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Diversity
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Conservation Genetics for Management of Threatened Plant and Animal Species
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Conservation Genetics for Management of Threatened Plant and Animal Species

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Biodiversity Conservation".

Deadline for manuscript submissions: closed (31 August 2021) | Viewed by 38675

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Dr. Kym Ottewell

E-Mail Website
Guest Editor
Western Australian Department of Biodiversity, Conservation and Attractions, Perth, Australia
Interests: threatened fauna; conservation genetics; reintroductions; genetic monitoring; population genomics
Dr. Margaret Byrne

E-Mail Website
Guest Editor
Western Australian Department of Biodiversity, Conservation and Attractions, Perth, Australia
Interests: species conservation; population genetics; conservation units; threatened species management; evolutionary genetics

Special Issue Information

Dear Colleagues,

Genetic diversity is fundamental to the maintenance of species diversity and ecosystem resilience, and especially the capacity of species to adapt to changing and challenging environmental conditions. Globally, species and ecosystems continue to decline as more species are added to threatened species lists every year. The field of conservation genetics offers a range of techniques and statistical approaches that enable us to describe and monitor various aspects of genetic diversity and make inferences about the underlying ecological and evolutionary processes driving these patterns in threatened species. Whilst conservation genetic analytical approaches are sophisticated and well-advanced, there is now growing interest from managers to incorporate management of genetic diversity in conservation programs.
For this Special Issue, we aim to highlight conservation genetic (or genomic) papers that demonstrate applied outcomes that inform practical threatened species management. We invite submissions of either review or original research articles that may cover a broad range of species or genetic approaches but that focus on how conservation genetic information is (or could be) used to underpin management actions for species recovery. We also particularly welcome papers that retrospectively document the outcomes of practical management actions undertaken to conserve or improve genetic diversity for threatened species, whether successful or unsuccessful. Through exposition of a diversity of approaches, we will demonstrate to conservation managers and researchers how conservation genetics can inform on-ground species management.
Some example topics of interest include:

  • species and subspecies delimitation, and identification of management units
  • distribution of genetic diversity across populations
  • using admixture for conservation purposes
  • genetic erosion
  • changes in mating patterns / managing inbreeding in small populations
  • hybridisation
  • genetic monitoring tools / approaches
  • corridors / connectivity research
  • reintroductions / restoration using genetic principles

Dr. Kym Ottewell
Dr. Margaret Byrne
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. Diversity 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 2100 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

  • Genetic diversity
  • Conservation management
  • Threatened species
  • Restoration
  • Genetic monitoring

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Published Papers (10 papers)

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Editorial

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4 pages, 188 KiB  
Editorial
Conservation Genetics for Management of Threatened Plant and Animal Species
by Kym Ottewell and Margaret Byrne
Diversity 2022, 14(4), 251; https://doi.org/10.3390/d14040251 - 28 Mar 2022
Cited by 2 | Viewed by 2369
Abstract
Globally, species and ecosystems continue to decline, and the impact on threatened species is increasing [...] Full article
(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)

Research

Jump to: Editorial, Other

13 pages, 1012 KiB  
Article
Genetic Differentiation among Subspecies of Banksia nivea (Proteaceae) Associated with Expansion and Habitat Specialization
by Jane Sampson and Margaret Byrne
Diversity 2022, 14(2), 98; https://doi.org/10.3390/d14020098 - 30 Jan 2022
Cited by 7 | Viewed by 3059
Abstract
Subspecies are traditionally defined using phenotypic differences associated with different geographical areas. Yet patterns of morphological and genetic variation may not coincide and thereby fail to reflect species’ evolutionary history. The division of the shrub Banksia nivea Labill. into one widespread (B. [...] Read more.
Subspecies are traditionally defined using phenotypic differences associated with different geographical areas. Yet patterns of morphological and genetic variation may not coincide and thereby fail to reflect species’ evolutionary history. The division of the shrub Banksia nivea Labill. into one widespread (B. nivea subsp. nivea) and two geographically localized subspecies (B. nivea subsp. uliginosa (A.S. George) A.R. Mast & K.R. Thiele and B. nivea subsp. Morangup (M. Pieroni 94/2)) in south-west Australia has been based mainly on variation in leaf shape and pistil length, although flowering time and habitat differences are also evident, and subsp. uliginosa occurs on a different substrate. To assess the genetic divergence of B. nivea subspecies, we genotyped representatives from each subspecies for nuclear microsatellite and non-coding chloroplast sequence variation. We used distance and parsimony-based methods to assess genetic relatedness. Patterns were consistent with the existing taxonomy of subsp. nivea and uliginosa but not subsp. Morangup. Phylogenetic analyses revealed evidence for a more recent divergence of subsp. uliginosa associated with expansion from dryer sandy soils into the winter-wet ironstone soils in the southwest of Western Australia, consistent with progressive long-term climatic drying. Nuclear microsatellites showed low to moderate diversity, high population differentiation overall, and genetic structuring of subspecies in different biogeographical areas. We propose this pattern reflects the predicted impact of a patchy distribution, small populations, and restrictions to gene flow driven by both distance and biogeographic differences in subspecies’ habitats. Full article
(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)
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12 pages, 1842 KiB  
Article
Genetic Diversity and Population Structure of Mesoamerican Scarlet Macaws in an Ex Situ Breeding Population in Mexico
by Patricia Escalante-Pliego, Noemí Matías-Ferrer, Patricia Rosas-Escobar, Gabriela Lara-Martínez, Karol Sepúlveda-González and Rodolfo Raigoza-Figueras
Diversity 2022, 14(1), 54; https://doi.org/10.3390/d14010054 - 14 Jan 2022
Cited by 1 | Viewed by 3319
Abstract
Given the interest in the conservation of the Mesoamerican scarlet macaw (Ara macao cyanoptera), the Xcaret Park formed an initial reproductive population about 30 years ago, which has progressively grown to a considerable population in captivity. In this work, we focus on [...] Read more.
Given the interest in the conservation of the Mesoamerican scarlet macaw (Ara macao cyanoptera), the Xcaret Park formed an initial reproductive population about 30 years ago, which has progressively grown to a considerable population in captivity. In this work, we focus on the evaluation of the genetic diversity of the captive population, taking two groups into account: its founding (49) and the current breeding individuals (166). The genetic analysis consisted of genotyping six nuclear microsatellite loci that are characterized by their high variability. Tests for all loci revealed a Hardy–Weinberg equilibrium in four loci of the founders and in no loci of the breeding groups. The results showed that the genetic variation in the Xcaret population was relatively high (founders He = 0.715 SE = 0.074, breeding pairs He = 0.763 SE = 0.050), with an average polymorphism of 7.5 (4–10) alleles per locus in founders and 8.3 (4–14) in breeding pairs. No significant differences in the evaluated genetic diversity indexes were found between both groups. This indicates that the genetic variability in Xcaret has been maintained, probably due to the high number of pairs and the reproductive management strategy. Bayesian analysis revealed five different genetic lineages present in different proportions in the founders and in the breeding pairs, but no population structure was observed between founders and breeding individuals. The analyzed captive individuals showed levels of genetic diversity comparable to reported values from Ara macao wild populations. These data indicate that the captive population has maintained a similar genetic diversity as the metapopulation in the Mayan Forest and is an important resource for reintroduction projects, some of which began more than five years ago and are still underway. Full article
(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)
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22 pages, 4635 KiB  
Article
Applying Population Viability Analysis to Inform Genetic Rescue That Preserves Locally Unique Genetic Variation in a Critically Endangered Mammal
by Joseph P. Zilko, Dan Harley, Alexandra Pavlova and Paul Sunnucks
Diversity 2021, 13(8), 382; https://doi.org/10.3390/d13080382 - 16 Aug 2021
Cited by 17 | Viewed by 5023
Abstract
Genetic rescue can reduce the extinction risk of inbred populations, but it has the poorly understood risk of ‘genetic swamping’—the replacement of the distinctive variation of the target population. We applied population viability analysis (PVA) to identify translocation rates into the inbred lowland [...] Read more.
Genetic rescue can reduce the extinction risk of inbred populations, but it has the poorly understood risk of ‘genetic swamping’—the replacement of the distinctive variation of the target population. We applied population viability analysis (PVA) to identify translocation rates into the inbred lowland population of Leadbeater’s possum from an outbred highland population that would alleviate inbreeding depression and rapidly reach a target population size (N) while maximising the retention of locally unique neutral genetic variation. Using genomic kinship coefficients to model inbreeding in Vortex, we simulated genetic rescue scenarios that included gene pool mixing with genetically diverse highland possums and increased the N from 35 to 110 within ten years. The PVA predicted that the last remaining population of lowland Leadbeater’s possum will be extinct within 23 years without genetic rescue, and that the carrying capacity at its current range is insufficient to enable recovery, even with genetic rescue. Supplementation rates that rapidly increased population size resulted in higher retention (as opposed to complete loss) of local alleles through alleviation of genetic drift but reduced the frequency of locally unique alleles. Ongoing gene flow and a higher N will facilitate natural selection. Accordingly, we recommend founding a new population of lowland possums in a high-quality habitat, where population growth and natural gene exchange with highland populations are possible. We also recommend ensuring gene flow into the population through natural dispersal and/or frequent translocations of highland individuals. Genetic rescue should be implemented within an adaptive management framework, with post-translocation monitoring data incorporated into the models to make updated predictions. Full article
(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)
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20 pages, 2465 KiB  
Article
Disentangling the Genetic Relationships of Three Closely Related Bandicoot Species across Southern and Western Australia
by Rujiporn Thavornkanlapachai, Esther Levy, You Li, Steven J. B. Cooper, Margaret Byrne and Kym Ottewell
Diversity 2021, 13(1), 2; https://doi.org/10.3390/d13010002 - 22 Dec 2020
Cited by 4 | Viewed by 3205
Abstract
The taxonomy of Australian Isoodon bandicoots has changed continuously over the last 20 years, with recent genetic studies indicating discordance of phylogeographic units with current taxonomic boundaries. Uncertainty over species relationships within southern and western Isoodon, encompassing I. obesulus, I. auratus [...] Read more.
The taxonomy of Australian Isoodon bandicoots has changed continuously over the last 20 years, with recent genetic studies indicating discordance of phylogeographic units with current taxonomic boundaries. Uncertainty over species relationships within southern and western Isoodon, encompassing I. obesulus, I. auratus, and I. fusciventer, has been ongoing and hampered by limited sampling in studies to date. Identification of taxonomic units remains a high priority, as all are threatened to varying extents by ongoing habitat loss and feral predation. To aid diagnosis of conservation units, we increased representative sampling of I. auratus and I. fusciventer from Western Australia (WA) and investigated genetic relationships of these with I. obesulus from South Australia (SA) and Victoria (Vic) using microsatellite markers and mitochondrial DNA. mtDNA analysis identified three major clades concordant with I. obesulus (Vic), I. auratus, and I. fusciventer; however, I. obesulus from SA was polyphyletic to WA taxa, complicating taxonomic inference. Microsatellite data aided identification of evolutionarily significant units consistent with existing taxonomy, with the exception of SA I. obesulus. Further, analyses indicated SA and Vic I. obesulus have low diversity, and these populations may require more conservation efforts than others to reduce further loss of genetic diversity. Full article
(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)
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13 pages, 864 KiB  
Article
Genomic Screening Reveals That the Endangered Eucalyptus paludicola (Myrtaceae) Is a Hybrid
by Kor-jent van Dijk, Michelle Waycott, Joe Quarmby, Doug Bickerton, Andrew H. Thornhill, Hugh Cross and Edward Biffin
Diversity 2020, 12(12), 468; https://doi.org/10.3390/d12120468 - 10 Dec 2020
Cited by 5 | Viewed by 3268
Abstract
A hybrid origin for a conservation listed taxon will influence its status and management options. Here, we investigate the genetic origins of a nationally endangered listed taxon—Eucalyptus paludicola—a tree that is restricted to the Fleurieu Peninsula and Kangaroo Island of South [...] Read more.
A hybrid origin for a conservation listed taxon will influence its status and management options. Here, we investigate the genetic origins of a nationally endangered listed taxon—Eucalyptus paludicola—a tree that is restricted to the Fleurieu Peninsula and Kangaroo Island of South Australia. Since its description in 1995, there have been suggestions that this taxon may potentially be a stable hybrid species. Using a high throughput sequencing approach, we developed a panel of polymorphic loci that were screened across E. paludicola and its putative parental species E. cosmophylla and E. ovata. Bayesian clustering of the genotype data identified separate groups comprising E. ovata and E. cosmophylla while E. paludicola individuals were admixed between these two, consistent with a hybrid origin. Hybrid class assignment tests indicate that the majority of E. paludicola individuals (~70%) are F1 hybrids with a low incidence of backcrossing. Most of the post-F1 hybrids were associated with revegetation sites suggesting they may be maladapted and rarely reach maturity under natural conditions. These data support the hypothesis that E. paludicola is a transient hybrid entity rather than a distinct hybrid species. We briefly discuss the conservation implications of our findings. Full article
(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)
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22 pages, 1330 KiB  
Article
Genetic Consequences of Multiple Translocations of the Banded Hare-Wallaby in Western Australia
by Daniel J. White, Kym Ottewell, Peter B. S. Spencer, Michael Smith, Jeff Short, Colleen Sims and Nicola J. Mitchell
Diversity 2020, 12(12), 448; https://doi.org/10.3390/d12120448 - 27 Nov 2020
Cited by 14 | Viewed by 4885
Abstract
Many Australian mammal species now only occur on islands and fenced mainland havens free from invasive predators. The range of one species, the banded hare-wallaby (Lagostrophus fasciatus), had contracted to two offshore islands in Western Australia. To improve survival, four conservation [...] Read more.
Many Australian mammal species now only occur on islands and fenced mainland havens free from invasive predators. The range of one species, the banded hare-wallaby (Lagostrophus fasciatus), had contracted to two offshore islands in Western Australia. To improve survival, four conservation translocations have been attempted with mixed success, and all occurred in the absence of genetic information. Here, we genotyped seven polymorphic microsatellite markers in two source (Bernier Island and Dorre Island), two historic captive, and two translocated L. fasciatus populations to determine the impact of multiple translocations on genetic diversity. Subsequently, we used population viability analysis (PVA) and gene retention modelling to determine scenarios that will maximise demographic resilience and genetic richness of two new populations that are currently being established. One translocated population (Wadderin) has undergone a genetic bottleneck and lost 8.1% of its source population’s allelic diversity, while the other (Faure Island) may be inbred. We show that founder number is a key parameter when establishing new L. fasciatus populations and 100 founders should lead to high survival probabilities. Our modelling predicts that during periodic droughts, the recovery of source populations will be slower post-harvest, while 75% more animals—about 60 individuals—are required to retain adequate allelic diversity in the translocated population. Our approach demonstrates how genetic data coupled with simulations of stochastic environmental events can address central questions in translocation programmes. Full article
(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)
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21 pages, 3437 KiB  
Article
Genetic Patterns and Climate Modelling Reveal Challenges for Conserving Sclerolaena napiformis (Amaranthaceae s.l.) an Endemic Chenopod of Southeast Australia
by Michael D. Amor, Neville G. Walsh and Elizabeth A. James
Diversity 2020, 12(11), 417; https://doi.org/10.3390/d12110417 - 4 Nov 2020
Cited by 2 | Viewed by 2909
Abstract
Sclerolaena napiformis is a perennial chenopod endemic to southeast Australia. Human-mediated habitat loss and fragmentation over the past century has caused a rapid decline in abundance and exacerbated reduced connectivity between remnant populations across three disjunct regions. To assess conservation requirements, we measured [...] Read more.
Sclerolaena napiformis is a perennial chenopod endemic to southeast Australia. Human-mediated habitat loss and fragmentation over the past century has caused a rapid decline in abundance and exacerbated reduced connectivity between remnant populations across three disjunct regions. To assess conservation requirements, we measured the genetic structure of 27 populations using double digest RADseq). We combined our genetic data with habitat models under projected climate scenarios to identify changes in future habitat suitability. There was evidence of regional differentiation that may pre-date (but also may be compounded) by recent habitat fragmentation. We also found significant correlation between genetic and geographic distance when comparing sites across regions. Overall, S. napiformis showed low genetic diversity and a relatively high proportion of inbreeding/selfing. Climate modelling, based on current occupancy, predicts a reduction in suitable habitat for S. napiformis under the most conservative climate change scenario. We suggest that the best conservation approach is to maximise genetic variation across the entire species range to allow dynamic evolutionary processes to proceed. We recommend a conservation strategy that encourages mixing of germplasm within regions and permits mixed provenancing across regions to maximise genetic novelty. This will facilitate shifts in genetic composition driven by individual plant fitness in response to the novel environmental conditions this species will experience over the next 50 years. Full article
(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)
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11 pages, 16204 KiB  
Communication
Pug-Headedness Anomaly in a Wild and Isolated Population of Native Mediterranean Trout Salmo trutta L., 1758 Complex (Osteichthyes: Salmonidae)
by Francesco Palmas, Tommaso Righi, Alessio Musu, Cheoma Frongia, Cinzia Podda, Melissa Serra, Andrea Splendiani, Vincenzo Caputo Barucchi and Andrea Sabatini
Diversity 2020, 12(9), 353; https://doi.org/10.3390/d12090353 - 15 Sep 2020
Cited by 13 | Viewed by 3636
Abstract
Skeletal anomalies are commonplace among farmed fish. The pug-headedness anomaly is an osteological condition that results in the deformation of the maxilla, pre-maxilla, and infraorbital bones. Here, we report the first record of pug-headedness in an isolated population of the critically endangered native [...] Read more.
Skeletal anomalies are commonplace among farmed fish. The pug-headedness anomaly is an osteological condition that results in the deformation of the maxilla, pre-maxilla, and infraorbital bones. Here, we report the first record of pug-headedness in an isolated population of the critically endangered native Mediterranean trout Salmo trutta L., 1758 complex from Sardinia, Italy. Fin clips were collected for the molecular analyses (D-loop, LDH-C1* locus. and 11 microsatellites). A jaw index (JI) was used to classify jaw deformities. Ratios between the values of morphometric measurements of the head and body length were calculated and plotted against values of body length to identify the ratios that best discriminated between malformed and normal trout. Haplotypes belonging to the AD lineage and the genotype LDH-C1*100/100 were observed in all samples, suggesting high genetic integrity of the population. The analysis of 11 microsatellites revealed that observed heterozygosity was similar to the expected one, suggesting the absence of inbreeding or outbreeding depression. The frequency of occurrence of pug-headedness was 12.5% (two out of 16). One specimen had a strongly blunted forehead and an abnormally short upper jaw, while another had a slightly anomaly asymmetrical jaw. Although sample size was limited, variation in environmental factors during larval development seemed to be the most likely factors to trigger the deformities. Full article
(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)
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Other

Jump to: Editorial, Research

8 pages, 251 KiB  
Opinion
Reducing the Extinction Risk of Populations Threatened by Infectious Diseases
by Gael L. Glassock, Catherine E. Grueber, Katherine Belov and Carolyn J. Hogg
Diversity 2021, 13(2), 63; https://doi.org/10.3390/d13020063 - 4 Feb 2021
Cited by 9 | Viewed by 5156
Abstract
Extinction risk is increasing for a range of species due to a variety of threats, including disease. Emerging infectious diseases can cause severe declines in wild animal populations, increasing population fragmentation and reducing gene flow. Small, isolated, host populations may lose adaptive potential [...] Read more.
Extinction risk is increasing for a range of species due to a variety of threats, including disease. Emerging infectious diseases can cause severe declines in wild animal populations, increasing population fragmentation and reducing gene flow. Small, isolated, host populations may lose adaptive potential and become more susceptible to extinction due to other threats. Management of the genetic consequences of disease-induced population decline is often necessary. Whilst disease threats need to be addressed, they can be difficult to mitigate. Actions implemented to conserve the Tasmanian devil (Sarcophilus harrisii), which has suffered decline to the deadly devil facial tumour disease (DFTD), exemplify how genetic management can be used to reduce extinction risk in populations threatened by disease. Supplementation is an emerging conservation technique that may benefit populations threatened by disease by enabling gene flow and conserving their adaptive potential through genetic restoration. Other candidate species may benefit from genetic management via supplementation but concerns regarding outbreeding depression may prevent widespread incorporation of this technique into wildlife disease management. However, existing knowledge can be used to identify populations that would benefit from supplementation where risk of outbreeding depression is low. For populations threatened by disease and, in situations where disease eradication is not an option, wildlife managers should consider genetic management to buffer the host species against inbreeding and loss of genetic diversity. Full article
(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)
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