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Genes
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Genetics in Wildlife and Fisheries Conservation and Management
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Genetics in Wildlife and Fisheries Conservation and Management

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (20 April 2022) | Viewed by 23994

Special Issue Editors

Dr. Janna Willoughby

E-Mail Website
Guest Editor
School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL 36849, USA
Interests: adaptation; captive breeding; conservation; evolution; genetics
Dr. Elizabeth Kierepka

E-Mail Website
Guest Editor
North Carolina Museum of Natural Sciences, North Carolina State University, Raleigh, NC 27601, USA
Interests: adaptation; captive breeding; conservation; evolution; genetics

Special Issue Information

Dear Colleagues,

Globally changing climate conditions mean that our need to understand how populations vary with myriad environmental conditions is critically important for conservation and management. For wildlife populations in particular, conservation efforts are focused on mitigating the effects of changing environmental conditions, management of invasive species, and reintroduction of endangered species, among many other concerns. In response to these concerns, basic and applied genetic studies on wildlife populations are needed because they provide critical information on multiple processes that impact population viability (e.g., genetic diversity, connectivity, and effective population size). With the recent growth of genomic and computational resources, we now have the ability to leverage data at genomic and landscape scales that were previously limited by sequencing technology and processing power.

The aim of this Special Issue is to better understand how population genetics can inform wildlife conservation and management. Relevant studies could occur through many avenues, including (but not limited to) landscape-scale characterization of genetic variability and differentiation, characterization of the patterns of rapid evolution, identification of candidate adaptive genes, as well as the examination of the complex interplay between various conservation concerns, including inbreeding, transposable elements, and adaptation. Submissions using any genetic or genomic approach or simulations of such data using wildlife populations as model organisms to understand conservation and management are encouraged.

Dr. Janna Willoughby
Dr. Elizabeth Kierepka
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • conservation 
  • evolution 
  • genetic 
  • genomic 
  • management 
  • wildlife

Published Papers (7 papers)

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Research

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20 pages, 2643 KiB  
Article
Genetic Analysis and Status of Brown Bear Sub-Populations in Three National Parks of Greece Functioning as Strongholds for the Species’ Conservation
by Tzoulia-Maria Tsalazidou-Founta, Evangelia A. Stasi, Maria Samara, Yorgos Mertzanis, Maria Papathanassiou, Pantelis G. Bagos, Spyros Psaroudas, Vasiliki Spyrou, Yorgos Lazarou, Athanasios Tragos, Yannis Tsaknakis, Elpida Grigoriadou, Athanasios Korakis, Maria Satra, Charalambos Billinis and ARCPROM project
Genes 2022, 13(8), 1388; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13081388 - 04 Aug 2022
Viewed by 1880
Abstract
In order to optimize the appropriate conservation actions for the brown bear (Ursus arctos L.) population in Greece, we estimated the census (Nc) and effective (Ne) population size as well as the genetic status of brown bear sub-populations in three National Parks [...] Read more.
In order to optimize the appropriate conservation actions for the brown bear (Ursus arctos L.) population in Greece, we estimated the census (Nc) and effective (Ne) population size as well as the genetic status of brown bear sub-populations in three National Parks (NP): Prespa (MBPNP), Pindos (PINDNP), and Rhodopi (RMNP). The Prespa and Pindos sub-populations are located in western Greece and the Rhodopi population is located in eastern Greece. We extracted DNA from 472 hair samples and amplified through PCR 10 microsatellite loci. In total, 257 of 472 samples (54.5%) were genotyped for 6–10 microsatellite loci. Genetic analysis revealed that the Ne was 35, 118, and 61 individuals in MBPNP, PINDNP, and RMNP, respectively, while high levels of inbreeding were found in Prespa and Rhodopi but not in Pindos. Moreover, analysis of genetic structure showed that the Pindos population is genetically distinct, whereas Prespa and Rhodopi show mutual overlaps. Finally, we found a notable gene flow from Prespa to Rhodopi (10.19%) and from Rhodopi to Prespa (14.96%). Therefore, targeted actions for the conservation of the bears that live in the abovementioned areas must be undertaken, in order to ensure the species’ viability and to preserve the corridors that allow connectivity between the bear sub-populations in Greece. Full article
(This article belongs to the Special Issue Genetics in Wildlife and Fisheries Conservation and Management)
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9 pages, 999 KiB  
Article
A Meta-Analytical Investigation of the Gap between Measured and Predicted Inter-Population Genetic Diversity in Species of High Conservation Concern—The Case of the Critically Endangered European Mink Mustela lutreola L., 1761
by Jakub Skorupski, Johan Michaux and Przemysław Śmietana
Genes 2021, 12(10), 1555; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12101555 - 29 Sep 2021
Viewed by 1843
Abstract
Although properly designed sampling in population genetic studies is of key importance for planning evidence-informed conservation measures, sampling strategies are rarely discussed. This is the case for the European mink Mustela lutreola, a critically endangered species. In order to address this problem, [...] Read more.
Although properly designed sampling in population genetic studies is of key importance for planning evidence-informed conservation measures, sampling strategies are rarely discussed. This is the case for the European mink Mustela lutreola, a critically endangered species. In order to address this problem, a meta-analysis aiming to examine the completeness of mtDNA haplotype sampling in recent studies of M. lutreola inter-population genetic diversity was conducted. The analysis was performed using the sample-size-based rarefaction and extrapolation sampling curve method for three populations—the Northeastern (Russia, Belarus and Estonia), the Western (France and Spain), and the Southeastern (Romania). The extrapolated values of the Shannon–Wiener index were determined, assuming full sample coverage. The gap between the measured and predicted inter-population genetic diversity was estimated, indicating that the identified level of sample coverage was the lowest for the NE population (87%), followed by the SE population (96%) and the W population (99%). A guide for sampling design and accounting for sampling uncertainty in future population genetic studies on European mink is provided. The relatively low sample coverage for the Russian population clearly indicates an urgent need to take conservation measures for European mink in this country. Full article
(This article belongs to the Special Issue Genetics in Wildlife and Fisheries Conservation and Management)
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16 pages, 2171 KiB  
Article
Selective Breeding for Disease-Resistant PRNP Variants to Manage Chronic Wasting Disease in Farmed Whitetail Deer
by Nicholas Haley, Rozalyn Donner, Kahla Merrett, Matthew Miller and Kristen Senior
Genes 2021, 12(9), 1396; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12091396 - 10 Sep 2021
Cited by 9 | Viewed by 4654
Abstract
Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy (TSE) of cervids caused by a misfolded variant of the normal cellular prion protein, and it is closely related to sheep scrapie. Variations in a host’s prion gene, PRNP, and its primary [...] Read more.
Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy (TSE) of cervids caused by a misfolded variant of the normal cellular prion protein, and it is closely related to sheep scrapie. Variations in a host’s prion gene, PRNP, and its primary protein structure dramatically affect susceptibility to specific prion disorders, and breeding for PRNP variants that prevent scrapie infection has led to steep declines in the disease in North American and European sheep. While resistant alleles have been identified in cervids, a PRNP variant that completely prevents CWD has not yet been identified. Thus, control of the disease in farmed herds traditionally relies on quarantine and depopulation. In CWD-endemic areas, depopulation of private herds becomes challenging to justify, leading to opportunities to manage the disease in situ. We developed a selective breeding program for farmed white-tailed deer in a high-prevalence CWD-endemic area which focused on reducing frequencies of highly susceptible PRNP variants and introducing animals with less susceptible variants. With the use of newly developed primers, we found that breeding followed predictable Mendelian inheritance, and early data support our project’s utility in reducing CWD prevalence. This project represents a novel approach to CWD management, with future efforts building on these findings. Full article
(This article belongs to the Special Issue Genetics in Wildlife and Fisheries Conservation and Management)
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12 pages, 1150 KiB  
Article
Novel Microsatellite Markers Used for Determining Genetic Diversity and Tracing of Wild and Farmed Populations of the Amazonian Giant Fish Arapaima gigas
by Paola Fabiana Fazzi-Gomes, Jonas da Paz Aguiar, Diego Marques, Gleyce Fonseca Cabral, Fabiano Cordeiro Moreira, Marilia Danyelle Nunes Rodrigues, Caio Santos Silva, Igor Hamoy and Sidney Santos
Genes 2021, 12(9), 1324; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12091324 - 27 Aug 2021
Cited by 4 | Viewed by 2765
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Genetics in Wildlife and Fisheries Conservation and Management)
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12 pages, 1916 KiB  
Article
Illegal, Unreported, and Unregulated Fisheries Threatening Shark Conservation in African Waters Revealed from High Levels of Shark Mislabelling in Ghana
by Narkie Akua Agyeman, Carmen Blanco-Fernandez, Sophie Leonie Steinhaussen, Eva Garcia-Vazquez and Gonzalo Machado-Schiaffino
Genes 2021, 12(7), 1002; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12071002 - 29 Jun 2021
Cited by 13 | Viewed by 5154
Abstract
Mislabelling of fish and fish products has attracted much attention over the last decades, following public awareness of the practice of substituting high-value with low-value fish in markets, restaurants, and processed seafood. In some cases, mislabelling includes illegal, unreported, and unregulated (IUU) fishing, [...] Read more.
Mislabelling of fish and fish products has attracted much attention over the last decades, following public awareness of the practice of substituting high-value with low-value fish in markets, restaurants, and processed seafood. In some cases, mislabelling includes illegal, unreported, and unregulated (IUU) fishing, contributing to overexploit substitute species that are undetectable when sold under wrong names. This is the first study of DNA barcoding to assess the level of mislabelling in fish marketed in Ghana, focusing on endangered shark species. Genetic identification was obtained from 650 base pair sequences within the cytochrome c oxidase I (COI) gene. All except one of 17 shark fillets analysed were wrongly labelled as compared with none of 28 samples of small commercial pelagic fish and 14 commercial shark samples purchased in Europe. Several substitute shark species in Ghana are endangered (Carcharhinus signatus and Isurus oxyrinchus) and critically endangered (Squatina aculeata). Shark products commercialized in Europe (n = 14) did not reveal mislabelling, thus specific shark mislabelling cannot be generalized. Although based on a limited number of samples and fish markets, the results that reveal trade of endangered sharks in Ghana markets encourage Ghanaian authorities to improve controls to enforce conservation measures. Full article
(This article belongs to the Special Issue Genetics in Wildlife and Fisheries Conservation and Management)
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Review

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10 pages, 892 KiB  
Review
Comparison of Minimally Invasive Monitoring Methods and Live Trapping in Mammals
by Andrea Miranda Paez, Mekala Sundaram and Janna R. Willoughby
Genes 2021, 12(12), 1949; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12121949 - 03 Dec 2021
Cited by 2 | Viewed by 3190
Abstract
The conservation and management of wildlife requires the accurate assessment of wildlife population sizes. However, there is a lack of synthesis of research that compares methods used to estimate population size in the wild. Using a meta-analysis approach, we compared the number of [...] Read more.
The conservation and management of wildlife requires the accurate assessment of wildlife population sizes. However, there is a lack of synthesis of research that compares methods used to estimate population size in the wild. Using a meta-analysis approach, we compared the number of detected individuals in a study made using live trapping and less invasive approaches, such as camera trapping and genetic identification. We scanned 668 papers related to these methods and identified data for 44 populations (all focused on mammals) wherein at least two methods (live trapping, camera trapping, genetic identification) were used. We used these data to quantify the difference in number of individuals detected using trapping and less invasive methods using a regression and used the residuals from each regression to evaluate potential drivers of these trends. We found that both trapping and less invasive methods (camera traps and genetic analyses) produced similar estimates overall, but less invasive methods tended to detect more individuals compared to trapping efforts (mean = 3.17 more individuals). We also found that the method by which camera data are analyzed can significantly alter estimates of population size, such that the inclusion of spatial information was related to larger population size estimates. Finally, we compared counts of individuals made using camera traps and genetic data and found that estimates were similar but that genetic approaches identified more individuals on average (mean = 9.07 individuals). Overall, our data suggest that all of the methods used in the studies we reviewed detected similar numbers of individuals. As live trapping can be more costly than less invasive methods and can pose more risk to animal well-fare, we suggest minimally invasive methods are preferable for population monitoring when less-invasive methods can be deployed efficiently. Full article
(This article belongs to the Special Issue Genetics in Wildlife and Fisheries Conservation and Management)
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15 pages, 2239 KiB  
Review
Noninvasive Genetic Assessment Is an Effective Wildlife Research Tool When Compared with Other Approaches
by Miriam A. Zemanova
Genes 2021, 12(11), 1672; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12111672 - 23 Oct 2021
Cited by 12 | Viewed by 3356
Abstract
Wildlife research has been indispensable for increasing our insight into ecosystem functioning as well as for designing effective conservation measures under the currently high rates of biodiversity loss. Genetic and genomic analyses might be able to yield the same information on, e.g., population [...] Read more.
Wildlife research has been indispensable for increasing our insight into ecosystem functioning as well as for designing effective conservation measures under the currently high rates of biodiversity loss. Genetic and genomic analyses might be able to yield the same information on, e.g., population size, health, or diet composition as other wildlife research methods, and even provide additional data that would not be possible to obtain by alternative means. Moreover, if DNA is collected non-invasively, this technique has only minimal or no impact on animal welfare. Nevertheless, the implementation rate of noninvasive genetic assessment in wildlife studies has been rather low. This might be caused by the perceived inefficiency of DNA material obtained non-invasively in comparison with DNA obtained from blood or tissues, or poorer performance in comparison with other approaches used in wildlife research. Therefore, the aim of this review was to evaluate the performance of noninvasive genetic assessment in comparison with other methods across different types of wildlife studies. Through a search of three scientific databases, 113 relevant studies were identified, published between the years 1997 and 2020. Overall, most of the studies (94%) reported equivalent or superior performance of noninvasive genetic assessment when compared with either invasive genetic sampling or another research method. It might be also cheaper and more time-efficient than other techniques. In conclusion, noninvasive genetic assessment is a highly effective research approach, whose efficacy and performance are likely to improve even further in the future with the development of optimized protocols. Full article
(This article belongs to the Special Issue Genetics in Wildlife and Fisheries Conservation and Management)
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