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Huang Z, Li Y, Yu K, Ma L, Pang B, Qin Q, Li J, Wang D, Gao H, Kan B. Genome-wide Expanding of Genetic Evolution and Potential Pathogenicity in Vibrio alginolyticus. Emerg Microbes Infect 2024:2350164. [PMID: 38687697 DOI: 10.1080/22221751.2024.2350164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Vibrio alginolyticus, an emergent species of Vibrio genus, exists in aquatic and marine environments. It has undergone genetic diversification, but its detailed genomic diversity is still unclear. Here, we performed a multi-dimensional comparative genomic analysis to explore the population phylogeny, virulence-related genes and potential drug resistance genes of 184 V. alginolyticus isolates. Although genetic diversity is complex, we analyzed the population structure using three sub-datasets, including the subdivision for three lineages into sublineages and the distribution of strains in the marine ecological niche. Accessory genes, most of which reclassified V. alginolyticus genomes as different but with relatively close affinities, were nonuniformly distributed among these isolates. We demonstrated that the spread of some post-evolutionary isolates (mainly L3 strains isolated from Chinese territorial seas) was likely to be closely related to human activities, whereas other more ancestral strains (strains in the L1 and L2) tended to be locally endemic and formed clonal complex groups. In terms of pathogenicity, the potential virulence factors were mainly associated with toxin, adherence, motility, chemotaxis, and the type III secretion system (T3SS). We also found five types of antibacterial drug resistance genes. The prevalence of β-lactam resistance genes was 100%, which indicated that there may be a potential risk of natural resistance to β-lactam drugs. Our study reveals insights into genomic characteristics, evolution and potential virulence-associated gene profiles of V. alginolyticus.
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Affiliation(s)
- Zhenzhou Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. Beijing 102206, P.R. China
- Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang 310021, P.R. China
| | - Yanjun Li
- The Sixth Medical Center of PLA General Hospital, Beijing, 100048, P.R. China
| | - Keyi Yu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. Beijing 102206, P.R. China
| | - Lizhi Ma
- The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, 100039, P.R. China
| | - Bo Pang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. Beijing 102206, P.R. China
| | - Qin Qin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. Beijing 102206, P.R. China
| | - Jie Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. Beijing 102206, P.R. China
| | - Duochun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. Beijing 102206, P.R. China
| | - He Gao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. Beijing 102206, P.R. China
| | - Biao Kan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. Beijing 102206, P.R. China
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2
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Bossu CM, Rodriguez M, Rayne C, Chromczak DA, Higgins PG, Trulio LA, Ruegg KC. Genomic approaches to mitigating genetic diversity loss in declining populations. Mol Ecol 2023; 32:5228-5240. [PMID: 37610278 DOI: 10.1111/mec.17109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023]
Abstract
The accelerating pace of global biodiversity loss is exacerbated by habitat fragmentation and subsequent inbreeding in small populations. To address this problem, conservation practitioners often turn to assisted breeding programmes with the aim of enhancing genetic diversity in declining populations. Although genomic information is infrequently included in these efforts, it has the potential to significantly enhance the success of such programmes. In this study, we showcase the value of genomic approaches for increasing genetic diversity in assisted breeding efforts, specifically focusing on a highly inbred population of Western burrowing owls. To maximize genetic diversity in the resulting offspring, we begin by creating an optimal pairing decision tree based on sex, kinship and patterns of homozygosity across the genome. To evaluate the effectiveness of our strategy, we compare genetic diversity, brood size and nestling success rates between optimized and non-optimized pairs. Additionally, we leverage recently discovered correlations between telomere length and fitness across species to investigate whether genomic optimization could have long-term fitness benefits. Our results indicate that pairing individuals with contrasting patterns of homozygosity across the genome is an effective way to increase genetic diversity in offspring. Although short-term field-based metrics of success did not differ significantly between optimized and non-optimized pairs, offspring from optimized pairs had significantly longer telomeres, suggesting that genetic optimization can help reduce the risk of inbreeding depression. These findings underscore the importance of genomic tools for informing efforts to preserve the adaptive potential of small, inbred populations at risk of further decline.
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Affiliation(s)
- Christen M Bossu
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Marina Rodriguez
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Christine Rayne
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Debra A Chromczak
- Burrowing Owl Researcher & Consultant, Riegelsville, Pennsylvania, USA
| | | | - Lynne A Trulio
- Department of Environmental Studies, San José State University, San Jose, California, USA
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
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3
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Steventon C, Wicker L, Legione AR, Devlin JM, Harley D, Dobson E. A RETROSPECTIVE ANALYSIS OF MORBIDITY AND MORTALITY IN THE CAPTIVE LEADBEATER'S POSSUM ( GYMNOBELIDEUS LEADBEATERI) POPULATION FROM 1970 TO 2021. J Zoo Wildl Med 2023; 54:511-519. [PMID: 37817616 DOI: 10.1638/2022-0126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 10/12/2023] Open
Abstract
The Leadbeater's possum (Gymnobelideus leadbeateri) is a critically endangered nocturnal marsupial with a restricted range in the Central Highlands of Victoria, Australia. There are two genetically distinct populations divided by location: highland and lowland. Lowland possums exist in one remnant swamp forest and entered captivity in 2012 when ∼60 individuals remained. Today, with less than 20 lowland individuals remaining, any information that informs the yet-unsuccessful breeding program is critical. This study encompasses a retrospective analysis of the causes of mortality and significant histological lesions in captive highland and lowland individuals across seven institutions internationally from 1970 to 2021. During this time, 245 possums lived in captivity. Postmortem records exist for 99 animals, including 349 histopathology diagnoses from 80 reports and 264 gross necropsy diagnoses from 78 reports. Diagnoses were assigned into two categories based on the importance to the individual (causing death or morbidity to a single animal [n = 194]), or importance to the wider population (causing death or morbidity to more than one animal or was related to reproduction [n = 155]). Individual animals had multiple diagnoses, which were tallied as individual data points. Renal disease was diagnosed 57 times; the most common finding was chronic nephropathy (43/57). Cardiovascular disease was diagnosed 33 times; atherosclerosis associated with obesity was common (n = 10/33). Both categories suggest causal association with captive husbandry but elicit no comment on the lack of success of the breeding program. Reproductive disease was diagnosed 36 times in 24 animals (14 females and 10 males). In females, 11 cases of uterine inflammation and associated clinical signs were associated with ascending infection or neoplasia. Of the seven lowland male possums with mortality data, five were infertile (azoospermia or testicular atrophy). More investigation into the reproductive health of this population is indicated to understand the lack of success in the current breeding program.
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Affiliation(s)
- Chloe Steventon
- Australian Wildlife Health Centre, Healesville Sanctuary, Zoos Victoria, Healesville, VIC 3777, Australia,
| | - Leanne Wicker
- Wildlife Conservation and Science, Zoos Victoria, Healesville, VIC 3777, Australia
| | - Alistair R Legione
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Joanne M Devlin
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Dan Harley
- Wildlife Conservation and Science, Zoos Victoria, Healesville, VIC 3777, Australia
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Liu Y, Hou L, Liu L, Sulaman A, Muhammad F. Mitochondrial DNA reveals two recent diverged lineages in Amphioctopusaegina (Gray, 1849) (Cephalopoda, Octopodidae) across the Leizhou Peninsula: a marine ecoregion barrier. Zookeys 2023; 1179:299-311. [PMID: 37745623 PMCID: PMC10514695 DOI: 10.3897/zookeys.1179.96015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 08/07/2023] [Indexed: 09/26/2023] Open
Abstract
Amphioctopusaegina is an economically important species that has been intensively exploited in the marine areas along the Chinese coast. However, the genetic variation and population genetic structure, which would provide valuable information for their fisheries management, have rarely been investigated. In this study, the genetic variation within and among four A.aegina populations throughout its full distribution range were estimated based on mitochondrial cytochrome b DNA sequences. Our results indicated low (Qinzhou) to high (Dongshan) genetic diversities among the four populations. Analysis of molecular variance (AMOVA), ΦST statistics, phylogenetic tree and haplotype networks revealed two significant (p < 0.01) divergent lineages with a ΦST value of 0.7116 between them, one from a population in Qinzhou and the other from the remaining three populations of Dongshan, Huizhou and Zhanjiang. However, the low genetic distance (0.0032) and only two fixed substitutions between them suggest their recent divergence is possibly due to the last glacial period barriers to gene flow produced by the Leizhou Peninsula. The observed lineage divergence suggests that populations of A.aegina in China are genetically subdivided and may represent evolutionary lineages that should be managed individually.
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Affiliation(s)
- Yantao Liu
- National Engineering Research Centre of Marine Facilities Aquaculture, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Long Hou
- National Engineering Research Centre of Marine Facilities Aquaculture, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Liqin Liu
- National Engineering Research Centre of Marine Facilities Aquaculture, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Amna Sulaman
- Center of Excellence in Marine Biology, University of Karachi, Karachi, PakistanUniversity of KarachiKarachiPakistan
| | - Faiz Muhammad
- Center of Excellence in Marine Biology, University of Karachi, Karachi, PakistanUniversity of KarachiKarachiPakistan
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5
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Marks AJ, Goldingay RL. Are Urban Populations of a Gliding Mammal Vulnerable to Decline? Animals (Basel) 2023; 13:2098. [PMID: 37443895 DOI: 10.3390/ani13132098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Small populations are at high risk of extinction, and they are likely to need management intervention. Successful management, however, relies on sufficient long-term demographic data in order to determine whether apparent declines are natural fluctuations or the product of threatening processes. In this study, we monitored a small urban population of squirrel gliders (Petaurus norfolcensis) in Queensland, Australia, over a 16 year period. A reference population in a larger forest patch was also studied in order to investigate whether its demographic trends were similar. Using mark-recapture data to generate estimates of apparent survival and population size, we found evidence of a decline within the small population but not in the reference population over the monitoring period. We suggest that the influence of multiple factors may have led to the decline, but, ultimately, that the genetic condition of the small population may be responsible. Understanding demographic trends is an important context for management interventions of small populations, although causes of decline need to be identified for successful management. The squirrel glider provides a useful case study for small urban populations and particularly for arboreal mammals.
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Affiliation(s)
- Anita J Marks
- Faculty of Science and Engineering, Southern Cross University, East Lismore, NSW 2480, Australia
| | - Ross L Goldingay
- Faculty of Science and Engineering, Southern Cross University, East Lismore, NSW 2480, Australia
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6
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Song WH, Li JJ. The effects of intraspecific variation on forecasts of species range shifts under climate change. Sci Total Environ 2023; 857:159513. [PMID: 36257416 DOI: 10.1016/j.scitotenv.2022.159513] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
As global climate change is altering the distribution range of macroalgae across the globe, it is critical to assess its impact on species range shifts to inform the biodiversity conservation of macroalgae. Latitude/environmental gradients could cause intraspecific variability, which may result in distinct responses to climate change. It remains unclear whether geographical variation occurs in the response of species' populations to climate change. We tested this assumption using the brown alga Sargassum thunbergii, a habitat-forming macroalgae encompassing multiple divergent lineages along the Northwest Pacific. Previous studies revealed a distinct lineage of S. thunbergii in rear-edge populations. Given the phylogeographic structure and temperature gradients, we divided these populations into the southern and northern groups. We assessed the physiological responses of the two groups to temperature changes and estimated their niche differences using n-dimensional hypervolumes. A higher photosynthetic rate and antioxidative abilities were detected in the southern group of S. thunbergii than in the northern group. In addition, significant niche differentiation was detected between the two groups, suggesting the possibility for local adaptation. Given these results, we inferred that the southern group (rear-edge populations) may be more resilient to climate change. To examine climate-driven range shifts of S. thunbergii, we constructed species- and lineage-level species distribution models (SDMs). Predictions of both levels showed considerable distribution contracts along the Chinese coasts in the future. For the southern group, the lineage-level model predicted less habitat loss than the species-level model. Our results highlight the importance of considering intraspecific variation in climate change vulnerability assessments for coastal species.
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Affiliation(s)
- Wang-Hui Song
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing 210024, China
| | - Jing-Jing Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing 210024, China.
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7
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Robledo-Ruiz DA, Gan HM, Kaur P, Dudchenko O, Weisz D, Khan R, Lieberman Aiden E, Osipova E, Hiller M, Morales HE, Magrath MJL, Clarke RH, Sunnucks P, Pavlova A. Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater. Gigascience 2022; 11:6554768. [PMID: 35348671 PMCID: PMC8963300 DOI: 10.1093/gigascience/giac025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/13/2022] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
Background The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required. Results We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene. Conclusions The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.
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Affiliation(s)
| | - Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia.,GeneSEQ Sdn Bhd, 48300 Rawang, Selangor, Malaysia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth WA 6009,Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erez Lieberman Aiden
- UWA School of Agriculture and Environment, The University of Western Australia, Perth WA 6009,Australia.,The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX 77030, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 101307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 101307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Hernán E Morales
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Denmark
| | - Michael J L Magrath
- Department of Wildlife Conservation and Science, Zoos Victoria, Parkville, VIC 3052, Australia
| | - Rohan H Clarke
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
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8
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Abstract
Human impact is noticeable around the globe, indicating that a new era might have begun: the Anthropocene. Continuing human activities, including land-use changes, introduction of non-native species and rapid climate change, are altering the distributions of countless species, often giving rise to human-mediated hybridization events. While the interbreeding of different populations or species can have detrimental effects, such as genetic extinction, it can be beneficial in terms of adaptive introgression or an increase in genetic diversity. In this paper, I first review the different mechanisms and outcomes of anthropogenic hybridization based on literature from the last five years (2016-2020). The most common mechanisms leading to the interbreeding of previously isolated taxa include habitat change (51% of the studies) and introduction of non-native species (34% intentional and 19% unintentional). These human-induced hybridization events most often result in introgression (80%). The high incidence of genetic exchange between the hybridizing taxa indicates that the application of a genic view of speciation (and introgression) can provide crucial insights on how to address hybridization events in the Anthropocene. This perspective considers the genome as a dynamic collection of genetic loci with distinct evolutionary histories, giving rise to a heterogenous genomic landscape in terms of genetic differentiation and introgression. First, understanding this genomic landscape can lead to a better selection of diagnostic genetic markers to characterize hybrid populations. Second, describing how introgression patterns vary across the genome can help to predict the likelihood of negative processes, such as demographic and genetic swamping, as well as positive outcomes, such as adaptive introgression. It is especially important to not only quantify how much genetic material introgressed, but also what has been exchanged. Third, comparing introgression patterns in pre-Anthropocene hybridization events with current human-induced cases might provide novel insights into the likelihood of genetic swamping or species collapse during an anthropogenic hybridization event. However, this comparative approach remains to be tested before it can be applied in practice. Finally, the genic view of introgression can be combined with conservation genomic studies to determine the legal status of hybrids and take appropriate measures to manage anthropogenic hybridization events. The interplay between evolutionary and conservation genomics will result in the constant exchange of ideas between these fields which will not only improve our knowledge on the origin of species, but also how to conserve and protect them.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and ConservationWageningen University & ResearchWageningenThe Netherlands
- Forest Ecology and Forest ManagementWageningen University & ResearchWageningenThe Netherlands
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9
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Hogg CJ, Morrison C, Dudley JS, Alquezar‐Planas DE, Beasley‐Hall PG, Magrath MJL, Ho SYW, Lo N, Johnson RN, Grueber CE. Using phylogenetics to explore interspecies genetic rescue options for a critically endangered parrot. Conservat Sci and Prac 2021. [DOI: 10.1111/csp2.483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Carolyn J. Hogg
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - Caitlin Morrison
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
- Australian Museum Research Institute Sydney New South Wales Australia
| | - Jessica S. Dudley
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | | | - Perry G. Beasley‐Hall
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
- School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
| | - Michael J. L. Magrath
- Wildlife Conservation and Science, Zoos Victoria Melbourne Victoria Australia
- School of BioSciences University of Melbourne Victoria Australia
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - Nathan Lo
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - Rebecca N. Johnson
- Australian Museum Research Institute Sydney New South Wales Australia
- National Museum of Natural History, Smithsonian Institution Washington District of Columbia USA
| | - Catherine E. Grueber
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
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10
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Forsdick NJ, Martini D, Brown L, Cross HB, Maloney RF, Steeves TE, Knapp M. Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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11
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Robledo-Ruiz DA, Pavlova A, Clarke RH, Magrath MJL, Quin B, Harrisson KA, Gan HM, Low GW, Sunnucks P. A novel framework for evaluating in situ breeding management strategies in endangered populations. Mol Ecol Resour 2021; 22:239-253. [PMID: 34288508 DOI: 10.1111/1755-0998.13476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 06/29/2021] [Accepted: 07/15/2021] [Indexed: 11/30/2022]
Abstract
Conservation breeding management aims to reduce inbreeding and maximize the retention of genetic diversity in endangered populations. However, breeding management of wild populations is still rare, and there is a need for approaches that provide data-driven evidence of the likelihood of success of alternative in situ strategies. Here, we provide an analytical framework that uses in silico simulations to evaluate, for real wild populations, (i) the degree of population-level inbreeding avoidance, (ii) the genetic quality of mating pairs, and (iii) the potential genetic benefits of implementing two breeding management strategies. The proposed strategies aim to improve the genetic quality of breeding pairs by splitting detrimental pairs and allowing the members to re-pair in different ways. We apply the framework to the wild population of the Critically Endangered helmeted honeyeater by combining genomic data and field observations to estimate the inbreeding (i.e., pair-kinship) and genetic quality (i.e., Mate Suitability Index) of all mating pairs for seven consecutive breeding seasons. We found no evidence of population-level inbreeding avoidance and that ~91.6% of breeding pairs were detrimental to the genetic health of the population. Furthermore, the framework revealed that neither proposed management strategy would significantly improve the genetic quality or reduce inbreeding of the mating pairs in this population. Our results demonstrate the usefulness of our analytical framework for testing the efficacy of different in situ breeding management strategies and for making evidence-based management decisions.
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Affiliation(s)
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Rohan H Clarke
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Michael J L Magrath
- Department of Wildlife Conservation and Science, Zoos Victoria, Parkville, Vic., Australia.,School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - Bruce Quin
- Department of Environment, Land, Water and Planning, Woori Yallock, Vic., Australia
| | - Katherine A Harrisson
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Vic., Australia.,Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Vic., Australia
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Vic., Australia.,Deakin Genomics Centre, Deakin University, Geelong, Vic., Australia
| | - Gabriel W Low
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
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12
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Flesch EP, Graves TA, Thomson JM, Proffitt KM, White PJ, Stephenson TR, Garrott RA. Evaluating wildlife translocations using genomics: A bighorn sheep case study. Ecol Evol 2020; 10:13687-13704. [PMID: 33391673 PMCID: PMC7771163 DOI: 10.1002/ece3.6942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 08/12/2020] [Accepted: 09/25/2020] [Indexed: 01/10/2023] Open
Abstract
Wildlife restoration often involves translocation efforts to reintroduce species and supplement small, fragmented populations. We examined the genomic consequences of bighorn sheep (Ovis canadensis) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0-10 translocations. Using the Illumina High Density Ovine array, we generated datasets of 6,155 to 33,289 single nucleotide polymorphisms and completed clustering, population tree, and kinship analyses. Our analyses determined that natural gene flow did not occur between most populations, including two pairs of native herds that had past connectivity. We synthesized genomic evidence across analyses to evaluate 24 different translocation events and detected eight successful reintroductions (i.e., lack of signal for recolonization from nearby populations) and five successful augmentations (i.e., reproductive success of translocated individuals) based on genetic similarity with the source populations. A single native population founded six of the reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Augmentations consisting of 18-57 animals including males and females succeeded, whereas augmentations of two males did not result in a detectable genetic signature. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration.
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Affiliation(s)
- Elizabeth P. Flesch
- Fish and Wildlife Ecology and Management ProgramEcology DepartmentMontana State UniversityBozemanMTUSA
| | - Tabitha A. Graves
- Northern Rocky Mountain Science CenterU.S. Geological SurveyWest GlacierMTUSA
| | | | | | - P. J. White
- Yellowstone Center for ResourcesNational Park ServiceMammothWYUSA
| | - Thomas R. Stephenson
- Sierra Nevada Bighorn Sheep Recovery ProgramCalifornia Department of Fish and WildlifeBishopCAUSA
| | - Robert A. Garrott
- Fish and Wildlife Ecology and Management ProgramEcology DepartmentMontana State UniversityBozemanMTUSA
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13
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Sadanandan KR, Low GW, Sridharan S, Gwee CY, Ng EYX, Yuda P, Prawiradilaga DM, Lee JGH, Tritto A, Rheindt FE. The conservation value of admixed phenotypes in a critically endangered species complex. Sci Rep 2020; 10:15549. [PMID: 32968132 PMCID: PMC7511927 DOI: 10.1038/s41598-020-72428-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/17/2020] [Indexed: 11/19/2022] Open
Abstract
In today's environmental crisis, conservationists are increasingly confronted with terminally endangered species whose last few surviving populations may be affected by allelic introgression from closely related species. Yet there is a worrying lack of evidence-based recommendations and solutions for this emerging problem. We analyzed genome-wide DNA markers and plumage variability in a critically endangered insular songbird, the Black-winged Myna (BWM, Acridotheres melanopterus). This species is highly threatened by the illegal wildlife trade, with its wild population numbering in the low hundreds, and its continued survival urgently depending on ex-situ breeding. Its three subspecies occur along a geographic gradient of melanism and are variably interpreted as three species. However, our integrative approach revealed that melanism poorly reflects the pattern of limited genomic differentiation across BWM subspecies. We also uncovered allelic introgression into the most melanistic subspecies, tertius, from the all-black congeneric Javan Myna (A. javanicus), which is native to the same islands. Based on our results, we recommend the establishment of three separate breeding programs to maintain subspecific traits that may confer local adaptation, but with the option of occasional cross-breeding between insurance populations in order to boost genetic diversity and increase overall viability prospects of each breeding program. Our results underscore the importance of evidence-based integrative approaches when determining appropriate conservation units. Given the rapid increase of terminally endangered organisms in need of ex-situ conservation, this study provides an important blueprint for similar programs dealing with phenotypically variable species.
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Affiliation(s)
- Keren R Sadanandan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
| | - Gabriel W Low
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Sheeraja Sridharan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- Department of Biological Sciences, University of Alberta, 116 St & 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Elize Y X Ng
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Pramana Yuda
- Universitas Atma Jaya, Jl. Babarsari 44, Janti, Caturtunggal, Kec. Depok, Kabupaten Sleman, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Jessica G H Lee
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826, Singapore
| | - Anaïs Tritto
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826, Singapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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14
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Zilko JP, Harley D, Hansen B, Pavlova A, Sunnucks P. Accounting for cryptic population substructure enhances detection of inbreeding depression with genomic inbreeding coefficients: an example from a critically endangered marsupial. Mol Ecol 2020; 29:2978-2993. [PMID: 32627274 DOI: 10.1111/mec.15540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/16/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022]
Abstract
Characterizing inbreeding depression in wildlife populations can be critical to their conservation. Coefficients of individual inbreeding can be estimated from genome-wide marker data. The degree to which sensitivity of inbreeding coefficients to population genetic substructure alters estimates of inbreeding depression in wild populations is not well understood. Using generalized linear models, we tested the power of two frequently used inbreeding coefficients that are calculated from genome-wide SNP markers, FH and F^III , to predict four fitness traits estimated over two decades in an isolated population of the critically endangered Leadbeater's possum. FH estimates inbreeding as excess observed homozygotes relative to equilibrium expectations, whereas F^III quantifies allelic similarity between the gametes that formed an individual, and upweights rare homozygotes. We estimated FH and F^III from 1,575 genome-wide SNP loci in individuals with fitness trait data (N = 179-237 per trait), and computed revised coefficients, FH by group and F^IIIby group , adjusted for population genetic substructure by calculating them separately within two different genetic groups of individuals identified in the population. Using FH or F^III in the models, inbreeding depression was detected for survival to sexual maturity, longevity and whether individuals bred during their lifetime. F^IIIby group (but not FH by group ) additionally revealed significant inbreeding depression for lifetime reproductive output (total offspring assigned to each individual). Estimates of numbers of lethal equivalents indicated substantial inbreeding load, but differing between inbreeding estimators. Inbreeding depression, declining population size, and low and declining genetic diversity suggest that genetic rescue may assist in preventing extinction of this unique Leadbeater's possum population.
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Affiliation(s)
- Joseph P Zilko
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
| | - Dan Harley
- Zoos Victoria, Parkville, Vic, Australia
| | - Birgita Hansen
- Centre for eResearch and Digital Innovation, Federation University, Ballarat, Vic, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
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15
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Paim TDP, Hay EHA, Wilson C, Thomas MG, Kuehn LA, Paiva SR, McManus C, Blackburn HD. Dynamics of genomic architecture during composite breed development in cattle. Anim Genet 2020; 51:224-234. [PMID: 31961956 PMCID: PMC7065137 DOI: 10.1111/age.12907] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022]
Abstract
Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.
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Affiliation(s)
- T do P Paim
- Instituto Federal de Educação, Ciência e Tecnologia Goiano, Avenida Oeste n. 350, Iporá, 76.200-000, Brazil.,Universidade de Brasília, Asa Norte, Campus Darcy Ribeiro, ICC Sul, Brasília, 70.910-900, Brazil
| | - E H A Hay
- US Department of Agriculture, Fort Keogh Livestock and Range Research Laboratory, Agricultural Research Service, 243 Fort Keogh Road, Miles City, 59301, USA
| | - C Wilson
- US Department of Agriculture, National Laboratory for Genetic Resources Preservation, Agricultural Research Service, National Animal Germplasm Program, 1111 S Mason St., Fort Collins, 80521, USA
| | - M G Thomas
- Department of Animal Sciences, Colorado State University, 350 W. Pitkin St., Fort Collins, 80523-1171, USA
| | - L A Kuehn
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, 844 Rd 313, Clay Center, 68933, USA
| | - S R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final) Caixa Postal 02372, Brasília, 70.770-917, Brazil
| | - C McManus
- Universidade de Brasília, Asa Norte, Campus Darcy Ribeiro, ICC Sul, Brasília, 70.910-900, Brazil
| | - H D Blackburn
- US Department of Agriculture, National Laboratory for Genetic Resources Preservation, Agricultural Research Service, National Animal Germplasm Program, 1111 S Mason St., Fort Collins, 80521, USA
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16
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Liddell E, Cook CN, Sunnucks P. Evaluating the use of risk assessment frameworks in the identification of population units for biodiversity conservation. Wildl Res 2020. [DOI: 10.1071/wr18170] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
ContextManaging small, isolated populations requires conservation practitioners to weigh up the risks of inbreeding depression and outbreeding depression when assessing alternative management actions aimed at preventing species extinction. Accordingly, it is important that research intended to guide these management decisions provides the relevant evidence to inform them.
AimsTo determine the extent to which studies that use genetic analyses to characterise population units for conservation consider the key theoretical concepts necessary for making sound management recommendations regarding the desirability of gene flow among units, notably the consequences and relative risks of inbreeding depression and outbreeding depression.
MethodsA systematic search was conducted of peer-reviewed literature for studies that attempted to identify population units of threatened birds and mammals. Using content analysis, the theoretical framing of these studies was assessed, based on the discussion of key concepts concerning differences among populations.
Key resultsThere has been a significant increase over time in the number of published studies that use genetics to identify population units for conservation. Many do not consider theoretical concepts relevant to the effective management of fragmented populations of threatened species. Mammals were more common than birds as focal species of studies, but the number of concepts used in the framing of the studies was similar for these two taxa, despite differences in their ecology and biology that might be expected to affect perceptions of distinctiveness. Nevertheless, species of greater conservation concern tended to have a slightly more comprehensive theoretical framing.
ConclusionsThere is great potential for more studies to implement theoretical guidelines and practical decision support tools when considering the best course of action for identifying appropriate population units for conservation management.
ImplicationsThe gap in the identified literature is likely to be impacting the ability of conservation practitioners to make evidence-informed decisions about how to manage the genetic health of threatened species; it would be valuable to improve this situation.
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17
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Quigley KM, Bay LK, van Oppen MJH. The active spread of adaptive variation for reef resilience. Ecol Evol 2019; 9:11122-11135. [PMID: 31641460 PMCID: PMC6802068 DOI: 10.1002/ece3.5616] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
The speed at which species adapt depends partly on the rates of beneficial adaptation generation and how quickly they spread within and among populations. Natural rates of adaptation of corals may not be able to keep pace with climate warming. Several interventions have been proposed to fast-track thermal adaptation, including the intentional translocation of warm-adapted adults or their offspring (assisted gene flow, AGF) and the ex situ crossing of warm-adapted corals with conspecifics from cooler reefs (hybridization or selective breeding) and field deployment of those offspring. The introgression of temperature tolerance loci into the genomic background of cooler-environment corals aims to facilitate adaptation to warming while maintaining fitness under local conditions. Here we use research on selective sweeps and connectivity to understand the spread of adaptive variants as it applies to AGF on the Great Barrier Reef (GBR), focusing on the genus Acropora. Using larval biophysical dispersal modeling, we estimate levels of natural connectivity in warm-adapted northern corals. We then model the spread of adaptive variants from single and multiple reefs and assess if the natural and assisted spread of adaptive variants will occur fast enough to prepare receiving central and southern populations given current rates of warming. We also estimate fixation rates and spatial extent of fixation under multiple release scenarios to inform intervention design. Our results suggest that thermal tolerance is unlikely to spread beyond northern reefs to the central and southern GBR without intervention, and if it does, 30+ generations are needed for adaptive gene variants to reach fixation even under multiple release scenarios. We argue that if translocation, breeding, and reseeding risks are managed, AGF using multiple release reefs can be beneficial for the restoration of coral populations. These interventions should be considered in addition to conventional management and accompanied by strong mitigation of CO2 emissions.
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Affiliation(s)
- Kate M. Quigley
- Australian Institute of Marine ScienceTownsvilleQldAustralia
| | - Line K. Bay
- Australian Institute of Marine ScienceTownsvilleQldAustralia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine ScienceTownsvilleQldAustralia
- School of BioSciencesThe University of MelbourneParkvilleVic.Australia
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18
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Rey O, Eizaguirre C, Angers B, Baltazar‐Soares M, Sagonas K, Prunier JG, Blanchet S. Linking epigenetics and biological conservation: Towards a
conservation epigenetics
perspective. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13429] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Olivier Rey
- CNRS UMR 5244, Interactions Hôtes‐Pathogènes‐Environnements (IHPE) Université de Perpignan Via Domitia Perpignan France
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Bernard Angers
- Department of Biological Sciences Université de Montréal Montreal QC Canada
| | | | - Kostas Sagonas
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Jérôme G. Prunier
- Evolution et Diversité Biologique, École Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA), CNRS, UPS, UMR5174 Institut de Recherche pour le Développement (IRD) Toulouse France
| | - Simon Blanchet
- Evolution et Diversité Biologique, École Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA), CNRS, UPS, UMR5174 Institut de Recherche pour le Développement (IRD) Toulouse France
- Station d'Ecologie Théorique et Expérimentale, UMR5321, CNRS Université Paul Sabatier (UP) Moulis France
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19
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Harrisson KA, Magrath MJ, Yen JD, Pavlova A, Murray N, Quin B, Menkhorst P, Miller KA, Cartwright K, Sunnucks P. Lifetime Fitness Costs of Inbreeding and Being Inbred in a Critically Endangered Bird. Curr Biol 2019; 29:2711-2717.e4. [DOI: 10.1016/j.cub.2019.06.064] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/31/2019] [Accepted: 06/21/2019] [Indexed: 11/20/2022]
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20
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Bell DA, Robinson ZL, Funk WC, Fitzpatrick SW, Allendorf FW, Tallmon DA, Whiteley AR. The Exciting Potential and Remaining Uncertainties of Genetic Rescue. Trends Ecol Evol 2019; 34:1070-1079. [PMID: 31296345 DOI: 10.1016/j.tree.2019.06.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 02/03/2023]
Abstract
Restoring gene flow into small, isolated populations can alleviate genetic load and decrease extinction risk (i.e., genetic rescue), yet gene flow is rarely augmented as a conservation strategy. Due to this discrepancy between opportunity and action, a recent call was made for widespread genetic rescue attempts. However, several aspects of augmenting gene flow are poorly understood, including the magnitude and duration of beneficial effects and when deleterious effects are likely to occur. We discuss the remaining uncertainties of genetic rescue in order to promote and direct future research and to hasten progress toward implementing this potentially powerful conservation strategy on a broader scale.
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Affiliation(s)
- Donovan A Bell
- Wildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA.
| | - Zachary L Robinson
- Wildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - W Chris Funk
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI, USA; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Fred W Allendorf
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - David A Tallmon
- Biology and Marine Biology Program, University of Alaska Southeast, Juneau, AK, USA
| | - Andrew R Whiteley
- Wildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
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21
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Atkins ZS, Amor MD, Clemann N, Chapple DG, While GM, Gardner MG, Haines ML, Harrisson KA, Schroder M, Robert KA. Allopatric divergence drives the genetic structuring of an endangered alpine endemic lizard with a sky‐island distribution. Anim Conserv 2019. [DOI: 10.1111/acv.12519] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Z. S. Atkins
- Department of Ecology, Environment and Evolution La Trobe University Bundoora Vic. Australia
| | - M. D. Amor
- Department of Ecology, Environment and Evolution La Trobe University Bundoora Vic. Australia
| | - N. Clemann
- Department of Environment, Land, Water& Planning Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - D. G. Chapple
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - G. M. While
- School of Biological Sciences University of Tasmania Hobart TAS Australia
| | - M. G. Gardner
- College of Science and Engineering Flinders University Adelaide Australia
- Evolutionary Biology Unit South Australian Museum Adelaide SA Australia
| | - M. L. Haines
- Biological Sciences University of Wisconsin‐Milwaukee Milwaukee WI USA
| | - K. A. Harrisson
- Department of Ecology, Environment and Evolution La Trobe University Bundoora Vic. Australia
- Department of Environment, Land, Water& Planning Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - M. Schroder
- NSW National Parks and Wildlife ServiceSnowy Mountains Region Jindabyne NSW Australia
| | - K. A. Robert
- Department of Ecology, Environment and Evolution La Trobe University Bundoora Vic. Australia
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22
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von Takach Dukai B, Jack C, Borevitz J, Lindenmayer DB, Banks SC. Pervasive admixture between eucalypt species has consequences for conservation and assisted migration. Evol Appl 2019; 12:845-860. [PMID: 30976314 PMCID: PMC6439489 DOI: 10.1111/eva.12761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/05/2018] [Accepted: 12/21/2018] [Indexed: 01/12/2023] Open
Abstract
Conservation management often uses information on genetic population structure to assess the importance of local provenancing for ecological restoration and reintroduction programs. For species that do not exhibit complete reproductive isolation, the estimation of population genetic parameters may be influenced by the extent of admixture. Therefore, to avoid perverse outcomes for conservation, genetically informed management strategies must determine whether hybridization between species is relevant, and the extent to which observed population genetic patterns are shaped by interspecific versus intraspecific gene flow. We used genotyping by sequencing to identify over 2,400 informative single nucleotide polymorphisms across 18 populations of Eucalyptus regnans F. Muell., a foundation tree species of montane forests in south-eastern Australia. We used these data to determine the extent of hybridization with another species, Eucalyptus obliqua L'Hér., and investigate how admixture influences genetic diversity parameters, by estimating metrics of genetic diversity and examining population genetic structure in datasets with and without admixed individuals. We found hybrid individuals at all sites and two highly introgressed populations. Hybrid individuals were not distributed evenly across environmental gradients, with logistic regression identifying hybrids as being associated with temperature. Removal of hybrids resulted in increases in genetic differentiation (F ST), expected heterozygosity, observed heterozygosity and the inbreeding coefficient, and different patterns of isolation by distance. After removal of hybrids and introgressed populations, mountain ash showed very little population genetic structure, with a small effect of isolation by distance, and very low global F ST(0.03). Our study shows that, in plants, decisions around provenancing of individuals for restoration depend on knowledge of whether hybridization is influencing population genetic structure. For species in which most genetic variation is held within populations, there may be little benefit in planning conservation strategies around environmental adaptation of seed sources. The possibility for adaptive introgression may also be relevant when species regularly hybridize.
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Affiliation(s)
- Brenton von Takach Dukai
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Cameron Jack
- ANU Bioinformatics Consultancy, John Curtin School of Medical ResearchAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Justin Borevitz
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
- Centre of Excellence in Plant Energy BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - David B. Lindenmayer
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Sam C. Banks
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthwest TerritoriesAustralia
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23
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Fitzpatrick SW, Funk WC. Genomics for Genetic Rescue. In: Hohenlohe PA, Rajora OP, editors. Population Genomics: Wildlife. Cham: Springer International Publishing; 2021. pp. 437-71. [DOI: 10.1007/13836_2019_64] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Slender AL, Louter M, Gardner MG, Kleindorfer S. Thick-billed grasswren (Amytornis modestus) songs differ across subspecies and elicit different subspecific behavioural responses. T ROY SOC SOUTH AUST 2018. [DOI: 10.1080/03721426.2018.1483185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Amy L. Slender
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Marina Louter
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Michael G. Gardner
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- Evolutionary Biology Unit, Adelaide, SA, Australia
| | - Sonia Kleindorfer
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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25
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Perrier C, Ferchaud AL, Sirois P, Thibault I, Bernatchez L. Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish. Mol Ecol 2017; 26:6317-6335. [PMID: 29024140 DOI: 10.1111/mec.14361] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 01/01/2023]
Abstract
Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated with lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated with inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated with inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.
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Affiliation(s)
- Charles Perrier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Pascal Sirois
- Chaire de Recherche sur les Espèces Aquatiques Exploitées, Laboratoire des Sciences Aquatiques, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Isabel Thibault
- Direction de l'expertise sur la Faune Aquatique, Ministère des Forêts de la Faune et des Parcs du Québec, Québec, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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Pavlova A, Beheregaray LB, Coleman R, Gilligan D, Harrisson KA, Ingram BA, Kearns J, Lamb AM, Lintermans M, Lyon J, Nguyen TTT, Sasaki M, Tonkin Z, Yen JDL, Sunnucks P. Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow. Evol Appl 2017; 10:531-550. [PMID: 28616062 PMCID: PMC5469170 DOI: 10.1111/eva.12484] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/29/2017] [Indexed: 12/15/2022] Open
Abstract
Genetic diversity underpins the ability of populations to persist and adapt to environmental changes. Substantial empirical data show that genetic diversity rapidly deteriorates in small and isolated populations due to genetic drift, leading to reduction in adaptive potential and fitness and increase in inbreeding. Assisted gene flow (e.g. via translocations) can reverse these trends, but lack of data on fitness loss and fear of impairing population "uniqueness" often prevents managers from acting. Here, we use population genetic and riverscape genetic analyses and simulations to explore the consequences of extensive habitat loss and fragmentation on population genetic diversity and future population trajectories of an endangered Australian freshwater fish, Macquarie perch Macquaria australasica. Using guidelines to assess the risk of outbreeding depression under admixture, we develop recommendations for population management, identify populations requiring genetic rescue and/or genetic restoration and potential donor sources. We found that most remaining populations of Macquarie perch have low genetic diversity, and effective population sizes below the threshold required to retain adaptive potential. Our simulations showed that under management inaction, smaller populations of Macquarie perch will face inbreeding depression within a few decades, but regular small-scale translocations will rapidly rescue populations from inbreeding depression and increase adaptive potential through genetic restoration. Despite the lack of data on fitness loss, based on our genetic data for Macquarie perch populations, simulations and empirical results from other systems, we recommend regular and frequent translocations among remnant populations within catchments. These translocations will emulate the effect of historical gene flow and improve population persistence through decrease in demographic and genetic stochasticity. Increasing population genetic connectivity within each catchment will help to maintain large effective population sizes and maximize species adaptive potential. The approach proposed here could be readily applicable to genetic management of other threatened species to improve their adaptive potential.
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Affiliation(s)
- Alexandra Pavlova
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
| | | | - Rhys Coleman
- Applied ResearchMelbourne WaterDocklandsVICAustralia
| | - Dean Gilligan
- Freshwater Ecosystems ResearchNSW Department of Primary Industries – FisheriesBatemans BayNSWAustralia
| | - Katherine A. Harrisson
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
- Department of Ecology Environment and EvolutionSchool of Life Sciences, La Trobe UniversityBundoora, Victoria3083Australia
| | - Brett A. Ingram
- Department of Economic DevelopmentJobs, Transport and ResourcesFisheries VictoriaAlexandraVICAustralia
| | - Joanne Kearns
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
| | - Annika M. Lamb
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
| | - Mark Lintermans
- Institute for Applied EcologyUniversity of CanberraCanberraACTAustralia
| | - Jarod Lyon
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
| | - Thuy T. T. Nguyen
- Agriculture VictoriaAgriBio, Centre for AgriBioscienceBundooraVICAustralia
| | - Minami Sasaki
- School of Biological SciencesFlinders UniversityAdelaideSAAustralia
| | - Zeb Tonkin
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
| | - Jian D. L. Yen
- School of Physics and AstronomyClayton Campus, Monash UniversityClaytonVICAustralia
| | - Paul Sunnucks
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
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