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Study on the Global Stability for a Generalized SEIR Epidemic Model. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:8215214. [PMID: 35978893 PMCID: PMC9377876 DOI: 10.1155/2022/8215214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/15/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022]
Abstract
In the current study, a generalized SEIR epidemic model is studied. The generalized fractional-order SEIR model (susceptible-infected-recovered (SIR) epidemic) model differentiated the population into susceptible population, exposure population, infected population, and rehabilitation population and has fundamental mentoring importance for the forecast of the probable outburst of infectious ailments. The fundamental duplicated quantity R0 is inferred. When R0 < 1, the disease-free equilibrium (DFE) is particular and tending towards stability. When R0 > 1, the endemic equilibrium is sole. In addition, certain circumstances are set up to make sure the local progressive stability of disease-free and endemic equilibrium. Considering the influence of the individual behavior, a broader SEIR epidemic model is raised, which classified the population into susceptible, exposure, infected, and rehabilitation. What is more, the basic reproduction number, that regulates whether the infection will die out or not, is obtained by the spectral radius of the next-generation matrix; moreover, the global stability of DFE and endemic equilibrium are analyzed by a geometry method.
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Magid M, Wold JR, Moraga R, Cubrinovska I, Houston DM, Gartrell BD, Steeves TE. Leveraging an existing whole genome resequencing population dataset to characterize toll‐like receptor gene diversity in a threatened bird. Mol Ecol Resour 2022; 22:2810-2825. [PMID: 35635119 PMCID: PMC9543821 DOI: 10.1111/1755-0998.13656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/29/2022] [Accepted: 05/26/2022] [Indexed: 11/27/2022]
Abstract
Species recovery programs are increasingly using genomic data to measure neutral genetic diversity and calculate metrics like relatedness. While these measures can inform conservation management, determining the mechanisms underlying inbreeding depression requires information about functional genes associated with adaptive or maladaptive traits. Toll‐like receptors (TLRs) are one family of functional genes, which play a crucial role in recognition of pathogens and activation of the immune system. Previously, these genes have been analysed using species‐specific primers and PCR. Here, we leverage an existing short‐read reference genome, whole‐genome resequencing population data set, and bioinformatic tools to characterize TLR gene diversity in captive and wild tchūriwat’/tūturuatu/shore plover (Thinornis novaeseelandiae), a threatened bird endemic to Aotearoa New Zealand. Our results show that TLR gene diversity in tchūriwat’/tūturuatu is low, and forms two distinct captive and wild genetic clusters. The bioinformatic approach presented here has broad applicability to other threatened species with existing genomic resources in Aotearoa New Zealand and beyond.
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Affiliation(s)
- Molly Magid
- University of Canterbury School of Biological Sciences Christchurch NZ
| | - Jana R. Wold
- University of Canterbury School of Biological Sciences Christchurch NZ
| | - Roger Moraga
- Tea Break Bioinformatics, Ltd Palmerston North NZ
| | - Ilina Cubrinovska
- University of Canterbury School of Biological Sciences Christchurch NZ
| | | | - Brett D. Gartrell
- Wildbase Massey University Institute of Veterinary, Animal, and Biomedical Sciences, Palmerston North, Manawatu NZ
| | - Tammy E. Steeves
- University of Canterbury School of Biological Sciences Christchurch NZ
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Howell LG, Johnston SD, O’Brien JK, Frankham R, Rodger JC, Ryan SA, Beranek CT, Clulow J, Hudson DS, Witt RR. Modelling Genetic Benefits and Financial Costs of Integrating Biobanking into the Captive Management of Koalas. Animals (Basel) 2022; 12:ani12080990. [PMID: 35454237 PMCID: PMC9028793 DOI: 10.3390/ani12080990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Managed wildlife breeding faces high costs and genetic diversity challenges associated with caring for small populations. Biobanking (freezing of sex cells and tissues for use in assisted breeding) and associated reproductive technologies could help alleviate these issues in koala captive management by enhancing retention of genetic diversity in captive-bred animals and lowering program costs through reductions in the size of the required live captive colonies. Australia’s zoos and wildlife hospitals provide rare opportunities to refine and cost-effectively integrate these tools into conservation outcomes for koalas due to extensive already-existing infrastructure, technical expertise, and captive animals. Abstract Zoo and wildlife hospital networks are set to become a vital component of Australia’s contemporary efforts to conserve the iconic and imperiled koala (Phascolarctos cinereus). Managed breeding programs held across zoo-based networks typically face high economic costs and can be at risk of adverse genetic effects typical of unavoidably small captive colonies. Emerging evidence suggests that biobanking and associated assisted reproductive technologies could address these economic and genetic challenges. We present a modelled scenario, supported by detailed costings, where these technologies are optimized and could be integrated into conservation breeding programs of koalas across the established zoo and wildlife hospital network. Genetic and economic modelling comparing closed captive koala populations suggest that supplementing them with cryopreserved founder sperm using artificial insemination or intracytoplasmic sperm injection could substantially reduce inbreeding, lower the required colony sizes of conservation breeding programs, and greatly reduce program costs. Ambitious genetic retention targets (maintaining 90%, 95% and 99% of source population heterozygosity for 100 years) could be possible within realistic cost frameworks, with output koalas suited for wild release. Integrating biobanking into the zoo and wildlife hospital network presents a cost-effective and financially feasible model for the uptake of these tools due to the technical and research expertise, captive koala colonies, and ex situ facilities that already exist across these networks.
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Affiliation(s)
- Lachlan G. Howell
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University Geelong, Melbourne Burwood Campus, 221 Burwood Highway, Burwood, VIC 3125, Australia
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
- Correspondence: (L.G.H.); (R.R.W.)
| | - Stephen D. Johnston
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia;
| | - Justine K. O’Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society, Bradleys Head Rd., Mosman, NSW 2088, Australia;
| | - Richard Frankham
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia;
| | - John C. Rodger
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
| | - Shelby A. Ryan
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
| | - Chad T. Beranek
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
| | - John Clulow
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
| | - Donald S. Hudson
- Port Stephens Koala & Wildlife Preservation Society LTD., t/a Port Stephens Koala Hospital, One Mile, NSW 2316, Australia;
| | - Ryan R. Witt
- School of Environmental and Life Sciences, Biology Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; (J.C.R.); (S.A.R.); (C.T.B.); (J.C.)
- FAUNA Research Alliance, P.O. Box 5092, Kahibah, NSW 2290, Australia
- Correspondence: (L.G.H.); (R.R.W.)
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Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern. Mol Ecol 2021; 30:5949-5965. [PMID: 34424587 PMCID: PMC9290615 DOI: 10.1111/mec.16141] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022]
Abstract
Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature-predominantly in human health, agriculture and ecoevolutionary biology-to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
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Affiliation(s)
- Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, Virginia, USA.,Centre for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - David Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Marissa F Le Lec
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Joseph Guhlin
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand.,Genomics Aotearoa, Dunedin, Otago, New Zealand
| | - Anna W Santure
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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