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Potter S, Moritz C, Piggott MP, Bragg JG, Afonso Silva AC, Bi K, McDonald-Spicer C, Turakulov R, Eldridge MDB. Museum skins enable identification of introgression associated with cytonuclear discordance. Syst Biol 2024:syae016. [PMID: 38577768 DOI: 10.1093/sysbio/syae016] [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] [Received: 03/10/2022] [Indexed: 04/06/2024] Open
Abstract
Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale datasets and coalescent modelling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridisation. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least four operational taxonomic units (OTUs) across four species which diverged 183-278 kya. ABC modelling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.
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Affiliation(s)
- Sally Potter
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Maxine P Piggott
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Jason G Bragg
- National Herbarium of New South Wales, The Royal Botanical Gardens and Domain Trust, Sydney, NSW, Australia
| | | | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Christiana McDonald-Spicer
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | | | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
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Potter S, Bragg JG, Turakulov R, Eldridge MDB, Deakin J, Kirkpatrick M, Edwards RJ, Moritz C. Limited introgression between rock-wallabies with extensive chromosomal rearrangements. Mol Biol Evol 2021; 39:6448774. [PMID: 34865126 PMCID: PMC8788226 DOI: 10.1093/molbev/msab333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Indexed: 12/16/2022] Open
Abstract
Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in speciation. Here, we pursue that goal using an extensive sampling of populations and genomes of Petrogale from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their divergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated divergence compared with autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in evaluating the role of Robertsonian fusions and structural variation in divergence, speciation, and patterns of molecular evolution.
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Affiliation(s)
- Sally Potter
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia.,Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Jason G Bragg
- National Herbarium of New South Wales, The Royal Botanical Gardens and Domain Trust, Sydney, NSW, Australia
| | - Rustamzhon Turakulov
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Janine Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX, United States of America
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
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Stevenson WS, Morel-Kopp MC, Chen Q, Liang HP, Bromhead CJ, Wright S, Turakulov R, Ng AP, Roberts AW, Bahlo M, Ward CM. GFI1B mutation causes a bleeding disorder with abnormal platelet function. J Thromb Haemost 2013; 11:2039-47. [PMID: 23927492 DOI: 10.1111/jth.12368] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [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: 05/28/2013] [Accepted: 07/31/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND GFI1B is a transcription factor important for erythropoiesis and megakaryocyte development but previously unknown to be associated with human disease. METHODS A family with a novel bleeding disorder was identified and characterized. Genetic linkage analysis and massively parallel sequencing were used to localize the mutation causing the disease phenotype on chromosome 9. Functional studies were then performed in megakaryocytic cell lines to determine the biological effects of the mutant transcript. RESULTS We have identified a family with an autosomal dominant bleeding disorder associated with macrothrombocytopenia, red cell anisopoikilocytosis, and platelet dysfunction. The severity of bleeding is variable with some affected individuals experiencing spontaneous bleeding while other family members exhibit only abnormal bleeding with surgery. A single nucleotide insertion was identified in GFI1B that predicts a frameshift mutation in the fifth zinc finger DNA-binding domain. This mutation alters the transcriptional activity of the protein, resulting in a reduction in platelet α-granule content and aberrant expression of key platelet proteins. CONCLUSIONS GFI1B mutation represents a novel human bleeding disorder, and the described phenotype identifies GFI1B as a critical regulator of platelet shape, number, and function.
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Affiliation(s)
- W S Stevenson
- Department of Haematology, Royal North Shore Hospital, Sydney, NSW, Australia; Northern Blood Research Centre, Kolling Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia
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Turakulov R, Jorm A, Jacomb P, Tan X, Easteal S. Erratum to “Association of dopamine-β-hydroxylase and androgen receptor gene polymorphisms with Eysenck’s P and other personality traits” [Personality and Individual Differences 37 (2004) 191–202]. Personality and Individual Differences 2005. [DOI: 10.1016/j.paid.2005.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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