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Graham ZA, Padilla Perez DJ. Correlated evolution of conspicuous colouration and burrowing in crayfish. Proc Biol Sci 2024; 291:20240632. [PMID: 38981529 PMCID: PMC11335007 DOI: 10.1098/rspb.2024.0632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 05/02/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024] Open
Abstract
Conspicuous colours have fascinated biologists for centuries, leading to research on the evolution and functional significance of colour traits. In many cases, research suggests that conspicuous colours are adaptive and serve a function in sexual or aposematic signalling. In other cases, a lack of evidence for the adaptive value of conspicuous colours garners interest from biologists, such as when organisms that live underground and are rarely exposed to the surface are nevertheless colourful. Here, we use phylogenetic comparative methods to investigate colour evolution throughout freshwater crayfishes that vary in burrowing ability. Within the taxa we analysed, conspicuous colours have evolved independently over 50 times, and these colours are more common in semi-terrestrial crayfishes that construct extensive burrows. The intuitive but not evolutionarily justified assumption when presented with these results is to assume that these colours are adaptive. But contrary to this intuition, we discuss the hypothesis that colouration in crayfish is neutral. Supporting these ideas, the small population sizes and reduced gene flow within semi-terrestrial burrowing crayfishes may lead to the fixation of colour-phenotype mutations. Overall, our work brings into question the traditional view of animal colouration as a perfectly adapted phenotype.
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Affiliation(s)
- Zackary A. Graham
- Department of Organismal Biology, Ecology, and Zoo Science, West Liberty University, 208 University Drive, West Liberty, WV26074, USA
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2
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Neculae A, Barnett ZC, Miok K, Dalosto MM, Kuklina I, Kawai T, Santos S, Furse JM, Sîrbu OI, Stoeckel JA, Pârvulescu L. Living on the edge: Crayfish as drivers to anoxification of their own shelter microenvironment. PLoS One 2024; 19:e0287888. [PMID: 38165988 PMCID: PMC10760702 DOI: 10.1371/journal.pone.0287888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/14/2023] [Indexed: 01/04/2024] Open
Abstract
Burrowing is a common trait among crayfish thought to help species deal with adverse environmental challenges. However, little is known about the microhabitat ecology of crayfish taxa in relation to their burrows. To fill this knowledge gap, we assessed the availability of oxygen inside the crayfish shelter by series of in-vivo and in-silico modelling experiments. Under modeled condition, we found that, except for the entrance region of the 200 mm, a flooded burrow microenvironment became anoxic within 8 h, on average. Multiple 12-hour day-night cycles, with burrows occupied by crayfish for 12 h and empty for 12 h, were not sufficient for refreshing the burrow microenvironment. We then examined the degree to which crayfish species with different propensities for burrowing are tolerant of self-created anoxia. From these experiments, primary and secondary burrowers showed best and most consistent tolerance-exhibiting ≥ 64% survival to anoxia and 25-91% survival of ≥ 9 h at anoxia, respectively. Tertiary burrowers exhibited little to no tolerance of anoxia with 0-50% survival to anoxia and only one species exhibiting survival (2%) of ≥ 9 h at anoxia. Results suggest that moderate to strongly burrowing crayfish can quickly draw down the dissolved oxygen in burrow water but appear to have conserved a legacy of strong tolerance of anoxia from their monophyletic ancestors-the lobsters-whereas tertiary burrowers have lost (or never evolved) this ability.
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Affiliation(s)
- Adrian Neculae
- Faculty of Physics, West University of Timisoara, Timisoara, Romania
| | - Zanethia C. Barnett
- Center for Bottomland Hardwoods Research, Southern Research Station, USDA Forest Service, Oxford, MS, United States of Ameirca
| | - Kristian Miok
- Crayfish Research Centre, Institute for Advanced Environmental Research, West University of Timisoara, Timisoara, Romania
| | - Marcelo M. Dalosto
- Laboratório de Carcinologia, Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Iryna Kuklina
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Tadashi Kawai
- Central Fisheries Research Institute, Yoichi, Hokkaido, Japan
| | - Sandro Santos
- Laboratório de Carcinologia, Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - James M. Furse
- Coastal and Marine Research Centre, Griffith University, Gold Coast, Queensland, Australia
| | - Ovidiu I. Sîrbu
- Department of Biochemistry and Pharmacology, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - James A. Stoeckel
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, United States of America
| | - Lucian Pârvulescu
- Crayfish Research Centre, Institute for Advanced Environmental Research, West University of Timisoara, Timisoara, Romania
- Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University of Timisoara, Timisoara, Romania
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Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci Rep 2019; 9:10756. [PMID: 31341205 PMCID: PMC6656734 DOI: 10.1038/s41598-019-47145-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023] Open
Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia.
- Deakin Genomics Centre, Deakin University, Geelong, Australia.
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, North Miami, Florida, 33181, USA
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Adam D Miller
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
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Decker P. Phylogenetic and morphological discord indicates introgressive hybridisation in two genera of Australian millipedes (Diplopoda, Polydesmida, Paradoxosomatidae). Zookeys 2019:1-14. [PMID: 30598611 PMCID: PMC6306475 DOI: 10.3897/zookeys.809.30087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/26/2018] [Indexed: 11/12/2022] Open
Abstract
Discord between molecular and morphological datasets was observed in two pairs of species of Australian millipedes in the family Paradoxosomatidae using morphological and molecular phylogenetic analysis (mitochondrial COI rDNA and 16 rRNA, and nuclear 28S rRNA). Close to the presumed distributional boundary between Pogonosternumnigrovirgatum (Carl, 1912) and Pogonosternumjeekeli Decker, 2017, near Dargo in Central Gippsland, Victoria, Pogonosternum specimens were collected which are phylogenetically closer to P.jeekeli in COI and 16S sequences, but are morphologically closer to P.nigrovirgatum. At Mount Osmond, Adelaide, South Australia, eight morphologically typical Somethuscastaneus (Attems, 1944) specimens were collected are phylogenetically closer to S.castaneus in 28S genealogy, but three of the eight are closer to S.lancearius Jeekel, 2002 in COI genealogy. These two cases are discussed in terms of hybridisation, past introgressive hybridisation events and aberrant morphology.
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Affiliation(s)
- Peter Decker
- Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826 Görlitz, Germany Senckenberg Museum of Natural History Görlitz Görlitz Germany
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Kallal RJ, Hormiga G. Systematics, phylogeny and biogeography of the Australasian leaf-curling orb-weaving spiders (Araneae: Araneidae: Zygiellinae), with a comparative analysis of retreat evolution. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Robert J Kallal
- The George Washington University, Department of Biological Sciences, Washington, D.C., USA
| | - Gustavo Hormiga
- The George Washington University, Department of Biological Sciences, Washington, D.C., USA
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The origins of diversity in ancient landscapes: Deep phylogeographic structuring in a pseudoscorpion (Pseudotyrannochthoniidae: Pseudotyrannochthonius) reflects Plio-Pleistocene climate fluctuations. ZOOL ANZ 2018. [DOI: 10.1016/j.jcz.2018.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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More evolution underground: Accelerated mitochondrial substitution rate in Australian burrowing freshwater crayfishes (Decapoda: Parastacidae). Mol Phylogenet Evol 2017; 118:88-98. [PMID: 28966124 DOI: 10.1016/j.ympev.2017.09.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/18/2017] [Accepted: 09/26/2017] [Indexed: 12/11/2022]
Abstract
To further understand the evolutionary history and mitogenomic features of Australia's highly distinctive freshwater crayfish fauna, we utilized a recently described rapid mitogenome sequencing pipeline to generate 24 new crayfish mitogenomes including a diversity of burrowing crayfish species and the first for Astacopsis gouldi, the world's largest freshwater invertebrate. Whole mitogenome-based phylogeny estimates using both Bayesian and Maximum Likelihood methods substantially strengthen existing hypotheses for systematic relationships among Australian freshwater crayfish with evidence of pervasive diversifying selection and accelerated mitochondrial substitution rate among the members of the clade representing strongly burrowing crayfish that may reflect selection pressures for increased energy requirement for adaptation to terrestrial environment and a burrowing lifestyle. Further, gene rearrangements are prevalent in the burrowing crayfish mitogenomes involving both tRNA and protein coding genes. In addition, duplicated control regions were observed in two closely related Engaeus species, together with evidence for concerted evolution. This study significantly adds to the understanding of Australian freshwater crayfish evolutionary relationships and suggests a link between mitogenome evolution and adaptation to terrestrial environments and a burrowing lifestyle in freshwater crayfish.
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Dawkins KL, Furse JM, Wild CH, Hughes JM. A novel genus and cryptic species harboured within the monotypic freshwater crayfish genus Tenuibranchiurus Riek, 1951 (Decapoda: Parastacidae). PeerJ 2017; 5:e3310. [PMID: 28560095 PMCID: PMC5445942 DOI: 10.7717/peerj.3310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/13/2017] [Indexed: 11/20/2022] Open
Abstract
Identifying species groups is an important yet difficult task, with there being no single accepted definition as to what constitutes a species, nor a set of criteria by which they should be delineated. Employing the General Lineage Concept somewhat circumvents these issues, as this concept allows multiple concordant lines of evidence to be used as support for species delimitation, where a species is defined as any independently evolving lineage. Genetically diverse groups have previously been identified within the monotypic parastacid genus Tenuibranchiurus Riek, 1951, but no further investigation of this diversity has previously been undertaken. Analysis of two mitochondrial DNA gene regions has previously identified two highly divergent groups within this taxon, representing populations from Queensland (Qld) and New South Wales (NSW), respectively. Additional testing within this study of both mitochondrial and nuclear DNA through species discovery analyses identified genetically diverse groups within these regions, which were further supported by lineage validation methods. The degree of genetic differentiation between Qld and NSW populations supports the recognition of two genera; with Qld retaining the original genus name Tenuibranchiurus, and NSW designated as Gen. nov. until a formal description is completed. Concordance between the species discovery and lineage validation methods supports the presence of six species within Tenuibranchiurus and two within Gen. nov. The recognition of additional species removes the monotypy of the genus, and the methods used can improve species identification within groups of organisms with taxonomic problems and cryptic diversity.
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Affiliation(s)
- Kathryn L Dawkins
- Australian Rivers Institute, Griffith University, Gold Coast, Queensland, Australia
| | - James M Furse
- Environmental Futures Research Institute, Griffith University, Gold Coast, Queensland, Australia.,Miyazaki International College, Miyazaki, Japan
| | - Clyde H Wild
- Environmental Futures Research Institute, Griffith University, Gold Coast, Queensland, Australia
| | - Jane M Hughes
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
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Decker P. Phylogenetic analysis of the Australian trans-Bass Strait millipede genus Pogonosternum (Carl, 1912) (Diplopoda, Polydesmida, Paradoxosomatidae) indicates multiple glacial refugia in southeastern Australia. Zookeys 2016:15-31. [PMID: 27110194 PMCID: PMC4829959 DOI: 10.3897/zookeys.578.8052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/10/2016] [Indexed: 11/12/2022] Open
Abstract
This study documents the first detailed phylogenetic analysis of an Australian paradoxosomatid millipede genus. Two mitochondrial genes (partial COI and 16S) as well as partial nuclear 28S rDNA were amplified and sequenced for 41 individuals of the southeastern Australian genus Pogonosternum Jeekel, 1965. The analysis indicates that five species groups of Pogonosternum occur across New South Wales, Victoria and Tasmania: Pogonosternumnigrovirgatum (Carl, 1912), Pogonosternumadrianae Jeekel, 1982, Pogonosternumlaetificum Jeekel, 1982 and two undescribed species. Pogonosternumconiferum (Jeekel, 1965) specimens cluster within Pogonosternumnigrovirgatum. Most of these five species groups exhibit a pattern of high intraspecific genetic variability and highly localized haplotypes, suggesting that they were confined to multiple Pleistocene refugia on the southeastern Australian mainland. The phylogenetic data also show that northwestern Tasmania was colonized by Pogonosternumnigrovirgatum, probably from central Victoria, and northeastern Tasmania by an as yet undescribed species from eastern Victoria.
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Owen CL, Bracken-Grissom H, Stern D, Crandall KA. A synthetic phylogeny of freshwater crayfish: insights for conservation. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140009. [PMID: 25561670 DOI: 10.1098/rstb.2014.0009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project (opentreeoflife.org) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world's freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts.
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Affiliation(s)
- Christopher L Owen
- Computational Biology Institute, George Washington University, Ashburn, VA 20132, USA
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
| | - David Stern
- Computational Biology Institute, George Washington University, Ashburn, VA 20132, USA
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA 20132, USA Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
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MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes. Mol Phylogenet Evol 2015; 85:180-8. [DOI: 10.1016/j.ympev.2015.02.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/20/2014] [Accepted: 02/13/2015] [Indexed: 11/22/2022]
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Lee YP, Gan HM, Tan MH, Lys I, Page R, Dias Wanigasekera B, Austin CM. The complete mitogenome of the New Zealand freshwater crayfish Paranephrops planifrons White 1842 (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3333-4. [DOI: 10.3109/19401736.2015.1018209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yin Peng Lee
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia,
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia,
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia,
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia,
| | - Mun Hua Tan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia,
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia,
| | - Isabelle Lys
- School of Science, Faculty of Health Sciences, Australian Catholic University, Banyo, Queensland, Australia, and
| | - Rachel Page
- School of Food and Nutrition, Massey University, Wellington, New Zealand
| | | | - Christopher M. Austin
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia,
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia,
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Toussaint EF, Condamine FL, Hawlitschek O, Watts CH, Porch N, Hendrich L, Balke M. Unveiling the Diversification Dynamics of Australasian Predaceous Diving Beetles in the Cenozoic. Syst Biol 2014; 64:3-24. [DOI: 10.1093/sysbio/syu067] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Emmanuel F.A. Toussaint
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Fabien L. Condamine
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Oliver Hawlitschek
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Chris H. Watts
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Nick Porch
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Lars Hendrich
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Michael Balke
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
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Rix MG, Edwards DL, Byrne M, Harvey MS, Joseph L, Roberts JD. Biogeography and speciation of terrestrial fauna in the south-western Australian biodiversity hotspot. Biol Rev Camb Philos Soc 2014; 90:762-93. [PMID: 25125282 DOI: 10.1111/brv.12132] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 06/28/2014] [Accepted: 07/02/2014] [Indexed: 01/21/2023]
Abstract
The south-western land division of Western Australia (SWWA), bordering the temperate Southern and Indian Oceans, is the only global biodiversity hotspot recognised in Australia. Renowned for its extraordinary diversity of endemic plants, and for some of the largest and most botanically significant temperate heathlands and woodlands on Earth, SWWA has long fascinated biogeographers. Its flat, highly weathered topography and the apparent absence of major geographic factors usually implicated in biotic diversification have challenged attempts to explain patterns of biogeography and mechanisms of speciation in the region. Botanical studies have always been central to understanding the biodiversity values of SWWA, although surprisingly few quantitative botanical analyses have allowed for an understanding of historical biogeographic processes in both space and time. Faunistic studies, by contrast, have played little or no role in defining hotspot concepts, despite several decades of accumulating quantitative research on the phylogeny and phylogeography of multiple lineages. In this review we critically analyse datasets with explicit supporting phylogenetic data and estimates of the time since divergence for all available elements of the terrestrial fauna, and compare these datasets to those available for plants. In situ speciation has played more of a role in shaping the south-western Australian fauna than has long been supposed, and has occurred in numerous endemic lineages of freshwater fish, frogs, reptiles, snails and less-vagile arthropods. By contrast, relatively low levels of endemism are found in birds, mammals and highly dispersive insects, and in situ speciation has played a negligible role in generating local endemism in birds and mammals. Quantitative studies provide evidence for at least four mechanisms driving patterns of endemism in south-western Australian animals, including: (i) relictualism of ancient Gondwanan or Pangaean taxa in the High Rainfall Province; (ii) vicariant isolation of lineages west of the Nullarbor divide; (iii) in situ speciation; and (iv) recent population subdivision. From dated quantitative studies we derive four testable models of historical biogeography for animal taxa in SWWA, each explicit in providing a spatial, temporal and topological perspective on patterns of speciation or divergence. For each model we also propose candidate lineages that may be worthy of further study, given what we know of their taxonomy, distributions or relationships. These models formalise four of the strongest patterns seen in many animal taxa from SWWA, although other models are clearly required to explain particular, idiosyncratic patterns. Generating numerous new datasets for suites of co-occurring lineages in SWWA will help refine our understanding of the historical biogeography of the region, highlight gaps in our knowledge, and allow us to derive general postulates from quantitative (rather than qualitative) results. For animals, this process has now begun in earnest, as has the process of taxonomically documenting many of the more diverse invertebrate lineages. The latter remains central to any attempt to appreciate holistically biogeographic patterns and processes in SWWA, and molecular phylogenetic studies should - where possible - also lead to tangible taxonomic outcomes.
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Affiliation(s)
- Michael G Rix
- Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia.,Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia
| | - Danielle L Edwards
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06520, U.S.A
| | - Margaret Byrne
- Science Division, Department of Parks and Wildlife, Locked Bag 104, Bentley DC, Western Australia 6983, Australia
| | - Mark S Harvey
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia.,School of Animal Biology, Centre for Evolutionary Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Facilities and Collections, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
| | - J Dale Roberts
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia.,School of Animal Biology, Centre for Evolutionary Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.,Centre of Excellence in Natural Resource Management, University of Western Australia, PO Box 5771, Albany, Western Australia 6332, Australia
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Gan HM, Tan MH, Gan HY, Lee YP, Schultz MB, Austin CM. The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:826-7. [PMID: 24845437 DOI: 10.3109/19401736.2014.919460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The mitogenome of the black yabby, Geocharax gracilis, was sequenced using the MiSeq Personal Sequencer. It has 15,924 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of G. gracilis mitogenome is 32.18% for T, 22.32% for C, 34.83% for A, and 10.68% for G, with an AT bias of 67.01%. The mitogenome gene order is typical for that of parastacid crayfish with the exception of some minor rearrangements involving tRNA genes.
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Affiliation(s)
- Han Ming Gan
- a School of Science, Monash University Malaysia, Jalan Lagoon Selatan , Bandar Sunway , Selangor , Malaysia and
| | - Mun Hua Tan
- a School of Science, Monash University Malaysia, Jalan Lagoon Selatan , Bandar Sunway , Selangor , Malaysia and
| | - Huan You Gan
- a School of Science, Monash University Malaysia, Jalan Lagoon Selatan , Bandar Sunway , Selangor , Malaysia and
| | - Yin Peng Lee
- a School of Science, Monash University Malaysia, Jalan Lagoon Selatan , Bandar Sunway , Selangor , Malaysia and
| | - Mark B Schultz
- b Faculty of Medical and Dental Health Sciences , The University of Melbourne, Bio21 Research Institute , Parkville , Victoria , Australia
| | - Christopher M Austin
- a School of Science, Monash University Malaysia, Jalan Lagoon Selatan , Bandar Sunway , Selangor , Malaysia and
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Griffin PC, Hoffmann AA. Limited genetic divergence among Australian alpine Poa tussock grasses coupled with regional structuring points to ongoing gene flow and taxonomic challenges. ANNALS OF BOTANY 2014; 113:953-65. [PMID: 24607721 PMCID: PMC3997636 DOI: 10.1093/aob/mcu017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/27/2014] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS While molecular approaches can often accurately reconstruct species relationships, taxa that are incompletely differentiated pose a challenge even with extensive data. Such taxa are functionally differentiated, but may be genetically differentiated only at small and/or patchy regions of the genome. This issue is considered here in Poa tussock grass species that dominate grassland and herbfields in the Australian alpine zone. METHODS Previously reported tetraploidy was confirmed in all species by sequencing seven nuclear regions and five microsatellite markers. A Bayesian approach was used to co-estimate nuclear and chloroplast gene trees with an overall dated species tree. The resulting species tree was used to examine species structure and recent hybridization, and intertaxon fertility was tested by experimental crosses. KEY RESULTS Species tree estimation revealed Poa gunnii, a Tasmanian endemic species, as sister to the rest of the Australian alpine Poa. The taxa have radiated in the last 0·5-1·2 million years and the non-gunnii taxa are not supported as genetically distinct. Recent hybridization following past species divergence was also not supported. Ongoing gene flow is suggested, with some broad-scale geographic structure within the group. CONCLUSIONS The Australian alpine Poa species are not genetically distinct despite being distinguishable phenotypically, suggesting recent adaptive divergence with ongoing intertaxon gene flow. This highlights challenges in using conventional molecular taxonomy to infer species relationships in recent, rapid radiations.
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Affiliation(s)
- Philippa C. Griffin
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Ary A. Hoffmann
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
- Pest and Environmental Adaptation Research Group, Department of Zoology, University of Melbourne, Parkville 3010, Victoria, Australia
- Long Term Ecological Research Network, http://www.ltern.org.au/
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Gan HM, Tan MH, Lee YP, Schultz MB, Austin CM. The complete mitogenome of the Australian land crayfishEngaeus lyelli(Clark 1936) (Crustacea: Decapoda: Parastacidae). ACTA ACUST UNITED AC 2014; 27:595-6. [DOI: 10.3109/19401736.2014.908361] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Gan HM, Schultz MB, Austin CM. Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 2014; 14:19. [PMID: 24484414 PMCID: PMC3915555 DOI: 10.1186/1471-2148-14-19] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 01/29/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline. RESULTS The complete mitochondrial genome of the parastacid freshwater crayfish, Engaeus lengana, was recovered by modest shotgun sequencing (1.2 giga bases) using the Illumina MiSeq benchtop sequencing platform. Genome assembly using the MITObim mitogenome assembler recovered the mitochondrial genome as a single contig with a 97-fold mean coverage (min. = 17; max. = 138). The mitogenome consists of 15,934 base pairs and contains the typical 37 mitochondrial genes and a non-coding AT-rich region. The genome arrangement is similar to the only other published parastacid mitogenome from the Australian genus Cherax. CONCLUSIONS We infer that the gene order arrangement found in Cherax destructor is common to Australian crayfish and may be a derived feature of the southern hemisphere family Parastacidae. Further, we report to our knowledge, the simplest and fastest protocol for the recovery and assembly of complete mitochondrial genomes using the MiSeq benchtop sequencer.
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Affiliation(s)
- Han Ming Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia.
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Schmidt DJ, Grund R, Williams MR, Hughes JM. Australian parasiticOgyrisbutterflies: east-west divergence of highly-specialized relicts. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel J. Schmidt
- Australian Rivers Institute; Griffith University; Nathan QLD 4111 Australia
| | - Roger Grund
- 9 Parkers Road, Torrens Park, SA, 5062, Australia
| | - Matthew R. Williams
- Department of Parks and Wildlife; Locked Bag 104, Bentley Delivery Centre WA 6983 Australia
| | - Jane M. Hughes
- Australian Rivers Institute; Griffith University; Nathan QLD 4111 Australia
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Vogt G. Abbreviation of larval development and extension of brood care as key features of the evolution of freshwater Decapoda. Biol Rev Camb Philos Soc 2012; 88:81-116. [DOI: 10.1111/j.1469-185x.2012.00241.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Rix MG, Harvey MS. Phylogeny and historical biogeography of ancient assassin spiders (Araneae: Archaeidae) in the Australian mesic zone: Evidence for Miocene speciation within Tertiary refugia. Mol Phylogenet Evol 2012; 62:375-96. [DOI: 10.1016/j.ympev.2011.10.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 10/11/2011] [Accepted: 10/13/2011] [Indexed: 11/26/2022]
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Griffin PC, Robin C, Hoffmann AA. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biol 2011; 9:19. [PMID: 21429199 PMCID: PMC3078099 DOI: 10.1186/1741-7007-9-19] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 03/23/2011] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Polyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems. RESULTS Using 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual) in a total of 60 individuals across 11 species of Australian Poa grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control) and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability.We applied this method to a group of sympatric Australian alpine Poa species, which we discovered to share an allopolyploid ancestor with a group of American Poa species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the trnH-psbA marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at <100 km with chloroplast but not nuclear markers, which may be a result of restricted seed flow and long-distance pollen flow in this wind-pollinated group. CONCLUSIONS Our results demonstrate that 454 sequencing of barcoded amplicon mixtures can be used to reliably sample all alleles of homeologous loci in polyploid species and successfully investigate phylogenetic relationships among species, as well as to investigate phylogeographic hypotheses. This next-generation sequencing method is more affordable than and at least as reliable as bacterial cloning. It could be applied to any experiment involving sequencing of amplicon mixtures.
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Affiliation(s)
- Philippa C Griffin
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Charles Robin
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Ary A Hoffmann
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
- Department of Zoology, University of Melbourne, Parkville 3010, Victoria, Australia
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Glaubrecht M, Brinkmann N, Pöppe J. Diversity and disparity ‘down under’: Systematics, biogeography and reproductive modes of the ‘marsupial’ freshwater Thiaridae (Caenogastropoda, Cerithioidea) in Australia. ZOOSYST EVOL 2009. [DOI: 10.1002/zoos.200900004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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