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Conservation Genetics as a Management Tool for Endangered, Vulnerable, and...
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Conservation Genetics as a Management Tool for Endangered, Vulnerable, and Threatened Species

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Conservation Biology and Biodiversity".

Deadline for manuscript submissions: 30 November 2024 | Viewed by 8708

Special Issue Editors

Dr. Claudia Greco

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Guest Editor
Italian Institute for Environmental Protection and Research, Ozzano dell’Emilia, 40064 Bologna, Italy
Interests: conservation genetics; forensics; biobank; zoology; biodiversity
Dr. Daniela Pacifico

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Guest Editor
CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy
Interests: food chemistry; circular economy; sustainable food industry; potato genetics
Dr. Irene Pellegrino

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Guest Editor
Department for the Sustainable Development and Ecological Transition, University of Piemonte Orientale, Alessandria, Italy
Interests: ornithology; phylogeography; taxonomy; phylogenetic; biogeography; zoology; avian haemosporidia

Special Issue Information

Dear Colleagues,

In recent decades, technological advances in the field of molecular biology of animals and plants enabled rapid and cost-effective production of large amounts of reliable genetic data.

Biological diversity is being depleted worldwide as a direct or indirect consequence of human actions; thus, the need for species conservation has arisen in recent years. Many species are already extinct, while many others have dramatically reduced population sizes, with consequent extinction risk. In many areas and for several species, this process has been expedited by local extinction of native populations commonly replaced by non-native species. Thus, several species require human intervention to ensure their survival. The genetic variability of a population corresponds to its ability to adapt to possible environmental changes and its evolutionary potential.

Genetic monitoring may lead to better species management, defining conservation units and reconstructing phylogenetic relationship and territory occupancy. Moreover, it could help to unmask illicit traffic, confirming specie, kinship, sex, etc.

Endemism should be protected from admixture, introgression, and hybridization.

Biobanks and museum specimens are essential resources when it comes to implementing conservation plans, characterizing historical native populations and clarifying the taxonomy of taxa.

Dr. Claudia Greco
Dr. Daniela Pacifico
Dr. Irene Pellegrino
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. Biology 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 2700 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 genetics
  • forensics
  • molecular markers
  • management
  • plants
  • animals

Published Papers (5 papers)

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Research

7 pages, 1100 KiB  
Communication
Ovotestis Isolation and Cryopreservation of Nesiohelix samarangae (Oriental Snail) as a Snail Model for Conserving Other Endangered Snail Species
by Jukyeong Jeong, Seungki Lee and Jung Kyu Choi
Biology 2024, 13(4), 205; https://doi.org/10.3390/biology13040205 - 22 Mar 2024
Viewed by 722
Abstract
This study aimed to develop a cryopreservation system for the reproductive organs of Nesiohelix samarangae (oriental snail) to support the conservation of their species. The reproductive glands of N. samarangae are divided into numerous acini by acinar boundaries. Within each acinus, the presence [...] Read more.
This study aimed to develop a cryopreservation system for the reproductive organs of Nesiohelix samarangae (oriental snail) to support the conservation of their species. The reproductive glands of N. samarangae are divided into numerous acini by acinar boundaries. Within each acinus, the presence of spermatogonia, spermatocytes, spermatids, and sperm were observed, indicating various stages of sperm development. The spermatocytes were irregular in shape and possessed large nuclei. Spermatids, on the other hand, were predominantly located within the lumen of the tissue and exhibited densely packed nuclei. Furthermore, sperm with tails attached were observed within the tissue. In order to preserve the oriental snail species, we utilized the vitrification method to freeze the reproductive organs. Comparing the two methods, it was observed that cryopreservation of ovotestis using 2% alginate encapsulation exhibited superior viability following thawing, surpassing the viability achieved with the non-encapsulated approach. In this study, the establishment of a cryopreservation system for the reproductive organs of the oriental snail not only contributes to the genetic conservation of the endangered snail species but also plays a role in maintaining genetic resources and diversity. Full article
(This article belongs to the Special Issue Conservation Genetics as a Management Tool for Endangered, Vulnerable, and Threatened Species)
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20 pages, 3743 KiB  
Article
Preserving Pure Siamese Crocodile Populations: A Comprehensive Approach Using Multi-Genetic Tools
by Thitipong Panthum, Nattakan Ariyaraphong, Wongsathit Wongloet, Pish Wattanadilokchatkun, Nararat Laopichienpong, Ryan Rasoarahona, Worapong Singchat, Syed Farhan Ahmad, Ekaphan Kraichak, Narongrit Muangmai, Prateep Duengkae, Yusuke Fukuda, Sam Banks, Yosapong Temsiripong, Tariq Ezaz and Kornsorn Srikulnath
Biology 2023, 12(11), 1428; https://doi.org/10.3390/biology12111428 - 13 Nov 2023
Viewed by 1456
Abstract
Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite [...] Read more.
Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite and mitochondrial DNA data to establish the criteria for identifying species and their hybrids; however, the results may have been influenced by biased allelic frequencies and genetic drift within the examined population. To overcome these limitations and identify the true signals of selection, alternative DNA markers and a diverse set of populations should be employed. Therefore, this study used DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm the genetic scenario of the parental species and their hybrids. A population of saltwater crocodiles from Australia was used to compare the distribution of species-diagnostic SNPs. Different analytical approaches were compared to diagnose the level of hybridization when an admixture was present, wherein three individuals had potential backcrossing. Approximately 17.00–26.00% of loci were conserved between the Siamese and saltwater crocodile genomes. Species-diagnostic SNP loci for Siamese and saltwater crocodiles were identified as 8051 loci and 1288 loci, respectively. To validate the species-diagnostic SNP loci, a PCR-based approach was used by selecting 20 SNP loci for PCR primer design, among which 3 loci were successfully able to differentiate the actual species and different hybridization levels. Mitochondrial and nuclear genetic information, including microsatellite genotyping and species-diagnostic DNA markers, were combined as a novel method that can compensate for the limitations of each method. This method enables conservation prioritization before release into the wild, thereby ensuring sustainable genetic integrity for long-term species survival through reintroduction and management programs. Full article
(This article belongs to the Special Issue Conservation Genetics as a Management Tool for Endangered, Vulnerable, and Threatened Species)
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16 pages, 1935 KiB  
Article
Optimizing Microsatellite Marker Panels for Genetic Diversity and Population Genetic Studies: An Ant Colony Algorithm Approach with Polymorphic Information Content
by Ryan Rasoarahona, Pish Wattanadilokchatkun, Thitipong Panthum, Thanyapat Thong, Worapong Singchat, Syed Farhan Ahmad, Aingorn Chaiyes, Kyudong Han, Ekaphan Kraichak, Narongrit Muangmai, Akihiko Koga, Prateep Duengkae, Agostinho Antunes and Kornsorn Srikulnath
Biology 2023, 12(10), 1280; https://doi.org/10.3390/biology12101280 - 25 Sep 2023
Cited by 1 | Viewed by 1512
Abstract
Microsatellites are polymorphic and cost-effective. Optimizing reduced microsatellite panels using heuristic algorithms eases budget constraints in genetic diversity and population genetic assessments. Microsatellite marker efficiency is strongly associated with its polymorphism and is quantified as the polymorphic information content (PIC). Nevertheless, [...] Read more.
Microsatellites are polymorphic and cost-effective. Optimizing reduced microsatellite panels using heuristic algorithms eases budget constraints in genetic diversity and population genetic assessments. Microsatellite marker efficiency is strongly associated with its polymorphism and is quantified as the polymorphic information content (PIC). Nevertheless, marker selection cannot rely solely on PIC. In this study, the ant colony optimization (ACO) algorithm, a widely recognized optimization method, was adopted to create an enhanced selection scheme for refining microsatellite marker panels, called the PIC–ACO selection scheme. The algorithm was fine-tuned and validated using extensive datasets of chicken (Gallus gallus) and Chinese gorals (Naemorhedus griseus) from our previous studies. In contrast to basic optimization algorithms that stochastically initialize potential outputs, our selection algorithm utilizes the PIC values of markers to prime the ACO process. This increases the global solution discovery speed while reducing the likelihood of becoming trapped in local solutions. This process facilitated the acquisition of a cost-efficient and optimized microsatellite marker panel for studying genetic diversity and population genetic datasets. The established microsatellite efficiency metrics such as PIC, allele richness, and heterozygosity were correlated with the actual effectiveness of the microsatellite marker panel. This approach could substantially reduce budgetary barriers to population genetic assessments, breeding, and conservation programs. Full article
(This article belongs to the Special Issue Conservation Genetics as a Management Tool for Endangered, Vulnerable, and Threatened Species)
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13 pages, 2380 KiB  
Article
Empirical Data Suggest That the Kashmir Musk Deer (Moschus cupreus, Grubb 1982) Is the One Musk Deer Distributed in the Western Himalayas: An Integration of Ecology, Genetics and Geospatial Modelling Approaches
by Amira Sharief, Bheem Dutt Joshi, Vineet Kumar, Hemant Singh, Vinay Kumar Singh, Shahid Ahmad Dar, Catherine Graham, Chinnasamy Ramesh, Iyaz Quyoom, Mukesh Thakur and Lalit Kumar Sharma
Biology 2023, 12(6), 786; https://doi.org/10.3390/biology12060786 - 29 May 2023
Cited by 3 | Viewed by 1813
Abstract
Insufficient research has been conducted on musk deer species across their distribution range, primarily because of their elusive behaviour and the fact they occupy remote high-altitude habitats in the Himalayas above 2500 m. The available distribution records, primarily derived from ecological studies with [...] Read more.
Insufficient research has been conducted on musk deer species across their distribution range, primarily because of their elusive behaviour and the fact they occupy remote high-altitude habitats in the Himalayas above 2500 m. The available distribution records, primarily derived from ecological studies with limited photographic and indirect evidence, fail to provide comprehensive information on the species distribution. Consequently, uncertainties arise when attempting to determine the presence of specific taxonomic units of musk deer in the Western Himalayas. This lack of knowledge hampers species-oriented conservation efforts, as there need to be more species-specific initiatives focused on monitoring, protecting, and combatting the illegal poaching of musk deer for their valuable musk pods. We used transect surveys (220 trails), camera traps (255 cameras), non-invasive DNA sampling (40 samples), and geospatial modelling (279 occurrence records) to resolve the taxonomic ambiguity, and identify the suitable habitat of musk deer (Moschus spp.) in Uttarkashi District of Uttarakhand and the Lahaul–Pangi landscape of Himachal Pradesh. All the captured images and DNA-based identification results confirmed the presence of only Kashmir musk deer (KDM) (Moschus cupreus) in Uttarakhand and Himachal Pradesh. The results suggest that KMD inhabit a narrow range of suitable habitats (6.9%) of the entire Western Himalayas. Since all evidence indicates that only KMD are present in the Western Himalayas, we suggest that the presence of other species of musk deer (Alpine musk deer and Himalayan musk deer) was wrongly reported. Therefore, future conservation plans and management strategies must focus only on KMD in the Western Himalayas. Full article
(This article belongs to the Special Issue Conservation Genetics as a Management Tool for Endangered, Vulnerable, and Threatened Species)
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Graphical abstract

13 pages, 2054 KiB  
Article
Effect of Translocation on Host Diet and Parasite Egg Burden: A Study of the European Bison (Bison bonasus)
by Christinna Herskind, Heidi Huus Petersen, Cino Pertoldi, Stine Karstenskov Østergaard, Marta Kołodziej-Sobocińska, Wojciech Sobociński, Małgorzata Tokarska and Trine Hammer Jensen
Biology 2023, 12(5), 680; https://doi.org/10.3390/biology12050680 - 04 May 2023
Viewed by 2140
Abstract
For the purpose of nature management and species conservation, European bison (Bison bonasus) are being increasingly reintroduced into nature reserves across Europe. The aim of this study was to investigate European bison’s adaptability to new areas through the study of their [...] Read more.
For the purpose of nature management and species conservation, European bison (Bison bonasus) are being increasingly reintroduced into nature reserves across Europe. The aim of this study was to investigate European bison’s adaptability to new areas through the study of their parasite-EPG (eggs per gram feces) and dietary diversity during twelve months after translocation. We compared the parasite-EPG from introduced European bison in Lille Vildmose, Denmark, with the parasite-EPG from populations from Bornholm, Denmark, and Białowieża Forest, Poland. From March 2021 to February 2022, fecal samples were collected from three populations. Samples from Lille Vildmose were examined through flotation, sedimentation, the Baermann technique, and nanopore sequencing. Fecal samples from Bornholm and Białowieża were examined through flotation and sedimentation. Nanopore sequencing of DNA from 63 European bison’s fecal samples collected during March–September in Lille Vildmose identified 8 species of nematodes within the digestive tract of the European bison, with Haemonchus contortus being the most frequently observed. In Lille Vildmose, a significantly higher excretion of nematode-EPG was observed during the summer period than in the spring, autumn, and winter. In addition, monthly differences in the excretion of nematode eggs were found, with this being significantly higher in June than in the months during autumn and winter (October–February). Significant differences in the nematode-EPG were only found between the excretion of nematode eggs in Białowieża Forest when compared to that of Lille Vildmose, with significantly higher excretion in Lille Vildmose (October–November). The results indicate that the development rates for nematodes may be affected by changes in temperature, with increasing temperatures speeding up their development time. Independent of this study design, wildlife vets together with the gamekeepers managing the herd found it necessary to treat the herd with antiparasitics for practical and animal welfare reasons in relation to translocation. Furthermore, 79 plant taxa were identified in the diet of the European bison. The broadest diet was observed in March suggesting that the European bison quickly adapted to their new habitat. The results suggest a seasonal shift in their diet, with this being most apparent from March to April. Full article
(This article belongs to the Special Issue Conservation Genetics as a Management Tool for Endangered, Vulnerable, and Threatened Species)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Tuscan Archipelago National Park: preservation and valorization of local landraces of Brassica and Phaseolus species
Authors: Lorella Andreani; Andrea Venturini; Giulia Spada; Giovanna Amorosi; Giuliana Gillone; Carolina Maria Miarelli; Fabiano Camangi; Agostino Stefani; Chiara Delogu
Affiliation: Council for Agricultural Research and Economics - Research Centre for Plant protection and Certification
Abstract: The maintenance of traditional agricultural practices in protected small islands is closely linked to the preservation of the land, the protection of natural resources, and the conservation of local traditions. For this purpose, the Tuscan Archipelago National Park promoted the census of ancient horticultural varieties preserved by some farmers on the island of Elba. The survey revealed a deep-rooted historical, cultural, social, and economic link between this germplasm and the island’s territory. A scientific characterization of the landrace under ethnobotanical, morphological, and genetic aspects was carried out. Among these local varieties, two landraces of the Brassica species and three landraces of the Phaseolus species were identified and analyzed in this study. To ascertain their distinguishability and uniqueness, similar varieties were also identified based on morpho-physiological characteristics or territorial proximity and compared with the Elban landraces. Morpho-phenological data were collected, and molecular analyses were carried out using Simple Sequence Repeats (SSR) markers. Ten different SSR loci were considered for the Phaseolus species and nine for the Brassica species. The Tuscan Archipelago landraces showed a high level of internal variability but were clearly distinct from each other and from the analyzed varieties, as shown by AMOVA (Analysis of Molecular Variance). Their distinctness was further highlighted by the UPGMA dendrogram obtained from the genetic distance matrix. The same results were confirmed by Principal Coordinate Analysis (PCoA). This study confirms the peculiarity of the Elban landraces, their biodiversity is a heritage to be safeguarded, which can also be used in future breeding programs. These ancient Elban landraces were allocated to local farmers (most were young farmers) to protect them from extinction and to promote more resilient varieties cultivation compared to commercial hybrids widely spread in the area. Local farmhouses also play a strategic role in safeguarding the germplasm and dissemination of sustainable agricultural practices. There is high demand for ancient Elban landraces, this has led to the development of a new local economy balanced between agricultural tradition and innovation.

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