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Beasley-Hall PG, Kinjo Y, Rose HA, Walker J, Foster CSP, Kovacs TGL, Bourguignon T, Ho SYW, Lo N. Shrinking in the dark: Parallel endosymbiont genome erosions are associated with repeated host transitions to an underground life. Insect Sci 2024. [PMID: 38462506 DOI: 10.1111/1744-7917.13339] [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] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 12/06/2023] [Accepted: 01/03/2024] [Indexed: 03/12/2024]
Abstract
Microbial symbioses have had profound impacts on the evolution of animals. Conversely, changes in host biology may impact the evolutionary trajectory of symbionts themselves. Blattabacterium cuenoti is present in almost all cockroach species and enables hosts to subsist on a nutrient-poor diet. To investigate if host biology has impacted Blattabacterium at the genomic level, we sequenced and analyzed 25 genomes from Australian soil-burrowing cockroaches (Blaberidae: Panesthiinae), which have undergone at least seven separate subterranean, subsocial transitions from above-ground, wood-feeding ancestors. We find at least three independent instances of genome erosion have occurred in Blattabacterium strains exclusive to Australian soil-burrowing cockroaches. These shrinkages have involved the repeated inactivation of genes involved in amino acid biosynthesis and nitrogen recycling, the core role of Blattabacterium in the host-symbiont relationship. The most drastic of these erosions have occurred in hosts thought to have transitioned underground the earliest relative to other lineages, further suggestive of a link between gene loss in Blattabacterium and the burrowing behavior of hosts. As Blattabacterium is unable to fulfill its core function in certain host lineages, these findings suggest soil-burrowing cockroaches must acquire these nutrients from novel sources. Our study represents one of the first cases, to our knowledge, of parallel host adaptations leading to concomitant parallelism in their mutualistic symbionts, further underscoring the intimate relationship between these two partners.
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Affiliation(s)
- Perry G Beasley-Hall
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Yukihiro Kinjo
- Evolutionary Genomics Unit, Okinawa Institute of Science & Technology Graduate University, Onna-son, Okinawa, Japan
| | - Harley A Rose
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - James Walker
- Australian Government Department of Agriculture Water and Environment, Canberra, Australia
| | - Charles S P Foster
- School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Toby G L Kovacs
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Thomas Bourguignon
- Australian Government Department of Agriculture Water and Environment, Canberra, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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Tea Y, Zhou Y, Ewart KM, Cheng G, Kawasaki K, DiBattista JD, Ho SYW, Lo N, Fan S. The spotted parrotfish genome provides insights into the evolution of a coral reef dietary specialist (Teleostei: Labridae: Scarini: Cetoscarus ocellatus). Ecol Evol 2024; 14:e11148. [PMID: 38476702 PMCID: PMC10932694 DOI: 10.1002/ece3.11148] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/25/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
With over 600 valid species, the wrasses (family Labridae) are among the largest and most successful families of the marine teleosts. They feature prominently on coral reefs where they are known not only for their impressive diversity in colouration and form but also for their functional specialisation and ability to occupy a wide variety of trophic guilds. Among the wrasses, the parrotfishes (tribe Scarini) display some of the most dramatic examples of trophic specialisation. Using abrasion-resistant biomineralized teeth, parrotfishes are able to mechanically extract protein-rich micro-photoautotrophs growing in and among reef carbonate material, a dietary niche that is inaccessible to most other teleost fishes. This ability to exploit an otherwise untapped trophic resource is thought to have played a role in the diversification and evolutionary success of the parrotfishes. In order to better understand the key evolutionary innovations leading to the success of these dietary specialists, we sequenced and analysed the genome of a representative species, the spotted parrotfish (Cetoscarus ocellatus). We find significant expansion, selection and duplications within several detoxification gene families and a novel poly-glutamine expansion in the enamel protein ameloblastin, and we consider their evolutionary implications. Our genome provides a useful resource for comparative genomic studies investigating the evolutionary history of this highly specialised teleostean radiation.
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Affiliation(s)
- Yi‐Kai Tea
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
| | - Yulu Zhou
- State Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life ScienceFudan UniversityShanghaiChina
| | - Kyle M. Ewart
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Guo Cheng
- State Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life ScienceFudan UniversityShanghaiChina
| | - Kazuhiko Kawasaki
- Department of AnthropologyPennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Joseph D. DiBattista
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
- School of Environment and ScienceGriffith UniversitySouthportQueenslandAustralia
| | - Simon Y. W. Ho
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Nathan Lo
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life ScienceFudan UniversityShanghaiChina
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Kovacs TGL, Walker J, Hellemans S, Bourguignon T, Tatarnic NJ, McRae JM, Ho SYW, Lo N. Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates. Syst Biol 2024:syae002. [PMID: 38320290 DOI: 10.1093/sysbio/syae002] [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: 01/16/2023] [Indexed: 02/08/2024] Open
Abstract
Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analysed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by phylogenetic analyses of mitochondrial genomes and UCE loci. Furthermore, Bayesian dating analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all thirteen major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ~115 million years ago despite both containing representatives of the genus Nocticola. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.
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Affiliation(s)
- Toby G L Kovacs
- School of Life and Environmental Sciences, University of Sydney, Sydney NSW 2006, Australia
| | - James Walker
- Department of Agriculture, Fisheries and Forestry, Canberra ACT 2601, Australia
| | - Simon Hellemans
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
- Faculty of Tropical AgriScience, Czech University of Life Sciences, Kamýcka 129, 16521 Prague, Czech Republic
| | - Nikolai J Tatarnic
- Collections & Research, Western Australian Museum, 49 Kew Street, Welshpool WA 6106, Australia
- Centre for Evolutionary Biology, The University of Western Australia, Perth WA 6009, Australia
| | - Jane M McRae
- Bennelongia Environmental Consultants, 5 Bishop Street, Jolimont WA 6014, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney NSW 2006, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney NSW 2006, Australia
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Floriano AM, Batisti Biffignandi G, Castelli M, Olivieri E, Clementi E, Comandatore F, Rinaldi L, Opara M, Plantard O, Palomar AM, Noël V, Vijay A, Lo N, Makepeace BL, Duron O, Jex A, Guy L, Sassera D. The evolution of intramitochondriality in Midichloria bacteria. Environ Microbiol 2023; 25:2102-2117. [PMID: 37305924 DOI: 10.1111/1462-2920.16446] [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] [Received: 10/25/2022] [Accepted: 05/31/2023] [Indexed: 06/13/2023]
Abstract
Midichloria spp. are intracellular bacterial symbionts of ticks. Representatives of this genus colonise mitochondria in the cells of their hosts. To shed light on this unique interaction we evaluated the presence of an intramitochondrial localization for three Midichloria in the respective tick host species and generated eight high-quality draft genomes and one closed genome, showing that this trait is non-monophyletic, either due to losses or multiple acquisitions. Comparative genomics supports the first hypothesis, as the genomes of non-mitochondrial symbionts are reduced subsets of those capable of colonising the organelles. We detect genomic signatures of mitochondrial tropism, including the differential presence of type IV secretion system and flagellum, which could allow the secretion of unique effectors and/or direct interaction with mitochondria. Other genes, including adhesion molecules, proteins involved in actin polymerisation, cell wall and outer membrane proteins, are only present in mitochondrial symbionts. The bacteria could use these to manipulate host structures, including mitochondrial membranes, to fuse with the organelles or manipulate the mitochondrial network.
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Affiliation(s)
- Anna Maria Floriano
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, Pavia, Italy
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Gherard Batisti Biffignandi
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Michele Castelli
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, Pavia, Italy
| | - Emanuela Olivieri
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, Pavia, Italy
- Pavia Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Pavia, Italy
| | - Emanuela Clementi
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, Pavia, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center 'Romeo ed Enrica Invernizzi', University of Milan, Milan, Italy
| | - Laura Rinaldi
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, CREMOPAR Regione Campania, Naples, Italy
| | - Maxwell Opara
- Zoonotic Parasites Research Group, Department of Parasitology and Entomology, Faculty of Veterinary Medicine, University of Abuja, Abuja, Nigeria
| | | | - Ana M Palomar
- Center of Rickettsiosis and Arthropod-Borne Diseases (CRETAV), San Pedro University Hospital, Center of Biomedical Research from La Rioja (CIBIR), Logroño, Spain
| | - Valérie Noël
- MIVEGEC (Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle), University of Montpellier (UM), Montpellier, France
| | - Amrita Vijay
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Benjamin L Makepeace
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Olivier Duron
- MIVEGEC (Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle), University of Montpellier (UM), Montpellier, France
| | - Aaron Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Davide Sassera
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, Pavia, Italy
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Lee IHT, Nong W, So WL, Cheung CKH, Xie Y, Baril T, Yip HY, Swale T, Chan SKF, Wei Y, Lo N, Hayward A, Chan TF, Lam HM, Hui JHL. The genome and sex-dependent responses to temperature in the common yellow butterfly, Eurema hecabe. BMC Biol 2023; 21:200. [PMID: 37749565 PMCID: PMC10521528 DOI: 10.1186/s12915-023-01703-1] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Lepidoptera (butterflies and moths) is one of the most geographically widespread insect orders in the world, and its species play important and diverse ecological and applied roles. Climate change is one of the biggest challenges to biodiversity this century, and lepidopterans are vulnerable to climate change. Temperature-dependent gene expression differences are of relevance under the ongoing climate crisis. However, little is known about how climate affects gene expression in lepidopterans and the ecological consequences of this, particularly with respect to genes with biased expression in one of the sexes. The common yellow butterfly, Eurema hecabe (Family Pieridae), is one of the most geographically widespread lepidopterans that can be found in Asia, Africa, and Australia. Nevertheless, what temperature-dependent effects there may be and whether the effects differ between the sexes remain largely unexplored. RESULTS Here, we generated high-quality genomic resources for E. hecabe along with transcriptomes from eight developmental stages. Male and female butterflies were subjected to varying temperatures to assess sex-specific gene expression responses through mRNA and microRNA transcriptomics. We find that there are more temperature-dependent sex-biased genes in females than males, including genes that are involved in a range of biologically important functions, highlighting potential ecological impacts of increased temperatures. Further, by considering available butterfly data on sex-biased gene expression in a comparative genomic framework, we find that the pattern of sex-biased gene expression identified in E. hecabe is highly species-specific, rather than conserved across butterfly species, suggesting that sex-biased gene expression responses to climate change are complex in butterflies. CONCLUSIONS Our study lays the foundation for further understanding of differential responses to environmental stress in a widespread lepidopteran model and demonstrates the potential complexity of sex-specific responses of lepidopterans to climate change.
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Affiliation(s)
- Ivy H T Lee
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Chris K H Cheung
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Yichun Xie
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Simon K F Chan
- Agriculture, Fisheries and Conservation Department, Hong Kong, China
| | - Yingying Wei
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong, China
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Hon-Ming Lam
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China.
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Wang YS, Zhang JW, Lo N, Bourguignon T, Guo L, Li BL, Che YL, Wang ZQ. Phylogenetic analysis of Blaberoidea reveals non-monophyly of taxa and supports the creation of multiple new subfamilies. Cladistics 2023; 39:198-214. [PMID: 37067219 DOI: 10.1111/cla.12535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/18/2023] Open
Abstract
The superfamily Blaberoidea is a highly species-rich group of cockroaches. High-level blaberoidean phylogenetics are still under debate owing to variable taxon sampling and incongruence between mitochondrial and nuclear evolution, as well as different methods used in various phylogenetic studies. We here present a phylogenetic analysis of Blaberoidea based on a dataset combining the mitochondrial genome with two nuclear markers from representatives of all recognized families within the superfamily. Our results support the monophyly of Blaberiodea, which includes Ectobiidae s.s. (=Ectobiinae), Pseudophyllodromiidae, Nyctiboridae, Blattellidae s.s. (=Blattellinae) and Blaberidae. Ectobiidae s.s. was recovered as sister to the remaining Blaberoidea in all inferences. Pseudophyllodromiidae was paraphyletic with respect to Anaplectoidea + Malaccina. Blattellidae s.s. excluding Anaplectoidea + Malaccina formed a monophyletic group that was sister to Blaberidae. Based on our results, we propose a revised classification for Blaberoidea: Anaplectoidinae subfam.nov. and Episorineuchora gen.nov., and two new combinations at species level within Pseudophyllodromiidae; Rhabdoblattellinae subfam.nov., Calolamprodinae subfam.nov., Acutirhabdoblatta gen.nov., as well as new combinations for three species within Blaberidae. Ancestral state reconstructions based on four morphological characters allow us to infer that the common ancestor of blaberoid cockroaches is likely to be a species with characteristics similar to those found in Ectobiidae, that is, front femur Type B, arolium present, abdomen with a visible gland and male genital hook on the left side.
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Affiliation(s)
- Yi-Shu Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing, 400715, China
| | - Jia-Wei Zhang
- College of Plant Protection, Southwest University, Beibei, Chongqing, 400715, China
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology Graduate University, Onna-son, 904-0495, Japan
| | - Lin Guo
- College of Plant Protection, Southwest University, Beibei, Chongqing, 400715, China
| | - Bian-Lun Li
- College of Plant Protection, Southwest University, Beibei, Chongqing, 400715, China
| | - Yan-Li Che
- College of Plant Protection, Southwest University, Beibei, Chongqing, 400715, China
| | - Zong-Qing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing, 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Beibei, Chongqing, 400715, China
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Noda S, Kitade O, Jasso-Selles DE, Taerum SJ, Takayanagi M, Radek R, Lo N, Ohkuma M, Gile GH. Molecular phylogeny of Spirotrichonymphea (Parabasalia) with emphasis on Spironympha, Spirotrichonympha, and three new genera Pseudospironympha, Nanospironympha, and Brugerollina. J Eukaryot Microbiol 2023; 70:e12967. [PMID: 36760170 DOI: 10.1111/jeu.12967] [Citation(s) in RCA: 2] [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: 09/10/2022] [Revised: 12/03/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
Spirotrichonymphea, one of the six classes of phylum Parabasalia, are characterized by bearing many flagella in spiral rows, and they occur exclusively in the guts of termites. Phylogenetic relationships among the 13 described genera are not well understood due to complex morphological evolution and a paucity of molecular data. One such understudied genus is Spironympha. It has been variously considered a valid genus, a subgenus of Spirotrichonympha, or an "immature" life cycle stage of Spirotrichonympha. To clarify this, we sequenced the small subunit rRNA gene sequences of Spironympha and Spirotrichonympha cells isolated from the hindguts of Reticulitermes species and Hodotermopsis sjostedti and confirmed the molecular identity of H. sjostedti symbionts using fluorescence in situ hybridization. Spironympha as currently circumscribed is polyphyletic, with both H. sjostedti symbiont species branching separately from the "true" Spironympha from Reticulitermes. Similarly, the Spirotrichonympha symbiont of H. sjostedti branches separately from the "true" Spirotrichonympha found in Reticulitermes. Our data support Spironympha from Reticulitermes as a valid genus most closely related to Spirotrichonympha, though its monophyly and interspecific relationships are not resolved in our molecular phylogenetic analysis. We propose three new genera to accommodate the H. sjostedti symbionts and two new species of Spirotrichonympha from Reticulitermes.
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Affiliation(s)
- Satoko Noda
- Graduate School of Science and Engineering, Ibaraki University, Mito, Japan.,Graduate School of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
| | - Osamu Kitade
- Graduate School of Science and Engineering, Ibaraki University, Mito, Japan
| | | | - Stephen J Taerum
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Miki Takayanagi
- Graduate School of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
| | - Renate Radek
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki, Japan
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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Van Der Wal C, Ahyong ST, Adams MWD, Ewart KM, Ho SYW, Lo N. Genomic analysis reveals strong population structure in the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Mol Phylogenet Evol 2023; 178:107629. [PMID: 36191898 DOI: 10.1016/j.ympev.2022.107629] [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: 03/24/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Australia is home to over 140 species of freshwater crayfish (Decapoda: Parastacidae), representing a centre of diversity for this group in the Southern Hemisphere. Species delimitation in freshwater crayfish is difficult because many species show significant variation in colouration and morphology. This is particularly evident in the genus Euastacus, which exhibits large variations in colour and spination throughout its putative range. To understand this variation, we investigated the genetic diversity, population structure, phylogeny, and evolutionary timescale of the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Our data set is sampled from over 70 individuals from across the ∼600 km range of the species, and includes a combination of two mitochondrial markers and more than 7000 single-nucleotide polymorphisms (SNPs) from the nuclear genome. Data were also obtained for representatives of the close relative, Euastacus vesper McCormack and Ahyong, 2017. Genomic SNP analyses revealed strong population structure, with multiple distinct populations showing little evidence of gene flow or migration. Phylogenetic analyses of mitochondrial data revealed similar structure between populations. Taken together, our analyses suggest that E. spinifer, as currently understood, represents a species complex, of which E. vesper is a member. Molecular clock estimates place the divergences within this group during the Pleistocene. The isolated and highly fragmented populations identified in our analyses probably represent relict populations of a previously widespread ancestral species. Periodic flooding events during the Pleistocene are likely to have facilitated the movement of these otherwise restricted freshwater crayfish within and between drainage basins, including the Murray-Darling and South East Coast Drainages. We present evidence supporting the recognition of populations in the southern parts of the range of E. spinifer as one or two separate species, which would raise the number of species within the E. spinifer complex to at least three. Our results add to the growing body of evidence that many freshwater crayfish exhibit highly fragmented, range-restricted distributions. In combination with the life-history traits of these species, the restricted distributions exacerbate the threats already placed on freshwater crayfish, which are among the five most endangered animal groups globally.
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Affiliation(s)
- Cara Van Der Wal
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia.
| | - Shane T Ahyong
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia; School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Maxim W D Adams
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Kyle M Ewart
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
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Jones BR, Brock PD, Mantovani B, Beasley-Hall P, Yeates DK, Lo N. Integrative taxonomy of the stick insect genus. INVERTEBR SYST 2022. [DOI: 10.1071/is21076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Austrocarausius Brock, 2000 is a stick insect (Phasmatodea: Lonchodidae) genus containing two species restricted to the tropical rainforests of northern Queensland. Recent specimen collections between the two species’ type localities, Lizard Island and Rockhampton, have suggested that Austrocarausius might represent more than the two nominal species. Here, we apply morphological and molecular analyses to revise the taxonomy of this genus. Using both field-collected and historic museum samples, we developed morphological species hypotheses and descriptions. Genetic sequencing of mitochondrial COI and 16S were undertaken for species delimitation and phylogenetic analysis, including an estimate of the evolutionary timescale of the genus. Based on these results, we propose nine new Austrocarausius species, increasing the number of species in the genus to eleven: A. nigropunctatus (Kirby, 1896), A. mercurius (Stål, 1877), A. coronatus sp. nov., A. decorus sp. nov., A. eirmosus sp. nov., A. gasterbulla sp. nov., A. tuberosus sp. nov., A. macropunctatus sp. nov., A. truncatus sp. nov. A. waiben sp. nov. and A. walkeri sp. nov. Our results suggest Austrocarausius species diversified over the last c. 25–70 Ma, resulting in the now endemic distributions in the tropical rainforests of the central and northern Queensland coasts. This is the first integrative systematic study of an Australian phasmid genus, combining morphological, molecular and biogeographical methods. Additional species of Austrocarausius likely remain undescribed as can be inferred from methodical sampling of rainforest patches along the Queensland coast.
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Khaleeq T, Lo N, King J, Turner A, Howland E, Graham T. 656 Making an Effective Ward Round Model in the Department of Trauma and Orthopaedic Surgery for University Hospitals of Birmingham Trust. Br J Surg 2022. [DOI: 10.1093/bjs/znac269.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background
Ward rounds in hospitals are crucial for decision-making in the context of patient treatment processes.
Objectives
Improve the standard of ward rounds with a review of care and planning.
Method
6 key elements were established using the Modern ward rounds report by the Royal College of Physicians and Nursing. This includes daily ward rounds which will be multidisciplinary, documented clearly and handed over to relevant staff; consisting of a board, bedside ward round and debrief; using Prompts in the form of REMIND mnemonic : R = Respect form, E = Electronic Prescribing, M = Mental Capacity, mobility status, I = Investigations, N = Nutrition and Hydration, NBM status, D=DVT assessment and Thromboprophylaxis; with practices being audited.
Results
After running a successful pilot in Respiratory in August 2021 the quality improvement project (QIP) was introduced in Trauma and Orthopaedic surgery.
88 patients were included in the initial audit prior to implementation and 91 in the re-audit. There was a 85% improvement seen in completion of respect and dementia forms with a 90% improvement in electronic prescribing. There was an 75% improvement in documentation of mobility status, investigations performed and NBM status. Fluid prescription, DVT assessment and LMWH prescription also improved by 85%.
Conclusions
A successful Pilot in Respiratory and Trauma and Orthopaedic Surgery shows the feasibility of the QIP in other departments. However, Education should also include Consultant and nurses. We are overcoming this but establishing a virtual module that can be made mandatory for induction of junior doctors, consultants, and nurses.
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Affiliation(s)
- T Khaleeq
- Queen Elizabeth Hospital , Birmingham , United Kingdom
| | - N Lo
- Queen Elizabeth Hospital , Birmingham , United Kingdom
| | - J King
- Queen Elizabeth Hospital , Birmingham , United Kingdom
| | - A Turner
- Queen Elizabeth Hospital , Birmingham , United Kingdom
| | - E Howland
- Queen Elizabeth hospital , Birmingham , United Kingdom
| | - T Graham
- Queen Elizabeth Hospital , Birmingham , United Kingdom
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11
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Arora J, Kinjo Y, Šobotník J, Buček A, Clitheroe C, Stiblik P, Roisin Y, Žifčáková L, Park YC, Kim KY, Sillam-Dussès D, Hervé V, Lo N, Tokuda G, Brune A, Bourguignon T. The functional evolution of termite gut microbiota. Microbiome 2022; 10:78. [PMID: 35624491 PMCID: PMC9137090 DOI: 10.1186/s40168-022-01258-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/16/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species but remains largely unknown in other taxa. We intend to fill this gap and provide a global understanding of the functional evolution of termite gut microbiota. RESULTS We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that essential nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways. CONCLUSIONS Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared ~ 150 million years ago. Therefore, the "world's smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception. Video Abstract.
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Affiliation(s)
- Jigyasa Arora
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.
| | - Yukihiro Kinjo
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Aleš Buček
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Crystal Clitheroe
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Petr Stiblik
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Yves Roisin
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Lucia Žifčáková
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Yung Chul Park
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Ki Yoon Kim
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - David Sillam-Dussès
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
- University Sorbonne Paris Nord, Laboratory of Experimental and Comparative Ethology, LEEC, UR 4443, Villetaneuse, France
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Gaku Tokuda
- Tropical Biosphere Research Center, Center of Molecular Biosciences, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic.
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12
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Maekawa K, Hayashi Y, Lo N. Termite sociogenomics: evolution and regulation of caste-specific expressed genes. Curr Opin Insect Sci 2022; 50:100880. [PMID: 35123120 DOI: 10.1016/j.cois.2022.100880] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/12/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Termite genomes have been sequenced in at least five species from four different families. Genome-based transcriptome analyses have identified large numbers of protein-coding genes with caste-specific expression patterns. These genes include those involved in caste-specific morphologies and roles, for example high fecundity and longevity in reproductives. Some caste-specific expressed genes belong to multi-gene families, and their genetic architecture and expression profiles indicate they have evolved via tandem gene duplication. Candidate regulatory mechanisms of caste-specific expression include epigenetic regulation (e.g. histone modification and non-coding RNA) and diversification of transcription factors and cis-regulatory elements. We review current knowledge in the area of termite sociogenomics, focussing on the evolution and regulation of caste-specific expressed genes, and discuss future research directions.
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Affiliation(s)
- Kiyoto Maekawa
- Faculty of Science, Academic Assembly, University of Toyama, Toyama, Japan
| | - Yoshinobu Hayashi
- Department of Biology, Keio University, Hiyoshi, Yokohama 223-8521, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, NSW, Australia
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13
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Lo N, Khan M, Sadia U, Jaipersad A. 354 Virtual Consultation in Vascular Practice: The New Normal. Br J Surg 2022. [DOI: 10.1093/bjs/znac039.238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Aim
Face to face vascular clinics were suspended at a major trauma centre at the beginning of the COVID-19 pandemic, however Royal Stoke Hospital Vascular team were still undertaking emergency vascular operations. Consequently, virtual telephone consultations were set up and delivered to facilitate post-operative follow ups. The objective of this improvement study is to compare the virtual clinic documentation against The Royal College of Surgeons of England (RCS Eng) Best Practice Guidance on Conducting Virtual Consultations, which was published in June 2020. This is important as good documentation is vital to patient care as well as being a medico-legal document.
Method
We retrospectively identified 30 vascular patients operated between May 2021 and June 2021; 10 of which had had a virtual telephone clinic and the majority underwent an amputation. We audited the clinic note documentation against the RCS Eng guidelines.
Results
Total of 9 RCS Eng guidelines were identified and audited. The first cycle revealed poor areas in documentation of the surgeon introducing themselves, confirmation of patient details, obtaining consent to proceed, summary of consult and plan discussed.
Findings were presented at the trust governance meeting. Areas which required improvement in documentation were highlighted. In addition to education of surgeons, it was decided to introduce a checklist as a requirement.
Conclusions
Clinic note documentation is of paramount importance as it has legal and medical ramifications. The education of surgeons and introduction of a checklist to ensure compliance with RCS Eng guidelines and we will re-audit to ensure improvement.
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Affiliation(s)
- N. Lo
- University Hospitals of North Midlands NHS Trust, Stoke- On-Trent, United Kingdom
| | - M. Khan
- University Hospitals of North Midlands NHS Trust, Stoke- On-Trent, United Kingdom
| | - U. Sadia
- University Hospitals of North Midlands NHS Trust, Stoke- On-Trent, United Kingdom
| | - A. Jaipersad
- University Hospitals of North Midlands NHS Trust, Stoke- On-Trent, United Kingdom
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Yashiro T, Tea YK, Van Der Wal C, Nozaki T, Mizumoto N, Hellemans S, Matsuura K, Lo N. Enhanced heterozygosity from male meiotic chromosome chains is superseded by hybrid female asexuality in termites. Proc Natl Acad Sci U S A 2021; 118:e2009533118. [PMID: 34903643 PMCID: PMC8713478 DOI: 10.1073/pnas.2009533118] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 11/18/2022] Open
Abstract
Although males are a ubiquitous feature of animals, they have been lost repeatedly in diverse lineages. The tendency for obligate asexuality to evolve is thought to be reduced in animals whose males play a critical role beyond the contribution of gametes, for example, via care of offspring or provision of nuptial gifts. To our knowledge, the evolution of obligate asexuality in such species is unknown. In some species that undergo frequent inbreeding, males are hypothesized to play a key role in maintaining genetic heterozygosity through the possession of neo-sex chromosomes, although empirical evidence for this is lacking. Because inbreeding is a key feature of the life cycle of termites, we investigated the potential role of males in promoting heterozygosity within populations through karyotyping and genome-wide single-nucleotide polymorphism analyses of the drywood termite Glyptotermes nakajimai We showed that males possess up to 15 out of 17 of their chromosomes as sex-linked (sex and neo-sex) chromosomes and that they maintain significantly higher levels of heterozygosity than do females. Furthermore, we showed that two obligately asexual lineages of this species-representing the only known all-female termite populations-arose independently via intraspecific hybridization between sexual lineages with differing diploid chromosome numbers. Importantly, these asexual females have markedly higher heterozygosity than their conspecific males and appear to have replaced the sexual lineages in some populations. Our results indicate that asexuality has enabled females to supplant a key role of males.
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Affiliation(s)
- Toshihisa Yashiro
- School of Life and Environmental Sciences, University of Sydney, Sydney NSW 2006, Australia;
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, Sydney NSW 2006, Australia
- Ichthyology, Australian Museum Research Institute, Sydney, NSW 2010, Australia
| | - Cara Van Der Wal
- School of Life and Environmental Sciences, University of Sydney, Sydney NSW 2006, Australia
| | - Tomonari Nozaki
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Nobuaki Mizumoto
- Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son 904-0495, Japan
| | - Simon Hellemans
- Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son 904-0495, Japan
| | - Kenji Matsuura
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney NSW 2006, Australia;
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15
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Che Y, Deng W, Li W, Zhang J, Kinjo Y, Tokuda G, Bourguignon T, Lo N, Wang Z. Vicariance and dispersal events inferred from mitochondrial genomes and nuclear genes (18S, 28S) shaped global Cryptocercus distributions. Mol Phylogenet Evol 2021; 166:107318. [PMID: 34562575 DOI: 10.1016/j.ympev.2021.107318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/02/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022]
Abstract
Cryptocercus Scudder, a genus of wingless, subsocial cockroaches, has low vagility but exhibits a disjunct distribution in eastern and western North America, and in China, South Korea and the Russian Far East. This distribution provides an ideal model for testing hypotheses of vicariance through plate tectonics or other natural barriers versus dispersal across oceans or other natural barriers. We sequenced 45 samples of Cryptocercus to resolve phylogenetic relationships among members of the genus worldwide. We identified four types of tRNA rearrangements among samples from the Qin-Daba Mountains. Our maximum-likelihood and Bayesian phylogenetic trees, based on mitochondrial genomes and nuclear genes (18S, 28S), strongly supported six major lineages of Cryptocercus, which displayed a clear geographical distribution pattern. We used Bayesian molecular dating to estimate the evolutionary timescale of the genus, and reconstructed Cryptocercus ancestral ranges using statistical dispersal-vicariance analysis (S-DIVA) in RASP. Two dispersal events and six vicariance events for Cryptocercus were inferred with high support. The initial vicariance event occurred between American and Asian lineages at 80.5 Ma (95% credibility interval: 60.0-104.7 Ma), followed by one vicariance event within the American lineage 43.8 Ma (95% CI: 32.0-57.5 Ma), and two dispersal 31.9 Ma (95% CI: 25.8-39.5 Ma), 21.7 Ma (95% CI: 17.3-27.1 Ma) plus four vicariance events c. 29.3 Ma, 27.2 Ma, 24.8 Ma and 16.7 Ma within the Asian lineage. Our analyses provide evidence that both vicariance and dispersal have played important roles in shaping the distribution and diversity of these woodroaches.
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Affiliation(s)
- Yanli Che
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China
| | - Wenbo Deng
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China
| | - Weijun Li
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China
| | - Jiawei Zhang
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China
| | - Yukihiro Kinjo
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Gaku Tokuda
- Tropical Biosphere Research Center, Center of Molecular Biosciences, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan; Faculty of Tropical AgriSciences, Czech University of Life Sciences, Kamycka 129, Prague CZ-165 00, Czech Republic
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China.
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16
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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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17
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Kinjo Y, Lo N, Martín PV, Tokuda G, Pigolotti S, Bourguignon T. Enhanced Mutation Rate, Relaxed Selection, and the "Domino Effect" are associated with Gene Loss in Blattabacterium, A Cockroach Endosymbiont. Mol Biol Evol 2021; 38:3820-3831. [PMID: 34426845 PMCID: PMC8382890 DOI: 10.1093/molbev/msab159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Indexed: 12/17/2022] Open
Abstract
Intracellular endosymbionts have reduced genomes that progressively lose genes at a timescale of tens of million years. We previously reported that gene loss rate is linked to mutation rate in Blattabacterium, however, the mechanisms causing gene loss are not yet fully understood. Here, we carried out comparative genomic analyses on the complete genome sequences of a representative set of 67 Blattabacterium strains, with sizes ranging between 511 and 645 kb. We found that 200 of the 566 analyzed protein-coding genes were lost in at least one lineage of Blattabacterium, with the most extreme case being one gene that was lost independently in 24 lineages. We found evidence for three mechanisms influencing gene loss in Blattabacterium. First, gene loss rates were found to increase exponentially with the accumulation of substitutions. Second, genes involved in vitamin and amino acid metabolism experienced relaxed selection in Cryptocercus and Mastotermes, possibly triggered by their vertically inherited gut symbionts. Third, we found evidence of epistatic interactions among genes leading to a "domino effect" of gene loss within pathways. Our results highlight the complexity of the process of genome erosion in an endosymbiont.
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Affiliation(s)
- Yukihiro Kinjo
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Paula Villa Martín
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Gaku Tokuda
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Simone Pigolotti
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
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18
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Arab DA, Lo N. Evolutionary Rates are Correlated Between Buchnera Endosymbionts and the Mitochondrial Genomes of Their Aphid Hosts. J Mol Evol 2021; 89:238-248. [PMID: 33730185 DOI: 10.1007/s00239-021-10001-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/20/2021] [Indexed: 10/21/2022]
Abstract
The evolution of bacterial endosymbiont genomes is strongly influenced by host-driven selection. Factors affecting host genome evolution will potentially affect endosymbiont genomes in similar ways. One potential outcome is correlations in molecular rates between the genomes of the symbiotic partners. Recently, we presented the first evidence of such correlations between the mitochondrial genomes of cockroaches and the genomes of their endosymbiont (Blattabacterium cuenoti). Here we investigate whether similar patterns are found in additional host-symbiont partners. We use partial genome data from multiple strains of the bacterial endosymbionts Buchnera aphidicola and Sulcia muelleri, and the mitochondrial genomes of their sap-feeding insect hosts. Both endosymbionts show phylogenetic congruence with the mitochondria of their hosts, a result that is expected due to their identical mode of inheritance. We compared root-to-tip distances and branch lengths of phylogenetically independent species pairs. Both analyses showed a highly significant correlation of molecular rates between the genomes of Buchnera and the mitochondrial genomes of their hosts. A similar correlation was detected between Sulcia and their hosts, but was not statistically significant. Our results indicate that evolutionary rate correlations between hosts and long-term symbionts may be a widespread phenomenon.
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Affiliation(s)
- Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
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19
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Tea YK, Xu X, DiBattista JD, Lo N, Cowman PF, Ho SYW. Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus). Syst Biol 2021; 71:1-12. [PMID: 33620490 DOI: 10.1093/sysbio/syab012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 05/29/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 01/22/2023] Open
Abstract
The fairy wrasses (genus Cirrhilabrus) are among the most successful of the extant wrasse lineages (Teleostei: Labridae), with their 61 species accounting for nearly 10% of the family. Although species complexes within the genus have been diagnosed on the basis of coloration patterns and synapomorphies, attempts to resolve evolutionary relationships among these groups using molecular and morphological data have largely been unsuccessful. Here we use a phylogenomic approach with a data set comprising 991 ultraconserved elements (UCEs) and mitochondrial COI to uncover the evolutionary history and patterns of temporal and spatial diversification of the fairy wrasses. Our analyses of phylogenetic signal suggest that most gene-tree incongruence is caused by estimation error, leading to poor resolution in a summary-coalescent analysis of the data. In contrast, analyses of concatenated sequences are able to resolve the major relationships of Cirrhilabrus. We determine the placements of species that were previously regarded as incertae sedis and find evidence for the nesting of Conniella, an unusual, monotypic genus, within Cirrhilabrus. Our relaxed-clock dating analysis indicates that the major divergences within the genus occurred around the Miocene-Pliocene boundary, followed by extensive cladogenesis of species complexes in the Pliocene-Pleistocene. Biogeographic reconstruction suggests that the fairy wrasses emerged within the Coral Triangle, with episodic fluctuations of sea levels during glacial cycles coinciding with shallow divergence events but providing few opportunities for more widespread dispersal. Our study demonstrates both the resolving power and limitations of UCEs across shallow timescales where there is substantial estimation error in individual gene trees.
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Affiliation(s)
- Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia.,Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, New South Wales 2010, Australia
| | - Xin Xu
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia.,College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Joseph D DiBattista
- Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, New South Wales 2010, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia
| | - Peter F Cowman
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, Queensland 4810, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia
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Abstract
Abstract
The pink cockatoo (Lophochroa leadbeateri; or Major Mitchell’s cockatoo) is one of Australia’s most iconic bird species. Two subspecies based on morphology are separated by a biogeographical divide, the Eyrean Barrier. Testing the genetic basis for this subspecies delineation, clarifying barriers to gene flow and identifying any cryptic genetic diversity will likely have important implications for conservation and management. Here, we used genome-wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA data to conduct the first range-wide genetic assessment of the species. The aims were to investigate the phylogeography of the pink cockatoo, to characterize conservation units and to reassess subspecies boundaries. We found consistent but weak genetic structure between the two subspecies based on nuclear SNPs. However, phylogenetic analysis of nuclear SNPs and mitochondrial DNA sequence data did not recover reciprocally monophyletic groups, indicating incomplete evolutionary separation between the subspecies. Consequently, we have proposed that the two currently recognized subspecies be treated as separate management units rather than evolutionarily significant units. Given that poaching is suspected to be a threat to this species, we assessed the utility of our data for wildlife forensic applications. We demonstrated that a subspecies identification test could be designed using as few as 20 SNPs.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rebecca N Johnson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, ACT, Australia
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Greta J Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
- Centre for Forensic Science, University of Technology Sydney, Broadway, NSW, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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Seymour M, Brown N, Carvalho GR, Wood C, Goertz S, Lo N, de Bruyn M. Ecological community dynamics: 20 years of moth sampling reveals the importance of generalists for community stability. Basic Appl Ecol 2020. [DOI: 10.1016/j.baae.2020.11.002] [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] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Větrovský T, Soukup P, Stiblik P, Votýpková K, Chakraborty A, Larrañaga IO, Sillam-Dussès D, Lo N, Bourguignon T, Baldrian P, Šobotník J, Kolařík M. Termites host specific fungal communities that differ from those in their ambient environments. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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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Lay CL, Shi M, Buček A, Bourguignon T, Lo N, Holmes EC. Unmapped RNA Virus Diversity in Termites and their Symbionts. Viruses 2020; 12:v12101145. [PMID: 33050289 PMCID: PMC7650761 DOI: 10.3390/v12101145] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Despite their ecological importance, nothing is known about the diversity and abundance of RNA viruses in termites (Termitoidae). We used a metatranscriptomics approach to determine the RNA virome structure of 50 diverse species of termite that differ in both phylogenetic position and colony composition. From these samples, we identified 67 novel RNA viruses, characterized their genomes, quantified their abundance and inferred their evolutionary history. These viruses were found within or similar to those from the Togaviridae, Iflaviridae, Polycipiviridae, Flaviviridae, Leviviridae, Narnaviridae, Mitoviridae, Lispivirdae, Phasmaviridae, Picobirnaviridae and Partitiviridae. However, all viruses identified were novel and divergent, exhibiting only 20% to 45% amino acid identity to previously identified viruses. Our analysis suggested that 17 of the viruses identified were termite-infecting, with the remainder likely associated with the termite microbiome or diet. Unclassified sobemo-like and bunya-like viruses dominated termite viromes, while most of the phylogenetic diversity was provided by the picobirna- and mitovirus-like viruses. Of note was the identification of a novel flavi-like virus most closely related to those found in marine vertebrates and invertebrates. Notably, the sampling procedure had the strongest association with virome composition, with greater RNA virome diversity in libraries prepared from whole termite bodies than those that only sampled heads.
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Affiliation(s)
- Callum Le Lay
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, New South Wales, Australia; (C.L.L.); (M.S.)
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
- School of Medical Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, New South Wales, Australia; (C.L.L.); (M.S.)
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
- School of Medical Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia
| | - Aleš Buček
- Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa 904-0495, Japan; (A.B.); (T.B.)
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa 904-0495, Japan; (A.B.); (T.B.)
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, New South Wales, Australia; (C.L.L.); (M.S.)
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
- School of Medical Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia
- Correspondence:
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Bourguignon T, Kinjo Y, Villa-Martín P, Coleman NV, Tang Q, Arab DA, Wang Z, Tokuda G, Hongoh Y, Ohkuma M, Ho SY, Pigolotti S, Lo N. Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes. Curr Biol 2020; 30:3848-3855.e4. [DOI: 10.1016/j.cub.2020.07.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/27/2020] [Accepted: 07/09/2020] [Indexed: 01/08/2023]
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Tea YK, Hobbs JPA, Vitelli F, DiBattista JD, Ho SYW, Lo N. Angels in disguise: sympatric hybridization in the marine angelfishes is widespread and occurs between deeply divergent lineages. Proc Biol Sci 2020; 287:20201459. [PMID: 32752983 DOI: 10.1098/rspb.2020.1459] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hybridization events are not uncommon in marine environments where physical barriers are attenuated. Studies of coral reef taxa have suggested that hybridization predominantly occurs between parapatric species distributed along biogeographic suture zones. By contrast, little is known about the extent of sympatric hybridization on coral reefs, despite the large amount of biogeographic overlap shared by many coral reef species. Here, we investigate if the propensity for hybridization along suture zones represents a general phenomenon among coral reef fishes, by focusing on the marine angelfishes (family Pomacanthidae). Although hybridization has been reported for this family, it has not been thoroughly surveyed, with more recent hybridization studies focusing instead on closely related species from a population genetics perspective. We provide a comprehensive survey of hybridization among the Pomacanthidae, characterize the upper limits of genetic divergences between hybridizing species and investigate the occurrence of sympatric hybridization within this group. We report the occurrence of hybridization involving 42 species (48% of the family) from all but one genus of the Pomacanthidae. Our results indicate that the marine angelfishes are among the groups of coral reef fishes with the highest incidences of hybridization, not only between sympatric species, but also between deeply divergent lineages.
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Affiliation(s)
- Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.,Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, New South Wales 2010, Australia
| | - Jean-Paul A Hobbs
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4069, Australia
| | - Federico Vitelli
- Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia 6027, Australia
| | - Joseph D DiBattista
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, New South Wales 2010, Australia.,School of Molecular and Life Sciences, Curtin University, Perth, Western Australia 6102, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
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Che Y, Wang D, Shi Y, Du X, Zhao Y, Lo N, Wang Z. Corrigendum to "A global molecular phylogeny and timescale of evolution for Cryptocercus woodroaches" [Mol. Phylogenet. Evol. 98 (2016) 201-209]. Mol Phylogenet Evol 2020; 152:106907. [PMID: 32777437 DOI: 10.1016/j.ympev.2020.106907] [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: 10/23/2022]
Affiliation(s)
- Yanli Che
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China; School of Life and Environment Sciences, University of Sydney, Sydney, NSW, Australia
| | - Dong Wang
- Chongqing International Travel Healthcare Center, Jiangbei, Chongqing 400020, PR China
| | - Yan Shi
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China
| | - Xiaohong Du
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China
| | - Yongquan Zhao
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China
| | - Nathan Lo
- School of Life and Environment Sciences, University of Sydney, Sydney, NSW, Australia
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China.
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27
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Taylor CL, Lydecker HW, Lo N, Hochuli DF, Banks PB. Invasive rabbits host immature Ixodes ticks at the urban-forest interface. Ticks Tick Borne Dis 2020; 11:101439. [PMID: 32295737 DOI: 10.1016/j.ttbdis.2020.101439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 11/08/2019] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 10/24/2022]
Abstract
Introduced wildlife may be important alternative hosts for generalist ticks that cause health issues for humans and companion animals in urban areas, but to date are rarely considered as part of the tick-host community compared to native wildlife. In Australia, European rabbits, Oryctolagus cuniculus, are a widespread and abundant invasive species common to a range of human-modified ecosystems. To understand the potential role of rabbits in the life cycle of Australian ticks, we investigated the seasonal abundance of all tick life stages (larva, nymph, and adult) on rabbits collected from pest control programs in two urban forest remnants in Sydney, Australia. We also recorded whether larvae, nymphs, and adults were attached to the head, body, or limbs of rabbits to reveal patterns of tick attachment. Of the 2426 Ixodes ticks collected from 42 rabbits, larvae were by far the most abundant life stage (2360), peaking in abundance in autumn, while small numbers of nymphs (62) and adults (4) were present in winter and summer respectively. Larvae were found all over the body, whereas adults and nymphs were predominantly attached to the head, suggesting that the mature life stages use the host landscape differently, or that adults or nymphs may be groomed off the body. The most abundant tick species, as determined by morphology and DNA sequencing, was Ixodes holocyclus, a generalist tick responsible for significant human and companion animal health concerns in Australia. Our findings highlight the importance of understanding the role of introduced wildlife in tick dynamics particularly in novel ecosystems where non-native hosts may be more abundant than native hosts.
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Affiliation(s)
- Casey L Taylor
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia.
| | - Henry W Lydecker
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia; Marie Bashir Institute for Infectious Disease and Biosecurity, The University of Sydney, Camperdown, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia
| | - Dieter F Hochuli
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia
| | - Peter B Banks
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia
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Hubbard NA, Siless V, Frosch IR, Goncalves M, Lo N, Wang J, Bauer CCC, Conroy K, Cosby E, Hay A, Jones R, Pinaire M, Vaz De Souza F, Vergara G, Ghosh S, Henin A, Hirshfeld-Becker DR, Hofmann SG, Rosso IM, Auerbach RP, Pizzagalli DA, Yendiki A, Gabrieli JDE, Whitfield-Gabrieli S. Brain function and clinical characterization in the Boston adolescent neuroimaging of depression and anxiety study. Neuroimage Clin 2020; 27:102240. [PMID: 32361633 PMCID: PMC7199015 DOI: 10.1016/j.nicl.2020.102240] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/28/2022]
Abstract
We present a Human Connectome Project study tailored toward adolescent anxiety and depression. This study is one of the first studies of the Connectomes Related to Human Diseases initiative and is collecting structural, functional, and diffusion-weighted brain imaging data from up to 225 adolescents (ages 14-17 years), 150 of whom are expected to have a current diagnosis of an anxiety and/or depressive disorder. Comprehensive clinical and neuropsychological evaluations and longitudinal clinical data are also being collected. This article provides an overview of task functional magnetic resonance imaging (fMRI) protocols and preliminary findings (N = 140), as well as clinical and neuropsychological characterization of adolescents. Data collection is ongoing for an additional 85 adolescents, most of whom are expected to have a diagnosis of an anxiety and/or depressive disorder. Data from the first 140 adolescents are projected for public release through the National Institutes of Health Data Archive (NDA) with the timing of this manuscript. All other data will be made publicly-available through the NDA at regularly scheduled intervals. This article is intended to serve as an introduction to this project as well as a reference for those seeking to clinical, neurocognitive, and task fMRI data from this public resource.
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Affiliation(s)
- N A Hubbard
- Massachusetts Institute of Technology, Cambridge, MA, United States; University of Nebraska-Lincoln, Lincoln, NE, United States
| | - V Siless
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - I R Frosch
- Massachusetts Institute of Technology, Cambridge, MA, United States
| | - M Goncalves
- Massachusetts Institute of Technology, Cambridge, MA, United States
| | - N Lo
- Massachusetts Institute of Technology, Cambridge, MA, United States
| | - J Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - C C C Bauer
- Massachusetts Institute of Technology, Cambridge, MA, United States
| | - K Conroy
- Boston University, Boston, MA, United States
| | - E Cosby
- Harvard Medical School, Boston, MA, United States; McLean Hospital, Belmont, MA, United States
| | - A Hay
- Boston University, Boston, MA, United States
| | - R Jones
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - M Pinaire
- Boston University, Boston, MA, United States
| | - F Vaz De Souza
- Harvard Medical School, Boston, MA, United States; Massachusetts General Hospital, Boston, MA, United States
| | - G Vergara
- Harvard Medical School, Boston, MA, United States; McLean Hospital, Belmont, MA, United States
| | - S Ghosh
- Massachusetts Institute of Technology, Cambridge, MA, United States; Harvard Medical School, Boston, MA, United States
| | - A Henin
- Harvard Medical School, Boston, MA, United States; Massachusetts General Hospital, Boston, MA, United States
| | - D R Hirshfeld-Becker
- Harvard Medical School, Boston, MA, United States; Massachusetts General Hospital, Boston, MA, United States
| | - S G Hofmann
- Boston University, Boston, MA, United States
| | - I M Rosso
- Harvard Medical School, Boston, MA, United States; McLean Hospital, Belmont, MA, United States
| | - R P Auerbach
- Columbia University, New York, NY, United States
| | - D A Pizzagalli
- Harvard Medical School, Boston, MA, United States; McLean Hospital, Belmont, MA, United States
| | - A Yendiki
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - J D E Gabrieli
- Massachusetts Institute of Technology, Cambridge, MA, United States
| | - S Whitfield-Gabrieli
- Massachusetts Institute of Technology, Cambridge, MA, United States; Northeastern University, Boston, MA, United States.
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Abstract
Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigations of hosts and symbionts are lacking. Here, we demonstrate a correlation in molecular rates between the genomes of an endosymbiont (Blattabacterium cuenoti) and the mitochondrial genomes of their hosts (cockroaches). We used partial genome data for multiple strains of B. cuenoti to compare phylogenetic relationships and evolutionary rates for 55 cockroach/symbiont pairs. The phylogenies inferred for B. cuenoti and the mitochondrial genomes of their hosts were largely congruent, as expected from their identical maternal and cytoplasmic mode of inheritance. We found a correlation between evolutionary rates of the two genomes, based on comparisons of root-to-tip distances and on comparisons of the branch lengths of phylogenetically independent species pairs. Our results underscore the profound effects that long-term symbiosis can have on the biology of each symbiotic partner.
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Affiliation(s)
- Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Thomas Bourguignon
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.,Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa, Japan.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Chongqing, People's Republic of China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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Bucek A, Šobotník J, He S, Shi M, McMahon DP, Holmes EC, Roisin Y, Lo N, Bourguignon T. Evolution of Termite Symbiosis Informed by Transcriptome-Based Phylogenies. Curr Biol 2019; 29:3728-3734.e4. [PMID: 31630948 DOI: 10.1016/j.cub.2019.08.076] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [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: 05/01/2019] [Revised: 07/11/2019] [Accepted: 08/30/2019] [Indexed: 10/25/2022]
Abstract
Termitidae comprises ∼80% of all termite species [1] that play dominant decomposer roles in tropical ecosystems [2, 3]. Two major events during termite evolution were the loss of cellulolytic gut protozoans in the ancestor of Termitidae and the subsequent gain in the termitid subfamily Macrotermitinae of fungal symbionts cultivated externally in "combs" constructed within the nest [4, 5]. How these symbiotic transitions occurred remains unresolved. Phylogenetic analyses of mitochondrial data previously suggested that Macrotermitinae is the earliest branching termitid lineage, followed soon after by Sphaerotermitinae [6], which cultivates bacterial symbionts on combs inside its nests [7]. This has led to the hypothesis that comb building was an important evolutionary step in the loss of gut protozoa in ancestral termitids [8]. We sequenced genomes and transcriptomes of 55 termite species and reconstructed phylogenetic trees from up to 4,065 orthologous genes of 68 species. We found strong support for a novel sister-group relationship between the bacterial comb-building Sphaerotermitinae and fungus comb-building Macrotermitinae. This key finding indicates that comb building is a derived trait within Termitidae and that the creation of a comb-like "external rumen" involving bacteria or fungi may not have driven the loss of protozoa from ancestral termitids, as previously hypothesized. Instead, associations with gut prokaryotic symbionts, combined with dietary shifts from wood to other plant-based substrates, may have played a more important role in this symbiotic transition. Our phylogenetic tree provides a platform for future studies of comparative termite evolution and the evolution of symbiosis in this taxon.
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Affiliation(s)
- Ales Bucek
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan; Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamycka 129, 16521 Prague, Czech Republic; Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Prague, Czech Repubic.
| | - Jan Šobotník
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamycka 129, 16521 Prague, Czech Republic
| | - Shulin He
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamycka 129, 16521 Prague, Czech Republic; Institute of Biology, Freie Universität Berlin, Königin-Luise-Strasse 1-3, 14195 Berlin, Germany
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dino P McMahon
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Strasse 1-3, 14195 Berlin, Germany; Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205 Berlin, Germany
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Yves Roisin
- Evolutionary Biology and Ecology, CP 160/12, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, 1050 Brussels, Belgium
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan; Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamycka 129, 16521 Prague, Czech Republic.
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Montagna M, Tong KJ, Magoga G, Strada L, Tintori A, Ho SYW, Lo N. Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction. Proc Biol Sci 2019; 286:20191854. [PMID: 31594499 PMCID: PMC6790769 DOI: 10.1098/rspb.2019.1854] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 12/24/2022] Open
Abstract
Insects are a highly diverse group of organisms and constitute more than half of all known animal species. They have evolved an extraordinary range of traits, from flight and complete metamorphosis to complex polyphenisms and advanced eusociality. Although the rich insect fossil record has helped to chart the appearance of many phenotypic innovations, data are scarce for a number of key periods. One such period is that following the End-Permian Extinction, recognized as the most catastrophic of all extinction events. We recently discovered several 240-million-year-old insect fossils in the Mount San Giorgio Lagerstätte (Switzerland-Italy) that are remarkable for their state of preservation (including internal organs and soft tissues), and because they extend the records of their respective taxa by up to 200 million years. By using these fossils as calibrations in a phylogenomic dating analysis, we present a revised time scale for insect evolution. Our date estimates for several major lineages, including the hyperdiverse crown groups of Lepidoptera, Hemiptera: Heteroptera and Diptera, are substantially older than their currently accepted post-Permian origins. We found that major evolutionary innovations, including flight and metamorphosis, appeared considerably earlier than previously thought. These results have numerous implications for understanding the evolution of insects and their resilience in the face of extreme events such as the End-Permian Extinction.
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Affiliation(s)
- Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - K. Jun Tong
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
| | - Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Laura Strada
- Dipartimento di Scienze della Terra ‘Ardito Desio’, Università degli Studi di Milano, Via Mangiagalli 34, 20133 Milano, Italy
| | - Andrea Tintori
- Dipartimento di Scienze della Terra ‘Ardito Desio’, Università degli Studi di Milano, Via Mangiagalli 34, 20133 Milano, Italy
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
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32
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Ewart KM, Johnson RN, Ogden R, Joseph L, Frankham GJ, Lo N. Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species. Mol Ecol Resour 2019; 19:1578-1592. [PMID: 31484222 DOI: 10.1111/1755-0998.13082] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 12/27/2018] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022]
Abstract
Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome-wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterized. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such samples. To achieve this, we generated thousands of SNPs from 47 red-tailed black cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site-associated DNA marker approach (DArTseq™ ). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5 to 123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species. We did identify a bias towards low diversity SNPs in older samples that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq-based method to produce reliable genome-wide SNP data from traditional museum specimens.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rebecca N Johnson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | - Greta J Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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Tea Y, Van Der Wal C, Ludt WB, Gill AC, Lo N, Ho SYW. Boomeranging around Australia: Historical biogeography and population genomics of the anti‐equatorial fish
Microcanthus strigatus
(Teleostei: Microcanthidae). Mol Ecol 2019; 28:3771-3785. [DOI: 10.1111/mec.15172] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Yi‐Kai Tea
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- Australian Museum Research Institute, Australian Museum Sydney NSW Australia
| | - Cara Van Der Wal
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- Australian Museum Research Institute, Australian Museum Sydney NSW Australia
| | - William B. Ludt
- National Museum of Natural History, Smithsonian Institution Washington DC USA
- Natural History Museum of Los Angeles County Los Angeles CA USA
| | - Anthony C. Gill
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- Australian Museum Research Institute, Australian Museum Sydney NSW Australia
- Macleay Museum University of Sydney Sydney NSW Australia
| | - Nathan Lo
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
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Chang WS, Pettersson JHO, Le Lay C, Shi M, Lo N, Wille M, Eden JS, Holmes EC. Novel hepatitis D-like agents in vertebrates and invertebrates. Virus Evol 2019; 5:vez021. [PMID: 31321078 PMCID: PMC6628682 DOI: 10.1093/ve/vez021] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hepatitis delta virus (HDV) is the smallest known RNA virus, encoding a single protein. Until recently, HDV had only been identified in humans, where it is strongly associated with co-infection with hepatitis B virus (HBV). However, the recent discovery of HDV-like viruses in metagenomic samples from birds and snakes suggests that this virus has a far longer evolutionary history. Herein, using additional meta-transcriptomic data, we show that highly divergent HDV-like viruses are also present in fish, amphibians, and invertebrates, with PCR and Sanger sequencing confirming the presence of the invertebrate HDV-like viruses. Notably, the novel viruses identified here share genomic features characteristic of HDV, such as a circular genome of only approximately 1.7 kb in length, and self-complementary, unbranched rod-like structures. Coiled-coil domains, leucine zippers, conserved residues with essential biological functions, and isoelectronic points similar to those in the human hepatitis delta virus antigens (HDAgs) were also identified in the putative non-human viruses. Importantly, none of these novel HDV-like viruses were associated with hepadnavirus infection, supporting the idea that the HDV–HBV association may be specific to humans. Collectively, these data not only broaden our understanding of the diversity and host range of HDV, but also shed light on its origin and evolutionary history.
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Affiliation(s)
- Wei-Shan Chang
- School of Life and Environmental Sciences and Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - John H-O Pettersson
- School of Life and Environmental Sciences and Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Callum Le Lay
- School of Life and Environmental Sciences and Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Mang Shi
- School of Life and Environmental Sciences and Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences and Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Michelle Wille
- The Peter Doherty Institute for Infection and Immunity, WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, VIC, Australia
| | - John-Sebastian Eden
- School of Life and Environmental Sciences and Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Centre for Virus Research, Westmead, NSW, Australia
| | - Edward C Holmes
- School of Life and Environmental Sciences and Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
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35
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Yashiro T, Lo N. Comparative screening of endosymbiotic bacteria associated with the asexual and sexual lineages of the termite Glyptotermes nakajimai. Commun Integr Biol 2019; 12:55-58. [PMID: 31143363 PMCID: PMC6527188 DOI: 10.1080/19420889.2019.1592418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 02/04/2019] [Revised: 02/28/2019] [Accepted: 03/05/2019] [Indexed: 02/01/2023] Open
Abstract
Males provide opportunities both for sexual reproduction and for sex-based phenotypic differences within animal societies. In termites, the ubiquitous presence of both male and female workers and soldiers indicate that males play a critical role in colonies of these insects. However, we have recently reported all-female asexual societies in a lineage of the termite Glyptotermes nakajimai – a dramatic transition from mixed-sex to all-female asexual societies. It is known that female-producing parthenogenesis in insects can be induced by maternally inherited endosymbiotic bacteria, such as Wolbachia, Cardinium, and Rickettsia. Here, we screen for the presence of endosymbiotic bacteria in the asexual and sexual lineages of G. nakajimai. Our bacterial screening of the asexual lineage did not reveal any likely causal agents for parthenogenetic reproduction, whereas screening of the sexual lineage resulted in Wolbachia being detected. Our findings suggest that the asexuality in G. nakajimai is likely to be maintained without manipulation by endosymbiotic bacteria.
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Affiliation(s)
- Toshihisa Yashiro
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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Wang M, Buček A, Šobotník J, Sillam-Dussès D, Evans TA, Roisin Y, Lo N, Bourguignon T. Historical biogeography of the termite clade Rhinotermitinae (Blattodea: Isoptera). Mol Phylogenet Evol 2019; 132:100-104. [DOI: 10.1016/j.ympev.2018.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/05/2018] [Accepted: 11/10/2018] [Indexed: 11/30/2022]
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Utami YD, Kuwahara H, Igai K, Murakami T, Sugaya K, Morikawa T, Nagura Y, Yuki M, Deevong P, Inoue T, Kihara K, Lo N, Yamada A, Ohkuma M, Hongoh Y. Genome analyses of uncultured TG2/ZB3 bacteria in 'Margulisbacteria' specifically attached to ectosymbiotic spirochetes of protists in the termite gut. ISME J 2019; 13:455-467. [PMID: 30287885 PMCID: PMC6331581 DOI: 10.1038/s41396-018-0297-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 11/09/2022]
Abstract
We investigated the phylogenetic diversity, localisation and metabolism of an uncultured bacterial clade, Termite Group 2 (TG2), or ZB3, in the termite gut, which belongs to the candidate phylum 'Margulisbacteria'. We performed 16S rRNA amplicon sequencing analysis and detected TG2/ZB3 sequences in 40 out of 72 termite and cockroach species, which exclusively constituted a monophyletic cluster in the TG2/ZB3 clade. Fluorescence in situ hybridisation analysis in lower termites revealed that these bacteria are specifically attached to ectosymbiotic spirochetes of oxymonad gut protists. Draft genomes of four TG2/ZB3 phylotypes from a small number of bacterial cells were reconstructed, and functional genome analysis suggested that these bacteria hydrolyse and ferment cellulose/cellobiose to H2, CO2, acetate and ethanol. We also assembled a draft genome for a partner Treponema spirochete and found that it encoded genes for reductive acetogenesis from H2 and CO2. We hypothesise that the TG2/ZB3 bacteria we report here are commensal or mutualistic symbionts of the spirochetes, exploiting the spirochetes as H2 sinks. For these bacteria, we propose a novel genus, 'Candidatus Termititenax', which represents a hitherto uncharacterised class-level clade in 'Margulisbacteria'. Our findings add another layer, i.e., cellular association between bacteria, to the multi-layered symbiotic system in the termite gut.
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Affiliation(s)
- Yuniar Devi Utami
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Hirokazu Kuwahara
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Katsura Igai
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Takumi Murakami
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Kaito Sugaya
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Takahiro Morikawa
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Yuichi Nagura
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Pinsurang Deevong
- Department of Microbiology, Kasetsart University, Bangkok, 10900, Thailand
| | - Tetsushi Inoue
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Kumiko Kihara
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Akinori Yamada
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Yuichi Hongoh
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan.
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Van Der Wal C, Ahyong ST, Ho SYW, Lins LSF, Lo N. Combining morphological and molecular data resolves the phylogeny of Squilloidea (Crustacea : Malacostraca). INVERTEBR SYST 2019. [DOI: 10.1071/is18035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The mantis shrimp superfamily Squilloidea, with over 185 described species, is the largest superfamily in the crustacean order Stomatopoda. To date, phylogenetic relationships within this superfamily have been comprehensively analysed using morphological data, with six major generic groupings being recovered. Here, we infer the phylogeny of Squilloidea using a combined dataset comprising 75 somatic morphological characters and four molecular markers. Nodal support is low when the morphological and molecular datasets are analysed separately but improves substantially when combined in a total-evidence phylogenetic analysis. We obtain a well resolved and strongly supported phylogeny that is largely congruent with previous estimates except that the Anchisquilloides-group, rather than the Meiosquilla-group, is the earliest-branching lineage in Squilloidea. The splits among the Anchisquilloides- and Meiosquilla-groups are followed by those of the Clorida-, Harpiosquilla-, Squilla- and Oratosquilla-groups. Most of the generic groups are recovered as monophyletic, with the exception of the Squilla- and Oratosquilla-groups. However, many genera within the Oratosquilla-group are not recovered as monophyletic. Further exploration with more extensive molecular sampling will be needed to resolve relationships within the Oratosquilla-group and to investigate the adaptive radiation of squilloids. Overall, our results demonstrate the merit of combining morphological and molecular datasets for resolving phylogenetic relationships.
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Beasley-Hall PG, Chui J, Arab DA, Lo N. Evidence for a complex evolutionary history of mound building in the Australian nasute termites (Nasutitermitinae). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Perry G Beasley-Hall
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Juanita Chui
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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Kinjo Y, Bourguignon T, Tong KJ, Kuwahara H, Lim SJ, Yoon KB, Shigenobu S, Park YC, Nalepa CA, Hongoh Y, Ohkuma M, Lo N, Tokuda G. Parallel and Gradual Genome Erosion in the Blattabacterium Endosymbionts of Mastotermes darwiniensis and Cryptocercus Wood Roaches. Genome Biol Evol 2018; 10:1622-1630. [PMID: 29860278 PMCID: PMC6022663 DOI: 10.1093/gbe/evy110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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] [Accepted: 05/29/2018] [Indexed: 12/23/2022] Open
Abstract
Almost all examined cockroaches harbor an obligate intracellular endosymbiont, Blattabacterium cuenoti. On the basis of genome content, Blattabacterium has been inferred to recycle nitrogen wastes and provide amino acids and cofactors for its hosts. Most Blattabacterium strains sequenced to date harbor a genome of ∼630 kbp, with the exception of the termite Mastotermes darwiniensis (∼590 kbp) and Cryptocercus punctulatus (∼614 kbp), a representative of the sister group of termites. Such genome reduction may have led to the ultimate loss of Blattabacterium in all termites other than Mastotermes. In this study, we sequenced 11 new Blattabacterium genomes from three species of Cryptocercus in order to shed light on the genomic evolution of Blattabacterium in termites and Cryptocercus. All genomes of Cryptocercus-derived Blattabacterium genomes were reduced (∼614 kbp), except for that associated with Cryptocercus kyebangensis, which comprised 637 kbp. Phylogenetic analysis of these genomes and their content indicates that Blattabacterium experienced parallel genome reduction in Mastotermes and Cryptocercus, possibly due to similar selective forces. We found evidence of ongoing genome reduction in Blattabacterium from three lineages of the C. punctulatus species complex, which independently lost one cysteine biosynthetic gene. We also sequenced the genome of the Blattabacterium associated with Salganea taiwanensis, a subsocial xylophagous cockroach that does not vertically transmit gut symbionts via proctodeal trophallaxis. This genome was 632 kbp, typical of that of nonsubsocial cockroaches. Overall, our results show that genome reduction occurred on multiple occasions in Blattabacterium, and is still ongoing, possibly because of new associations with gut symbionts in some lineages.
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Affiliation(s)
- Yukihiro Kinjo
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan.,Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Okinawa Institute of Science and Technology, Graduate University, Okinawa, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology, Graduate University, Okinawa, Japan.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Kwei Jun Tong
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Hirokazu Kuwahara
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Sang Jin Lim
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Kwang Bae Yoon
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Shuji Shigenobu
- National Institute for Basic Biology, NIBB Core Research Facilities, Okazaki, Japan
| | - Yung Chul Park
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Christine A Nalepa
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, USA
| | - Yuichi Hongoh
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan.,Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Gaku Tokuda
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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Yashiro T, Lo N, Kobayashi K, Nozaki T, Fuchikawa T, Mizumoto N, Namba Y, Matsuura K. Loss of males from mixed-sex societies in termites. BMC Biol 2018; 16:96. [PMID: 30249269 PMCID: PMC6154949 DOI: 10.1186/s12915-018-0563-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 02/18/2018] [Accepted: 08/09/2018] [Indexed: 11/13/2022] Open
Abstract
Background Sexual reproduction is the norm in almost all animal species, and in many advanced animal societies, both males and females participate in social activities. To date, the complete loss of males from advanced social animal lineages has been reported only in ants and honey bees (Hymenoptera), whose workers are always female and whose males display no helping behaviors even in normal sexual species. Asexuality has not previously been observed in colonies of another major group of social insects, the termites, where the ubiquitous presence of both male and female workers and soldiers indicate that males play a critical role beyond that of reproduction. Results Here, we report asexual societies in a lineage of the termite Glyptotermes nakajimai. We investigated the composition of mature colonies from ten distinct populations in Japan, finding six asexual populations characterized by a lack of any males in the reproductive, soldier, and worker castes of their colonies, an absence of sperm in the spermathecae of their queens, and the development of unfertilized eggs at a level comparable to that for the development of fertilized eggs in sexual populations of this species. Phylogenetic analyses indicated a single evolutionary origin of the asexual populations, with divergence from sampled sexual populations occurring about 14 million years ago. Asexual colonies differ from sexual colonies in having a more uniform head size in their all-female soldier caste, and fewer soldiers in proportion to other individuals, suggesting increased defensive efficiencies arising from uniform soldier morphology. Such efficiencies may have contributed to the persistence and spread of the asexual lineage. Cooperative colony foundation by multiple queens, the single-site nesting life history common to both the asexual and sexual lineages, and the occasional development of eggs without fertilization even in the sexual lineage are traits likely to have been present in the ancestors of the asexual lineage that may have facilitated the transition to asexuality. Conclusions Our findings demonstrate that completely asexual social lineages can evolve from mixed-sex termite societies, providing evidence that males are dispensable for the maintenance of advanced animal societies in which they previously played an active social role. Electronic supplementary material The online version of this article (10.1186/s12915-018-0563-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Toshihisa Yashiro
- School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, NSW, 2006, Australia. .,Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Nathan Lo
- School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, NSW, 2006, Australia
| | - Kazuya Kobayashi
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Tomonari Nozaki
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Taro Fuchikawa
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Nobuaki Mizumoto
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yusuke Namba
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kenji Matsuura
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
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Ewart KM, Frankham GJ, McEwing R, The DT, Hogg CJ, Wade C, Lo N, Johnson RN. Correction: A rapid multiplex PCR assay for presumptive species identification of rhinoceros horns and its implementation in Vietnam. PLoS One 2018; 13:e0202433. [PMID: 30096182 PMCID: PMC6086477 DOI: 10.1371/journal.pone.0202433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Ewart KM, Frankham GJ, McEwing R, The DT, Hogg CJ, Wade C, Lo N, Johnson RN. A rapid multiplex PCR assay for presumptive species identification of rhinoceros horns and its implementation in Vietnam. PLoS One 2018; 13:e0198565. [PMID: 29902212 PMCID: PMC6002117 DOI: 10.1371/journal.pone.0198565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/21/2018] [Indexed: 12/04/2022] Open
Abstract
Rhinoceros (rhinos) have suffered a dramatic increase in poaching over the past decade due to the growing demand for rhino horn products in Asia. One way to reverse this trend is to enhance enforcement and intelligence gathering tools used for species identification of horns, in particular making them fast, inexpensive and accurate. Traditionally, species identification tests are based on DNA sequence data, which, depending on laboratory resources, can be either time or cost prohibitive. This study presents a rapid rhino species identification test, utilizing species-specific primers within the cytochrome b gene multiplexed in a single reaction, with a presumptive species identification based on the length of the resultant amplicon. This multiplex PCR assay can provide a presumptive species identification result in less than 24 hours. Sequence-based definitive testing can be conducted if/when required (e.g. court purposes). This work also presents an actual casework scenario in which the presumptive test was successfully utlitised, in concert with sequence-based definitive testing. The test was carried out on seized suspected rhino horns tested at the Institute of Ecology and Biological Resources, the CITES mandated laboratory in Vietnam, a country that is known to be a major source of demand for rhino horns. This test represents the basis for which future 'rapid species identification tests' can be trialed.
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Affiliation(s)
- Kyle M. Ewart
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, New South Wales, Australia
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Greta J. Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Ross McEwing
- TRACE Wildlife Forensics Network, Edinburgh, Scotland
| | - Dang Tat The
- Institute of Ecology and Biological Resources, Hanoi, Vietnam
| | - Carolyn J. Hogg
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, New South Wales, Australia
- Zoo and Aquarium Association Australasia, Mosman, New South Wales, Australia
| | - Claire Wade
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Nathan Lo
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Rebecca N. Johnson
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, New South Wales, Australia
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Utami YD, Kuwahara H, Murakami T, Morikawa T, Sugaya K, Kihara K, Yuki M, Lo N, Deevong P, Hasin S, Boonriam W, Inoue T, Yamada A, Ohkuma M, Hongoh Y. Phylogenetic Diversity and Single-Cell Genome Analysis of "Melainabacteria", a Non-Photosynthetic Cyanobacterial Group, in the Termite Gut. Microbes Environ 2018; 33:50-57. [PMID: 29415909 PMCID: PMC5877343 DOI: 10.1264/jsme2.me17137] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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] [Indexed: 11/12/2022] Open
Abstract
Termite guts harbor diverse yet-uncultured bacteria, including a non-photosynthetic cyanobacterial group, the class "Melainabacteria". We herein reported the phylogenetic diversity of "Melainabacteria" in the guts of diverse termites and conducted a single-cell genome analysis of a melainabacterium obtained from the gut of the termite Termes propinquus. We performed amplicon sequencing of 16S rRNA genes from the guts of 60 termite and eight cockroach species, and detected melainabacterial sequences in 48 out of the 68 insect species, albeit with low abundances (0.02-1.90%). Most of the melainabacterial sequences obtained were assigned to the order "Gastranaerophilales" and appeared to form clusters unique to termites and cockroaches. A single-cell genome of a melainabacterium, designated phylotype Tpq-Mel-01, was obtained using a fluorescence-activated cell sorter and whole genome amplification. The genome shared basic features with other melainabacterial genomes previously reconstructed from the metagenomes of human and koala feces. The bacterium had a small genome (~1.6 Mb) and possessed fermentative pathways possibly using sugars and chitobiose as carbon and energy sources, while the pathways for photosynthesis and carbon fixation were not found. The genome contained genes for flagellar components and chemotaxis; therefore, the bacterium is likely motile. A fluorescence in situ hybridization analysis showed that the cells of Tpq-Mel-01 and/or its close relatives are short rods with the dimensions of 1.1±0.2 μm by 0.5±0.1 μm; for these bacteria, we propose the novel species, "Candidatus Gastranaerophilus termiticola". Our results provide fundamental information on "Melainabacteria" in the termite gut and expand our knowledge on this underrepresented, non-photosynthetic cyanobacterial group.
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Affiliation(s)
| | | | - Takumi Murakami
- Department of Biological Sciences, Tokyo Institute of Technology
| | | | - Kaito Sugaya
- Department of Biological Sciences, Tokyo Institute of Technology
| | - Kumiko Kihara
- Department of Biological Sciences, Tokyo Institute of Technology
| | - Masahiro Yuki
- Biomass Research Platform Team, RIKEN Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science
| | - Nathan Lo
- School of Biological Sciences, University of Sydney
| | | | - Sasitorn Hasin
- College of Innovative Management, Valaya Alongkorn Rajabhat University under the Royal Patronage
| | | | - Tetsushi Inoue
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University
| | - Akinori Yamada
- Department of Biological Sciences, Tokyo Institute of Technology.,Graduate School of Fisheries and Environmental Sciences, Nagasaki University
| | - Moriya Ohkuma
- Biomass Research Platform Team, RIKEN Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science.,Japan Collection of Microorganisms, RIKEN BioResource Center
| | - Yuichi Hongoh
- Department of Biological Sciences, Tokyo Institute of Technology.,Japan Collection of Microorganisms, RIKEN BioResource Center
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Bourguignon T, Lo N, Dietrich C, Šobotník J, Sidek S, Roisin Y, Brune A, Evans TA. Rampant Host Switching Shaped the Termite Gut Microbiome. Curr Biol 2018; 28:649-654.e2. [PMID: 29429621 DOI: 10.1016/j.cub.2018.01.035] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/21/2017] [Accepted: 01/11/2018] [Indexed: 10/18/2022]
Abstract
The gut microbiota of animals exert major effects on host biology [1]. Although horizontal transfer is generally considered the prevalent route for the acquisition of gut bacteria in mammals [2], some bacterial lineages have co-speciated with their hosts on timescales of several million years [3]. Termites harbor a complex gut microbiota, and their advanced social behavior provides the potential for long-term vertical symbiont transmission, and co-evolution of gut symbionts and host [4-6]. Despite clear evolutionary patterns in the gut microbiota of termites [7], a consensus on how microbial communities were assembled during termite diversification has yet to be reached. Although some studies have concluded that vertical transmission has played a major role [8, 9], others indicate that diet and gut microenvironment have been the primary determinants shaping microbial communities in termite guts [7, 10]. To address this issue, we examined the gut microbiota of 94 termite species, through 16S rRNA metabarcoding. We analyzed the phylogeny of 211 bacterial lineages obtained from termite guts, including their closest relatives from other environments, which were identified using BLAST. The results provided strong evidence for rampant horizontal transfer of gut bacteria between termite host lineages. Although the majority of termite-derived phylotypes formed large monophyletic groups, indicating high levels of niche specialization, numerous other clades were interspersed with bacterial lineages from the guts of other animals. Our results indicate that "mixed-mode" transmission, which combines colony-to-offspring vertical transmission with horizontal colony-to-colony transfer, has been the primary driving force shaping the gut microbiota of termites.
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Affiliation(s)
- Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic.
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Carsten Dietrich
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Strategy and Innovation Technology Center, Siemens Healthcare, Erlangen, Germany
| | - Jan Šobotník
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Sarah Sidek
- Department of Biological Sciences, National University of Singapore, 117543 Singapore, Singapore
| | - Yves Roisin
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Theodore A Evans
- Department of Biological Sciences, National University of Singapore, 117543 Singapore, Singapore; School of Animal Biology, University of Western Australia, Perth, WA 6009, Australia
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Bourguignon T, Tang Q, Ho SYW, Juna F, Wang Z, Arab DA, Cameron SL, Walker J, Rentz D, Evans TA, Lo N. Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics. Mol Biol Evol 2018; 35:970-983. [DOI: 10.1093/molbev/msy013] [Citation(s) in RCA: 53] [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: 02/07/2023] Open
Affiliation(s)
- Thomas Bourguignon
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Qian Tang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Frantisek Juna
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | | | - James Walker
- Department of Agriculture and Water Resources, Cairns, QLD, Australia
| | - David Rentz
- School of Marine and Tropical Biology, James Cook University, Townsville, QLD, Australia
| | - Theodore A Evans
- School of Animal Biology, University of Western Australia, Perth, WA, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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Lo N, Simpson SJ, Sword GA. Epigenetics and developmental plasticity in orthopteroid insects. Curr Opin Insect Sci 2018; 25:25-34. [PMID: 29602359 DOI: 10.1016/j.cois.2017.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/26/2017] [Accepted: 11/06/2017] [Indexed: 06/08/2023]
Abstract
Developmental plasticity is a key driver of the extraordinary ecological success of insects. Epigenetic mechanisms provide an important link between the external stimuli that initiate polyphenisms, and the stable changes in gene expression that govern alternative insect morphs. We review the epigenetics of orthopteroid insects, focussing on recent research on locusts and termites, two groups which display high levels of phenotypic plasticity, and for which genome sequences have become available in recent years. We examine research on the potential role of DNA methylation, histone modifications, and non-coding RNAs in the regulation of gene expression in these insects. DNA methylation patterns in orthopteroids share a number of characteristics with those of hymenopteran insects, although methylation levels are much higher, and extend to introns and repeat elements. Future examinations of epigenetic mechanisms in these insects will benefit from comparison of tissues from aged-matched individuals from alternative morphs, and adequate biological replication.
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Affiliation(s)
- Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Stephen J Simpson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gregory A Sword
- Department of Entomology, Interdisciplinary Faculty of Ecology and Evolutionary Biology, Texas A&M University, TAMU 2475, College Station, TX 77843, USA
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Ritchie AM, Lo N, Ho SYW. The Impact of the Tree Prior on Molecular Dating of Data Sets Containing a Mixture of Inter- and Intraspecies Sampling. Syst Biol 2018; 66:413-425. [PMID: 27798404 DOI: 10.1093/sysbio/syw095] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/14/2016] [Indexed: 11/12/2022] Open
Abstract
In Bayesian phylogenetic analyses of genetic data, prior probability distributions need to be specified for the model parameters, including the tree. When Bayesian methods are used for molecular dating, available tree priors include those designed for species-level data, such as the pure-birth and birth-death priors, and coalescent-based priors designed for population-level data. However, molecular dating methods are frequently applied to data sets that include multiple individuals across multiple species. Such data sets violate the assumptions of both the speciation and coalescent-based tree priors, making it unclear which should be chosen and whether this choice can affect the estimation of node times. To investigate this problem, we used a simulation approach to produce data sets with different proportions of within- and between-species sampling under the multispecies coalescent model. These data sets were then analyzed under pure-birth, birth-death, constant-size coalescent, and skyline coalescent tree priors. We also explored the ability of Bayesian model testing to select the best-performing priors. We confirmed the applicability of our results to empirical data sets from cetaceans, phocids, and coregonid whitefish. Estimates of node times were generally robust to the choice of tree prior, but some combinations of tree priors and sampling schemes led to large differences in the age estimates. In particular, the pure-birth tree prior frequently led to inaccurate estimates for data sets containing a mixture of inter- and intraspecific sampling, whereas the birth-death and skyline coalescent priors produced stable results across all scenarios. Model testing provided an adequate means of rejecting inappropriate tree priors. Our results suggest that tree priors do not strongly affect Bayesian molecular dating results in most cases, even when severely misspecified. However, the choice of tree prior can be significant for the accuracy of dating results in the case of data sets with mixed inter- and intraspecies sampling. [Bayesian phylogenetic methods; model testing; molecular dating; node time; tree prior.].
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Affiliation(s)
- Andrew M Ritchie
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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Bai Q, Wang L, Wang Z, Lo N, Che Y. Exploring the diversity of Asian Cryptocercus (Blattodea : Cryptocercidae): species delimitation based on chromosome numbers, morphology and molecular analysis. INVERTEBR SYST 2018. [DOI: 10.1071/is17003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Woodroaches from the genus Cryptocercus Scudder, 1862 are known to display low levels of morphological divergence, yet significant genetic divergence and variability in chromosome number. Compared with Cryptocercus taxa from North America, the diversity of the genus in Asia has received relatively little attention. We performed morphological and karyotypic examinations of multiple taxa from several previously unsampled mountainous areas of central and south-western China, and identified nine candidate species primarily on the basis of chromosome number. We then investigated diversity across all Asian Cryptocercus, through phylogenetic analyses of 135 COI sequences and 74 28S rRNA sequences from individuals of 28 localities, including species delimitation analysis in General Mixed Yule Coalescent (GMYC) and Automatic Barcode Gap Discovery (ABGD). Phylogenetic results indicated that individuals from the same locality constituted well supported clades. The congruence of GMYC and ABGD results were in almost perfect accord, with 28 candidate species described on the basis of karyotypes (including the nine identified in this study). We provide evidence that each valley population in the Hengduan Mountains contains a separate evolving lineage. We conclude that the principal cause of the rich Cryptocercus diversity in China has been the uplift of the Qinghai-Tibet Plateau.
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