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Life
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Evolutionary and Conservation Genetics
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Evolutionary and Conservation Genetics

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Evolutionary Biology".

Deadline for manuscript submissions: closed (31 July 2021) | Viewed by 35869

Special Issue Editors

Dr. Daria Sanna

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Guest Editor
Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
Interests: evolutionary genetics; conservation genetics; population genetics; molecular taxonomy; phylogenetics; phylogeography
Special Issues, Collections and Topics in MDPI journals
Dr. Marco Casu

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Guest Editor
Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
Interests: zoology; genetics; conservation genetics; molecular taxonomy; ichthyology; one health
Special Issues, Collections and Topics in MDPI journals
Dr. Fabio Scarpa

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Guest Editor
Department of Biomedical Science, University of Sassari, 07100 Sassari, Italy
Interests: genetics; genomics; phylodynamics; bioinformatics; biostatistics; population genetics; one health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In this new millennium, in which mankind is facing many great difficulties such as those related to climate change and to the global spread of SARS-CoV-2 pandemic, the role of scientific research in all fields is of pivotal importance for the increasing of our knowledge on organisms and biological phenomena. In this context, evolutionary genetics lays the basis for understanding the evolutionary mechanisms of each type of organism (animals, plants, viruses, etc.), providing support for the management and conservation of those taxonomic units which require specific protection or monitoring. For these reasons, this Special Issue aims to combine the contributions of research groups working all over the world in the field of evolutionary genetics, population genetics, molecular taxonomy, and conservation genetics, in order to join together a group of papers that highlight the importance of the study of genetic variability in organisms for the safeguarding of the biodiversity.

Dr. Daria Sanna
Dr. Marco Casu
Dr. Fabio Scarpa
Guest Editors

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Keywords

  • Evolutionary Genetics
  • Population Genetics
  • Conservation Genetics
  • Phylogeography
  • Phylogenetics
  • Phylodynamics
  • Molecular Taxonomy

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Related Special Issue

Published Papers (9 papers)

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Editorial

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6 pages, 210 KiB  
Editorial
Evolutionary and Conservation Genetics
by Fabio Scarpa, Marco Casu and Daria Sanna
Life 2021, 11(11), 1160; https://doi.org/10.3390/life11111160 - 30 Oct 2021
Cited by 6 | Viewed by 1967
Abstract
Genetic variation, evolution, and conservation are three strictly interconnected words, but none of them exist without the others, unless wanting to waive a complete and operational sense [...] Full article
(This article belongs to the Special Issue Evolutionary and Conservation Genetics)

Research

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16 pages, 8966 KiB  
Article
Bio-Ecological Features Update on Eleven Rare Cartilaginous Fish in the Central-Western Mediterranean Sea as a Contribution for Their Conservation
by Antonello Mulas, Andrea Bellodi, Pierluigi Carbonara, Alessandro Cau, Martina Francesca Marongiu, Paola Pesci, Cristina Porcu and Maria Cristina Follesa
Life 2021, 11(9), 871; https://doi.org/10.3390/life11090871 - 25 Aug 2021
Cited by 10 | Viewed by 7650
Abstract
Cartilaginous fish are commonly recognized as key species in marine ecosystems for their fundamental ecological role as top predators. Nevertheless, effective management plans for cartilaginous fish are still missing, due to the lack of knowledge on their abundance, distribution or even life-history. In [...] Read more.
Cartilaginous fish are commonly recognized as key species in marine ecosystems for their fundamental ecological role as top predators. Nevertheless, effective management plans for cartilaginous fish are still missing, due to the lack of knowledge on their abundance, distribution or even life-history. In this regard, this paper aims at providing new information on the life-history traits, such as age, maturity, reproductive period, in addition to diet characteristics of eleven rare cartilaginous fish inhabiting the Central-Western Mediterranean Sea belonging to the orders Chimaeriformes (Chimaera monstrosa), Hexanchiformes (Heptranchias perlo and Hexanchus griseus), Myliobatiformes (Aetomylaeus bovinus and Myliobatis aquila), Rajiformes (Dipturus nidarosiensis and Leucoraja circularis), Squaliformes (Centrophorus uyato, Dalatias licha and Oxynotus centrina) and Torpediniformes (Tetronarce nobiliana), useful for their assessment and for future management actions. Particularly, the present paper provides for the first time the age estimation of D. nidarosienis and L. circularis which were both found capable of becoming older than ten years. In addition, the present study updates the sizes of first maturity of C. uyato and D. licha, which appeared to be capable of reproducing earlier than what was previously hypothesized, representing very valuable information for a better understanding of these rare species populations status and, eventually, their conservation. On the basis of the stomach content analysis, it was possible to identify five different predator groups. Full article
(This article belongs to the Special Issue Evolutionary and Conservation Genetics)
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16 pages, 2113 KiB  
Article
Molecular Taxonomy and Diversification of Atlantic Skates (Chondrichthyes, Rajiformes): Adding More Pieces to the Puzzle of Their Evolutionary History
by Valentina Crobe, Alice Ferrari, Robert Hanner, Robin W. Leslie, Dirk Steinke, Fausto Tinti and Alessia Cariani
Life 2021, 11(7), 596; https://doi.org/10.3390/life11070596 - 22 Jun 2021
Cited by 7 | Viewed by 3281
Abstract
Conservation and long-term management plans of marine species need to be based upon the universally recognized key-feature of species identity. This important assignment is particularly challenging in skates (Rajiformes) in which the phenotypic similarity between some taxa and the individual variability in others, [...] Read more.
Conservation and long-term management plans of marine species need to be based upon the universally recognized key-feature of species identity. This important assignment is particularly challenging in skates (Rajiformes) in which the phenotypic similarity between some taxa and the individual variability in others, hampers accurate species identification. Here, 432 individual skate samples collected from four major ocean areas of the Atlantic were barcoded and taxonomically analysed. A BOLD project ELASMO ATL was implemented with the aim of establishing a new fully available and well curated barcode library containing both biological and molecular information. The evolutionary histories of the 38 skate taxa were estimated with two concatenated mitochondrial markers (COI and NADH2) through Maximum Likelihood and Bayesian inference. New evolutionary lineages within the genus Raja were discovered off Angola, where paleogeographic history coupled with oceanographic discontinuities could have contributed to the establishment of isolated refugia, playing a fundamental role among skates’ speciation events. These data successfully resolved many taxonomic ambiguities, identified cryptic diversity within valid species and demonstrated a highly cohesive monophyletic clustering among the order, laying the background for further inference of evolutionary patterns suitable for addressing management and conservation issues. Full article
(This article belongs to the Special Issue Evolutionary and Conservation Genetics)
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32 pages, 9545 KiB  
Article
Genomic, Habitat, and Leaf Shape Analyses Reveal a Possible Cryptic Species and Vulnerability to Climate Change in a Threatened Daisy
by Colette Blyth, Matthew J. Christmas, Douglas C. Bickerton, Martin F. Breed, Nicole R. Foster, Greg R. Guerin, Alex R. G. Mason and Andrew J. Lowe
Life 2021, 11(6), 553; https://doi.org/10.3390/life11060553 - 11 Jun 2021
Cited by 2 | Viewed by 3409
Abstract
Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but distinct leaf shape. Remnant populations face threats from [...] Read more.
Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but distinct leaf shape. Remnant populations face threats from habitat fragmentation and climate change. We analysed range-wide genomic data and leaf shape variation to assess population diversity and divergence and to inform conservation management strategies. We detected three distinct genetic groupings and a likely cryptic species. Samples identified as O. pannosa subsp. cardiophylla from the Flinders Ranges in South Australia were genetically distinct from all other samples and likely form a separate, range-restricted species. Remaining samples formed two genetic clusters, which aligned with leaf shape differences but not fully with current subspecies classifications. Levels of genetic diversity and inbreeding differed between the three genetic groups, suggesting each requires a separate management strategy. Additionally, we tested for associations between genetic and environmental variation and carried out habitat suitability modelling for O. pannosa subsp. pannosa populations. We found mean annual maximum temperature explained a significant proportion of genomic variance. Habitat suitability modelling identified mean summer maximum temperature, precipitation seasonality and mean annual rainfall as constraints on the distribution of O. pannosa subsp. pannosa, highlighting increasing aridity as a threat for populations located near suitability thresholds. Our results suggest maximum temperature is an important agent of selection on O. pannosa subsp. pannosa and should be considered in conservation strategies. We recommend taxonomic revision of O. pannosa and provide conservation management recommendations. Full article
(This article belongs to the Special Issue Evolutionary and Conservation Genetics)
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13 pages, 1932 KiB  
Article
Integrated Biomarker Response for Environmental Assessment Using the Gastropod Phorcus turbinatus along the Northern and the Northeastern Coasts of Tunisia
by Wafa Boulajfene, Montassar Lasram and Sabiha Zouari-Tlig
Life 2021, 11(6), 529; https://doi.org/10.3390/life11060529 - 7 Jun 2021
Cited by 6 | Viewed by 2056
Abstract
This work aims to assess the spatial and temporal variations of four biomarkers activities and to integrate their biological responses in a battery using the gastropod Phorcus turbinatus. The monitoring was carried out during the period between April 2014 and January 2015 [...] Read more.
This work aims to assess the spatial and temporal variations of four biomarkers activities and to integrate their biological responses in a battery using the gastropod Phorcus turbinatus. The monitoring was carried out during the period between April 2014 and January 2015 at six stations along the northern and the northeastern coasts of Tunisia. The Fulton condition factor was estimated and the activities of catalase, acetylcholinesterase and glutathione-S-transferase were evaluated by spectrophotometry. A multi-biomarker battery approach was used to assess ecosystems’ condition and to identify environmental impacts on the organisms. The results suggest that the enzymatic activities of CAT and GST depend especially on seasons. As for AChE activity, it was similar between seasons and stations. The values of the integrated biological response were maximal at Jarzouna in summer and at Sidi Daoued in winter, indicating the presence of severe stressors suffered by the organisms. This perturbation may be due to the enrichment of the waters by xenobiotics, namely polycyclic aromatic hydrocarbons, insecticides, phosphate wastes, PCBs and pesticides. Thus, P. turbinatus seems to be a good bioindicator of chemical pollution, constituting an adequate tool for a bio-monitoring program. Full article
(This article belongs to the Special Issue Evolutionary and Conservation Genetics)
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21 pages, 9239 KiB  
Article
Molecular Insights into the Genetic Variability of ORF Virus in a Mediterranean Region (Sardinia, Italy)
by Elisabetta Coradduzza, Daria Sanna, Angela M. Rocchigiani, Davide Pintus, Fabio Scarpa, Rosario Scivoli, Roberto Bechere, Maria A. Dettori, Maria A. Montesu, Vincenzo Marras, Renato Lobrano, Ciriaco Ligios and Giantonella Puggioni
Life 2021, 11(5), 416; https://doi.org/10.3390/life11050416 - 4 May 2021
Cited by 8 | Viewed by 2711
Abstract
Orf virus (ORFV) represents the causative agent of contagious ecthyma, clinically characterized by mild papular and pustular to severe proliferative lesions, mainly occurring in sheep and goats. In order to provide hints on the evolutionary history of this virus, we carried out a [...] Read more.
Orf virus (ORFV) represents the causative agent of contagious ecthyma, clinically characterized by mild papular and pustular to severe proliferative lesions, mainly occurring in sheep and goats. In order to provide hints on the evolutionary history of this virus, we carried out a study aimed to assess the genetic variation of ORFV in Sardinia that hosts a large affected small ruminant population. We also found a high worldwide mutational viral evolutionary rate, which resulted, in turn, higher than the rate we detected for the strains isolated in Sardinia. In addition, a well-supported genetic divergence was found between the viral strains isolated from sheep and those from goats, but no relevant connection was evidenced between the severity of lesions produced by ORFV and specific polymorphic patterns in the two species of hosts. Such a finding suggests that ORFV infection-related lesions are not necessarily linked to the expression of one of the three genes here analyzed and could rather be the effect of the expression of other genes or rather represents a multifactorial character. Full article
(This article belongs to the Special Issue Evolutionary and Conservation Genetics)
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13 pages, 921 KiB  
Article
Male Deep-Sea Shrimps Aristeus antennatus at Fishing Grounds: Growth and First Evaluation of Recruitment by Multilocus Genotyping
by Alba Abras, Jose-Luis García-Marín, Sandra Heras, Manuel Vera, Melania Agulló, Laia Planella and María Inés Roldán
Life 2021, 11(2), 116; https://doi.org/10.3390/life11020116 - 4 Feb 2021
Cited by 5 | Viewed by 2694
Abstract
The population biology of the deep-sea shrimp Aristeus antennatus, as with other exploited demersal species, is usually studied using data from fishery statistics. Such statistical analyses have shown female-biased sex ratios during the spawning season in this species. Because the abundance of [...] Read more.
The population biology of the deep-sea shrimp Aristeus antennatus, as with other exploited demersal species, is usually studied using data from fishery statistics. Such statistical analyses have shown female-biased sex ratios during the spawning season in this species. Because the abundance of males increases at greater depths that are not exploited by fisheries (virgin grounds), knowledge on their recruitment is limited. Here, the growth and recruitment of A. antennatus males at fishing grounds was evaluated. This was achieved by integrating information on previously identified breeding behaviours and by tracing the young-of-year cohort through genotyping at 10 microsatellite loci. Using a codend and a codend cover with distinct meshed windows, four groups of males were collected in winter and in a subsequent spawning summer season. Summer collections were mostly composed of pre-adult males, reaching sizes that are to be expected from the growth of winter juveniles; however, many specimens also originated from nearby grounds. This result indicates the horizontal dispersal of male juveniles via intermediate and deep oceanographic currents. Such dispersal complements passive larval dispersal in surface waters, and contributes to the weak genetic divergence among regional fishing grounds. These features could be shared by other deep-sea crustacean and fish species, and should be considered for the sustainable exploitation of demersal fisheries. Full article
(This article belongs to the Special Issue Evolutionary and Conservation Genetics)
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Review

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19 pages, 8963 KiB  
Review
Anthropogenic Drivers Leading to Population Decline and Genetic Preservation of the Eurasian Griffon Vulture (Gyps fulvus)
by Monica Pirastru, Paolo Mereu, Laura Manca, Daniela Bebbere, Salvatore Naitana and Giovanni G. Leoni
Life 2021, 11(10), 1038; https://doi.org/10.3390/life11101038 - 1 Oct 2021
Cited by 7 | Viewed by 3873
Abstract
Human activities are having increasingly devastating effects on the health of marine and terrestrial ecosystems. Studying the adaptive responses of animal species to changes in their habitat can be useful in mitigating this impact. Vultures represent one of the most virtuous examples of [...] Read more.
Human activities are having increasingly devastating effects on the health of marine and terrestrial ecosystems. Studying the adaptive responses of animal species to changes in their habitat can be useful in mitigating this impact. Vultures represent one of the most virtuous examples of adaptation to human-induced environmental changes. Once dependent on wild ungulate populations, these birds have adapted to the epochal change resulting from the birth of agriculture and livestock domestication, maintaining their essential role as ecological scavengers. In this review, we retrace the main splitting events characterising the vultures’ evolution, with particular emphasis on the Eurasian griffon Gyps fulvus. We summarise the main ecological and behavioural traits of this species, highlighting its vulnerability to elements introduced into the habitat by humans. We collected the genetic information available to date, underlining their importance for improving the management of this species, as an essential tool to support restocking practices and to protect the genetic integrity of G. fulvus. Finally, we examine the difficulties in implementing a coordination system that allows genetic information to be effectively transferred into management programs. Until a linking network is established between scientific research and management practices, the risk of losing important wildlife resources remains high. Full article
(This article belongs to the Special Issue Evolutionary and Conservation Genetics)
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17 pages, 517 KiB  
Review
Genomic Approaches for Conservation Management in Australia under Climate Change
by Isabelle R. Onley, Katherine E. Moseby and Jeremy J. Austin
Life 2021, 11(7), 653; https://doi.org/10.3390/life11070653 - 4 Jul 2021
Cited by 11 | Viewed by 6664
Abstract
Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and [...] Read more.
Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change. Full article
(This article belongs to the Special Issue Evolutionary and Conservation Genetics)
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