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

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 21856

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Dr. Claudia Greco

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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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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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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

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Keywords

conservation genetics
forensics
molecular markers
management
plants
animals

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Published Papers (9 papers)

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15 pages, 2598 KiB

Open AccessArticle

Genetic Assessment of a Captive Population of Eurasian Stone-Curlew (Burhinus oedicnemus), Source for the Reinforcement of Wild Populations

by Loïc Lesobre, Alessia Ostolani, Hiba Abi Hussein, Dimitri Giunchi, Mohamed Aourir, Yassine Teyar and Mariella Baratti

Biology 2024, 13(12), 982; https://doi.org/10.3390/biology13120982 - 27 Nov 2024

Viewed by 1168

Abstract

Although ex situ conservation programs are increasingly valuable support tools for in situ conservation measures, success depends on these captive individuals to be genetically representative of the recipient population. The Eurasian stone-curlew (Burhinus oedicnemus) inhabit steppes that represent some of the most degraded and exploited habitats worldwide. A captive breeding program was implemented in Morocco as a pre-emptive effort for the conservation of the North African subspecies Burhinus oedicnemus saharae. However, the genetic origins of the founders of the captive flock were unknown. We applied a multi-locus approach to characterize the genetic ancestry of the current captive breeding flock by comparing it to wild populations from both Western and Eastern Morocco. Mitochondrial DNA and microsatellite markers were employed to assess levels of genetic diversity and relatedness within each sample, as well as potential genetic differentiation between wild and captive samples through PCA and admixture analyses. We recovered similar genetic diversity estimates, low levels of relatedness, and little differentiation between captive and wild samples. These results confirmed the Moroccan origin of the founders. We provide recommendations for the optimization of the Eurasian Stone Curlew conservation breeding program but also for future conservation breeding programs to ensure the effective conservation of genetic diversity and wild populations. 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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19 pages, 1629 KiB

Open AccessArticle

Combining Historical and Molecular Data to Study Nearly Extinct Native Italian Grey Partridge (Perdix perdix) at the Turn of the Twentieth Century

by Claudia Greco, Cristiano Tabarroni, Irene Pellegrino, Livia Lucentini, Leonardo Brustenga, Lorenza Sorbini and Nadia Mucci

Biology 2024, 13(9), 709; https://doi.org/10.3390/biology13090709 - 10 Sep 2024

Cited by 1 | Viewed by 1421

Abstract

The grey partridge (Perdix perdix Linnaeus, 1758), is a polytypic species with seven recognized subspecies, including P. p. italica (Hartert, 1917), which is endemic to Italy. Until World War II, the species was widespread across Europe but severely declined due to anthropogenic causes, jeopardizing the Italian subspecies gene pool. Genetic characterization and haplotype identification were performed by analyzing the 5′-end of the mitochondrial control region (CR). A total of 15 haplotypes were detected, seven of which were present in the population before 1915. Among them, three haplotypes were never detected again in the individuals collected after 1915. Interestingly, eight of the 15 haplotypes detected in Italian museum samples belonged exclusively to individuals collected after 1915. The obtained data highlight a high presence of specimens originating from other European populations and, despite all the conservation efforts, suggest an uncertain situation of the subspecies in Italy. This research was strongly backed up by extensive bibliographic research on historical documents, allowing the identification of hundreds of restocking events all over Italy. This is an integral part of this research and has laid the foundations for identifying and circumscribing historical periods in which introductions from the rest of Europe had different pressures, aiming to define a baseline. 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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26 pages, 4559 KiB

Open AccessArticle

Genetic and Phenotypic Evaluation of European Maize Landraces as a Tool for Conservation and Valorization of Agrobiodiversity

by Carlotta Balconi, Agustin Galaretto, Rosa Ana Malvar, Stéphane D. Nicolas, Rita Redaelli, Violeta Andjelkovic, Pedro Revilla, Cyril Bauland, Brigitte Gouesnard, Ana Butron, Alessio Torri, Ana Maria Barata, Natalija Kravic, Valérie Combes, Pedro Mendes-Moreira, Danela Murariu, Hrvoje Šarčević, Beate Schierscher-Viret, Morgane Vincent, Anne Zanetto, Bettina Kessel, Delphine Madur, Tristan Mary-Huard, André Pereira, Domnica Daniela Placinta, Alexandre Strigens, Alain Charcosset and Sandra Goritschnig Show full author list Hide full author list

Biology 2024, 13(6), 454; https://doi.org/10.3390/biology13060454 - 19 Jun 2024

Cited by 8 | Viewed by 2722

Abstract

The ECPGR European Evaluation Network (EVA) for Maize involves genebanks, research institutions, and private breeding companies from nine countries focusing on the valorization of maize genetic resources across Europe. This study describes a diverse collection of 626 local landraces and traditional varieties of maize (Zea mays L.) from nine European genebanks, including criteria for selection of the collection and its genetic and phenotypic diversity. High-throughput pool genotyping grouped the landraces into nine genetic groups with a threshold of 0.6 admixture, while 277 accessions were designated admixed and likely to have resulted from previous breeding activities. The grouping correlated well with the geographic origins of the collection, also reflecting the various pathways of introduction of maize to Europe. Phenotypic evaluations of 588 accessions for flowering time and plant architecture in multilocation trials over three years confirmed the great diversity within the collection, although phenotypic clusters only partially correlated with the genetic grouping. The EVA approach promotes conservation of genetic resources and opens an opportunity to increase genetic variability for developing improved varieties and populations for farmers, with better adaptation to specific environments and greater tolerance to various stresses. As such, the EVA maize collection provides valuable sources of diversity for facing climate change due to the varieties’ local adaptation. 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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7 pages, 1100 KiB

Open AccessCommunication

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

Cited by 1 | Viewed by 1732

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 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

Open AccessArticle

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

Cited by 2 | Viewed by 2787

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 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

Open AccessArticle

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 10 | Viewed by 3063

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, 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

Open AccessArticle

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 7 | Viewed by 3359

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 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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13 pages, 2054 KiB

Open AccessArticle

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 - 4 May 2023

Viewed by 3081

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 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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9 pages, 1067 KiB

Open AccessBrief Report

Unveiling MHC-DAB Polymorphism Within the Western Balkan Salmonid Hotspot: Preliminary Outcomes from Native Trouts of Ohrid Lake and the Drin-Skadar Drainage (Albania)

by Lorenzo Talarico, Arnold Rakaj and Lorenzo Tancioni

Biology 2024, 13(12), 1060; https://doi.org/10.3390/biology13121060 - 18 Dec 2024

Viewed by 580

Abstract

Due to their involvement in pathogen-mediated immune responses, the hypervariable genes of the Major Histocompatibility Complex (MHC) have become a paradigm for investigating the evolution and maintenance of genetic (adaptive) diversity, contextually providing insight into the viability of wild populations, which is meaningful for conservation. Here, we provide the first preliminary characterization of MHC polymorphism and evolution in trouts from Albania, a known hotspot of Salmonid diversity harboring ecologically and phylogenetically distinct native (threatened) taxa. Overall, 36 trout—including Lake Ohrid-endemic Salmo ohridanus and S. letnica, and both riverine and lacustrine native brown trout (the S. trutta complex) from the Drin-Skadar drainage—were genotyped at the MHC-DAB locus through next-generation amplicon sequencing. We identified 34 alleles (including 30 novel alleles), unveiling remarkable population/taxon MHC-DAB distinctiveness. Despite apparent functional (supertype) similarity, S. letnica and the S. trutta complex showed MHC-typical high sequence/allele diversity and evidence of global/codon-specific positive selection, particularly at antigen-binding sites. Conversely, deep-water-adapted S. ohridanus revealed unexpectedly reduced allelic/supertype diversity and relaxed selection. Evolution by reticulation and signals of trans-species polymorphism emerged from sequence genealogies. Further investigations and increased sampling will provide a deeper understanding of the evolutionary mechanisms yielding the observed pattern of MHC diversity across Albanian trout taxa and populations. 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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