subspecies (D. b. minor, D. b. michaeli and D. b. bicornis) in an attempt to resolve their taxonomy and to establish baseline genetic assessments for managing populations. However, there has been a lack of genetic information based on the variable mitochondrial DNA (mtDNA) control region of the KZN metapopulation and a direct comparison of microsatellite variability between the D. b. minor populations of KZN and Zimbabwe.  The specific objectives of this study were to: (1) determine the DNA sequence of the mtDNA control region of three subspecies and estimate the level of variation within the HiP source and KZN metapopulation and compare the results with D. b. minor outside KZN and the other two subspecies; (2) use ten microsatellite DNA markers to estimate the levels of heterozygosity and allelic diversity in the HiP source and KZN metapopulation and compare results to previously published microsatellite data (specifically native Zimbabwe D. b. minor; and (3) use VORTEX Population Viability Analysis (PVA) and HiP vital rates to model the effects of increasing population size and supplementation, and investigate what management scenarios would be most effective for minimizing the loss of genetic variation caused by genetic drift with HiP...</p>


2021 ◽  
Author(s):  
◽  
Rosalynn Marie Anderson-Lederer

<p>The African black rhinoceros (Diceros bicornis) is critically endangered. Like other megafauna, the species is managed in parks and is often translocated to expand their range into reserves where they have been extirpated. Management of genetic variation has been identified as an important consideration in long-term management plans for many wild and captive endangered species including black rhino. In this thesis I examined the contemporary levels of genetic variation within the black rhinoceros (D. b. minor) in KwaZulu-Natal (KZN), South Africa, and specifically the relict source population at Hluhluwe-iMfolozi Game Reserve (HiP), and how this information can be incorporated into management decisions to improve the long-term viability and persistence of the population. Previous studies have examined levels of genetic variation and differentiation among the three black rhino subspecies (D. b. minor, D. b. michaeli and D. b. bicornis) in an attempt to resolve their taxonomy and to establish baseline genetic assessments for managing populations. However, there has been a lack of genetic information based on the variable mitochondrial DNA (mtDNA) control region of the KZN metapopulation and a direct comparison of microsatellite variability between the D. b. minor populations of KZN and Zimbabwe.  The specific objectives of this study were to: (1) determine the DNA sequence of the mtDNA control region of three subspecies and estimate the level of variation within the HiP source and KZN metapopulation and compare the results with D. b. minor outside KZN and the other two subspecies; (2) use ten microsatellite DNA markers to estimate the levels of heterozygosity and allelic diversity in the HiP source and KZN metapopulation and compare results to previously published microsatellite data (specifically native Zimbabwe D. b. minor; and (3) use VORTEX Population Viability Analysis (PVA) and HiP vital rates to model the effects of increasing population size and supplementation, and investigate what management scenarios would be most effective for minimizing the loss of genetic variation caused by genetic drift with HiP...</p>


2021 ◽  
Author(s):  
Sergio A Gonzalez-Mollinedo ◽  
Thomas Schrei ◽  
Brad Locke

In this study, samples from 33 Guatemalan Beaded Lizard (Heloderma charlesbogerti) were analyzed for genetic diversity. Twenty-three samples were obtained from wild individuals from two separate population areas, and 10 samples were obtained from captive individuals. Because the seasonally dry tropical forest habitat sampled for this study, is degraded and fragmented, it was hypothesized that beaded lizard populations were small and isolated and would be subject to genetic erosion and an elevated extinction risk. To test this hypothesis, eight microsatellite markers were employed to analyze 22 individual samples from the population of Cabanas, Zacapa, a single individual from the eastern-most population and 10 captive individuals of unknown origin. An average of three alleles per maker was reported for the Cabanas population, evidencing a low genetic diversity. In addition, a recent bottleneck event was detected and an effective population size of 19.6 was estimated. Demographic reconstruction using a Bayesian approach was inconclusive possibly due to a small dataset and shallow coalescence trees obtained with the generated data. No clear structuring pattern was detected for the Cabanas population and most samples from individuals in captivity were found to have similar alleles to the ones from Cabanas. Population designation is challenging without the genotyping of every wild population, but unique alleles were found in captive individuals of unknown origin that could suggest that different genotypes might exist within other, less studied, wild populations. Low genetic diversity, and a small effective population size represent a risk for the Cabanas population facing the threats of isolation, habitat loss and climate change. These findings suggest that genetic management of the Cabanas population might be utilized to avoid high rates of inbreeding and subsequent inbreeding depression.


Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2633
Author(s):  
Poh Chiang Chew ◽  
Annie Christianus ◽  
Jaapar M. Zudaidy ◽  
Md Yasin Ina-Salwany ◽  
Chou Min Chong ◽  
...  

In this study, a mixture of Tor tambra and T. tambroides with unknown genetic background were collected from 11 localities in Malaysia for broodstock development and sperm cryo-banking. This study aims to assess the microsatellite (simple sequence repeat, SSR) variation, genetic diversity, genetic differentiation, level of gene flow, population structure, genetic relatedness and their demographic aspects among these Tor populations, in addition to establishing their SSR profile by employing 22 SSR markers via fragment analysis. Total genomic DNA was extracted from 181 samples (91 cryopreserved milt samples and 90 scale samples of live broodfish). Results showed the Tor spp. collection retained their genetic variation but exhibited excessive homozygosity among individuals within population. Moderate genetic differentiation was shown among the populations, with highly significant (p < 0.001) fixation indices (FST, FIS and FIT). A low gene flow over all loci (Nm 1.548) indicates little genetic variation transfer between populations. The genetic structures of all the populations were successfully resolved into four main clusters by an unweighted pair group method with arithmetic mean (UPGMA) dendrogram generated based on Nei’s genetic distances. The population structures based on principal coordinates analysis (PCoA) and the Bayesian model also suggested four distinct clusters following geographical regions and eight closely related populations. This study provided a useful baseline reference for better genetic management and utilization of the Tor spp. stocks in their breeding and conservation programmes.


Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1324
Author(s):  
Paola Fabiana Fazzi-Gomes ◽  
Jonas da Paz Aguiar ◽  
Diego Marques ◽  
Gleyce Fonseca Cabral ◽  
Fabiano Cordeiro Moreira ◽  
...  

The Amazonian symbol fish Arapaima gigas is the only living representative of the Arapamidae family. Environmental pressures and illegal fishing threaten the species’ survival. To protect wild populations, a national regulation must be developed for the management of A. gigas throughout the Amazon basin. Moreover, the reproductive genetic management and recruitment of additional founders by aquaculture farms are needed to mitigate the damage caused by domestication. To contribute to the sustainable development, we investigated the genetic diversity of wild and cultivated populations of A. gigas and developed a panel composed by 12 microsatellite markers for individual and population genetic tracing. We analyzed 368 samples from three wild and four farmed populations. The results revealed low rates of genetic diversity in all populations, loss of genetic diversity and high inbreeding rates in farmed populations, and genetic structuring among wild and farmed populations. Genetic tracing using the 12 microsatellite markers was effective, and presented a better performance in identifying samples at the population level. The 12-microsatellite panel is appliable to the legal aspects of the trade of the A. gigas, such as origin discrimination, reproductive genetic management by DNA profiling, and evaluation and monitoring of genetic diversity.


Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 386
Author(s):  
Carlos I. Campos ◽  
Melinda A. Martinez ◽  
Daniel Acosta ◽  
Jose A. Diaz-Luque ◽  
Igor Berkunsky ◽  
...  

A key aspect in the conservation of endangered populations is understanding patterns of genetic variation and structure, which can provide managers with critical information to support evidence-based status assessments and management strategies. This is especially important for species with small wild and larger captive populations, as found in many endangered parrots. We used genotypic data to assess genetic variation and structure in wild and captive populations of two endangered parrots, the blue-throated macaw, Ara glaucogularis, of Bolivia, and the thick-billed parrot, Rhynchopsitta pachyrhyncha, of Mexico. In the blue-throated macaw, we found evidence of weak genetic differentiation between wild northern and southern subpopulations, and between wild and captive populations. In the thick-billed parrot we found no signal of differentiation between the Madera and Tutuaca breeding colonies or between wild and captive populations. Similar levels of genetic diversity were detected in the wild and captive populations of both species, with private alleles detected in captivity in both, and in the wild in the thick-billed parrot. We found genetic signatures of a bottleneck in the northern blue-throated macaw subpopulation, but no such signal was identified in any other subpopulation of either species. Our results suggest both species could potentially benefit from reintroduction of genetic variation found in captivity, and emphasize the need for genetic management of captive populations.


2021 ◽  
Vol 4 (2) ◽  
pp. 122-127
Author(s):  
N.H. Desha ◽  
M.S.A. Bhuiyan ◽  
F. Islam ◽  
A.K.F.H. Bhuiyan

The study was conducted to investigate the effect of non-genetic factors on growth performance of Indigenous chicken under village condition of Bangladesh. A total of 1070 eggs from Indigenous chicken were set and 628 chicks were hatched. Data were recorded on hatching performance and body weight of chicks from week 1 (BWWK1) to week 15 (BWWK15). The non-genetic factors considered were sex, batch, farm, brooding system and feeding system. Least squares means for fertility (%), hatchability (%) and mortality on hatching day (%) of eggs were 70.81, 77.52, and 19.63, respectively. Body weight of male and female birds at 1st, 3rd, 5th, 7th, 9th,11th, 13th and 15th weeks of age were 45.97 and 38.44 g, 129.36 and 104.94 g, 266.82 and 213.92 g, 453.93 and 390.72 g, 470.58 and 394.75 g, 614.60 and 489.48 g, 693.72 and 462.77 g, 833.94 and 650.77 g, respectively. Artificially hatched birds gained better body weight than the naturally hatched birds up to 11 weeks of age. The coal brooding system was superior to electric and natural brooding. Hand mixed feed gave better growth of birds than commercial feed and scavenging feed resources. Better growth of birds in farm 2 was observed suggesting replication of management system of farm 2 to get better growth. Further, batch, farm, brooding system and feeding system were found to contribute significant (p<0.05) differences in the body weight at various weeks of their age. These results indicated due adjustment of non-genetic management systems for obtaining better growth performance of Indigenous chicken to enhance commercialization of the indigenous chicken flocks in rural areas of the country.


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