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Hoare RJB, Patrick BH, Buckley TR, Brav-Cubitt T. Wing pattern variation and DNA barcodes defy taxonomic splitting in the New Zealand Pimelea Looper Notoreas perornata (Walker) (Lepidoptera: Geometridae: Larentiinae): the importance of populations as conservation units. Zootaxa 2023; 5346:1-27. [PMID: 38221354 DOI: 10.11646/zootaxa.5346.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Indexed: 01/16/2024]
Abstract
The endemic Notoreas perornata (Walker, 1863) complex (Lepidoptera: Geometridae: Larentiinae) from the North Island and northern South Island of New Zealand is reviewed. Larvae feed on Pimelea spp. (Thymelaeaceae), frequently in highly fragmented and threatened shrubland habitats. Allopatric populations tend to differ in size and wing pattern characteristics, but not in genitalia; moreover extensive variation renders recognition of subspecies / allopatric species based on any species concept problematic. A mitochondrial DNA gene tree is not congruent with morphology and indicates rapid recent divergence that has not settled into diagnosable lineages. Based on our results, we synonymise Notoreas simplex Hudson, 1898 with N. perornata (Walker, 1863), and retain N. perornata as a single, highly diverse but monotypic species. All known populations are illustrated to display variation. For conservation purposes, we recommend the continued recognition within the species of 10 populations or groups of populations that appear to be on the way to diverging at subspecific level based on morphological and/or DNA data. The conservation status of all these populations is reviewed. One conservation unit, comprising the populations from Westland, has not been seen since 1998 and is feared possibly extinct.
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Affiliation(s)
- Robert J B Hoare
- Manaaki Whenua-Landcare Research; Private Bag 92170; St Johns 1072; Auckland; New Zealand.
| | | | - Thomas R Buckley
- Manaaki Whenua-Landcare Research; Private Bag 92170; St Johns 1072; Auckland; New Zealand.
| | - Talia Brav-Cubitt
- Manaaki Whenua-Landcare Research; Private Bag 92170; St Johns 1072; Auckland; New Zealand.
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Dopheide A, Brav-Cubitt T, Podolyan A, Leschen RAB, Ward D, Buckley TR, Dhami MK. Fast-tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation. Mol Ecol Resour 2022. [PMID: 36345645 DOI: 10.1111/1755-0998.13733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
Abstract
Despite recent advances in high-throughput DNA sequencing technologies, a lack of locally relevant DNA reference databases limits the potential for DNA-based monitoring of biodiversity for conservation and biosecurity applications. Museums and national collections represent a compelling source of authoritatively identified genetic material for DNA database development, yet obtaining DNA barcodes from long-stored specimens may be difficult due to sample degradation. Here we demonstrate a sensitive and efficient laboratory and bioinformatic process for generating DNA barcodes from hundreds of invertebrate specimens simultaneously via the Illumina MiSeq system. Using this process, we recovered full-length (334) or partial (105) COI barcodes from 439 of 450 (98%) national collection-held invertebrate specimens. This included full-length barcodes from 146 specimens which produced low-yield DNA and no visible PCR bands, and which produced as little as a single sequence per specimen, demonstrating high sensitivity of the process. In many cases, the identity of the most abundant sequences per specimen were not the correct barcodes, necessitating the development of a taxonomy-informed process for identifying correct sequences among the sequencing output. The recovery of only partial barcodes for some taxa indicates a need to refine certain PCR primers. Nonetheless, our approach represents a highly sensitive, accurate and efficient method for targeted reference database generation, providing a foundation for DNA-based assessments and monitoring of biodiversity.
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Affiliation(s)
| | | | | | | | - Darren Ward
- Manaaki Whenua Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Thomas R Buckley
- Manaaki Whenua Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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3
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Buckley TR, Hoare RJB, Leschen RAB. Key questions on the evolution and biogeography of New Zealand alpine insects. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2130367] [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: 10/10/2022]
Affiliation(s)
- Thomas R. Buckley
- Manaaki Whenua – Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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4
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McCartney AM, Hilario E, Choi S, Guhlin J, Prebble JM, Houliston G, Buckley TR, Chagné D. An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome. Mol Ecol Resour 2021; 21:2125-2144. [PMID: 33955186 PMCID: PMC8362059 DOI: 10.1111/1755-0998.13406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/18/2021] [Accepted: 04/20/2021] [Indexed: 12/17/2022]
Abstract
We used long read sequencing data generated from Knightia excelsa, a nectar-producing Proteaceae tree endemic to Aotearoa (New Zealand), to explore how sequencing data type, volume and workflows can impact final assembly accuracy and chromosome reconstruction. Establishing a high-quality genome for this species has specific cultural importance to Māori and commercial importance to honey producers in Aotearoa. Assemblies were produced by five long read assemblers using data subsampled based on read lengths, two polishing strategies and two Hi-C mapping methods. Our results from subsampling the data by read length showed that each assembler tested performed differently depending on the coverage and the read length of the data. Subsampling highlighted that input data with longer read lengths but perhaps lower coverage constructed more contiguous, kmers and gene-complete assemblies than short read length input data with higher coverage. The final genome assembly was constructed into 14 pseudochromosomes using an initial flye long read assembly, a racon/medaka/pilon combined polishing strategy, salsa2 and allhic scaffolding, juicebox curation, and Macadamia linkage map validation. We highlighted the importance of developing assembly workflows based on the volume and read length of sequencing data and established a robust set of quality metrics for generating high-quality assemblies. Scaffolding analyses highlighted that problems found in the initial assemblies could not be resolved accurately by Hi-C data and that assembly scaffolding was more successful when the underlying contig assembly was of higher accuracy. These findings provide insight into how quality assessment tools can be implemented throughout genome assembly pipelines to inform the de novo reconstruction of a high-quality genome assembly for nonmodel organisms.
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Affiliation(s)
- Ann M. McCartney
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
| | - Elena Hilario
- Genomics AotearoaDunedinNew Zealand
- The New Zealand Institute for Plant and Food Research (Plant & Food Research)SandringhamNew Zealand
| | - Seung‐Sub Choi
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Joseph Guhlin
- Genomics AotearoaDunedinNew Zealand
- University of OtagoDunedinNew Zealand
| | - Jessica M. Prebble
- Genomics AotearoaDunedinNew Zealand
- Manaaki Whenua Landcare ResearchLincolnNew Zealand
| | - Gary Houliston
- Genomics AotearoaDunedinNew Zealand
- Manaaki Whenua Landcare ResearchLincolnNew Zealand
| | - Thomas R. Buckley
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - David Chagné
- Genomics AotearoaDunedinNew Zealand
- Plant & Food ResearchFitzherbert, Palmerston NorthNew Zealand
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5
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Wu C, Twort VG, Newcomb RD, Buckley TR. Divergent Gene Expression Following Duplication of Meiotic Genes in the Stick Insect Clitarchus hookeri. Genome Biol Evol 2021; 13:6245840. [PMID: 33885769 DOI: 10.1093/gbe/evab060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 01/02/2023] Open
Abstract
Some animal groups, such as stick insects (Phasmatodea), have repeatedly evolved alternative reproductive strategies, including parthenogenesis. Genomic studies have found modification of the genes underlying meiosis exists in some of these animals. Here we examine the evolution of copy number, evolutionary rate, and gene expression in candidate meiotic genes of the New Zealand geographic parthenogenetic stick insect Clitarchus hookeri. We characterized 101 genes from a de novo transcriptome assembly from female and male gonads that have homology with meiotic genes from other arthropods. For each gene we determined copy number, the pattern of gene duplication relative to other arthropod orthologs, and the potential for meiosis-specific expression. There are five genes duplicated in C. hookeri, including one also duplicated in the stick insect Timema cristinae, that are not or are uncommonly duplicated in other arthropods. These included two sister chromatid cohesion associated genes (SA2 and SCC2), a recombination gene (HOP1), an RNA-silencing gene (AGO2) and a cell-cycle regulation gene (WEE1). Interestingly, WEE1 and SA2 are also duplicated in the cyclical parthenogenetic aphid Acyrthosiphon pisum and Daphnia duplex, respectively, indicating possible roles in the evolution of reproductive mode. Three of these genes (SA2, SCC2, and WEE1) have one copy displaying gonad-specific expression. All genes, with the exception of WEE1, have significantly different nonsynonymous/synonymous ratios between the gene duplicates, indicative of a shift in evolutionary constraints following duplication. These results suggest that stick insects may have evolved genes with novel functions in gamete production by gene duplication.
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Affiliation(s)
- Chen Wu
- School of Biological Sciences, The University of Auckland, New Zealand.,Manaaki Whenua-Landcare Research, Auckland, New Zealand.,New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Victoria G Twort
- School of Biological Sciences, The University of Auckland, New Zealand.,Manaaki Whenua-Landcare Research, Auckland, New Zealand.,Zoology Unit, Finnish Museum of Natural History, LUOMUS, University of Helsinki, Finland
| | - Richard D Newcomb
- School of Biological Sciences, The University of Auckland, New Zealand.,New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Thomas R Buckley
- School of Biological Sciences, The University of Auckland, New Zealand.,Manaaki Whenua-Landcare Research, Auckland, New Zealand
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6
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Bradler S, Buckley TR. Editorial: Stick Insect Research in the Era of Genomics: Exploring the Evolution of a Mesodiverse Insect Order. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.619418] [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: 11/13/2022] Open
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7
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Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, Martin FJ, Flicek P, Petersen B, Kang L, Michalak P, Buckley TR, Wilson M, Cheng Y, Miller H, Schott RK, Jordan MD, Newcomb RD, Arroyo JI, Valenzuela N, Hore TA, Renart J, Peona V, Peart CR, Warmuth VM, Zeng L, Kortschak RD, Raison JM, Zapata VV, Wu Z, Santesmasses D, Mariotti M, Guigó R, Rupp SM, Twort VG, Dussex N, Taylor H, Abe H, Bond DM, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Van Stijn T, Clarke S, Ryder O, Edwards SV, Salzberg SL, Anderson L, Nelson N, Stone C. The tuatara genome reveals ancient features of amniote evolution. Nature 2020; 584:403-409. [PMID: 32760000 PMCID: PMC7116210 DOI: 10.1038/s41586-020-2561-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/26/2020] [Indexed: 12/21/2022]
Abstract
The tuatara (Sphenodon punctatus)-the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2-is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which-at approximately 5 Gb-is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
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Affiliation(s)
- Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand.
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg Museum, Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Marc Tollis
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - David Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - David L Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Alexander Suh
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Terry Bertozzi
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - José H Grau
- Amedes Genetics, Amedes Medizinische Dienstleistungen, Berlin, Germany
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Berlin, Germany
| | - Chris Organ
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - Paul P Gardner
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
| | - Pawel Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Thomas R Buckley
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Melissa Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Ryan K Schott
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Melissa D Jordan
- The New Zealand Institute for Plant and Food Research, Auckland, New Zealand
| | - Richard D Newcomb
- The New Zealand Institute for Plant and Food Research, Auckland, New Zealand
| | - José Ignacio Arroyo
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Tim A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Jaime Renart
- Instituto de Investigaciones Biomédicas 'Alberto Sols' CSIC-UAM, Madrid, Spain
| | - Valentina Peona
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Claire R Peart
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Vera M Warmuth
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Lu Zeng
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - R Daniel Kortschak
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Joy M Raison
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Zhiqiang Wu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marco Mariotti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shawn M Rupp
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Victoria G Twort
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Nicolas Dussex
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Helen Taylor
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Hideaki Abe
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Donna M Bond
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - James M Paterson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Vanessa L Gonzalez
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | | | - Stephan Pabinger
- Austrian Institute of Technology (AIT), Center for Health and Bioresources, Molecular Diagnostics, Vienna, Austria
| | | | - Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Oliver Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay Anderson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Nicola Nelson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Clive Stone
- Ngatiwai Trust Board, Whangarei, New Zealand
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Mathieu C, Hermans SM, Lear G, Buckley TR, Lee KC, Buckley HL. A Systematic Review of Sources of Variability and Uncertainty in eDNA Data for Environmental Monitoring. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00135] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Simon S, Letsch H, Bank S, Buckley TR, Donath A, Liu S, Machida R, Meusemann K, Misof B, Podsiadlowski L, Zhou X, Wipfler B, Bradler S. Old World and New World Phasmatodea: Phylogenomics Resolve the Evolutionary History of Stick and Leaf Insects. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00345] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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10
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Walker LA, Vink CJ, Holwell GI, Buckley TR. A preliminary molecular phylogeny for New Zealand sheet-web spiders (Cambridgea) and comparison of web-building behaviour. New Zealand Journal of Zoology 2019. [DOI: 10.1080/03014223.2019.1672760] [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] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Affiliation(s)
- Leilani A. Walker
- Faculty of Environmental and Health Sciences, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Cor J. Vink
- Natural History, Canterbury Museum, Christchurch, New Zealand
| | - Gregory I. Holwell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Thomas R. Buckley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
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Hoare RJ, Patrick BH, Buckley TR. A new leaf-mining moth from New Zealand, Sabulopteryxbotanica sp. nov. (Lepidoptera, Gracillariidae, Gracillariinae), feeding on the rare endemic shrub Teucriumparvifolium (Lamiaceae), with a revised checklist of New Zealand Gracillariidae. Zookeys 2019; 865:39-65. [PMID: 31379443 PMCID: PMC6663935 DOI: 10.3897/zookeys.865.34265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 03/04/2019] [Accepted: 05/03/2019] [Indexed: 11/25/2022] Open
Abstract
Sabulopteryxbotanica Hoare & Patrick, sp. nov. (Lepidoptera, Gracillariidae, Gracillariinae) is described as a new species from New Zealand. It is regarded as endemic, and represents the first record of its genus from the southern hemisphere. Though diverging in some morphological features from previously described species, it is placed in genus Sabulopteryx Triberti, based on wing venation, abdominal characters, male and female genitalia and hostplant choice; this placement is supported by phylogenetic analysis based on the COI mitochondrial gene. The life history is described: the larva is an underside leaf-miner on the endemic divaricating shrub Teucriumparvifolium (Lamiaceae), and exits the mine to pupate in a cocoon in a folded leaf of the host plant. The remarkable history of the discovery and rediscovery of this moth is discussed: for many years it was only known from a single sap-feeding larva found in a leaf-mine in a pressed herbarium specimen of the host. The adult was discovered by BHP in Christchurch Botanic Gardens in 2013. Most distribution records of the moth come from a recent search for mines and cocoons on herbarium specimens of T.parvifolium. Sabulopteryxbotanica has high conservation status, and is regarded as 'Nationally Vulnerable' according to the New Zealand Department of Conservation threat classification system, based on the rarity and declining status of its host plant. However, the presence of apparently thriving populations of S.botanica on cultivated plants of T.parvifolium, especially at the type locality, Christchurch Botanic Gardens, suggests that encouraging cultivation of the plant could greatly improve the conservation status of the moth. A revised checklist of New Zealand Gracillariidae is presented, assigning all species to the currently recognised subfamilies. The Australian Macarostolaida (Meyrick, 1880) is newly recorded from New Zealand (Auckland), where it is established on Eucalyptus.
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Affiliation(s)
- Robert J.B. Hoare
- New Zealand Arthropod Collection (NZAC), Manaaki Whenua–Landcare Research, Private Bag 92170, Auckland, New ZealandNew Zealand Arthropod CollectionAucklandNew Zealand
| | - Brian H. Patrick
- Wildlands Consultants Ltd, PO Box 9276, Tower Junction, Christchurch 8149, New ZealandWildlands Consultants LtdChristchurchNew Zealand
| | - Thomas R. Buckley
- New Zealand Arthropod Collection (NZAC), Manaaki Whenua–Landcare Research, Private Bag 92170, Auckland, New ZealandNew Zealand Arthropod CollectionAucklandNew Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New ZealandThe University of AucklandAucklandNew Zealand
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12
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Dopheide A, Tooman LK, Grosser S, Agabiti B, Rhode B, Xie D, Stevens MI, Nelson N, Buckley TR, Drummond AJ, Newcomb RD. Estimating the biodiversity of terrestrial invertebrates on a forested island using DNA barcodes and metabarcoding data. Ecol Appl 2019; 29:e01877. [PMID: 30811075 DOI: 10.1002/eap.1877] [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: 09/11/2018] [Revised: 01/13/2019] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
Invertebrates are a major component of terrestrial ecosystems, however, estimating their biodiversity is challenging. We compiled an inventory of invertebrate biodiversity along an elevation gradient on the temperate forested island of Hauturu, New Zealand, by DNA barcoding of specimens obtained from leaf litter samples and pitfall traps. We compared the barcodes and biodiversity estimates from this data set with those from a parallel DNA metabarcoding analysis of soil from the same locations, and with pre-existing sequences in reference databases, before exploring the use of combined data sets as a basis for estimating total invertebrate biodiversity. We obtained 1,282 28S and 1,610 COI barcodes from a total of 1,947 invertebrate specimens, which were clustered into 247 (28S) and 366 (COI) OTUs, of which ≤ 10% were represented in GenBank. Coleoptera were most abundant (730 sequenced specimens), followed by Hymenoptera, Diptera, Lepidoptera, and Amphipoda. The most abundant OTU from both the 28S (153 sequences) and COI (140 sequences) data sets was an undescribed beetle from the family Salpingidae. Based on the occurrences of COI OTUs along the elevation gradient, we estimated there are ~1,000 arthropod species (excluding mites) on Hauturu, including 770 insects, of which 344 are beetles. A DNA metabarcoding analysis of soil DNA from the same sites resulted in the identification of similar numbers of OTUs in most invertebrate groups compared with the DNA barcoding, but less than 10% of the DNA barcoding COI OTUs were also detected by the metabarcoding analysis of soil DNA. A mark-recapture analysis based on the overlap between these data sets estimated the presence of approximately 6,800 arthropod species (excluding mites) on the island, including ~3,900 insects. Estimates of New Zealand-wide biodiversity for selected arthropod groups based on matching of the COI DNA barcodes with pre-existing reference sequences suggested over 13,200 insect species are present, including 4,000 Coleoptera, 2,200 Diptera, and 2,700 Hymenoptera species, and 1,000 arachnid species (excluding mites). These results confirm that metabarcoding analyses of soil DNA tends to recover different components of terrestrial invertebrate biodiversity compared to traditional invertebrate sampling, but the combined methods provide a novel basis for estimating invertebrate biodiversity.
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Affiliation(s)
- Andrew Dopheide
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142, New Zealand
- Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - Leah K Tooman
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142, New Zealand
| | - Stefanie Grosser
- Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Geschwister-Scholl-Platz 1, 80539, 80539, Munich, Germany
| | - Barbara Agabiti
- Centre for Computational Evolution, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Birgit Rhode
- Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - Dong Xie
- Centre for Computational Evolution, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Mark I Stevens
- South Australian Museum, North Terrace, GPO Box 234, Adelaide, South Australia, 5001, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, GPO Box 2471, Adelaide, South Australia, 5001, Australia
| | - Nicola Nelson
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Thomas R Buckley
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - Alexei J Drummond
- Centre for Computational Evolution, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Richard D Newcomb
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142, New Zealand
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13
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Seldon F L S DS, Buckley TR. The genus Mecodema Blanchard 1853 (Coleoptera: Carabidae: Broscini) from the North Island, New Zealand. Zootaxa 2019; 4598:zootaxa.4598.1.1. [PMID: 31716064 DOI: 10.11646/zootaxa.4598.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/03/2019] [Indexed: 11/04/2022]
Abstract
Mecodema (Coleoptera: Carabidae: Broscini) is a hyperdiverse endemic New Zealand genus of ground beetles with only a few geographically widespread species found throughout the two main islands, as well as many offshore islands. Using specimens from a number of private and institutional collections, in addition new specimens were acquired by extensive pitfall trapping, we describe or redescribe all of the known North Island Mecodema species. Additionally, we redescribe three South Island species from the former genus Metaglymma, as morphological evidence shows that these species are nested within Mecodema. Species descriptions are formed by using 128 morphological characters, which include external characters, as well as both male and female internal structures. There are four new combinations: Mecodema antarctica comb. n., M. aberrans comb. n., M. moniliferum comb. n. and M. tibiale comb. n. We synonymise M. occiputale under Mecodema curvidens, and M. sulcatum under Mecodema oblongum, and reinstate M. scitulum Broun (northwest Hunua Range, Auckland). Twenty four new species are described: Mecodema argentum sp. n., M. atuanui sp. n., M. dunnorum sp. n., M. genesispotini sp. n., M. godzilla sp. n., M. jacinda sp. n., M. kipjac sp. n., M. kokoroiho sp. n., M. mohi sp. n., M. ngaiatonga sp. n., M. ngaitahuhu sp. n., M. papake sp. n., M. perexiguus sp. n., M. rusticulus sp. n., M. temata sp. n., M. teparawhau sp. n., M. teroroa sp. n., M. tewhara sp. n., M. tuhoe sp. n., M. undecimus sp. n., M. wharekahika sp. n., M. xylanthrax sp. n., M. yconomus sp. n., M. zonula sp. n. North Island regional species endemism is very high in Northland (15/16 endemic species), with species becoming more widespread in the southern regions, e.g. Wellington only has two endemic species from a total of eight species. This research increases the total number of described Mecodema species to 102, and will allow a modern taxonomic framework for completion of the revision of the South Island species.
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Affiliation(s)
- David S Seldon F L S
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. Manaaki Whenua - Landcare Research, Private Bag 92170, Auckland 1142, New Zealand..
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14
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Twort VG, Newcomb RD, Buckley TR. New Zealand Tree and Giant Wētā (Orthoptera) Transcriptomics Reveal Divergent Selection Patterns in Metabolic Loci. Genome Biol Evol 2019; 11:1293-1306. [PMID: 30957857 PMCID: PMC6486805 DOI: 10.1093/gbe/evz070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2019] [Indexed: 01/01/2023] Open
Abstract
Exposure to low temperatures requires an organism to overcome physiological challenges. New Zealand wētā belonging to the genera Hemideina and Deinacrida are found across a wide range of thermal environments and therefore subject to varying selective pressures. Here we assess the selection pressures across the wētā phylogeny, with a particular emphasis on identifying genes under positive or diversifying selection. We used RNA-seq to generate transcriptomes for all 18 Deinacrida and Hemideina species. A total of 755 orthologous genes were identified using a bidirectional best-hit approach, with the resulting gene set encompassing a diverse range of functional classes. Analysis of ortholog ratios of synonymous to nonsynonymous amino acid changes found 83 genes that are under positive selection for at least one codon. A wide variety of Gene Ontology terms, enzymes, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways are represented among these genes. In particular, enzymes involved in oxidative phosphorylation, melanin synthesis, and free-radical scavenging are represented, consistent with physiological and metabolic changes that are associated with adaptation to alpine environments. Structural alignment of the transcripts with the most codons under positive selection revealed that the majority of sites are surface residues, and therefore have the potential to influence the thermostability of the enzyme, with the exception of prophenoloxidase where two residues near the active site are under selection. These proteins provide interesting candidates for further analysis of protein evolution.
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Affiliation(s)
- Victoria G Twort
- School of Biological Sciences, University of Auckland, New Zealand.,Manaaki Whenua - Landcare Research, Auckland, New Zealand.,Department of Biology, Lund University, Lund, Sweden
| | - Richard D Newcomb
- School of Biological Sciences, University of Auckland, New Zealand.,The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Thomas R Buckley
- School of Biological Sciences, University of Auckland, New Zealand.,Manaaki Whenua - Landcare Research, Auckland, New Zealand
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15
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Langton‐Myers SS, Holwell GI, Buckley TR. Weak premating isolation betweenClitarchusstick insect species despite divergent male and female genital morphology. J Evol Biol 2019; 32:398-411. [DOI: 10.1111/jeb.13424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/30/2019] [Accepted: 02/01/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Shelley S. Langton‐Myers
- Manaaki Whenua – Landcare Research Auckland New Zealand
- School of Biological SciencesThe University of Auckland Auckland New Zealand
- EcoQuest Education Foundation ‐ Te Rarangahau Taiao Whakatiwai New Zealand
| | - Gregory I. Holwell
- School of Biological SciencesThe University of Auckland Auckland New Zealand
| | - Thomas R. Buckley
- Manaaki Whenua – Landcare Research Auckland New Zealand
- School of Biological SciencesThe University of Auckland Auckland New Zealand
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16
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Wipfler B, Letsch H, Frandsen PB, Kapli P, Mayer C, Bartel D, Buckley TR, Donath A, Edgerly-Rooks JS, Fujita M, Liu S, Machida R, Mashimo Y, Misof B, Niehuis O, Peters RS, Petersen M, Podsiadlowski L, Schütte K, Shimizu S, Uchifune T, Wilbrandt J, Yan E, Zhou X, Simon S. Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects. Proc Natl Acad Sci U S A 2019; 116:3024-3029. [PMID: 30642969 PMCID: PMC6386694 DOI: 10.1073/pnas.1817794116] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyneoptera represents one of the major lineages of winged insects, comprising around 40,000 extant species in 10 traditional orders, including grasshoppers, roaches, and stoneflies. Many important aspects of polyneopteran evolution, such as their phylogenetic relationships, changes in their external appearance, their habitat preferences, and social behavior, are unresolved and are a major enigma in entomology. These ambiguities also have direct consequences for our understanding of the evolution of winged insects in general; for example, with respect to the ancestral habitats of adults and juveniles. We addressed these issues with a large-scale phylogenomic analysis and used the reconstructed phylogenetic relationships to trace the evolution of 112 characters associated with the external appearance and the lifestyle of winged insects. Our inferences suggest that the last common ancestors of Polyneoptera and of the winged insects were terrestrial throughout their lives, implying that wings did not evolve in an aquatic environment. The appearance of the first polyneopteran insect was mainly characterized by ancestral traits such as long segmented abdominal appendages and biting mouthparts held below the head capsule. This ancestor lived in association with the ground, which led to various specializations including hardened forewings and unique tarsal attachment structures. However, within Polyneoptera, several groups switched separately to a life on plants. In contrast to a previous hypothesis, we found that social behavior was not part of the polyneopteran ground plan. In other traits, such as the biting mouthparts, Polyneoptera shows a high degree of evolutionary conservatism unique among the major lineages of winged insects.
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Affiliation(s)
- Benjamin Wipfler
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-University Jena, 07743 Jena, Germany;
- Center of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Harald Letsch
- Department für Botanik und Biodiversitätsforschung, Universität Wien, 1030 Vienna, Austria
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84604
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20002
| | - Paschalia Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Daniela Bartel
- Department of Integrative Zoology, Universität Wien, 1090 Vienna, Austria
| | - Thomas R Buckley
- New Zealand Arthropod Collection, Manaaki Whenua - Landcare Research, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Janice S Edgerly-Rooks
- Department of Biology, College of Arts and Sciences, Santa Clara University, Santa Clara, CA 95053
| | - Mari Fujita
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen 518083, China
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Yuta Mashimo
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Oliver Niehuis
- Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, 79104 Freiburg, Germany
| | - Ralph S Peters
- Center of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Kai Schütte
- Tierökologie und Naturschutz, Universität Hamburg, 20146 Hamburg, Germany
| | - Shota Shimizu
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Toshiki Uchifune
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
- Yokosuka City Museum, Fukadadai, Kanagawa 238-0016, Japan
| | - Jeanne Wilbrandt
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Evgeny Yan
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-University Jena, 07743 Jena, Germany
- Borissiak Palaeontological Institute, Russian Academy of Sciences, 123 Moscow, Russia
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100083, China
| | - Sabrina Simon
- Biosystematics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
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Davis SR, Brav-Cubitt T, Buckley TR, Leschen RAB. Systematics of the New Zealand Weevil Etheophanus Broun (Curculionidae: Molytinae). Zootaxa 2019; 4543:341-374. [PMID: 30647293 DOI: 10.11646/zootaxa.4543.3.2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Indexed: 11/04/2022]
Abstract
Etheophanus Broun is considered a molytine based on the form of the pharyngeal plate, presence of a small spiculum relictum in the male, and presence of a pair of small internal apodemes on the antero-lateral corners of the 5th abdominal ventrite of the female. Examination of primary type specimens and newer material confirm one new species Etheophanus kuscheli sp. n. and two synonomies (Etheophanus nitidellus Broun, 1923 [= Etheophanus obscurus Broun, 1923] and Etheophanus striatus Broun, 1910 [=Etheophanus punctiventris Broun, 1914]). Generic and species diagnoses, a key to the species, and lectotype designations for three species are included. Phylogenetic reconstructions based on a combined analysis of the nuclear 28S rRNA and mitochondrial cytochrome c oxidase subunit I genes confirmed the status of E. kuscheli and a species complex, the E. nitidellus/E. optandus clade distributed in the southern portion of the South Island. The relationship E. pinguis [northern North Island] (E. striatus [southern North Island, northern South Island] (E. kuscheli [northwestern South Island] (E. nitidellus, E. optandus [southwestern North Island]) corresponds to geographic patterns found in other beetle lineages. Etheophanus striatus is composed of three lineages, one widespread in the north and south islands and two allopatric populations in the northwest South Island. The E. nitidellus/E. optandus complex includes four distinct lineages, one restricted to Fiordland, the other three sympatric in the region affected by the Haast Corridor.
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Affiliation(s)
- Steven R Davis
- Division of Invertebrate Zoology, American Museum of Natural History, 200 Central Park West at 79th Street, New York, NY 10024-5192, USA..
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Dopheide A, Xie D, Buckley TR, Drummond AJ, Newcomb RD. Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13086] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Andrew Dopheide
- School of Biological SciencesThe University of Auckland Auckland New Zealand
- The New Zealand Institute for Plant & Food Research Auckland New Zealand
- Manaaki Whenua ‐ Landcare Research Auckland New Zealand
| | - Dong Xie
- Centre for Computational EvolutionThe University of Auckland Auckland New Zealand
| | - Thomas R. Buckley
- School of Biological SciencesThe University of Auckland Auckland New Zealand
- Manaaki Whenua ‐ Landcare Research Auckland New Zealand
| | - Alexei J. Drummond
- Centre for Computational EvolutionThe University of Auckland Auckland New Zealand
| | - Richard D. Newcomb
- School of Biological SciencesThe University of Auckland Auckland New Zealand
- The New Zealand Institute for Plant & Food Research Auckland New Zealand
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19
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Büscher TH, Buckley TR, Grohmann C, Gorb SN, Bradler S. The Evolution of Tarsal Adhesive Microstructures in Stick and Leaf Insects (Phasmatodea). Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00069] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Wu C, Twort VG, Crowhurst RN, Newcomb RD, Buckley TR. Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction. BMC Genomics 2017; 18:884. [PMID: 29145825 PMCID: PMC5691397 DOI: 10.1186/s12864-017-4245-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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] [Received: 08/21/2017] [Accepted: 10/31/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. RESULTS The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria, the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. CONCLUSIONS The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri genome size yet are surprisingly absent from the T. cristinae genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick insects.
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Affiliation(s)
- Chen Wu
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Victoria G. Twort
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
- Department of Biology, Lund University, Lund, Sweden
| | - Ross N. Crowhurst
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Richard D. Newcomb
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Thomas R. Buckley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
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Twort VG, Dennis AB, Park D, Lomas KF, Newcomb RD, Buckley TR. Positive selection and comparative molecular evolution of reproductive proteins from New Zealand tree weta (Orthoptera, Hemideina). PLoS One 2017; 12:e0188147. [PMID: 29131842 PMCID: PMC5683631 DOI: 10.1371/journal.pone.0188147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/01/2017] [Indexed: 11/18/2022] Open
Abstract
Animal reproductive proteins, especially those in the seminal fluid, have been shown to have higher levels of divergence than non-reproductive proteins and are often evolving adaptively. Seminal fluid proteins have been implicated in the formation of reproductive barriers between diverging lineages, and hence represent interesting candidates underlying speciation. RNA-seq was used to generate the first male reproductive transcriptome for the New Zealand tree weta species Hemideina thoracica and H. crassidens. We identified 865 putative reproductive associated proteins across both species, encompassing a diverse range of functional classes. Candidate gene sequencing of nine genes across three Hemideina, and two Deinacrida species suggests that H. thoracica has the highest levels of intraspecific genetic diversity. Non-monophyly was observed in the majority of sequenced genes indicating that either gene flow may be occurring between the species, or that reciprocal monophyly at these loci has yet to be attained. Evidence for positive selection was found for one lectin-related reproductive protein, with an overall omega of 7.65 and one site in particular being under strong positive selection. This candidate gene represents the first step in the identification of proteins underlying the evolutionary basis of weta reproduction and speciation.
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Affiliation(s)
- Victoria G. Twort
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
- * E-mail:
| | | | | | | | - Richard D. Newcomb
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | - Thomas R. Buckley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
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Dearden PK, Gemmell NJ, Mercier OR, Lester PJ, Scott MJ, Newcomb RD, Buckley TR, Jacobs JME, Goldson SG, Penman DR. The potential for the use of gene drives for pest control in New Zealand: a perspective. J R Soc N Z 2017. [DOI: 10.1080/03036758.2017.1385030] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Peter K. Dearden
- Genomics Aotearoa, Bioprotection Research Centre, and Biochemistry Department, University of Otago, Dunedin, Aotearoa New Zealand
| | - Neil J. Gemmell
- Anatomy Department, University of Otago, Dunedin, Aotearoa New Zealand
| | - Ocean R. Mercier
- Te Kawa a Māui—School of Māori Studies, Victoria University of Wellington, Wellington, Aotearoa New Zealand
| | - Philip J. Lester
- School of Biological Sciences, Victoria University of Wellington, Wellington, Aotearoa New Zealand
| | - Maxwell J. Scott
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, USA
| | - Richard D. Newcomb
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, Aotearoa New Zealand
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa New Zealand
| | - Thomas R. Buckley
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa New Zealand
- Landcare Research Ltd, Auckland, Aotearoa New Zealand
| | - Jeanne M. E. Jacobs
- AgResearch, Lincoln Research Centre, Christchurch, Aotearoa New Zealand
- Bioprotection Research Centre, Lincoln University, Canterbury, Aotearoa New Zealand
| | - Stephen G. Goldson
- Bioprotection Research Centre, Lincoln University, Canterbury, Aotearoa New Zealand
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Wu C, Jordan MD, Newcomb RD, Gemmell NJ, Bank S, Meusemann K, Dearden PK, Duncan EJ, Grosser S, Rutherford K, Gardner PP, Crowhurst RN, Steinwender B, Tooman LK, Stevens MI, Buckley TR. Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution. BMC Genomics 2017; 18:795. [PMID: 29041914 PMCID: PMC5644144 DOI: 10.1186/s12864-017-4197-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/08/2017] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events. RESULTS Our genome assembly was ~375 Mbp in size with a scaffold N50 of ~230 Kbp and sequencing coverage of ~180×. DNA elements, LTRs and simple repeats and LINEs formed the largest components and SINEs were very rare. Phylogenomics (370,877 amino acids) placed H. duospinosa within the Neanuridae. We recovered orthologs of the conserved sex determination genes thought to play a role in sex determination. Analysis of CpG content suggested the absence of DNA methylation, and consistent with this we were unable to detect orthologs of the DNA methyltransferase enzymes. The small subunit rRNA gene contained a possible retrotransposon. The Hox gene complex was broken over two scaffolds. For chemosensory ability, at least 15 and 18 ionotropic glutamate and gustatory receptors were identified, respectively. However, we were unable to identify any odorant receptors or their obligate co-receptor Orco. Twenty-three chitinase-like genes were identified from the assembly. Members of this multigene family may play roles in the digestion of fungal cell walls, a common food source for these saproxylic organisms. We also detected 59 and 96 genes that blasted to bacteria and fungi, respectively, but were located on scaffolds that otherwise contained arthropod genes. CONCLUSIONS The genome of H. duospinosa contains some unusual features including a Hox complex broken over two scaffolds, in a different manner to other arthropod species, a lack of odorant receptor genes and an apparent lack of environmentally responsive DNA methylation, unlike many other arthropods. Our detection of candidate horizontal gene transfer candidates confirms that this phenomenon is occurring across Collembola. These findings allow us to narrow down the regions of the arthropod phylogeny where key innovations have occurred that have facilitated the evolutionary success of Hexapoda.
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Affiliation(s)
- Chen Wu
- Landcare Research, Private Bag, Auckland, 92170, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Melissa D Jordan
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Richard D Newcomb
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Sarah Bank
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Karen Meusemann
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
- Evolutionary Biology & Ecology, Institute for Biology, University of Freiburg, Freiburg, Germany
| | - Peter K Dearden
- Genetics Otago, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Elizabeth J Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sefanie Grosser
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-, Martinsried, Germany
| | - Kim Rutherford
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Paul P Gardner
- Biomolecular Interactions Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ross N Crowhurst
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Bernd Steinwender
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Leah K Tooman
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Mark I Stevens
- South Australian Museum, North Terrace, GPO Box 234, Adelaide, SA, 5001, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Thomas R Buckley
- Landcare Research, Private Bag, Auckland, 92170, New Zealand.
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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Painting CJ, Myers S, Holwell GI, Buckley TR. Phylogeography of the New Zealand giraffe weevil Lasiorhynchus barbicornis (Coleoptera: Brentidae): A comparison of biogeographic boundaries. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Buckley TR. Applications of phylogenetics to solve practical problems in insect conservation. Curr Opin Insect Sci 2016; 18:35-39. [PMID: 27939708 DOI: 10.1016/j.cois.2016.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Phylogenetic approaches have much promise for the setting of conservation priorities and resource allocation. There has been significant development of analytical methods for the measurement of phylogenetic diversity within and among ecological communities as a way of setting conservation priorities. Application of these tools to insects has been low as has been the uptake by conservation managers. A critical reason for the lack of uptake includes the scarcity of detailed phylogenetic and species distribution data from much of insect diversity. Environmental DNA technologies offer a means for the high throughout collection of phylogenetic data across landscapes for conservation planning.
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Affiliation(s)
- Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland, New Zealand; School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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Wu C, Crowhurst RN, Dennis AB, Twort VG, Liu S, Newcomb RD, Ross HA, Buckley TR. De Novo Transcriptome Analysis of the Common New Zealand Stick Insect Clitarchus hookeri (Phasmatodea) Reveals Genes Involved in Olfaction, Digestion and Sexual Reproduction. PLoS One 2016; 11:e0157783. [PMID: 27336743 PMCID: PMC4919086 DOI: 10.1371/journal.pone.0157783] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 03/15/2016] [Accepted: 06/03/2016] [Indexed: 11/21/2022] Open
Abstract
Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White). The female olfactory gene repertoire revealed ten odorant binding proteins with three recently duplicated, 12 chemosensory proteins, 16 odorant receptors, and 17 ionotropic receptors. The majority of these olfactory genes were over-expressed in female antennae and have the inferred function of odorant reception. Others that were predominantly expressed in male terminalia (n = 3) and female midgut (n = 1) suggest they have a role in sexual reproduction and digestion, respectively. Over-represented transcripts in the midgut were enriched with digestive enzyme gene families. Clitarchus hookeri is likely to harbour nine members of an endogenous cellulase family (glycoside hydrolase family 9), two of which appear to be specific to the C. hookeri lineage. All of these cellulase sequences fall into four main phasmid clades and show gene duplication events occurred early in the diversification of Phasmatodea. In addition, C. hookeri genome is likely to express γ-proteobacteria pectinase transcripts that have recently been shown to be the result of horizontal transfer. We also predicted 711 male terminalia-enriched transcripts that are candidate accessory gland proteins, 28 of which were annotated to have molecular functions of peptidase activity and peptidase inhibitor activity, two groups being widely reported to regulate female reproduction through proteolytic cascades. Our study has yielded new insights into the genetic basis of odour detection, nutrient digestion, and male sexual traits in stick insects. The C. hookeri reference transcriptome, together with identified gene families, provides a comprehensive resource for studying the evolution of sensory perception, digestive systems, and reproductive success in phasmids.
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Affiliation(s)
- Chen Wu
- Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Ross N. Crowhurst
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Alice B. Dennis
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Victoria G. Twort
- Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Shanlin Liu
- China National GeneBank, BGI-Shenzhen, Shen Zhen, China
| | - Richard D. Newcomb
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Howard A. Ross
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Thomas R. Buckley
- Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Drummond AJ, Newcomb RD, Buckley TR, Xie D, Dopheide A, Potter BC, Heled J, Ross HA, Tooman L, Grosser S, Park D, Demetras NJ, Stevens MI, Russell JC, Anderson SH, Carter A, Nelson N. Evaluating a multigene environmental DNA approach for biodiversity assessment. Gigascience 2015; 4:46. [PMID: 26445670 PMCID: PMC4595072 DOI: 10.1186/s13742-015-0086-1] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [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: 11/03/2014] [Accepted: 09/15/2015] [Indexed: 12/30/2022] Open
Abstract
Background There is an increasing demand for rapid biodiversity assessment tools that have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing (NGS) that span the tree of life, comparing them with traditional biodiversity monitoring tools within ten 20×20 meter plots along a 700 meter elevational gradient. Results From six eDNA datasets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 109 NCBI taxonomy-defined phyla or equivalent, ranging from 31 to 60 for a given eDNA marker. Estimates of alpha and gamma diversity were sensitive to the number of sequence reads, whereas beta diversity estimates were less sensitive. The average within-plot beta diversity was lower than between plots for all markers. The soil beta diversity of COI and 18S markers showed the strongest response to the elevational variation of the eDNA markers (COI: r=0.49, p<0.001; 18S: r=0.48, p<0.001). Furthermore pairwise beta diversities for these two markers were strongly correlated with those calculated from traditional vegetation and invertebrate biodiversity measures. Conclusions Using a soil-based eDNA approach, we demonstrate that standard phylogenetic markers are capable of recovering sequences from a broad diversity of eukaryotes, in addition to prokaryotes by 16S. The COI and 18S eDNA markers are the best proxies for aboveground biodiversity based on the high correlation between the pairwise beta diversities of these markers and those obtained using traditional methods. Electronic supplementary material The online version of this article (doi:10.1186/s13742-015-0086-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexei J Drummond
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; Department of Computer Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Richard D Newcomb
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand ; The Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142 New Zealand
| | - Thomas R Buckley
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand ; Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | - Dong Xie
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; Department of Computer Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Andrew Dopheide
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand ; The Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142 New Zealand
| | - Benjamin Cm Potter
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Joseph Heled
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; Department of Computer Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Howard A Ross
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Leah Tooman
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; The Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142 New Zealand
| | - Stefanie Grosser
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | - Duckchul Park
- Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | - Nicholas J Demetras
- Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton, 3240 New Zealand
| | - Mark I Stevens
- South Australian Museum, North Terrace, Adelaide, SA 5000 Australia ; School of Pharmacy and Medical Sciences, University of South Australia, GPO Box 2471, Adelaide, SA 5001 Australia
| | - James C Russell
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand ; Department of Statistics, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Sandra H Anderson
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Anna Carter
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140 New Zealand
| | - Nicola Nelson
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140 New Zealand
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Bradler S, Cliquennois N, Buckley TR. Single origin of the Mascarene stick insects: ancient radiation on sunken islands? BMC Evol Biol 2015; 15:196. [PMID: 26377339 PMCID: PMC4573937 DOI: 10.1186/s12862-015-0478-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The study of islands as model systems plays a key role in understanding many evolutionary processes. Knowledge of the historical events leading to present-day island communities is pivotal for exploring fundamental mechanisms of speciation and adaptation. The remote Mascarene archipelago (Mauritius, Réunion, Rodrigues), considered to be the product of an age-progressive trend of north-to-south volcanic activity in the Indian Ocean, hosts a remarkably diverse, endemic and threatened concentration of flora and fauna that has traditionally been considered to be biogeographically related to Madagascar and Africa. To explore the evolutionary diversity of the Mascarene stick insects (Phasmatodea), we constructed a global phylogeny from approximately 2.4 kb of mitochondrial and nuclear sequence data of more than 120 species representing all major phasmatodean lineages. RESULTS Based on the obtained time-calibrated molecular tree we demonstrate that the current phasmid community of the Mascarene archipelago, which consists of members of four presumably unrelated traditional subfamilies, is the result of a single ancient dispersal event from Australasia and started radiating between 16-29 million years ago, significantly predating the age of Mauritius (8-10 million years). CONCLUSIONS We propose that the Mascarene stick insects diversified on landmasses now eroded away, presumably to the north of Mauritius. In consequence, ancient islands have probably persisted in the Indian Ocean until the emergence of Mauritius and not only served as stepping stones for colonisation events during sea-level lowstands, but as long-lasting cradles of evolution. These ancient landmasses most likely allowed for adaptive speciation and served as significant sources of diversity that contributed to the biomes of the Mascarene archipelago and the megadiverse Madagascar.
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Affiliation(s)
- Sven Bradler
- Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Georg-August-University Göttingen, Berliner Str. 28, 37073, Göttingen, Germany.
| | - Nicolas Cliquennois
- Collège français, Lot 02 F 15 Tomboarivo, B.P. 141, 110, Antsirabe, Madagascar
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
- Allan Wilson Centre, Auckland, New Zealand
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Ward DF, Leschen RA, Buckley TR. More from ecologists to support natural history museums. Trends Ecol Evol 2015; 30:373-4. [DOI: 10.1016/j.tree.2015.04.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 10/23/2022]
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Abstract
For animals that exhibit a scramble competition mating system, sexual selection pressures on mate searching ability are expected to be strong. Scramble competition mating systems evolve when populations provide females with equal accessibility to all male competitors, yet sex ratio and population density influences mating systems and varies seasonally. The stick insect species,Clitarchus hookeri, is frequently found in copula, yet very little is known about it’s mating behaviour. We preformed behavioural tests and assayed antennal sensory morphology to determine whether males used chemosensory cues to detect females. Through natural field observations we found populations to be significantly male-biased earlier in the season, while later, populations began to display equal sex ratios. With increasing female availability mating pair proportions steadily increased, while copulation duration declined. These results supportC. hookerias a scramble competitor, and demonstrate males may alter their behaviour in response to the seasonal variation in female density.
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Affiliation(s)
- Shelley S. Myers
- Landcare Research, Private Bag 92170, Auckland 1142, New Zealand
- The School of Biological Sciences, The University of Auckland, 1142, New Zealand
- Allan Wilson Centre, Auckland, New Zealand
| | - Thomas R. Buckley
- Landcare Research, Private Bag 92170, Auckland 1142, New Zealand
- The School of Biological Sciences, The University of Auckland, 1142, New Zealand
- Allan Wilson Centre, Auckland, New Zealand
| | - Gregory I. Holwell
- The School of Biological Sciences, The University of Auckland, 1142, New Zealand
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Buckley TR, Myers SS, Bradler S. Revision of the stick insect genus Clitarchus Stål (Phasmatodea: Phasmatidae): new synonymies and two new species from northern New Zealand. Zootaxa 2014; 3900:451-82. [PMID: 25543751 DOI: 10.11646/zootaxa.3900.4.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 11/04/2022]
Abstract
We describe two new species of Clitarchus Stål from Northland, New Zealand. Clitarchus rakauwhakanekeneke sp. nov. is described from the Poor Knights Islands and Clitarchus tepaki sp. nov. is described from the Te Paki / North Cape area and the Karikari Peninsula at the northernmost tip of New Zealand. Two new synonymies are proposed including Clitarchus multidentatus Brunner (syn. nov.) and Clitarchus tuberculatus Salmon (syn. nov.) as synonyms of Clitarchus hookeri (White). Clitarchus magnus Brunner, recorded from Thailand, is transferred to Ramulus Saussure and given the replacement name Ramulus changmaiense nom. nov. The holotype of C. multidentatus was recorded as being collected from New Caledonia; however we believe this is a labelling error and the specimen was collected from New Zealand. These taxonomic changes render Clitarchus endemic to New Zealand and consisting of three species; C. hookeri, C. rakauwhakanekeneke and C. tepaki. Keys to the adult males and females of Clitarchus species are given in addition to notes on host plants, ecology and geographic distributions.
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Affiliation(s)
- Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland, New Zealand. School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand Allan Wilson Centre, Auckland, New Zealand;
| | - Shelley S Myers
- Landcare Research, Private Bag 92170, Auckland, New Zealand. School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand Allan Wilson Centre, Auckland, New Zealand;
| | - Sven Bradler
- Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Georg-August-Universität Göttingen, Berliner Strasse 28, 37073 Göttingen, Germany.;
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Dunning LT, Dennis AB, Sinclair BJ, Newcomb RD, Buckley TR. Divergent transcriptional responses to low temperature among populations of alpine and lowland species of New Zealand stick insects (Micrarchus). Mol Ecol 2014; 23:2712-26. [DOI: 10.1111/mec.12767] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 04/10/2014] [Accepted: 04/16/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Luke T. Dunning
- Landcare Research; Private Bag 92170 Auckland New Zealand
- School of Biological Sciences; The University of Auckland; Private Bag 92019 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
| | - Alice B. Dennis
- Landcare Research; Private Bag 92170 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
| | - Brent J. Sinclair
- Department of Biology; The University of Western Ontario; London ON Canada N6G 1L3
| | - Richard D. Newcomb
- School of Biological Sciences; The University of Auckland; Private Bag 92019 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
- The New Zealand Institute of Plant & Food Research Limited; Private Bag 92169 Auckland New Zealand
| | - Thomas R. Buckley
- Landcare Research; Private Bag 92170 Auckland New Zealand
- School of Biological Sciences; The University of Auckland; Private Bag 92019 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
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Murienne J, Daniels SR, Buckley TR, Mayer G, Giribet G. A living fossil tale of Pangaean biogeography. Proc Biol Sci 2014; 281:20132648. [PMID: 24285200 PMCID: PMC3866409 DOI: 10.1098/rspb.2013.2648] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 10/31/2013] [Indexed: 11/12/2022] Open
Abstract
The current distributions of widespread groups of terrestrial animals and plants are supposedly the result of a mixture of either vicariance owing to continental split or more recent trans-oceanic dispersal. For organisms exhibiting a vicariant biogeographic pattern-achieving their current distribution by riding on the plates of former supercontinents-this view is largely inspired by the belief that Pangaea lacked geographical or ecological barriers, or that extinctions and dispersal would have erased any biogeographic signal since the early Mesozoic. We here present a time-calibrated molecular phylogeny of Onychophora (velvet worms), an ancient and exclusively terrestrial panarthropod group distributed throughout former Pangaean landmasses. Our data not only demonstrate that trans-oceanic dispersal does not need be invoked to explain contemporary distributions, but also reveal that the early diversification of the group pre-dates the break-up of Pangaea, maintaining regionalization even in landmasses that have remained contiguous throughout the history of the group. These results corroborate a growing body of evidence from palaeontology, palaeogeography and palaeoclimatic modelling depicting ancient biogeographic regionalization over the continuous landmass of Pangaea.
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Affiliation(s)
- Jerome Murienne
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- CNRS, Université Paul Sabatier, ENFA, UMR 5174 EDB (Laboratoire Évolution et Diversité Biologique), Université de Toulouse, 118 route de Narbonne, Toulouse 31062, France
| | - Savel R. Daniels
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - Thomas R. Buckley
- Landcare Research, Auckland Mail Centre, Private Bag 92170, Auckland 1142, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
| | - Georg Mayer
- Animal Evolution and Development, Institute of Biology, University of Leipzig, Talstraße 33, Leipzig 04103, Germany
| | - Gonzalo Giribet
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Novis PM, Smissen R, Buckley TR, Gopalakrishnan K, Visnovsky G. Inclusion of chloroplast genes that have undergone expansion misleads phylogenetic reconstruction in the Chlorophyta. Am J Bot 2013; 100:2194-2209. [PMID: 24148615 DOI: 10.3732/ajb.1200584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Chlorophytes comprise a substantial proportion of green plant diversity. However, sister-group relationships and circumscription of the classes Chlorophyceae, Trebouxiophyceae, and Ulvophyceae have been problematic to resolve. Some analyses support a sister relationship between the trebouxiophycean Leptosira and chlorophyceans, potentially altering the circumscription of two classes, also supported by a shared fragmentation in the chloroplast gene rpoB. We sought to determine whether the latter is a synapomorphy or whether the supporting analyses are vulnerable to systematic bias. METHODS We sequenced a portion of rpoB spanning the fragmented region in strains for which it had not previously been sampled: four Chlorophyceae, six counterclockwise (CCW) group (ulvophyceans and trebouxiophyceans) and one streptophyte. We then explored the effect of subsampling proteins and taxa on phylogenetic reconstruction from a data set of 41 chloroplast proteins. KEY RESULTS None of the CCW or streptophyte strains possessed the split in rpoB, including inferred near relatives of Leptosira, but it was found in all chlorophycean strains. We reconstructed alternative phylogenies (Leptosira + Chlorophyceae and Leptosira + Chlorellales) using two different protein groups (Rpo and Rps), both subject to coding-region expansion. A conserved region of RpoB remained suitable for analysis of more recent divergences. CONCLUSIONS The Rps sequences can explain earlier findings linking Leptosira with the Chlorophyceae and should be excluded from phylogenetic analyses attempting to resolve deep nodes because their expansion violates the assumptions of substitution models. We reaffirm that Leptosira is a trebouxiophycean and that fragmentation of rpoB has occurred at least twice in chlorophyte evolution.
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Affiliation(s)
- Phil M Novis
- Allan Herbarium, Landcare Research, P.O. Box 69040, Lincoln 7640, New Zealand
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Dunning LT, Dennis AB, Thomson G, Sinclair BJ, Newcomb RD, Buckley TR. Positive selection in glycolysis among Australasian stick insects. BMC Evol Biol 2013; 13:215. [PMID: 24079656 PMCID: PMC3850572 DOI: 10.1186/1471-2148-13-215] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [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: 05/02/2013] [Accepted: 09/23/2013] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The glycolytic pathway is central to cellular energy production. Selection on individual enzymes within glycolysis, particularly phosphoglucose isomerase (Pgi), has been associated with metabolic performance in numerous organisms. Nonetheless, how whole energy-producing pathways evolve to allow organisms to thrive in different environments and adopt new lifestyles remains little explored. The Lanceocercata radiation of Australasian stick insects includes transitions from tropical to temperate climates, lowland to alpine habitats, and winged to wingless forms. This permits a broad investigation to determine which steps within glycolysis and what sites within enzymes are the targets of positive selection. To address these questions we obtained transcript sequences from seven core glycolysis enzymes, including two Pgi paralogues, from 29 Lanceocercata species. RESULTS Using maximum likelihood methods a signature of positive selection was inferred in two core glycolysis enzymes. Pgi and Glyceraldehyde 3-phosphate dehydrogenase (Gaphd) genes both encode enzymes linking glycolysis to the pentose phosphate pathway. Positive selection among Pgi paralogues and orthologues predominately targets amino acids with residues exposed to the protein's surface, where changes in physical properties may alter enzyme performance. CONCLUSION Our results suggest that, for Lancerocercata stick insects, adaptation to new stressful lifestyles requires a balance between maintaining cellular energy production, efficiently exploiting different energy storage pools and compensating for stress-induced oxidative damage.
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Affiliation(s)
- Luke T Dunning
- Landcare Research, Private Bag 92170, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
- Imperial College London, Silwood Park Campus, Buckhurst Road, SL5 7PY, Ascot, Berks, UK
| | - Alice B Dennis
- Landcare Research, Private Bag 92170, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
| | - Geoffrey Thomson
- Landcare Research, Private Bag 92170, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Brent J Sinclair
- Department of Biology, The University of Western Ontario, London, ON, Canada N6G 1L3
| | - Richard D Newcomb
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
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Dunning LT, Dennis AB, Park D, Sinclair BJ, Newcomb RD, Buckley TR. Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 2013; 8:24-31. [DOI: 10.1016/j.cbd.2012.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/19/2012] [Accepted: 10/20/2012] [Indexed: 12/22/2022]
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Affiliation(s)
| | - Richard A. B. Leschen
- New Zealand Arthropod Collection; Landcare Research; Private Bag 92170; Auckland; New Zealand
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Marshall DC, Hill KBR, Marske KA, Chambers C, Buckley TR, Simon C. Limited, episodic diversification and contrasting phylogeography in a New Zealand cicada radiation. BMC Evol Biol 2012; 12:177. [PMID: 22967046 PMCID: PMC3537654 DOI: 10.1186/1471-2148-12-177] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 08/15/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The New Zealand (NZ) cicada fauna contains two co-distributed lineages that independently colonized the isolated continental fragment in the Miocene. One extensively studied lineage includes 90% of the extant species (Kikihia + Maoricicada + Rhodopsalta; ca 51 spp.), while the other contains just four extant species (Amphipsalta - 3 spp. + Notopsalta - 1 sp.) and has been little studied. We examined mitochondrial and nuclear-gene phylogenies and phylogeography, Bayesian relaxed-clock divergence timing (incorporating literature-based uncertainty of molecular clock estimates) and ecological niche models of the species from the smaller radiation. RESULTS Mitochondrial and nuclear-gene trees supported the monophyly of Amphipsalta. Most interspecific diversification within Amphipsalta-Notopsalta occurred from the mid-Miocene to the Pliocene. However, interspecific divergence time estimates had large confidence intervals and were highly dependent on the assumed tree prior, and comparisons of uncorrected and patristic distances suggested difficulty in estimation of branch lengths. In contrast, intraspecific divergence times varied little across analyses, and all appear to have occurred during the Pleistocene. Two large-bodied forest taxa (A. cingulata, A. zelandica) showed minimal phylogeographic structure, with intraspecific diversification dating to ca. 0.16 and 0.37 Ma, respectively. Mid-Pleistocene-age phylogeographic structure was found within two smaller-bodied species (A. strepitans - 1.16 Ma, N. sericea - 1.36 Ma] inhabiting dry open habitats. Branches separating independently evolving species were long compared to intraspecific branches. Ecological niche models hindcast to the Last Glacial Maximum (LGM) matched expectations from the genetic datasets for A. zelandica and A. strepitans, suggesting that the range of A. zelandica was greatly reduced while A. strepitans refugia were more extensive. However, no LGM habitat could be reconstructed for A. cingulata and N. sericea, suggesting survival in microhabitats not detectable with our downscaled climate data. CONCLUSIONS Unlike the large and continuous diversification exhibited by the Kikihia-Maoricicada-Rhodopsalta clade, the contemporaneous Amphipsalta-Notopsalta lineage contains four comparatively old (early branching) species that show only recent diversification. This indicates either a long period of stasis with no speciation, or one or more bouts of extinction that have pruned the radiation. Within Amphipsalta-Notopsalta, greater population structure is found in dry-open-habitat species versus forest specialists. We attribute this difference to the fact that NZ lowland forests were repeatedly reduced in extent during glacial periods, while steep, open habitats likely became more available during late Pleistocene uplift.
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Affiliation(s)
- David C Marshall
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd, Storrs, CT, 06269, USA
| | - Kathy B R Hill
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd, Storrs, CT, 06269, USA
| | - Katharine A Marske
- Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen, Denmark
- Landcare Research, Private Bag 92170, Auckland, New Zealand
| | - Colleen Chambers
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd, Storrs, CT, 06269, USA
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd, Storrs, CT, 06269, USA
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Marske KA, Leschen RAB, Buckley TR. CONCERTED VERSUS INDEPENDENT EVOLUTION AND THE SEARCH FOR MULTIPLE REFUGIA: COMPARATIVE PHYLOGEOGRAPHY OF FOUR FOREST BEETLES. Evolution 2012; 66:1862-77. [DOI: 10.1111/j.1558-5646.2011.01538.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Marske KA, Leschen RA, Buckley TR. Reconciling phylogeography and ecological niche models for New Zealand beetles: Looking beyond glacial refugia. Mol Phylogenet Evol 2011; 59:89-102. [DOI: 10.1016/j.ympev.2011.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 11/12/2010] [Accepted: 01/13/2011] [Indexed: 02/07/2023]
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Buckley TR, Stringer I, Gleeson D, Howitt R, Attanayake D, Parrish R, Sherley G, Rohan M. A revision of the New Zealand Placostylus land snails using mitochondrial DNA and shell morphometric analyses, with implications for conservation. New Zealand Journal of Zoology 2011. [DOI: 10.1080/03014223.2010.527997] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- TR Buckley
- a Landcare Research , Auckland, New Zealand
| | - I Stringer
- b Department of Conservation , Wellington, New Zealand
| | - D Gleeson
- a Landcare Research , Auckland, New Zealand
| | - R Howitt
- a Landcare Research , Auckland, New Zealand
| | | | - R Parrish
- c Karaka RD1 , Papakura, New Zealand
| | - G Sherley
- d United Nations Environmental Programme , Matautu Uta, Apia, Samoa
| | - M Rohan
- b Department of Conservation , Wellington, New Zealand
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O'Neill SB, Buckley TR, Jewell TR, Ritchie PA. Phylogeographic history of the New Zealand stick insect Niveaphasma annulata (Phasmatodea) estimated from mitochondrial and nuclear loci. Mol Phylogenet Evol 2009; 53:523-36. [PMID: 19596452 DOI: 10.1016/j.ympev.2009.07.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 07/05/2009] [Accepted: 07/06/2009] [Indexed: 11/28/2022]
Abstract
We have assessed the utility of a single-copy nuclear locus and mitochondrial DNA (mtDNA) in a phylogeographic study of the New Zealand stick insect Niveaphasma annulata (Hutton). We amplified sequences from the mitochondrial cytochrome oxidase subunit I (COI) gene and the single-copy nuclear gene elongation factor-1alpha (EF1alpha) from 97 individuals. Allelic phase at the EF1alpha locus was determined using Denaturing Gradient Gel Electrophoresis. Phylogenetic analyses showed broad congruence between the geographic distribution of three major COI clades and EF1alpha alleles, which suggested that the phylogenetic patterns reflect population history rather than lineage sorting. However, the geographic boundaries of these clades were not always in exact agreement between the two loci. Our data indicate that Niveaphasma annulata was most likely separated into a number of refugia during Pleistocene glacial advances. Subsequent to glacial retreat these refugial populations have expanded and now form a number of zones of secondary contact. We contrast these patterns with those observed from other New Zealand taxa. Our study offers compelling evidence for the use of nuclear genes alongside mtDNA for future phylogeographic studies.
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Affiliation(s)
- Shay B O'Neill
- Allan Wilson Centre for Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Buckley TR, Attanayake D, Bradler S. Extreme convergence in stick insect evolution: phylogenetic placement of the Lord Howe Island tree lobster. Proc Biol Sci 2009; 276:1055-62. [PMID: 19129110 DOI: 10.1098/rspb.2008.1552] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The 'tree lobsters' are an enigmatic group of robust, ground-dwelling stick insects (order Phasmatodea) from the subfamily Eurycanthinae, distributed in New Guinea, New Caledonia and associated islands. Its most famous member is the Lord Howe Island stick insect Dryococelus australis (Montrouzier), which was believed to have become extinct but was rediscovered in 2001 and is considered to be one of the rarest insects in the world. To resolve the evolutionary position of Dryococelus, we constructed a phylogeny from approximately 2.4 kb of mitochondrial and nuclear sequence data from representatives of all major phasmatodean lineages. Our data placed Dryococelus and the New Caledonian tree lobsters outside the New Guinean Eurycanthinae as members of an unrelated Australasian stick insect clade, the Lanceocercata. These results suggest a convergent origin of the 'tree lobster' body form. Our reanalysis of tree lobster characters provides additional support for our hypothesis of convergent evolution. We conclude that the phenotypic traits leading to the traditional classification are convergent adaptations to ground-living behaviour. Our molecular dating analyses indicate an ancient divergence (more than 22 Myr ago) between Dryococelus and its Australian relatives. Hence, Dryococelus represents a long-standing separate evolutionary lineage within the stick insects and must be regarded as a key taxon to protect with respect to phasmatodean diversity.
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Affiliation(s)
- Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland 1142, New Zealand.
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Langhoff P, Authier A, Buckley TR, Dugdale JS, Rodrigo A, Newcomb RD. DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and Planotortrix. Mol Ecol Resour 2009; 9:691-8. [PMID: 21564726 DOI: 10.1111/j.1755-0998.2009.02537.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular techniques such as DNA barcoding have become popular in assisting species identification especially for cryptic species complexes. We have analysed data from a 468-bp region of the mitochondrial cytochrome oxidase subunit I (COI) gene from 200 specimens of 12 species of endemic New Zealand leafroller moths (Tortricidae) from the genera Planotortrix and Ctenopseustis to assess whether the DNA barcoding region can distinguish these species. Among the 200 sequences analysed, 72 haplotypes were recovered, with each genus forming a separate major clade. Maximum likelihood phylogenetic methods were used to test whether species fell into reciprocally monophyletic clades. The optimal phylogeny showed that four species within the genus Ctenopseustis (C. obliquana, C. herana, C. filicis and C. fraterna) and three within Planotortrix (P. octo, P. excessana and P. avicenniae) are polyphyletic. Shimodaira-Hasegawa tests rejected a null hypothesis of monophyly for the species C. obliquana, C. herana, P. octo and P. excessana. Comparisons of within and between species levels of sequence divergence for the same set of seven species showed cases where maximum levels of within-species divergence were greater than some levels of between-species divergence. DNA barcoding using this region of the COI gene is able to distinguish the two genera and some species within each genus; however, many species cannot be identified using this method. Finally, we discuss the possible reasons for this polyphyly, including incomplete lineage sorting, introgression, horizontal gene transfer and incorrect taxonomy.
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Affiliation(s)
- Pia Langhoff
- Molecular Olfaction Group, HortResearch, Private Bag 92169, Auckland 1003, New Zealand Landcare Research, Private Bag 92170, Auckland 1142, New Zealand Landcare Research, Private Bag 6, Nelson 7042, New Zealand Bioinformatics Institute, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Yeates GW, Buckley TR. First records of mermithid nematodes (Nematoda: Mermithidae) parasitising stick insects (Insecta: Phasmatodea). New Zealand Journal of Zoology 2009. [DOI: 10.1080/03014220909510137] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
The dominance of angiosperms has played a direct role in the diversification of insects, especially Coleoptera. The shift to angiosperm feeding from other diets is likely to have increased the rate of speciation in Phytophaga. However, Phytophaga is only one of many hyperdiverse lineages of beetles and studies of host-shift proliferation have been somewhat limited to groups that primitively feed on plants. We have studied the diet-diverse beetle family Erotylidae (Cucujoidea) to determine if diet is correlated with high diversification rates and morphological evolution by first reconstructing ancestral diets and then testing for associations between diet and species number and diet and ovipositor type. A Bayesian phylogenetic analysis of morphological data that was previously published in Leschen (2003, Pages 1-108 in Fauna of New Zealand, 47; 53 terminal taxa and 1 outgroup, 120 adult characters and 1 diet character) yielded results that are similar to the parsimony analyses of Leschen (2003). Ancestral state reconstructions based on Bayesian and parsimony inference were largely congruent and both reconstructed microfungal feeding (the diet of the outgroup Biphyllidae) at the root of the Erotylidae tree. Shifts among microfungal, saprophagous, and phytophagous diets were most frequent. The largest numbers of species are contained in lineages that are macrofungal feeders (subfamily Erotylinae) and phytophagous (derived Languriinae), although the Bayesian posterior predictive tests of character state correlation were unable to detect any significant associations. Ovipositor morphology correlated with diet (i.e., acute forms were associated with phytophagy and unspecialized forms were associated with a mixture of diets). Although there is a general trend to increased species number associated with the shift from microfungal feeding to phytophagy (based on character mapping and mainly restricted to shifts in Languriinae), there is a large radiation of taxa feeding on macrofungi. Cycad feeding is scattered in more deeply diverged taxa and may have preceded the evolution of angiosperm feeding in some groups. Preliminary analysis of diet mapped onto higher beetle phylogenies suggests that about half of the major Coleoptera lineages may have had fungus-feeding ancestors. We discuss the roles of stochastic models and prior distributions of the reconstruction of ancestral character states in the context of the current data.
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Affiliation(s)
- Richard A B Leschen
- New Zealand Arthropod Collection, Landcare Research, drivate Bag 92170, Auckland, New Zealand.
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Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT. Incorporating Molecular Evolution into Phylogenetic Analysis, and a New Compilation of Conserved Polymerase Chain Reaction Primers for Animal Mitochondrial DNA. Annu Rev Ecol Evol Syst 2006. [DOI: 10.1146/annurev.ecolsys.37.091305.110018] [Citation(s) in RCA: 429] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chris Simon
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
- School of Biological Sciences, Victoria University of Wellington, Wellington 6014, New Zealand
| | | | - Francesco Frati
- Department of Evolutionary Biology, University of Siena, 53100 Siena, Italy;
| | - James B. Stewart
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada; ,
- Department of Laboratory Medicine, Division of Metabolic Diseases, Karolinska Institutet, Norvum 141 86, Stockholm, Sweden
| | - Andrew T. Beckenbach
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada; ,
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Marshall DC, Simon C, Buckley TR. Accurate Branch Length Estimation in Partitioned Bayesian Analyses Requires Accommodation of Among-Partition Rate Variation and Attention to Branch Length Priors. Syst Biol 2006; 55:993-1003. [PMID: 17345679 DOI: 10.1080/10635150601087641] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- David C Marshall
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, Connecticut 06269, USA.
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Buckley TR, Cordeiro M, Marshall DC, Simon C. Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale). Syst Biol 2006; 55:411-25. [PMID: 16684720 DOI: 10.1080/10635150600697283] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Lineage sorting and introgression can lead to incongruence among gene phylogenies, complicating the inference of species trees for large groups of taxa that have recently and rapidly radiated. In addition, it can be difficult to determine which of these processes is responsible for this incongruence. We explore these issues with the radiation of New Zealand alpine cicadas of the genus Maoricicada Dugdale. Gene trees were estimated from four putative independent loci: mitochondrial DNA (2274 nucleotides), elongation factor 1-alpha (1275 nucleotides), period (1709 nucleotides), and calmodulin (678 nucleotides). We reconstructed phylogenies using maximum likelihood and Bayesian methods from 44 individuals representing the 19 species and subspecies of Maoricicada and two outgroups. Species-level relationships were reconstructed using a novel extension of gene tree parsimony, whereby gene trees were weighted by their Bayesian posterior probabilities. The inferred gene trees show marked incongruence in the placement of some taxa, especially the enigmatic forest and scrub dwelling species, M. iolanthe. Using the species tree estimated by gene tree parsimony, we simulated coalescent gene trees in order to test the null hypothesis that the nonrandom placement of M. iolanthe among gene trees has arisen by chance. Under the assumptions of constant population size, known generation time, and panmixia, we were able to reject this null hypothesis. Furthermore, because the two alternative placements of M. iolanthe are in each case with species that share a similar song structure, we conclude that it is more likely that an ancient introgression event rather than lineage sorting has caused this incongruence.
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